Skip to main content

Advertisement

Proceedings of the Frontiers of Retrovirology Conference 2016

Article metrics

Table of contents

Oral presentations

Session 1: Entry & uncoating

O1 Host cell polo-like kinases (PLKs) promote early prototype foamy virus (PFV) replication

Irena Zurnic, Sylvia Hütter, Ute Lehmann, Nicole Stanke, Juliane Reh, Tobias Kern, Fabian Lindel, Gesche Gerresheim, Martin Hamann, Erik Müllers, Paul Lesbats, Peter Cherepanov, Erik Serrao, Alan Engelman, Dirk Lindemann

O2 A novel entry/uncoating assay reveals the presence of at least two species of viral capsids during synchronized HIV-1 infection

Claire Da Silva Santos, Kevin Tartour, Andrea Cimarelli

O3 Dynamics of nuclear envelope association and nuclear import of HIV-1 complexes

Rya Burdick, Jianbo Chen, Jaya Sastri, Wei-Shau Hu, Vinay Pathak

O4 Human papillomavirus protein E4 potently enhances the susceptibility to HIV infection

Oliver T. Keppler

Session 2: Reverse transcription & integration

O5 Structure and function of HIV-1 integrase post translational modifications

Karine Pradeau, Sylvia Eiler, Nicolas Levy, Sarah Lennon, Sarah Cianferani, Stéphane Emiliani, Marc Ruff

O6 Regulation of retroviral integration by RNA polymerase II associated factors and chromatin structure

Vincent Parissi

Session 3: Transcription and latency

O7 A novel single-cell analysis pipeline to identify specific biomarkers of HIV permissiveness

Sylvie Rato, Antonio Rausell, Miguel Munoz, Amalio Telenti, Angela Ciuffi

O8 A capsid-dependent integration program linking T cell activation to HIV-1 gene expression

Alexander Zhyvoloup, Anat Melamed, Ian Anderson, Delphine Planas, Janos Kriston-Vizi, Robin Ketteler, Chen-Hsuin Lee, Andy Merritt, Petronela Ancuta, Charles Bangham, Ariberto Fassati

O9 Characterisation of new RNA polymerase III and RNA polymerase II transcriptional promoters in the Bovine Leukemia Virus genome

Anthony Rodari, Benoit Van Driessche, Mathilde Galais, Nadége Delacourt, Sylvain Fauquenoy, Caroline Vanhulle, Anna Kula, Arsène Burny, Olivier Rohr, Carine Van Lint

O10 Tissue-specific dendritic cells differentially modulate latent HIV-1 reservoirs

Thijs van Montfort, Renee van der Sluis, Dave Speijer, Ben Berkhout

Session 4: RNA trafficking & packaging

O11 A novel cis-acting element affecting HIV replication

Bo Meng, Andrzej Rutkowski, Neil Berry, Lars Dölken, Andrew Lever

O12 Tolerance of HIV’s late gene expression towards stepwise codon adaptation

Thomas Schuster, Benedikt Asbach, Ralf Wagner

Session 5: Assembly & release

O13 Importance of the tax-inducible actin-bundling protein fascin for transmission of human T cell leukemia virus Type 1 (HTLV-1)

Christine Gross, Veit Wiesmann, Martina Kalmer, Thomas Wittenberg, Jan Gettemans, Andrea K. Thoma-Kress

O14 Lentiviral nef proteins antagonize TIM-mediated inhibition of viral release

Minghua Li, Eric O. Freed, Shan-Lu Liu

Session 6: Pathogenesis & evolution

O15 SEVI and semen prolong the half-life of HIV-1

Janis Müller, Jan Münch

O16 CD169+ macrophages mediate retrovirus trans-infection of permissive lymphocytes to establish infection in vivo

Xaver Sewald, Pradeep Uchil, Mark Ladinsky, Jagadish Beloor, Ruoxi Pi, Christin Herrmann, Nasim Motamedi, Thomas Murooka, Michael Brehm, Dale Greiner, Thorsten Mempel, Pamela Bjorkman, Priti Kumar, Walther Mothes

O17 Efficient replication of a vpu containing SIVagm construct in African Green Monkeys requires an HIV-1 nef gene

Simone Joas, Erica Parrish, Clement Wesley Gnanadurai, Edina Lump, Christina M. Stürzel, Nicholas F. Parrish, Ulrike Sauermann, Katharina Töpfer, Tina Schultheiss, Steven Bosinger, Guido Silvestri, Cristian Apetrei, Nicholas Huot, Michaela Müller-Trutwin, Daniel Sauter, Beatrice H. Hahn, Christiane Stahl-Hennig, Frank Kirchhoff

O18 Reprogramming initiates mobilization of endogenous mutagenic LINE-1, Alu and SVA retrotransposons in human induced pluripotent stem cells with consequences for host gene expression

Gerald Schumann, Sabine Jung-Klawitter, Nina V. Fuchs, Kyle R. Upton, Martin Muñoz-Lopez, Ruchi Shukla, Jichang Wang, Marta Garcia-Canadas, Cesar Lopez-Ruiz, Daniel J. Gerhardt, Attila Sebe, Ivana Grabundzija, Patricia Gerdes, Sylvia Merkert, Andres Pulgarin, Anja Bock, Ulrike Held, Anett Witthuhn, Alexandra Haase, Ernst J. Wolvetang, Ulrich Martin, Zoltán Ivics, Zsuzsanna Izsvák, J. Garcia-Perez, Geoffrey J. Faulkner

O19 NF-κB activation induces expression of human endogenous retrovirus and particle production

Tara Hurst, Aris Katzourakis, Gkikas Magiorkinis

Session 7a and b: Innate sensing & intrinsic immunity

O20 Identification of the phosphatase acting on T592 in SAMHD1 during M/G1 transition

Kerstin Schott, Rita Derua, Janna Seifried, Andreas Reuter, Heike Schmitz, Christiane Tondera, Alberto Brandariz-Nuñez, Felipe Diaz-Griffero, Veerle Janssens, Renate König

O21 Vpx overcomes a SAMHD1-independent block to HIV reverse transcription that is specific to resting CD4 T cells

Hanna-Mari Baldauf, Lena Stegmann, Sarah-Marie Schwarz, Maud Trotard, Margarethe Martin, Gina Lenzi, Manja Burggraf, Xiaoyu Pan, Oliver I. Fregoso, Efrem S. Lim, Libin Abraham, Elina Erikson, Laura Nguyen, Ina Ambiel, Frank Rutsch, Renate König, Baek Kim, Michael Emerman, Oliver T. Fackler, Oliver T. Keppler

O22 The role of SAMHD1 in antiviral restriction and immune sensing in the mouse

Sabine Wittmann, Rayk Behrendt, Bianca Volkmann, Kristin Eissmann, Thomas Gramberg

O23 T cells expressing reduced restriction factors are preferentially infected in therapy naïve HIV-1 patients

Sebastian Bolduan, Herwig Koppensteiner, Stefanie Regensburg, Ruth Brack-Werner, Rika Draenert, Michael Schindler

O24 cGAS-mediated innate immunity spreads through HIV-1 env-induced membrane fusion sites from infected to uninfected primary HIV-1 target cells

Aurélie Ducroux, Shuting Xu, Aparna Ponnurangam, Sergej Franz, Angelina Malassa, Ellen Ewald, Christine Goffinet

O25 Perturbation of innate RNA and DNA sensing by human T cell leukemia virus type 1 oncoproteins

Sin-Yee Fung, Ching-Ping Chan, Chun-Kit Yuen, Kin-Hang Kok, Chin-Ping Chan, Dong-Yan Jin

O26 Induction and anti-viral activity of Interferon α subtypes in HIV-1 infection

Ulf Dittmer

O27 Vpu-mediated counteraction of tetherin is a major determinant of HIV-1 interferon resistance

Dorota Kmiec, Shilpa Iyer, Christina Stürzel, Daniel Sauter, Beatrice Hahn, Frank Kirchhoff

O28 DNA repair protein Rad18 restricts HIV-1 and LINE-1 life cycle

Yasuo Ariumi, Mariko Yasuda-Inoue, Koudai Kawano, Satoshi Tateishi, Priscilla Turelli

O29 Natural mutations in IFITM3 allow escape from post-translational regulation and toggle antiviral specificity

Alex Compton, Nicolas Roy, Françoise Porrot, Anne Billet, Nicoletta Casartelli, Jacob Yount, Chen Liang, Oliver Schwartz

Session 8: Adaptive immunity & immune evasion

O30 Observing evolution in HIV-1 infection: phylogenetics and mutant selection windows to infer the influence of the autologous antibody response on the viral quasispecies

Carsten Magnus, Lucia Reh, Penny Moore, Therese Uhr, Jacqueline Weber, Lynn Morris, Alexandra Trkola

O31 Dose and subtype specific analyses of the anti-HIV effects of IFN-alpha family members

Rashel V. Grindberg, Erika Schlaepfer, Gideon Schreiber, Viviana Simon, Roberto F. Speck

Session 9: Novel antiviral strategies

O32 LEDGIN-mediated inhibition of the integrase-LEDGF/p75 interaction reduces reactivation of residual latent HIV

Zeger Debyser, Lenard Vranckx, Jonas Demeulemeester, Suha Saleh, Eric Verdin, Anna Cereseto, Frauke Christ, Rik Gijsbers

O33 NKG2D-mediated clearance of reactivated viral reservoirs by natural killer cells

O34 Inhibition of HIV reactivation in brain cells by AAV-mediated delivery of CRISPR/Cas9

O35 CRISPR-Cas9 as antiviral: potent HIV-1 inhibition, but rapid virus escape and the subsequent design of escape-proof antiviral strategies

Ben Berkhout, Gang Wang, Na Zhao, Atze T. Das

Session 10: Recent advances in HIV vaccine development

O36 Priming with a potent HIV-1 DNA vaccine frames the quality of T cell and antibody responses prior to a poxvirus and protein boost

Benedikt Asbach, Josef Köstler, Beatriz Perdiguero, Mariano Esteban, Bertram L. Jacobs, David C. Montefiori, Celia C. LaBranche, Nicole L. Yates, Georgia D. Tomaras, Guido Ferrari, Kathryn E. Foulds, Mario Roederer, Gary Landucci, Donald N. Forthal, Michael S. Seaman, Natalie Hawkins, Steven G. Self, Sanjay Phogat, James Tartaglia, Susan W. Barnett, Brian Burke, Anthony D. Cristillo, Song Ding, Jonathan L. Heeney, Giuseppe Pantaleo, Ralf Wagner

O37 Passive immunisation with a neutralising antibody against HIV-1 Env prevents infection of the first cells in a mucosal challenge rhesus monkey model

Christiane Stahl-Hennig, Viktoria Stab, Armin Ensser, Ulrike Sauermann, Bettina Tippler, Dennis Burton, Matthias Tenbusch, Klaus Überla

O38 HIV antibody Fc-glycoforms drive B cell affinity maturation

Galit Alter, Giuseppe Lofano, Anne-Sophie Dugast, Viraj Kulkarni, Todd Suscovich

Poster presentations

Topic 1: Entry & uncoating

P1 Dynein light chain is required for murine leukemia virus infection

Tatiana Opazo, Felipe Barraza, Diego Herrera, Andrea Garces, Tomas Schwenke, Diego Tapia, Jorge Cancino, Gloria Arriagada

P2 Peptide paratope mimics of the broadly neutralising HIV-1 antibody b12

Christina Haußner, Dominik Damm, Anette Rohrhofer, Barbara Schmidt, Jutta Eichler

P3 Investigating cellular pathways involved in the transmission of HIV-1 between dendritic cells and T cells using RNAi screening techniques

Rebecca Midgley, James Wheeldon, Vincent Piguet

P4 Co-receptor tropism in HIV-1, HIV-2 monotypic and dual infections

Priyanka Khopkar, Megha Rohamare, Smita Kulkarni

P5 Characterisation of the role of CIB1 and CIB2 as HIV-1 helper factors

Ana Godinho-Santos, Allan Hance, Joao Goncalves, Fabrizio Mammano

P6 Buffering deleterious polymorphisms in the highly constrained C2 region of HIV-1 envelope by the flexible V3 domain

Romain Gasser, Meriem Hamoudi, Martina Pellicciotta, Zhicheng Zhou, Clara Visdeloup, Philippe Colin, Martine Braibant, Bernard Lagane, Matteo Negroni

P7 Entry inhibition of HERV-K(HML-2) by an Env-IgG fusion protein

Jula Wamara, Norbert Bannert

Topic 2: Reverse transcription & integration

P8 The R263K/H51Y resistance substitutions in HIV integrase decreases levels of integrated HIV DNA over time

Thibault Mesplede, Nathan Osman, Kaitlin Anstett, Jiaming Calvin Liang, Hanh Thi Pham, Mark Wainberg

P9 The Retrovirus Integration Database (RID)

Wei Shao, Jigui Shan, Mary Kearney, Xiaolin Wu, Frank Maldarelli, John Mellors, Brian Luke, John Coffin, Stephen Hughes

P10 The small molecule 3G11 inhibits HIV-1 reverse transcription

Thomas Fricke, Silvana Opp, Caitlin Shepard, Dmitri Ivanov, Baek Kim, Jose Valle-Casuso, Felipe Diaz-Griffero

P11 Dual and opposite regulation of HIV-1 integration by hRAD51: impact on therapeutical approaches using homologous DNA repair modulators

Vincent Parissi

P12 A flexible motif essential for integration by HIV-1 integrase

Marine Kanja, Pierre Cappy, Matteo Negroni, Daniela Lener

P13 Interaction between HIV-1 integrase and the host protein Ku70: identification of the binding site and study of the influence on integrase-proteasome interplay

Ekaterina Knyazhanskaya, Andrey Anisenko, Timofey Zatsepin, Marina Gottikh

P14 Normalisation based method for deep sequencing of somatic retroelement integrations in human genome

Alexander Komkov, Anastasia Minervina, Gaiaz Nugmanov, Vadim Nazarov, Konstantin Khodosevich, Ilgar Mamedov, Yuri Lebedev

Topic 3: Transcription and latency

P15 BCA2/RABRING7 restricts HIV-1 transcription by preventing the nuclear translocation of NF-κB

Marta Colomer-Lluch, Ruth Serra-Moreno

P16 MATR3 post-transcriptional regulation of HIV-1 transcription during latency

Ambra Sarracino, Anna Kula, Lavina Gharu, Alexander Pasternak, Carine Van Lint, Alessandro Marcello

P17 HIV-1 tat intersects the SUMO pathway to regulate HIV-1 promoter activity

Ann Marie McCartin, Anurag Kulkarni, Valentin Le Douce, Virginie Gautier

P18 Conservation in HIV-1 Vpr guides tertiary gRNA folding and alternative splicing

Ann Baeyens, Evelien Naessens, Anouk Van Nuffel, Karin Weening, Anne-Marie Reilly, Eva Claeys, Wim Trypsteen, Linos Vandekerckhove, Sven Eyckerman, Kris Gevaert, Bruno Verhasselt

P19 The majority of reactivatable latent HIV are genetically distinct

Hoi Ping Mok, Nicholas Norton, Axel Fun, Jack Hirst, Mark Wills, Andrew Lever

P20 Do mutations in the tat exonic splice enhancer contribute to HIV-1 latency?

Nicholas Norton, Hoi Ping Mok, Jack Hirst, Andrew Lever

P21 Culture-to-Ct: A fast and direct RT-qPCR HIV gene reactivation screening method using primary T cell culture

Valentin Le Douce, Ann Marie McCartin, Virginie Gautier

P22 A novel approach to define populations of early silenced proviruses

Dalibor Miklik, Filip Senigl, Jiri Hejnar

Topic 4: RNA trafficking & packaging

P23 Functional analysis of the structure and conformation of HIV-1 genome RNA DIS

Jun-ichi Sakuragi, Sayuri Sakuragi, Masaru Yokoyama, Tatsuo Shioda, Hironori Sato

P24 Regulation of foamy viral env splicing controls gag and pol expression

Jochen Bodem, Rebecca Moschall, Sarah Denk, Steffen Erkelenz, Christian Schenk, Heiner Schaal

Topic 5: Assembly & release

P25 Transfer of HTLV-1 p8 to target T cells depends on VASP: a novel interaction partner of p8

Norbert Donhauser, Ellen Socher, Sebastian Millen, Heinrich Sticht, Andrea K. Thoma-Kress

P26 COL4A1 and COL4A2 are novel HTLV-1 tax targets with a putative role in virus transmission

Christine Gross, Sebastian Millen, Melanie Mann, Klaus Überla, Andrea K. Thoma-Kress

P27 The C terminus of foamy virus gag protein is required for particle formation, and virus budding: starting assembly at the C terminus?

