Full Genome Sequences of Human Immunodeficiency Virus Type 1 Subtypes G and A/G Intersubtype Recombinants

Abstract

Multiple genetic subtypes and intersubtype recombinant strains have been identified among isolates of HIV-1. The greatest diversity of strains has been recovered from Central Africa, where mixtures of subtypes and recombinant forms have been recovered. However, many of the HIV-1 subtypes and recombinants have been characterized by partial rather than full-length genome sequencing. Here we report the first two virtually full-length genome sequences from HIV-1 subtype G, isolated in Sweden and Finland but originating in Congo and Kenya, and from two Djibouti isolates sharing the A/G recombinant structure of Nigerian isolate, IbNG. By comparison with reference sequences of other subtypes, it appears that the subtype G strains are largely nonrecombinant, while the Djibouti strains show alternating segments from subtypes A and G. In the cytoplasmic domain of the gp41 protein of the Djibouti viruses the E, G, and IbNG strains form a single cluster, separate from subtype A, clouding the subtype origin of these particular segments. Within the resolution of current technology, the structure of the Djibouti strains is identical to that of IbNG, establishing for the first time the geographic spread of this recombinant in Africa. The geographic spread of the IbNG-like strains suggests that, like the subtype E recombinants, these should be given a specific name to facilitate future identification and tracking; the name "IbNG subtype" is proposed.

Prevalence and risk determinants of HIV-1 and HIV-2 infections in pregnant women in Bissau

“…On the other hand, the modest genital shedding of HIV-2 15e17 probably reduces the efficiency of sexual transmission, as suggested by the considerably slower spread of HIV-2 among sex workers 16,18 and the marked reduction in HIV-2 in Angola and Mozambique at the end of 1990s. 1 HIV-1 in Guinea-Bissau is mainly represented by the A/G (CRF 02_AG) recombinant strain, 19,20 and the finding of clusters, which contained sequences separated by short branches, suggests that the virus had time to evolve in the country. 20 However, it is likely that HIV-1 arrived some years after HIV-2 as it was completely absent in a study population already showing a significant prevalence of HIV-2 in 1980s, 21 and was first documented in three out of 2539 pregnant women (0.1%) by Månsson et al in 1988.…”

Biologic and Genetic Characterization of a Panel of 60 Human Immunodeficiency Virus Type 1 Isolates, Representing Clades A, B, C, D, CRF01_AE, and CRF02_AG, for the Development and Assessment of Candidate Vaccines

“…Each strain was characterized by sequencing of the complete genome, except for a small portion of the long terminal repeat. Thirty-nine viruses were sequenced previously (2,11,12,19,(21)(22)(23)(24)60). Twenty-one new complete genome sequences were generated for this study.…”

Worldwide molecular epidemiology of HIV

“…71,105 The subtypes A, E, G, H, J and K have been described to be prevalent in Burkina Faso, Mali, Nigeria, Ivory Coast, Gabon, and Democratic Republic of Congo, from where they have spread to South Europe, and Asia. 6,16,55,89,106,122 In South America, HIV-1 subtype B has been predominant in Brazil, followed by subtypes F, and C, with small proportion of subtype D. 13,15,28,30,39,94,114,116,127 In Argentina, Bolivia, Peru, Paraguay, Uruguay and Venezuela 21 and also in Caribbean Islands 140 these same subtypes have been found since the mid-1990s.…”