Ancient, independent evolution and distinct molecular features of the novel human T-lymphotropic virus type 4
- William M Switzer1Email author,
- Marco Salemi2,
- Shoukat H Qari†1,
- Hongwei Jia†1,
- Rebecca R Gray2,
- Aris Katzourakis3,
- Susan J Marriott4,
- Kendle N Pryor4,
- Nathan D Wolfe5, 6,
- Donald S Burke7,
- Thomas M Folks8 and
- Walid Heneine1
© Switzer et al; licensee BioMed Central Ltd. 2009
Received: 23 October 2008
Accepted: 02 February 2009
Published: 02 February 2009
Human T-lymphotropic virus type 4 (HTLV-4) is a new deltaretrovirus recently identified in a primate hunter in Cameroon. Limited sequence analysis previously showed that HTLV-4 may be distinct from HTLV-1, HTLV-2, and HTLV-3, and their simian counterparts, STLV-1, STLV-2, and STLV-3, respectively. Analysis of full-length genomes can provide basic information on the evolutionary history and replication and pathogenic potential of new viruses.
We report here the first complete HTLV-4 sequence obtained by PCR-based genome walking using uncultured peripheral blood lymphocyte DNA from an HTLV-4-infected person. The HTLV-4(1863LE) genome is 8791-bp long and is equidistant from HTLV-1, HTLV-2, and HTLV-3 sharing only 62–71% nucleotide identity. HTLV-4 has a prototypic genomic structure with all enzymatic, regulatory, and structural proteins preserved. Like STLV-2, STLV-3, and HTLV-3, HTLV-4 is missing a third 21-bp transcription element found in the long terminal repeats of HTLV-1 and HTLV-2 but instead contains unique c-Myb and pre B-cell leukemic transcription factor binding sites. Like HTLV-2, the PDZ motif important for cellular signal transduction and transformation in HTLV-1 and HTLV-3 is missing in the C-terminus of the HTLV-4 Tax protein. A basic leucine zipper (b-ZIP) region located in the antisense strand of HTLV-1 and believed to play a role in viral replication and oncogenesis, was also found in the complementary strand of HTLV-4. Detailed phylogenetic analysis shows that HTLV-4 is clearly a monophyletic viral group. Dating using a relaxed molecular clock inferred that the most recent common ancestor of HTLV-4 and HTLV-2/STLV-2 occurred 49,800 to 378,000 years ago making this the oldest known PTLV lineage. Interestingly, this period coincides with the emergence of Homo sapiens sapiens during the Middle Pleistocene suggesting that early humans may have been susceptible hosts for the ancestral HTLV-4.
The inferred ancient origin of HTLV-4 coinciding with the appearance of Homo sapiens, the propensity of STLVs to cross-species into humans, the fact that HTLV-1 and -2 spread globally following migrations of ancient populations, all suggest that HTLV-4 may be prevalent. Expanded surveillance and clinical studies are needed to better define the epidemiology and public health importance of HTLV-4 infection.
Deltaretroviruses are a diverse group of human and simian T-lymphotropic viruses (HTLV and STLV, respectively) that until lately were composed of only two distinct human groups called HTLV types 1 and 2 [1–7]. Two new HTLVs, HTLV-3 and HTLV-4, were recently identified in primate hunters in Cameroon effectively doubling the genetic diversity of deltaretroviruses in humans [6, 8]. Collectively, members of the HTLV groups and their STLV analogues are called primate T-lymphotropic viruses (PTLV) with PTLV-1, PTLV-2, and PTLV-3 being composed of HTLV-1/STLV-1, HTLV-2/STLV-2, and HTLV-3/STLV-3, respectively. The PTLV-4 group currently has only one member, HTLV-4, since a simian counterpart has yet to be identified .
STLV-1 has a broad geographic distribution in nonhuman primates (NHPs) in both Asia and Africa thus providing humans with historical and contemporaneous opportunities for exposure to this virus [2, 4, 5, 9, 10]. Indeed, phylogenetic analysis of simian T-lymphotropic viruses type 1 (STLV-1) and global HTLV-1 sequences suggests that different STLV-1s were introduced into humans multiple times in the past resulting in at least six phylogenetically distinct HTLV-1 subtypes [1–5, 11]. Recently, a new HTLV-1 subtype was found in Cameroon that was closest phylogenetically to STLV-1 from monkeys hunted in this region and which shared greater that 99% nucleotide identity . Since similar high sequence identities are typically seen in both vertical and horizontal linked transmission cases of HTLV-1 [12–14], the finding of this new HTLV-1 subtype in Cameroon suggests a relatively recent cross-species transmission of STLV-1 to this primate hunter and that these zoonotic infections continue to occur in persons naturally exposed to NHPs.