Guochao Wei, Matthew J. Betts, Yang Liu, Timo Kehl, Robert B. Russell, Martin Löchelt

P28 Generation of an antigen-capture ELISA and analysis of Rec and Staufen-1 effects on HERV-K(HML-2) virus particle production

Oliver Hohn, Saeed Mostafa, Kirsten Hanke, Stephen Norley, Norbert Bannert

P29 Antagonism of BST-2/tetherin is a conserved function of primary HIV-2 Env glycoproteins

Chia-Yen Chen, Masashi Shingai, Pedro Borrego, Nuno Taveira, Klaus Strebel

P30 Mutations in the packaging signal region of the HIV-1 genome cause a late domain mutant phenotype

Chris Hellmund, Bo Meng, Andrew Lever

P31 p6 regulates membrane association of HIV-1 gag

Melanie Friedrich, Friedrich Hahn, Christian Setz, Pia Rauch, Kirsten Fraedrich, Alina Matthaei, Petra Henklein, Maximilian Traxdorf, Torgils Fossen, Ulrich Schubert

Topic 6: Pathogenesis & evolution

P32 Molecular and structural basis of protein evolution during viral adaptation

Aya Khwaja, Meytal Galilee, Akram Alian

P33 HIV-1 enhancement and neutralisation by soluble gp120 and its role for the selection of the R5-tropic “best fit”

Birco Schwalbe, Heiko Hauser, Michael Schreiber

P34 An insertion of seven amino acids in the Env cytoplasmic tail of Human Immunodeficiency Virus type 2 (HIV-2) selected during disease progression enhances viral replication

François Dufrasne, Mara Lucchetti, Patrick Goubau, Jean Ruelle

P35 Cell-associated HIV-1 unspliced to multiply spliced RNA ratio at 12 weeks ART correlates with markers of immune activation and apoptosis and predicts the CD4 T-cell count at 96 weeks ART

Mirte Scherpenisse, Ben Berkhout, Alexander Pasternak

P36 Faster progression in non-B subtype HIV-1-infected patients than Korean subclade of subtype B is accompanied by higher variation and no induction of gross deletion in non-B nef gene by Korean red ginseng treatment

Young-Keol Cho, Jungeun Kim, Daeun Jeong

P37 Aberrant expression of ERVWE1 endogenous retrovirus and overexpression of TET dioxygenases are characteristic features of seminoma

Katerina Trejbalova, Martina Benesova, Dana Kucerova, Zdenka Vernerova, Rachel Amouroux, Petra Hajkova, Jiri Hejnar

P38 Life history of the oldest lentivirus: characterisation of ELVgv integrations and the TRIM5 selection pattern in dermoptera

Daniel Elleder, Tomas Hron, Helena Farkasova, Abinash Padhi, Jan Paces

P39 Characterisation of a highly divergent endogenous retrovirus in the equine germ line

Henan Zhu, Robert Gifford, Pablo Murcia

P40 The emergence of pandemic retroviral infection in small ruminants

Maria Luisa Carrozza, Anna-Maria Niewiadomska, Maurizio Mazzei, Mounir Abi-Said, Joseph Hughes, Stéphane Hué, Robert Gifford

P41 Near full-length genome (NFLG) Characterisation of HIV-1 subtype B identified in South Africa

Adetayo Obasa, Graeme Jacobs, Susan Engelbrecht

P42 Acquisition of Vpu-mediated tetherin antagonism by an HIV-1 group O strain

Katharina Mack, Kathrin Starz, Daniel Sauter, Matthias Geyer, Frederic Bibollet-Ruche, Christina Stürzel, Marie Leoz, Jean Christophe Plantier, Beatrice H. Hahn, Frank Kirchhoff

P43 The human endogenous retrovirus type K is involved in cancer stem cell markers expression and in human melanoma malignancy

Ayele Argaw-Denboba, Emanuela Balestrieri, Annalucia Serafino, Ilaria Bucci, Chiara Cipriani, Corrado Spadafora, Paolo Sinibaldi-Vallebona, Claudia Matteucci

P44 Natural infection of Indian non-human primates by unique lentiviruses

S. Nandi Jayashree, Ujjwal Neogi, Anil K. Chhangani, Shravan Sing Rathore, Bajrang R. J. Mathur

P45 Free cervical cancer screening among HIV-positive women receiving antiretroviral treatment in Nigeria

Adeyemi Abati

P46 Molecular evolutionary status of feline immunodeficiency virus in Turkey

B. Taylan Koç, Tuba Çiğdem Oğuzoğlu

Topic 7: Innate sensing & intrinsic immunity

P47 Cell-to-cell contact with HTLV-1-infected T cells reduces dendritic cell immune functions and contributes to infection in trans.

Takatoshi Shimauchi, Stephan Caucheteux, Jocelyn Turpin, Katja Finsterbusch, Charles Bangham, Yoshiki Tokura, Vincent Piguet

P48 Deciphering the mechanisms of HIV-1 exacerbation induced by Mycobacterium tuberculosis in monocytes/macrophages

Shanti Souriant, Luciana Balboa, Karine Pingris, Denise Kviatcowsky, Brigitte Raynaud-Messina, Céline Cougoule, Ingrid Mercier, Marcelo Kuroda, Pablo González-Montaner, Sandra Inwentarz, Eduardo Jose Moraña, Maria del Carmen Sasiain, Olivier Neyrolles, Isabelle Maridonneau-Parini, Geanncarlo Lugo-Villarino, Christel Vérollet

P49 The SAMHD1-mediated inhibition of LINE-1 retroelements is regulated by phosphorylation

Alexandra Herrmann, Sabine Wittmann, Caitlin Shepard, Dominique Thomas, Nerea Ferreirós Bouzas, Baek Kim, Thomas Gramberg

P50 Activities of nuclear envelope protein SUN2 in HIV infection

Xavier Lahaye, Anvita Bhargava, Takeshi Satoh, Matteo Gentili, Silvia Cerboni, Aymeric Silvin, Cécile Conrad, Hakim Ahmed-Belkacem, Elisa C. Rodriguez, Jean-François Guichou, Nathalie Bosquet, Matthieu Piel, Roger Le Grand, Megan King, Jean-Michel Pawlotsky, Nicolas Manel

P51 Activation of TLR7/8 with a small molecule agonist induces a novel restriction to HIV-1 infection of monocytes

Henning Hofmann, Benedicte Vanwalscappel, Nicolin Bloch, Nathaniel Landau

P52 Steady state between the DNA polymerase and Rnase H domain activities of reverse transcriptases determines the sensitivity of retroviruses to inhibition by APOBEC3 proteins

Stanislav Indik, Benedikt Hagen

P53 HIV restriction in mature dendritic cells is related to p21 induction and p21-mediated control of the dNTP pool and SAMHD1 activity.

José Carlos Valle-Casuso, Awatef Allouch, Annie David, Françoise Barré-Sinoussi, Michaela Müller-Trutwin, Monsef Benkirane, Gianfranco Pancino, Asier Saez-Cirion

P54 IFITM protens restrict HIV-1 protein synthesis

Wing-Yiu Lee, Chen Liang, Richard Sloan

P55 Characterisation and functional analysis of the novel restriction factor Serinc5

Bianca Schulte, Silvana Opp, Felipe Diaz-Griffero

P56 piRNA sequences are common in Human Endogenous Retroviral Sequences (HERVs): An antiretroviral restriction mechanism?

Jonas Blomberg, Luana Vargiu, Patricia Rodriguez-Tomé, Enzo Tramontano, Göran Sperber

P57 Ferroportin restricts HIV-1 infection in sickle cell disease

Namita Kumari, Tatiana Ammosova, Sharmeen Diaz, Patricia Oneal, Sergei Nekhai

P58 APOBEC3G modulates the response to antiretroviral drugs in humanized mice

Audrey Fahrny, Gustavo Gers-Huber, Annette Audigé, Roberto F. Speck, Anitha Jayaprakash, Ravi Sachidanandam, Matt Hernandez, Marsha Dillon-White, Viviana Simon

P59 High-throughput epigenetic analysis of evolutionarily young endogenous retrovirus presents in the mule deer (Odocoileus hemionus) genome

Tomas Hron, Helena Farkasova, Daniel Elleder

P60 Characterisation of the expression of novel endogenous retroviruses and immune interactions in a macaque model

Neil Berry, Emmanuel Maze, Claire Ham, Neil Almond, Greg Towers, Robert Belshaw

P61 HIV-1 restriction by orthologs of SERINC3 and SERINC5

Patrícia de Sousa-Pereira, Joana Abrantes, Massimo Pizzato, Pedro J. Esteves, Oliver T. Fackler, Oliver T. Keppler, Hanna-Mari Baldauf

P62 TRIM19/PML restricts HIV infection in a cell type-dependent manner

Bianca Volkmann, Tanja Kahle, Kristin Eissmann, Alexandra Herrmann, Sven Schmitt, Sabine Wittmann, Laura Merkel, Nina Reuter, Thomas Stamminger, Thomas Gramberg

P63 Recent invasion of the mule deer genome by a retrovirus

Helena Farkasova, Tomas Hron, Daniel Elleder

P64 Does the antiviral protein SAMHD1 influence mitochondrial function?

Ilaria Dalla Rosa, Kate Bishop, Antonella Spinazzola, Harriet Groom

P65 cGAMP transfers intercellularly via HIV-1 Env-mediated cell–cell fusion sites and triggers an innate immune response in primary target cells

Shuting Xu, Aurélie Ducroux, Aparna Ponnurangam, Sergej Franz, Gabrielle Vieyres, Mathias Müsken, Thomas Zillinger, Angelina Malassa, Ellen Ewald, Veit Hornung, Winfried Barchet, Susanne Häussler, Thomas Pietschmann, Christine Goffinet

P66 Pre-infection transcript levels of FAM26F in PBMCS inform about overall plasma viral load in acute and postacute phase after SIV-infection

Ulrike Sauermann, Aneela Javed, Nicole Leuchte, Gabriela Salinas, Lennart Opitz, Christiane Stahl-Hennig, Sieghart Sopper

P67 Sequence-function analysis of three T cell receptors targeting the HIV-1 p17 epitope SLYNTVATL

Christiane Mummert, Christian Hofmann, Angela G. Hückelhoven, Silke Bergmann, Sandra M. Müller-Schmucker, Ellen G. Harrer, Jan Dörrie, Niels Schaft, Thomas Harrer

P68 An immunodominant region of the envelope glycoprotein of small ruminant lentiviruses may function as decoy antigen

Laure Cardinaux, M.-L. Zahno, H.-R. Vogt, R. Zanoni, G. Bertoni

P69 Impact of immune activation, immune exhaustion, broadly neutralising antibodies and viral reservoirs on disease progression in HIV-infected children

Maximilian Muenchhoff, Philip Goulder, Oliver Keppler

Topic 9: Novel antiviral strategies

P70 Identification of natural compounds as new antiviral products by bioassay-guided fractionation

Alexandra Herrmann, Stephanie Rebensburg, Markus Helfer, Michael Schindler, Ruth Brack-Werner

P71 The PPARG antagonism disconnects the HIV replication and effector functions in Th17 cells

Yuwei Zhang, Huicheng Chen, Delphine Planas, Annie Bernier, Annie Gosselin, Jean-Pierre Routy, Petronela Ancuta

P72 Characterisation of a multiresistant subtype AG reverse transcriptase: AZT resistance, sensitivity to RNase H inhibitors and inhibitor binding

Birgitta Wöhrl, Anna Schneider, Angela Corona, Imke Spöring, Mareike Jordan, Bernd Buchholz, Elias Maccioni, Roberto Di Santo, Jochen Bodem, Enzo Tramontano, Kristian Schweimer

P73 Insigths into the acetylation pattern of HDAC inhibitors and their potential role in HIV therapy

Christian Schölz, Brian Weinert, Sebastian Wagner, Petra Beli, Yasuyuki Miyake, Jun Qi, Lars Jensen, Werner Streicher, Anna McCarthy, Nicholas Westwood, Sonia Lain, Jürgen Cox, Patrick Matthias, Matthias Mann, James Bradner, Chunaram Choudhary

P74 HPV-derived and seminal amyloid peptides enhance HIV-1 infection and impair the efficacy of broadly neutralising antibodies and antiretroviral drugs

Marcel Stern, Oliver T. Keppler

P75 D(−)lentiginosine inhibits both proliferation and virus expression in cells infected by HTLV-1 in vitro

Elena Valletta, Caterina Frezza, Claudia Matteucci, Francesca Marino-Merlo, Sandro Grelli, Anna Lucia Serafino, Antonio Mastino, Beatrice Macchi

P76 HIV-1 resistance analyses of the Cape Winelands districts, South Africa

Sello Mikasi, Graeme Jacobs, Susan Engelbrecht

Topic 10: Recent advances in HIV vaccine development

P77 Induction of complex retrovirus antigen-specific immune responses by adenovirus-based vectors depends on the order of vector administration

Meike Kaulfuß, Sonja Windmann, Wibke Bayer

P78 Direct impact of structural properties of HIV-1 Env on the regulation of the humoral immune response

Rebecca Heß, Michael Storcksdieck gen. Bonsmann, Viktoria Stab, Carsten Kirschning, Bernd Lepenies, Matthias Tenbusch, Klaus Überla

P79 Lentiviral virus-like particles mediate gerenration of T-follicular helper cells in vitro

Anne Kolenbrander, Klaus Überla, Vladimir Temchura

P80 Recruitment of HIV-1 Vpr to DNA damage sites and protection of proviral DNA from nuclease activity

Kenta Iijima, Junya Kobayashi, Yukihito Ishizaka

Oral presentations

Session 1: Entry & uncoating

O1 Host cell polo-like kinases (PLKs) promote early prototype foamy virus (PFV) replication

Irena Zurnic1,2, Sylvia Hütter2, Ute Lehmann3, Nicole Stanke2, Juliane Reh4, Tobias Kern2,4, Fabian Lindel2,4, Gesche Gerresheim2, Martin Hamann2,4, Erik Müllers2,4, Paul Lesbats5, Peter Cherepanov5, Erik Serrao6, Alan Engelman6, Dirk Lindemann2
1Molecular Virology and Gene Therapy, Molecular Medicine, Leuven, Belgium; 2Technical University Dresden, Molecular Virology, Dresden, Germany; 3Potsdam University, Potsdam, Germany; 4Center for regenerative therapies Dresden, Dresden, Germany; 5The Francis Crick Institute, London, Great Britain; 6Dana Farber Cancer Institute, Boston, MA United States

Correspondence: Irena Zurnic

Retrovirology 2016, 13(Suppl 1): O1

Question: Foamy viruses (FV), and in particular PFV, have emerged in recent years as attractive gene therapy vector candidates. Since the lack of knowledge on molecular events in FV replication is a major hurdle for broader usage of foamy virus vectors, we aimed at elucidating PFV biology by investigating interactions of its capsid protein, Gag, with host cell components.

Methodology and result: To this end, we identified members of the mammalian PLK family as PFV Gag interactants in a commercial yeast-two-hybrid (Y2H) screen and validated these results in detailed Y2H experiments for PLK1–3. In the yeast system, the intact PLK kinase and substrate recognition motifs were required for interactions with PFV Gag, in which a unique S224-T-P226 motif served as a PLK binding determinant. PFV Gag mutants harbouring alanine substitutions of STP residues (iSTP) or phosphomimetic mutations of the T225 (pmSTP) failed to interact with PLK1–3 in yeast. These findings were corroborated by colocalization studies of ectopically expressed, fluorescently tagged proteins in mammalian cells, where mCherry-tagged PFV Gag was able to recruit eGFP-tagged PLK1 and 2 to condensed mitotic chromatin in an STP motif-dependent manner.

When characterizing PFV virions containing wild type or STP mutant Gag proteins, we observed that the mutations did not interfere with particle assembly, release or reverse transcription, but led to a 70 % titer reduction relative to wild type in single-round infection experiments. These replication defects became more prominent in the replication-competent PFV context. Therefore, the lack of Gag STP mutant interaction with PLK proteins upon viral entry into host cells was likely underlying this replication deficit. This hypothesis was strengthened by the finding that enzymatic PLK inhibition in host cells during transduction with wild type PFV mimicked the replication phenotype of PFV STP mutants. In addition to the overall reduced infectivity of the mutants, we also observed that the STP mutations in particle-associated Gag lead to differential sensitivity to integrase inhibition by dolutegravir and resulted in decreased integration efficiency.

Conclusions: Taken together, our results demonstrate that PLK proteins influence PFV replication by virtue of their interaction with the Gag protein, ensuring timely and efficient transduction.

