Molecular epidemiology of HIV-1 in Switzerland: evidence for a silent mutation in the C2V3 region distinguishing intravenous drug users from homosexual men. Swiss HIV Cohort Study

OBJECTIVES: To study the molecular epidemiology of HIV-1 strains found in Switzerland and to determine possible genetic linkages among strains sorted by risk group or geographic region. DESIGN: A cross-sectional, clinic-based survey of HIV-1 molecular sequences and linked patient history from Swiss people. METHODS: Specimens were collected from 215 HIV-1-infected people in HIV outpatient clinics of four tertiary referral centers (Lausanne, St. Gallen, Zurich, and Basel) between May and August 1996, mainly from homosexual men, injecting drug users (IDU), and heterosexually infected people. In addition, specimens collected between 1991 and 1995 in the HIV outpatient clinic at University of Geneva were included into this survey. These specimens were collected primarily for an ongoing, prospective cohort (Swiss HIV Cohort Study). Direct C2V3C3 sequences of the env gene were determined from 158 samples of peripheral blood mononuclear cells. Genetic data were analyzed with the available patient history on each specimen. RESULTS: As found in other previous studies in Europe, primarily subtype B viruses were identified, whereas seven (4%) of 158 were non-subtype B: one subtype D, four subtype A, and two subtype E. Five of seven non-B subtypes occurred in immigrants from African or Asian countries and all seven were found exclusively in individuals who had been infected by heterosexual contact. No significant clustering of strains within different study sites or risk groups was found. A silent mutation (LAI env 834) occurred significantly more often in IDU than in homosexual men (p<.001). CONCLUSIONS: Although the lack of significant clustering of strains by risk group or geographic region may result from early introduction of subtype B viruses in Switzerland, the strong association of a silent mutation with IDU suggests that, early in the epidemic, there was a unique founder virus among IDUs. The HIV epidemic in Switzerland is still predominantly caused by subtype B viruses.     

Genetic characterization of HIV-1 strains circulating in Kazakhstan

To determine the HIV-1 genetic diversity in Kazakhstan, 85 blood samples from HIV-seropositive donors were collected between 2001 and 2003. The study population consisted of 91.8% injecting drug users (IDUs); the remainder was infected sexually or iatrogenically. A genomic region that included part of the polymerase gene was sequenced for all 85 samples, and from these, 6 samples were randomly selected for nearly full genome sequencing. Subtype A was the most common genetic form (94.1%), followed by CRF02_AG (4.7%) and subtype C (1.2%). All subtype A sequences clustered closely with samples from countries of the former Soviet Union (FSU). From these sequences, 47 (58.8%) presented the secondary protease inhibitor mutation V77I that has been linked to a genetic lineage in the FSU epidemic. In addition, most had the other 2 mutations that characterize the "V77I haplotype." All 6 nearly full-length sequences were subtype A and clustered with other FSU strains. The CRF02_AG strains from this population clustered with strains from Uzbekistan, reflecting the spread of the CRF02_AG epidemic in Central Asia. The HIV epidemic in Kazakhstan is predominantly in IDUs and is indigenous to the geographic region, and most of the strains are genetically similar to those circulating in the FSU and other parts of Central Asia.     

HIV diversity, recombination and disease progression: how does fitness "fit" into the puzzle?

HIV appears to have diverged into several lineages upon multiple zoonotic introductions from the nonhuman primates. The HIV-2 and HIV-1 groups M, N, and O likely represent different cross-species transmission events. The radial evolution of group M in multiple clades or subtypes is likely due to adaptation and expansions in the human hosts. It is not well understood why HIV strains such as HIV-1 subtype C in particular or group M in general have spread disproportionately as compared to other subtypes, groups, or types, which often remained geographically constrained to local epidemics. Host genetic effects, transmission bottlenecks, social/behavioral and environmental limitations, founder effect and other viral factors could have contributed to variable spread through the human population. Even after transmission, viruses evolve at different rates during disease progression. Recent studies have explored phenotypic differences between HIV types, groups, and subtypes in attempts to explain or understand this radial evolution and expansion. This review explores some of the important aspects relating to fitness during disease progression, during global distribution of different HIV subtypes, and related to circulation of recombinant forms in the epidemic.     

