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Published in final edited form as: Virology. 2018 Mar;516:158–164. doi: 10.1016/j.virol.2017.12.035

Spumaretroviruses: Updated taxonomy and nomenclature

Arifa S Khan a,*, Jochen Bodem b, Florence Buseyne c,d, Antoine Gessain c,d, Welkin Johnson e, Jens H Kuhn f, Jacek Kuzmak g, Dirk Lindemann h, Maxine L Linial i, Martin Löchelt j, Magdalena Materniak-Kornas g, Marcelo A Soares k, William M Switzer l
PMCID: PMC11318574  NIHMSID: NIHMS2012787  PMID: 29407373

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

1. Introduction

Spumaretroviruses belong to the subfamily Spumaretrovirinae in the family Retroviridae. They are highly prevalent in animals of diverse non-primate mammalian families [Bovidae (cloven-hooved ruminants), Felidae (cats), Equidae (horses and relatives), and Rhinolophidae (horseshoe bats)], as well as nonhuman primates (NHPs), including apes, Old World monkeys (OWM), New World monkeys (NWM), and prosimians (Rethwilm and Lindemann, 2013; Rethwilm and Bodem, 2013). Members of the subfamily Spumaretrovirinae, commonly referred to as foamy viruses, have a broad tissue and cell tropism and virus infection is generally latent, except in some tissues of the oral cavity (Falcone et al., 1999; Murray et al., 2008).

The earliest reports of foamy virus isolates were of simian origin (NWM, OWM, and apes) and were originally classified serologically using neutralization assays (Hooks and Gibbs, 1975; Meiering and Linial, 2001). The first “human” spumaretrovirus isolate was obtained from cultures of a human nasopharyngeal carcinoma in 1971 and was originally designated “human foamy virus (HFV)” (Achong et al., 1971a, 1971b), but was later found to be of chimpanzee origin based upon sequence identity to chimpanzee foamy virus and renamed as prototype foamy virus (PFV) (Meiering and Linial, 2001; Herchenroder et al., 1994). Cross-species transmissions of simian foamy viruses (SFVs) to humans have occurred by exposure to fluids or tissues from infected NHPs (Betsem et al., 2011; Calattini et al., 2007; Engel et al., 2013; Heneine et al., 2003, 1998; Mouinga-Ondémé et al., 2012; Schweizer et al., 1995; Stenbak et al., 2014; Switzer et al., 2004, 2012; Wolfe et al., 2004; Khan, 2009; Brooks et al., 2002; Callahan et al., 1999). Although foamy viruses are exogenously transmitted viruses, endogenous foamy virus sequences have been identified and characterized in genomes of many species, including aye-aye (Daubentonia madagascariensis), sloth (Choloepus hoffmanni), Cape golden mole (Chrysochloris asiatica), coelacanth (Latimeria chalumnae), platyfish (Xiphophorus maculatus), and zebrafish (Danio rerio) (Katzourakis et al., 2014, 2009; Aiewsakun and Katzourakis, 2017; Han and Worobey, 2012a, 2012b, 2014; Ruboyianes and Worobey, 2016). In fact, molecular evolution studies have indicated that spumaretroviruses have co-speciated with their hosts for millions of years (Katzourakis et al., 2014, 2009; Ghersi et al., 2015; Switzer et al., 2005a). Recently, phylogenetic analyses using amphibian and fish genomes have estimated the date of retrovirus emergence at > 450 million years ago (Aiewsakun and Katzourakis, 2017) with foamy viruses inferred to be the most ancient retrovirus. A recent increase in the number of foamy virus isolates and sequences using a variety of novel molecular and genomic techniques highlights the need for updating and expanding spumaretrovirus taxonomy (Mouinga-Ondémé et al., 2012; Ghersi et al., 2015; Ayouba et al., 2013; Liu et al., 2008; Wu et al., 2012; Muniz et al., 2013; Troncoso et al., 2015; Blasse et al., 2013; Calattini et al., 2006, 2004; Goldberg et al., 2009; Huang et al., 2013; Jones-Engel et al., 2007; Mouinga-Ondémé et al., 2010; Richard et al., 2015; Yoshikawa et al., 2014; Kehl et al., 2013; Hechler et al., 2012).

