The changing molecular epidemiology of HIV type 1 among northern Thai drug users, 1999 to 2002

CRF01_AE and subtype B have dominated the HIV-1 epidemic in Thailand since 1989. We reported a new circulating recombinant form of HIV-1, CRF15_01B, as well as other unique CRF01_AE/B recombinants among prevalent HIV infections in Thailand. We sought to study this challenging molecular picture through assessment of subtypes among recent HIV-1 seroconverters in northern Thai drug users. A total of 847 HIV-1 seronegative drug users (342 IDU and 505 non-IDU) were enrolled, from 1999 to 2002, in a prospective study; 39 HIV-1 incident cases were identified and characteristics were collected. The overall HIV-1 incidence rate was 2.54/100PY, but it was 10.0/100PY among male IDU. HIV was strongly associated with injection history; 38 of 39 seroconverters gave a history of IDU. A near full-length genome of HIV-1 was recovered by PCR amplification and sequenced from peripheral mononuclear cell extracted DNA of 38 seroconverters. Phylogenetic analysis revealed that 33 (86.8%) were CRF01_AE and 5 (13.2%) were CRF01_AE/B recombinants. These recombinants had different structure but shared some common breakpoints, indicating an ongoing recombination process. Recombinant infection increased with year of sampling (0 to 57.1%). The molecular epidemiology of HIV-1 among drug users in northern Thailand has thus entered a new era. CRF01_AE remains predominant while pure subtype B is becoming rare, and now a substantial component of the epidemic. These findings support the need for CRF01_AE and subtype B components in clade-matched vaccine strategies for Thai phase III trials. Ongoing molecular surveillance of circulating HIV-1 strains is imperative for the evaluation of HIV vaccine efficacy.     

Randomized, double-blind, placebo-controlled efficacy trial of a bivalent recombinant glycoprotein 120 HIV-1 vaccine among injection drug users in Bangkok, Thailand

BACKGROUND: In Thailand, phase 1/2 trials of monovalent subtype B and bivalent subtype B/E (CRF01_AE) recombinant glycoprotein 120 human immunodeficiency virus type 1 (HIV-1) vaccines were successfully conducted from 1995 to 1998, prompting the first HIV-1 vaccine efficacy trial in Asia. METHODS: This randomized, double-blind, placebo-controlled efficacy trial of AIDSVAX B/E (VaxGen), which included 36-months of follow-up, was conducted among injection drug users (IDUs) in Bangkok, Thailand. The primary end point was HIV-1 infection; secondary end points included plasma HIV-1 load, CD4 cell count, onset of acquired immunodeficiency syndrome-defining conditions, and initiation of antiretroviral therapy. RESULTS: A total of 2546 IDUs were enrolled between March 1999 and August 2000; the median age was 26 years, and 93.4% were men. The overall HIV-1 incidence was 3.4 infections/100 person-years (95% confidence interval [CI], 3.0-3.9 infections/100 person-years), and the cumulative incidence was 8.4%. There were no differences between the vaccine and placebo arms. HIV-1 subtype E (83 vaccine and 81 placebo recipients) accounted for 77% of infections. Vaccine efficacy was estimated at 0.1% (95% CI, -30.8% to 23.8%; P=.99, log-rank test). No statistically significant effects of the vaccine on secondary end points were observed. CONCLUSION: Despite the successful completion of this efficacy trial, the vaccine did not prevent HIV-1 infection or delay HIV-1 disease progression.     

Identification of subtype B, multiple circulating recombinant forms and unique recombinants of HIV type 1 in an MSM cohort in China

To study HIV-1 genetic diversity among HIV-positive men who have sex with men (MSM) in China, a cohort consisting of HIV-positive MSM was established in 2005 and was monitored every 2 years. In 2007, 44 HIVpositiveMSM subjects were genotyped, and the results showed HIV-1 subtype B decreased from 77.5% to41.9%, but non-B subtypes increased rapidly represented by CRF01_AE from 3.7% to 30.2% compared to 2005.In addition, one case of CRF07_BC was first identified in this population, which mainly circulated among HIV-1-infected injection drug users (IDUs) in China. There were 11 unique recombinant forms (URFs) consisting ofa recombination of CRF01_AE with subtype B or CRF07_BC. The subtype-specific phylogenic tree analysis showed that the genetic distance within subtype B group viruses was larger than the genetic distance within the CRF01_AE group (p 0.001). Of the identified viruses in the Chinese MSM population, over 80% of subtype B viruses might originate from the United States and Brazil, and over 85% of the CRF01_AE viruses mightoriginate from Thailand. In addition, epidemic study data showed that some of the HIV-1-infected MSM had foreign sexual partners (13.6%) and heterosexual activities (43.2%). The patients infected with HIV-1 URF viruses had more heterosexual encounters (54.5%) and more sexual partners (72.7%) compared to those infected with subtype B (44.4%; 33.3%) and CRF01_AE (23.1%; 69.2%) viruses. Taken together, we suspected that the genetic complexity of HIV-1 viruses identified in Chinese MSM populations was more likely a result of multiple introductions of viruses from the general population infected with HIV-1 through IDUs or heterosexual transmission.     

