Genetic diversity of HIV in Africa

Peeters, Martine; Touré-Kâne, Coumba; Nkengasong, John N.

doi:10.1097/00002030-200312050-00002

Cited by 237 publications

(175 citation statements)

References 139 publications

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“…There are regions in the world where multiple subtypes circulate in the human population (4,42); although intersubtype recombinants have emerged in these regions, individual subtypes remain. Multiple factors probably affect the maintenance of the subtype and emergence of a recombinant strain, such as the compatibilities of various cis-and͞or transacting elements, and the replication fitness of the virus.…”

Section: Restrictions In Intersubtype Recombination and Their Implicamentioning

confidence: 99%

Identification of a major restriction in HIV-1 intersubtype recombination

Chin

Rhodes

Chen

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

111

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Genetic recombination increases diversity in HIV-1 populations, thereby allowing variants to escape from host immunity or antiviral therapies. In addition to the currently described nine subtypes of HIV-1, many of the circulating strains are intersubtype recombinants. In this study, we determined the recombination rate between two HIV-1 subtype C viruses and between a subtype B virus and a subtype C virus during a single round of virus replication. Although HIV-1 subtype C recombines at a high rate, similar to that of HIV-1 subtype B, the recombination rate between a subtype B virus and a subtype C virus is much lower than the intrasubtype recombination rate. A 3-nt sequence difference in the dimerization initiation signal (DIS) region between HIV-1 subtypes B and C accounts for most of the reduction of intersubtype recombination. By matching the DIS sequences, the B͞C intersubtype recombination rate was elevated 4-fold; by introducing mismatches in the 3-nt sequences, the B͞B intrasubtype recombination rate was reduced 4-fold. Further analyses showed that the intermolecular template-switching frequency was unaffected by the sequence identity of the DIS region. These results support the hypothesis that mismatched sequences in the DIS region alter the formation of heterozygous virions, thereby lowering the observable recombination rate. Here, we present the discovery of a major restriction in HIV-1 intersubtype recombination. These results have important implications for virus evolution, the mechanism of HIV-1 RNA packaging, high negative interference in recombination, and the generation of circulating intersubtype recombinants within the infected population.subtype ͉ RNA dimerization

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Section: Restrictions In Intersubtype Recombination and Their Implicamentioning

confidence: 99%

Identification of a major restriction in HIV-1 intersubtype recombination

Chin

Rhodes

Chen

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

111

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“…The diffusion of the AIDS pandemic has provided an alarming indication of the massive impact of recombination on the evolution of retroviruses. Indeed, by scattering and rearranging mutations already existing along the HIV-1 genome, recombination stands nowadays as a worldwide hindrance for molecular and serological diagnosis, vaccine development, and treatment against AIDS (2,3). Features of the HIV-1 infectious cycle, such as the poor fidelity of the RT (4), which boosts the probability of co-packaging non-identical viral RNAs, and the dynamic nature of HIV-1 infection, where de novo infection of CD4 ϩ T cells amplifies the possibility of copy choice to occur during the repeated cycles of reverse transcription (5), can explain the extremely high level of genetic recombination documented (6).…”

mentioning

confidence: 99%

The Structure of HIV-1 Genomic RNA in the gp120 Gene Determines a Recombination Hot Spot in Vivo

Galetto¹,

Moumen²,

Giacomoni³

et al. 2004

Journal of Biological Chemistry

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By frequently rearranging large regions of the genome, genetic recombination is a major determinant in the plasticity of the human immunodeficiency virus type I (HIV-1) population. In retroviruses, recombination mostly occurs by template switching during reverse transcription. The generation of retroviral vectors provides a means to study this process after a single cycle of infection of cells in culture. Using HIV-1-derived vectors, we present here the first characterization and estimate of the strength of a recombination hot spot in HIV-1 in vivo. In the hot spot region, located within the C2 portion of the gp120 envelope gene, the rate of recombination is up to ten times higher than in the surrounding regions. The hot region corresponds to a previously identified RNA hairpin structure. Although recombination breakpoints in vivo cluster in the top portion of the hairpin, the bias for template switching in this same region appears less marked in a cell-free system. By modulating the stability of this hairpin we were able to affect the local recombination rate both in vitro and in infected cells, indicating that the local folding of the genomic RNA is a major parameter in the recombination process. This characterization of reverse transcription products generated after a single cycle of infection provides insights in the understanding of the mechanism of recombination in vivo and suggests that specific regions of the genome might be prompted to yield different rates of evolution due to the presence of circumscribed recombination hot spots.

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“…80,109 Replication of HIV, like all RNA viruses that lack enzymes for editing the freshly replicated nucleotides strands, is liable to error prone. 113 The earliest case of HIV-1 group M infection was identified in human blood specimen collected in 1959 in Kinshasa, Democratic Republic of Congo 157,158 while the most ancient case of group O infection was found in a Norwegian patient that would be infected in the early 1960s.…”

Section: Genomic Variabilitymentioning

confidence: 99%

“…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.…”

Section: Genomic Variabilitymentioning

confidence: 99%

“…This virus emerged among several African countries and became epidemic in the African continent, predominantly in West and West Central Africa, where it represents between 50 to 70% of the circulating strains. 2,24,38,83,91,109,143 Thus, from Africa CRF02_AG they were introduced in Europe and its epidemic has lately been rapidly spreading in France, 137 Belgium, 126 Italy, 90 and United Kingdom. 134 African and European immigrants are responsible by a large panel of CRFs in United Kingdom, such as CRF01_AE, CRF14_BG, CRF03_AB, CRF05_DF, CRF06_cpx, and CRF11_cpx, together with CRF02_AG and several URFs.…”

Section: Circulating Recombinant Formsmentioning

confidence: 99%

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Worldwide molecular epidemiology of HIV

Requejo

2006

Rev. Saúde Pública

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Human immunodeficiency virus (HIV) is the worldwide disseminated causative agent of acquired immunodeficiency syndrome (AIDS). HIV is a member of the Lentivirus genus of Retroviridae family and is grouped in two types named HIV-1 and HIV-2. These viruses have a notable ability to mutate and adapt to the new conditions of human environment. A large incidence of errors at the transcriptional level results in changes on the genetic bases during the reproductive cycle. The elevated genomic variability of HIV has carried important implications for the diagnosis, treatment and prevention as well as epidemiologic investigations. The present review describes important definitions and geographical distribution of subtypes, circulating recombinant forms and other genomic variations of HIV. The present study aimed at leading students of Biomedical Sciences and public health laboratory staff guidance to general and specific knowledge about the genomic variability of the HIV.

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Genetic diversity of HIV in Africa

Cited by 237 publications

References 139 publications

Identification of a major restriction in HIV-1 intersubtype recombination

Identification of a major restriction in HIV-1 intersubtype recombination

The Structure of HIV-1 Genomic RNA in the gp120 Gene Determines a Recombination Hot Spot in Vivo

Worldwide molecular epidemiology of HIV

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