Virtually Full-Length Subtype F and F/D Recombinant HIV-1 from Africa and South America

Abstract

For reliable classification of HIV-1 strains appropriate reference sequences are needed. The HIV-1 genetic subtype F has a wide geographic spread, causing significant epidemics in South America, Africa, and some regions of Europe. Previously only two full-length sequences of each of the HIV-1 subtype F subclusters F1 and F2 have been described. To extend the knowledge of subtype F variation on a complete genome level, three new virtually full-length F1 sequences were cloned and sequenced, two from Africa and one from South America. Comparison of the new and previously described sequences showed that monophyletic clustering of the subcluster F1 of subtype F is consistent and highly supported in all genome regions. Two additional full-length strains were shown to be mosaics of subtypes F and D. These epidemiologically unrelated F/D sequences showed similar chimeric structure, suggesting that they may represent a previously undescribed circulating recombinant form (CRF). This was supported by partial sequences from three additional unlinked F/D recombinants. Genetic distances in the phylogenetic trees suggest that the recombination event leading to the putative CRF occurred relatively long ago, close to the divergence of the F1 and F2 subclusters. Furthermore, all five F/D recombinants are linked to the Democratic Republic of Congo, suggesting that the original recombination event took place in central Africa.

Genetic Diversity and the Human Immunodeficiency Virus Type-1: Implications and Impact

“…This is in keeping with reports, from other English speaking Caribbean Islands, which did not include Jamaican samples (Gittens, 2003;. Subtype B is also the predominant subtype in North America, Western Europe, Australia and South America (Distler, 1995;Laukkanen, 2000;.…”

Worldwide molecular epidemiology of HIV

“…153 Subtype D has been responsible for 5 to 40% in countries of East and Central Africa where it has been circulating together with subtype A. 74,109 Subtype E (renamed as CRF01_AE) has been common in Vietnam and neighbor countries, in the majority of infected intravenous drug users (IDUs). 22,71 Subtype E has been predominant in Thailand (>80%), with small proportion of subtype B, also in majority of IDUs.…”

“…39 Other recombinant forms such as B/C, C/B, B/F, F/D, and the triplet B/C/F are consistent with the three main circulating subtypes. 74,94,116,127 The genetic arrangement caused by the subtype recombinations has made it difficult the understanding of CRF genomic composition, and then its ensuing definition. All representing subtype E strains initially described in Southeast Asia seem to be recombinant forms of subtypes A and E, and thus they have been designated CRF01_AE.…”

HIV-1 Diversity and Its Implications in Diagnosis, Transmission, Disease Progression, and Antiretroviral Therapy

“…Subtype C is the overwhelming prevailing strain in Southern Africa (Bartolo et al, 2009b;Gonzalez et al, 2010;Lahuerta et al, 2008;Papathanasopoulos et al, 2010), in India and neighbor countries (Neogi et al, 2009a;Neogi et al, 2009b) and in the southern region of Brazil (Monteiro-Cunha et al, 2011). Subtype D strains are found mainly in East Africa, and to a lesser extent in West Africa (Conroy et al, 2010;Harris et al, 2002;Laukkanen et al, 2000;Songok et al, 2004). Subtype F predominates in Central Africa (Carr et al, 2010b;Soares et al, 2010), South America (Avila et al, 2002;Munerato et al, 2010) and Eastern Europe (Fernandez-Garcia et al, 2009;Paraschiv, Foley, and Otelea, 2011).…”

“…Some CRFs have high impact in local AIDS epidemics, such as CRF01_AE in Southeast Asia (Gao et al, 1996;Magiorkinis et al, 2002) and CRF02_AG in Western and Central Africa (Cornelissen et al, 2000;Fischetti et al, 2004a;Fischetti et al, 2004b). CRF11_cpx was the first second generation CRF described in 2000 in patients from Cameroon (TscherningCasper et al, 2000).…”