Hepatitis C virus (HCV) 5'NC sequence variants and their association with hepatitis C risk groups.

BACKGROUND: Genotype distribution of hepatitis C virus (HCV) is relatively uniform in Prague, Czech Republic. Unlike the other developed countries where HCV genotype 3 is increasingly associated with injection drug users (IDU), subtype 1b remains the most prevalent HCV subtype in Prague, regardless of risk factors. OBJECTIVE: We wished to determine if subtype 1b strains could be further differentiated by comparing the conserved 5'NC sequences of the strains infecting IDU and non-IDU populations. STUDY DESIGN: All prospectively collected serum samples that were HCV RNA positive were genotyped according to the 5'NC and NS5b regions. All 5'NC sequences were further analyzed for new mutations and these data were compared to patient epidemiologic information. RESULTS: We found eight 5'NC sequence variants among 96 specimens tested. Further analysis of subtype 1b strains showed that a variant with a nucleotide insertion at -138 positions was found only among non-IDU subjects, while the variant with T-->C substitution at -94 was found only among the IDUs. CONCLUSIONS: These observations suggest that the current HCV transmission between the IDU and non-IDU populations is uncommon, and may reflect the beginning of divergence of HCV genotypes in the IDU population in Prague.     

Co-existence of HIV-1 subtypes B' and E infections among Thai injecting drug users

Subtypes B' and E are the two major subtypes of HIV-1 among injecting drug users (IDU) in Thailand. However, there are not many reports on subtype distribution during the early epidemic. Random blood specimens collected during 1994-2000 from 3,286 IDU at the Thanyarak Hospital were tested for HIV antibody and subtyped by using peptide binding enzyme immunoassay. The prevalence rate of HIV infection was 36.8%. All HIV-seropositive IDU were ascertained for "year of first HIV seropositivity" from their medical records. Of 1,512 HIV-seropositive samples, 1,408 (93.1%) were typeable. During 1987-1988, the proportion of subtype B' was as high as 80% but decreased rapidly to 27.6% during 1999-2000. At the same time, the proportions of subtype E increased correspondingly (Chi-square test for the trend, p < 0.05). The relatively high proportion of subtype E among IDU since an early stage of the epidemic suggests early co-existence of both subtypes and needs further investigation.     

Prevalences, genotypes, and risk factors for HIV transmission in South America

HIV cross-sectional studies were conducted among high-risk populations in 9 countries of South America. Enzyme-linked immunosorbent assay screening and Western blot confirmatory testing were performed, and env heteroduplex mobility assay genotyping and DNA sequencing were performed on a subset of HIV-positive subjects. HIV prevalences were highest among men who have sex with men (MSM; 2.0%-27.8%) and were found to be associated with multiple partners, noninjection drug use (non-IDU), and sexually transmitted infections (STIs). By comparison, much lower prevalences were noted among female commercial sex workers (FCSWs; 0%-6.3%) and were associated mainly with a prior IDU and STI history. Env subtype B predominated among MSM throughout the region (more than 90% of strains), whereas env subtype F predominated among FCSWs in Argentina and male commercial sex workers in Uruguay (more than 50% of strains). A renewed effort in controlling STIs, especially among MSM groups, could significantly lessen the impact of the HIV epidemic in South America.     

Genetic variants of hepatitis C virus in HIV-infected drug users

The prevalence of genetic variants (subtypes) of hepatitis C virus (HCV) among HIV-infected and noninfected intravenous drug users (IDU) in Russia is studied. HIV and HCV infections spread in the population of IDUs in Russia irrespective of each other. HCV subtypes 1b, 2a, and 3a (35.2, 18.3, and 29.6%, respectively) are the most prevalent in Russia. The profile of HCV subtype distribution in Russia differs from that in Europe; a "domestic" origin of HCV infection among IDUs is suggested. The authors conclude that identification of HCV subtype should be included in the protocol of examination of HIV-infected patients.     

