The explosive human immunodeficiency virus type 1 epidemic among injecting drug users of Kathmandu, Nepal, is caused by a subtype C virus of restricted genetic diversity

K. J. AJ, Dhar C, D. Souza G, Berry N, Vyakarnam A. Deep sequencing of near full-length HIV-1 genomes from plasma identifies circulating subtype C and infrequent occurrence of AC recombinant form in Southern India

India has the third largest number of HIV-1-infected individuals accounting for approximately 2.1 million people, with a predominance of circulating subtype C strains and a low prevalence of subtype A and A1C and BC recombinant forms, identified over the past two decades. Recovery of near full-length HIV-1 genomes from a plasma source coupled with advances in next generation sequencing (NGS) technologies and development of universal methods for amplifying whole genomes of HIV-1 circulating in a target geography or population provides the opportunity for a detailed analysis of HIV-1 strain identification, evolution and dynamics. Here we describe the development and implementation of approaches for HIV-1 NGS analysis in a southern Indian cohort. Plasma samples (n = 20) were obtained from HIV-1-confirmed individuals living in and around the city of Bengaluru. Near full-length genome recovery was obtained for 9 Indian HIV-1 patients, with recovery of full-length gag and env genes for 10 and 2 additional subjects, respectively. Phylogenetic analyses indicate the majority of sequences to be represented by subtype C viruses branching within a monophyletic clade, comprising viruses from India, Nepal, Myanmar and China and closely related to a southern African cluster, with a low prevalence of the A1C recombinant form also present. Development of algorithms for bespoke recovery and analysis at a local level will further aid clinical management of HIV-1 infected Indian subjects and delineate the progress of the HIV-1 pandemic in this and other geographical regions.

Overview of HIV molecular epidemiology among people who inject drugs in Europe and Asia

HIV strains continuously evolve, tend to recombine, and new circulating variants are being discovered. Novel strains complicate efforts to develop a vaccine against HIV and may exhibit higher transmission efficiency and virulence, and elevated resistance to antiretroviral agents. The United Nations Joint Programme on HIV/AIDS (UNAIDS) set an ambitious goal to end HIV as a public health threat by 2030 through comprehensive strategies that include epidemiological input as the first step of the process. In this context, molecular epidemiology becomes invaluable as it captures trends in HIV evolution rates that shape epidemiological pictures across several geographical areas. This review briefly summarizes the molecular epidemiology of HIV among people who inject drugs (PWID) in Europe and Asia. Following high transmission rates of subtype G and CRF14_BG among PWID in Portugal and Spain, two European countries, Greece and Romania, experienced recent HIV outbreaks in PWID that consisted of multiple transmission clusters including subtypes B, A, F1, and recombinants CRF14_BG and CRF35_AD. The latter was first identified in Afghanistan. Russia, Ukraine, and other Former Soviet Union (FSU) states are still facing the devastating effects of epidemics in PWID produced by A_FSU (also known as IDU-A), B_FSU (known as IDU-B), and CRF03_AB. In Asia, CRF01_AE and subtype B (Western B and Thai B) travelled from PWID in Thailand to neighboring countries. Recombination hotspots in South China, Northern Myanmar, and Malaysia have been generating several intersubtype and inter-CRF recombinants (e.g. CRF07_BC, CRF08_BC, CRF33_01B etc.), increasing the complexity of HIV molecular patterns.

HIV and risk environment for injecting drug users: the past, present, and future

We systematically reviewed reports about determinants of HIV infection in injecting drug users from 2000 to 2009, classifying findings by type of environmental influence. We then modelled changes in risk environments in regions with severe HIV epidemics associated with injecting drug use. Of 94 studies identified, 25 intentionally examined risk environments. Modelling of HIV epidemics showed substantial heterogeneity in the number of HIV infections that are attributed to injecting drug use and unprotected sex. We estimate that, during 2010-15, HIV prevalence could be reduced by 41% in Odessa (Ukraine), 43% in Karachi (Pakistan), and 30% in Nairobi (Kenya) through a 60% reduction of the unmet need of programmes for opioid substitution, needle exchange, and antiretroviral therapy. Mitigation of patient transition to injecting drugs from non-injecting forms could avert a 98% increase in HIV infections in Karachi; whereas elimination of laws prohibiting opioid substitution with concomitant scale-up could prevent 14% of HIV infections in Nairobi. Optimisation of effectiveness and coverage of interventions is crucial for regions with rapidly growing epidemics. Delineation of environmental risk factors provides a crucial insight into HIV prevention. Evidence-informed, rights-based, combination interventions protecting IDUs' access to HIV prevention and treatment could substantially curtail HIV epidemics.

