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Figure 5 | Retrovirology

Figure 5

From: New STLV-3 strains and a divergent SIVmus strain identified in non-human primate bushmeat in Gabon

Figure 5

Phylogenetic analysis of partial SIV pol sequences. Phylogenetic relationships of the newly derived SIVs in partial pol sequences to representatives of the other SIV lineages. Reference sequences used were as follow: SIVwrcPbt (western red colobus monkey, Piliocolobus badius temminckii) 05GMX02_AM937062, SIVwrcPbb (western red colobus monkey, Piliocolobus badius badius) 98CI04_AM713177, SIVwrcPbb97CI14_AM745105, SIVtal (talapoin monkey, Miopithecus ogoouensis) 00CM266_AY655744, SIVtal01CM8023_AM182197, SIVmon (mona monkey, Cercopithecus mona) 99CMCML1_AY340701, SIVgsn (greater spot nosed monkey, Cercopithecus nictitans) 99CM166_AF468659, SIVgsn99CM71_AF468658, SIVsyk (Sykes monkey, Cercopithecus albogularis) KE51_AY523867, SIVsyk173_L06042, SIVmus-1 (Mustached monkey, Cercopithecus cephus) 01CM1085_AY340700, SIVmus- 1.01CMCM1239_EF070330, SIVmus-2 01CM1246_EF070329, SIVdeb (DeBrazza monkey, Cercopithecus neglectus) 99CMCM40_AY523865, SIVdeb99CMCM5_AY523866, SIVden (Dents monkey, Cercopithecus denti) CD1_AJ580407, SIVsun (Suntailed monkey, Cercopithecus solatus) L14_AF131870, SIVlho (L’Hoest monkey, Cercopithecus l’hoesti) 7_AF075269, SIVmnd-1 (Mandrill, Mandrillus sphinx) Gab1_M27470, SIVmnd-2 M14_AF328295, SIVdrl (Drill, Mandrilus leucophaeus) FAO_AY159321, SIVolc (olive colobus monkey, Procolobus verus) 97CI12_FM165200, SIVcol (black and white colobus monkey, Colobus guereza) CGU1_AF301156, SIVagmver (Afican green monkey, Chlorocebus vervet)155_M29975, SIVagmgri (Afican green monkey, Chlorocebus grivet) 677_M66437, SIVagmTAN (Afican green monkey, Chlorocebus tantalus) 1_U58991, SIVrcm (red-capped mangabey, Cercocebus torquatus) GAB1_AF382829, SIVrcmNG411_AF349680, SIVrcm-02CM8081_ HM803689, SIVagi (Agile mangabey, Cercocebus agilis) 00CM312_ HM803690, SIVcpzPts (Chimpanzee, Pan troglodytes schweinfurtii) TAN1_AF447763, SIVcpzPtt_(Chimpanzee, Pan troglodytes troglodytes) AF103818, SIVsmm (Sooty mangabey, Cercocebus atys) US-H9_M80194, HIV-2Rod_ M15390, SIVreg (Red eared guenon, Cercopithecus erythrotis) REG016_ HM363408, SIVreg-REG001_ HM363406, SIVblc (Black colobus monkey, Colobus satanas) BCM91_ HM363421, SIVbcm-BCM307_ HM363423, SIVprg (preussis monkey, Cercopithecus preussi insularis) PRG138_ HM363425, SIVprg-PRG056_ HM363424, SIVwol (Wolf’s monkeys, Cercopithecus mona wolfi) 09DRC5_JN020273, SIVtrc (Tshuapa red colobus (Piliocolobus tholloni) 09DRC67_JN020274, SIVtrc-09DRC73_JN020275, SIVasc (redtailed monkey, Cercopithecus ascanius) 09DRC93_JN020276, SIVasc-09DRC99_JN020277, SIVasc-10DRC110_JN020278, SIVasc-10DRC149_JN020279. The newly identified SIV strains in this study are highlighted in grey rectangles and in bold text.. Within the SIVrcm clade, acronyms CM, Ng and Gab corresponded to the geographical origin of these SIVrcm strains (CM = Cameroon, Ng = Nigeria and Gab = Gabon). The unrooted trees were inferred from 300 bp nucleotides. The analyses were performed using discrete gamma distribution and GTR model. The starting tree was obtained by using phyML. One thousand bootstrap replications were performed to assess confidence in topology (only values ≥ 80% are shown and represented by an asterisk). Scale bar represents the number of nucleotide substitution per site.

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