Figure 6

Phylogenetic analysis of partial SIVrcm gag, pol and env sequences. Phylogenetic relationships of the newly derived SIVrcm sequences in partial a/gag, b/pol and c/env sequences to the previously described SIVrcm strains from Cameroon, Nigeria and Gabon as well as with SIVagi from Cameroon. Reference sequences used were as follow: SIVmnd-2 M14_AF328295, SIVdrlFAO_AY159321, SIVrcmGAB1_AF382829, SIVrcmNG411_AF349680, SIVrcm-02CM8081_ HM803689, SIVagi-00CM312_ HM803690, SIVsmmUS-H9_M80194, HIV-2Rod_ M15390. The newly identified strains in this study are in bold text and specific sub-clades are shown in grey rectangles for gag and pol. The rooted trees were inferred from 470, 1800, 500 bp nucleotides for gag, pol and env respectively with representatives of the other SIV lineages. Only sequences of interest are showed with the closer SIVs outgroup in the complete tree topology (SIVmnd-2 and drl for gag and pol trees, SIVsmm and HIV-2 for env tree). SIV strains from Cameroon and Nigeria are underlined and in italic respectively. 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.