Identification of an HIV-1 BG Intersubtype Recombinant Form (CRF73_BG), Partially Related to CRF14_BG, Which Is Circulating in Portugal and Spain

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.

HIV-1 Unique Recombinant Forms Identified in Slovenia and Their Characterization by Near Full-Length Genome Sequencing

“…On the other hand, CRF19_cpx spread was observed in southern Spain, where several transmission networks of young native Spanish MSM were determined, with tMRCAs in the period from 2007 to 2010 [36][37][38]. This, coupled with the recent characterization of new recombinant forms of subtypes B and G described in Spain and Portugal, could suggest that the URF identified in this study might also have originated in Europe [39,40].…”

Molecular Epidemiology of HIV-1 Subtype G in the Russian Federation

“…The most remarkable example is Portugal, where subtype G is the second most prevalent HIV-1 clade (>10%), after subtype B (>40%) [12,13,14]. In addition to Portugal, Spain has experienced an enormous spread of HIV; their epidemics are characterized by substantial viral diversity and distinct molecular properties compared to other European countries [15,16,17]. Non-B subtypes, particularly subtype G, were also very prevalent, with subtype G found in approximately 30% of all diagnoses [7].…”

Local Epidemics Gone Viral: Evolution and Diffusion of the Italian HIV-1 Recombinant Form CRF60_BC

“…Despite their origin, some CRFs gained epidemiological relevance in previously B subtype-restricted countries with lower HIV-1 prevalence. Within the last years, multiple new CRFs have been identified in European countries such as Russia (Liitsola et al, 1998; Lukashov et al, 1999; Baryshev et al, 2014), Portugal, Spain (Delgado et al, 2002; Fernandez-Garcia et al, 2016), Italy (Simonetti et al, 2014), United Kingdom (Foster et al, 2014), Luxembourg (Struck et al, 2015), and France (Leoz et al, 2013; Recordon-Pinson et al, 2018).…”