Nef-mediated MHC class I down-regulation unmasks clonal differences in virus suppression by SIV-specific CD8(+) T cells independent of IFN-gamma and CD107a responses

CD8(+) T lymphocytes (CTL) play a role in controlling HIV/SIV infection. CTL antiviral activity is dependent on recognition of antigenic peptides associated with MHC class I molecules on infected target cells, and CTL activation can be impaired by Nef-mediated down-regulation of MHC class I molecules. We tested the ability of a series of rhesus macaque CD8(+) T-cell clones specific for the SIV Gag CM9 peptide to suppress SIV infection of autologous CD4(+) T cells. We used a set of SIV(mac)239 viruses with either wild-type Nef or Nef mutations that impair MHC class I down-regulation. All CTL clones efficiently suppressed virus replication in cells infected with mutant viruses with altered Nef function, phenotypically MHC class I(high) or MHC class I(intermediate). However, the ability of the clones to suppress virus replication was variably reduced in the presence of wild-type Nef (MHC class I(low)) despite the observations that all CTL clones showed similar IFN-gamma responses to titrated amounts of cognate peptide as well as to SIV-infected cells. In addition, the CTL clones showed variable CD107a (CTL degranulation marker) responses that did not correlate with their capacity to suppress virus replication. Thus, the clonal differences are not attributable to TCR avidity or typical effector responses, and point to a potential as yet unknown mechanism for CTL-mediated suppression of viral replication. These data emphasize that current assays for evaluating CTL responses in infected or vaccinated individuals do not fully capture the complex requirements for effective CTL-mediated control of virus replication.

Prevalence of infections, HIV risk behaviors and factors associated with HIV infection among male injecting drug users attending a needle/syringe exchange program in Dhaka, Bangladesh

Injecting drug users (IDU) in Bangladesh are at the early stages of an HIV epidemic. To understand the dynamics of the HIV epidemic, male IDU (n = 561) were recruited from the needle/syringe exchange program in Dhaka in 2002, who underwent a risk-behavior survey and were tested for HIV, syphilis, hepatitis C, and hepatitis B. Correlates of HIV infection were determined by conducting bivariate and multiple regression analyses. The median age of the IDU was 35 years, 39.6% had no formal education, approximately half were married and/or living with their regular sex partner and 26% were currently homeless. The median age at first injection was 29 years. HIV was detected in 5.9% of the IDU and homelessness was the only factor independently associated with HIV (OR = 5.5). Urgent measures must be undertaken to prevent escalation of the HIV epidemic. The study's limitations are noted.

Bangladesh moves from being a low-prevalence nation for HIV to one with a concentrated epidemic in injecting drug users

Bangladesh has been conducting annual serological surveillance for HIV and syphilis since 1998 among most at-risk populations including sex workers, males having sex with males, injecting drug users (IDUs) and heroin smokers. During the seventh round conducted between January and June 2006, 10,368 people were sampled and the overall HIV prevalence was 0.9%. The highest HIV rate was recorded in male IDUs from the capital city Dhaka (7%), and the rates have risen significantly over the rounds (P < 0.001). In Dhaka, most of the HIV-positive IDUs (10.5%) were localized in one neighbourhood, while in the remaining neighbourhoods 1% were positive (P < 0.001). In all other groups, HIV prevalence was <1%. Active syphilis rates were highest in female IDUs (9.9%) followed by female street-based sex workers (8.6%). However, rates in female sex workers in Dhaka declined significantly over the years (P < 0.001). Bangladesh has to act urgently to prevent escalation of the epidemic.

Coverage to curb the emerging HIV epidemic among injecting drug users in Pakistan: delivering prevention services where most needed

BACKGROUND

HIV Surveillance data from IDUs is suggestive of an escalating epidemic in major cities of Pakistan. The relatively widespread presence and interlinking of IDU and high-risk sexual networks, combined with low levels of HIV knowledge and prevention methods, indicate that there is potential for a rapid spread of HIV to other high-risk groups and its further expansion to general population through bridging groups.

METHODS

We reviewed Second Generation Surveillance data which provides mapping, biological and behavioural information from IDUs in eight major cities across Pakistan. Geographic mapping provided information about the location and size of the population, which was followed by a behavioural survey, conducted with a representative sample of 2432 IDUs. In addition, blood samples were also obtained which were tested for HIV.

RESULTS

Despite availability of syringe and needle exchange programmes in larger cities, drug users continued to reuse syringes (78.1%), injected in groups (73.3%) where extensive sharing of needle and injecting paraphernalia took place (50%). 12.6% of the respondents reported to having sexual relationships with female sex workers and 14.7% had sex with males in the past 6 months. 65% never used condoms. In addition 5.3% reported exchange of sex for money and drugs. Fairly low levels of coverage were reported from most of the cities.

CONCLUSION

Despite an existing nationwide harm reduction programme, increasing rates of HIV infection among IDUs underscore the need to identify gaps in the existing prevention strategy. Data available on coverage shows that effective harm reduction activities are unable to reach a substantial number of IDUs to actually avert or delay the emerging IDUs epidemic. There is an urgent need to expand coverage, and to integrate harm reduction in the mainstream of public health.