O2 A novel entry/uncoating assay reveals the presence of at least two species of viral capsids during synchronized HIV-1 infection

Claire Da Silva Santos, Kevin Tartour, Andrea Cimarelli
CIRI, Lyon, France

Correspondence: Andrea Cimarelli

Retrovirology 2016, 13(Suppl 1): O2

After viral-to-cellular membrane fusion, a nucleoprotein complex enclosing the viral genome and composed of viral as well as cellular proteins is released in the cell cytoplasm. The behavior of viral cores once inside the cell is notoriously difficult to apprehend especially given the metamorphic nature of these structures over time. To better understand the behavior of HIV-1 capsids, we have developed a novel assay that we named EURT, forEntry/Uncoating assay based on core-packagedRNA availability andTranslation. This novel entry-uncoating assay is based on the degree of exposure of a virion core-packaged mRNA reporter to the translation machinery of the target cell and it provides a measure of the status of viral capsids, as reporter RNA translation is prevented in hyperstable viral capsids. Using EURT, we highlight here that two kinds of viral cores coexist during HIV-1 infection: one that we define as open, in which the viral genome is readily accessible to the cytoplasmic environment and to the translation machinery and another that we define as close, in which access to the RNA is prevented until viral capsid is destabilized. The results we have obtained so far indicate that the former species represents a dead-end product of infection, likely derived from improper or inefficient assembly of infectious virion units. Interestingly, IFNα that negatively impacts HIV-1 replication increases the proportion of open viral cores to the detriment of closed ones, suggesting a core-destabilizing activity driven by interferon-regulated proteins. These and other results examining the relationship between core opening and reverse transcription will be presented.

Work in our laboratory is supported by the ANRS and Sidaction.

O3 Dynamics of nuclear envelope association and nuclear import of HIV-1 complexes

Rya Burdick, Jianbo Chen, Jaya Sastri, Wei-Shau Hu, Vinay Pathak
National Cancer Institute, Frederick, MD, United States

Correspondence: Vinay Pathak

Retrovirology 2016, 13(Suppl 1): O3

HIV-1 must travel through the cytoplasm to reach the nuclear envelope (NE) of an infected cell, transport through a nuclear pore to enter the nucleus, and integrate its genome into the chromosomal DNA of the host cell. Recently, we have labeled HIV-1 virions with APOBEC3F fused to yellow fluorescent protein (A3F-YFP), which remains stably associated with viral complexes, and visualized the viral complexes in infected cells to gain new insights into the early stages of viral replication. We showed that reverse transcription is not required for nuclear import of HIV-1 complexes, indicating that alterations in the viral capsid (CA) structure that accompany reverse transcription are dispensable for their nuclear import. We found that HIV-1 CA mutations that altered the stability of the viral core significantly reduced the association of viral complexes with the nuclear envelope (NE) and their nuclear import. In addition, we found that nuclear viral complexes remain near NE and are not randomly distributed in the nuclei.

The dynamics of HIV-1 association with the NE and nuclear import in infected cells are not well understood. To gain insights into the dynamics of HIV-1 association with the NE, we analysed A3F-labeled HIV-1 complexes in living cells, and observed that most contacts between HIV-1 and NE form transient associations while few form stable associations, which are essential for nuclear import. Furthermore, HIV-1 capsid and host Nup358 played critical roles in forming the stable associations. Additionally, we observed the translocation of viral complexes from the cytoplasm to the NE during nuclear import. We determined that viral complexes have long residence times at the NE prior to import. After import, viral complexes exhibit a brief fast phase as they move away from the point of entry, followed by a long slow phase, suggesting they are associated with chromatin and/or other nuclear macromolecules. These studies provide novel insights into the dynamics of HIV-1 NE association, nuclear import, and nuclear movements.

O4 Human papillomavirus protein E4 potently enhances the susceptibility to HIV infection

Oliver T. Keppler
LMU Munich, Max von Pettenkofer-Institut, Virology, Munich, Germany

Correspondence: Oliver T. Keppler

Retrovirology 2016, 13(Suppl 1): O4

Sexually transmitted infections of the anogenital tract are important cofactors for HIV transmission, and acute infections by mucotropic human papillomaviruses (HPV) enhance the risk of HIV acquisition. Little is known about the molecular mechanisms involved in this increased susceptibility.

Here we show that the abundant E4 protein, which is encoded by both oncogenic and non-oncogenic HPV types, drastically enhances HIV infection. E4 is expressed in HPV-infected, ultimately disintegrating keratinocytes in the outermost cell layers of the anogenital mucosa. N-terminally cleaved forms of E4 self-assembled into cationic, intermediate amyloid fibrils that captured and concentrated cell-free HIV particles, protecting their infectivity and promoting their envelope-independent binding and envelope-dependent fusion to primary target cells. E4 drastically lowered the virus titer required for productive HIV infection in lymphoid organ cultures ex vivo and infection enhancement occurred efficiently in vaginal fluid. Moreover, HIV-permissive target cells were found to be recruited into HPV-induced lesions in the anogential mucosa.

Thus the concept emerges that aggregating cleavage products originating from body fluids, including semen, and from co-infecting pathogens can alone or in combination modulate the susceptibility to sexual transmission of HIV. In conjunction with the observational epidemiological evidence these findings provide a molecular rationale to extend anti-HPV vaccine programs to individuals at risk for HIV acquisition. The development of a new generation of broad-range vaccines that protect from infection with all circulating, oncogenic and non-oncogenic mucosal HPV types may lower the global incidence of HIV infection.

Session 2: Reverse transcription & integration

O5 Structure and function of HIV-1 integrase post translational modifications

Karine Pradeau1, Sylvia Eiler1, Nicolas Levy1, Sarah Lennon2, Sarah Cianferani2, Stéphane Emiliani3, Marc Ruff1
1IGBMC, Integrative structural Biology, Illkirch, France; 2Institut Pluridisciplinaire Hubert Curien, Strasbourg, France; 3Institut Cochin, Paris, France

Correspondence: Marc Ruff

Retrovirology 2016, 13(Suppl 1): O5

After retroviral infection of a target cell, during the early phase of replication, the HIV-1 genomic viral RNA is reverse transcribed by the viral reverse transcriptase (RT) to generate the double-stranded viral DNA that interact with viral and cellular proteins to form the pre-integration complex (PIC). Viral integrase (IN) is a key component of the PIC and is involved in several steps of replication notably in reverse transcription, nuclear import, chromatin targeting and integration. Viral components such as IN cannot perform these functions on their own and need to recruit host cell proteins to efficiently carry out the different processes. IN is a disordered protein showing high inter-domain flexibility. This flexibility accounts for IN ability to interact with multiple partners allowing its multiple functions in viral replication. Yet the molecular mechanisms and dynamics of these processes, the role of cellular co-factors as well as of post-translational modifications remain largely unknown.

To produce and purify proteins participating in these transient macromolecular complexes we develop new technologies for high molecular weight transient complexes production as well as for functional and structural analysis. We demonstrated that the low solubility and inter-domain flexibility can be circumvented by forming stable and specific complexes with substrates such as DNA or protein co-factors and by post-translational modifications (PTMs). We purified HIV-1 IN alone and in complex with viral and cellular proteins produced in E. coli, insect and mammalian cells (Levy et al. 2016, Nature Communications 7:10932). Comparison of IN purified from E. coli, insect and mammalian cells production showed that IN purified from mammalian cell production showed higher solubility, increased 3′ processing activity as well as 5 PTMs (one phosphorylation and four acetylation). Mutant of the phosphorylated and acetylated sites were generated and their effect on viral replication and 3′ processing are analysed. Structural analysis of acetylation in the IN catalytic core domain suggest that acetylation participate in the modulation of IN multimerization.

O6 Regulation of retroviral integration by RNA polymerase II associated factors and chromatin structure

Vincent Parissi
CNRS, UMR5234 MFP Lab, Bordeaux, France

Correspondence: Vincent Parissi

Retrovirology 2016, 13(Suppl 1): O6

HIV-1 integration occurs in highly Pol II transcribed and spliced regions of the chromatin thanks to the interaction between the retroviral intasome and the cellular tethering factor LEDGF/p75. These regions of the host genome are enriched in transcription and remodeling factors that are expected to modulate the chromatin access to the incoming intasome and its functional association with the targeted nucleosome. Since this final step has been shown to be regulated by both intasomes and chromatin structure we investigated these regulation processes focusing on the analysis of the IN/nucleosome interaction and on the role of the cellular proteins associated with the Pol II transcription apparatus. We found that HIV-1 IN specifically binds to the amino-terminal tail of human histone H4, a major component of the nucleosome. This interaction was found required for optimal association and integration onto nucleomes. Functional and structural analysis of this interaction led us to validate the presence of an unedited histone tail binding motif in the CTD of HIV-1 IN that behaves as an ancestral SH3/β-chromobarrel chromatin-reader domain and point out the critical role of the IN/H4 association during the retroviral integration process. Additionally, the analysis of the role of Pol II associated remodeling factors on this functional association led us to found that FACT (facilitates chromatin transcription) complex, a chromatin remodeler associated with Pol II and recently reported to bind LEDGF/p75, can regulate the access to the nucleosome and histone tails to the incoming intasomes. Mechanistic studies indicate that FACT generates partially dissociated nucleosomes structures that are highly favored substrates for HIV-1 integration. This partial nucleosome dissociation decreases the chromatin density in the vicinity of the integration site and, thus, allows the final association between intasomes and the targeted nucleosome. Consequently, our work highlights new host/pathogen interactions that could constitute novel and attractive targets for future potential therapeutic applications in addition to provide a better understanding of this crucial integration step of the retroviral replication.

Session 3: Transcription and latency

O7 A novel single-cell analysis pipeline to identify specific biomarkers of HIV permissiveness

Sylvie Rato1, Antonio Rausell2, Miguel Munoz1, Amalio Telenti3, Angela Ciuffi1
1Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland; 2Imagine Institute, Paris Descartes University, Paris, France; 3J. Craig Venter Institute, La Jolla, CA, United States

Correspondence: Sylvie Rato

Retrovirology 2016, 13(Suppl 1): O7

Background: Cellular permissiveness to HIV infection is highly heterogeneous across individuals, as well as across cells from the same individual. To investigate the major source of this difference and identify biomarkers, we developed a novel pipeline based on single-cell analysis, where (i) cellular heterogeneity was evaluated at transcriptome level, and (ii) HIV permissiveness was correlated to cell surface protein expression.

Methods: Activated CD4+ T cells from a high and low permissive donor were used for single-cell RNA-seq analysis (fluidigm C1™ technology).

Activated cells from the high permissive donor were infected with a GFP encoding HIV-based vector. Expression of 332 cell surface proteins (LegendScreen™) was assessed by FACS and correlated with GFP expression.

Candidate biomarkers were validated in activated cells sorted according to their protein expression level and infected by HIV vector.

Results: Transcriptomic profiles of 85 high and 81 low permissive single cells were successfully obtained. Transcriptional heterogeneity observed at single-cell level identified TCR-mediated cell activation as a major determinant of cellular heterogeneity.

Cell surface expression analysis of 332 proteins identified 76 candidates correlating with successful HIV infection, including CD25, a typical activation marker.

Candidate biomarkers of HIV permissiveness were selected based on correlations between gene expression and activation (single-cell RNA-Seq) and between surface protein expression and HIV permissiveness (LegendScreen™), and tested for their ability to capture permissive cells.

Eleven candidate biomarkers were successfully validated, showing enrichment of HIV permissive cells.

Conclusions: In this study, we developed a single-cell pipeline to investigate cell heterogeneity and identify gene candidates affecting HIV permissiveness. Our data showed that, at the single-cell level, the status of cellular activation was the major driver of cell heterogeneity towards HIV permissiveness. Moreover, we identified several cell surface biomarkers characterizing the HIV permissive cell. This single-cell analysis pipeline represents a valuable tool for biomarker identification.

Acknowledgements

FP7 European grant n°305762/Hit Hidden HIV and Swiss SNF grant 166412.

O8 A capsid-dependent integration program linking T cell activation to HIV-1 gene expression

Alexander Zhyvoloup1, Anat Melamed2, Ian Anderson1, Delphine Planas3, Janos Kriston-Vizi4, Robin Ketteler4, Chen-Hsuin Lee1, Andy Merritt5, Petronela Ancuta3, Charles Bangham2, Ariberto Fassati1
1University College London, Infection, London, Great Britain; 2Imperial College, Medicine, London, Great Britain; 3University of Montreal, Microbiology & Infection, Montreal, Great Britain; 4University College London, LMCB, London, Great Britain; 5MRC Technology, Centre for Therapeutic discovery, London, Great Britain

Correspondence: Ariberto Fassati

Retrovirology 2016, 13(Suppl 1): O8

To identify key steps of the HIV-1 life cycle that are dependent on capsid (CA), we have developed differential high throughput chemical screening. The CA point mutation N74D makes HIV-1 independent of several host factors. Taking advantage of this phenotype, CD4+ T cells were co-infected with two HIV-1 vectors (WT-GFP and N74D-mCherry), which were identical except for the CA N74D mutation. Compound libraries were screened to find molecules that selectively inhibited infection of WT over N74D, which, by implication, should affect directly or indirectly the interaction between host factors and HIV-1 CA.

We found that digoxin selectively inhibited infection of WT in both CD4 T cell lines and primary memory CD4 T cells, repressing HIV-1 gene expression. The antiretroviral activity of digoxin was dependent on the Na/K ATPase. To identify the mechanism of digoxin selectivity, we infected CD4 T cells with WT or N74D virus in the presence of digoxin then analysed in parallel the cellular transcriptional profile by RNAseq and integration site selection by deep sequencing. RNAseq showed that digoxin up-regulated 221 genes and down-regulated 336 genes ≥fourfold. Within the up-regulated genes, the main biological functions affected by digoxin were regulation of cell cycle, chromatin remodeling, RNA processing, cell survival. Within the down-regulated gene group, the main biological functions impinged by digoxin were antigen presentation, T cell activation and metabolism. Two main gene networks down-regulated by the drug were CD40L and CD38 markers of T cell activation.

We examined >400,000 unique integration sites and discovered that WT virus had a stronger bias relative to N74D virus to integrate within or near genes susceptible to down-regulation by digoxin. Of those, integration within or near genes involved in T cell activation was twofold more frequent for WT virus than N74D virus and 3.8-fold more frequent than integration near any gene. Thus WT virus is more sensitive to digoxin than N74D because it integrates more frequently within or near genes down-regulated by the drug. We discovered a functional connection between integration preference and T cell activation and metabolism that is dependent on CA, which may affect the establishment of latency and the control of viral reactivation.

O9 Characterisation of new RNA polymerase III and RNA polymerase II transcriptional promoters in the Bovine Leukemia Virus genome

Anthony Rodari1, Benoit Van Driessche1, Mathilde Galais1, Nadége Delacourt1, Sylvain Fauquenoy1, Caroline Vanhulle1, Anna Kula1, Arsène Burny2, Olivier Rohr3, Carine Van Lint1
1University of Brussels, Molecular Virology, Gosselies, Belgium; 2University of Brussels, Laboratory of Experimental Hematology, Brussels, Belgium; 3University of Strasbourg, Institut Universitaire de Technologie (IUT) Louis Pasteur de Schiltigheim, Schiltigheim, France

Correspondence: Anthony Rodari

Retrovirology 2016, 13(Suppl 1): O9

Bovine leukemia virus (BLV), the etiologic agent of enzootic bovine leucosis, is a B-lymphotropic oncogenic retrovirus closely related to the human T cell leukemia virus I and II (HTLV-I and II). It is widely accepted that BLV latency, due to the RNA polymerase II (RNAPII) 5′LTR-driven transcriptional and epigenetic repression, is a viral strategy used to escape from the host immune system and contribute to tumor development. However, by deep sequencing and bioinformatics analysis, a highly expressed BLV micro-RNA (miRNA) cluster has been recently reported, suggesting that the silencing dogma in BLV transcriptional regulation is only partially correct. In addition, these viral miRNAs are produced through a non-canonical process, involving RNA polymerase III (RNAPIII).

