Data from: Hepatitis C virus genotype 1 and 2 recombinant genomes and the phylogeographic history of the 2k/1b lineage

Recombination is an important driver of genetic diversity, though it is
relatively uncommon in hepatitis C virus (HCV). Recent investigation of
sequence data acquired from HCV clinical trials produced 21 full-genome
recombinant viruses belonging to three putative inter-subtype forms 2b/1a,
2b/1b, and 2k/1b. The 2k/1b chimera is the only known HCV circulating
recombinant form (CRF), provoking interest in its genetic structure and
origin. Discovered in Russia in 1999, 2k/1b cases have since been detected
throughout the former Soviet Union, Western Europe, and North America.
Although 2k/1b prevalence is highest in the Caucasus mountain region
(i.e., Armenia, Azerbaijan, and Georgia), the origin and migration
patterns of CRF 2k/1b have remained obscure due to a paucity of available
sequences. We assembled an alignment which spans the entire coding region
of the HCV genome containing all available 2k/1b sequences (>500
nucleotides; n=109) sampled in 19 countries from public databases (102
individuals), additional newly sequenced genomic regions (from 48 of these
102 individuals), unpublished isolates with newly sequenced regions (5
additional individuals), and novel complete genomes (2 additional
individuals) generated in this study. Analysis of this expanded dataset
reconfirmed the monophyletic origin of 2k/1b with a recombination
breakpoint at position 3,187 (95% confidence interval: 3,172–3,202; HCV
GT1a reference strain H77). Phylogeography is a valuable tool used to
reveal viral migration dynamics. Inference of the timed history of spread
in a Bayesian framework identified Russia as the ancestral source of the
CRF 2k/1b clade. Further, we found evidence for migration routes leading
out of Russia to other former Soviet Republics or countries under the
Soviet sphere of influence. These findings suggest an interplay between
geopolitics and the historical spread of CRF 2k/1b.