Diversity of V3 Region Sequences of Human Immunodeficiency Viruses Type 1 from the Central African Republic

Abstract

Nucleotide sequences of the central portion of gp120, including the third hypervariable (V3) loop, were obtained from lymphocytes cocultivated with SupT1 cells from 29 AIDS patients in Bangui, Central African Republic. These sequences displayed significantly greater diversity (average distance, 23%) than has been previously observed in isolates from comparably restricted geographical areas. Isolates belonging to four major subtypes of HIV-1 were found; the only subtype not represented was the North American/European subtype B. Unlike the situation in Zaire and Uganda, where subtypes A and D account equally for virtually all isolates of HIV-1, the predominant subtypes in the Central African Republic, accounting for two-thirds of the isolates, were subtypes A (10 isolates) and E (9 isolates). Subtype E represents a group of variants that have previously been found only in Thailand. Only one isolate belonging to subtype D was found. Also recovered were two isolates of subtype C, a subtype associated with southern African and Indian isolates but not previously detected in central Africa. These isolates, although clearly clustering with subtype C, formed a distinct subset, differing from one another by 8.8% and from the Indian and South African subtype C isolates by an average of 22.5%. High interpatient, intrasubtype variation was also seen among the CAR subtype A (average pairwise difference, 19.3%) and subtype E (10.9%) isolates. The diversity of V3 sequences in this set has implications for immunization protocols that rely on the recognition of V3. This study underscores the necessity of basing intervention strategies on knowledge of the particular sequences present in the target population or geographical area.

Subtype-Specific Conformational Differences within the V3 Region of Subtype B and Subtype C Human Immunodeficiency Virus Type 1 Env Proteins

“…The V3 loop plays a central role in the life cycle of HIV-1 but, like other regions of the genome, displays subtype-specific sequence variation (42,44,51). We are interested in the possibility that these sequence differences can impact virus biology in a subtype-specific way.…”

Human retroviruses and AIDS 1997

“…Consensus, PCR-clones, cell culture, DNA. [Murphy et al(1993)]. Accession numbers L11482-L11483, L11497, L11508-L11510 and L11514-L11515.…”

“…This holds true for the E subtypes sequences that originated in Thailand, as well as the E subtype isolate from the Central African Republic for which gag sequence was obtained. [McCutchan et al(1992)]; [Louwagie et al(1993)]; and [Murphy et al(1993)]. Complete genomes of subtype A and subtype E viruses became available in late 1996 [Gao et al(1996b)], genbank accession numbers U51188-U51190.…”

“…Subtype A sequences were also determined in this study. 2) CF.4067: This sequence was associated with the C subtype in first analysis of the C2V3 region ( [Murphy et al(1993)]), but when a full gpl20 sequence became available from this isolate, and phylogenetic analysis was performed including some of the new subtype G sequences, it was more closely associated with G. The frill length sequence was kindly provided prior to publication by Dr. MP Kieny of Transgene, Strasbourg Cedex, France. It is part of a set of 14 HTV-1 gpl20 isolates from Bangui, Central African Republic.…”

“…Accession numbers U22010, U27426. 17) UZl.BUK3a: This sequence is from a 39 year old male Caucasian heterosexual who lived in Uzbekistan [Bobkov et al(1996a) [Murphy et al(1993)], with accession number L11497. It was later classified as subtype H, [Janssens et al(1994b)].…”