In this report, we used chromatin immunoprecipitation assays to demonstrate the in vivo recruitment of a bona fide RNAPIII complex to the BLV miRNA cluster both in BLV-latently infected cell lines and in ovine BLV-infected primary cells, through a canonical type 2 RNAPIII promoter. In addition, by specific knockdown of the RPC6 RNAPIII subunit, we showed a direct functional link between RNAPIII transcription and BLV miRNAs expression. Furthermore, in BLV-latently infected cell lines and in ovine BLV-infected primary cells, we showed that both the tumor- and the quiescent-related isoforms of RPC7 RNAPIII subunits were recruited to the miRNA cluster, consistent with previous studies showing that the viral miRNAs are transcribed at all stages of BLV disease. Epigenetically, we demonstrated that the BLV miRNA cluster was enriched in positive epigenetic marks in agreement with the high expression level of the viral miRNAs previously reported. Interestingly, we also demonstrated the in vivo recruitment of RNAPII at the 3′LTR/host genomic junction, associated with positive epigenetic marks. Functionally, we showed that the BLV LTR exhibited a strong antisense promoter activity and identified cis-acting elements of an RNAPII-dependent promoter. Finally, we provided evidence for an in vivo collision between RNAPIII and RNAPII convergent transcriptions.

Taken together, our results provide new insights into alternative ways used by BLV to counteract silencing of the viral 5′LTR promoter.

O10 Tissue-specific dendritic cells differentially modulate latent HIV-1 reservoirs

Thijs van Montfort1, Renee van der Sluis1, Dave Speijer2, Ben Berkhout1
1Academic Medical Center, Medical Microbiology, Amsterdam, Netherlands; 2Academic Medical Center, Medical Biochemistry, Amsterdam, Netherlands

Correspondence: Thijs van Montfort

Retrovirology 2016, 13(Suppl 1): O10

Method: Early after HIV-1 acquisition, cellular viral reservoirs are formed containing latent, but infectious, HIV-1. Cells belonging to these latent reservoirs can, when activated, reestablish new viral infections in the absence of antiretroviral therapy (ART). How latently infected cells are activated in patients is still unclear. To examine whether cellular signaling between cells can activate latent HIV-1, we co-cultured tissue-specific immune cells, including a large panel of dendritic cell subsets with latently infected cells. Next, we measured reversal of HIV-1 latency using our in vitro latency model. Moreover, by using specific signaling pathway inhibitors we determined which intracellular signaling pathways are important for reversion: making latent HIV replication competent upon cell–cell contact.

Results: Our results demonstrate that blood or genital tract dendritic cells do not activate latent provirus in effector T-cells, whereas gut or lymphoid dendritic cells induce virus production from latently infected effector T-cells. Dendritic cells were also able to activate latent HIV-1 in resting T cells from patients as measured with the virus outgrowth assay. We could show that activation was not triggered via classical T-cell stimulation pathways, but that activation occurred via the mTORC1 pathway.

Conclusion: In this study, we show that HIV-1 provirus residing in the effector T-cells is activated from latency by tissue-specific dendritic cell subsets and other immune cells with remarkably different efficiencies. Our results suggest that the observed rapid depletion of T cells in the gut can be attributed to the large quantities of gut dendritic cells that constantly promote virus propagation from latently infected cells.

Session 4: RNA trafficking & packaging

O11 A novel cis-acting element affecting HIV replication

Bo Meng1, Andrzej Rutkowski1, Neil Berry2, Lars Dölken1,3, Andrew Lever1
1University of Cambridge, Division of Infectious Diseases, Cambridge, Great Britain; 2National Institute for Biological Standards and Control, Division of Virology, Potters Bar, Great Britain; 3Julius-Maximilians-Universität Würzburg, Institute for Virology and Immunbiology, Würzburg, Germany

Correspondence: Bo Meng

Retrovirology 2016, 13(Suppl 1): O11

Background: HIV RNA is known to contain a large number of cis-acting sequences such as the TAR stem loop, packaging signal and the Rev responsive element with which HIV controls its lifecycle.

Methods: Bioinformatics analysis across HIV sequences has identified regions with high sequence homology to motifs associated with subcellular trafficking of RNA in other systems. The motifs were synonymously mutated in HIV and viral replication kinetics examined.

Results: Upon disruption of these elements, we observed a phenotypic effect on virus replication manifest as a slow virus growth rate but showed cell type specificity, being most apparent in physiologically relevant T cells but not commonly used cell lines. This effect seems to act at the early stage of the virus life cycle as the overall production of HIV-1 Gag protein is reduced leading to a diminished amount of intracellular viral protein.

Conclusions: Studies to date implicate a transcriptional or post-transcriptional defect involving members of the ESCRT group of cellular proteins.

O12 Tolerance of HIV’s late gene expression towards stepwise codon adaptation

Thomas Schuster, Benedikt Asbach, Ralf Wagner
1Institute of Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany

Correspondence: Thomas Schuster

Retrovirology 2016, 13(Suppl 1): O12

Different organisms show differences in the frequency of occurrence of synonymous codons (codon usage bias). In contrast to humans, HIV uses in general the most A-rich codon for a certain amino acid. Codon usage influences protein production on various levels, starting from gene expression over RNA metabolism to translation.

Previous studies of our group showed that adapting the gag gene to human codon usage (huGag) led not only to a significantly increased protein production but also caused independency of Rev, an accessory protein of HIV which mediates the export of unspliced and incompletely spliced HIV mRNAs. The aim of this work is to gain insight into the effects of codon adaptation on gag expression, especially regarding length and position. For this, subgenomic gag reporter constructs were generated that extend the humanized part of the gene stepwise from 5′end to 3′end as well as from 3′end to 5′end. Those constructs were then transfected into HEK293T cells. Gag expression was investigated on protein level by p24 ELISA as well as on RNA level by Northern blot analysis and qPCR.

It became apparent that humanization of the very 5′ end is necessary for enhanced protein production and Rev-independent expression. Moreover, increasing the length of the humanized sequence starting from the 5′ end directly correlated with p24 levels. Contrary to that, such a correlation is lacking for constructs humanized progressively in 3′ to 5′ direction. Interestingly, even humanization of the whole gag except of the 5′part remained Rev-dependent and thus did not show enhanced gag expression. Inhibition of Rev-mediated export with LMB confirmed the Rev-independency of huGag and showed that Rev-dependency decreased with increasing length of the optimized sequence part. Relative quantification of the RNA levels corroborated the results obtained on protein level. The existence of cryptic splicing products could be ruled out by Northern Blot analysis.

In summary, codon adaptation of the 5′ part of HIV gag seems to be necessary for enhanced and Rev-independent Gag expression. Clarification of the underlying molecular mechanisms could help to understand how HIV benefits from the deviant codon usage.

Session 5: Assembly & release

O13 Importance of the tax-inducible actin-bundling protein fascin for transmission of human T cell leukemia virus Type 1 (HTLV-1)

Christine Gross1, Veit Wiesmann2, Martina Kalmer1, Thomas Wittenberg2, Jan Gettemans3, Andrea K. Thoma-Kress1
1Institute of Clinical and Molecular Virology, Friedrich-Alexander-Universität Erlangen-Nuremberg, Erlangen, Germany; 2Fraunhofer Institute for Integrated Circuits IIS, Erlangen, Germany; 3Ghent University, Department of Biochemistry, Faculty of Medicine and Health Sciences, Campus Rommelaere, Ghent, Belgium

Correspondence: Christine Gross

Retrovirology 2016, 13(Suppl 1): O13

Transmission of Human T-cell leukemia virus type 1 (HTLV-1) between CD4+ T-cells requires cell–cell contacts and remodeling of the host cell cytoskeleton. The viral transactivator Tax is crucial for formation of the virological synapse (VS), a specialized cell–cell contact. At the VS, polarized budding of virions into synaptic clefts and transfer of viral biofilms to target cells takes place. Furthermore, HTLV-1 is transmitted via cellular protrusions. The actin-bundling protein Fascin is Tax-dependently upregulated in HTLV-1-infected T-cells and important for the formation of protrusive structures. Here, we report that Fascin is required for HTLV-1 transmission. Repression of endogenous Fascin by short hairpin RNAs or delocalization of Fascin by nanobodies impaired virus transmission and release using single-cycle replication-dependent HTLV-1 reporter vectors in 293T cells. Beyond, HTLV-1 release and cell-to-cell transmission were enhanced by Tax-induced Fascin in Jurkat T-cells in co-culture with Raji/CD4+ B-cells. In chronically HTLV-1-infected T-cells, virus release, transfer of gag p19 to target cells and transactivation of co-cultured reporter T-cells was decreased upon knockdown of Fascin. Spotting the mechanism, confocal laser scanning microscopy revealed that Fascin and actin accumulate at cell–cell contacts suggesting that Fascin enhances T-cell conjugate formation. However, Fascin was not necessary for Tax-induced T-cell aggregation as exploited by automatic image analysis and flow cytometry-based aggregation assays. Yet, Fascin potentially regulates dissemination of infected cells as knockdown of Fascin reduced adhesion of HTLV-1-infected MT-2 cells. Immunofluorescence analysis of cell–cell-contacts between HTLV-1-positive MS-9 cells co-cultured with Jurkat T-cells revealed the following: (1) short Fascin-containing protrusions extend from infected cells and clutch target cells, (2) Fascin and gag localize in long-distance cellular protrusions in close proximity or partially co-localize, and (3) clusters of Fascin are interspersed by clusters of gag reminiscent of viral biofilms. Taken together, we found that endogenous and Tax-induced Fascin is crucial for HTLV-1 transmission, potentially by redirecting viral proteins to budding sites.

O14 Lentiviral nef proteins antagonize TIM-mediated inhibition of viral release

Minghua Li1, Eric O. Freed2, Shan-Lu Liu1
1The Ohio State University, Center for Retrovirus Research, Columbus, GA, United States; 2National Cancer Institute, HIV Dynamics and Replication, Frederick, MD, United States

Correspondence: Shan-Lu Liu

Retrovirology 2016, 13(Suppl 1): O14

We recently reported that the T cell immunoglobulin and mucin domain (TIM) proteins inhibit release of HIV-1 and other enveloped viruses by interacting with virion- and cell-associated phosphatidylserine (PS) (Li et al., PNAS 111, 2014). In this study, we demonstrate that the Nef proteins of HIV-1 and other lentiviruses antagonize TIM-mediated restriction. We show that TIM-1 exhibits stronger inhibition of the release of Nef-deficient relative to Nef-expressing HIV-1 particles and that ectopic expression of Nef relieves this restriction. Consistent with this finding, knockdown of endogenous TIM-3 in human PBMCs effectively enhances the production of Nef-deficient HIV-1 particles. HIV-1 Nef does not appear to downregulate TIM-1 expression on the cell surface, nor does it disrupt TIM-1 incorporation into HIV-1 virions. Interestingly, we observed that coexpression of SERINC3 and SERINC5 potentiates TIM-1 inhibition of HIV-1 release, and that depletion of SERINC proteins in viral-producer cells rescues TIM-mediated inhibition of HIV-1 release. These results suggest that SERINCs are involved in TIM-mediated restriction of HIV-1 release. In addition to HIV-1 Nef, the Nef proteins of simian immunodeficiency virus (SIV) strains and HIV-2 also antagonize the antiviral activity of TIM-1, suggesting an evolutionarily conserved role of the lentiviral nef gene in antagonizing TIMs. Collectively, our work reveals a new role for lentiviral Nef in antagonizing TIM, and highlights a complex interplay between lentiviral Nef and cellular restriction by TIMs and SERINCs.

Session 6: Pathogenesis & evolution

O15 SEVI and semen prolong the half-life of HIV-1

Janis Müller, Jan Münch
1Institute of Molecular Virology, Ulm, Germany

Correspondence: Janis Müller

Retrovirology 2016, 13(Suppl 1): O15

Human Immunodeficiency Virus Type 1 (HIV-1), the causative agent of Acquired Immunodeficiency Syndrome (AIDS), has currently infected 35 million people and caused 1.5 million deaths in 2013 with no cure available. 85 % of all new infections occur following sexual intercourse where semen is the main vector of HIV-1 transmission. Instead of being a passive carrier, semen enhances HIV infectivity, an activity that is attributed to amyloid fibrils present in semen. These fibrils self-assemble from peptides derived from prostatic acidic phosphatase (PAP) or semenogelins where SEVI (Semen-derived Enhancer of Virus Infection) formed from PAP248–286 is the best characterised. The cationic surface of semen amyloid allows capturing negatively charged HIV-1 virions and increases attachment to and thus infection of target cells. Interestingly, HIV-1 particles are relatively labile and have a reported half-life of only a few hours in serum, probably due to gp120 shedding and membrane rupture induced by shearing forces. We hypothesized that amyloid, by binding and concentrating, may stabilize virions resulting in a prolonged infectious half-life. We thus performed HIV-1 decay kinetics in buffer, and in the presence of SEVI or human semen at 37 °C. We found that the infectious half-life of HIV-1 in buffer was 2.5 ± 1.3 h, independent on the virus concentration used. Incubation with physiological concentrations of SEVI increased infection rates and additionally extended the viral half-life to 12.1 ± 2.7 h (p < 0.0001). This effect was observed using lab adapted NL4-3 as well as transmitted/founder (T/F) HIV-1 variants. Furthermore, HIV-1 incubated in semen reached half-lives up to 10.2 ± 3.2 h (p < 0.0001). This effect was abrogated by depleting semen of amyloid, suggesting it accounts for the observed phenomenon. Normalizing for initial infection rates revealed that the extended half-lives in the presence of SEVI or semen are independent of infectivity enhancing effects. Conclusively, semen increases HIV infection not only by promoting attachment of virions to target cells but also by increasing the infectious half-life. Consequently, antagonizing semen amyloid might not only lower the infectivity but also the stability of HIV-1 particles in semen, and might find application in microbicides designed to impede HIV spread.

O16 CD169+ macrophages mediate retrovirus trans-infection of permissive lymphocytes to establish infection in vivo

Xaver Sewald1,2, Pradeep Uchil2, Mark Ladinsky3, Jagadish Beloor4, Ruoxi Pi2, Christin Herrmann2, Nasim Motamedi1,2, Thomas Murooka5, Michael Brehm6, Dale Greiner6, Thorsten Mempel5, Pamela Bjorkman3, Priti Kumar4, Walther Mothes2
1Max von Pettenkofer Institute, LMU Munich, Dept. of Virology, Munich, Germany; 2Yale University, School of Medicine, Dept. of Microbial Pathogenesis, New Haven, CT, United States; 3California Institute of Technology, Division of Biology and Biological Engineering, Pasadena, CA, United States; 4Yale University, School of Medicine, Department of Medicine, New Haven, CT, United States; 5Harvard Medical School, Center for Immunology and Inflammatory Diseases, Boston, MA, United States; 6University of Massachusetts Medical School, Program in Molecular Medicine, Worcester, MA, United States

Correspondence: Xaver Sewald

Retrovirology 2016, 13(Suppl 1): O16

Background: Retroviruses can infect an organism at mucosal surfaces after sexual and mother to child transmission. They can also be transmitted horizontally through contact with body fluids such as blood, semen and saliva of retrovirus-infected individuals. Irrespective of the path retroviruses take to establish an infection within the host, retroviruses pass through secondary lymphoid organs such as lymph nodes and the spleen. Unfortunately, the critical events and the mechanism leading to the initial infection and subsequent spread of retroviruses at secondary lymphoid organs are currently unknown.

Results: Here, we show that sinus-lining macrophages of secondary lymphoid tissue contribute to establish infection by lymph- and blood-derived human immunodeficiency virus and murine leukemia virus. We identify the I-type lectin CD169/Siglec-1 to mediate Env-independent capture of retroviral particles followed by efficient trans-infection of permissive lymphocytes in peripheral lymph nodes and spleen. Using blocking antibodies and mice lacking CD169, we demonstrate that CD169-dependent trans-infection is required for the establishment of viral infection in mice. Applying intravital microscopy and EM tomography we visualize the formation of infectious synapses between CD169+ macrophages and target cells and subsequent virus transmission across cell–cell contacts in vivo.

Conclusions: Our results highlight the central role of CD169-expressing macrophages in retrovirus transmission and identify trans-infection as an important mechanism to establish retrovirus infection in vivo. Given the strategic position of CD169+ macrophages at the interface between extracellular body fluids such as lymph and blood to lymphoid tissues, our data suggest that retroviruses spread in vivo by a combination of cell-free spread within extracellular fluid followed by the CD169-dependent capture of cell-free virus and efficient trans-infection of permissive lymphocytes.

Reference

  1. 1.

    Sewald X*, Ladinsky M, Uchil P, Beloor J, Pi R, Herrmann C, Motamedi N, Murooka T, Brehm M, Greiner D, Shultz L, Mempel T, Bjorkman P, Kumar P*, Walther Mothes*. Retroviruses use CD169-mediated trans-infection of permissive lymphocytes to establish infection. Science. 2015;350(6260):563–7 (*corresponding author).

