Identification and characterization of highly divergent simian foamy viruses in a wide range of new world primates from Brazil

Abstract

Foamy viruses naturally infect a wide range of mammals, including Old World (OWP) and New World primates (NWP), which are collectively called simian foamy viruses (SFV). While NWP species in Central and South America are highly diverse, only SFV from captive marmoset, spider monkey, and squirrel monkey have been genetically characterized and the molecular epidemiology of SFV infection in NWPs remains unknown. We tested a large collection of genomic DNA (n = 332) comprising 14 genera of NWP species for the presence of SFV polymerase (pol) sequences using generic PCR primers. Further molecular characterization of positive samples was carried out by LTR-gag and larger pol sequence analysis. We identified novel SFVs infecting nine NWP genera. Prevalence rates varied between 14-30% in different species for which at least 10 specimens were tested. High SFV genetic diversity among NWP up to 50% in LTR-gag and 40% in pol was revealed by intragenus and intrafamilial comparisons. Two different SFV strains infecting two captive yellow-breasted capuchins did not group in species-specific lineages but rather clustered with SFVs from marmoset and spider monkeys, indicating independent cross-species transmission events. We describe the first SFV epidemiology study of NWP, and the first evidence of SFV infection in wild NWPs. We also document a wide distribution of distinct SFVs in 14 NWP genera, including two novel co-speciating SFVs in capuchins and howler monkeys, suggestive of an ancient evolutionary history in NWPs for at least 28 million years. A high SFV genetic diversity was seen among NWP, yet these viruses seem able to jump between NWP species and even genera. Our results raise concerns for the risk of zoonotic transmission of NWP SFV to humans as these primates are regularly hunted for food or kept as pets in forest regions of South America.

Figure 1. Geographic distribution of distinct Cebus (A), Ateles (B) and Alouatta (C) primate species in Brazil.

Data are according to the Database of Georeferenced Occurrence Localities of Neotropical Primates, Department of Zoology, Universidade Federal de Minas Gerais, Brazil (http://www.icb.ufmg.br/zoo/primatas/home_bdgeoprim.htm). Primate center and wild animal site locations within Brazil (see Table 4) are shown: Pará (PA), Mato Grosso (MT), Rondônia (RO), Paraíba (PB), and Brazil/Argentina frontier (RS).

Figure 2. Taxonomical classification of SFV-positive NWP specimens based on phylogenetic inference of 500-bp cytochrome B (cytB) sequences.

GenBank accession numbers of reference ctyB sequences are provided. Topology and divergence dates were inferred using a relaxed molecular clock and a Yule tree prior using BEAST v1.6.2. X axis is in millions of years. Posterior probabilities >0.8 are provided at nodes.

Figure 3. Identification of broad simian foamy virus (SFV) diversity in New World primates (NWPs).

Phylogenetic inference of 265-bp SFV long terminal repeat (LTR)/gag (A) and 276-bp polymerase (pol) (B) sequences from neotropical primate species. SFV sequences retrieved from GenBank are shown with their respective accession numbers, while the remaining SFV are those generated in the study. The newly characterized SFV lineages infecting capuchins (SFVcap) and howler monkeys (SFVhow) can be seen in both panels. Scale bar for the SFV LTR/gag tree is in nucleotide substitutions per site. Statistical support for branch nodes in the LTR/gag tree are provided as bootstrap values from neighbor-joining (NJ) and maximum likelihood (ML) methods and posterior probabilities from Bayesian inference (BI) in the order NJ/ML/BI. # indicates statistical support was not provided by the respective program. Topology and divergence dates for the pol tree were inferred using a relaxed molecular clock and a Yule tree prior using BEAST v1.6.2. X axis is in millions of years. Posterior probabilities >0.8 are provided at nodes.

Figure 4. Co-evolutionary relationships of simian foamy virus (SFV) polymerase (pol) (green branches and text) and primate cytochrome B (cytB) (brown branches and text) Bayesian-inferred phylogenetic trees based on reconciliation analysis.

One of nine potentially optimal reconciled trees with 12 cospeciations (black circles), three host switches (blue arrows with dashed lines), 1 duplication (black square), and 15 sorting events (truncated branches without corresponding taxa).

Figure 5

Correlation of (A) branch lengths (substitutions per site) and (B) coalescence times (genetic distances) of primate cytochrome B and SFV polymerase (pol) Bayesian-inferred phylogenetic trees.