Emergence of a New HIV Type 1 CRF01_AE Variant in Guangxi, Southern China

Abstract The distribution of HIV-1 subtypes and genetic characterization of CRF01_AE in Guangxi, southern China were identified. The distribution of HIV-1 genotypes based on gag, pol, and partial env sequences (n=349) was as follows: CRF01_AE (66.5%), CRF08_BC (19.2%), CRF07_BC (7.2%), URF (4.6%), subtype B (1.7%), and subtype B' (0.9%). CRF01_AE predominated in all geographic regions and risk populations and there were multiple introductions of CRF01_AE strains in Guangxi. We found a peculiar CRF01_AE monophyletic lineage distinct from other CRF01_AE viruses, and we designated it "CRF01_AE-v" for convenience. CRF01_AE-v circulating in both heterosexuals and injecting drug users (IDUs) had accounted for 39.7% of CRF01_AE. It showed a selective advantage in the Guangxi population and formed its own characteristic compared with all the CRF01_AE references. Our results suggested that CRF01_AE-v was a new variant of CRF01_AE and it might lead to a new epidemic in Guangxi.     

Evaluation of a sensitive/less sensitive testing algorithm using the bioMérieux Vironostika-LS assay for detecting recent HIV-1 subtype B' or E infection in Thailand

The performance of the bioMérieux Vironostika-LS EIA (less sensitive enzyme immunoassay) was assessed to detect recent seroconversion among injecting drug users (IDUs) in Bangkok, Thailand who were infected with either HIV-1 subtypes B' or E (also known as circulating recombinant form CRF01_AE). To evaluate the Vironostika-LS EIA in non-B subtypes, we collected longitudinal specimens (n = 796) from 115 IDUs (subtype B' infection, n = 24; subtype E infection, n = 91). After testing HIV-positive specimens with the Vironostika-LS EIA, standardized optical densities (SODs) were calculated using median values to determine the window period, which is the time from seroconversion on a standard EIA to seroconversion on the Vironostika-LS EIA for a given SOD, for either subtype. For an SOD cutoff of 1.0, Vironostika-LS EIA results showed a mean window period of 239 days (95% confidence interval [95% CI], 208-287 days) for subtype B' and 356 days (95% CI, 318-402 days) for subtype E in Thailand. This outcome demonstrates that the Vironostika-LS EIA has significantly different performance characteristics in detecting recent seroconversion between different HIV-1 subtypes. Accurate identification of recent infection and estimation of incidence for HIV-1 strains other than North American subtype B, using the Vironostika-LS EIA, requires knowledge of specimen subtype and use of appropriate cutoffs and mean window periods.     

Molecular epidemiology of HIV Type 1 in preparation for a Phase III prime-boost vaccine trial in Thailand and a new approach to HIV Type 1 genotyping

To characterize HIV-1 genotypes in candidate populations for a prime-boost phase III vaccine trial in Thailand, specimens from prevalent and incident HIV-1 infections from a family planning clinic population in Rayong Province and a community cohort in Chon Buri Province, collected from 1998 to 2001, were genotyped. A new multiregion hybridization assay, MHAbce, capable of distinguishing HIV-1 CRF01_AE, subtype B, and subtype C and their recombinants, was developed and applied to prevalent infections. Most incident and selected prevalent infections were studied by complete genome sequencing. By MHAbce, 168 of 194 prevalent infections were genotyped. Of these, 90.5% were CRF01_AE, 2.4% were subtype B, and 7.2% showed discordant or dual probe reactivity, indicative of recombination or dual infection, respectively. Among 23 incident infections, 20 were sequenced. Eighteen CRF01_AE, one subtype B, and one CRF01/B recombinant strains were seen. Two CRF01/B and one CRF01/C recombinant were identified among selected prevalent infections. These results indicate that incident and prevalent HIV-1 infections in Rayong and Chon Buri during 1998-2001 were 90% CRF01_AE, 3% subtype B, and 7% either recombinant or dual. This study frames the genetic diversity of HIV-1 in these cohorts in their preparatory phase for the ongoing ALVACHIV (vCP1521) prime, AIDSVAX B/E boost, phase III vaccine trial and will provide a benchmark for interpretation and analysis.     

