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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.

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