Far from black and white: Insights into the diversity of SIV

Retrovirology is pleased to announce the publication of its 1000th article, a fantastic milestone for the journal.

The article is from researchers at the University of Wisconsin-Madison, USA, analysing new simian immunodeficiency viruses (SIVs) identified from nine black-and-white colobus monkeys (Colobus guereza) from the Kibale National Park in Uganda. With limited taxonomic and geographic sampling of non-human primates, particularly in East Africa, the research presents an interesting insight into the diversity of SIV.

Black-and-white colobus monkey. Image courtesy of Minnesota Zoo www.mnzoo.com

The researchers used “unbiased” deep-sequencing techniques to sequence the entire coding region for each virus, a method that does not depend on genetic similarity to viruses previously identified.  The authors identified two distinct SIVs sharing only 72% nucleotide identity, calling the viruses SIVkcol-1 and SIVkcol-2, detected in three and four animals respectively.  Intriguingly, no monkeys were found to be co-infected.

The viruses are most closely related to SIVcol, a SIV previously identified in black-and-white colobus monkeys from Cameroon, with SIVkcol-1 more closely related to SIVcol than to SIVkcol-2.  Both SIVs contain genomic structures similar to those of complex retroviruses and SIVcol, including three structural genes (gag, pol and env) and accessory genes (vif, vpr, tat, rev and nef).  Comparing inter-host genetic diversity, SIVkcol-1 was shown to be slightly more diverse than SIVkcol-2 (88.7 ± 5.3% nucleotide identity compared to 93.9 ± 5.9%).

The researchers have identified a number of important functional motifs for SIVkcol-1 and SIVkcol-2.  In particular, the authors have identified SIVkcol-2 as the first lentivirus that contains only 16 conserved cysteines within the extracellular subunit of the envelope protein.  These conserved cysteines contribute to envelope function, such as binding to host cell receptors.  This finding is significant as SIVcol and all other primate lentiviruses contain 18 conserved cysteine residues, referred to as the “18 Cys state”.  It is interesting to speculate which “state” may have existed first.

Further insights were revealed when analysing crucial binding sites for the SIV Gag p6 protein, the motifs PT/SAP and YPXL.  Both motifs can be present at the same time, but the presence of one motif can compensate for the absence of the other.  SIVkcol-1 and SIVkcol-2 only have the YPXL motif, identical to SIVcol, providing evidence for an unusual feature of Colobus-infecting SIVs.

Phylogenetic analyses were conducted with the SIVkcol-1 and SIVkcol-2 sequences, with the authors constructing four separate evolutionary trees for the gag, pol, env and nef genes.  All phylogenies indicated SIVkcol-1, SIVkcol-2 and SIVcol formed a distinct lineage, with SIVkcol-2 in a separate branch ancestral to SIVcol and SIVkcol-1.  Bayesian inference identified the TMRCA (time to the most recent common ancestor), estimating that the split between SIVkcol-1/col and SIVkcol-2 occurred at least 10,656 years before present, although the authors admit the accuracy of such estimates is still under debate.

In summary, the researchers have identified two distinct SIVs from the same black-and-white colobus population, increasing the understanding of SIV diversity.  The two new viruses have many unique features, in particular, a unique cysteine architecture in SIVkcol-2 env and loss of the PT/SAP Gag binding motif, the significance of which warrants further investigation.  There is clearly considerable potential for further insights into SIV in the non-human primate population in this under-sampled region. Furthermore,  the use of deep sequencing in this study has highlighted its value in identifying unknown or poorly characterised viruses and this approach should be considered in future studies.

Figure courtesy of Lauck et al., Retrovirology, 2013

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