Molecular Detection of HIV-1 Subtype B,CRF01_AE,CRF33_01B,and Newly Emerging Recombinant Lineages in Malaysia

A molecular genotyping assay for human immunodeficiency virus type 1 (HIV-1) circulating in Southeast Asia is difficult to design because of the high level of genetic diversity. We developed a multiplex real-time polymerase chain reaction (PCR) assay to detect subtype B, CRF01_AE, CRF33_01B, and three newly described circulating recombinant forms, (CRFs) (CRF53_01B, CRF54_01B, and CRF58_01B). A total of 785 reference genomes were used for subtype-specific primers and TaqMan probes design targeting the gag, pol, and env genes. The performance of this assay was compared and evaluated with direct sequencing and phylogenetic analysis. A total of 180 HIV-infected subjects from Kuala Lumpur, Malaysia were screened and 171 samples were successfully genotyped, in agreement with the phylogenetic data. The HIV-1 genotype distribution was as follows: subtype B (16.7%); CRF01_AE (52.8%); CRF33_01B (24.4%); CRF53_01B (1.1%); CRF54_01B (0.6%); and CRF01_AE/B unique recombinant forms (4.4%). The overall accuracy of the genotyping assay was over 95.0%, in which the sensitivities for subtype B, CRF01_AE, and CRF33_01B detection were 100%, 100%, and 97.7%, respectively. The specificity of genotyping was 100%, inter-subtype specificities were > 95% and the limit of detection of 10³ copies/mL for plasma. The newly developed real-time PCR assay offers a rapid and cost-effective alternative for large-scale molecular epidemiological surveillance for HIV-1.     

Human immunodeficiency virus type 1 subtype and other factors associated with extrapulmonary Cryptococcosis among patients in Thailand with AIDS

Delineating factors associated with extrapulmonary cryptococcosis (EPC), a major disease burden among Thailand's AIDS patients, can clarify its pathogenesis and guide preventive interventions. From November 1993 through June 1996, enhanced surveillance of 2261 human immunodeficiency virus (HIV)-seropositive patients in a hospital near Bangkok showed EPC among 561 of 1553 AIDS patients (36.1%). Univariate analysis results were confirmed by multivariate analyses of data on 1259 patients. Logistic regression models identified factors significantly associated with EPC to be male sex (adjusted odds ratio [aOR], 2.0; 95% confidence interval [CI], 1.3-2.9), age <33 years (aOR, 1.5; 95% CI, 1.2-1.9), severe immunosuppression (aOR, 1.8; 95% CI, 1.3-2.6), not injecting drugs (aOR, 3.0; 95% CI, 1.7-5.5), and infection with HIV-1 circulating from CRF01_AE (formerly subtype E) versus subtype B (aOR, 2.3; 95% CI, 1.2-4.5). The association with CRF01_AE may result from undetermined markers of exposure or viral subtype effects on host immune responses. Better understanding of the epidemiology of EPC may reduce EPC incidence through targeted primary prevention and treatment.     

The lack of epidemiological link between the HIV type 1 infections in Hong Kong and Mainland China

Blood samples were collected from 139 newly reported HIV-1 infections in Hong Kong over a 3-year period between 1999 and 2001, representing 22.8% of all reported cases. A majority of the patients were male (85.6%), Chinese (74%), and adult (97.1%) and acquired HIV-1 through sexual transmission (88.2%). The B and CRF01_AE were the major subtypes detected--49.6% and 44.6%, respectively. Over time, the frequency of CRF01_AE subtype increased, the B subtype decreased, and new subtypes of C (4) 2.8%, B' (1) 0.7%, and CRF07_BC (3) 2.2% emerged. The CRF01_AE subtype was commoner in female, Chinese, heterosexuals, and injection drug users whereas B subtype was commoner in male, white, and people with homosexual/bisexual contacts. There was no common source of infection from the analysis except a discernible cluster of Vietnamese injection drug users with the CRF01_AE subtype. The molecular findings did not suggest an epidemiological link between HIV infection in Hong Kong and Mainland China. Hong Kong's longstanding and extensive methadone treatment network may have contributed to the phenomenon.     