The taxonomic history of Spumaretrovirinae has been based only on the few early virus isolates. Although “foamy virus” was discovered in rhesus monkey kidney cultures in 1955 (Rustigian et al., 1955), simian foamy retroviruses were not formally classified until the Second Report (1976) of the International Committee on Taxonomy of Viruses [ICTV], which assigned bovine syncytial virus (BSV), feline syncytial virus (FSV), hamster syncytial virus (HSV), human foamy virus (HFV), and simian foamy virus (SFV) to the “genus-less” subfamily Spumavirinae (not italicized at the time) (Fenner, 1976). In the Third (1979) ICTV Report, the still genus-less subfamily Spumavirinae contained only four viruses (BSV, FSV, HFV, and SFV) (Matthews, 1979). By the Fifth (1991) ICTV Report, all three subfamilies (Oncovirinae, Lentivirinae, and Spumavirinae) of the Retroviridae were abandoned and seven genera created, including Spumavirus, which contained BSV, FSV, HFV, and SFV (Coffin et al., 1991), with HFV designated as the type species. This taxonomy was upheld in the Sixth (1995) ICTV Report, but HFV was referred to as human spumavirus (Coffin et al., 1995). The Seventh (2000) ICTV Report for the first time differentiated between species and viruses. Chimpanzee foamy virus was designated the type species and chimpanzee foamy virus (formerly human spumavirus) was assigned to it (according to the ICTV rules, virus names are not italicized). The other species were Bovine foamy virus (containing bovine foamy virus; formerly bovine syncytial virus), Feline foamy virus (containing feline foamy virus, formerly feline syncytial virus), Simian foamy virus 1 (containing simian foamy virus type 1), and Simian foamy virus 3 (containing simian foamy virus type 3) (Hunter et al., 2000). In the Eighth (2005) ICTV Report, based upon the distinct replication pathway of foamy viruses, which contains features homologous to both retroviruses and hepadnaviruses (Linial, 1999), the subfamily Spumaretrovirinae was reinstated for the genus Spumavirus. The species Simian foamy virus 1 was renamed Macaque simian foamy virus and the virus assigned to this species, simian foamy virus 1, was renamed macaque simian foamy virus. Similarly, the species Simian foamy virus 3 was renamed African green monkey simian foamy virus and the virus in this species, simian foamy virus 3, was renamed African green monkey simian foamy virus; the species Chimpanzee foamy virus was renamed Simian foamy virus and the virus in this species, chimpanzee foamy virus was renamed simian foamy virus. In addition, the species Equine foamy virus was established for equine foamy virus. No changes were made to Bovine foamy virus and Feline foamy virus (Linial et al., 2005). The most recent, Ninth (2011) ICTV Report, lists six spumavirus species for six viruses (Stoye et al., 2012), and this current classification is shown in Table 1.

Table 1.

Current spumaretrovirus taxonomy according to ICTVa.

Family Subfamily Genus Species Virus name
Retroviridae Spumaretrovirinae Spumavirus African green monkey simian foamy virus African green monkey simian foamy virus (SFVagm)b
Bovine foamy virus bovine foamy virus (BFV)
Equine foamy virus equine foamy virus (EFV)
Feline foamy virus feline foamy virus (FFV)
Macaque simian foamy virus macaque simian foamy virus (SFVmac)c
Simian foamy virus d simian foamy virus, human isolate (SFVcpz(hu))e
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b

Synonym: simian foamy virus 3 (SFV-3).

c

Synonym: simian foamy virus 1 (SFV-1).

d

Type species.

e

Synonyms: chimpanzee foamy virus (CFV), human foamy virus (HFV) and prototype foamy virus (PFV).

The current taxonomy for spumaretroviruses is outdated as it does not accommodate new foamy viruses discovered in NHPs of various species, including OWM and NWM (Ghersi et al., 2015; Muniz et al., 2013, 2015). Furthermore, formal nomenclature for designating virus isolates is lacking, particularly for simian foamy viruses, which has led to some confusion in virus descriptions and references in publications and retrieval of sequences deposited in public databases. The critical need for updating spumaretrovirus taxonomy and for developing a consensus nomenclature for different foamy viruses was recognized by the scientific community and discussed at the International Foamy Virus Conference held in 2014 in Puławy, Poland (Materniak et al., 2015) and in 2016 in Paris, France (Buseyne et al., 2016). Here, we present an updated and expanded spumaretrovirus taxonomy based upon current knowledge that accounts for host-virus co-speciation and cross-species transmission. Furthermore, the proposed virus nomenclature can be applied to all spumaretroviruses, including non-primate and primate viruses.

