Infectious Endogenous Retroviruses in Cats and Emergence of Recombinant Viruses

Endogenous retroviruses (ERVs) comprise a significant percentage of the mammalian genome, and it is poorly understood whether they will remain as inactive genomes or emerge as infectious retroviruses. Although several types of ERVs are present in domestic cats, infectious ERVs have not been demonstrated. Here, we report a previously uncharacterized class of endogenous gammaretroviruses, termed ERV-DCs, that is present and hereditary in the domestic cat genome. We have characterized a subset of ERV-DC proviral clones, which are numbered according to their genomic insertions. One of these, ERV-DC10, located in the q12-q21 region on chromosome C1, is an infectious gammaretrovirus capable of infecting a broad range of cells, including human. Our studies indicate that ERV-DC10 entered the genome of domestic cats in the recent past and appeared to translocate to or reintegrate at a distinct locus as infectious ERV-DC18. Insertional polymorphism analysis revealed that 92 of 244 domestic cats had ERV-DC10 on a homozygous or heterozygous locus. ERV-DC-like sequences were found in primate and rodent genomes, suggesting that these ERVs, and recombinant viruses such as RD-114 and BaEV, originated from an ancestor of ERV-DC. We also found that a novel recombinant virus, feline leukemia virus subgroup D (FeLV-D), was generated by ERV-DCenvtransduction into feline leukemia virus in domestic cats. Our results indicate that ERV-DCs behave as donors and/or acceptors in the generation of infectious, recombinant viruses. The presence of such infectious endogenous retroviruses, which could be harmful or beneficial to the host, may affect veterinary medicine and public health.

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Ancestral Mutations Acquired in Refrex-1, a Restriction Factor against Feline Retroviruses, during its Cooption and Domestication

Journal of Virology ◽

10.1128/jvi.01904-15 ◽

2015 ◽

Vol 90 (3) ◽

pp. 1470-1485 ◽

Cited By ~ 7

Author(s):

Jumpei Ito ◽

Takuya Baba ◽

Junna Kawasaki ◽

Kazuo Nishigaki

Keyword(s):

Field Model ◽

Leukemia Virus ◽

Endogenous Retroviruses ◽

Chimeric Virus ◽

Feline Leukemia Virus ◽

Domestic Cats ◽

Terminal Domain ◽

Viral Particles ◽

Triangular Relationships ◽

Retroviral Infections

ABSTRACTEndogenous retroviruses (ERVs) are remnants of ancestral retroviral infections of germ cells. Retroviral endogenization is an adaptation process for the host genome, and ERVs are gradually attenuated or inactivated by mutation. However, some ERVs that have been “domesticated” by their hosts eventually gain physiological functions, such as placentation or viral resistance. We previously reported the discovery of Refrex-1, a soluble antiretroviral factor in domestic cats that specifically inhibits infection by feline leukemia virus subgroup D (FeLV-D), a chimeric virus of FeLV, and a feline ERV, ERV-DC. Refrex-1 is a truncated envelope protein (Env) encoded by both ERV-DC7 and ERV-DC16 proviral loci. Here, we reconstituted ancestral and functional Env from ERV-DC7 and ERV-DC16 envelope genes (env) by inducing reverse mutations. Unexpectedly, ERV-DC7 and ERV-DC16 full-length Env (ERV-DC7 fl and ERV-DC16 fl), reconstructed by removing stop codons, did not produce infectious viral particles. ERV-DC7 fl and ERV-DC16 fl were highly expressed in cells but were not cleaved into surface subunits (SU) and transmembrane subunits, nor were they incorporated into virions. G407R/N427I-A429T and Y431D substitutions within the SU C-terminal domain of ERV-DC7 fl and ERV-DC16 fl, respectively, caused these dysfunctions. The residues glycine 407 and tyrosine 431 are relatively conserved among infectious gammaretroviruses, and their substitution causes the same dysfunctions as the tested retroviruses. Our results reveal that specific mutations within the SU C-terminal domain suppressed Env cleavage and incorporation into virions and indicate that these mutations contributed to the domestication of Refrex-1 through multistep events that occurred in the postintegration period.IMPORTANCEDomestic cats are colonized with various exogenous retroviruses (exRVs), such as feline leukemia virus (FeLV), and their genomes contain numerous ERVs, some of which are replication-competent proviruses. The feline hosts, exRVs, and ERVs have complicated genetic interactions and provide an interesting field model for triangular relationships: recombination between FeLV and ERV-DC, which is a feline ERV, generated FeLV-D, a chimeric virus, and FeLV-D is restricted by Refrex-1, an antiretroviral factor corresponding to truncated Env of ERV-DC7 and ERV-DC16. Here, we reconstructed ancestral, functional Env from ERV-DC7 and ERV-DC16envby inducing reverse mutations to elucidate how Refrex-1 was generated from its ancestor. Our results reveal that they were repeatedly inactivated by mutations preventing Env maturation. Our results provide insights into how ERVs were “domesticated” by their hosts and identify the mutations that mediated these evolutions. Notably, experiments that restore inactivated ERVs might uncover previously unrecognized features or properties of retroviruses.