O17 Efficient replication of a vpu containing SIVagm construct in African Green Monkeys requires an HIV-1 nef gene

Simone Joas1, Erica Parrish2, Clement Wesley Gnanadurai1,3, Edina Lump1, Christina M. Stürzel1, Nicholas F. Parrish2, Ulrike Sauermann4, Katharina Töpfer4, Tina Schultheiss4, Steven Bosinger5, Guido Silvestri5, Cristian Apetrei6, Nicholas Huot7, Michaela Müller-Trutwin7, Daniel Sauter1, Beatrice H. Hahn2, Christiane Stahl-Hennig4, Frank Kirchhoff1
1Ulm University Medical Center, Institute of Molecular Virology, Ulm, Germany; 2University of Pennsylvania, Departments of Medicine and Microbiology, Philadelphia, PA, United States; 3University of Georgia, Department of Pathology, Athens, GA, United States; 4German Primate Centre, Göttingen, Germany; 5Emory University, Emory Vaccine Center and Yerkes National Primate Research Center, Atlanta, GA, United States; 6University of Pittsburgh, Center for Vaccine Research, Pittsburgh, PA, United States; 7Institut Pasteur, Unité de Régulation des Infections Rétrovirales, Paris, France

Correspondence: Simone Joas

Retrovirology 2016, 13(Suppl 1): O17

The presence of a vpu gene and the lack of Nef-mediated downmodulation of the T cell receptor (TCR) CD3 distinguish HIV-1 and its simian precursors from primate lentiviruses that replicate efficiently in their natural host without causing disease. For example, SIVagm from African Green Monkeys (AGMs), which does not encode vpu but downmodulates CD3, is generally not pathogenic in its natural host species. Here, we generated HIV-1-like derivatives of SIVagm containing a functional vpu and/or an HIV-1 nef allele. Although all chimeric viruses replicated with similar efficiencies in cell culture, their replication fitness in infected AGMs was strikingly different. While insertion of vpu alone prevented SIVagm infection in vivo, insertion of HIV-1 nef attenuated viral replication after acute infection. SIVagm containing both vpu and HIV-1 nef maintained high viral loads for more than 4 years without causing disease, whereas individual introduction of vpu disrupted and of HIV-1 nef impaired viral replicaton in AGMs. Thus, Vpu and Nef cooperate to allow efficient viral replication in vivo and host factors seem to play a key role in the non-pathogenic course of SIVagm infection in AGMs.

To study the genetic and functional evolution of Vpu and Nef in the AGMs infected with SIVagm or the chimeric variants thereof, the 3′ halves of the viral genomes were amplified by single-genome amplification (SGA). The great majority of the PCR fragments contained intact vpu and nef ORFs, and sequence alignments revealed that these accessory genes were highly conserved. All Vpus tested were active in downmodulating CD4, NTB-A and CD1d. Furthermore, all AGM-derived vpu alleles suppressed NF-kB activation, reduced AGM Tetherin cell surface expression and promoted infectious virus release. The nef alleles maintained the functional properties of the parental SIVagm and HIV-1 nef genes. Notably, none of the HIV-1 nef alleles became active in downmodulating CD3 or in counteracting AGM tetherin, irrespectively of the presence of a vpu gene.

O18 Reprogramming initiates mobilization of endogenous mutagenic LINE-1, Alu and SVA retrotransposons in human induced pluripotent stem cells with consequences for host gene expression

Gerald Schumann1, Sabine Jung-Klawitter1, Nina V. Fuchs1, Kyle R. Upton2, Martin Muñoz-Lopez3, Ruchi Shukla2, Jichang Wang4, Marta Garcia-Canadas3, Cesar Lopez-Ruiz3, Daniel J. Gerhardt2, Attila Sebe1, Ivana Grabundzija4, Patricia Gerdes2, Sylvia Merkert5, Andres Pulgarin3, Anja Bock1, Ulrike Held1, Anett Witthuhn5, Alexandra Haase5, Ernst J. Wolvetang6, Ulrich Martin5, Zoltán Ivics1, Zsuzsanna Izsvák4, J. Garcia-Perez3, Geoffrey J. Faulkner2
1Paul-Ehrlich-Institut, Medical Biotechnology, Langen, Germany; 2Mater Research Institute, Brisbane, Australia; 3GENYO, Granada, Germany; 4Max-Delbrück-Center for Molecular Medicine, Berlin, Germany; 5Hanover Medical School, Hanover, Germany; 6Australian Institute for Bioengineering and Nanotechnology, Brisbane, Australia

Correspondence: Gerald Schumann

Retrovirology 2016, 13(Suppl 1): O18

Human induced pluripotent stem cells (hiPSCs) can differentiate into every cell type of the adult body and hold substantial promise for regenerative medicine and as in vitro models of disease and development. However, reprogramming and subsequent cultivation of hiPSCs can induce genetic and epigenetic abnormalities that can result in tumorigenic hiPSCs. Thus, it is unclear if hiPSCs or their derivatives are safe for administration. Genomic mutations may undermine their use in regenerative medicine. Activation of the human endogenous mobile retrotransposons LINE-1 (Long Interspersed Element-1, L1), Alu and SVA has the potential to cause such mutations. In differentiated cells, L1 is primarily suppressed by methylation of its CpG-rich promoter, but we show that reprogramming triggers transcription of functional L1 elements via demethylation and specific transcription factors that are absent from differentiated cells. To investigate if the observed L1 activation in hiPSCs leads to L1-mediated mobilization, we applied retrotransposon capture-sequencing (RC-seq) to 8 hiPSC lines, their parental cells and human embryonic stem cell lines (hESCs). We identified, mapped and validated individual L1, Alu and SVA de novo retrotransposition events that occurred during reprogramming into hiPSCs and cultivation of hiPSCs and hESCs, and timed the period during hiPSC cultivation when individual de novo insertions occurred. Each hiPSC was estimated to carry ~1 L1 de novo insertion. As ~50 % of all de novo retrotransposition events occurred in protein-coding genes that are actively transcribed in hiPSCs, including genes playing roles in oncogenesis, development or signal transduction, we investigated effects of these intronic insertions on host gene expression in hiPSCs. To exemplify the consequences of even short intronic L1 de novo insertions, we analysed effects of the 390-bp L1 de novo insertion L1-dn13 in CADPS2 intron 7 on CADPS2 transcription in hiPSCs, and demonstrate significant interference of L1-dn13 with allelic CADPS2 gene expression. Our experiments demonstrate incidence, and functional impact of reprogramming-activated endogenous retrotransposition in hiPSCs and imply consequences for the biological safety of hiPSC-derived cell therapies.

O19 NF-κB activation induces expression of human endogenous retrovirus and particle production

Tara Hurst, Aris Katzourakis, Gkikas Magiorkinis
1University of Oxford, Zoology, Oxford, Great Britain

Correspondence: Tara Hurst

Retrovirology 2016, 13(Suppl 1): O19

Question: Human endogenous retroviruses (HERVs) are prevalent in the human genome, mainly as defective proviruses or solo long terminal repeats (LTRs). The presence of HERVs can potentially alter human gene expression since the LTRs contain binding sites for numerous transcription factors, as well as for steroid hormone and nuclear receptors. While these sites have been predicted by sequence analysis, they have not been shown to be functional in vivo.

Methods: In order to assess the responsiveness of these binding sites, we used a cell line that is known to be permissive for HERV expression. The human embryonic carcinoma cell line, NCCIT, has been demonstrated to express HERVs and to produce mature particles. This is likely facilitated by the loss of the usual epigenetic suppression of HERV expression, such as by global hypomethylation that is frequently observed in cancer cells. The cells were treated with drugs, hormones and cytokines, then HERV-K env and pol expression was analysed by quantitative PCR (qPCR).

Results: We found that the cytokines interleukin-1α (IL-1α) and tumour necrosis factor α (TNFα), as well as the Toll-like receptor-4 (TLR4) ligand lipopolysaccharide (LPS), increased HERV transcription in the NCCITs. Further, these ligands dramatically increased HERV-K particle production by these cells.

Conclusions: Since these ligands activate innate immune signalling pathways to the transcription factor nuclear factor-κB (NF-κB), we hypothesise that the HERV-K LTRs are responsive to NF-κB binding. Thus, pro-inflammatory conditions could lead to increased HERV-K expression if the LTRs are de-repressed for other reasons, such as in the context of cancer.

Session 7a and b: Innate sensing & intrinsic immunity

O20 Identification of the phosphatase acting on T592 in SAMHD1 during M/G1 transition

Kerstin Schott1, Rita Derua2, Janna Seifried1, Andreas Reuter3, Heike Schmitz1, Christiane Tondera1, Alberto Brandariz-Nuñez4, Felipe Diaz-Griffero4, Veerle Janssens2, Renate König1,5
1Paul-Ehrlich-Institute, Host-Pathogen Interactions, Langen, Germany; 2KU Leuven, Department of Cellular and Molecular Medicine, Laboratory of Protein Phosphorylation and Proteomics, Leuven, Belgium; 3Paul-Ehrlich-Institute, Division of Allergology, Langen, Germany; 4Albert Einstein College of Medicine, Department of Microbiology and Immunology, New York City, NY, United States; 5Sanford Burnham Prebys Medical Discovery Institute, Immunity and Pathogenesis Program, La Jolla, CA, Germany

Correspondence: Kerstin Schott

Retrovirology 2016, 13(Suppl 1): O20

SAMHD1 is a critical HIV-1 restriction factor in non-dividing, myeloid and resting CD4+ T cells. As a dNTPase, SAMHD1 reduces dNTP levels below those required for reverse transcription. The restrictive activity of SAMHD1 is negatively regulated by phosphorylation: in cycling cells, SAMHD1 is phosphorylated at T592 and unable to restrict HIV-1 infection. Upon entry into a non-cycling state, T592 phosphorylation is lost and SAMHD1 rendered active against HIV-1.

SAMHD1 is phosphorylated by CDKs/cyclin A2, but the phosphatase acting on SAMHD1 is currently unknown. Using tandem affinity purification followed by MS analysis, we identified the Aα subunit of protein phosphatase 2A (PP2A) to potentially interact with SAMHD1. PP2A holoenzymes are composed of a scaffolding (A), catalytic (C) and variable regulatory (B) subunit, which can be recruited out of 4 different families. Specific PP2A holoenzymes are known to reverse CDK1-mediated phosphorylation events at the end of mitosis—consistent with the fact that SAMHD1 loses T592 phosphorylation rapidly upon entry into G1, as we could observe in synchronized HeLa ‘Kyoto’ cells using a thymidine block/release protocol.

After pull-down of PP2A-B55α trimers, SAMHD1 was specifically enriched. In line with this observation, only PP2A-B55α trimers were able to efficiently remove SAMHD1 phosphorylation at T592 in in vitro-dephosphorylation assays. We verified the specificity as (i) the inhibitor okadaic acid prevented dephosphorylation by PP2A and (ii) the protein phosphatase 1 (PP1) had no influence. Upon incubation with equilibrated units of de novo purified PP2A dimers or PP1, MS-based quantification of (non-)phosphorylated SAMHD1 peptides revealed that only PP2A dimers were able to remove phosphorylation at T592 in vitro. Furthermore, silencing of PP2A-B55α trimers in vivo using specific siRNAs led to increased T592 phosphorylation in HeLa ‘Kyoto’ cells. To characterise dephosphorylation at T592 at M/G1 transition in more detail, we chemically induced exit from mitosis in HeLa ‘Kyoto’ cells and observed impaired T592 dephosphorylation upon silencing of PP2A-B55α trimers. Taken together, we determined PP2A-B55α holoenzymes responsible for dephosphorylating SAMHD1 during M/G1 transition and rendering SAMHD1 active against HIV-1.

O21 Vpx overcomes a SAMHD1-independent block to HIV reverse transcription that is specific to resting CD4 T cells

Hanna-Mari Baldauf1,2, Lena Stegmann2, Sarah-Marie Schwarz2, Maud Trotard3, Margarethe Martin2, Gina Lenzi4, Manja Burggraf5, Xiaoyu Pan3, Oliver I. Fregoso6, Efrem S. Lim6, Libin Abraham3, Elina Erikson2, Laura Nguyen4, Ina Ambiel2,3, Frank Rutsch7, Renate König5, Baek Kim4, Michael Emerman6, Oliver T. Fackler3, Oliver T. Keppler1,2
1Max von Pettenkofer Institute, Virology, Munich, Germany; 2Institute for Medical Virology, Frankfurt a. M., Germany; 3Department of Infectious Diseases, Integrative Virology, Heidelberg, Germany; 4Center for Drug Discovery, Department of Pediatrics, Atlanta, GA, United States; 5Paul-Ehrlich-Institute, Host-Pathogen-Interactions, Langen, Germany; 6Fred Hutchinson Cancer Research Center, Seattle, WA, United States; 7Department of General Pediatrics, Münster, Germany

Correspondence: Hanna-Mari Baldauf

Retrovirology 2016, 13(Suppl 1): O21

In contrast to activated CD4 T cells, resting CD4 T cells from peripheral blood are highly resistant to productive HIV-1 infection. Infection of resting CD4 T cells is restricted at the level of reverse transcription. This block can be overcome by virion-packaged Vpx proteins that target SAMHD1 for proteasomal degradation and elevate cellular dNTP pools. Here we find that Vpx proteins from distinct SIV lineages, SIVrcm and SIVmnd-2, enhanced the HIV-1 susceptibility in the absence of SAMHD1 degradation or elevation of dNTP pools in resting CD4 T cells, but not macrophages. This infection enhancement was paralleled by a dramatic increase of RT intermediates and total HIV-1 cDNA. Single amino acid changes enabled the prototypic SAMHD1-degrading Vpxmac239 to enhance early post-entry step of HIV infection in rcm/mnd2-like fashion. Importantly, Vpx enhanced HIV infection of resting PMBCs of an AGS patient that lacks expression of functional SAMHD1. These results demonstrate that Vpx, in addition to SAMHD1, overcomes a previously unappreciated post-entry restriction of HIV-1 that is specific to resting CD4 T cells.

O22 The role of SAMHD1 in antiviral restriction and immune sensing in the mouse

Sabine Wittmann1, Rayk Behrendt2, Bianca Volkmann1, Kristin Eissmann1, Thomas Gramberg1
1Universitätsklinikum Erlangen, Institute of Virology, Erlangen, Germany; 2Technical University Dresden, Institute for Immunology, Dresden, Germany

Correspondence: Thomas Gramberg

Retrovirology 2016, 13(Suppl 1): O22

SAMHD1 acts as a dNTP triphosphohydrolase and blocks the replication of retroviruses and retroelements in nondividing cells. Here, we use SAMHD1 knockout mice to analyze the regulation and the mechanism of SAMHD1 restriction and to determine the impact of SAMHD1 on antiviral sensing. Previously, we found that the lack of SAMHD1 triggers a spontaneous upregulation of IFN-inducible genes (ISGs) in various murine cell types. We therefore infected SAMHD1 knockout mice lacking the type I IFN receptor (IFNAR) with HIV reporter virus and analysed splenocytes of the mice 72 h postinfection. We found a strong increase in infected splenocytes of SAMHD1/IFNAR KO mice compared to SAMHD1 KO mice, suggesting an IFN-depended antiviral mechanism in the absence of SAMHD1 in vivo. In addition, we found that, similar to human SAMHD1, the antiviral activity of mouse SAMHD1 is regulated through phosphorylation and is limited to nondividing cells. Comparing the susceptibility to infection with intracellular dNTP levels and SAMHD1 phosphorylation showed that both functions are important determinants of the antiviral activity of murine SAMHD1. In contrast, we found the proposed RNase activity of SAMHD1 to be less important and could not detect any effect of mouse or human SAMHD1 on the level of incoming viral RNA. Our findings show that murine SAMHD1 blocks retroviral infection at the level of reverse transcription and is regulated through a cell cycle-dependent phosphorylation at threonine 603. Together, we show that the antiviral block mediated by murine SAMHD1 is mechanistically similar to what is known for the human protein, making the SAMHD1 KO mouse model a valuable tool to study the impact of SAMHD1 on the replication of different viruses in vivo.

O23 T cells expressing reduced restriction factors are preferentially infected in therapy naïve HIV-1 patients

Sebastian Bolduan1, Herwig Koppensteiner1, Stefanie Regensburg1, Ruth Brack-Werner1, Rika Draenert2, Michael Schindler1,3
1Helmholtz Center Munich, Institute of Virology, Neuherberg, Germany; 2Ludwig-Maximilians-University Munich, Munich, Germany; 3University Hospital Tuebingen, Institute of Medical Virology, Tuebingen, Germany

Correspondence: Michael Schindler

Retrovirology 2016, 13(Suppl 1): O23

Question: So-called host cell restriction factors (RFs) potently suppress HIV-1 replication in cell lines and primary cell culture models. In theory, RFs might represent attractive targets for the development of novel antiviral treatment strategies but their importance for virus control in vivo is controversial.

