Genome characterization of a simian foamy virus from a human bitten by an African green monkey

Abstract

We obtained the near-complete simian foamy virus (SFV) genome from an infected human bitten by an African green monkey (Chlorocebus aethiops; SFVcae_hu501). The genome is 13,062 nucleotides long with the classical SFV genome structure. Phylogenetically, SFVcae_hu501 clustered closely with SFV from Ch. aethiops (SFVagm_LK3).

Keywords: phylogeny; retroviruses; whole-genome sequencing; zoonoses; zoonotic infections.

Fig 1

Evolutionary relationships of FVs from various mammals inferred by maximum-likelihood analysis of the gag-pol-env concatemer (~7.0 kb). Shimodaira-Hasegawa support values are provided on the branch to the left of the node. Sequences were aligned using Multiple Alignment using Fast Fourier Transform (https://mafft.cbrc.jp/alignment/server/), and phylogeny was inferred using FastTree version 2.0 using the GTR nucleotide substitution model and 1,000 bootstrap replicates (12). Old World apes (OWAs): SFVpve, Pan troglodytes verus (chimpanzee), GenBank accession number U04327; SFVpsc_huHSRV.13, Pan troglodytes schweinfurthii (chimpanzee), Y07725; SFVppy_bella, Pongo pygmaeus (orangutan), AJ544579; SFVggo_Gg, Gorilla (gorilla), NC_039029; OWMs: SFVpxx_hu9406 (human infected with baboon SFV), MF472626 (“xx” in the SFV name indicates the simian species is unknown); SFVcae_LK3, Chlorocebus aethiops (African green monkey), M74895; SFVmcy_FV21, Macaca cyclopsis (macaque), X54482. New World monkeys (NWMs): SFVcja_FXV, Callithrix jacchus (common marmoset), GU356395; SFVsxa_Z17, Sapajus xanthosternos (capuchin), KP143760; SFVaxx_Hooks40, Ateles species (spider monkey), EU010385; SFVssc_1224, Saimiri sciureus (squirrel monkey), GU356394. Prosimian (Pro): SFVocr_1557, Otolemur crassicaudatus (brown greater galago), KM233624. Non-simian mammals (NSMs): EFVeca_1, Equus caballus (equine), AF201902; BFVbta_BSV11, Bos taurus (bovine), U94514; and FFVfca_FUV7, Felis catus (feline), Y08851.