2. Updated 2017 spumaretrovirus classification

The recent increase in the number of primate and non-primate spumaretroviruses warranted an update of the current ICTV classification as well as establishment of a more consistent nomenclature. This updated taxonomy, which was proposed by the authors to the Executive Committee of the ICTV on June 8, 2017, is shown in Table 2. The following changes were proposed based on analyses of sequences of spumaretrovirus genomes available in public databases:

Table 2.

Updated spumaretrovirus taxonomy as proposed in June 2017a.

Family Subfamily Genus Species Virus (name)
Retroviridae Spumaretrovirinae Simiispumavirus Eastern chimpanzee simian foamy virus b,c simian foamy virus Pan troglodytes schweinfurthii (SFVpsc)
Western chimpanzee simian foamy virus simian foamy virus Pan troglodytes verus (SFVpve)
Central chimpanzee simian foamy virus simian foamy virus Pan troglodytes troglodytes (SFVptr)
Western lowland gorilla simian foamy virus simian foamy virus Gorilla gorilla gorilla (SFVggo)
Bornean orangutan simian foamy virus simian foamy virus Pongo pygmaeus pygmaeus (SFVppy)
Taiwanese macaque simian foamy virus d simian foamy virus Macaca cyclopis (SFVmcy)
Rhesus macaque simian foamy virus simian foamy virus Macaca mulatta (SFVmmu)
Japanese macaque simian foamy virus simian foamy virus Macaca fuscata (SFVmfu)
Grivet simian foamy virus e simian foamy virus Chlorocebus aethiops (SFVcae)
Guenon simian foamy virus simian foamy virus Cercopithecus nictitans (SFVcni)
Spider monkey simian foamy virus simian foamy virus Ateles species (SFVaxx)
White-tufted-ear marmoset simian foamy virus simian foamy virus Callithrix jacchus (SFVcja)
Squirrel monkey simian foamy virus simian foamy virus Saimiri sciureus (SFVssc)
Yellow-breasted capuchin simian foamy virus simian foamy virus Sapajus xanthosternos (SFVsxa)
Prosimiispumavirus Brown greater galago prosimian foamy virus c simian foamy virus Otolemur crassicaudatus (SFVocr)
Bovispumavirus Bovine foamy virus c bovine foamy virus Bos taurus (BFVbta)
Felispumavirus Feline foamy virus c feline foamy virus Felis catus (FFVfca)
Puma feline foamy virus feline foamy virus Puma concolor (FFVpco)
Equispumavirus Equine foamy virus c equine foamy virus Equus caballus (EFVeca)
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a

Based upon available complete virus genome sequences.

b

The former species Simian spumavirus.

c

Type species.

d

The former species Macaque simian foamy virus.

e

The former species African green monkey simian foamy virus.

  • the existing genus Spumavirus was replaced by five genera named Bovispumavirus, Equispumavirus, Felispumavirus, Prosimiispumavirus, and Simiispumavirus because the spumaretrovirus phylogeny largely reflects the host phylogeny (Fig. 1), supporting the hypothesis of spumaretrovirus-host co-evolution (Switzer et al., 2004, 2005a; Katzourakis et al., 2014, 2009; Ghersi et al., 2015);

  • the established species Bovine foamy virus, Feline foamy virus, and Equine foamy virus were included in the new genera Bovispumavirus, Felispumavirus, and Equispumavirus, respectively. Additionally, the species Puma feline foamy virus was included in genus Felispumavirus;

  • a new species, Brown greater galago simian foamy virus, was included in a new genus Prosimiispumavirus;

  • the previously established species were included in the new genera, and new species were established for previously unclassified spumaretroviruses. Species names were chosen based upon the viral host animal names. The previous species simian foamy virus was renamed Eastern chimpanzee simian foamy virus. The species Macaque simian foamy virus and African green monkey simian foamy virus were renamed Taiwanese macaque simian foamy virus and Grivet simian foamy virus, respectively, and together with Eastern chimpanzee simian foamy virus were included in genus Simiispumavirus. Eleven additional NHP spumaretrovirus species were added to this genus. Each proposed species is represented by at least one virus for which a complete genome sequence has been deposited in public databases.