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Presence of Endogenous Viral Elements Negatively Correlates with Feline Leukemia Virus Susceptibility in Puma and Domestic Cat Cells

Journal of Virology ◽

10.1128/jvi.01274-20 ◽

2020 ◽

Vol 94 (21) ◽

Author(s):

Elliott S. Chiu ◽

Sue VandeWoude

Keyword(s):

Copy Number ◽

Puma Concolor ◽

Leukemia Virus ◽

Domestic Cat ◽

Feline Leukemia Virus ◽

Domestic Cats ◽

Endogenous Virus ◽

Content Type ◽

Copy Numbers ◽

Felid Species

ABSTRACT While feline leukemia virus (FeLV) has been shown to infect felid species other than the endemic domestic cat host, differences in FeLV susceptibility among species has not been evaluated. Previous reports have noted a negative correlation between endogenous FeLV (enFeLV) copy number and exogenous FeLV (exFeLV) infection outcomes in domestic cats. Since felids outside the genus Felis do not harbor enFeLV genomes, we hypothesized absence of enFeLV results in more severe disease consequences in felid species lacking these genomic elements. We infected primary fibroblasts isolated from domestic cats (Felis catus) and pumas (Puma concolor) with FeLV and quantitated proviral and viral antigen loads. Domestic cat enFeLV env and long terminal repeat (LTR) copy numbers were determined for each individual and compared to FeLV viral outcomes. FeLV proviral and antigen levels were also measured in 6 naturally infected domestic cats and 11 naturally infected Florida panthers (P. concolor coryi). We demonstrated that puma fibroblasts are more permissive to FeLV than domestic cat cells, and domestic cat FeLV restriction was highly related to enFeLV-LTR copy number. Terminal tissues from FeLV-infected Florida panthers and domestic cats had similar exFeLV proviral copy numbers, but Florida panther tissues have higher FeLV antigen loads. Our work indicates that enFeLV-LTR elements negatively correlate with exogenous FeLV replication. Further, Puma concolor samples lacking enFeLV are more permissive to FeLV infection than domestic cat samples, suggesting that endogenization can play a beneficial role in mitigating exogenous retroviral infections. Conversely, presence of endogenous retroelements may relate to new host susceptibility during viral spillover events. IMPORTANCE Feline leukemia virus (FeLV) can infect a variety of felid species. Only the primary domestic cat host and related small cat species harbor a related endogenous virus in their genomes. Previous studies noted a negative association between the endogenous virus copy number and exogenous virus infection in domestic cats. This report shows that puma cells, which lack endogenous FeLV, produce more virus more rapidly than domestic cat fibroblasts following cell culture challenge. We document a strong association between domestic cat cell susceptibility and FeLV long terminal repeat (LTR) copy number, similar to observations in natural FeLV infections. Viral replication does not, however, correlate with FeLV env copy number, suggesting that this effect is specific to FeLV-LTR elements. This discovery indicates a protective capacity of the endogenous virus against the exogenous form, either via direct interference or indirectly via gene regulation, and may suggest evolutionary outcomes of retroviral endogenization.

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Endogenous feline leukemia virus siRNA transcription may interfere with exogenous FeLV infection

10.1101/2021.01.12.426481 ◽

2021 ◽

Author(s):

Elliott S. Chiu ◽

Sue VandeWoude

Keyword(s):