我国云南省艾滋病病毒感染的长期不进展者人免疫缺陷 …

目的 人类免疫缺陷病毒１型（ＨＩＶ－１）ｔａｔ基因是该病毒的调控基因之一。本研究是探讨ｔａｔ基因变异是否影响ＨＩＶ－１感染者的病程进展。方法 从云南ＨＩＶ流行区的２２例感染后临床进程不同的人抽取外周血,提取核酸,用套式聚合酶链反应（ＰＣＲ）扩增ＨＩＶ－１的ｔａｔ基因,并进行了核酸序列测定和分析。     

Genetic characterization of hepatitis C virus strains in Estonia: fluctuations in the predominating subtype with time

During the last decade, there has been a dramatic increase in intravenous drug use in young adults in Estonia with an increased incidence of both hepatitis B and C as a consequence. Since genetic data are limited regarding hepatitis C virus (HCV) strains in Estonia, the aim of the study was to characterize HCV strains in different risk groups to determine their relatedness to strains from other geographical regions. Three hundred fifty-three anti-HCV positive sera collected during 1994-2004 from hospitalized patients, blood donors and health care workers were used as source of HCV RNA. Two hundred nine (59%) of the sera were positive for HCV RNA by PCR directed to the 5'-UTR region. For 174 strains the HCV subtype was determined by analyses of the NS5B and/or the 5'UTR-core regions. 1b (71%) was the most common subtype followed by 3a (24%), 2c (2%), 1a (1%), and 2a (1%). The 1b and 3a strains were similar to strains from other regions of the former USSR. Within genotype 1b there were several HCV lineages. However, for 3a there seemed to be two separate introductions into Estonia. There was a relative shift from subtype 1b to 3a in 1999-2000 with a further replacement of 3a with 1b in intravenous drug users in 2001 and onwards (P < 0.05). However, both subtypes were found to co-circulate in the community independent of risk factors. One patient was infected with the 2k/1b recombinant presumed to originate from St. Petersburg being the first isolate of this recombinant recovered outside Russia.     

HIV-1 subtyping in Salvador, Bahia, Brazil: a city with African sociodemographic characteristics

To investigate the prevalence of the HIV-1 subtypes in different populations from Salvador, Bahia, Brazil, blood samples from 72 HIV-1-seropositive injecting drug users (IDUs) and 62 individuals infected sexually were analyzed using the heteroduplex mobility assay (HMA). In the IDU group, 89.5% were classified as subtype B, 3% as subtype F, and 7.5% showed a B/F HMA profile. In the sexual transmission (ST) group, 95% were identified as B subtype, 3.4% showed a B/F profile, and 1.6% a B/C/E HMA profile. All Brazilian samples that showed multiple reactivities in the HMA analysis clustered on sequencing with B North American/ European HIV-1 isolates in the phylogenetic analysis, whereas the F subtypes clustered with F Brazilian HIV-I isolates. Serologic reactivities of IDU's sera were examined using a panel of synthetic V3 loop peptides representative of the different HIV-1 subtypes. No difference in serologic reactivity between F and B subtype plasma could be observed. Predominance of HIV-I subtype B was identified in both study groups, whereas subtype F was detected only among IDUs in a frequency lower than described for other Brazilian regions.     

中国HIV-1型B、C亚型主要流行株外膜蛋白基因V3-V4区序列的变异分析

目的　研究我国人类免疫缺陷病毒 1型 (HIV 1)B、C亚型主要流行株在感染过程中基因变异的特点及其与选择压力的关系。方法　应用巢式聚合酶链反应 (nested PCR)对 2 5 8例HIV 1感染者血样中的HIV 1外膜蛋白 (env)基因进行扩增 ,并使用ABI 377型测序仪对扩增产物测序后 ,选择其中 37份B亚型和 35份C亚型HIV 1毒株env基因包括V3～V4区的序列进行比较分析 ,并计算和分析氨基酸同义替换与非同义替换的比值 (Ks Ka)。结果　B亚型毒株V3～V4区的基因离散率高于C亚型毒株。无论B亚型 ,还是C亚型毒株 ,其V4区基因序列较V3区变异更大。在C亚型毒株中 ,V3区基因序列变异甚至比V3上游区和C3区小。B和C亚型毒株整个V3～V4基因区的Ks Ka比值均 <1,差异有非常显著性 (P <0 0 0 1) ,其中B亚型毒株以V3区的Ks Ka比值最小 ,而C亚型毒株则以V4区的Ks Ka比值最小。结论　B和C亚型毒株env基因的变异主要发生在V4区而不是V3区。C亚型毒株V3区较V3上游区和C3区还要保守 ,是本研究的特殊发现。这两种亚型在我国快速流行中发生的变异是在选择压力下发生的 ,而不是随机进化的结果 ,而且选择压力对这两种亚型毒株V3、V4区的作用程度也不一样。这将为我国艾滋病防治策略的制定和疫苗研究提供科学的依据。     