Although a simian T-lymphotropic virus type 2 (STLV-2) has been identified in two troops of captive bonobos (Pan paniscus), the zoonotic relationship of this divergent virus to HTLV-2 is less clear [15–17]. Like STLV-1, STLV-3 also has a broad and ancient geographic distribution across Africa [9, 10, 18–23]. Thus, while only three distinct HTLV-3 strains have been identified to date in Cameroon [6, 8, 24], it is conceivable that HTLV-3 may be prevalent throughout Africa and, like HTLV-1 and HTLV-2, potentially could be spread globally through migrations of infected human populations. Expanded screening is needed to define the prevalence of HTLV-3 in human populations. Likewise, the epidemiology of HTLV-4 is not well understood since only a single human infection has been reported and a simian counterpart has yet to be identified . Although limited sequencing of very small gene regions showed that HTLV-4 is most genetically related to STLV-2 and HTLV-2, but is a distinct lineage separate from all known PTLVs , understanding the evolutionary relationship of HTLV-4 to known PTLVs requires additional phylogenetic analyses using longer sequences or the complete viral genome.
Like HIV, both HTLV-1 and -2 have spread globally and are pathogenic human viruses [1, 2, 5, 7, 25]. HTLV-1 causes adult T-cell leukemia/lymphoma (ATL), HTLV-1 associated myelopathy/tropical spastic paraperesis (HAM/TSP), and other inflammatory diseases in less than 5% of those infected [2, 5, 7]. HTLV-2 is less pathogenic than HTLV-1 and has been associated with a neurologic disease similar to HAM/TSP . The recent identification of HTLV-3 and HTLV-4 in only four persons limits an evaluation of the disease potential and secondary transmissibility of these novel viruses [6, 8, 24]. However, complete genomic sequences of these viruses can provide insights on the genetic structure and whether functional motifs that are important for viral expression and HTLV-induced leukemogenesis are preserved [6, 8, 24, 26–30]. In addition, determination of the viral sequence will be important to develop improved diagnostic assays to better understand the epidemiology of this novel human virus.
In this paper, we report the first full-length sequence of HTLV-4 and demonstrate by detailed phylogenetic analysis that this virus clearly falls outside the diversity of all other PTLVs. The observed low nucleotide substitution rate, absence of evident genetic recombination, and conserved genomic structure of HTLV-4 demonstrate the genetic stability of this virus. In addition, molecular dating suggests that the HTLV-4 lineage split from the progenitor of PTLV-2 about 200 millennia ago and is older than the ancestors of HTLV-1, HTLV-2, and HTLV-3. We also highlight biologically important molecular features in HTLV-4 that are unique or common to HTLV-1, HTLV-2, and HTLV-3.
Comparison of the HTLV-4(1863LE) proviral genome with prototypical PTLVs
Percent Nucleotide Identity and Amino Acid Similarity of HTLV4(1863LE) with other PTLV Prototypes1.
Dating the origin of HTLV-4(1863LE) and other PTLVs
The long branch leading to the HTLV-4 strain suggests an ancient, independent evolution of this human retrovirus. Hence, additional molecular analyses were performed to estimate the divergence times of the HTLV and PTLV lineages. Although we and others have reported finding a clock-like behavior of PTLV sequences using partial LTR or env sequences [3, 18–20], we were unable to confirm these results. Instead, the clock hypothesis was strongly rejected (p < 0.00001) for the 1st + 2nd codon position alignment of full-length PTLV genomes without LTRs, as well as for separate alignments of full-length gag, pol, env and tax genes (p < 0.00001 in each case) suggesting significant evolutionary rate heterogeneity among the different viral lineages. Indeed, sequence analysis showed unequal base composition for some lineages and substitution saturation at the 3rd codon position (cdp) for all PTLVs (Additional file 1, Fig. S1). Substitution saturation was not observed in the 1st and 2nd cdps (Additional file 1, Fig. S1) and these sites were thus suitable for estimating posterior evolutionary rates and divergence dates of PTLV by using Bayesian analysis with a MCMC algorithm.
PTLV evolutionary rates1 at 1st + 2nd codon positions of different gene regions assuming a Bayesian relaxed molecular clock.
0.23 (0.168 – 0.303)
3.02 × 10-7
2.89 × 10-7
1.65 – 4.78 × 10-7
0.417 (0.356 – 0. 475)
7.92 × 10-7
7.57 × 10-7
3.93 – 12.7 × 10-7
0.29 (0.228 – 0.359)
4.08 × 10-7
3.9 × 10-7
2.25 – 6.44 × 10-7
0.311 (0.215 – 0.421)
4.32 × 10-7
4.17 × 10-7
2.34 – 6.47 × 10-7
PTLV evolutionary time-scale calculated with a Bayesian relaxed molecular clock using 1st + 2nd codon positions of different gene regions1.