Mononuclear Cells ◽

Cell Function ◽

Leukemia Virus ◽

Endogenous Retroviruses ◽

Domestic Cat ◽

Feline Leukemia Virus ◽

Infectious Agents ◽

Biological Functions ◽

Peripheral Blood Mononuclear ◽

Solo Ltrs

AbstractEndogenous retroviruses (ERVs) are increasingly recognized for biological impacts on host cell function and susceptibility to infectious agents, particularly in relation to interactions with exogenous retroviral progenitors (XRVs). ERVs can simultaneously promote and restrict XRV infections using different mechanisms that are virus- and host-specific. The majority of endogenous-exogenous retroviral interactions have been evaluated in experimental mouse or chicken systems which are limited in their ability to extend findings to naturally infected outbred animals. Feline leukemia virus (FeLV) has a relatively well-characterized endogenous retrovirus with a coexisting virulent exogenous counterpart and is endemic worldwide in domestic cats. We have previously documented an association between endogenous FeLV LTR copy number and abrogated exogenous FeLV in naturally infected cats and experimental infections in tissue culture. Analyses described here examine limited FeLV replication in experimentally infected peripheral blood mononuclear cells. We further examine NCBI Sequence Read Archive RNA transcripts to evaluate enFeLV transcripts and RNA interference precursors. We find that lymphoid-derived tissues, which are experimentally less permissive to exogenous FeLV infection, transcribe higher levels of enFeLV under basal conditions. Transcription of enFeLV-LTR segments is significantly greater than other enFeLV genes. We documented transcription of a 21-nt miRNA just 3′ to the enFeLV 5′-LTR in the feline miRNAome of all datasets evaluated (n=27). Our findings point to important biological functions of enFeLV transcription linked to solo LTRs distributed within the domestic cat genome, with potential impacts on domestic cat exogenous FeLV susceptibility and pathogenesis.ImportanceEndogenous retroviruses (ERVs) are increasingly implicated in host cellular processes and susceptibility to infectious agents, specifically regarding interactions with exogenous retroviral progenitors (XRVs). Exogenous feline leukemia virus (FeLV) and its endogenous counterpart (enFeLV) represent a well characterized, naturally occurring XRV-ERV dyad. We have previously documented an abrogated FeLV infection in both naturally infected cats and experimental fibroblast infections that harbor higher enFeLV proviral loads. Using an in silico approach, we provide evidence of miRNA-transcription that are produced in tissues most important for FeLV infection, replication, and transmission. Our findings point to important biological functions of enFeLV transcription linked to solo-LTRs distributed within the feline genome, with potential impacts on domestic cat exogenous FeLV susceptibility and pathogenesis. This body of work provides additional evidence of RNAi as a mechanism of viral interference and is a demonstration of ERV exaptation by the host to defend against related XRVs.

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Presence of endogenous viral elements negatively correlates with FeLV susceptibility in puma and domestic cat cells

10.1101/2020.06.23.168351 ◽

2020 ◽

Author(s):

Elliott S. Chiu ◽

Sue VandeWoude

Keyword(s):

Copy Number ◽

Puma Concolor ◽

Leukemia Virus ◽

Domestic Cat ◽

Feline Leukemia Virus ◽

Host Susceptibility ◽

Domestic Cats ◽

Endogenous Virus ◽

Copy Numbers ◽

Felid Species

AbstractWhile feline leukemia virus (FeLV) has been shown to infect felid species other than the endemic domestic cat host, differences in FeLV susceptibility among species has not been evaluated. Previous reports have noted a negative correlation between enFeLV copy number and exogenous FeLV infection outcomes in domestic cats. Since felids outside the genus Felis do not harbor enFeLV genomes, we hypothesized absence of enFeLV results in more severe disease consequences in felid species lacking these genomic elements. We infected primary fibroblasts isolated from domestic cats (Felis catus) and pumas (Puma concolor) with FeLV and quantitated proviral and viral antigen loads. Domestic cat enFeLV env and LTR copy numbers were determined for each individual and compared to FeLV viral outcomes. FeLV proviral and antigen levels were also measured in 6 naturally infected domestic cats and 11 naturally infected Florida panthers (P. concolor coryi). We demonstrated that puma fibroblasts are more permissive to FeLV than domestic cat cells, and domestic cat FeLV restriction was highly related to enFeLV LTR copy number. Terminal tissues from FeLV-infected Florida panthers and domestic cats had similar exFeLV proviral copy numbers, but Florida panther tissues have higher FeLV antigen loads. Our work indicates enFeLV LTR elements negatively regulate exogenous FeLV replication. Further, Puma concolor lacking enFeLV are more permissive to FeLV infection than domestic cats, suggesting endogenization can play a beneficial role in mitigating exogenous retroviral infections. Conversely, presence of endogenous retroelements may relate to new host susceptibility during viral spillover events.ImportanceFeline leukemia virus (FeLV) can infect a variety of felid species. Only the primary domestic cat host and related small cat species harbor a related endogenous virus in their genomes. Previous studies noted a negative association between the endogenous virus copy number and exogenous virus infection in domestic cats. This report shows that puma cells, which lack endogenous FeLV, produce more virus more rapidly than domestic cat fibroblasts following cell culture challenge. We document a strong association between domestic cat cell susceptibility and FeLV long terminal repeat (LTR) copy number, similar to observations in natural FeLV infections. Viral replication does not, however, correlate with FeLV env copy number, suggesting this effect is specific to FeLV LTR elements. This discovery indicates a protective capacity of the endogenous virus against the exogenous form, either via direct interference or indirectly via gene regulation, and may suggest evolutionary outcomes of retroviral endogenization.

