Identification of a New HIV-1 BC Intersubtype Circulating Recombinant Form (CRF108_BC) in Spain

Abstract

The extraordinary genetic variability of human immunodeficiency virus type 1 (HIV-1) group M has led to the identification of 10 subtypes, 102 circulating recombinant forms (CRFs) and numerous unique recombinant forms. Among CRFs, 11 derived from subtypes B and C have been identified in China, Brazil, and Italy. Here we identify a new HIV-1 CRF_BC in Northern Spain. Originally, a phylogenetic cluster of 15 viruses of subtype C in protease-reverse transcriptase was identified in an HIV-1 molecular surveillance study in Spain, most of them from individuals from the Basque Country and heterosexually transmitted. Analyses of near full-length genome sequences from six viruses from three cities revealed that they were BC recombinant with coincident mosaic structures different from known CRFs. This allowed the definition of a new HIV-1 CRF designated CRF108_BC, whose genome is predominantly of subtype C, with four short subtype B fragments. Phylogenetic analyses with database sequences supported a Brazilian ancestry of the parental subtype C strain. Coalescent Bayesian analyses estimated the most recent common ancestor of CRF108_BC in the city of Vitoria, Basque Country, around 2000. CRF108_BC is the first CRF_BC identified in Spain and the second in Europe, after CRF60_BC, both phylogenetically related to Brazilian subtype C strains.

Keywords: HIV-1; HIV-1 genetic diversity; HIV-1 molecular epidemiology; HIV-1 phylogeny; circulating recombinant form.

Figure 1

Maximum likelihood tree of C_2 cluster. Similar sequences retrieved from databases and subtype references are also included. Only bootstrap values ≥90% are shown. Sequences obtained in our laboratory are in blue and bold type. Database sequences are labeled with subtype, two-letter ISO code of the country of collection, virus names, and GenBank accession. Subtype reference sequences are labeled with “Ref.”.

Figure 2

(A) Bootscan analyses of 6 NFLG and 1 semigenome sequences of viruses of the C_2 cluster. The horizontal axis represents the position in the HXB2 genome of the midpoint of a 250 nt window moving in 20 in increments, and the vertical axis represents the bootstrap value supporting clustering of the query sequence with subtype references. Vertical dashed lines denote breakpoint locations; (B) Mosaic structure of HIV-1 BC intersubtype circulating recombinant form (CRF108_BC). Breakpoint positions in the HXB2 genome are indicated.

Figure 3

Maximum likelihood tree of NFLGs of CRF108_BC and all CRF_BCs identified to date. Only bootstrap values ≥90% are shown. CRF108_BC sequences are in blue and bold type. Database Scheme 108. BC, BLAST searches for similar sequences were done with subtype C and B fragments at the Los Alamos HIV Sequence Database. With regard to the subtype C fragments, searches were done with the two largest fragments in gag-pol and tat-rev-vpu-env-nef, respectively. A phylogenetic tree with all subtype C concatenated fragments from the NFLGs of CRF108_BC, and most similar database sequences showed the closest relationship with the Brazilian virus 02BR2022 from Sao Paulo (Figure 4). Similarity searches with the four subtype B fragments and subsequent phylogenetic analyses with individual or concatenated fragments failed to identify any database virus related to the subtype B parental strain of CRF108_BC.

Figure 4

Phylogenetic tree of concatenated subtype C fragments of CRF108_BC. Only bootstrap values ≥90% are shown. CRF108_BC sequences are in blue and bold type. Database sequences are labeled with subtype, two-letter ISO code of the country of sample collection, virus name, and GenBank accession.

Figure 5

Maximum clade credibility tree of PR–RT sequences of CRF108_BC and 50 subtype C sequences from databases. Sequences belonging to the CRF108_BC cluster are in blue and bold type. Database sequences are labeled with subtype, two-letter ISO country-code, virus name, and GenBank accession. Colors of terminal and internal branches represent sampling locations and most probable locations of the corresponding nodes, respectively, according to the legend. For the nodes corresponding to the cluster and its closest ancestor, the most probable locations and the mean tMRCA (with 95% HPD intervals) are indicated. Nodes supported by PP (posterior probability) = 0.998–1 and PP = 0.95–0.9979 are marked with filled and unfilled circles, respectively. 29 branches corresponding to sequences from Botswana, Cyprus, Ethiopia, Georgia, Israel, Kenya, Malawi, Senegal, South Africa, Sweden, Tanzania, United Kingdom, Yemen, and Zambia were collapsed for better viewing.