Fig. 1.

Fig. 1.

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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).

In addition to the viruses included in the updated taxonomy submitted to the ICTV in 2017, there are other foamy virus isolates that are phylogenetically distinct from the currently included ones and were not included in the proposal because of the lack of a complete coding genome sequence. These are shown in Table 3 and are envisioned to be included in future taxonomic updates, along with other available sequences at that time. It should be noted that simian foamy virus Macaca fascicularis (SFVmfa) is also included in this table (and in Fig. 1) since it is expected to be classified in the next update based upon a published full-genome sequence (Sakai et al., 2016). Additionally, based upon recent discussions related to viruses identified by metagenomics, sequences that are distinct phylogenetically from those of the currently classified viruses and have been completely sequenced in their coding regions may be classified officially by the ICTV even in the absence of virus isolates (Simmonds et al., 2017).

Table 3.

Projected updates for spumaretrovirus taxonomya.

Family Subfamily Genus Species Virus names and designations
Retroviridae Spumaretrovirinae Simiispumavirus Cynomolgus macaque simian foamy virus simian foamy virus Macaca fascicularis (SFVmfa)b
Drill simian foamy virus simian foamy virus Mandrillus leucophaeus (SFVmle)c
Mandrill simian foamy virus simian foamy virus Mandrillus sphinx (SFVmsp)c
Yellow baboon simian foamy virus simian foamy virus Papio cynocephalus (SFVpcy)c
Chispumavirus Intermediate horseshoe bat foamy virus d chiropteran foamy virus Rhinolophus affinis (CFVraf)c
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a

Potential candidates for new species based upon phylogenetic distance from current ones.

b

To be included in next update since full-genome sequence has been published.

c

To be included in update when sequence of at least full genome open reading frames is publicly available.

d

Potential candidate for type species.

3. Updated 2017 spumaretrovirus nomenclature

Previously, different spumaretroviruses were named by adding three-letter lower-case abbreviations to “SFV” (simian foamy virus) derived from the common names of the hosts from which the viruses were isolated. For instance, SFVmac was used for simian spumaretroviruses infecting macaques and SFVagm was used for simian spumaretroviruses infecting grivets (African green monkeys, agm) (Meiering and Linial, 2001). However, this general designation of viruses does not distinguish strains infecting hosts of different species or subspecies. The genus Macaca (macaques) includes more than 20 species the members of which are distributed throughout Asia, with one also in Africa, and the genus Chlorocebus (African green monkeys) includes six species, the members of which are distributed across sub-Saharan Africa. The most confusing virus name was “simian foamy virus”, which referred to foamy viruses from all NHPs except macaques and African green monkeys.

Here we propose a spumaretrovirus nomenclature similar to that used for simian immunodeficiency virus and simian T-lymphotropic virus isolates. Accordingly, all spumaretrovirus names will contain the words “foamy virus” preceded by an adjectival classifier indicating the host (e.g., bovine, feline, simian) followed by the name of the species, or in some cases subspecies, of the particular host. The virus host name and “foamy virus” are abbreviated in capital letters (e.g., feline foamy virus is abbreviated FFV, simian foamy virus is abbreviated SFV) followed by lower-case three-letter abbreviations for the host species name. These abbreviations are comprised of the first letter of the host genus and the first two letters of the species or subspecies (e.g., simian foamy virus Macaca cyclopis is abbreviated SFVmcy) (Tables 2 and 3), or the first letter of the species or subspecies and the next unique letter, when the letters are the same (e.g. simian foamy viruses isolated from New World primate species such as Leontopithecus chrysomelas and Leonthopithecus chrysopygus would be abbreviated as SFVlcm and SFVlcp, respectively). In the case of an unknown host species, the first letter of the genus name is followed by “xx” (italics letters). Virus isolate names are designated by using the virus abbreviation followed by an underscore that appends additional, isolate-identifying information such as the host from which it was isolated (for instance, “hu” for human), isolate designation, and other identifying information. For example, simian foamy virus Pan troglodytes schweinfurthii, human isolate HSRV, clone 13 will be designated as SFVpsc_huHRSV.13, and feline foamy virus Felis catus strain FUV7 will be designated as FFVfca_FUV7 (Table 4). Similarly, in case of inter-species transmission involving nonhuman primates, SFV from western red colobus monkey (Philiocolobus badius badius) isolated from a wild chimpanzee subspecies Pan troglodyes verus (Leendertz et al., 2008) will be designated as SFVpba_pveLeo. Furthermore, for recombinant viruses (including naturally-occurring and those genetically-engineered), the designation “[RF]” is included at the end (e.g., SFVmcy_FV34[RF] (Galvin et al., 2013)).