2005—2008年广东省CDC艾滋病自愿咨询检测人群特征分析

目的分析广东省疾病预防控制中心（CDC）艾滋病自愿咨询检测（VCT）人群特征,为预防HIV传播提供科学依据。方法对2005年1月至2008年12月来广东省CDC门诊寻求VCT服务的人群进行检测前咨询并填写个案登记表,用描述性方法分析其特征及艾滋病病毒（HIV）抗体检测结果。结果咨询检测者2951人,主要来自于广州市以外地区,初诊者多于复诊者,以20～39岁的青壮年为主,男性多于女性,以已婚者居多;本科文化程度者所占比例较大;职业分布主要以干部职员为主,其次为商业服务人员;咨询检测原因依次为异性性接触、同性性接触、吸毒。共发现HIV抗体阳性者299人,检出率10．1％（x^2=61．27,P〈0．01）。HIV检出率2008年高于2007年,2007、2008年高于2006年,HIV检出率逐年升高。结论广东省CDC门诊VCT高危人群相对集中,主要为青壮年男性,来自外市区,已婚者,受教育水平高,有一定社会地位,咨询的主要原因为异性性接触。VCT能早期发现HIV感染者,2005—2008年HIV阳性检出率逐年升高,建议加强VCT建设,根据人群特征制定防治措施,更有助于提高艾滋病预防效果。     

Genetic analysis of incident HIV-1 strains among injection drug users in Bangkok: evidence for multiple transmission clusters during a period of high incidence

During 1995-1996, 1,209 HIV-1-negative injection drug users (IDUs) attending methadone treatment clinics operated by the Bangkok Metropolitan Administration in Bangkok, Thailand, were enrolled in a prospective cohort study. Through 1998, 133 of these IDUs had seroconverted to HIV-1; 130 of these seroconverters were included in this study. HIV-1 CRF01_AE and subtype B strains accounted for 79% and 21% of the incident infections, respectively. To examine phylogenetic relationships among these incident HIV-1 strains, we used several phylogenetic inference methodologies to analyze the env (C2-V4) sequences in blood samples collected soon after seroconversion. These analyses consistently revealed eight phylogenetic clusters comprising 21 incident strains (bootstrap method, >80%; six CRF01_AE and two subtype B clusters). Two factors were found to be associated with the eight clusters. The first factor was temporal: seven of the eight clusters comprised 17 sequences from IDUs whose estimated dates of seroconversion were within a period of high incidence from July 1996 through January 1997. The second factor was a possible geographic association: four clusters were observed among IDUs who had attended the same methadone treatment clinics. These phylogenetic clusters likely represent subgroups within larger HIV transmission networks among IDUs in Bangkok. Despite prevention efforts, the incidence of HIV-1 infection among the Bangkok IDU population continues to be high. A better understanding of transmission networks and factors associated with such networks can help guide prevention efforts.     

The early phase of an HIV epidemic in a population exposed previously to HCV in the Philippines

