Simplified strategy for detection of recombinant human immunodeficiency virus type 1 group M isolates by gag/env heteroduplex mobility assay. Study Group on Heterogeneity of HIV Epidemics in African Cities

Identification of a new circulating recombinant form of human immunodeficiency virus type 1, CRF124_cpx involving subtypes A, G, H, and CRF27_cpx in Angola

Angola, located in Central Africa, has around 320,000 (270,000–380,000) people living with human immunodeficiency virus (HIV)/AIDS, equivalent to 1% of the country’s population at the end of 2021. A previous study conducted in 2012, using Angolan samples collected between 2008 and 2010 revealed a high prevalence of HIV-1 recombinants, around 42% of sequences, with 21% showing the same UH profile in partial pol region which were grouped into a monophyletic cluster with high bootstrap support. Thus, the objective of the present work was to obtain complete genomes of those sequences and characterize them, aiming at a description of a new circulating recombinant form (CRF). Whole blood from nine HIV-1 UH pol-infected individuals had their genomic DNA extracted, and nested PCR was used to amplify seven overlapping fragments targeting the full-length HIV-1 genome. The final classification was based on maximum likelihood trees, and recombination analyses were performed using a bootscan from the Simplot program. BLAST and Los Alamos Database inspections were used to search other similar H-like pol sequences. Complete genome amplification was possible for three samples, partial genomes were obtained for the other three, and only pol was available for the remaining three sequences. Bootscan analysis of the two whole-genome and three partial genome sequences retrieved from people living with HIV/AIDS (PLHIVA) without epidemiological linkage showed the same complex recombination profile involving HIV-1 subtypes A/G/H/CRF27_cpx, with a total of six recombinant breakpoints, aiming to classify a new HIV-1 CRF124_cpx. We found no other full-length HIV-1 genomes with the same mosaic profile; however, we identified 33 partial pol sequences, mainly sampled from Angola between 2001 to 2019, with the same H-like profile. Bayesian analysis of H and H-like pol sequences indicates that CRF124_cpx probably originated in Angola at mid-1970s, indicating that this CRF has been circulating in the country for a long time. In summary, our study describes a new CRF circulating principally in Angola and highlights the importance of continuing molecular surveillance studies, especially in countries with high molecular diversity of HIV.

HIV-1 drug resistance and genetic diversity in a cohort of people with HIV-1 in Nigeria

OBJECTIVE

This study was designed to provide information on the genetic diversity of HIV-1 and drug resistance mutations in Nigeria, as there is limited understanding of variants circulating in the country.

METHODS

We used an advanced next-generation sequencing platform, Primer ID, to: investigate the presence of high and low abundance drug resistance mutations; characterize preexisting Integrase Strand Transfer Inhibitor (INSTI) mutations in antiretroviral therapy (ART)-experienced but dolutegravir-naive individuals; detect recent HIV-1 infections and characterize subtype diversity from a cohort of people with HIV-1 (PWH).

RESULTS

HIV-1 subtype analysis revealed the predominance of CRF02_AG and subtype G in our study population. At detection sensitivity of 30% abundance, drug resistance mutations (DRMs) were identified in 3% of samples. At a sensitivity level of 10%, DRMs were identified in 27.3% of samples. We did not detect any major INSTI mutation associated with dolutegravir-resistance. Only one recent infection was detected in our study population.

CONCLUSION

Our study suggests that dolutegravir-containing antiretroviral regimens will be effective in Nigeria. Our study also further emphasizes the high genetic diversity of HIV-1 in Nigeria and that CRF02_AG and subtype G are the dominant circulating forms of HIV-1 in Nigeria. These two circulating forms of the virus are largely driving the epidemic in the country.

