Evolution and characterization of endogenous avian retroviruses in galliform birds.

Abstract

Endogenous retroviruses have been found in all vertebrate hosts examined, although little is known about the distribution, evolution, and transmission of these viruses in birds. In this dissertation, I use a phylogenetic approach to investigate horizontal transmission and cospeciation of endogenous avian retroviruses found in galliform birds. I found avian sarcoma and leukosis virus (ASLV) <italic>gag</italic> genes in 26 species of galliform birds from North America, Central America, eastern Europe, Asia, and Africa. Nineteen of the 26 host species from whom ASLVs were sequenced were not previously known to contain ASLVs, I assessed congruence between ASLV phylogenies based on a total of 110 <italic>gag</italic> gene sequences and ASLV-host phylogenies based on mitochondrial 12S rDNA and ND2 sequences to infer coevolutionary history for ASLVs and their hosts. Widespread distribution of ASLVs among diverse, endemic galliform host species suggests an ancient association. Congruent ASLV and host phylogenies for two-species of <italic>Perdix</italic>, two species of <italic>Gallus</italic> and for <italic>Lagopus lagopus</italic> and <italic>L. mutus</italic> also indicate an old association with vertical transmission and cospeciation for these ASLVs and hosts. Inference of horizontal transmission of ASLVs among some Tetraoninae species (grouse and ptarmigan) is supported by ASLV monophyletic groups reflecting geographic distribution and proximity of hosts rather than host species phylogeny. To further investigate these elements I sequenced a full-length retrovirus, here named Tetraonine endogenous retrovirus (TERV), from <italic>Bonasa umbellus</italic> (Ruffed Grouse). This is the first report of a full-length ASLV provirus sequence from a bird other than the Domestic Chicken. I found a replication-defective proviral sequence consisting of putative <italic>Gag</italic> and <italic> Env</italic> proteins flanked by long terminal repeats (LTRs). The untranslated regions (UTRs) were highly conserved compared to published avian retroviruses, and contained elements necessary for transcription, replication, and packaging. Phylogenetic analyses of different gene regions suggest that TERV may have arisen via recombination between different retroviral lineages infecting birds. RT-PCR analysis showed that retroviral <italic>gag</italic> sequences closely related to TERV are transcribed, supporting the hypothesis that TERV is an active endogenous retrovirus able to move between host genomes if packaged with a replication competent retrovirus.