The evolving molecular epidemiology of HIV-1 envelope subtypes in injecting drug users in Bangkok, Thailand

Ml, Kalish; Baldwin, Albert S.; Raktham, Suwanee; Wasi, Chantapong; Cc, Luo; Schochetman, Gerald; Td, Mastro; Young, Nancy L.; Vanichseni, Suphak; Rübsamen‐Waigmann, Helga

doi:10.1097/00002030-199508000-00004

Cited by 156 publications

(66 citation statements)

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“…First, it was noted that the withinsubtype interhost genetic divergence had increased significantly compared to that noted in earlier surveys (9,10,17,(22)(23)(24)(25). Second, the barriers that maintained the segregation of subtypes on the basis of risk factors started to efface; the representation of CRF01_AE among IDUs increased, especially among new infections (26), to the point where CRF01_AE accounted for 80 to 90% of the cases in Bangkok and the northern province of Chiang Mai (27,28). Coinfections (29) and superinfections (30) with subtype B and CRF01_AE were documented, and intersubtype recombinants were detected among individuals with either IDU (28,31) or heterosexual (32,33) exposure.…”

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confidence: 95%

Molecular Evolution of the HIV-1 Thai Epidemic between the Time of RV144 Immunogen Selection to the Execution of the Vaccine Efficacy Trial

Kijak

Tovanabutra

Rerks-Ngarm

et al. 2013

J Virol

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The RV144 HIV-1 vaccine trial (Thailand, 2003 to 2009), using immunogens genetically matched to the regional epidemic, demonstrated the first evidence of efficacy for an HIV-1 vaccine. Here we studied the molecular evolution of the HIV-1 epidemic from the time of immunogen selection to the execution of the efficacy trial. We studied HIV-1 genetic diversity among 390 volunteers who were deferred from enrollment in RV144 due to preexisting HIV-1 infection using a multiregion hybridization assay, full-genome sequencing, and phylogenetic analyses. The subtype distribution was 91.7% CRF01_AE, 3.5% subtype B, 4.3% B/CRF01_AE recombinants, and 0.5% dual infections. CRF01_AE strains were 31% more diverse than the ones from the 1990s Thai epidemic. Sixty-nine percent of subtype B strains clustered with the cosmopolitan Western B strains. Ninety-three percent of B/CRF01_AE recombinants were unique; recombination breakpoint analysis showed that these strains were highly embedded within the larger network that integrates recombinants from East/Southeast Asia. Compared to Thai sequences from the early 1990s, the distance to the RV144 immunogens increased 52% to 68% for CRF01_AE Env immunogens and 12% to 29% for subtype B immunogens. Forty-three percent to 48% of CRF01_AE sequences differed from the sequence of the vaccine insert in Env variable region 2 positions 169 and 181, which were implicated in vaccine sieve effects in RV144. In conclusion, compared to the molecular picture at the early stages of vaccine development, our results show an overall increase in the genetic complexity of viruses in the Thai epidemic and in the distance to vaccine immunogens, which should be considered at the time of the analysis of the trial results.

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confidence: 95%

Molecular Evolution of the HIV-1 Thai Epidemic between the Time of RV144 Immunogen Selection to the Execution of the Vaccine Efficacy Trial

Kijak

Tovanabutra

Rerks-Ngarm

et al. 2013

J Virol

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“…Then, an increase of HIV-1 CRF01_AE infections was detected among female sex workers in Thailand, and soon thereafter, CRF01_AE spread to IDUs, suggesting an early and complicated interconnection between epidemics among drug users and commercial sex workers (49). By 1995, CRF01_AE was widespread among Thai IDUs (20,56), and IDU populations in other countries, such as Vietnam and Malaysia, had experienced rapid increases in CRF01_AE infections (21,43,46). In 1996 and 1997, an outbreak of CRF01_AE, genetically highly similar to the Vietnamese strain, was detected among IDUs in China (22).…”

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confidence: 99%

Unequal Evolutionary Rates in the Human Immunodeficiency Virus Type 1 (HIV-1) Pandemic: the Evolutionary Rate of HIV-1 Slows Down When the Epidemic Rate Increases