Table 4.

Proposed spumaretrovirus isolate nomenclature.

Host Spumaretrovirus name and designation Isolate description: type, strain, isolate [Previous
designation(s)]		 New isolate designation GenBank accession
number		 Reference(s) a
Bovine bovine foamy virus Bos taurus (BFVbta) BSV-11 [BSV, BFV] BFVbta_BSV11b U94514 c (Renshaw and Casey, 1994)
BFV-Riems BFVbta_Riems JX307862 c (Hechler et al., 2012)
BFV100 BFVbta_100 JX307861 c (Hechler et al., 2012)
Feline feline foamy virus Felis catus (FFVfca) type FUV7 [FSV, FFV] FFVfca_FUV7b Y08851 c (Bodem et al., 1996; Winkler et al., 1997)
type F17/951 FFVfca_F17/951 U85043 c (Helps and Harbour, 1997)
feline foamy virus Puma concolor (FFVpco) X102 FFVpco_X102 KC292054 c (Kehl et al., 2013)
Equine equine foamy virus Equus caballus (EFVeca) isolate clone 1 [EFV] EFVeca_1b AF201902 c (Tobaly-Tapiero et al., 2000)
Chiropteran chiropteran foamy virus Rhinolophus affinis (CFVraf) isolate 1 [RaFV-1] CFVraf_1 JQ814855 d (Wu et al., 2012)
Prosimian simian foamy virus Otolemur crassicaudatus (SFVocr) type 5, strain 1557 [SFV type 5; SFVgal] SFVocr_1557b KM233624 c (Katzourakis et al., 2014)
Simian—New World monkeys simian foamy virus Ateles species (SFVaxx) serotype 8, strain S-140, Hooks40 [SFV type 8; SFVspm] SFVaxx_Hooks40 EU010385 c (Thumer et al., 2007)
simian foamy virus Callithrix jacchus (SFVcja) isolate FXV [SFVmar] SFVcja_FXV GU356395 c (Pacheco et al., 2010)
simian foamy virus Saimiri sciureus (SFVssc) serotype 4, strain 1224 [SFV type 4; SFVsqu] SFVssc_1224 GU356394 c (Pacheco et al., 2010)
simian foamy virus Sapajus xanthosternos (SFVsxa) isolate Z17 SFVsxa_Z17 KP143760 c (Troncoso et al., 2015)
Simian—apes simian foamy virus Pan troglodytes schweinfurthii (SFVpsc) human isolate HSRV clone 13 [PFV; CFV; HSRV; SFVcpz (hu); HFV] SFVpsc_huHSRV.13b KX08159 c (Wagner and Bodem, 2017)
simian foamy virus Pan troglodytes troglodytes (SFVptr) human isolate BAD327 SFVptr_huBAD327 JQ867463 c (Rua et al., 2012)
human isolate AG15 SFVptr_huAG15 JQ867462 c (Rua et al., 2012)
simian foamy virus Pan troglodytes verus (SFVpve) [SFVcpz] SFVpve NC_001364 c (Herchenroder et al., 1994)
serotype 6, strain CV-1, Pan-1 [SFV type 6; SFVcpz] SFVpve_Pan1
serotype 7, strain CV-11, Pan-2 [ SFV type 7; SFVcpz] SFVpve_Pan2
simian foamy virus Gorilla gorilla gorilla (SFVggo) [SFV-Gg; SFVgor] SFVggo_Gg HM245790 c (Schulze et al., 2011)
human isolate BAK74 SFVggo_huBAK74 JQ867464 c (Rua et al., 2012)
human isolate BAD468 SFVggo_huBAD468 JQ867465 c (Rua et al., 2012)
simian foamy virus Pongo pygmaeus pygmaeus (SFVppy) serotype 11, strain bella [SFV type 11; SFVora] SFVppy_bella AJ544579 c (Verschoor et al., 2003)
Simian—Old World monkeys simian foamy virus Chlorocebus aethiops (SFVcae) strain LK3 [African green monkey SFV; SFVagm; SFVagm-3] SFVcae_LK3 M74895 c (Renne et al., 1992)
serotype 3, strain FV2014 [SFV 3; SFV type 3; SFVagm] SFVcae_FV2014 MF582544 c (Nandakumar et al., 2018)
simian foamy virus Cercopithecus nictitans (SFVcni) human isolate AG16 SFVcni_huAG16 JQ867466 c (Rua et al., 2012)
simian foamy virus Macaca cyclopis (SFVmcy) serotype 1, strain FV21 [SFV-1; macaque SFV; SFV type 1; SFVmac; SFVmcy-1] SFVmcy_FV21 NC_010819 c (Kupiec et al., 1991)
serotype 2, strain FV34 [SFV type 2; SFVmac; SFVmcy-2] SFVmcy_FV34[RF]d KF026286.1 c (Galvin et al., 2013)
simian foamy virus Macaca fascicularis (SFVmfa) isolate Cy5061 SFVmfa_Cy5061 LC094267 c (Sakai et al., 2016)
simian foamy virus Macaca fuscata (SFVmfu) Isolate WK1, clone pJM356 [Japanese macaque SFV; SFVjm] SFVmfu_WK1.pJM356 AB923518 c (Yoshikawa et al., 2014)
simian foamy virus Macaca mulatta (SFVmmu) isolate K3T SFVmmu_K3T MF280817 c (Nandakumar et al., 2017)
simian foamy virus Mandrillus leucophaeus (SFVmle) isolate Mnd205 SFVmle_Mnd205 AY583777 d (Calattini et al., 2004)
simian foamy virus Mandrillus sphinx (SFVmsp) isolate Mnd301 SFVmsp_Mnd301 AY583775 d (Calattini et al., 2004)
simian foamy virus Papio cynocephalus (SFVpcy) serotype 10 [SFV type 10; SFVbab] SFVpcy AF049083 d
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a