Methods: Here, we profiled the expression of RFs including p21, SAMHD1 and Tetherin in primary blood-derived mononuclear cells (PBMC) from untreated, therapy-naïve HIV-1 patients and quantified cellular infection levels.

Results: There was overall no correlation between the expression of the individual RFs and HIV-1 control versus progression in patients. However, we identified a T cell population that was negative for intracellular CD2 and expresses low levels of SAMHD1, p21 and the recently identified inhibitor of HIV-1 infectivity SerinC5. CD2-negative T-cells with low RF expression levels were highly HIV-infected in comparison to their CD2+ counterparts and the extent of CD2-negative T-cell infection was a marker of HIV-1 progression. Altogether, we report an association of RF expression levels with the extent of HIV-1 infection in primary T cells directly isolated from untreated patients.

Conclusions: Our study supports the in vivo importance of RFs for HIV-1 control and highlights RFs as promising targets for therapeutic intervention.

O24 cGAS-mediated innate immunity spreads through HIV-1 env-induced membrane fusion sites from infected to uninfected primary HIV-1 target cells

Aurélie Ducroux, Shuting Xu, Aparna Ponnurangam, Sergej Franz, Angelina Malassa, Ellen Ewald, Christine Goffinet
Twincore, Experimental Virology, Hanover, Germany

Correspondence: Christine Goffinet

Retrovirology 2016, 13(Suppl 1): O24

Upon HIV infection, reverse transcribed DNA present in the cytoplasm can be sensed by cellular pattern recognition receptors, resulting in the induction of antiviral type I IFN and expression of interferon-stimulated genes that exert numerous antiviral functions. Specifically, upon DNA binding, the protein cyclic GMP-AMP Synthase (cGAS) synthesizes the unique second messenger cGAMP that binds to STING to activate downstream IFN signaling. It has been proposed that this signaling pathway is engaged upon HIV infection, especially in the absence of TREX1, a cellular exonuclease that degrades excess viral DNA that escapes the viral core. However, HIV-1 perfectly inhibits and evades intrinsic immune responses. Most of these studies have been performed with cell-free HIV-1 particles.

We established an HIV-1 cell-to-cell transmission model using HIV-1-infected human PBLs and autologous macrophages as donor and target cell populations, respectively. Upon cell-to-cell transmission, HIV-1 infection led to a robust interferon response, an observation which was not recapitulated in assays using cell-free HIV-1 particles although the resulting percentage of infected target macrophages was in a similar range as in the condition of cell-to-cell transmission. Specifically, IFN-beta mRNA expression and release of bioactive type I IFN in the culture supernatant were induced.

To understand the specific signatures of the cellular responses to each infection mode, the expression of known cellular key players was decreased using siRNA in target macrophages showing that this IFN induction required STING, but not cGAS. Moreover, direct contact of donor and target cells and functional HIV-1 Env-mediated fusion were necessary. HIV-1-infected PBLs, but not their cell-free virions, contained SVPDE-sensitive, IFN-inducing small molecules, most conceivably cGAMP. These data are in line with intercellular transfer of cGAMP from infected PBLs to target macrophages, where cGAMP binds to STING and triggers a type I IFN induction in a fashion that bypasses the necessity of functional cGAS in macrophages.

We propose that, in HIV-1-infected tissues, cGAMP-mediated innate immunity spreads predominantly via direct cell–cell contacts that result in cytoplasmic mixing of HIV-1-infected and neighboring target cells.

O25 Perturbation of innate RNA and DNA sensing by human T cell leukemia virus type 1 oncoproteins

Sin-Yee Fung1, Ching-Ping Chan1, Chun-Kit Yuen2, Kin-Hang Kok2, Chin-Ping Chan1, Dong-Yan Jin1
1The University of Hong Kong, School of Biomedical Sciences, Pokfulam, Hong Kong; 2The University of Hong Kong, Department of Microbiology, Pokfulam, Hong Kong

Correspondence: Dong-Yan Jin

Retrovirology 2016, 13(Suppl 1): O25

Human T-cell leukemia virus type 1 (HTLV-1) chronically infects 5–20 million people worldwide, causing adult T-cell leukemia (ATL) and tropical spastic paraparesis in a small subset of them. Interferon (IFN) α is a key innate immune effector and its combination with zidovudine, which is a nucleoside reverse transcriptase inhibitor, is the recommended standard first-line therapy for ATL. It is thought that viral RNA and proviral genome in HTLV-1-infected cells are sensed by the host sensor proteins to induce type I IFNs. Exactly how HTLV-1 perturbs this induction remains to be fully understood. In this study we report on the perturbation of innate RNA and DNA sensing by HTLV-1 oncoproteins Tax and HBZ. The induction of IFN-β production was blunted in HTLV-1-transformed ATL cells and in T lymphocytes freshly infected with HTLV-1. Interestingly, HTLV-1 oncoproteins Tax and HBZ displayed differential activity to perturb innate RNA sensing mediated by RIG-I and PACT as well as innate DNA sensing mediated by cGAS, cGAMP and STING. The perturbation occurred at a step prior to IRF3 activation since neither Tax nor HBZ was capable of suppressing the activity of a dominant active phosphomimetic IRF3 mutant IRF3-5D. Tax and HBZ were found to associate with TBK1, IKKε, STING and IRF3. In vitro phosphorylation assay indicated the suppression of TBK1-mediated phosphorylation of IRF3 and other substrates by Tax. Taken together, our findings suggested that HTLV-1 oncoproteins Tax and HBZ differentially modulate innate RNA and DNA sensing in infected cells. Our findings might reveal new strategies and compounds that could be used to improve IFN-based anti-HTLV-1 and anti-ATL therapy. Supported by HKRGC (HKU171091/14M, HKU271215/15 and C7011-15R), HMRF (HKM-15-M01 and 15140682) and SK Yee Medical Research Fund (2011).

O26 Induction and anti-viral activity of Interferon α subtypes in HIV-1 infection

Ulf Dittmer
University Hospital Essen, Institute for Virology, Essen, Germany

Correspondence: Ulf Dittmer

Retrovirology 2016, 13(Suppl 1): O26

HIV-1 is transmitted primarily across mucosal surfaces and rapidly spreads within the intestinal mucosa during acute infection. The type I interferons (IFNs) likely serve as a first line of defense, but the relative expression and antiviral properties of the 12 IFNα subtypes against HIV-1 infection remain unknown. We evaluated the expression of all IFNα subtypes in HIV-1-exposed plasmacytoid dendritic cells and PBMC of HIV-infected individuals. We also determined the relative antiviral potency of each IFNα subtype ex vivo using the human intestinal Lamina Propria Aggregate Culture or an PBMC model. IFNα8, IFNα6, IFNα14, IFNα17, and IFNα21 were the most potent in restricting HIV-1 infection in vitro. IFNα2, the clinically-approved subtype, and IFNα1 were both highly expressed but exhibited relatively weak antiviral activity. The relative potencies correlated the induction levels of HIV-1 restriction factors Mx2 and Tetherin/BST-2.

We also demonstrate in a humanized mouse model that, when delivered at the same high clinical dose, the human IFNα14 subtype has very potent anti-HIV-1 activity in vivo whereas IFNα2 does not. In both post-exposure prophylaxis and treatment of acute infections, IFNα14 but not IFNα2 significantly suppressed HIV-1 replication and proviral loads. Whereas ineffective IFNα2 therapy was associated with CD8+ T cell activation, successful IFNα14 therapy was associated with increased intrinsic and innate immunity including significantly higher induction of tetherin and MX2, increased APOBEC3G signature mutations in HIV-1 proviral DNA, and higher frequencies of TRAIL + NK cells. These results identify IFNα14 as a potent new therapeutic that operates via mechanisms distinct from antiretroviral drugs. The ability of IFNα14 to reduce both viremia and proviral loads in vivo suggests that it has strong potential as a component of a cure strategy for HIV-1 infections.

O27 Vpu-mediated counteraction of tetherin is a major determinant of HIV-1 interferon resistance

Dorota Kmiec1, Shilpa Iyer2, Christina Stürzel1, Daniel Sauter1, Beatrice Hahn2, Frank Kirchhoff1
1Ulm University, Ulm, Germany; 2University of Pennsylvania, Philadelphia, PA; United States

Correspondence: Dorota Kmiec

Retrovirology 2016, 13(Suppl 1): O27

HIV-1 groups M, N, O and P are the result of independent zoonotic transmissions of SIVs infecting great apes in Africa. Among these, only Vpu proteins of pandemic HIV-1 group M strains evolved potent activity against the restriction factor tetherin which inhibits virus release from infected cells. Thus, effective Vpu-mediated tetherin antagonism may have been a prerequisite for the global spread of HIV-1. To determine whether this particular function enhances primary HIV-1 replication and interferon resistance, we introduced mutations into the vpu gene of HIV-1 group M and N strains to specifically disrupt their ability to antagonize tetherin, but not other Vpu functions, such as degradation of CD4, down-modulation of CD1d and NTB-A, and suppression of NF-κB activity. Lack of particular human-specific adaptations reduced the ability of HIV-1 group M Vpu proteins to enhance virus production and release from primary CD4+ T cells at high levels of type I IFN from about fivefold to twofold. Interestingly, transmitted-founder HIV-1 strains exhibited higher virion release capacity than chronic control HIV-1 strains irrespective of Vpu function, and group M viruses produced higher levels of cell-free virions than an N group HIV-1 strain. Thus, efficient virus release from infected cells seems to play an important role in the spread of HIV-1 in the human population and requires a fully functional Vpu protein that counteracts human tetherin.

O28 DNA repair protein Rad18 restricts HIV-1 and LINE-1 life cycle

Yasuo Ariumi1, Mariko Yasuda-Inoue1, Koudai Kawano1, Satoshi Tateishi2, Priscilla Turelli3
1Kumamoto University, Center for AIDS Research, Kumamoto, Japan; 2Kumamoto University, Institute of Molecular Embryology and Genetics, Kumamoto, Japan; 3EPFL, Lausanne, Switzerland

Correspondence: Yasuo Ariumi

Retrovirology 2016, 13(Suppl 1): O28

Introduction: Long interspersed element type 1 (LINE-1, L1) is a mobile genetic element comprising about 17 % of the human genome. L1 utilizes an endonuclease to insert L1 cDNA into the target genomic DNA, which induces double-strand DNA breaks (DSBs). Likewise, human immunodeficiency virus-1 (HIV-1) integration induces DSBs in the human genome and activates DNA damage signaling pathway resulting in a recruitment of DNA repair protein(s). This may facilitate HIV-1 and L1 integration in the human genome. Therefore, host DNA repair machinery has been involved in both HIV-1 and L1 life cycle.

Results: In this study, we have demonstrated that Rad18 post-replication repair protein restricts both HIV-1 and L1 life cycle. Notably, HIV-1 infection or L1 retrotransposition efficiency was enhanced in the Rad18 deficient or the knockdown cells. In contrast, overexpression of Rad18 strongly suppressed L1 retrotransposition as well as L1-mediated Alu retrotransposition. The RING-finger and the Rad6 (E2 ubiquitin-conjugated enzyme)-binding domains but not the Polη-binding domain were required for the inhibitory effect on L1 retrotransposition, suggesting that the ubiquitin E3 ligase activity of Rad18 is important for regulation of L1 mobility. Furthermore, Rad18 sequestered L1 ORF1p in RAD18-nuclear bodies and bound with L1 ORF1p. Similarly, HIV-1 integrase colocalized with Rad18 in Rad18-nuclear bodies and bound with Rad18, indicating an interaction of Rad18 with HIV-1 integrase. Moreover, we found that Rad18 suppressed the late step of HIV-1 replication.

Conclusion: Altogether, these results suggest a potential role of Rad18 DNA repair protein in HIV-1 life cycle and L1 retrotransposition process.

O29 Natural mutations in IFITM3 allow escape from post-translational regulation and toggle antiviral specificity

Alex Compton, Nicolas Roy, Françoise Porrot, Anne Billet, Nicoletta Casartelli, Jacob Yount, Chen Liang, Oliver Schwartz
Institut Pasteur, Paris, France

Correspondence: Alex Compton

Retrovirology 2016, 13(Suppl 1): O29

The interferon-induced transmembrane (IFITM) proteins protect host cells from diverse virus infections. IFITM also incorporate into HIV-1 virions and inhibit virus fusion and cell-to-cell spread, with IFITM3 showing the greatest potency. Here we report that amino-terminal mutants of IFITM3 preventing ubiquitination and endocytosis are more abundantly incorporated into virions and exhibit enhanced inhibition of HIV-1 fusion. An analysis of primate genomes revealed that IFITM3 is the most ancient antiviral family member of the IFITM locus and has undergone repeated duplication in independent host lineages. Some IFITM3 genes in non-human primates, including those that arose following gene duplication, carry amino-terminal mutations that modify protein localization and function. This suggests that “runaway“IFITM3 variants could be selected for altered antiviral activity. Furthermore, we show that adaptations in IFITM3 result in a trade-off in antiviral specificity, as variants exhibiting enhanced activity against HIV-1 poorly restrict Influenza A virus. Overall, we provide the first functional evidence that variation in IFITM3 genes may boost the antiviral coverage of host cells and provide selective functional advantages.

Session 8: Adaptive immunity & immune evasion

O30 Observing evolution in HIV-1 infection: phylogenetics and mutant selection windows to infer the influence of the autologous antibody response on the viral quasispecies

Carsten Magnus1, Lucia Reh2, Penny Moore3, Therese Uhr2, Jacqueline Weber2, Lynn Morris3, Alexandra Trkola2
1ETH Zurich, D-BSSE, Computational Evolution, Basel, Switzerland; 2University of Zurich, Instiute of Medical Virology, Zurich, Switzerland; 3University of the Witwatersrand, Faculty of Health Sciences, Johannesburg, South Africa

Correspondence: Carsten Magnus

Retrovirology 2016, 13(Suppl 1): O30

Question: During HIV-1 infection, a constant interplay of antibodies and the autologous viral quasi-species shapes the developing antibody response and potentially leads to viral escape. A better understanding of these co-evolutionary processes is urgently needed both for designing a vaccine scheme eliciting an effective antibody response and for preventing viral escape in passive immunisation with broadly neutralising antibodies (bnAbs). Of particular importance is the right dosage of these bnAbs as too low concentrations may lead to fast escape of the virus. Thus, we study here at which antibody concentrations a viral escape variant can outcompete its viral ancestor, referred to as mutant selection window (MSW).

Methods: To determine the MSWs of an ancestor/escape pair in respect to a specific bnAb, we analysed experimentally derived inhibition measures (IC50) with a mathematical model. As within-host viral transmission can happen via free-virus transmission and through direct spread between infected and target cells (cell–cell transmission), we calculated the MSW for both transmission routes. With the MSW framework, we characterised the selective pressure of a bnAb lineage leading to viral escape in the HIV-infected individual CAP256 using in vivo-derived longitudinally sampled virus strains and isolated autologous bnAbs. We identified potential CAP256 ancestor/escape pairs based on the viral phylogeny.

Results: We found that escape mutants can out-compete their sensitive ancestral strains for wide concentration ranges in both transmission pathways. The MSW of these viral pairs in respect to the autologous bnAbs additionally allowed us to identify (i) which autologous virus strain will be out-competed (ii) which strain could be a possible ancestor of an escape variant and (iii) whether escape predominantly occurs via free virus or cell–cell transmission.

Conclusions: Our method provides important implications for antibody-based treatment strategies and vaccine design. Not only will the MSW framework allow the selection of the appropriate antibody dosage to suppress the development of escape mutants but, in addition, may help to design a vaccine scheme that mimics the co-evolutionary processes of a natural HIV-1 infection leading to a protective broadly neutralising antibody response in uninfected individuals.

O31 Dose and subtype specific analyses of the anti-HIV effects of IFN-alpha family members

Rashel V. Grindberg1, Erika Schlaepfer1, Gideon Schreiber2, Viviana Simon3, Roberto F. Speck1
1University Hospital Zurich, Infectious Disease and Hospital Epidemiology, Zurich, Switzerland; 2Weizmann Institute of Science, Department of Biological Chemistry, Rehovot, Israel; 3Icahn School of Medicine at Mount Sinai, Department of Microbiology, New York City, NY, United States

Correspondence: Rashel V. Grindberg

Retrovirology 2016, 13(Suppl 1): O31

Interferons (IFN) are cytokines that are fundamental to innate and adaptive immune responses and are named so by their ability to “interfere” with viral replication. The family of human IFN-alpha’s (IFN-α) is encoded on chromosome 9 and comprises 13 different subtypes [1]. These molecules signal through the IFN-α receptors 1 and 2, prompting Jak/Stat activation and induction of interferon stimulated genes (ISGs) [2]. IFN-α 1 and 2 were the first two alpha subtypes characterised [3]. IFN-α2 has a higher specificity and activity than IFN-α1 and so became the prototype IFN for most subsequent studies. Data reporting the anti-viral effects of the other subtypes is sparse.