Phylogeny of partial gag, pol and env genes show predominance of HIV-1G and CRF02_AG with emerging recombinants in south-eastern Nigeria

Human Immunodeficiency Virus is characterized by high degree of genetic diversity with marked differences in its geographic distribution even within a country. This study was designed to identify the strains of HIV-1 circulating among infected individuals in southeastern parts of Nigeria. Genomic DNA was extracted from blood samples of 30 HIV-1 infected individuals from Anambra, Delta and Imo states of southeastern Nigeria. Portions of the genome corresponding to entire p24 gag, entire protease and C2-V3 env genes were amplified by nested PCR, sequenced using Sanger's method and phylogenetically analysed. Out of the 30 samples sequenced, 17, 28 and 14 readable sequences were obtained for gag, pol and env regions respectively. The most prevalent subtypes were CRF02_AG (41.2% in gag, 57.1% in pol protease and 50.0% in env) and G (29.4% in gag, 35.7% in pol protease and 35.7% in env). Other subtypes identified include A (17.7% in gag, 7.1% in env) and J (7.1% in env). Also 2 sequences each in gag (11.8%) and pol protease (7.1%) regions were unclassified but preliminary analysis showed they are recombinants. Furthermore, 71.4% of the isolates with sequences in the 3 regions and 26.7% of those with sequences in 2 genomic regions were recombinant forms. CRF02_AG and subtype G are the predominant HIV-1 strains circulating among infected individuals in southeastern Nigeria. Preliminary analysis results of unclassified sequences suggest that they are new recombinants.

HIV-1 transmission networks in high risk fishing communities on the shores of Lake Victoria in Uganda: A phylogenetic and epidemiological approach

BACKGROUND

Fishing communities around Lake Victoria in sub-Saharan Africa have been characterised as a population at high risk of HIV-infection.

METHODS

Using data from a cohort of HIV-positive individuals aged 13-49 years, enrolled from 5 fishing communities on Lake Victoria between 2009-2011, we sought to identify factors contributing to the epidemic and to understand the underlying structure of HIV transmission networks. Clinical and socio-demographic data were combined with HIV-1 phylogenetic analyses. HIV-1 gag-p24 and env-gp-41 sub-genomic fragments were amplified and sequenced from 283 HIV-1-infected participants. Phylogenetic clusters with ≥2 highly related sequences were defined as transmission clusters. Logistic regression models were used to determine factors associated with clustering.

RESULTS

Altogether, 24% (n = 67/283) of HIV positive individuals with sequences fell within 34 phylogenetically distinct clusters in at least one gene region (either gag or env). Of these, 83% occurred either within households or within community; 8/34 (24%) occurred within household partnerships, and 20/34 (59%) within community. 7/12 couples (58%) within households clustered together. Individuals in clusters with potential recent transmission (11/34) were more likely to be younger 71% (15/21) versus 46% (21/46) in un-clustered individuals and had recently become resident in the community 67% (14/21) vs 48% (22/46). Four of 11 (36%) potential transmission clusters included incident-incident transmissions. Independently, clustering was less likely in HIV subtype D (adjusted Odds Ratio, aOR = 0.51 [95% CI 0.26-1.00]) than A and more likely in those living with an HIV-infected individual in the household (aOR = 6.30 [95% CI 3.40-11.68]).

CONCLUSIONS

A large proportion of HIV sexual transmissions occur within house-holds and within communities even in this key mobile population. The findings suggest localized HIV transmissions and hence a potential benefit for the test and treat approach even at a community level, coupled with intensified HIV counselling to identify early infections.

Evolutionary Dynamics of Tat in HIV-1 Subtypes B and C

Evolutionary characteristics of HIV-1 have mostly studied focusing its structural genes, Gag, Pol and Env. However, regarding the process of HIV-1's evolution, few studies emphasize on genetic changes in regulatory proteins. Here we investigate the evolutionary dynamics of HIV-1, targeting one of its important regulatory proteins, Tat. We performed a phylogenetic analysis and employed a Bayesian coalescent-based approach using the BEAST package to investigate the evolutionary changes in Tat over time in the process of HIV-1 evolution. HIV-1 sequences of subtypes B and C from different parts of the world were obtained from the Los Alamos database. The mean estimated nucleotide substitution rates for Tat in HIV-1 subtypes B and C were 1.53x10^-3 (95% highest probability density- HPD Interval: 1.09 x10^-3 to 2.08x10^-3) and 2.14x10^-3 (95% HPD Interval: 1.35 x10^-3 to 2.91x10^-3) per site per year, respectively, which is relatively low compared to structural proteins. The median times of the most recent common ancestors (tMRCA) were estimated to be around 1933 (95% HPD, 1907–1952) and 1956 (95% HPD, 1934–1970) for subtypes B and C, respectively. Our analysis shows that subtype C appeared in the global population two decades after the introduction of subtype B. A Gaussian Markov random field (GMRF) skyride coalescent analysis demonstrates that the early expansion rate of subtype B was quite high, rapidly progressing during the 1960s and 1970s to the early 1990s, after which the rate increased up to the 2010s. In contrast, HIV-1 subtype C exhibited a relatively slow occurrence rate until the late 1980s when there was a sharp increase up to the end of 1990s; thereafter, the rate of occurrence gradually slowed. Our study highlights the importance of examining the internal/regulatory genes of HIV-1 to understand its complete evolutionary dynamics. The study results will therefore contribute to better understanding of HIV-1 evolution.

