Near-Full-Length Genome Sequencing of Divergent African HIV Type 1 Subtype F Viruses Leads to the Identification of a New HIV Type 1 Subtype Designated K

Abstract

We recently reported a high divergence among African subtype F strains. Three well-separated groups (F1, F2, and F3) have been shown based on the phylogenetic analysis of the p24 gag and envelope sequences with genetic distances similar to those observed for known subtypes. In this study, we characterized the near-full-length genomes of two strains from epidemiological unlinked individual belonging to each of the subgroups: F1 (96FR-MP411), F2 (95CM-MP255 and 95CM-MP257), and F3 (96CM-MP535 and 97ZR-EQTB11). Phylogenetic analysis of the near-full-length sequences and for each of the genes separately showed the same three groups, supported by high bootstrap values. Diversity plotting, BLAST subtyping, and bootstrap plotting confirmed that the divergent F strains correspond to nonrecombinant viruses. The divergence between F1 and F2 is consistently lower than that seen in any other intersubtype comparison, with the exception of subtypes B and D. Based on all the different analyses, we propose to divide subtype F into two subclades, with F1 gathering the known subtype F strains from Brazil and Finland, and our African strain (96FR-MP411), and F2 containing the 95CM-MP255 and 95CM-MP257 strains from Cameroon. The F3 strains, 97ZR-EQTB11 from the Democratic Republic of Congo and 96CM-MP535 from Cameroon, meet the criteria of a new subtype designated as K. The equidistance of subtype K to the other subtypes of HIV-1 suggests that this subtype existed as long as the others, the lower distance between B and D, and between F1 and F2 suggest a more recent subdivision for these latter strains.

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

“…In addition to each of the Group M subtypes and several CRFs, HIV-1 Groups N, O, and P as well as HIV-2 strains have been identified in the country. [3][4][5][6][7][8][9][10][11][12][13][14][15][16][17] The first AIDS case in Cameroon was diagnosed in 1985. 18 Since then, about 540,000 cases have been officially reported.…”

Distinct Human Immunodeficiency Virus Type 1 Subtype A Virus Circulating in West Africa: Sub-Subtype A3

“…Pairwise distance analysis has previously been used to distinguish between subtypes and sub-subtypes (1,11,26,37). Intersubtype and intrasubtype distances were calculated for the full-length sequences based on reference strains (Fig.…”

“…In addition, there are a number of circulating recombinant forms (CRFs) in the world, which are associated with significant transmission and disease in various populations worldwide (23). Detailed phylogenetic studies have revealed evidence of sub-subtypes, which are characterized as regional subclusters composed of distinct lineages that are closely related to a given subtype (11,21,(36)(37)(38). Sub-subtypes F2 (36) and A2 (11) have been identified and characterized.…”

“…Sub-subtypes F2 (36) and A2 (11) have been identified and characterized. There have also been suggestions that certain previously identified subtypes could have been categorized as sub-subtypes (19,26,(36)(37)(38). For example, there is evidence suggesting that the previously identified subtype D viruses might have been more appropriately named sub-subtype B2 (26,38).…”

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

“…Subtypes H and J were described in Central Africa Mokili et al, 1999;Yamaguchi et al, 2010) and in Angola (Bartolo et al, 2005;Bartolo et al, 2009d). Subtype K was identified in DRC and Cameroon (Triques et al, 2000).…”