(169,200 – 600,200)
(136,400 – 559,900)
(172,300 – 638,900)
(104,050 – 353,100)
(68,650 – 201,300)
(60,450 – 220,600)
(72,450 – 244,800)
(50,400 – 143,250)
(50,200 – 115,200)
(40,410 – 79,340)
(41,600 – 84,000)
(40,900 – 76,100)
HTLV-1(Mel)/PTLV1a, b 2
(40,000 – 57,900)
(40,000 – 58,400)
(40,000 – 58,400)
(40,000 – 58,500)
(85,050 – 321,800)
(63,850 – 334,750)
(89,650 – 378,000)
(49,800 – 218,250)
(57,000 – 226,550)
(41,300 – 205,100)
(51,850 – 223,350)
(29,850 – 135,200)
(11,650 – 87,100)
(9,800 – 82,800)
(8,150 – 58,100)
(12,100 – 70,050)
(15,750 – 58,200)
(13,900 – 54,900)
(13,750 – 54,100)
(12,800 – 41,050)
HTLV-2a, b 3
(14,350 – 30,000)
(12,000 – 28,700)
(12,000 – 28,350)
(12,000 – 27,950)
(28,800 – 120,700)
(25,010 – 129,800)
(32,950 – 122,200)
(16,400 – 81,150)
Genomic organization and characterization of the HTLV-4(1863LE) structural and enzymatic proteins, and the LTR
Translation of predicted protein open reading frames (ORFs) across the viral genome identified all major Gag, Pro (protease), Pol, and Env proteins, as well as the regulatory proteins, Tax and Rex (Fig. 1). Translation of the overlapping gag and pro and pro and pol ORFs occurs by one or more successive -1 ribosomal frameshifts that align the different ORFs. The conserved slippage nucleotide sequence 6(A)-8nt-6(G)-11nt-6(C) is present in the Gag-Pro overlap starting at nucleotide 1997. Similarly, the Pro-Pol overlap slippage sequence (TTTAAAC) was identical to that seen in HTLV-1 and HTLV-2 but which is different from that found in HTLV-3 by a single nucleotide substitution at the beginning of this motif (GTTAAAC) . Importantly, the asparagine codon (AAC) crucial for the slippage mechanism is conserved in all HTLVs.
The structural and group-specific precursor Gag protein consisted of 424 amino acids (aa), and is predicted to be cleaved into the three core proteins p19 (matrix), p24 (capsid), and p15 (nucleocapsid) similar to HTLV-1, HTLV-2, and HTLV-3. Across PTLVs, Gag is one of the most conserved proteins, with the HTLV-4 Gag having 82% to 86% similarity to HTLV-1, PTLV-2, and PTLV-3 (Table 1). The Gag capsid protein (214 aa) showed about 90% to 93% similarity to other PTLV capsids, while the matrix (129 aa) and nucleocapsid (81 aa) proteins were somewhat less conserved, showing less than 85% similarity to HTLV-1, PTLV-2, and PTLV-3 (Table 1). The conservation of the capsid protein supports the observed cross-reactivity to Gag seen with plasma from the HTLV-4-infected person in Western blot (WB) assays employing HTLV-1 antigens [6, 38].
The predicted size of the HTLV-4 (1863LE) Env polyprotein is 485 aa, which is slightly shorter than the Env of PTLV-2 (486 aa), PTLV-1 (488 aa), and PTLV-3 (491–492 aa). The Env surface (SU) protein (307 aa) showed the most genetic divergence from other PTLVs with only 70% – 81% similarity, while the transmembrane (TM) protein (178 aa) was highly conserved across all PTLVs, sharing 85% – 94% similarity, supporting the use of recombinant HTLV-1 TM protein (GD21) on WB strips to identify divergent PTLVs, including HTLV-4. The HTLV-4(1863LE) SU showed about 86% similarity to the HTLV-2 type specific SU peptide (K55) despite the observed weak reactivity of anti-HTLV-4(1863LE) antibodies to [6, 38] K55 spiked onto WB strips. This amino acid similarity is somewhat greater than the 67.4% and 72.1% similarity of the HTLV-1 and HTLV-3 SUs to K55, respectively, allowing serologic discrimination of HTLV-2 from HTLV-1 in this region. In contrast, the HTLV-4(1863LE), HTLV-2, and HTLV-3 SUs share from 68.8% to 70.8% similarity to the HTLV-1 type specific SU peptide (MTA-1). Although these results are limited to testing the sera of a single HTLV-4-infected individual, they suggest that higher antibody reactivity to the HTLV-2-type specific peptide may be observed in HTLV-4-infected persons .