Autochthonous horizontal transmission of a CRF02_AG strain revealed by a human immunodeficiency virus type 1 diversity survey in a small city in inner state of Rio de Janeiro, Southeast Brazil

As part of an ongoing study on the features of AIDS spread towards small cities and rural areas, we present a molecular survey of human immunodeficiency virus type 1 (HIV-1) polymerase sequences recovered between 2004 and 2006 from 71 patients receiving care in the city of Saquarema, inner state of Rio de Janeiro. Phylogenetic reconstructions found the two prevalent lineages in the state (subtypes B [59 strains, 83.1%], F1 [6 strains; 8.4%], and BF1 recombinants [four strains; 5.6%]), as well as two (2.8%) CRF02_AG strains, which seems to be an emerging lineage in the capital. These CRF02_AG sequences were recovered from a married heterosexual couple who never traveled abroad, thus providing the first molecular evidence of autochthonous horizontal transmission of this lineage of major global importance. Also, three phylogenetic clusters of strains recovered from a total of 18.3% of the cohort were uncovered. Their close genetic relatedness suggests they were recovered from patients who probably took part in the same chain of viral spread. In conjunction with our previous surveys from inner Rio de Janeiro, these results suggest that although small cities harbor unique molecular features of HIV-1 infection, they also clearly reflect and may rapidly absorb the diversity recorded in large urban centers.

Population mobility and spread of HIV across the Indo-Nepal border

The article reviews information on the epidemiology of HIV/AIDS and behavioural networking to examine the role of population mobility in spreading HIV across the Indo-Nepal border. Documents were collected through a systematic search of electronic databases and web-based information resources, and the review focuses on studies about types of the virus, prevalence of HIV, and sexual and injecting networking. HIV-1 (subtype C) and HIV-2 were identified in Nepal. The prevalence of HIV was higher among male labour migrants and female sex workers (FSWs) who returned from India, especially from Mumbai, than in similar non-migrant groups. In the early 2000s, about 6-10% of Mumbai returnee men, compared to up to 4% of India returnee men and up to 3% of non-migrant men in the far-west Nepal, were identified with HIV. Likewise, when the prevalence of HIV among sex workers in Kathmandu was found to be 17% in 1999-2000, up to 44% of India returnee and 73% of Mumbai returnee FSWs were identified with the virus. These data are, however, based on small samples with questionable representativeness of the target populations and need to be interpreted cautiously. They also generate a biased impression that HIV was coming into Nepal from India. Recently, the possibility of a two-way flow of HIV across the Indo-Nepal border through injecting and sexual networking have been indicated by serological and behavioural data from a south-eastern cluster of Nepal and a north-eastern district of India. Although similar behavioural networks exist along other segments of the border, serological data are unavailable to assess whether and how extensively this phenomenon has caused the spread of HIV. Collaborative research and interventions covering both sides of the border are desirable to fully understand and address the prospect of HIV epidemics associated with cross-border population mixing.

Phylogenetic analysis of env, gag, and tat genes of HIV type 1 detected among the injecting drug users in West Bengal, India

A recent occurrence of HIV-1 seropositivity among a group of injecting drug users (IDUs) in Darjeeling, a hilly district in northern West Bengal, revealed overall 11.8% HIV seroprevalence. Our study based on env (C2-V3), gag (p24-p7), and tat (exon-1) genomic regions of HIV-1 detected among this population showed that Darjeeling IDU sequences belonged to subtype C. Interestingly, the IDU sequences from Darjeeling were again found to be closer to the C strains from Manipur, a northeastern state in India, which is linked to the Golden Triangle via the Manipur-Myanmar border, rather than the IDU C sequences from Nepal, a neighboring country of India. The outgroup reference strains from different sites of IDU-driven epidemics in the world like Russia, Vietnam, Thailand, and Spain belonged to the nonsubtype C group and formed separate clusters from the subtype C cluster in our analysis. These results indicate a rapid spread of HIV-1 by possible drug trafficking along international boundaries, which might also help in the invasion of HIV-1 among IDUs of Darjeeling through the Manipur-Myanmar border of India.

Molecular epidemiology of HIV Type 1 in Ukraine: birthplace of an epidemic

During the 1990s, HIV-1 spread rapidly through drug networks in Ukraine and from there throughout the former Soviet Union. To examine the origins of this epidemic, the genetics of HIV-1 in Ukraine were studied. Proviral DNA from PBMC was extracted and PCR amplified. Part of pol and nearly full genomes of HIV-1 were sequenced and characterized. The predominant genetic form in 163 strains was subtype A (66%), followed by subtypes B (30%), C (2%), D (1%), and a new AB recombinant form (1%). HIV strains from Kiev were diverse having subtypes A, B, C, and D. In Crimea, Donetsk, Poltava, and Odessa, however, the strains were overwhelmingly subtype A, while in Nikolaev subtype B predominated. After the near simultaneous introduction of subtypes A and B in Ukraine, subtype B remained where it was introduced while subtype A spread widely, creating the fastest growing epidemic in the world.

Background demographics and risk behaviors of injecting drug users in Karachi, Pakistan

OBJECTIVE

To find the prevalence of HIV infection and risk behaviors among injecting drug users (IDUs) in Karachi, Pakistan.

DESIGN

A cross-sectional study of IDUs conducted in Karachi, Pakistan from February through June 1996.

