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Discovery and full genome characterization of two highly divergent simian immunodeficiency viruses infecting black-and-white colobus monkeys (Colobus guereza) in Kibale National Park, Uganda.

ABSTRACT: African non-human primates (NHPs) are natural hosts for simian immunodeficiency viruses (SIV), the zoonotic transmission of which led to the emergence of HIV-1 and HIV-2. However, our understanding of SIV diversity and evolution is limited by incomplete taxonomic and geographic sampling of NHPs, particularly in East Africa. In this study, we screened blood specimens from nine black-and-white colobus monkeys (Colobus guereza occidentalis) from Kibale National Park, Uganda, for novel SIVs using a combination of serology and "unbiased" deep-sequencing, a method that does not rely on genetic similarity to previously characterized viruses.We identified two novel and divergent SIVs, tentatively named SIVkcol-1 and SIVkcol-2, and assembled genomes covering the entire coding region for each virus. SIVkcol-1 and SIVkcol-2 were detected in three and four animals, respectively, but with no animals co-infected. Phylogenetic analyses showed that SIVkcol-1 and SIVkcol-2 form a lineage with SIVcol, previously discovered in black-and-white colobus from Cameroon. Although SIVkcol-1 and SIVkcol-2 were isolated from the same host population in Uganda, SIVkcol-1 is more closely related to SIVcol than to SIVkcol-2. Analysis of functional motifs in the extracellular envelope glycoprotein (gp120) revealed that SIVkcol-2 is unique among primate lentiviruses in containing only 16 conserved cysteine residues instead of the usual 18 or more.Our results demonstrate that the genetic diversity of SIVs infecting black-and-white colobus across equatorial Africa is greater than previously appreciated and that divergent SIVs can co-circulate in the same colobine population. We also show that the use of "unbiased" deep sequencing for the detection of SIV has great advantages over traditional serological approaches, especially for studies of unknown or poorly characterized viruses. Finally, the detection of the first SIV containing only 16 conserved cysteines in the extracellular envelope protein gp120 further expands the range of functional motifs observed among SIVs and highlights the complex evolutionary history of simian retroviruses.

SUBMITTER: Lauck M

PROVIDER: S-EPMC4016034 | biostudies-literature | 2013 Oct

REPOSITORIES: biostudies-literature

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Discovery and full genome characterization of two highly divergent simian immunodeficiency viruses infecting black-and-white colobus monkeys (Colobus guereza) in Kibale National Park, Uganda.

Lauck Michael M Switzer William M WM Sibley Samuel D SD Hyeroba David D Tumukunde Alex A Weny Geoffrey G Taylor Bill B Shankar Anupama A Ting Nelson N Chapman Colin A CA Friedrich Thomas C TC Goldberg Tony L TL O'Connor David H DH

Retrovirology 20131021

<h4>Background</h4>African non-human primates (NHPs) are natural hosts for simian immunodeficiency viruses (SIV), the zoonotic transmission of which led to the emergence of HIV-1 and HIV-2. However, our understanding of SIV diversity and evolution is limited by incomplete taxonomic and geographic sampling of NHPs, particularly in East Africa. In this study, we screened blood specimens from nine black-and-white colobus monkeys (Colobus guereza occidentalis) from Kibale National Park, Uganda, for ...[more]

PMID: 24139306

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Project description:Black-and-white colobus (Colobus guereza Rüppell, 1835) are arboreal Old World monkeys inhabiting large parts of the deciduous and evergreen forests of sub-Saharan Africa. Two of the eight subspecies of Colobus guereza are endemic to Ethiopia: C. g. gallarum and C. g. guereza. However, the validity of the Ethiopian taxa is debated and observed morphological differences were attributed to clinal variation within C. g. guereza. To date, no molecular phylogeny of the Ethiopian guerezas is available to facilitate their taxonomic classification. We used mitochondrial DNA markers from 94 samples collected across Ethiopia to reconstruct a phylogeny of respective mitochondrial lineages. In our phylogenetic reconstruction, augmented by orthologous sequence information of non-Ethiopian black-and-white colobus from GenBank, we found two major Ethiopian mitochondrial clades, with one being largely congruent with the distribution of C. g. guereza. The second clade was found only at two locations in the eastern part of the putative range of C. g. gallarum. This second lineage clustered with the lowland form, C. g. occidentalis, from central Africa, whereas the C. g. guereza lineages clustered with C. g. caudatus and C. g. kikuyuensis from Kenya and northern Tanzania. These two guereza lineages diverged around 0.7 million years ago. In addition, mitochondrial sequence information does not support unequivocally a distinction of C. g. caudatus and C. g. kikuyuensis. Our findings indicate a previous biogeographic connection between the ranges of C. g. occidentalis and C. g. gallarum and a possible secondary invasion of Ethiopia by members of the C. g. guereza-C. g. caudatus-C. g. kikuyuensis clade. Given these phylogenetic relationships, our study supports the two-taxa hypothesis, making C. g. gallarum an Ethiopian endemic, and, in combination with the taxon's very restricted range, makes it one of the most endangered subspecies of black-and-white colobus.

Dataset Information

Discovery and full genome characterization of two highly divergent simian immunodeficiency viruses infecting black-and-white colobus monkeys (Colobus guereza) in Kibale National Park, Uganda.

Publications

Discovery and full genome characterization of two highly divergent simian immunodeficiency viruses infecting black-and-white colobus monkeys (Colobus guereza) in Kibale National Park, Uganda.

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