A new circulating recombinant form,CRF15_01B,reinforces the linkage between IDU and heterosexual epidemics in Thailand

HIV-1 subtype B and CRF01_AE have been in circulation in Thailand and Southeast Asia for more than a decade. Initially separated by risk group, the two strains are increasingly intermixed, and two recombinant strains of essentially reciprocal structure have been recently reported. Here we identify additional CRF_01B recombinants and provide the evidence that HIV-1 strains now pass freely between the two high-risk populations. HIV isolates that showed discordance between CRF01_AE and subtype B in multi-region genotyping assays were selected for the study. They were drawn from 3 different cohorts in Thailand representing different risk behaviors and demographic characteristics: a drug user cohort in the north, a family planning clinic attendee cohort in the southeast, and a cohort study of the mucosal virology and immunology of HIV-1 infection in Thailand. The DNA from these isolates was PCR amplified to recover the full HIV-1 genome and subjected to sequencing and phylogenetic analysis. We establish that one particular CRF_01B recombinant, with the external envelope of subtype B and the rest of the genome from CRF01_AE, is circulating widely in Thailand. Termed CRF15_01B (also referred to as CRF15), the strain was primarily heterosexually transmitted, although injecting drug use (IDU) also played a role. In aggregate data from the studies, CRF15 constituted 1.7% of all HIV-1 infections (95% confidence interval 0.5-4.4%) and was dispersed widely in the country. The previously separate heterosexual and IDU epidemics have apparently been bridged by a new CRF. The entry of CRF15 into the mainstream of the epidemic signals new complexity in the long stable molecular picture in Thailand. These recombinants must be considered in ongoing or projected efficacy evaluations of HIV-1 vaccines and antiviral therapies.     

The molecular epidemiology of HIV type 1 among Vietnamese Australian injecting drug users in Melbourne, Australia

The proportion of human immunodeficiency virus type 1 (HIV-1) among Vietnamese injecting drug users (IDUs) in Melbourne, Australia exceeds that of the background population. To investigate the molecular epidemiology of HIV-1 among this group, the C2-V4 region of the HIV-1 envelope was directly sequenced from 11 Vietnamese Australians and 19 non-Vietnamese Australian controls. A significant difference in the distribution of the HIV-1 subtypes was demonstrated, with greater than 50% of Vietnamese Australian IDU shown to be infected with CRF01_AE-the predominant subtype in Southeast Asia, rather than subtype B, which dominates the Australian epidemic and which was found in 89.5% of the non-Vietnamese controls. The genetic diversity of the CRF01_AE epidemic in Vietnamese Australian IDUs was substantially lower that that of the background subtype B, consistent with a more recent introduction of a limited number of viral strains from Vietnam. These results support public health policy targeting Australian IDUs of Vietnamese ethnicity as a distinct vulnerable population.     

Importation of multiple HIV type 1 strains into West Papua, Indonesia (Irian Jaya).

HIV-1 from 16 sexually transmitted disease clinic patients in Timika, West Papua, Indonesia was amplified by RT-PCR and subtyped by a combination of envelope and gag region heteroduplex mobility analysis (HMA) and direct PCR DNA sequencing. HMA showed the presence of 14 subtype E (CRF01_AE) and 2 subtype B HIV-1. Phylogenetic analysis of a 540-bp V3-V4 region of gp120 showed that 9 of 10 CRF01_AE variants clustered tightly with a median distance of 1.3% (range, 0.5 to 2.2%) whereas 1 CRF01_AE variant diverged significantly from the others (median distance, 10.7%; range, 10.1 to 11.8%). One subtype B virus envelope was typical of United States/European strains whereas the other appeared to be related to Thai subtype B' variants. These results reflect the independent introduction of multiple HIV-1 strains into West Papua, with the rapid spread in the majority of infected patients tested of a single strain of HIV-1E (CRF01_AE).     

我国男男性行为人群中HIV-1病毒亚型分布及其演变

男男性行为人群(MSM)仍是我国HIV感染的高危人群,欧美B亚型、CRF01_AE和CRF07_BC亚型是其人群中流行的主要病毒亚型。近年来,MSM中HIV-1亚型的流行趋势发生改变,欧美B亚型所占比例显著下降,CRF01_AE和CRF07_BC亚型所占比例则明显增加,并且出现新的重组亚型。运用分子生物学技术分析我国男男性行为人群中HIV-1病毒亚型分布和变化趋势,可有助于阐明MSM人群中HIV-1的流行规律,追踪传染来源和确定相关危险因素,并为MSM人群精准干预提供重要的参考依据。     

HIV-1 CRF01_AE in intravenous drug users in Hanoi, Vietnam

To investigate the molecular epidemiology of HIV-1 among intravenous drug users (IDUs) in Hanoi we collected 17 samples from individuals living in 12 locations in and around Hanoi. The HIV-1 env V3 and gag p17 regions were directly sequenced from the proviral PBMC population. The majority of the IDUs were infected with HIV-1 CRF01_AE and one individual carried a p17/V3 CRF01/subtype C recombinant. The CRF01 viruses found among these individuals did not seem to be directly epidemiologically linked to each other. The sequences were, however, related to previously reported CRF01 sequences from Vietnam and China. Thus, IDUs in Hanoi seem to have derived their infections in Vietnam, but not from the same source. The discovery of the CRF01/C recombinant shows that new viral forms easily can be generated in IDU transmission chains.     