Here we analysed 12 IFN family members and 6 mutant IFN variants, engineered to have various binding efficiencies, for their ability to inhibit HIV-1 replication in primary human cells such as peripheral blood mononuclear cells, purified CD4+ T-cells as well as monocyte derived macrophages. We tested a range of concentrations (10 U/ml, 100 U/ml and 1000 U/ml) for each of the IFNs. We found a significant difference in activities of the natural IFN variants at lower dosages, which was lost at higher concentrations. Similarly, at lower dosages, the IFN mutants with stronger (60×) binding affinity showed a higher inhibition than the mutants with lower (40×) affinity. However, this difference was also reduced with increasing concentrations, indicating that differential antiviral efficacies between IFN subtypes can be compensated for with higher amounts. These results are consistent with RNA-seq, differential expression and biological network analyses of IFNα-2, IFNα-14 and IFN mutant stimulated macrophages at high and low doses.

Together, these observations bring into focus the importance of understanding putative differential IFN antiviral activity as a function of binding affinity, potency and dosage.

References

  1. 1.

    Gibbert K, et al. Br J Pharmacol. 2013;168(5):1048–58.

  2. 2.

    Hyrcza MD, et al. J Virol. 2007;81(7):3477–86.

  3. 3.

    Paul F, Pellegrini S, Uze G. Gene. 2015;567(2):132–7.

Session 9: Novel antiviral strategies

O32 LEDGIN-mediated inhibition of the integrase-LEDGF/p75 interaction reduces reactivation of residual latent HIV

Zeger Debyser1, Lenard Vranckx1, Jonas Demeulemeester1, Suha Saleh1, Eric Verdin2, Anna Cereseto2,3, Frauke Christ1, Rik Gijsbers1
1KU Leuven, Leuven, Belgium; 2Gladstone Institute of Virology and Immunology, University of California, San Francisco, CA, United States; 3Centre for Integrative Biology (CIBIO), Trento, Italy

Correspondence: Zeger Debyser

Retrovirology 2016, 13(Suppl 1): O32

Persistence of latent, replication-competent HIV provirus is the main impediment towards a cure for HIV/AIDS. Therefore, different therapeutic strategies to eliminate this latent reservoir are currently being explored. Persistence is in part a consequence of proviral integration. LEDGF/p75 acts as the pivotal chromatin tethering-factor targeting HIV integration into active transcription units through its interaction with HIV-1 integrase. We investigated the role of integration site selection in the establishment of HIV persistence employing LEDGF/p75 knockout cells. To evaluate whether the reactivation potential of the quiescent proviral reservoir was dependent on integration site selection during reservoir establishment, LEDGF/p75 WT and KD/KO cell lines were infected with HIVNL4.3-tCD34 or a double reporter virus that allowed direct visualization of the quiescent pool by FACS analysis. We show for the first time that LEDGF/p75 depletion hampers HIV-1 reactivation in cell culture.

Next we demonstrate that LEDGINs, a novel class of integration inhibitors inhibiting the interaction between HIV integrase and the LEDGF/p75 host cofactor, relocate 3D nuclear location and retarget HIV proviral integration out of transcription units, resulting in a HIV reservoir that is refractory to reactivation by different latency-reversing agents both in cell lines an primary CD4+ T-cells. We here propose a novel strategy to reduce the functional HIV reservoir during primary HIV infection by means of drug-induced retargeting of HIV integration and support the potential of these drugs to reduce the likeliness of viral rebound. Pushing the provirus into quiescence could drive the basic reproduction number of HIV below a threshold required for sustained infection even after treatment interruption.

O33 NKG2D-mediated clearance of reactivated viral reservoirs by natural killer cells

Permission for the publication has not been granted.

O34 Inhibition of HIV reactivation in brain cells by AAV-mediated delivery of CRISPR/Cas9

Permission for the publication has not been granted.

O35 CRISPR-Cas9 as antiviral: potent HIV-1 inhibition, but rapid virus escape and the subsequent design of escape-proof antiviral strategies

Ben Berkhout, Gang Wang, Na Zhao , Atze T. Das
Academic Medical Center of the University of Amsterdam, Laboratory of Experimental Virology, Amsterdam, Netherlands

Correspondence: Ben Berkhout

Retrovirology 2016, 13(Suppl 1): O35

Several recent studies demonstrated that the CRISPR-associated endonuclease Cas9 can be used for guide RNA (gRNA)-directed, sequence-specific cleavage of HIV proviral DNA in infected cells. We here demonstrate profound inhibition of HIV-1 replication by harnessing T cells with Cas9 and an antiviral gRNA. However, the virus rapidly and consistently escaped from this inhibition. Sequencing of the HIV-1 escape variants revealed nucleotide insertions, deletions and substitutions around the Cas9/gRNA cleavage site that are typical for DNA repair by the non-homologous end-joining (NHEJ) pathway. We thus demonstrate the potency of CRISPR-Cas9 as an antiviral approach, but any therapeutic strategy should consider these viral escape options. We will present several combinatorial therapeutic approaches designed to block virus escape. More specifically, we tested the simultaneous attack by different guide RNAs on HIV-1 DNA, but also the combinatorial attack on both HIV-1 RNA and DNA forms by combining RNAi and CRISPR-Cas approaches.

Session 10: Recent advances in HIV vaccine development

O36 Priming with a potent HIV-1 DNA vaccine frames the quality of T cell and antibody responses prior to a poxvirus and protein boost

Benedikt Asbach1, Josef Köstler2, Beatriz Perdiguero3, Mariano Esteban3, Bertram L. Jacobs4, David C. Montefiori5, Celia C. LaBranche5, Nicole L. Yates5, Georgia D. Tomaras5, Guido Ferrari5, Kathryn E. Foulds6, Mario Roederer6, Gary Landucci7, Donald N. Forthal7, Michael S. Seaman8, Natalie Hawkins9, Steven G. Self9, Sanjay Phogat10, James Tartaglia10, Susan W. Barnett11, Brian Burke11, Anthony D. Cristillo12, Song Ding13, Jonathan L. Heeney14, Giuseppe Pantaleo15, Ralf Wagner1
1University Regensburg, Institute for Medical Microbiology and Hygiene, Regensburg, Germany; 2University Regensburg, Institute for Clinical Microbiology and Hygiene, Regensburg, Germany; 3Centro Nacional de Biotecnología, Madrid, Spain; 4Arizona State University, Biodesign Institute, Tempe, AZ, United States; 5Duke University Medical Center, Durham, NC, United States; 6National Institutes of Health, Vaccine Research Center, Bethesda, MD, United States; 7University of California, Irvine, CA, United States; 8Beth Israel Deaconess Medical Center, Center for Virology and Vaccine Research, Boston, MA, United States; 9Fred Hutchinson Cancer Research Center, Statistical Center for HIV/AIDS Research and Prevention, Seattle, WA, United States; 10Sanofi Pasteur, Swiftwater, PA, United States; 11Novartis Vaccines and Diagnostics, Inc., Cambridge, MA, United States; 12Advanced BioScience Laboratories, Inc., Rockville, MD, United States; 13EuroVacc Foundation, Lausanne, Switzerland; 14University of Cambridge, Department of Veterinary Medicine, Cambridge, Great Britain; 15University of Lausanne, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland

Correspondence: Benedikt Asbach

Retrovirology 2016, 13(Suppl 1): O36

The use of heterologous immunisation regimens, and the employment of various improved vector systems as well as antigen designs, has proven to lead to vigorous increases in immunogenicity in the assessment of HIV-1 vaccine candidates in non-human primates. In order to resolve interdepencies between different delivery modalities, we compared three different poxvirus boost regimens after a DNA prime. Three groups of rhesus macaques were each immunized with the same DNA vaccine encoding for Gag, PolNef, and gp140 at weeks 0, 4 and 8. At week 20, the groups were boosted either (i) by administering the poxviral replication-competent NYVAC-KC-vector by scarification, or (ii) by i.m. injection, or (iii) by i.m. injection of the replication-deficient NYVAC-vector, carrying the same antigens. Finally, macaques were boosted with adjuvanted, recombinant gp120 protein at weeks 28, 32, and 49 in order to enhance humoral responses. The regimen elicited very potent CD4+ and CD8+ T cell responses in a well-balanced manner, peaking 2 weeks after the NYVAC-boost. T cell responses subsequently declined and were hardly influenced by subsequent protein boosts. T-cells were broadly reactive and polyfunctional, with high fractions of cells secreting all three cytokines assessed. All animals exhibited antigen-specific humoral responses already after the poxvirus boost, that by trend slightly increased following protein administration. Polyclonal reactivity of IgG antibodies was highest against C clade Env-proteins, yet with substantial cross-reactivity towards other clades. Serum IgA responses were absent. Substantial ADCC activity, and very high ADCVI activity were observed in sera obtained after the last protein boost.

As no differences were evident between the groups, it can be concluded that the potent priming induced by the DNA vaccine initially framed the epitope specificity and polyfunctionality of the T cell responses in a way that the subsequent poxvirus boost only led to an increase in the response magnitudes without skewing the quality. This emphasizes the importance of selecting the best mixture of vector systems in heterologous vaccination regimens.

O37 Passive immunisation with a neutralising antibody against HIV-1 Env prevents infection of the first cells in a mucosal challenge rhesus monkey model

Christiane Stahl-Hennig1, Viktoria Stab2, Armin Ensser3, Ulrike Sauermann1, Bettina Tippler2, Dennis Burton4, Matthias Tenbusch2, Klaus Überla3
1German Primate Center, Infection Models, Göttingen, Germany; 2Ruhr-University Bochum, Department of Molecular and Medical Virology, Bochum, Germany; 3Friedrich-Alexander University Erlangen-Nuremberg, Institute of Clinical and Molecular Virology, Erlangen, Germany; 4The Scripps Research Institute, Department of Immunology and Microbial Science, La Jolla, CA, United States

Correspondence: Christiane Stahl-Hennig

Retrovirology 2016, 13(Suppl 1): O37

Pretreatment with antibodies targeting the HIV-1 Env protein has been shown to prevent systemic infection in non-human primate models for AIDS. To investigate whether these antibodies can block infection of the “first cell” at the viral portal of entry, genetically tagged challenge viruses based on simian immunodeficiency virus (SIV) were constructed. They use HIV-1 Env for entry into target cells during the first replication cycle, but switch to SIV Env for all subsequent rounds of infection. Macaques were passively immunized with the HIV-1 Env specific neutralising antibody PGT121 a day before rectal exposure to the switching challenge virus. Ten days after viral inoculation a 100-fold reduction of HIV-1 Env-mediated infection events was observed in various organs and blood compared to control animals treated with a HIV-unrelated antibody. A lesser level of inhibition of infection was also detected against a HIV Env pseudotype, which is resistant to PGT121 neutralisation. Thus, antiviral antibodies can reach sufficient levels at mucosal surfaces to provide sterilizing immunity in a very strict sense.

O38 HIV antibody Fc-glycoforms drive B cell affinity maturation

Galit Alter1, Giuseppe Lofano2, Anne-Sophie Dugast1, Viraj Kulkarni3, Todd Suscovich1
1Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, United States; 2Novartis Vaccines and Diagnostics S.r.l. (a GSK Company), Research Center, Siena, Italy; 3National Cancer Institute, Center for Cancer Research, Frederick, MD, United States

Correspondence: Galit Alter

Retrovirology 2016, 13(Suppl 1): O38

HIV broadly neutralising antibodies (bNAbs) confer protection following passive immunisation, but the mechanisms that allow these humoral immune responses to evolve in a fraction of infected individuals is unclear. Features of bNAbs suggest that extensive germinal center (GC) reactions are required to drive these unusual super-high affinity responses required to drive broad viral neutralisation. However, the mechanisms that underlie this extensive affinity maturation are poorly understood. Given that antigens are delivered to follicular dendritic cells (FDCs), the key antigen presenting cells in the GC, in the form of antibody immune complexes, here we speculated that key features of immune complexes may drive enhanced affinity maturation. Thus using a set of high-throughput, comprehensive Fc-characterizing assays that capture the remarkable biodiversity of antibody Fc-effector functions, linked to multivariate computational tools, we profiled differences in immune complex (IC) biology among individuals that develop neutralising antibodies (“neutralizers”) in an unbiased manner. “Neutralizers” possessed higher Fc-mediated antibody effector functions, HIV-specific antibody titers, and overall enhanced binding to Fc-receptors as compared to subjects that did not possess broadly neutralising antibodies. Interestingly, enhanced antibody effector function in “Neutalizers” was not associated with overall changes in antibody subclass distribution but was associated with the selective production of antibodies that were more highly sialylated. Interestingly, ICs generated with “neutralizer” antibodies drove enhanced antibody class switch and affinity maturation following immunisation of mice compared to ICs generated with “non-neutralizer” antibodies. Moreover, ICs generated with solely sialylated antibodies demonstrated en equally enhanced capacity to drive B cell maturation by class switch, to expand GC B cell numbers, and drive enhanced antibody affinity maturation. These data argue that the generation of particular antigen-specific sialylated Fc-profiles drives enhanced antibody maturation, potentially contributing the prolonged affinity maturation required for the evolution of broadly neutralising antibody responses. Thus rational vaccine design strategies that induce enhanced sialylated HIV-specific antibodies may enhance affinity maturation and therefore accelerate the induction of broadly neutralising antibodies against HIV.

Poster presentations

Topic 1: Entry & uncoating

P1 Dynein light chain is required for murine leukemia virus infection

Tatiana Opazo1,2, Felipe Barraza1,2, Diego Herrera1,2, Andrea Garces1, Tomas Schwenke1,2, Diego Tapia1, Jorge Cancino1, Gloria Arriagada1,2
1Universidad Andres Bello, Ciencias Biologicas, Viña del Mar, Chile; 2Millenium Nucleus Biology of Neuropsiquiatric Disorders NuMIND, Valparaiso, Chile

Correspondence: Gloria Arriagada

Retrovirology 2016, 13(Suppl 1): P1

Question: How Murine Leukemia virus (MLV) travels from the cell membrane towards the nucleus, and the mechanism of nuclear entry of MLV viral DNA in dividing cells, still remain unclear. It seems likely that the MLV preintegration complex (PIC) interacts with cellular proteins to perform those tasks. We have recently published that microtubule motor cytoplasmic dynein complex (DC) and its regulator proteins interact with MLV preintegration complex at early stages of infection, suggesting a direct interaction between the incoming viral particles and the DC, and have shown an essential role for the dynein regulators dynactin and NudEL on MLV infection.

Methods: Here we show a shRNA screening of the dynein chains on MLV infection.

Results: We found that silencing or over expressing a specific light chain of the cytoplasmic DC profoundly reduced the efficiency of infection and increases the infection of MLV in a dose dependent manner, respectively. The block of restriction was determined to be in a step after reverse transcription, but before nuclear entry, by MLV reporter viruses, without altering traffic of cellular components.

Conclusions: We propose that the light chains of the cytoplasmic DC are an important piece of the host machinery needed for MLV infection.

P2 Peptide paratope mimics of the broadly neutralising HIV-1 antibody b12

Christina Haußner1, Dominik Damm2, Anette Rohrhofer2, Barbara Schmidt2, Jutta Eichler1
1Friedrich-Alexander-University Erlangen-Nuremberg, Department of Chemistry and Pharmacy, Erlangen, Germany; 2Institute of Microbiology and Hygiene, Clinical Virology and Infection Immunology, Regensburg, Germany

Correspondence: Barbara Schmidt

Retrovirology 2016, 13(Suppl 1): P2

Introduction: Broadly neutralising antibodies (bnAbs) against envelope structures of HIV-1 are promising candidates for antiviral prophylaxis or therapy. We hypothesized that peptides mimicking the complementarity-determining regions (CDRs) of the bnAb b12, which recognizes the CD4 binding site of the HIV-1 envelope glycoprotein gp120, may be able to inhibit the entry of HIV-1 into target cells in a b12-related fashion.

Methods: Peptides presenting the sequences of the heavy chain CDRs of b12 were synthesized by solid-phase synthesis. The virus neutralising activity of b12 itself, as well as the paratope mimetic peptides, was tested using a reporter cell line. To further clarify the mechanism of inhibition, the proviral clone HIV-1NL4-3 was sequentially passaged in increasing concentrations of either b12 or paratope mimetic peptides. After obtaining resistant viruses, they were sequenced and analysed for cross-resistance against each inhibitor.