The glucose transporter GLUT1 has been shown to be the HTLV-1 and -2 envelope receptor and a retrovirus binding domain (RBD) for GLUT1 has been identified in the SU of these viruses [39, 40]. Analysis of the HTLV-4 Env protein revealed a putative RBD located at positions 85 – 138 of the SU that shared about 80%, 78%, and 87% amino acid similarity with the RBDs of HTLV-1(ATK), HTLV-2(MoT), and that identified by analysis of the HTLV-3(2026ND) Env, respectively. In addition, both aspartic acid and the tyrosine residues located as positions 106 and 114 of HTLV-1(ATK) are highly conserved in the putative HTLV-4 RBD and all other PTLV RBDs (data not shown), supporting a critical role for these residues as the receptor binding core as previously suggested .
Characterization of Regulatory and Accessory Proteins of HTLV-4(1863LE)
Although important functional motifs are highly conserved in PTLVs, phenotypic differences between HTLV-1 and HTLV-2 Tax proteins have lead to speculation that these differences account for the different pathologies associated with both HTLVs . Recently, the C-terminus of Tax1, but not Tax2, has been shown to contain a conserved PDZ binding domain present in cellular proteins involved in signal transduction and induction of IL-2-independent growth required for T-cell transformation [29, 44, 45] and may contribute to the phenotypic differences between these two viral groups. The consensus PDZ domain has been defined as S/TXV-COOH, where the first amino acid is serine or threonine, X is any amino acid, followed by valine and the carboxyl terminus. Tax4 does not contain a PDZ domain (Fig. 10), suggesting that like HTLV-2, HTLV-4 may possibly be less pathogenic than HTLV-1.
Here we report the first complete nucleotide sequence and genomic characterization of the recently discovered HTLV-4. We show that the genome of this novel human virus is genetically equidistant from HTLV-1, HTLV-2, and HTLV-3. Robust phylogenetic and molecular clock analysis confirms that HTLV-4 clearly falls outside the diversity of PTLV-1, PTLV-2, and PTLV-3, demonstrating that HTLV-4 is the only known member of a distinct PTLV group we call PTLV-4. Combined, these results strongly support the HTLV-4/PTLV-4 nomenclature proposed for this virus . The phylogenetic stability seen across HTLV-4 and other PTLV genomes also demonstrates the absence of major recombination events occurring in PTLV despite evidence of dual infections in humans and primates [9, 49]. Furthermore, these results support the distinct evolutionary history of HTLV-4 and other PTLVs demonstrating that they are not recent genetic recombinants from pre-existing viral genomes. This finding contrasts with other retroviruses like HIV in which frequent recombination contributes substantially to genetic diversity .
Bayesian MCMC statistical methods have recently been developed to accurately infer dates of evolutionary events, to investigate the origin of viral epidemics, and to estimate historical population dynamics [32, 51]. Molecular dating of the HTLV-4 predecessor using these robust methods suggests that this novel PTLV lineage originated almost 200 millennia ago, which predates the inferred origin of the ancestors of HTLV-1, HTLV-2, and HTLV-3 by about 76,000 – 191,000 ya . Two equally parsimonious hypotheses on the origin of HTLV-4 can thus be proposed by the inferred ancient existence of the PTLV-4 lineage. First, it is possible that HTLV-4(1863LE) is a current descendent of the ancestral PTLV-4 that infected humans as they evolved in Africa and represents a strain circulating within humans living in this geographic region. Interestingly, the inferred date of the HTLV-4 ancestor also coincides with the appearance of Homo sapiens sapiens, estimated to have occurred around 200 – 400 K ya, suggesting the emergent human lineage may have been a suitable host for the ancestral PTLV-4. If this is not just an evolutionary historical coincidence of both virus and host, then HTLV-4 may indeed be the oldest human deltaretrovirus as inferred from the molecular dating of all four HTLV groups. Alternatively, HTLV-4(1863LE) could also be the result of a more recent zoonotic infection with a very divergent STLV present in NHPs in the forests of Cameroon. Additional information on the diversity of HTLV-4 and its likely simian counterpart will be needed to determine whether HTLV-4(1863LE) truly originated as H. sapiens sapiens evolved, and persists in humans today, or represents a more recent zoonotic transmission from an NHP. As of yet, a simian counterpart of HTLV-4 has not been identified in Cameroon or elsewhere despite the identification of other novel STLVs in this region [9, 10, 22]. Nonetheless, the inability to find "STLV-4" may be due to sampling and screening biases in the selection of NHP species and the geographic locations examined [9, 32].
