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Background  Although simian foamy viruses (SFV) are the only exogenous retroviruses to infect New World monkeys (NWMs), little is known about their evolutionary history and epidemiology. Previous reports show distinct SFVs among NWMs but were limited to small numbers of captive or wild monkeys from five ( Cebus ,  Saimiri ,  Ateles ,  Alouatta , and  Callithrix ) of the 15 NWM genera. Other studies also used only PCR testing or serological assays with limited validation and may have missed infection in some species. We developed and validated new serological and PCR assays to determine the prevalence of SFV in blood specimens from a large number of captive NWMs in the US (n = 274) and in captive and wild-caught NWMs (n = 236) in Peruvian zoos, rescue centers, and illegal trade markets. Phylogenetic and co-speciation reconciliation analyses of new SFV polymerase ( pol ) and host mitochondrial cytochrome  B  sequences, were performed to infer SFV and host co-evolutionary histories.    Results  124/274 (45.2 %) of NWMs captive in the US and 59/157 (37.5 %) of captive and wild-caught NWMs in Peru were SFV WB-positive representing 11 different genera ( Alouatta ,  Aotus ,  Ateles ,  Cacajao ,  Callithrix ,  Cebus ,  Lagothrix ,  Leontopithecus ,  Pithecia ,  Saguinus  and  Saimiri ). Seroprevalences were lower at rescue centers (10/53, 18.9 %) compared to zoos (46/97, 47.4 %) and illegal trade markets (3/7, 8/19, 42.9 %) in Peru. Analyses showed that the trees of NWM hosts and SFVs have remarkably similar topologies at the level of species and sub-populations suggestive of co-speciation. Phylogenetic reconciliation confirmed 12 co-speciation events (p < 0.002) which was further supported by obtaining highly similar divergence dates for SFV and host genera and correlated SFV-host branch times. However, four ancient cross-genus transmission events were also inferred for Pitheciinae to Atelidae,  Cacajao  to ancestral  Callithrix  or  Cebus  monkeys, between  Callithrix  and  Cebus  monkeys, and  Lagothrix  to  Alouatta .    Conclusions  We demonstrate a broad distribution and stable co-speciation history of SFV in NWMs at the species level. Additional studies are necessary to further explore the epidemiology and natural history of SFV infection of NWMs and to determine the zoonotic potential for persons exposed to infected monkeys in captivity and in the wild.    Electronic supplementary material  The online version of this article (doi:10.1186/s12977-015-0214-0) contains supplementary material, which is available to authorized users.

Wide distribution and ancient evolutionary history of simian foamy viruses in New World primates