An effective tool for identifying HIV-1 subtypes B, C, CRF01_AE, their recombinant forms, and dual infections in Southeast Asia by the multi-region subtype specific PCR (MSSP) assay

The RV144 Thai vaccine trial has been the only vaccine study to show efficacy in preventing HIV infection. Ongoing molecular surveillance of HIV-1 in Southeast Asia is vital for vaccine development and evaluation. In this study a novel tool, the multi-region subtype specific PCR (MSSP) assay, that was able to identify subtypes B, C, CRF01_AE for Thailand, other Southeast Asian countries, India and China is described. The MSSP assay is based on a nested PCR strategy and amplifies eight short regions distributed along the HIV-1 genome using subtype-specific primers. A panel of 41 clinical DNA samples obtained primarily from opiate users in northern Thailand was used to test the assay performance. The MSSP assay provided 73-100% sensitivity and 100% specificity for the three subtypes in each genome region. The assay was then field-tested on 337 sera from HIV infected northern Thai drug users collected between 1999 and 2002. Subtype distribution was CRF01_AE 77.4% (n=261), subtype B 3.3% (n=11), CRF01_AE/B recombinant 12.2% (n=41), CRF01_AE/C recombinant 0.6% (n=2), and non-typeable 6.5% (n=22). The MSSP assay is a simple, cost-effective, and accurate genotyping tool for laboratory settings with limited resources and is sensitive enough to capture the recombinant genomes and dual infections.

Use of the heteroduplex mobility assay and cell sorting to select genome sequences of the CCR5 gene in HEK 293T cells edited by transcription activator-like effector nucleases

Engineered nucleases such as zinc finger nucleases (ZFN) and transcription activator-like effector nucleases (TALEN) are one of the most promising tools for modifying genomes. These site-specific enzymes cause double-strand breaks that allow gene disruption or gene insertion, thereby facilitating genetic manipulation. The major problem associated with this approach is the labor-intensive procedures required to screen and confirm the cellular modification by nucleases. In this work, we produced a TALEN that targets the human CCR5 gene and developed a heteroduplex mobility assay for HEK 293T cells to select positive colonies for sequencing. This approach provides a useful tool for the quick detection and easy assessment of nuclease activity.

Inferring viral population structures using heteroduplex mobility and DNA sequence analyses

Heteroduplex mobility (HMA) and tracking assays (HTA) are used to assess genetic relationships between DNA molecules. While distinguishing relationships between clonal or nearly clonal molecules is relatively straightforward, inferring population structures is more complex. To address this issue, HIV-1 quasispecies with varying levels of diversity were studied using both HTA and DNA sequencing. Viral diversity estimates and the temporal features of virus evolution were found to be generally concordant between HTA and DNA sequencing. In addition, the distribution of pairwise differences and the rates of virus divergence were similar between the two methods. These findings support the use of HTA to characterize variant populations of DNA and strengthen previous inferences concerning the evolution of HIV-1 over the course of infection.

