Extensive Homologous Recombination among Widely Divergent TT Viruses

Abstract

Analyses of a collection of full-length TT virus genomes showed nearly half of them to be recombinant. The results were highly significant and revealed homologous recombination both within and among genotypes, often involving extremely divergent lineages. Recombination breakpoints were significantly more common in the noncoding region of the TT virus genome than in the coding region.TT virus (TTV) is a newly discovered nonenveloped DNA virus that was initially considered to be a possible agent of viral hepatitis, since it was first recovered from a patient with posttransfusion hepatitis of unknown etiology (12,15). Subsequent studies, however, have shown it to be very widespread and to occur at an extremely high prevalence even in healthy populations (1,9,18,20), casting doubt on its causal role in human disease. Its circular, single-stranded, negative-sense DNA genome, approximately 3,850 nucleotides in length (10, 11), bears little or no identifiable similarity to other known viruses, and TTV appears to represent a new virus family, tentatively designated Circinoviridae (11).For a DNA virus, TTV exhibits an astonishingly large amount of genetic diversity. To date, more than 16 genotypes separated by more than 30% divergence at the nucleotide level have been described (6,7,14,16,18,22), incorporating three hypervariable regions (13). Understanding the origins of such diversity is a fundamental problem in virology. While the role played by mutation has long been considered, it is becoming increasingly apparent that recombination also plays a key role in the evolution of many virus groups (19,24). The recent availability of several full-length TTV sequences (3,6,10,11,16), along with evidence for mixed infection by multiple genetic types (2,4,17,21), prompted this investigation into whether recombination might also play a role in the evolution of TTV.A total of 15 full-length or near-full-length TTV genomes with the following isolate names (accession numbers) were collected from GenBank: TA278 (AB017610) (16); GH1 (AF122913) (11); TUS01 (AB017613) (16); SAN-BAN (AB025946) (6); JA20 (AF122914), JA9 (AF122915), JA10 (AF122919), JA4 (AF122917), JA1 (AF122916), JA2B (AF122918), US32 (AF122921), and US35 (AF122920) (3); and BDH1 (AF116842), TTVCHN1 (AF079173), and TTVCHN2 (AF129887). The sequences were aligned using CLUSTAL W (23) and adjusted by hand. The resulting 3,853-nucleotide fulllength TTV alignment is available from the author on request.The aligned data set was analyzed by various methods to identify possible recombinant isolates, to characterize their putative recombination breakpoints, and to test results suggestive of recombination for statistical significance. First, an exploratory tree analysis (5) was performed by sliding a 400-nucleotide window down the sequence alignment in 200-nucleotide increments, generating a series of trees for the different regions. All trees were reconstructed with the PAUP* program (version 4; Sinauer Associates, Sunderland, Mass.) using the neighbor-joining algorithm with di...

Detection of Tt Virus Among Chimpanzees in the Wild Using a Noninvasive Technique

“…It should be noted that the proximity of strains TUSO1 (genotype 11) and JA1 (genotype 2) in the phylogenetic tree is a consequence of the recombinant nature of strain TUSO1, as previously reported (Worobey, 2000).…”

In Vivo and In Vitro Intragenomic Rearrangement of TT Viruses

“…Intragenomic rearrangement involving larger fragments within one TT virus genome, however, has not been described previously. Homologous recombination between TT virus types has been discussed, and putative recombination breakpoints in the noncoding region have been identified (4,60). The phylogenetic analysis of amplified sequences from a very short region within ORF1 also suggested recombinational events (25).…”

Isolation of Multiple TT Virus Genotypes from Spleen Biopsy Tissue from a Hodgkin's Disease Patient: Genome Reorganization and Diversity in the Hypervariable Region

“…The use of different regions of the genome for establishing phylogeny has frequently been questioned and debated (3,39,45,55). Recombination between TT isolates has been discussed (28,59), although according to our experience this may represent PCR artifacts (generating genomes or partial genomes by PCR amplification on DNA templates harboring several closely related TTV genomes) (unpublished data). The TT-like mini viruses have been lumped together with the TTV into the proposed genus Anellovirus, based on a similar genome organization and similar modes of transmission and infection (12).…”