Investigating retroviral super-infection in wild chimpanzees (Pan troglodytes verus)

Background

While the molecular epidemiology of retroviruses in wild primate populations has received much attention, the related question of the frequency and nature of super-infection events has remained largely neglected. Here, we explicitly investigated it, focusing on simian foamy viruses (SFV) infecting wild chimpanzees (Pan troglodytes verus), as an example.

Methods

We first compared the costs and benefits of end-point dilution PCR (EPD-PCR) (currently considered a gold standard method) and multiple bulk PCR cloning, when applied to non-invasive samples. For the latter method, we had to develop a specific analytical framework aimed at deciphering relevant biological information from method-induced biases. We then applied multiple bulk PCR cloning to samples collected from chimpanzees belonging to different age classes.

Results and discussion

We found that, when applied to faeces, proper EPD-PCR analysis will sometimes require the consumption of unrealistic large amounts of biological material (i.e. when “native” EPD-PCR conditions are encountered). However, super-infection status, as well as the underlying main strain sequences, could be robustly inferred from multiple bulk PCR analyses (which are more parsimonious), using a combination of statistic and network analyses. Applying this method to individuals belonging to different age classes, we finally found that wild chimpanzees actually accumulated distinct chimpanzee-specific SFV throughout their lives.