The inference of an ancient split of HTLV-4(1863LE) from the PTLV-2 lineage, combined with the wide geographic distribution of STLVs and a history of STLVs crossing into humans [2, 8–10, 18–21], all imply that HTLV-4 infection may be more prevalent. Repeated and historical cross-species infections of humans with various STLV-1 strains led to the emergence and dissemination of several HTLV-1 subtypes in West-Central Africa [2, 4–6]. Similar evidence suggests that the newly identified HTLV-3 infections also potentially arose from multiple, independent past or contemporary introductions of different STLV-3 strains into humans [6, 8, 31]. Given that both HTLV-1 and HTLV-2 followed human population migrations out of Africa and across the globe as humans evolved, HTLV-4 and HTLV-3 may also have spread globally. A more precise determination of the origin and distribution of HTLV-4 infection will require further studies, such as expanded surveillance in both humans and NHPs. However, serosurveys for HTLV-4 may be complicated by the inability to discriminate this infection from HTLV-2 since they both show similar WB profiles and the sensitivity of serological assays for identifying HTLV-4 is currently unknown [6, 35]. Thus, additional diagnostic tools are required to determine the level of HTLV-4 penetration into the general population and to search for the potential primate origin of HTLV-4(1863LE). Screening for HTLV-4 will be facilitated by the development and application of serologic and molecular assays based on the sequences reported here. For example, since the HTLV-4 Gag matrix and nucleocapsid and the envelope surface proteins are divergent from PTLV-1, PTLV-2, and PTLV-3 it may be possible to use them in serologic assays to differentiate the four PTLV groups.
Virus classification is a topic of ongoing discussion and suggestions for nomenclature are typically based on lumping or splitting of taxa into distinct groups. Deltaretrovirus species are classified by the International Committee on Taxonomy of Viruses (ICTV) by differences in genome sequence and viral oncogenes, antigenic properties, natural host range, and pathogenicity. For example, HTLV-1 and HTLV-2 are distinguished mostly by phylogenetic diversity and variable disease outcomes of each virus. Recently, a new deltaretrovirus species, STLV-5, was proposed based on limited analyses of small tax/rex sequences from a Macaca arctoides (strain MarB43) that was originally classified as STLV-1 [4, 10]. Herein, we show by using robust phylogenetic analysis of major coding regions and complete viral genomes that expansion of the current PTLV nomenclature from four to six putative major taxonomic species or groups should be considered. Our natural classification of PTLV groups is based on rigorous phylogenetic inference that demonstrates with high confidence the formation of very distinctive monophyletic lineages outside the diversity of all known viral groups, combined with genetic distances demonstrating the putative new lineage is nearly equidistant from all previously characterized groups, and the placement of the new PTLV groups near the root of the PTLV phylogeny. The first four PTLV phylogroups consist of HTLV-1/STLV-1, HTLV-2, HTLV-3/STLV-3, and HTLV-4. We confirm the existence of the putative STLV-5(MarB43) lineage, while the sixth group consists of the STLV-2(PanP) and STLV-2(PP1664) viruses. However, for simplicity we suggest maintaining the STLV-2 nomenclature historically used for this particular viral group. Each proposed new viral group clearly falls outside the diversity of their nearest PTLV relatives (PTLV-1 and HTLV-2, respectively), is monophyletic with strong bootstrap support and posterior probabilities, and are all roughly genetically equidistant from other PTLVs, and hence should all be classified as distinct viral species. As with all viral nomenclature, PTLV classification as proposed here will require approval of ICTV.
In addition to understanding viral evolutionary history, analysis of full-length genomes can also provide basic information on the replication and pathogenic potential of new viruses. Thus, we examined in detail the genetic structure and sequence of HTLV-4 to determine if important functional motifs involved in viral expression and HTLV-induced leukemogenesis are preserved [26–30, 44]. All enzymatic, regulatory, and structural proteins are well conserved in HTLV-4(1863LE), including conserved functional motifs in Tax that are important for viral gene expression and T-cell proliferation, suggesting HTLV-4 is replication competent. We also observed several important molecular features of the HTLV-4 genome involved in viral expression and pathogenicity that are either similar or distinct from other HTLVs. For example, the absence of a PDZ domain in the Tax protein of HTLV-4(1863LE), known to be important in cellular signal transduction and T-cell transformation [29–31], is similar to what is seen in HTLV-2 but not in HTLV-1 and HTLV-3 . The absence of PDZ suggests that the HTLV-4 Tax may be more phenotypically similar to the HTLV-2 than the HTLV-1 Tax. Furthermore, the high amino acid identity of the Tax4 and Tax2 proteins also suggests that Tax4 may function similarly to Tax2 . However, whether the absence of a PDZ domain in HTLV-4 is associated with an absence of specific cellular and/or clinical outcomes like HTLV-2 will require further investigation.
