Abstract
HIV-1 exhibits a characteristically high genetic diversity, with the M group, responsible for the pandemic, being classified into nine subtypes, 72 circulating recombinant forms (CRFs) and numerous unique recombinant forms (URFs). Here we characterize the near full-length genome sequence of an HIV-1 BG intersubtype recombinant virus (X3208) collected in Galicia (Northwest Spain) which exhibits a mosaic structure coincident with that of a previously characterized BG recombinant virus (9601_01), collected in Germany and epidemiologically linked to Portugal, and different from currently defined CRFs. Similar recombination patterns were found in partial genome sequences from three other BG recombinant viruses, one newly derived, from a virus collected in Spain, and two retrieved from databases, collected in France and Portugal, respectively. Breakpoint coincidence and clustering in phylogenetic trees of these epidemiologically-unlinked viruses allow to define a new HIV-1 CRF (CRF73_BG). CRF73_BG shares one breakpoint in the envelope with CRF14_BG, which circulates in Portugal and Spain, and groups with it in a subtype B envelope fragment, but the greatest part of its genome does not appear to derive from CRF14_BG, although both CRFs share as parental strain the subtype G variant circulating in the Iberian Peninsula. Phylogenetic clustering of partial pol and env segments from viruses collected in Portugal and Spain with X3208 and 9691_01 indicates that CRF73_BG is circulating in both countries, with proportions of around 2–3% Portuguese database HIV-1 isolates clustering with CRF73_BG. The fact that an HIV-1 recombinant virus characterized ten years ago as a URF has been shown to represent a CRF suggests that the number of HIV-1 CRFs may be much greater than currently known.
Highlights
HIV-1 is characterized for its high genetic diversity, derived from elevated mutation and recombination rates
In analyses of HIV-1 protease-reverse transcriptase (PR-RT) and V3 sequences from samples collected in different regions of Spain, from a total of more than 8,000 individuals whose samples were studied, we identified a subtype G PR-RT cluster of five viruses which in the V3 region were of subtype B and formed a cluster with two other sequences of Spanish viruses obtained by us, branching apart from CRF14_BG viruses
The total number of viruses clustering with 9196_01 in PR-RT and/or V3 region was 38, from different individuals, 31 of which were from Portugal (12 in PR-RT and 19 in the V3 region) and seven from Spain
Summary
HIV-1 is characterized for its high genetic diversity, derived from elevated mutation and recombination rates. Nonsubtype B viruses are common in most of them, these usually have been associated to travel and migration and have been acquired in or are epidemiologically linked to other continents, most frequently sub-Saharan Africa [1,2,3] Notable exceptions to this rule are Portugal, where a subtype G variant circulates at a high prevalence among the local HIV-1-infected population [4,5], and the Spanish region of Galicia, north of Portugal, where the mentioned subtype G variant [6,7] and a recently originated subtype F cluster [8] are spreading locally. Recombination of the Spanish-Portuguese or Iberian subtype G (GIb) variant with subtype B has given rise to CRF14_BG, initially identified among injecting drug users (IDUs) in Galicia [6,7], and circulating in other Spanish regions [9,10] and in Portugal [5,11,12], and to diverse unique BG recombinant viruses [6,7,13,14]
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