RESULTS

Of the 242 IDUs, 11 (4%) refused HIV testing. One (0.4%; 95% confidence interval (CI) = 0.37-0.48%) was HIV positive. All subjects were male. Over the past 6 months 47% had engaged in receptive needle sharing, 38% had perceived a change in their social network, 22% had had sexual intercourse, of whom only 7% always used condoms, and none had washed their needles with bleach. Younger age (28 vs. 31 years; p = 0.01), younger age at first injection (25 vs. 28 years; p = 0.001), fewer years of schooling (3 vs. 5 years; p = 0.001), lower monthly income (70 dollars vs. 80 dollars; p = 0.03), inhaling fumes of heroin from a foil in the year before injecting (OR = 4.8; CI = 2.2-10.3), injecting first time with heroin (OR = 3.6; CI = 1.2-12.6), having a temporary job (OR = 2.5; CI = 1.2-5.2), and a perceived change in one's social network (OR = 4.4; CI = 2.4-7.9) were all associated with receptive needle sharing. IDUs who knew about HIV spread through contaminated needles were less likely to share (OR = 0.4; CI 0.2-0.8). In the final logistic regression model receptive needle sharing was associated with inhaling of fumes of heroin on a foil in the year prior to injecting (adjusted OR = 5.6; CI = 2.6-12.0), a perceived change in one's social network (adjusted OR = 4.0; CI = 2.2-7.4), and inversely associated with age at first time of injection (beta = -0.07; p = 0.002).

CONCLUSION

Background HIV prevalence was low among IDUs in Karachi despite high-risk behavior in 1996. In order to control HIV transmission among IDUs in Pakistan, continual HIV surveillance with well-coordinated and effective HIV risk reduction, and drug demand reduction programs need to be implemented among drug users.

Molecular epidemiology of HIV-1 infection in a small Brazilian county: usefulness of envelope and polymerase sequences to epidemiologic studies

OBJECTIVE

The AIDS epidemic in Brazil is spreading from the large urban centers to small counties and the innermost parts of the country; however, data on the features of HIV-1 infection in these places are scarce. To study the routes of HIV-1 spread and assess the existence of transmission networks in such a setting, we performed a genetic analysis of viral sequences from the small county of Miracema, Rio de Janeiro State.

METHODS

HIV-1 envelope and polymerase sequences recovered from 63 adult patients (from a cohort of 78 patients) were phylogenetically analyzed.

RESULTS

A polyphyletic pattern ensued. Six clusters of sequences sharing close genetic relatedness were also recovered from 29 (46%) patients. Envelope and polymerase phylogenies yielded essentially the same results.

CONCLUSIONS

The polyphyletic pattern suggests multiple viral introductions in the region. Intracluster cases, including those with no known direct epidemiologic link, probably took part in the same chain of viral transmission. Such a pattern suggests the existence of sexual networks and the emergence of multiple new infections within a relatively short period, a potential molecular marker of high incidence.

Epidemic of HIV coupled with hepatitis C virus among injecting drug users of Himalayan West Bengal, Eastern India, Bordering Nepal, Bhutan, and Bangladesh

A study was conducted in June 2004 to find out the epidemiology of HIV infection among injecting drug users (IDUs) of Darjeeling District of West Bengal, eastern India. The district headquarter, Darjeeling town, also known as "Queen of Hills," is a beautiful spot situated in Himalayan West Bengal that attracts a large number of tourists each year from all over the world. Another unique feature of the district is that it has international boundaries with three countries, Nepal, Bhutan, and Bangladesh. Siliguri, the part of the district on plains, acts as a transit station for these countries as well as to the entire Himalayan region of West Bengal and neighboring state, Sikkim. It is also a transit point to all northeastern states of India: Assam, Arunachal Pradesh, Nagaland, Manipur, Mizoram, Meghalaya, and Tripura. Two hundred twenty-eight study subjects (IDUs) were included in this community-based cross-sectional study from all four subdivisions of the district. Informed consent was obtained, and then personal interviews, followed by blood testing were performed using unlinked anonymous procedure. The study revealed that overall HIV seroprevalence among IDUs was 11.8% (n = 27; 95% confidence interval, 7.9-16.7), whereas seroprevalence of hepatitis C was found to be 47.7% (n = 97). Prevalence of HIV was higher in subjects from hill districts (13.5%) compared with subjects from the plains (9.2%). It also revealed that most IDUs (75.3%) used "brown sugar," an impure form of heroin, as their major addictive substance followed by injection norphine. Sharing of injecting equipment was found to be as high as 67% among IDUs, and sharing of drugs from common ampules was found to be 35.5% of the studied subjects (n = 93). Most subjects (96%) were found to clean their injecting paraphernalia with plain water. Most IDUs (98%) were found to inject intravenously. About 52% of IDUs visited sex workers one or more times within the last 1 year, and 15% of the interviewed subjects (n = 93) reported to suffer from sexually transmitted diseases during the same period. All the IDUs knew about HIV/AIDS. About 69% of the subjects knew that apparently healthy looking person might have HIV infection. HIV was found to be associated significantly with age of the injectors and duration of injecting practices. The study revealed the epidemic of HIV and hepatitis C among IDU populations at this bordering district of West Bengal for the first time that requires urgent intervention at local, national, and international levels.