We also identified unique putative c-Myb and Pbx-1 transcription factor binding sites in the U3 region of the LTR of HTLV-4(1863LE). c-Myb is a proto-oncogene that is expressed in T cells induced by mitogen or antigenic stimulation and is involved in cell cycle progression and proliferation of T lymphocytes, such that continuous deregulation of cell cycling may play a role in leukemogenesis . c-Myb has been shown to bind to the HTLV-1 and feline leukemia virus LTRs to increase viral transcription [53, 54]. Like c-Myb, dysregulation of the homeoprotein Pbx-1 can also increase leukemogenesis by disturbing hematopoiesis . We demonstrate here that the potential c-Myb binding site in the HTLV-4 LTR specifically binds c-Myb, suggesting that it may also promote LTR-mediated viral expression and which may help overcome the loss of the distal 21-bp repeat element observed in the HTLV-4 LTR. For example, Pbx-1 has been demonstrated to up-regulate transcription of another retrovirus, murine leukemia virus (MuLV), by binding to conserved Pbx-1 transcription factor sites present in MuLV LTRs . The presence of putative c-Myb and Pbx-1 binding sites in the HTLV-4 LTR may provide novel mechanisms of transcriptional control at both the viral and cellular levels not previously known for HTLV. Nevertheless, involvement of the putative novel binding sites in viral transcription and leukemogenesis will require additional studies.
Although originally reported to be exclusive to HTLV-1 , we now provide additional evidence for a putative HBZ region among all PTLVs, including HTLV-4(1863LE). Despite the absence of canonical bZIP domains, preliminary experiments show that proteins are transcribed from the HTLV-3, and -4 antisense mRNAs and all were potent inhibitors of Tax induction of HTLV LTR activity with similar cellular localizations like that of the HTLV-1 HBZ (unpublished data). These results not only confirm the predicted HBZ sequences and proteins in these viruses but also demonstrate the potential importance of HBZ in PTLV replication. The finding of a potential bZIP region on the antisense strand of all PTLV genomes also indicates that the nomenclature for this protein should be renamed from HBZ to AEP for antisense encoding protein as suggested . The potential role of AEP in HTLV-induced oncogenesis may be less clear since HTLV-1 and HTLV-2 infection result in different clinical outcomes, while pathologies for HTLV-3 and HTLV-4 have not yet been reported. Additional studies are required to confirm the potential effect of the predicted AEP transcripts and proteins on HTLV-4 and PTLV expression and any role they may have on leukemogenesis.
The novel HTLV-4 genome independently evolved from an ancient deltaretrovirus lineage and contains many of the functional motifs important for viral expression and possibly oncogenesis, including two novel transcription factor binding sites in the LTR. More studies are needed to further characterize the unique molecular features of HTLV-4 identified here, and to determine whether HTLV-4 is endemic and pathogenic in humans to better understand the public health importance of this novel human virus.
DNA preparation and PCR-based genome walking
DNA was prepared from uncultured PBMCs available from person 1863LE identified in the original PTLV surveillance study in Cameroon reported in detail elsewhere . DNA integrity was confirmed by β-actin polymerase chain reaction (PCR) as previously described . All DNA preparation and PCR assays were performed in a laboratory where only human specimens are processed and tested according to recommended precautions to prevent contamination. To obtain the full-length genomic sequence of HTLV-4 we first PCR-amplified small regions of each major coding region by using nested PCR and degenerate PTLV primers (Fig. 1). The tax (730-bp), polymerase (pol) (662-bp), and envelope (env) (319-bp) sequences were amplified by using primers and conditions provided elsewhere [6, 31]. An additional short HTLV-4 sequence, 440-bp in length, that overlaps the end of tax and the beginning of the 3'LTR was amplified using standard PCR conditions and 45°C annealing with the external primers PGTAXF7a 5'TGATGGIWSICCIATGATTTCCGG 3', PGTAXF7b 5'TGATGGGTCTCCTATGATTTCCGG3' and PGTATA1+2R1 5'TCCTGAACYGTCYYYRCGCTTTTATAG3' and the internal primers PGTAXF8 5'TGCCCIAARIMIGGICAGCCATCTTT3' and PGTATA1+2R1.
HTLV-4(1863LE)-specific primers were then designed from sequences obtained in each of the four viral regions described above and were used in nested, long-template PCRs (Expand High Fidelity kit containing both Taq and Tgo DNA polymerases (Roche)) to fill in the gaps in the genome as depicted in Fig. 1. The external and internal primer sequences for the LTR-pol fragment are 1863LF2 5'CCAAGGACAAAACTAGCAGGGACT3' and 1863PR4 5'GGGGATGGTAAAGGCGAAGTAGGG3', and 1863LF3 5'CGTCCCAGCCCAGCCTCAAAACCA 3'and 1863PR5 5'GGGAATCTGGAAGAAAGCGTCCGT3', respectively. The external and internal primer sequences for the pol-env fragment are 1863PF3 5'GTCCTCTCATGGTCTCCCAGTTTCCCAG 3' and 1863ER 5'GCTGGAGTGGTAGGAGGAGATAC3', and 1863PF5 5'CACTTCCTGGGCCAAATCATACATCCAGATC3' and 1863ER3 5'GGCTGGCCTGAA GTACTGGGATGCC3', respectively. The external and internal primer sequences for the env-tax fragment are 1863EF1 5'CCTGCCAAAACCTGATCACCTATTC3' and 1863TR1 5'CGACAACTCGTCCATCGATGG3' and 1863EF2 5'CCCTGTATCTCTTCCCACACTGGGTA C3' and 1863TR2 5'GGGGAGCATAATCCACCGGAGATGG3', respectively. The remaining 3' end of the genome was obtained by using the primers 1863pXF1 5'AACTCCGCCAATACACCCAACAGG3' and 1863LR1 5'GGAGGGGTTTGAGTACAGCGGGCT3' in a single round of PCR amplification.