Higher cross-subtype IFN-γ ELISpot responses to Gag and Nef peptides in Brazilian HIV-1 subtype B- and F1- than in C-infected subjects

HIV-1 diversity has been considered a huge challenge for the HIV-1 vaccine development. To overcome it, immunogens based on centralized sequences, as consensus, have been tested. In Brazil, the co-circulation of three subtypes offers a suitable scenario to test T cell cross-subtype responses to consensus sequences. Furthermore, we included peptides based on closest viral isolates (CVI) from each subtype analyzed to compare with T cell responses detected against the consensus sequences. The study included 32 subjects infected with HIV-1 subtype B (n=13),C (n=11), and F1 (n=8). Gag and Nef-specific T cell responses were evaluated by IFN-γ-ELISpot assay. Peptides based on CVI sequences were similar to consensus in both reducing genetic distance and detecting T cell responses. A high cross-subtype response between B and F1 in both regions was observed in HIV-1 subtype B and F1-infected subjects. We also found no significant difference in responses to subtype B and C consensus peptides among subtype B-infected subjects. In contrast, the magnitude of T cell responses to consensus C peptides in the Gag region was higher than to consensus B peptides among HIV-1 subtype C-infected subjects. Regarding Nef, subtype C-infected subjects showed higher values to consensus C than to consensus F1 peptides. Moreover, subtype F1-infected subjects presented lower responses to subtype C peptides than to subtype F1 and B. A similar level of responses was detected with group M based peptides in subtype B and F1 infected subjects. However, among subtype C infected subjects, this set of peptides detected lower levels of response than consensus C. Overall, the level of cross-subtype response between subtypes B and F1 was higher than between subtype C and B or C and F1. Our data suggests that the barrier of genetic diversity in HIV-1 group M for vaccine design may be dependent on the subtypes involved.

A gp41-based heteroduplex mobility assay provides rapid and accurate assessment of intrasubtype epidemiological linkage in HIV type 1 heterosexual transmission Pairs

A critical step in HIV-1 transmission studies is the rapid and accurate identification of epidemiologically linked transmission pairs. To date, this has been accomplished by comparison of polymerase chain reaction (PCR)-amplified nucleotide sequences from potential transmission pairs, which can be cost-prohibitive for use in resource-limited settings. Here we describe a rapid, cost-effective approach to determine transmission linkage based on the heteroduplex mobility assay (HMA), and validate this approach by comparison to nucleotide sequencing. A total of 102 HIV-1-infected Zambian and Rwandan couples, with known linkage, were analyzed by gp41-HMA. A 400-base pair fragment within the envelope gp41 region of the HIV proviral genome was PCR amplified and HMA was applied to both partners' amplicons separately (autologous) and as a mixture (heterologous). If the diversity between gp41 sequences was low (<5%), a homoduplex was observed upon gel electrophoresis and the transmission was characterized as having occurred between partners (linked). If a new heteroduplex formed, within the heterologous migration, the transmission was determined to be unlinked. Initial blind validation of gp-41 HMA demonstrated 90% concordance between HMA and sequencing with 100% concordance in the case of linked transmissions. Following validation, 25 newly infected partners in Kigali and 12 in Lusaka were evaluated prospectively using both HMA and nucleotide sequences. Concordant results were obtained in all but one case (97.3%). The gp41-HMA technique is a reliable and feasible tool to detect linked transmissions in the field. All identified unlinked results should be confirmed by sequence analyses.

Immune and viral correlates of "secondary viral control" after treatment interruption in chronically HIV-1 infected patients

Upon interruption of antiretroviral therapy, HIV-infected patients usually show viral load rebound to pre-treatment levels. Four patients, hereafter referred to as secondary controllers (SC), were identified who initiated therapy during chronic infection and, after stopping treatment, could control virus replication at undetectable levels for more than six months. In the present study we set out to unravel possible viral and immune parameters or mechanisms of this phenomenon by comparing secondary controllers with elite controllers and non-controllers, including patients under HAART. As candidate correlates of protection, virus growth kinetics, levels of intracellular viral markers, several aspects of HIV-specific CD4+ and CD8+ T cell function and HIV neutralizing antibodies were investigated. As expected all intracellular viral markers were lower in aviremic as compared to viremic subjects, but in addition both elite and secondary controllers had lower levels of viral unspliced RNA in PBMC as compared to patients on HAART. Ex vivo cultivation of the virus from CD4+ T cells of SC consistently failed in one patient and showed delayed kinetics in the three others. Formal in vitro replication studies of these three viruses showed low to absent growth in two cases and a virus with normal fitness in the third case. T cell responses toward HIV peptides, evaluated in IFN-γ ELISPOT, revealed no significant differences in breadth, magnitude or avidity between SC and all other patient groups. Neither was there a difference in polyfunctionality of CD4+ or CD8+ T cells, as evaluated with intracellular cytokine staining. However, secondary and elite controllers showed higher proliferative responses to Gag and Pol peptides. SC also showed the highest level of autologous neutralizing antibodies. These data suggest that higher T cell proliferative responses and lower replication kinetics might be instrumental in secondary viral control in the absence of treatment.