Evolution of subtype C HIV-1 Env in a slowly progressing Zambian infant

BACKGROUND

Given the high prevalence of mother to child infection, the development of a better understanding of African subtype C HIV-1 transmission and natural evolution is of significant importance. In this study, we genotypically and phenotypically characterized subtype C viruses isolated over a 67-month follow-up period from an in utero-infected Zambian infant. Changes in genotype and phenotype were correlated to alterations of the host humoral immune response.

RESULTS

A comparison of baseline maternal and infant samples indicated that the infant sequences are monophyletic and contain a fraction of the diversity observed in the mother. This finding suggests that selective transmission occurred from mother to child. Peaks in infant HIV-1 Env genetic diversity and divergence were noted at 48 months, but were not correlated with changes in co-receptor usage or syncytia phenotype. Phylogenetic analyses revealed an accumulation of mutations over time, as well as the reappearance of ancestral lineages. In the infant C2-V4 region of Env, neither the median number of putative N-glycosylation sites or median sequence length showed consistent increases over time. The infant possessed neutralizing antibodies at birth, but these decreased in effectiveness or quantity with time. De novo humoral responses were detected in the child after 12 months, and corresponded with an increase in Env diversity.

CONCLUSION

Our study demonstrates a correlation between HIV-1 Env evolution and the humoral immune response. There was an increase in genetic diversification in the infant viral sequences after 12 months, which coincided with increases in neutralizing antibody titers. In addition, episodes of viral growth and successive immune reactions in the first 5-6 years were observed in this slow progressor infant with delayed onset of AIDS. Whether this pattern is typical of slow progressing subtype C HIV-1 infected infant needs to be further substantiated.

HIV in Nepal: is the violent conflict fuelling the epidemic?

Singh and colleagues discuss the HIV epidemic in Nepal, including the local and international response from the health and development community.

Determination of gag and env subtypes of HIV-1 detected among injecting drug users (IDUs) in Manipur, India: evidence for intersubtype recombination

The majority of HIV-1 transmission in Manipur, one of the northeastern states of India, is through the sharing of needles and syringes among the injecting drug users (IDUs). A total of 28 HIV seropositive samples were used to determine the HIV-1 subtypes with respect to both gag and envelope genes. The specific regions within gag and envelope genes were amplified from PBMC DNA by nested PCR using appropriate primers. These amplicons were used in heteroduplex mobility assay followed by DNA sequencing. Phylogenetic analysis of the nucleotide sequences of respective regions showed that 89% of samples (25/28) were infected with subtype C with respect to both gag and envelope genes; however, 11% of the samples (3/28) showed subtype discordance with respect to the envelope (C2-V3) and gag (p24-p7) genomic regions. Simplot analysis of the discordant samples showed the presence of intersubtype recombination between subtype C and Thai B; two samples were found to be subtype C in envelope but Thai B in gag, whereas, one sample was found to be subtype Thai B in envelope and 'C' in gag region.

Prevalence and risk factors of chlamydia and gonorrhea among rural Nepali women

OBJECTIVES

The epidemiology of sexually transmitted infections (STI) in rural, developing world populations is poorly understood. We estimated the prevalence and risk factors of Neisseria gonorrhoeae and Chlamydia trachomatis in a female population in rural Nepal.

METHODS

We conducted a cross sectional study in a sample of 1177 postpartum women participating in a micronutrient supplementation trial in Nepal. Urine samples were collected to test for the two infections using the ligase chain reaction (LCR).

RESULTS

C trachomatis was detected in 1.0% (95% confidence intervals (CI): 0.4 to 1.5) and N gonorrhoeae in 2.3% (95% CI: 1.2 to 3.4) of women. None of the women tested positive for both. Self report of all three symptoms of lower abdominal pain, pain and burning on urination, and vaginal discharge was associated with the presence of gonorrhoea (odds ratio (OR): 12.1, 95% CI: 1.3 to 115.0). Neonatal eye discharge was associated with maternal gonococcal infection (OR = 5.2, 95% CI: 1.1 to 24.9). Incidence of low birth weight was not related to these maternal infections, but very preterm delivery (<32 weeks) was higher among women positive for gonorrhoea (OR = 4.7, 95% CI: 1.0 to 22.0). In a multivariable analysis, low body mass index (<18.5) and cattle ownership were associated with gonorrhoea (p <0.05), whereas woman's literacy was associated with chlamydia (p = 0.06).

CONCLUSION

We found the rates of N gonorrhoeae and C trachomatis to be low among women in this rural population of Nepal.