PCR products were purified with a Qiaquick PCR purification kit (Qiagen), and sequenced in both directions with a BigDye terminator cycle kit and automated sequencers (Applied Biosystems). Selected PCR products were also cloned into the pCR4-TOPO vector using the TOPO TA Cloning kit (Invitrogen) and recombinant plasmid DNA was prepared using the Qiagen plasmid purification kit prior to automated sequencing.
Percent nucleotide divergence was calculated using the GAP program in the Genetic Computer Group's (GCG) Wisconsin package . Examination of functional genetic motifs involved in viral expression, regulation, and HTLV-induced oncogenesis was done by detailed comparison of the HTLV-4 genome with full-length PTLV sequences [26–29, 31, 44]. Identification of potential transcription factor binding sites in the HTLV-4 genome was performed using the program TESS (Transcription Element Search System) . Secondary structure of the LTR RNA was determined using the program RNAstructure v4.2 program . Comparison of full-length PTLV genomes available at GenBank and determination of genetic recombination was done using HTLV-4(1863LE) as the query sequence and the F84 (maximum likelihood) model and a transition/transversion ratio of 2.28 implemented in the program SimPlot . Prediction of splice acceptor (sa) and splice donor (sd) sites was done using an artificial neural network implemented in the NetGene2 program  and with the Spliceview program .
Nucleotide substitution saturation was evaluated using pair-wise transition and transversion versus divergence plots using the DAMBE program . Unequal nucleotide composition was measured by using the TREE-PUZZLE program . Phylogenetic trees were inferred with the parameters estimated from the Clustal W  sequence alignments of each gene and the full-length genome after removing indels by using Modeltest v3.7  and Neighbor-Joining (NJ) methods in the MEGA v4.0  program and maximum-likelihood (ML) analysis in PAUP* , TREE-PUZZLE , and PhyML . The reliability of the inferred tree topology was tested with 100 (PAUP*) to 1000 bootstrap replicates (NJ and PhyML) or 100,000 puzzling steps (TREE-PUZZLE). Trees were viewed and edited using FigTree v1.1.2 .
PTLV evolutionary rates and divergence times
In order to estimate a reliable divergence time for the cenancestor (most recent common ancestor) of the HTLV-4(1863LE) lineage, we generated separate alignments of gag, pol, env, and tax genes from all full-length PTLV genomes available at GenBank by using Clustal W. Sequence gaps and 3rd codon positions were removed, and minor adjustments in the alignment were made manually. The best fitting evolutionary model for the aligned sequences was determined using a hierarchical likelihood ratio test as described elsewhere . A variant of the GTR model, allowing four different substitution rate categories (rA↔C = rA↔T = rG↔T = 1, rA↔G = 9.35, rC↔G = 0.67, rC↔T = 5.79), with gamma-distributed rate heterogeneity (a = 0.694) and an estimated proportion of invariable sites (0.185), was determined to best fit the data.
The molecular clock hypothesis, or constant rate of evolution, for the PTLV tree was tested with the likelihood ratio test . Likelihoods were calculated using the best fitting nucleotide substitution model either with or without the enforcement of the global clock constraint with the program PAML . The PTLV evolutionary rate assuming the global molecular clock model was estimated by using the divergence time of 40,000 – 60,000 years ago (ya) for the Melanesian HTLV-1 lineage (HTLV-1mel) and 12,000–30,000 ya for the most recent common ancestor of HTLV-2a/HTLV-2b native American strains according to the formula: evolutionary rate (r) = branch length (bl)/divergence time (t) . Such divergence dates were based on well-established genetic and archaeological evidence suggesting that ancestors of indigenous Melanesians and Australians migrated from Southeast Asia or the introduction of ancestral indigenous Indians into North America via the Bering Straight during those times [3, 4, 32]. The evolutionary rate was also estimated by employing a Bayesian Markov Chain Monte Carlo (MCMC) molecular clock method, allowing for either a strict or a relaxed molecular clock , implemented in the BEAST software package . For each analysis, we used the calibration dates discussed above as a strong prior for the time of the most recent common ancestor (tMRCA) of the HTLV-1Mel/HTLV-1a,b and HTLV-2a,b lineages, respectively. In practice, the upper and lower divergence times estimated from anthropological data were used to define the interval of a strong uniform prior distribution from which the MCMC sampler would sample possible divergence times for the corresponding node in the tree. For each model, the Bayesian calculation consisted of three independent 100,000,000 generations MCMC with sampling every 1,000th generation. Convergence of the MCMC was assessed by calculating the effective sampling size (ESS) of the runs using the program Tracer . All parameter estimates showed significant ESSs (>150). The tree with the maximum product of the posterior clade probabilities (maximum clade credibility tree) was chosen from the posterior distribution of 5,000 sampled trees (after burning in the first 5001 sampled trees) with the program TreeAnnotator version 1.4.6 included in the BEAST software package . Both the constant coalescent and Yule Process were used as tree priors and gave identical results.
