Recombination in feline immunodeficiency virus genomes from naturally infected cougars

Bruen, Trevor C.; Poss, Mary

doi:10.1016/j.virol.2007.03.023

Cited by 10 publications

(12 citation statements)

References 42 publications

(70 reference statements)

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“…In contrast, the PLVB breakpoints occur almost exclusively in the 3= half of the genome, with only one of nine breakpoints being located in the 5= half. This finding is in agreement with a previous study of PLVB that analyzed the sequences from WY and MT (11).…”

Section: Viral Sequencessupporting

confidence: 93%

“…Animal capture locations are indicated as follows: circles, bobcats (PLVA); squares, mountain lions (PLVA); small triangles, mountain lions (PLVB); stars, PLVA/PLVB-coinfected mountain lions. Large upside-down triangles represent approximate capture locations for previously reported PLV sequences included in this study (11,15). The exact locations for Florida panther samples are not shown.…”

Section: Figmentioning

confidence: 99%

“…Several previous reports have described the phylogenetic relationships among FIVs based upon nucleotide sequence alignments from short regions of the pol or env genes (4,(6)(7)(8)(9)(10). Additional studies comparing phylogenetic relationships among fulllength sequences of lion lentivirus (LLV) isolates across Africa and PLVB isolates from central North America demonstrate that complex evolutionary histories cannot be fully resolved through single-gene analyses (11,13,14,17). Since only one full-length PLVA sequence has been evaluated, no genomic evolutionary studies have been conducted on this clade (15).…”

mentioning

confidence: 99%

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Evolution of Puma Lentivirus in Bobcats (Lynx rufus) and Mountain Lions (Puma concolor) in North America

Lee

Bevins²,

Serieys

et al. 2014

J Virol

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Mountain lions (Puma concolor) throughout North and South America are infected with puma lentivirus clade B (PLVB).A second, highly divergent lentiviral clade, PLVA, infects mountain lions in southern California and Florida. Bobcats (Lynx rufus) in these two geographic regions are also infected with PLVA, and to date, this is the only strain of lentivirus identified in bobcats. We sequenced full-length PLV genomes in order to characterize the molecular evolution of PLV in bobcats and mountain lions. Low sequence homology (88% average pairwise identity) and frequent recombination (1 recombination breakpoint per 3 isolates analyzed) were observed in both clades. Viral proteins have markedly different patterns of evolution; sequence homology and negative selection were highest in Gag and Pol and lowest in Vif and Env. A total of 1.7% of sites across the PLV genome evolve under positive selection, indicating that host-imposed selection pressure is an important force shaping PLV evolution. PLVA strains are highly spatially structured, reflecting the population dynamics of their primary host, the bobcat. In contrast, the phylogeography of PLVB reflects the highly mobile mountain lion, with diverse PLVB isolates cocirculating in some areas and genetically related viruses being present in populations separated by thousands of kilometers. We conclude that PLVA and PLVB are two different viral species with distinct feline hosts and evolutionary histories. IMPORTANCEAn understanding of viral evolution in natural host populations is a fundamental goal of virology, molecular biology, and disease ecology. Here we provide a detailed analysis of puma lentivirus (PLV) evolution in two natural carnivore hosts, the bobcat and mountain lion. Our results illustrate that PLV evolution is a dynamic process that results from high rates of viral mutation/ recombination and host-imposed selection pressure.

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Section: Viral Sequencessupporting

confidence: 93%

Section: Figmentioning

confidence: 99%

mentioning

confidence: 99%

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Evolution of Puma Lentivirus in Bobcats (Lynx rufus) and Mountain Lions (Puma concolor) in North America

Lee

Bevins²,

Serieys

et al. 2014

J Virol

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“…On the other hand, the rapid change of functional proteins, such as VP1, due to recombination might play a potential role in the rapid evolution of BTV. Homologous recombination is important process driving genotype diversity for some RNA viruses (11,20,38). Recombination, especially between different serotypes, may speed up the evolution of BTV and result in a rapid change in its epidemiology.…”

Section: Discussionmentioning

confidence: 99%

Intragenic Recombination as a Mechanism of Genetic Diversity in Bluetongue Virus

Ding

et al. 2010

J Virol

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Bluetongue (BT), caused by Bluetongue virus (BTV), is an economically important disease affecting sheep, deer, cattle, and goats. Since 1998, a series of BT outbreaks have spread across much of southern and central Europe. To study why the epidemiology of the virus happens to change, it is important to fully know the mechanisms resulting in its genetic diversity. Gene mutation and segment reassortment have been considered as the key forces driving the evolution of BTV. However, it is still unknown whether intragenic recombination can occur and contribute to the process in the virus. We present here several BTV groups containing mosaic genes to reveal that intragenic recombination can take place between the virus strains and play a potential role in bringing novel BTV lineages.