reference provided for published sequences

b

Type species.

c

full-length genome.

d

partial sequence.

4. Conclusions

The updated and expanded spumaretrovirus taxonomy presented here was initially submitted to the ICTV on June 8, 2017, and is now approved by the ICTV Executive Committee. The proposal awaits ratification by vote of the International Union of Microbiological Societies (IUMS) Virology Division, which will occur in the first quarter of 2018. The new taxonomy format is easily expandable to accommodate new genera and species for classification of newly discovered foamy viruses. Additionally, we have established a spumaretrovirus nomenclature that considers host-virus co-speciation and cross-species transmission, and incorporates host animal species information and strain and/or animal identification codes in spumaretrovirus names and their abbreviations. This collaborative effort is aimed toward unifying classification and designations of spumaretroviruses to facilitate easy comparisons of reported foamy virus isolates.

Supplementary Material

Supp material

Acknowledgements

We appreciate the expertise provided by Prof. Dr. Gerrit Kloss for deriving the Latin names of the genera in Spumaretrovirinae.

Footnotes

Disclaimer

The views and conclusions that are contained in this document are those of the authors and should not be interpreted as necessarily representing the official policies, either expressed or implied, of the US Department of Health and Human Services, the U.S. Centers for Disease Control and Prevention, or of the institutions and companies affiliated with the authors. The work by J.H.K. was supported through Battelle Memorial Institute's prime contract with the U.S. National Institute of Allergy and Infectious Diseases (NIAID) under contract number HHSN272200700016I.

Appendix A. Supplementary material

Supplementary data associated with this article can be found in the online version at http://dx.doi.org/10.1016/j.virol.2017.12.035.

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