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Endogenous feline leukemia virus siRNA transcription may interfere with exogenous FeLV infection

Journal of Virology ◽

10.1128/jvi.00070-21 ◽

2021 ◽

Author(s):

Elliott S. Chiu ◽

Coby A. McDonald ◽

Sue VandeWoude

Keyword(s):

Mononuclear Cells ◽

Cell Function ◽

Leukemia Virus ◽

Endogenous Retroviruses ◽

Domestic Cat ◽

Feline Leukemia Virus ◽

Infectious Agents ◽

Biological Functions ◽

Peripheral Blood Mononuclear ◽

Solo Ltrs

Endogenous retroviruses (ERVs) are increasingly recognized for biological impacts on host cell function and susceptibility to infectious agents, particularly in relation to interactions with exogenous retroviral progenitors (XRVs). ERVs can simultaneously promote and restrict XRV infections using mechanisms that are virus- and host-specific. The majority of endogenous-exogenous retroviral interactions have been evaluated in experimental mouse or chicken systems which are limited in their ability to extend findings to naturally infected outbred animals. Feline leukemia virus (FeLV) has a relatively well-characterized endogenous retrovirus with a coexisting virulent exogenous counterpart and is endemic worldwide in domestic cats. We have previously documented an association between endogenous FeLV LTR copy number and abrogated exogenous FeLV in naturally infected cats and experimental infections in tissue culture. Analyses described here examine limited FeLV replication in experimentally infected peripheral blood mononuclear cells which correlates with higher enFeLV transcripts in these cells compared to fibroblasts. We further examine NCBI Sequence Read Archive RNA transcripts to evaluate enFeLV transcripts and RNA interference precursors. We find that lymphoid-derived tissues, which are experimentally less permissive to exogenous FeLV infection, transcribe higher levels of enFeLV under basal conditions. Transcription of enFeLV-LTR segments is significantly greater than other enFeLV genes. We documented transcription of a 21-nt miRNA just 3’ to the enFeLV 5’-LTR in the feline miRNAome of all datasets evaluated (n=27). Our findings point to important biological functions of enFeLV transcription linked to solo LTRs distributed within the domestic cat genome, with potential impacts on domestic cat exogenous FeLV susceptibility and pathogenesis. Importance Endogenous retroviruses (ERVs) are increasingly implicated in host cellular processes and susceptibility to infectious agents, specifically regarding interactions with exogenous retroviral progenitors (XRVs). Exogenous feline leukemia virus (FeLV) and its endogenous counterpart (enFeLV) represent a well characterized, naturally occurring XRV-ERV dyad. We have previously documented an abrogated FeLV infection in both naturally infected cats and experimental fibroblast infections that harbor higher enFeLV proviral loads. Using an in silico approach, we provide evidence of miRNA-transcription that are produced in tissues most important for FeLV infection, replication, and transmission. Our findings point to important biological functions of enFeLV transcription linked to solo-LTRs distributed within the feline genome, with potential impacts on domestic cat exogenous FeLV susceptibility and pathogenesis. This body of work provides additional evidence of RNAi as a mechanism of viral interference and is a demonstration of ERV exaptation by the host to defend against related XRVs.

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Epidemiologic survey of feline leukemia virus in domestic cats on Tsushima Island, Japan: management strategy for Tsushima leopard cats

Journal of Veterinary Diagnostic Investigation ◽

10.1177/1040638717725551 ◽

2017 ◽

Vol 29 (6) ◽

pp. 889-895 ◽

Cited By ~ 1

Author(s):

Isaac Makundi ◽

Yushi Koshida ◽

Kyohei Kuse ◽

Takahiro Hiratsuka ◽

Jumpei Ito ◽

...