Dichotomy in cross-clade reactivity and neutralization by HIV-1 sera: Implications for active and passive immunotherapy

The identification of broadly reactive and cross-clade neutralizing antibodies will facilitate the development of a more universally effective vaccine for human immunodeficiency virus (HIV). Antibodies in sera from individuals infected with Clade B HIV bind native primary viral isolates, and virus binding correlates with neutralization and stable clinical disease. In this study, we quantified cross-clade antibody reactivity and neutralization by Clades B and C sera. Primary viral isolates were captured by serum IgG bound to anti-human IgG and quantitated as p24 released by lysis of captured virus. Neutralization was determined using PHA-stimulated PBMC. Clade B antibodies reacted more frequently with Clade B R5 virus, but positive sera captured quantitatively more X4 virus than R5 and R5X4 virus. Clade B sera reacted less frequently and captured less Clade C virus than Clade B virus. Antibodies in Clade C sera captured Clades B and C isolates with equal frequency and quantity. There was no difference in neutralization of Clade B virus by either group of sera; however, Clade C sera neutralized Clade C virus, whereas Clade B sera were ineffective against Clade C virus. Thus, there are distinct differences in cross-clade reactivity of and neutralization by antibodies induced in response to Clade C infection compared to Clade B infection. Understanding antibody responses to native virions after Clade C infection and cross clade antibody behavior has implications for understanding pathogenesis and vaccine development.

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.

HIV-1 infection among injection and ex-injection drug users from Rio de Janeiro, Brazil: prevalence, estimated incidence and genetic diversity

BACKGROUND AND OBJECTIVES

Due to their behavioral conditions and vulnerability, injection drug users (IDUs) are prone to multiple simultaneous or sequential infections with distinct HIV-1 subtypes and variants, making them a key population for molecular epidemiology surveillance. In the present study, we evaluated HIV-1 infection seroprevalence, genetic diversity and estimated incidence among IDUs and ex-injection drug users (ex-IDUs) from Rio de Janeiro, Brazil.

STUDY DESIGN

Six hundred and eight IDUs and ex-IDUs, recruited between 1999 and 2001, were interviewed and agreed to donate 30 ml of blood. The serologic status for HIV infection was determined by two ELISAs and confirmed by IFA. CD4+ T-cell percentages were assessed by flow cytometry. HIV-1 positive samples were submitted to viral load quantification. DNA samples were PCR amplified and HIV-1 subtypes were determined using env and gag HMA.

RESULTS AND CONCLUSIONS

Forty-eight (7.89%) individuals were seropositive for HIV-1 infection. The seroincidence of HIV-1 infection was estimated as 0.76%. HIV-1 env and gag subtyping identified 29 (69%) samples as belonging to subtype B, 7 (16.7%) to subtype F, and 6 (14.3%) discordant env/gag genomes infections, indicating the circulation of recombinant viruses in this population.

Timing and reconstruction of the most recent common ancestor of the subtype C clade of human immunodeficiency virus type 1

Human immunodeficiency virus type 1 (HIV-1) subtype C is responsible for more than 55% of HIV-1 infections worldwide. When this subtype first emerged is unknown. We have analyzed all available gag (p17 and p24) and env (C2-V3) subtype C sequences with known sampling dates, which ranged from 1983 to 2000. The majority of these sequences come from the Karonga District in Malawi and include some of the earliest known subtype C sequences. Linear regression analyses of sequence divergence estimates (with four different approaches) were plotted against sample year to estimate the year in which there was zero divergence from the reconstructed ancestral sequence. Here we suggest that the most recent common ancestor of subtype C appeared in the mid- to late 1960s. Sensitivity analyses, by which possible biases due to oversampling from one district were explored, gave very similar estimates.

HIV-1 subtype distribution and the problem of drug resistance

Genetic diversity is a hallmark of HIV-1 infection with regard to the expansion of distinct viral subtypes (clades A, B, C, D, E, F, G, K, and O) in different geographical regions. Here, we discuss the issues of HIV-1 sensitivity to antiretroviral drugs and drug resistance in the context of HIV-1 subtype diversity. Virtually all available evidence suggests that all subtypes of HIV display similar sensitivity to antiviral drugs, but viruses from some subtypes or geographical regions may occasionally have a greater propensity to develop resistance against certain drugs than other viral variants. In some situations, the types of mutations associated with resistance may vary, as a result of subtle differences among subtypes with regard to the genetic code. This consideration notwithstanding, drug resistance is unlikely to become a more serious issue in developing than developed countries, and there is an urgency to make anti-HIV drugs available to all who are in need.

Astrocyte specific viral strains in HIV dementia

We molecularly characterized human immunodeficiency virus type 1 (HIV-1) present in pure populations of astrocytes, macrophages, and multinucleated giant cells isolated using laser capture microdissection from brain tissue of two patients who died with HIV-associated dementia. The V3 region of the HIV-1 envelope (env) gene was amplified from the pure-cell populations, and multiple clones were sequenced. In both patients, the V3 env sequences were distinct in astrocytes compared with neighboring macrophages or multinucleated giant cells and were characteristic of CCR5-using (R5) HIV-1. These results demonstrate cell-specific compartmentalization of distinct R5-like viral strains in the central nervous system microenvironment.

Drug-related HIV in South and South-East Asia

While there has been significant advancement in the knowledge on effective HIV prevention methods among injecting drug users (IDUs), and their demonstrated success, in particular the impact of availability and use of clean injecting equipment on reducing HIV prevalence among IDUs, in Australia, the US and the UK, progress made in implementation of actual interventions focused on IDUs in South and South-East Asia is less than satisfactory. This paper examines some of the critical issues related to the context and causes of inadequate drug-related HIV prevention programmes in Asia. It also raises questions relating to evidence-based interventions to be scaled up in the region, including the need for sufficient resources anda conducive policy and legalenvironment.