Maintaining low HIV type 1 env genetic diversity among injection drug users infected with a B/C recombinant and CRF01_AE HIV type 1 in southern China

HIV-1 outbreaks in Guangxi Province, southern China were initiated from two separate border cities in 1996 and 1997. Drug users in Pingxiang City, which borders Vietnam, were infected with CRF01_AE HIV-1, and drug users in Baise City, which borders Yunan Province, were infected with a novel B/C recombinant HIV-1. Since 1997, HIV-1 has been rapidly spreading in Guangxi, including its capital city Nanning. Survey data indicated that HIV-1 prevalence among IDUs in new outbreak regions increased 8 to 42% within 1 year. The B/C recombinants obtained from five separate regions in Guangxi, which span a 4-year time frame, were remarkable for their low intersubject env V3 diversity, less than 0.2%. Similarly, the CRF01_AE from IDUs over a 3-year time frame had low intersubject env V3 diversity of less than 1.6%. Different patterns of sequence variations in the V3 and V4 regions were observed for the B/C recombinant and the CRF01_AE HIV1. The rapid spreading of homogeneous HIV-1 strains in Guangxi may have important implications for HIV transmission as well as vaccine development and evaluation.     

MSM人群急性HIV-1感染者病毒亚型分析

目的研究2007-2009年男男性行为人群（MSM）艾滋病病毒-1型（HIV-1）的基因亚型,以监测MSM人群HIV病毒株的最新流行情况。方法采集95例MSM急性HIV-1感染者的外周全血,从外周全血浓缩白细胞中提取脱氧核糖核酸（DNA）,用巢式聚合酶链反应（Nested-PCR）对HIV-1的前病毒DNA进行扩增,然后检测并分析PCR扩增产物的核苷酸序列,确定病毒的基因亚型。结果 95例感染者平均年龄为（35.02±9.15）岁,其中20～50岁的青壮年45例（94.74%）,未婚51例（53.68%）,大专或大学及以上文化程度者30例（占31.58%）。感染者中共发现CRF01_AE亚型、B亚型、BC重组亚型（包括CRF07_BC和CRF08_BC）及C亚型4种亚型。其中CRF01_AE重组亚型56例（占58.95%）,B亚型28例（占29.47%）,BC重组亚型10例（占10.53%）,C亚型1例（1.05%）。结论 MSM人群急性HIV-1感染者年轻化,文化程度普遍偏低。小样本流行病学调查显示,急性HIV-1感染者中有CRF01_AE亚型、B亚型、BC重组亚型及C亚型4种亚型病毒株流行,CRF01_AE亚型为MSM人群的主要亚型。     

Surveillance of HIV type 1 recent infection and molecular epidemiology among different risk behaviors between 2007 and 2009 after the HIV type 1 CRF07_BC outbreak in Taiwan

The objective of this study was to analyze recent infections and the molecular epidemiology of human immunodeficiency virus type 1 (HIV-1) among different risk groups since the outbreak of circulating recombinant form CRF07_BC among intravenous drug users (IDUs) in 2004 in Taiwan. Phylogenetic analysis was performed using the env and pol fragment sequences amplified from these specimens. The BED IgG capture incidence EIA (BED-CEIA assay) was used to determine recent infections. Among the 683 HIV-1-positive individuals enrolled between 2007 and 2009, 394 (57.7%) were subtype B, 260 (38.1%) were CRF07_BC, 26 (3.8%) were CRF01_AE, two (0.3%) were CRF08_BC, and one (0.1%) was CRF06_cpx. While the percentage of CRF07_BC decreased (58.5-17.9%, p < 0.001) from 2007 to 2009, the percentage of subtype B increased (37.6% to 74.9%, p < 0.001). A concordant decrease in the proportion of recent infections to new infections among IDUs (63.6% to 9.8%, p < 0.001), accompanied with an increase of the proportion of recent infections in MSM (men having sex with men) (22.4-67.1%, p = 0.77) and heterosexual groups (13.1- 23.2%, p = 0.852), was observed. The decrease in CRF07_BC infections and the reduction in the proportion of recent infections among IDUs reflected the success of harm reduction strategies initiated by the government in 2005.