Spumaretroviruses: Updated taxonomy and nomenclature

Abstract

Spumaretroviruses, commonly referred to as foamy viruses, are complex retroviruses belonging to the subfamily Spumaretrovirinae, family Retroviridae, which naturally infect a variety of animals including nonhuman primates (NHPs). Additionally, cross-species transmissions of simian foamy viruses (SFVs) to humans have occurred following exposure to tissues of infected NHPs. Recent research has led to the identification of previously unknown exogenous foamy viruses, and to the discovery of endogenous spumaretrovirus sequences in a variety of host genomes. Here, we describe an updated spumaretrovirus taxonomy that has been recently accepted by the International Committee on Taxonomy of Viruses (ICTV) Executive Committee, and describe a virus nomenclature that is generally consistent with that used for other retroviruses, such as lentiviruses and deltaretroviruses. This taxonomy can be applied to distinguish different, but closely related, primate (e.g., human, ape, simian) foamy viruses as well as those from other hosts. This proposal accounts for host-virus co-speciation and cross-species transmission.

Keywords: Foamy virus; ICTV; International Committee on Taxonomy of Viruses; Retrovirus; Spumaretrovirinae; Spumaretrovirus; Spumavirus; Virus classification; Virus nomenclature; Virus taxonomy; Zoonosis.

Fig. 1.

Foamy virus phylogeny reflects long-term virus – host co-speciation. Evolutionary relationships were inferred using maximum likelihood analysis of an alignment comprising the polymerase gene (pol) and envelope gene (env) nucleotide sequences of 21 foamy viruses from diverse mammalian hosts. Branch tips are labeled with viral species names and the host common names; brackets indicate common names for subfamily/group within the class Mammalia. Nodes are labeled with bootstrap support values (based on 1000 replicates). An alignment (including insertions and deletions) beginning approximately in the middle of the pol gene and extending to approximately the middle of the env gene was generated using the MUSCLE algorithm as implemented in Geneious 10.1.3. For reference, alignment corresponded to nucleotide position 5089 – 7927 of SFVpsc (NCBI accession number KX08159). Alignment of all of the sequences are submitted in the Supplement. Unrooted tree was generated using PhyML with the HKY85 substitution model and the NNI search option. Tree was visualized using FigTree 1.4.2 (note that unrooted tree is shown as rooted for ease of visualization). Topology is similar to those published by others (Rethwilm and Bodem, 2013; Katzourakis et al., 2014; Switzer et al., 2005b). Input taxa and accession numbers were: SFVcni (JQ867466); SFVcae (NC_010820); SFVmfa (LC094267); SFVmcy (NC_010819); SFVmmu (MF280817); SFVmfu (AB923 518); SFVpve (NC_001364); SFVpsc (KX08159); SFVptr (JQ867463); SFVggo (HM245790); SFVppy (AJ5445 79); SFVsxa (KP143760); SFVcja (GU356395); SFVaxx (EU010385); SFVssc (GU356394); SFVocr (KM233 624); FFVfca (Y08851); FFVpco (KC292054); EFVeca (AF201902); BFVbta (NC_001831); CFVraf (JQ8148 55).