Diversity of mosaic structures and common ancestry of human immunodeficiency virus type 1 BF intersubtype recombinant viruses from Argentina revealed by analysis of near full-length genome sequences

Abstract

The findings that BF intersubtype recombinant human immunodeficiency type 1 viruses (HIV-1) with coincident breakpoints in pol are circulating widely in Argentina and that non-recombinant F subtype viruses have failed to be detected in this country were reported recently. To analyse the mosaic structures of these viruses and to determine their phylogenetic relationship, near fulllength proviral genomes of eight of these recombinant viruses were amplified by PCR and sequenced. Intersubtype breakpoints were analysed by bootscanning and examining the signature nucleotides. Phylogenetic relationships were determined with neighbour-joining trees. Five viruses, each with predominantly subtype F genomes, exhibited mosaic structures that were highly similar. Two intersubtype breakpoints were shared by all viruses and seven by the majority. Of the consensus breakpoints, all nine were present in two viruses, which exhibited identical recombinant structures, and four to eight breakpoints were present in the remaining viruses. Phylogenetic analysis of partial sequences supported both a common ancestry, at least in part of their genomes, for all recombinant viruses and the phylogenetic relationship of F subtype segments with F subtype viruses from Brazil. A common ancestry of the recombinants was supported also by the presence of shared signature amino acids and nucleotides, either unreported or highly unusual in F and B subtype viruses. These results indicate that HIV-1 BF recombinant viruses with diverse mosaic structures, including a circulating recombinant form (which are widespread in Argentina) derive from a common recombinant ancestor and that F subtype segments of these recombinants are related phylogenetically to the F subtype viruses from Brazil.

Molecular Epidemiology of HIV Type 1 CRF02_AG in Cameroon and African Patients Living in Italy

“…13 Recent data from Yaoundé also indicate that the CRF02_AG strain represents up to 50% of the total infection. 15 CRF02_AG prevalence has been increasing not only in West and West-Central Africa, 8,[13][14][15][19][20][21][22][23] but also in different countries of Europe, [24][25][26][27] such as Italy, [28][29][30][31][32] because of migrations from the sub-Saharan region. This viral variant is one of the most prevalent recombinant forms of HIV-1 in the world, responsible for at least 5% of infections.…”

Extremely Rapid Spread of Human Immunodeficiency Virus Type 1 BF Recombinants in Argentina

“…However, full-length genome sequencing led to the identification of a variety of subtype BF recombinants (2,14), with the circulating recombinant form CRF12_BF representing nearly 25% of those described. Currently, approximately 80% of HIV-1 isolates from Argentina are BF recombinants, with almost all the remaining 20% constituting subtype B viruses and scattered cases of subtypes A, C, BC, and F (1, 3).…”

Human Immunodeficiency Virus Type 1 Superinfection Was Not Detected following 215 Years of Injection Drug User Exposure

“…An individual infected with both group M and group O HIV-1 viruses was identified (71), although it is not known whether the infections were nearly simultaneous or sequential. Indirect evidence for infections with more then one subtype of HIV-1 group M viruses is seen in the large number of distinct intersubtype recombinants, each with a presumably independent origin (8,12,24,25,36,46,56,66,73,74,76), and in numerous cases of dual-subtype infections (4,6,(24)(25)(26)62). It is not known with what time intervals such dual infections are acquired.…”