Human immunodeficiency virus (HIV) sentinel surveillance program for injecting drug users has been conducted in Metro Cebu, the Philippines. A low prevalence (0-0.52%) of anti-HIV-positivity had been detected in this population from 2002 to 2007. However, a 10-fold increase in HIV prevalence was detected in the 2009 national HIV sentinel surveillance program. It prompted an additional outreach program to be conducted in Metro Cebu in January 2010, which recorded the highest HIV prevalence rate ever documented in the Philippines (75%, 44/59). HIV genes from fourteen 2009 to 2010 Metro Cebu strains were clustered closely in the phylogenetic tree, but no other strain collected outside Metro Cebu and none stored in the International Nucleotide Sequence Database was allocated to the same phylogenetic cluster. All these HIV infections have emerged in the anti-hepatitis C virus (HCV)-positive population (100%, 62/62) in Metro Cebu from 2009 to 2010. The five HCV strains from the individuals harboring the closely related HIV strains were categorized into different subtypes. These results strongly suggest that HIV infections occurred recently and spread rapidly among injecting drug users, while HCV had been circulating previously among them. Considering the fact that injecting drug use was the first mode of HIV transmission in Asia, extensive monitoring of injecting drug users and associated bridging populations is necessary. Therefore, HCV-guided characterization of the spread of HIV to populations that are vulnerable to blood-borne infections could play an important role in alerting health authorities to the early phase of an HIV epidemic.     

HIV risk perception and prevalence in a program for prevention of mother-to-child HIV transmission: comparison of women who accept voluntary counseling and testing and those tested anonymously

OBJECTIVE: To determine whether data from voluntary counseling and testing (VCT)/prevention of mother-to-child transmission (PMTCT) programs can be used for HIV surveillance. METHODS: Women attending an antenatal clinic at the district hospital in Entebbe, Uganda, from May 2002 to April 2003 were offered counseling and HIV testing with same-day results (VCT) and nevirapine for PMTCT was provided for HIV-positive women and their babies. Those who declined VCT were tested for HIV anonymously. RESULTS: Overall, 2635 women accepted VCT; 883 were tested anonymously. HIV prevalence was higher in VCT than in anonymously tested women in the first month of the program (20% vs. 11%, P=0.05) and in months with <70% VCT uptake (17% vs. 8%, P<0.001) but was similar in months with high uptake. Uptake of VCT was higher in women who had risk factors for HIV, especially those who believed themselves to have been exposed (84% vs. 73%, P<0.001). CONCLUSION: There was a bias to accepting VCT in women with HIV, or risk factors for HIV infection, the former most apparent when there was low coverage. Data from VCT/PMTCT programs cannot replace anonymous surveillance for monitoring of HIV epidemic trends where coverage is incomplete within clinics or communities.     

我国西南西北地区吸毒人群重组人类免疫缺陷病毒1型毒株的发现

目的寻找人类免疫缺陷病毒１型（ＨＩＶ１型）在中国可能的重组。方法从流行２种以上ＨＩＶ１亚型的地区收集ＨＩＶ感染者的血样。从ＰＭＣｓ中应用套式聚合酶链反应（ＰＣＲ）方法,对ＨＩＶ病毒的ｔａｔ和ｅｎｖ基因进行扩增,ＰＣＲ产物直接测序并进行序列分析。结果对中国Ｂ′亚型和Ｃ亚型流行区域收集的１４个ＨＩＶ１毒株进行序列分析,对ｅｎｖ基因进行测序后没有发现重组毒株的证据。对ｔａｔ基因的第一外显子进行序列分析时,１４个样品中的１０个样品发现了Ｂ′亚型和Ｃ亚型重组的ＨＩＶ１毒株。此外,四川省静脉吸毒者中发现了３个非重组的Ｂ′亚型毒株和１个非重组的Ｃ亚型毒株。结论首次在中国西南部的四川省和西部的新疆维吾尔自治区发现了Ｂ′亚型和Ｃ型的重组ＨＩＶ１毒株。相同的序列和重组方式,表明重组毒株具有相同的起源,同时表明这两个艾滋病流行区域密切相关。由于在新疆只发现了重组毒株,而在四川省则发现了Ｂ亚型、Ｃ亚型和Ｂ′／Ｃ重组毒株,重组很有可能发生在四川而不是新疆。     

中国人类免疫缺陷病毒（HIV—1）D亚型毒株gag,env和t …

目的 通过对ＨＩＶ－１毒株ｇａｇ,ｔａｔ,ｅｎｖ基因的序列分析,阐明Ｄ亚型ＨＩＶ－１毒株已在中国出现。方法 从１名四川非洲回国营务人员ＨＩＶ感染者（ＳＣ９ ７１２）淋巴细胞（ＰＢＭＣ）中提取前病毒ＤＮＡ,使用套式ＰＣＲ方法分别扩增ＨＩＶ－１的ｇａｇ基因区,ｅｎｖ基因的Ｃ２Ｖ３区和ｔａｔ基因的第一外显子。结果 发现ＳＣ９ ７１２在ｇａｇ区,ｅｎｖ区和ｔａｔ区与国际标准Ｄ亚型毒株的基因距离最近,其中在     