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“…Phylogenetic comparisons were made using discontinuous megablast (http://blast.ncbi.nlm.nih.gov/Blast. cgi) of part or all of FIV Petaluma strain nucleotides 216-727 (Talbott et al 1989), FIVPco nucleotides 184-751 (Bruen and Poss 2007), or FIVPleo accession number EU117992 nucleotides 262-802 (Pecon-Slattery et al 2008). A consensus sequence was taken for molecular clones that originated from the same viral isolate.…”

Section: In Silico Analyses Of Fiv Rnamentioning

confidence: 99%

The secondary structure of the 5′ end of the FIV genome reveals a long-range interaction between R/U5 and gag sequences, and a large, stable stem–loop

Kenyon¹,

Ghazawi²,

Cheung³

et al. 2008

RNA

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The secondary structure of the 59 end of the FIV genome reveals a long-range interaction between R/U5 and gag sequences, and a large, stable stem-loop JULIA C. KENYON ABSTRACT Feline immunodeficiency virus (FIV) is a lentivirus that infects cats and is related to human immunodeficiency virus (HIV).Although it is a common worldwide infection, and has potential uses as a human gene therapy vector and as a nonprimate model for HIV infection, little detail is known of the viral life cycle. Previous experiments have shown that its packaging signal includes two or more regions within the first 511 nucleotides of the genomic RNA. We have undertaken a secondary structural analysis of this RNA by minimal free-energy structural prediction, biochemical mapping, and phylogenetic analysis, and show that it contains five conserved stem-loops and a conserved long-range interaction between heptanucleotide sequences 59-CCCUGUC-39 in R/U5 and 59-GACAGGG-39 in gag. This long-range interaction is similar to that seen in primate lentiviruses where it is thought to be functionally important. Along with strains that infect domestic cats, this heptanucleotide interaction can also occur in speciesspecific FIV strains that infect pumas, lions, and Pallas' cats where the heptanucleotide sequences involved vary. We have analyzed spliced and genomic FIV RNAs and see little structural change or sequence conservation within single-stranded regions of the 59 UTR that are important for viral packaging, suggesting that FIV may employ a cotranslational packaging mechanism.Keywords: FIV; lentivirus; packaging signal; dimerization; RNA INTRODUCTIONFeline immunodeficiency virus (FIV) is a lentivirus related to human immunodeficiency virus (HIV), the causative agent of AIDS (Olmsted et al. 1989;Talbott et al. 1989). Like HIV, FIV causes in its host, the domestic cat, a prolonged disease that is characterized by progressive depletion of CD4 + T cells, ultimately leading to a fatal immunodeficiency (Pedersen et al. 1987;Yamamoto et al. 1988;Siebelink et al. 1990). Many other parallels exist between the two viruses and these render FIV infection in cats a potentially useful small animal model for HIV (Olmsted et al. 1989; and reviewed in Elder et al. 2008). In addition to this, FIV is being developed as a human gene therapy vector as, like all lentiviruses, it is able to transduce nondividing cells while being associated with fewer safety concerns than primate lentiviral vectors (reviewed in Saenz and Poeschla 2004). FIV also poses a serious veterinary concern in its own right, as it infects domestic cats and big cats alike, with a worldwide distribution and a high seroprevalence (Troyer et al. 2005). A better understanding of the mechanisms of FIV replication is needed in order to utilize the virus to its full potential as an HIV model or as a gene therapy vector, and to seek ways to combat its spread in feline species. Examining the structure of functionally important regions of the FIV RNA will not only aid this, but may also enhance our understand...

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Recombination in feline immunodeficiency virus genomes from naturally infected cougars

Cited by 10 publications

References 42 publications

Evolution of Puma Lentivirus in Bobcats (Lynx rufus) and Mountain Lions (Puma concolor) in North America

Evolution of Puma Lentivirus in Bobcats (Lynx rufus) and Mountain Lions (Puma concolor) in North America

Intragenic Recombination as a Mechanism of Genetic Diversity in Bluetongue Virus

The secondary structure of the 5′ end of the FIV genome reveals a long-range interaction between R/U5 and gag sequences, and a large, stable stem–loop

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