Berry

Ribeiro

Kothari

et al. 2007

J Virol

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HIV-1 sequences in intravenous drug user (IDU) networks are highly homogenous even after several years, while this is not observed in most sexual epidemics. To address this disparity, we examined the human immunodeficiency virus type 1 (HIV-1) evolutionary rate on the population level for IDU and heterosexual transmissions. All available HIV-1 env V3 sequences from IDU outbreaks and heterosexual epidemics with known sampling dates were collected from the Los Alamos HIV sequence database. Evolutionary rates were calculated using phylogenetic trees with a t test root optimization of dated samples. The evolutionary rate of HIV-1 subtype A1 was found to be 8.4 times lower in fast spread among IDUs in the former Soviet Union (FSU) than in slow spread among heterosexual individuals in Africa. Mixed epidemics (IDU and heterosexual) showed intermediate evolutionary rates, indicating a combination of fast-and slow-spread patterns. Hence, if transmissions occur repeatedly during the initial stage of host infection, before selective pressures of the immune system have much impact, the rate of HIV-1 evolution on the population level will decrease. Conversely, in slow spread, where HIV-1 evolves under the pressure of the immune system before a donor infects a recipient, the virus evolution at the population level will increase. Epidemiological modeling confirmed that the evolutionary rate of HIV-1 depends on the rate of spread and predicted that the HIV-1 evolutionary rate in a fast-spreading epidemic, e.g., for IDUs in the FSU, will increase as the population becomes saturated with infections and the virus starts to spread to other risk groups.The evolutionary rate of human immunodeficiency virus type 1 (HIV-1) has been shown to differ in different genes as well as in different regions of the same genes. Using molecularclock analyses, the rate of evolution of the env V3 region was estimated to be from 2.3 ϫ 10 Ϫ3 to 6.7 ϫ 10 Ϫ3 substitutions site Ϫ1 year Ϫ1 , while the rate for the whole env was estimated to be between 1.0 ϫ 10 Ϫ3 and 1.7 ϫ 10 Ϫ3 substitutions site Ϫ1 year Ϫ1 (25,26,33,54,63). Stronger diversifying pressure by the immune system on the V3 region is thought to be responsible for the higher rate, while genes, such as gag and pol, that are under less diversifying and more purifying selection pressure show lower rates (25,33,54

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“…Some strains may prevail, either due to different inherent biological properties of the viruses or to epidemiological host reasons. It is now recognized that clade E overwhelmed clade B in the IDU population in Thailand (9), and that clade C is expanding out of proportion in Africa (10).…”

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HIV-1 subtypes among intravenous drug users from two neighboring cities in São Paulo State, Brazil

Rossini

Diaz

Caseiro

et al. 2001

Braz J Med Biol Res

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In order to assess the molecular epidemiology of HIV-1 in two neighboring cities located near the epicenter of the HIV-1 epidemics in Brazil (Santos and São Paulo), we investigated 83 HIV-1 strains obtained from samples collected in 1995 from intravenous drug users. The V3 through V5 region of the envelope of gp 120 was analyzed by heteroduplex mobility analysis. Of the 95 samples, 12 (12.6%) were PCR negative (6 samples from each group); low DNA concentration was the reason for non-amplification in half of these cases. Of the 42 typed cases from São Paulo, 34 (81%, 95% confidence limits 74.9 to 87.0%) were B and 8 (19%, 95% confidence limits 12.9 to 25.0%) were F, whereas of the 41 typed cases from Santos, 39 (95%, 95% confidence limits 91.6 to 98.4%) were B and 2 (5%, 95% confidence limits 1.6 to 8.4%) were C. We therefore confirm the relationship between clade F and intravenous drug use in São Paulo, and the presence of clade C in Santos. The fact that different genetic subtypes of HIV-1 are co-circulating indicates a need for continuous surveillance for these subtypes as well as for recombinant viruses in Brazil.

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The evolving molecular epidemiology of HIV-1 envelope subtypes in injecting drug users in Bangkok, Thailand

Cited by 156 publications

References 0 publications

Molecular Evolution of the HIV-1 Thai Epidemic between the Time of RV144 Immunogen Selection to the Execution of the Vaccine Efficacy Trial

Molecular Evolution of the HIV-1 Thai Epidemic between the Time of RV144 Immunogen Selection to the Execution of the Vaccine Efficacy Trial

Unequal Evolutionary Rates in the Human Immunodeficiency Virus Type 1 (HIV-1) Pandemic: the Evolutionary Rate of HIV-1 Slows Down When the Epidemic Rate Increases

HIV-1 subtypes among intravenous drug users from two neighboring cities in São Paulo State, Brazil

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