Mortality of HIV-infected and uninfected children in a longitudinal cohort in rural south-west Uganda during 8 years of follow-up

OBJECTIVES

To determine the impact of HIV on child mortality and explore potential risk factors for mortality among HIV-infected and HIV-exposed uninfected children in a longitudinal cohort in rural Uganda.

METHODS

From July 2002 to March 2010, HIV-infected and HIV-exposed uninfected children aged 6 weeks-13 years were enrolled in an open population-based clinical cohort. Antiretroviral therapy (ART) was introduced in 2005. Clinical and laboratory data were collected every 3 months. Person-years at risk were calculated from time of enrolment until earliest date of ART initiation, death or last visit. Cox regression was used to estimate hazard ratios (HR) for mortality.

RESULTS

Eighty-nine (30.2%) HIV-infected and 206 (69.8%) HIV-exposed but uninfected children were enrolled. Twenty-one children died. The mortality rate was six times higher in ART-naive HIV-infected children than in HIV-exposed but uninfected children (HR = 6.4, 95% CI = 2.4-16.6). Among HIV-infected children, mortality was highest in those aged <2 years. Decreasing weight-for-age Z (WAZ) score was the strongest risk factor for mortality among HIV-infected children (HR for unit decrease in WAZ = 2.6, 95% CI = 1.6-4.1). Thirty-five children (aged 7 months-15.6 years; median, 5.4 years) started ART.

CONCLUSIONS

Mortality among HIV-infected children was highest among those aged <2 years. Intensified efforts to prevent mother-to-child transmission of HIV and ensure early HIV diagnosis and treatment are required to decrease child mortality caused by HIV in rural Africa.

HIV type 1 subtype distribution, multiple infections, sexual networks, and partnership histories in female sex workers in Kampala, Uganda

We investigated for the first time the subtype distribution, prevalence of multiple HIV-1 infections, sexual networks, and partnership histories in a cohort of women engaged in high-risk sexual behavior such as female sex workers (FSWs) and women employed in entertainment facilities. Viral RNA was extracted from blood samples collected from 324 HIV-1-positive women; the gp-41 and pol-IN genes were directly sequenced. Women found to have closely related viruses and those with recombinant viruses were further analyzed in the pol-IN gene by clonal sequencing to determine HIV-1 multiple infections. Individual partnership histories were used to provide information on when sex work was undertaken and where. Subtyping in both gp-41 and pol-IN was successfully done in 210/324 (64.8%) women. Subtype distribution in these two genes was 54.3% (n=114) A/A, 2.9% (n=6) C/C, 24.3% (n=51) D/D, 11.9% (n=25) A/D, 4.8% (n=10) D/A, 0.5% (n=1) C/A, 1.0% (n=2) B/A, and 0.5% (n=1) B/D. Sexual networks were identified in six pairs and one triplet of women with closely related subtype A viruses. Partnership histories showed that women having phylogenetically similar viruses had worked in the same localities. Five cases of multiple infections were confirmed: four dual infections and one triple infection. In this first molecular epidemiology study among FSWs in Kampala, subtype A was the predominant subtype. About 9% of a subgroup had multiple infections. Partnership histories and multiple infections observed in this population suggest sexual mixing of the FSWs and their clients confirming their high-risk characteristics.