Results: The paratope mimetic peptides were found to specifically recognize the b12 antigen, i.e. gp120 from b12-susceptible HIV-1, but not gp120 from b12-resistant HIV-1. Furthermore, the peptides were able to inhibit HIV-1 infection in cellular infections assays, at micromolar concentrations. A peptide with mutations at key amino acids within the three CDR loops was inactive. Viruses resistant against b12 and the paratope mimetic peptide, respectively, occurred after 15 and 6 passages, respectively. b12 selected one mutation (V370E), located directly in the CD4 binding site, while the mutations induced by the paratope mimetic peptide were in the vicinity of this site. The b12-resistant virus was also resistant against the paratope mimetic peptide. Vice versa, cross-resistance was also evident, but less pronounced.

Conclusion: Peptides which mimic the CDRs of the broadly neutralising antibody b12, exhibit antiviral activity. Ongoing chemical and structural optimization of the peptides is expected to enhance their antiviral activity, demonstrating the therapeutic potential of antibody paratope mimics.

P3 Investigating cellular pathways involved in the transmission of HIV-1 between dendritic cells and T cells using RNAi screening techniques

Rebecca Midgley, James Wheeldon, Vincent Piguet
Cardiff University, Dermatology, Cardiff, Great Britain

Correspondence: Rebecca Midgley

Retrovirology 2016, 13(Suppl 1): P3

Background: Dendritic cells (DC) are thought to be amoung the earliest targets of HIV-1 infection and act as a ‘Trojan Horse’ concealing the virus from the innate immune system and delivering it directly to T-cells via virological synapses to promote infection.

Question: DC studies have led to the identification of several restriction factors and cellular structures that aid viral transmission, however work still needs to be done on how the virus is trafficked through the cell to the virological synapse and how the virus evades degradation within DC.

Method: Advancements in RNAi screening libraries allows the investigation of multiple pathways which could potential be involved in viral transmission such as cell signalling. A high-throughput method has been developed using On-Target SMART pool siRNA (Dharmacon) in Monocyte derived dendritic cells (MDDC) to investigate the transfer of HIV-1 from DC to T-cells.

Results: Initial membrane traffic screening results analysed using network mapping software (Cytoscape 3.3.0) implicates a role of several genes involved in vesicle mediated transport at both the plasma and vesicle membrane and a role for actin cytoskeleton organisation in DC to T-cell HIV transfer.

Conclusion: The discovery of potential cellular targets involved in HIV-1 transmission between DC and T-cells could potentially lead to the discovery of potential drug targets to be developed to combat HIV-1 infection in the future.

P4 Co-receptor tropism in HIV-1, HIV-2 monotypic and dual infections

Priyanka Khopkar1,2, Megha Rohamare3, Smita Kulkarni1
1National AIDS Research Institute, Virology, Pune, India; 2Symbiosis International University, Department of Health and Biomedical Sciences, Pune, India; 3National Institute of Virology, Academic Department, Pune, India

Correspondence: Priyanka Khopkar

Retrovirology 2016, 13(Suppl 1): P4

Background: HIV entry is mediated through the retroviral envelope, CD4 and chemokine receptors (majorly CXCR4, CCR5). Co-receptor tropism plays a crucial role in HIV transmission and pathogenesis. HIV-1 co-receptor tropism is extensively studied; however scarce data exists on tropism exhibited during HIV-2 and HIV-1&2 dual infections from endemic regions. In the present study, we determined co-receptor tropism amongst Indian drug naïve patients with HIV-1 (n = 10); HIV-2 (n = 12) and HIV-1&2 dual infection (n = 13) confirmed by ELISA and Western Blot.

Methods: PBMC co-cultures using patient’s PBMCs were carried out and virus growth confirmed by various assays viz. for i) HIV-1: HIV-1 p24 antigen capture ELISA on culture supernatants and IFA on infected cells; ii) HIV-2: ExaVir™ load, TZM-bl infectivity assay on culture supernatants for CPE and IFA on infected cells; iii) HIV-1&2 dually infected viral cultures: presence of HIV-1 was confirmed by HIV-1 p24 antigen capture ELISA; independent IFAs were carried out for HIV-1 and HIV-2 and overall infection was assessed using TZM-bl infectivity assays and ExaVir™ load (Fig. 1). Co-receptor tropism was determined using GHOST cell assays in co-receptor specific cell lines (GHOST CXCR4; GHOST CCR5); the results were confirmed microscopically for syncytium formation and on FACS using FLOWJO software for green florescence protein production under the control of HIV tat.

Fig. 1
figure1

Confirmation of HIV-2 and HIV-1 and 2 virus isolations

Results: Our results suggest that amongst ten HIV-1 drug naïve primary isolates one isolate was CXCR4 tropic, four were CCR5 tropic and five were dual tropic viruses. Of twelve HIV-2 drug naïve primary isolates, eight were CCR5 tropic and four were dual tropic. In case of HIV-1&2 dually infected primary isolates, seven were CXCR4 tropic and six were dual tropic viruses (Fig. 2).

Fig. 2
figure2

Results of co-receptor tropism

Conclusion: During the early stage of HIV infection, the transmitting virus is almost invariably CCR5 tropic. In contrast to these findings our data suggests 50 % existence of dual tropism in Indian HIV-1 and HIV-2 infection. Although we report in vitro phenotypic co-receptor tropism for the first time on Indian HIV-1&2 dual infections, it is difficult to attribute our findings to the independent tropism of the two viruses, as it is a preliminary baseline finding that needs further genotypic confirmation.

P5 Characterisation of the role of CIB1 and CIB2 as HIV-1 helper factors

Ana Godinho-Santos1, Allan Hance2, Joao Goncalves1, Fabrizio Mammano2
1Research Institute for Medicines, University of Lisbon, Lisbon, Portugal; 2INSERM, University Paris-Diderot, Paris, France

Correspondence: Fabrizio Mammano

Retrovirology 2016, 13(Suppl 1): P5

Questions: Understanding how cellular proteins participate in HIV-1 replication provides insights into the mechanisms of individual steps of retroviral replication, and may identify potential novel antiviral targets. In this study we evaluated the contribution of the calcium- and integrin-binding 2 (CIB2) protein, previously identified by RNAi screening as a potential helper factor, and its homolog, CIB1.

Methods: Jurkat cells and primary CD4+ T-lymphocytes were transduced by lentiviral vectors expressing shRNA targeting either CIB1 or CIB2, resulting in efficient and specific knockdown of expression of these proteins.

Results: HIV-1 replicated with significantly lower efficiency in transduced cells, identifying CIB1 and CIB2 as non-redundant HIV-1 helper factors. By exploring individual steps of virus replication in CIB1- or CIB2-knockdown cells, we determined that CIB1 and CIB2 are required for efficient HIV-1 entry into target cells, both for CCR5- and CXCR4-tropic viruses. Also, both the cell-free and cell-associated entry pathways were affected by CIB proteins depletion. In contrast, knockdown of CIB1 and CIB2 had no impact on the infectivity of HIV-1 virions pseudotyped with the VSV-G envelope in either Jurkat cells or CD4+ T-lymphocytes. We found no evidence that the level of CIB1 and CIB2 expression influenced cell viability, cell proliferation, receptor-independent viral binding to the cell surface, later steps involved in the transport and uncoating of the viral capsid, nuclear import and integration, or the production, export and infectivity of progeny virions. CIB1 and CIB2 knockdown were found to reduce the expression of surface receptors implicated in HIV-1 infection, including CCR5, CXCR4 and integrin α4β7.

Conclusions: In this study we have shown CIB1 and CIB2 knockdown significantly inhibited HIV-1 replication, specifically affecting the viral entry step. CIB1 and CIB2 knockdown reduced the expression of surface receptors implicated in HIV-1 infection, suggesting at least one mechanism through which these proteins may promote viral infection.

P6 Buffering deleterious polymorphisms in the highly constrained C2 region of HIV-1 envelope by the flexible V3 domain

Romain Gasser1, Meriem Hamoudi1, Martina Pellicciotta1, Zhicheng Zhou2, Clara Visdeloup3, Philippe Colin2, Martine Braibant3, Bernard Lagane2, Matteo Negroni1
1Institut de Biologie Moleculaire et Cellulaire, Strasbourg, France; 2Institut Pasteur, Paris, France; 3Université François Rabelais, Tours, France

Correspondence: Matteo Negroni

Retrovirology 2016, 13(Suppl 1): P6

Covariation is an essential evolutionary process leading to the coevolution of parts of proteins and genomes. In organisms that are subject to strong selective pressure, coevolution is central to keep the balance between the opposite requirements of antigenic variation and retention of functionality. Being the viral component the most exposed to the environment, the envelope glycoprotein gp120 of HIV-1 constitutes the main target of the immune response raised against this virus. This is also reflected by the fact that its more external portions are characterised by extensive sequence heterogeneity leading to broad antigenic variation. We are interested in the study of coevolution within the HIV-1 envelope through the functional characterisation of chimerical envelopes of primary isolates of HIV-1 group M.

We observe that a single polymorphism, present at the level of the viral population in the conserved internal region C2, is sufficient to totally abolish Env functionality when inserted in an exogenous envelope backbone. Two main alterations of the functionality of the envelope are responsible for the loss of functionality: a decrease in the proportion of trimeric forms and a post-CCR5 binding defect, likely due to an interference with the subsequent conformational changes that lead to membrane fusion. We also observed that a complete restoration of functionality can be achieved by compensatory polymorphisms introduced at the level of the external and hypervariable region V3. Interestingly, this is accompanied by a change in antigenic profile and in the response to treatment with membrane-fusion inhibitors.

Altogether, these results indicate that (1) coevolution between V3 and C2 can control the formation of trimeric spikes on the viral particles, (2) even if two V3 loops bind CCR5 with similar affinity, the subsequent steps required to carry out membrane fusion can have markedly different outcomes, suggesting that the modes of binding can be different. (3) Finally, these results suggest that variable regions, besides harbouring intrinsic extensive antigenic diversity themselves, can also contribute to sequence diversification in more structurally constrained parts of the gp120, further increasing the genetic flexibility of the protein.

This research was supported by Sidaction and the ANRS.

P7 Entry inhibition of HERV-K(HML-2) by an Env-IgG fusion protein

Jula Wamara, Norbert Bannert
Robert Koch Institute, Department 1, FG18, Berlin, Germany

Correspondence: Jula Wamara

Retrovirology 2016, 13(Suppl 1): P7

The recognition of a cell-surface protein or a group of surface proteins and their specific interaction with the viral envelope protein represent the first stage and one of the key events of the viral infection process. For the human endogenous retrovirus HERV-K(HML-2), the cellular receptor(s) which mediate entry of the virus have not been yet identified.

We have generated a fusion protein comprising a codon-optimized version of the reconstituted envelope glycoprotein of HERV-K113 (OriCoEnvgp42) and the Fc-region of the human immunoglobulin protein (h-IgG). This fusion-protein is secreted from transfected cells and can be easily purified. OriCoEnvgp42-IgG interferes profoundly with the HERV-K(HML-2) virus/receptor interaction and inhibits virus entry in a concentration-dependent manner. In order to shed light on the receptor binding site of HERV-K(HML-2) Env, we aligned the protein sequence with the Env sequence of the most closely related Betaretrovirus, mouse mammalian tumor virus (MMTV). This allowed the putative HERV-K(HML-2) Env receptor binding site (RBS) to be predicted, based on the MMTV Env RBS. RBS mutants were then generated from a C-terminal truncated HERV-K(HML-2) Env and the OriCoEnvgp42. The RBS mutants Env_D139A and Env_Δ144–153 were expressed at wild-type levels, but in contrast to the reconstituted original Env did not facilitate entry of pseudotyped lentiviruses, indicating a defect in receptor binding. However, mutants derived from the OriCoEnvgp42-IgG fusion protein still interfered with the entry of reporter viruses pseudotyped with the reconstituted HERV-K(HML2) Env.

These data suggest the presence of additional, relevant RBS sequences and should help the complete RBS of HERV-K(HML-2) to be characterised. The OriCoEnvgp42-IgG fusion protein will be a very useful tool in elucidating the mechanisms of cell-entry by the virus.

Topic 2: Reverse transcription & integration

P8 The R263K/H51Y resistance substitutions in HIV integrase decreases levels of integrated HIV DNA over time

Thibault Mesplede, Nathan Osman, Kaitlin Anstett, Jiaming Calvin Liang, Hanh Thi Pham, Mark Wainberg
Jewish General Hospital, Lady Davis Institute, McGill AIDS Centre, Montreal, Canada

Correspondence: Mark Wainberg

Retrovirology 2016, 13(Suppl 1): P8

Background: HIV DNA that is integrated into cells can persist indefinitely within HIV-positive individuals, even when they are successfully treated with antiretroviral therapy (ART). This persistence of integrated HIV DNA within reservoirs contributes to an inability to achieve viral eradication.

No patient treated with the integrase inhibitor dolutegravir (DTG) in first-line therapy has ever developed resistance to this drug. Our group showed in culture that DTG can select for a R263K mutation in Integrase that confers low-level DTG resistance. Although rare, failure in treatment-experienced, integrase inhibitor-naïve individuals who are treated with DTG is associated with the emergence of the R263K substitution in integrase as well as plasma viral loads that are lower than those observed when treatment failure occurs with ART regimens that do not contain DTG. This is likely due to the fact that R263K confers only low-level resistance against DTG and also decreases both viral replication capacity and viral integrase activity in short-term infectivity assays. We sought to determine the effect of the DTG-specific R263K resistance substitution on integration during long-term infection.

Methods: We measured HIV integration by Alu-mediated QPCR over 5 weeks of infection of Jurkat cells with WT, R263K and H51Y/R263K viruses. Levels of integration were measured every week and expressed relative to integration of the WT virus after week 1. Means ± standard deviations were calculated and Student’s t test was used to evaluate significance of differences.

Results: The R263K substitution impaired HIV integration over time and was associated with a progressive decline in levels of integrated HIV DNA in peripheral blood mononuclear cells. Even further impairments were noted if both the R263K and H51Y substitutions were simultaneously present and this is because H51Y further impairs viral replication and integrase activity at the same time that it only slightly increases levels of drug resistance against DTG.

Conclusions: This raises the possibility that emergence of the R263K/H51Y substitutions in individuals who experience treatment failure with DTG might result in a progressive decline in the size of the viral reservoir. Further studies to study this hypothesis are underway in SIV-infected macaques.

P9 The Retrovirus Integration Database (RID)

Wei Shao1, Jigui Shan1, Mary Kearney2, Xiaolin Wu3, Frank Maldarelli2, John Mellors4, Brian Luke1, John Coffin5, Stephen Hughes2
1Leidos Biomedical Research, Inc, Advanced Biomedical Computing Center, Frederick, MD, United States; 2National Cancer Institute, HIV Dynamics and Replication Program, Frederick, MD, United States; 3Leidos Biomedical Research, Inc, Frderick National Lab for Cancer Research, Frederick, MD, United States; 4University of Pittsburgh, Division of Infectious Disease, Pittsburgh, PA, United States; 5Tuffs University, Boston, MA, United States

Correspondence: Wei Shao

Retrovirology 2016, 13(Suppl 1): P9

Retrovirus replication requires that the virus integrate a DNA copy of its genome into the host chromosomal DNA. Although there are numerous published studies that describe the distribution of retrovirus integration sites, there is no large publicly available centralized database that contains the available integration site information. Currently, most of the retrovirus integration site information is found in supplementary materials, which makes retrieving it for meta-analyses difficult. Thus, a comprehensive database that includes information about integration sites is critically needed.

We have built the NCI Retrovirus Integration Database (RID, Fig. 3) to record integration site information for all retroviruses, including HIV-1, HTLV, and MLV. RID is an in-progress MySql based relational database. Briefly, it has tables to store host, virus and subtypes, sample/patient and tissue and demographics information without (for integration sites in humans) revealing personally identifiable information. Chromosome, integration site, associated genes, exon/intron information, provirus orientation, and the references from which the information was collected are provided on the database. Additionally, we built several tools into the database to facilitate mapping of the integration sites to USCS genome browser, to plot the integration site patterns on a chromosome (Fig. 4), and to display provirus LTRs in their inserted genome sequence for PCR/probe design. We also created a robust, user friendly website that allows users to query the database and analyze the data dynamically. All the integration sites are mapped to human genome build hg19 for easy comparison between different datasets.

Fig. 3
figure3

NCI Retrovirus Integration Database

Fig. 4
figure4

Pattern plotting result. a One dataset, b comparison of two datasets

In conclusi