Keyword(s):

Management Strategy ◽

Leukemia Virus ◽

Feline Leukemia Virus ◽

Domestic Cats ◽

Epidemiologic Survey

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Acute visceral leishmaniasis in a domestic cat (Felis silvestris catus) from the state of Tocantins, Brazil

Semina Ciências Agrárias ◽

10.5433/1679-0359.2019v40n4p1723 ◽

2019 ◽

Vol 40 (4) ◽

pp. 1723

Author(s):

Sebastiana Adriana Pereira Sousa ◽

Helcileia Dias Santos ◽

Cristiane América de Carvalho ◽

Aline Marinho Machado ◽

Letícia Espindola de Oliveira ◽

...

Keyword(s):

Visceral Leishmaniasis ◽

Leukemia Virus ◽

Antibody Test ◽

The State ◽

Diagnostic Methods ◽

Domestic Cat ◽

Feline Leukemia Virus ◽

Mesenteric Lymph Nodes ◽

First Case ◽

Immunodeficiency Virus

Visceral leishmaniasis (VL) is expanding in the Brazilian territory. Dogs are considered an important urban reservoir; however, studies have demonstrated the presence of infected cats in some Brazilian states. This report aimed to describe a case of Leishmania (Leishmania) infantum infection in a two-month-old domestic feline from a Brazilian region with a high incidence of human visceral leishmaniasis. The analyzed samples were the cat’s blood, conjunctiva, spleen, liver, popliteal, submandibular and mesenteric lymph nodes, skin, lung and kidney. The diagnostic methods were: parasitological examination, polymerase chain reaction (PCR) and an immunoflurescence antibody test (IFAT). All tissues were positive. The title obtained using the IFAT was 1:160. The animal was negative for feline immunodeficiency virus (FIV) and feline leukemia virus (FeLV). This work addresses the first case of feline leishmaniasis in the state of Tocantins, and reveals data that may contribute to the knowledge of the disease, since it has been shown to be able to develop rapidly and fatally in kittens, with the ability to infect several tissues.

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Feline Pit2 Functions as a Receptor for Subgroup B Feline Leukemia Viruses

Journal of Virology ◽

10.1128/jvi.75.22.10563-10572.2001 ◽

2001 ◽

Vol 75 (22) ◽

pp. 10563-10572 ◽

Cited By ~ 25

Author(s):

Maria M. Anderson ◽

Adam S. Lauring ◽

Scott Robertson ◽

Clarissa Dirks ◽

Julie Overbaugh

Keyword(s):

High Efficiency ◽

Leukemia Virus ◽

Variable Region ◽

Feline Leukemia Virus ◽

Envelope Gene ◽

Lower Efficiency ◽

Critical Determinant ◽

Recombinant Viruses ◽

Ability To Act ◽

Leukemia Viruses

ABSTRACT Different subgroups of feline leukemia virus (FeLV) use different host cell receptors for entry. Subgroup A FeLV (FeLV-A) is the virus that is transmitted from cat to cat, suggesting that cells expressing the FeLV-A receptor are important targets at the earliest stages of infection. FeLV-B evolves from FeLV-A in the infected cat through acquisition of cellular sequences that are related to the FeLV envelope gene. FeLV-Bs have been shown to infect cells using the Pit1 receptor, and some variants can infect cells at a lower efficiency using Pit2. Because these observations were made using receptor proteins of human or rodent origin, the role that Pit1 and Pit2 may play in FeLV-B replication in the cat is unclear. In this study, the feline Pit receptors were cloned and tested for their ability to act as receptors for different FeLV-Bs. Some FeLV-Bs infected cells expressing feline Pit2 and feline Pit1 with equal high efficiency. Variable region A (VRA) in the putative receptor-binding domain (RBD) was a critical determinant for both feline Pit1 and feline Pit2 binding, although other domains in the RBD appear to influence how efficiently the FeLV-B surface unit can bind to feline Pit2 and promote entry via this receptor. An arginine residue at position 73 in VRA was found to be important for envelope binding to feline Pit2 but not feline Pit1. Interestingly, this arginine is not found in endogenous FeLV sequences or in recombinant viruses recovered from feline cells infected with FeLV-A. Thus, while FeLV-Bs that are able to use feline Pit2 can evolve by recombination with endogenous sequences, a subsequent point mutation during reverse transcription may be needed to generate a virus that can efficiently enter the cells using the feline Pit2 as its receptor. These studies suggest that cells expressing the feline Pit2 protein are likely to be targets for FeLV-B infection in the cat.

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