Determination of human immunodeficiency virus type 1 subtypes in Taiwan by vpu gene analysis

The genetic diversity of human immunodeficiency virus (HIV) type 1 (HIV-1) has been characterized mainly by analysis of the env and gag genes. Information on the vpu genes in the HIV sequence database is very limited. In the present study, the nucleotide sequences of the vpu genes were analyzed, and the genetic subtypes determined by analysis of the vpu gene were compared with those previously determined by analysis of the gag and env genes. The vpu genes were amplified by nested PCR of proviral DNA extracted from 363 HIV-1-infected individuals and were sequenced directly by use of the PCR products. HIV-1 subtypes were determined by sequence alignment and phylogenetic analysis with reference strains. The strains in all except one of the samples analyzed could be classified as subtype A, B, C, E, or G. The vpu subtype of one strain could not be determined. Of the strains analyzed, genetic subtypes of 247 (68.0%) were also determined by analysis of the env or gag gene. The genetic subtypes determined by vpu gene analysis were, in general, consistent with those determined by gag and/or env gene analysis except for those for two AG recombinant strains. All the strains that clustered with a Thailand subtype E strain in the vpu phylogenetic analyses were subtype E by env gene analysis and subtype A by gag gene analysis. In summary, our genetic typing revealed that subtype B strains, which constituted 73.8% of all strains analyzed, were most prevalent in Taiwan. While subtype E strains constituted about one-quarter of the viruses, they were prevalent at a higher proportion in the group infected by heterosexual transmission. Genetic analysis of vpu may provide an alternate method for determination of HIV-1 subtypes for most of the strains, excluding those in which intersubtype recombination has occurred.     

Predicted HIV-1 coreceptor usage among Kenya patients shows a high tendency for subtype d to be cxcr4 tropic

ABSTRACT: BACKGROUND: CCR5 antagonists have clinically been approved for prevention or treatment of HIV/AIDS and countries in Subsahara Africa with the highest burden of HIV/AIDS are due to adopt these regimens. However, HIV-1 can also use CXCR4 as a co-receptor. There is hence an urgent need to map out cellular tropism of country circulating HIV strains to guide the impending use of CCR5 antagonists. Objectives: To determine HIV-1 coreceptor usage among patients attending a comprehensive care centre in Nairobi, Kenya METHODS: Blood samples were obtained from HIV infected patients attending the comprehensive care centre, Kenyatta National Hospital in years 2008 and 2009. The samples were separated into plasma and peripheral blood mononuclear cells (PBMCs). Proviral DNA was extracted from PBMCs and Polymerase Chain reaction (PCR) done to amplify the HIV env fragment spanning the C2-V3 region. The resultant fragment was directly sequenced on an automated sequencer (ABI, 3100). Co-receptor prediction of the env sequences was done using Geno2pheno [co-receptor]. and. phylogenetic relationships determined using CLUSTAL W and Neighbor Joining method. RESULTS: A total of 67 samples (46 treatment experienced and 21 treatment naive) were successfully amplified and sequenced. Forty nine (73%) sequences showed a prediction for R5 tropism while 18(27%) were X4 tropic. Phylogenetic analysis showed that 46(69%) were subtype A, 11(16%) subtype C, and 10(15%) subtype D. No statistically significant associations were observed between cell tropism and CD4+ status, patient gender, age, or type of treatment regimen. There was a tendency for more X4 tropic strains being in the treatment experienced than the naive group 14/18 (78%), though not statistically significant (p=0.31). However, a strong association was observed between subtype D and CXCR4 co-receptor usage (p=0.015). CONCLUSION: HIV-1 R5 tropic strains were the most prevalent in the study population and HIV infected patients in Kenya may benefit from CCR5 antagonists. However, there is need for caution where subtype D infection is suspected or where antiretroviral salvage therapy is indicated.