Adherence to methadone is associated with a lower level of HIV-related risk behaviors in drug users

There have been limited studies on the potential role of methadone treatment in HIV prevention in Asia. Over an 8-week period, we assessed the profiles of drug-taking and HIV risk behaviors, and tried to identify their relationships with methadone adherence in 690 clients who attended Hong Kong's methadone treatment program. In the preceding month, 71% of respondents reported using drugs and two-thirds of those respondents who had injected drugs at some time in their lives injected then. Infrequent clients who attended methadone clinics <2 times in the previous week were twice more likely to have injected drugs in the last month and six times more likely to have >5 injections in the last week than frequent clinic attendees. Also, clients taking <60 mg methadone daily were twice more likely to have >5 injections in the last week than those taking > or = 60 mg methadone. The findings called for further studies on harm reduction programs for HIV prevention among drug users in Asian countries.

Phylogenetic and phenotypic analysis of HIV type 1 env gp120 in cases of subtype C mother-to-child transmission

Human immunodeficiency virus type 1 (HIV-1) subtype C constitutes a majority of the newly transmitted cases of HIV-1 in many developing countries. There is growing evidence suggesting that subtype C viruses may display characteristics that make them distinct from subtype B and other subtypes, and such differences may affect its transmission and pathogenesis in infected individuals. In this study, HIV-1 sequences from the C2-V4 region of the envelope gene were analyzed from four infected mother-infant pairs (MIPs) after perinatal transmission in Zambia. We found that all viral isolates from four Zambian MIPs were of the subtype C HIV-1 subgroup. All tested isolates were macrophage tropic and did not infect any tested T cell lines or form syncytia in vitro. In addition, the isolates appear to use exclusively the CCR5 coreceptor. Phylogenetic analyses clearly indicated two contrasting phylogenetic transmission patterns for the four MIPs analyzed in the present study. Three cases displayed a pattern of selective transmission of a single or a few variants, and one case was found to transmit multiple maternal HIV-1 variants to her infant. The differences in the mode and timing of transmission may account for the observed transmission pattern among four MIPs.

HIV type 1 subtypes circulating in eastern and northeastern regions of India

Genetic subtyping has been a powerful tool in tracking the global spread of HIV. To determine the HIV-1 subtypes circulating in eastern and northeastern regions of India blood samples were collected from female sex workers in Calcutta and intravenous drug users (IDUs) in Manipur. Fifty-four samples from Calcutta and 25 samples from Manipur were analyzed for HIV-1 subtyping by heteroduplex mobility assay (HMA). Twenty-six samples from these regions were sequenced. HMA and sequencing of the samples from these regions revealed subtype C as the major subtype, circulating within both eastern and northeastern regions. In Manipur, subtype ThaiB was also detected as the second major subtype. Some of the IDUs from Manipur were found to be dual infected with subtype C and ThaiB.

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.

Human immunodeficiency virus type 1 env sequences from Calcutta in eastern India: identification of features that distinguish subtype C sequences in India from other subtype C sequences

India is experiencing a rapid spread of human immunodeficiency virus type 1 (HIV-1), primarily through heterosexual transmission of subtype C viruses. To delineate the molecular features of HIV-1 circulating in India, we sequenced the V3-V4 region of viral env from 21 individuals attending an HIV clinic in Calcutta, the most populous city in the eastern part of the country, and analyzed these and the other Indian sequences in the HIV database. Twenty individuals were infected with viruses having a subtype C env, and one had viruses with a subtype A env. Analyses of 192 subtype C sequences that included one sequence for each subject from this study and from the HIV database revealed that almost all sequences from India, along with a small number from other countries, form a phylogenetically distinct lineage within subtype C, which we designate C(IN). Overall, C(IN) lineage sequences were more closely related to each other (level of diversity, 10.2%) than to subtype C sequences from Botswana, Burundi, South Africa, Tanzania, and Zimbabwe (range, 15.3 to 20.7%). Of the three positions identified as signature amino acid substitution sites for C(IN) sequences (K340E, K350A, and G429E), 56% of the C(IN) sequences contained all three amino acids while 87% of the sequences contained at least two of these substitutions. Among the non-C(IN) sequences, all three amino acids were present in 2%, while 22% contained two or more of these amino acids. These results suggest that much of the current Indian epidemic is descended from a single introduction into the country. Identification of conserved signature amino acid positions could assist epidemiologic tracking and has implications for the development of a vaccine against subtype C HIV-1 in India.