Genetic Characterization of HIV-1 Strains Among the Injecting Drug Users in Nagaland, India

Global HIV-1 surveillance has led to the detection of its new recombinant forms. This study was carried out for the first time to elucidate the genetic characterization and evolutionary relationship of HIV-1 strains among injecting drug users of Nagaland, northeastern India. A total of 156 injecting drug users participated in this study voluntarily. Among them 18 were seropositive for HIV-1 (11.5%).The Heteroduplex Mobility Assay (HMA) of HIV-1 based on p24-p7 region of gag gene and C2-V3 region of env gene revealed 11 samples to be subtype C (gag/env), 1 sample as subtype B (gag/env) and 6 samples to be recombinants between subtype C and B. Also, the sequencing and phylogenetic analysis of gag (p24-p7) and env (C2-V3) genes from eighteen samples of Nagaland IDUs with different global HIV-1 strains showed the presence of Indian, African, Thai and their recombinant forms. However, more recombinant strains based on different genomic regions of HIV-1 were detected using Multiregional Hybridization Assay (MHA) where 8 out of 18 samples were found to be recombinants between subtype C and B. Thus, multiregional hybridization assay along with heteroduplex mobility assay can serve as an efficient tool in the characterization of recombination pattern among the newly emerging HIV-1 recombinants.

Lack of high-level resistance mutations in HIV type 1 BF recombinant strains circulating in northeast Brazil

Abstract The genetic variability and the prevalence of drug resistance-associated mutations (DRAM) of HIV-1 isolates from 50 women and 8 children from Feira de Santana, Bahia, Brazil were investigated. DNA samples were obtained and pol sequences were generated by PCR and direct sequencing. Phylogenetic analysis showed that 39 (67.2%) samples were subtype B, four (6.9%) F, one (1.7%) C, and 14 (24.1%) BF recombinants. Four different BF recombination patterns were detected. Twelve (20.7%) samples shared the same breakpoint within the reverse transcriptase (RT) sequence. Fifty-five (94.8%) isolates showed several resistance-associated mutations in the RT and the protease (PR) genes. Ten (17.2%) isolates presented mutations associated with a high level of resistance: nine (15.5%) to nucleoside RT inhibitors (NRTI), four (6.9%) to nonnucleoside RT inhibitors (NNRTI), and three (5.2%) to PR inhibitors (PIs). Subtype B-infected patients had, on average, 0.5 high-level DRAM per sequence while no mutations were observed in BF recombinants, although the two groups were under ARV for a similar period of time. Our data indicate the predominance of the subtype B, followed by BF recombinants in this population, and the dissemination of a recombinant strain in Bahia, which could be related to adaptive advantages of these variants over the predominant subtype B.

Multiple HIV-1 infections with evidence of recombination in heterosexual partnerships in a low risk Rural Clinical Cohort in Uganda

We report on the frequency of multiple infections, generation of recombinants and consequences on disease progression in 35 HIV-1 infected individuals from 7 monogamous and 6 polygamous partnerships within a Rural Clinical Cohort in Uganda. The env-C2V3, gag-p24 and pol-IN genes were sequenced. Single genome amplified half genome sequences were used to map recombination breakpoints. Three participants were dually infected with subtypes A and D, one case with subtype A and A/D recombinant and the fifth with 2 phylogenetically distinct A/D recombinants. Occurrence of A/D recombination was observed in two multiple infected individuals. Rate of late stage WHO events using Cox regression was 3 times greater amongst multiple infected compared to singly infected individuals (hazard ratio 3.35; 95% CI 1.09, 10.3; p = 0.049). We have shown that polygamous relationships involving subtype discordant partnerships was a major contributor of multiple infections with generation of inter subtype recombinants in our cohort.