Approximately 1 million 293 cells were seeded on a 100 mm dish and incubated for 24 h at 37°C. Cells were then transfected with a c-Myb expression vector using Lipofectamine-PLUS (Invitrogen). Cells were lysed 48 hours using 1 × passive lysis buffer (Promega). Whole cell extract was stored at -80°C.
Electrophoretic mobility shift assay (EMSA)
The double-stranded oligonucleotide probe representing the c-Myb binding site within the HTLV-4 LTR (sense, 5'-TCGAGAAAGGTCAACTGTCTCACACAAAC-3'; antisense, 3'-TCGAGTTTGTGTGAGACAGTTGACCTTTC-5') was end-labeled with [α-32P]dCTP using Klenow enzyme (Invitrogen). The DNA-binding reaction was incubated for 1 h at room temperature using 5 ng of labeled probe and binding buffer (10 mM Tris [pH 7.9], 50 mM NaCl, 1 mM EDTA 10 mM dithiothreitol, 0.5% non-fat dry milk, 5% glycerol) supplemented with 2 ug of sheared salmon sperm DNA, 1 ug poly-dI-dC (Sigma St. Louis, MO), and 5 ug 293 cell extract in a final volume of 15 ul. The supershift was performed by adding 1 ug of anti-c-Myb monoclonal antibody (Upstate Biotechnology, Charlottesville, VA) or non-specific PC10 monoclonal antibody (Santa Cruz Biotechnology, Santa Cruz, CA) to the binding reaction for 1 h at room temperature. Unlabeled double-stranded (sense, 5'-TCGAGAAAGGTCGTATGTCTCACACAAAC-3'; antisense, 3'-TCGAGTTTGTGTGAGACATACGACCTTTC-5') non-specific oligonucleotide contained mutations at three positions (underlined) within the predicted c-Myb binding site. Specific and non-specific competitors were added in a 100-fold excess over labeled probe. DNA-protein complexes were resolved on a 4% non-denaturing polyacrylamide gel in 0.5× Tris-borate-EDTA at 150 V for 2.5 h.
Nucleotide sequence accession numbers
The complete HTLV-4(1863LE) proviral sequence has been deposited in GenBank with accession number EF488483. GenBank accession numbers for the complete PTLV genomes used in this paper are [HTLV-1(ATK) = J02029], [HTLV-1(ATL-YS) = U19949], [HTLV-1(Mel5) = L02534], [HTLV-1 (Boi) = L36905], [STLV-1(TE4) = Z46900], [STLV-1(Tan90) = AF074966], [HTLV-2(MoT) = M10060], [HTLV-2(Kay96) = AF356584], [HTLV-2(Gab) = Y13051], [HTLV-2(SP-WV) = AF139382], [HTLV-2(G2) = L11456], [HTLV-2(G12) = L11456], [HTLV-2(Efe) = Y14365], [STLV-2(Pan-p) = U90557], [STLV-2(pp1664) = Y14570], [HTLV-3(2026ND) = DQ093792], [HTLV-3(Pyl43) = DQ462191], [STLV-3(CTO604) = NC_003323], [STLV-3(Ph969) = Y07616], [STLV-3(TGE2117) = AY217650], [STLV-3(NG409) = AY222339], [STLV-3(Ppaf3) = AF517775], [STLV-5(MarB43) = AY590142].
N.D.W. is supported by a National Institutes of Health (NIH) Director's Pioneer Award Program (grant number DP1-OD000370) and an International Research Scientist Development Award from the NIH Fogarty International Center (K01 TW00003-1). This research was supported in part by the Global Viral Forecasting Initiative. Use of trade names is for identification only and does not imply endorsement by the U.S. Department of Health and Human Services, the Public Health Service, or the Centers for Disease Control and Prevention. The findings and conclusions in this report are those of the authors and do not necessarily represent the views of the Centers for Disease Control and Prevention. K.N.P. was supported by NIH grant #R25 M 69234, and work in the S.J.M.laboratory was supported by NIH grant #R21 AI078307.
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