Measuring the impact of needle exchange programs among injecting drug users through the National Behavioural Surveillance in Bangladesh

Bangladesh is a low HIV prevalence country, with buprenorphine injectors having the highest prevalence of HIV at 2.5% as of 1999. Using National HIV Behavioral Surveillance data, the impact of a needle exchange program (NEP) on sharing behavior among injecting drug users in two cities was measured. Results showed positive changes that varied with the different settings. Those who reported utilizing the NEP were compared with those who did not. Differences in Dhaka were significant for the average proportion of needles shared but not for the proportion of men who ever shared in the last week. In Rajshahi, where professional injectors were the norm, the impact of an NEP was greater and affected both the proportion of needles shared as well as the proportion of men never sharing. Behavioral surveillance methods have the potential to measure intervention impact through comparative analysis in certain settings.

Survey of reverse transcriptase from the heterosexual epidemic of human immunodeficiency virus type 1 CRF01_AE in Thailand from 1990 to 2000

Genetic diversity of the HIV-1 envelope gene has shown a steady increase over time in the Thai and other regional epidemics. A serial survey of subtype CRF01_AE polymerase gene (RT) diversity in Thailand was performed, using 48 novel and 15 reported sequences covering the period 1990--2000. These sequences were gathered from individuals whose sole risk factor for infection was heterosexual contact. By contrast to envelope, diversity was low and, despite a 40% increase early in the epidemic, has remained static since 1996. These results indicate that epidemic HIV-1 may be constrained within defined limits of genetic diversity at least in some genomic regions.

A recent outbreak of human immunodeficiency virus type 1 infection in southern China was initiated by two highly homogeneous, geographically separated strains, circulating recombinant form AE and a novel BC recombinant

New outbreaks of human immunodeficiency virus type 1 (HIV-1) among injecting drug users (IDUs) are spreading in China along heroin trafficking routes. Recently, two separate HIV-1 epidemics among IDUs were reported in Guangxi, Southern China, where partial sequencing of the env gene showed subtype C and circulating recombinant form (CRF) AE. We evaluated five virtually full-length HIV-1 genome sequences from IDUs in Guangxi to determine the genetic diversity and the presence of intersubtype recombinants. Sequence analysis showed two geographically separated, highly homogeneous HIV-1 strains. B/C intersubtype recombinants were found in three IDUs from Baise City, in a mountainous region near the Yunnan-Guangxi border. These were mostly subtype C, with portions of the capsid and reverse transcriptase (RT) genes from subtype B. The subtype B portion of the capsid was located in the N-terminal domain, which has been shown to influence virus core maturation, virus infectivity, and binding to cyclophilin A, whereas the subtype B portion of RT was located in the palm subdomain, which is the active site of the enzyme. These BC recombinants differed from a BC recombinant found in Xinjiang Province in northwestern China. CRF AE strains were found in IDUs from Nanning, the capital of Guangxi, and in IDUs from Pingxiang City near the China-Vietnam border. The AE and BC recombinants were both remarkable for their low interpatient diversity, less than 1% for the full genome. Rapid spread of HIV-1 among IDUs may foster the emergence of highly homogeneous strains, including novel recombinants in regions with multiple subtypes.

Emergence of new forms of human immunodeficiency virus type 1 intersubtype recombinants in central Myanmar

We have previously shown that HIV-1 env subtypes B' (a Thai-B cluster within subtype B) and E (CRF01_AE) are distributed in Yangon, the capital city of Myanmar. However, HIV strains from the rest of country have not yet been genetically characterized. In the present study, we determined env (C2/V3) and gag (p17) subtypes of 25 specimens from central Myanmar (Mandalay). Phylogenetic analyses identified 5 subtype C (20%), in addition to 10 CRF01_AE (40%) and 4 subtype B' (16%). Interestingly, the remaining six specimens (24%) showed discordance between gag and env subtypes; three gag subtype B'/env subtype C, one gag subtype B'/env subtype E, one gag subtype C/env subtype B', and one gag subtype C/env subtype E. These discordant specimens were found frequently among injecting drug users (4 of 12, 33%) and female commercial sex workers (2 of 8, 25%) engaging in high-risk behaviors. The recombinant nature of these HIV-1 strains was verified in three specimens, indicating the presence of new forms of HIV-1 intersubtype C/B' and C/B'/E recombinants with different recombination breakpoints. The data suggest that multiple subtypes of B', C, and CRF01_AE are cocirculating in central Myanmar, leading to the evolution of new forms of intersubtype recombinants among the risk populations exhibiting one of the highest HIV infection rates in the region.

T-helper-cell proliferative responses to whole-killed human immunodeficiency virus type 1 (HIV-1) and p24 antigens of different clades in HIV-1-infected subjects vaccinated with HIV-1 immunogen (Remune)

The discovery of multiple subtypes of human immunodeficiency virus type 1 (HIV-1) worldwide has created new challenges for the development of both therapeutic and preventive AIDS vaccines. We examined T-helper proliferative responses to HIV-1 clade A, B, C, G, and E whole-killed virus and to HIV-1 clade G and B core (p24) antigens in HIV-1-infected subjects taking potent antiviral drugs who received HIV immunogen (Remune) therapeutic vaccination. Subjects who were immunized mounted strong proliferative responses to both whole virus and core antigens of the different clades. These results suggest that a whole-killed immunogen may have broad applications as a therapeutic as well as a preventive vaccine in the current multiclade HIV-1 pandemic.