Infection by discordant strains of HIV-1 markedly enhances the neutralizing antibody response against heterologous virus

High-risk cohorts in East Africa and the United States show rates of dual HIV-1 infection--the concomitant or sequential infection by two HIV-1 strains--of 50% to 100% of those of primary infection, and our normal-risk HIV-positive cohort in Cameroon exhibits a rate of dual infection of 11% per year, signifying that these infections are not exceptional. Little is known regarding the effect of dual infections on host immunity, despite the fact that they provide unique opportunities to investigate how the immune response is affected when challenged with diverse HIV-1 antigens. Using heterologous primary isolates, we have shown here that dual HIV-1 infection by genetically distant strains correlates with significantly increased potency and breadth of the anti-HIV-1 neutralizing antibody response. When the neutralization capacities of sequential plasma obtained before and after the dual infection of 4 subjects were compared to those of matched plasma obtained from 23 singly infected control subjects, a significant increase in the neutralization capacity of the sequential sample was found for 16/28 dually infected plasma/virus pairs, while only 4/159 such combinations for the control subjects exhibited a significant increase (P < 0.0001). Similarly, there was a significant increase in the plasma dilution capable of neutralizing 50% of virus (IC(50)) for 18/24 dually infected plasma/virus pairs, while 0/36 controls exhibited such an increase (P < 0.0001). These results demonstrate that dual HIV-1 infection broadens and strengthens the anti-HIV-1 immune response, suggesting that vaccination schemes that include polyvalent, genetically divergent immunogens may generate highly protective immunity against any HIV-1 challenge strain.

The role of recombination in the emergence of a complex and dynamic HIV epidemic

Background

Inter-subtype recombinants dominate the HIV epidemics in three geographical regions. To better understand the role of HIV recombinants in shaping the current HIV epidemic, we here present the results of a large-scale subtyping analysis of 9435 HIV-1 sequences that involve subtypes A, B, C, G, F and the epidemiologically important recombinants derived from three continents.

Results

The circulating recombinant form CRF02_AG, common in West Central Africa, appears to result from recombination events that occurred early in the divergence between subtypes A and G, followed by additional recent recombination events that contribute to the breakpoint pattern defining the current recombinant lineage. This finding also corrects a recent claim that G is a recombinant and a descendant of CRF02, which was suggested to be a pure subtype. The BC and BF recombinants in China and South America, respectively, are derived from recent recombination between contemporary parental lineages. Shared breakpoints in South America BF recombinants indicate that the HIV-1 epidemics in Argentina and Brazil are not independent. Therefore, the contemporary HIV-1 epidemic has recombinant lineages of both ancient and more recent origins.

Conclusions

Taken together, we show that these recombinant lineages, which are highly prevalent in the current HIV epidemic, are a mixture of ancient and recent recombination. The HIV pandemic is moving towards having increasing complexity and higher prevalence of recombinant forms, sometimes existing as "families" of related forms. We find that the classification of some CRF designations need to be revised as a consequence of (1) an estimated > 5% error in the original subtype assignments deposited in the Los Alamos sequence database; (2) an increasing number of CRFs are defined while they do not readily fit into groupings for molecular epidemiology and vaccine design; and (3) a dynamic HIV epidemic context.

The Evolution of HIV-1 Diversity in Rural Cameroon and its Implications in Vaccine Design and Trials

West-Central Africa is an epicenter of the HIV pandemic; endemic to Cameroon are HIV-1 viruses belonging to all (sub)subtypes and numerous Circulating Recombinant Forms (CRFs). The rural villages of Cameroon harbor many strains of HIV-1, though these areas are not as well monitored as the urban centers. In the present study, 82 specimens obtained in 2000 and 2001 from subjects living in the rural villages of the South and West Regions of Cameroon were subtyped in gag, pol, and env and compared to 90 specimens obtained in 2006–2008 in the same regions, in order to analyze HIV-1 evolution in these rural areas. It was found that in the South Region, the proportion of unique recombinant forms (URFs) remained constant (∼40%), while the amount of URFs containing fragments of a CRF increased by 25%. (Sub)subtypes A1, F2, H, and K, and CRF09_cpx, identified in 2000 and 2001, were replaced by CRFs 01_AE, 13_cpx, 14_BG, and 18_cpx in 2006–2008. In the West Region, (sub)subtypes A2, C, G, and H, and CRFs 01_AE and 09_cpx, identified in 2000–2001, were replaced by sub-subtype A1 and CRFs 25_cpx and 37_cpx in 2006–2008. The proportion of URFs in the West Region dropped significantly over the time period by 43%. In both Regions, the proportion of CRF02_AG increased at all loci. These findings demonstrate that the evolution of HIV-1 is distinct for each endemic region, and suggests that the proportion of URFs containing CRF fragments is increasing as the genetic identity of the virus continues to shift dramatically. This highlights the concern that subtype-specific vaccines may not be relevant in Cameroon, and that the distribution of viral diversity in these regions of Cameroon must be carefully monitored.

Evidence for a "Founder Effect" among HIV-infected injection drug users (IDUs) in Pakistan

Background

We have previously reported a HIV-1 subtype A infection in a community of injection drug users (IDUs) in Karachi, Pakistan. We now show that this infection among the IDUs may have originated from a single source.

Methods

Phylogenetic analysis was performed of partial gag sequences, generated using PCR, from 26 HIV-positive IDU samples.

Results

Our results showed formation of a tight monophyletic group with an intra-sequence identity of < 98% indicating a "founder effect". Our data indicate that the HIV-1 epidemic in this community of IDUs may have been transmitted by an HIV positive overseas contract worker who admitted to having contact with commercial sex workers during stay abroad.

Conclusion

Specific measures need to implemented to control transmission of HIV infection in Pakistan through infected migrant workers.

HIV-1 subtype and viral tropism determination for evaluating antiretroviral therapy options: an analysis of archived Kenyan blood samples

BACKGROUND

Infection with HIV-1 is characterized by genetic diversity such that specific viral subtypes are predominant in specific geographical areas. The genetic variation in HIV-1 pol and env genes is responsible for rapid development of resistance to current drugs. This variation has influenced disease progression among the infected and necessitated the search for alternative drugs with novel targets. Though successfully used in developed countries, these novel drugs are still limited in resource-poor countries. The aim of this study was to determine HIV-1 subtypes, recombination, dual infections and viral tropism of HIV-1 among Kenyan patients prior to widespread use of antiretroviral drugs.

METHODS

Remnant blood samples from consenting sexually transmitted infection (STI) patients in Nairobi were collected between February and May 2001 and stored. Polymerase chain reaction and cloning of portions of HIV-1 gag, pol and env genes was carried out followed by automated DNA sequencing.

RESULTS

Twenty HIV-1 positive samples (from 11 females and 9 males) were analyzed. The average age of males (32.5 years) and females (26.5 years) was significantly different (p value < 0.0001). Phylogenetic analysis revealed that 90% (18/20) were concordant HIV-1 subtypes: 12 were subtype A1; 2, A2; 3, D and 1, C. Two samples (10%) were discordant showing different subtypes in the three regions. Of 19 samples checked for co-receptor usage, 14 (73.7%) were chemokine co-receptor 5 (CCR5) variants while three (15.8%) were CXCR4 variants. Two had dual/mixed co-receptor use with X4 variants being minor population.

CONCLUSION

HIV-1 subtype A accounted for majority of the infections. Though perceived to be a high risk population, the prevalence of recombination in this sample was low with no dual infections detected. Genotypic co-receptor analysis showed that most patients harbored viruses that are predicted to use CCR5.

High frequency of HIV-1 dual infections among HIV-positive individuals in Cameroon, West Central Africa

OBJECTIVES

To determine the frequency of dual inter- and intra-subtype HIV-1 infection among a cohort of 64 longitudinally-studied, HIV-1-positive individuals in Yaoundé, Cameroon.

METHODS

Blood was collected every 3-6 months for up to 36 months and RNA was extracted from plasma. Gag fragment (HxB2 location 1577-2040) was amplified by nested RT-PCR, and mixed-time-point Heteroduplex Assays (HDAs) were performed. As heteroduplexes in this assay indicate >or=5% genetic discordance in the gag fragment, their presence reveals dual infection. Results were confirmed by phylogenetic analysis.

RESULTS

Heteroduplexes were generated by specimens of 10 subjects (15.6%). Kaplan-Meier nonparametric estimate of maintenance of single infection was calculated; the rate/year of a 2 infection was found to be approximately 11%. Dual infection was identified in the final specimens of five subjects, after as much as 18 months follow-up, while for the remaining five subjects, dual infection was identified in interim specimens within an average of 10 months follow-up. Analysis of samples obtained after dual infection from each of these latter five subjects revealed two patterns: reversion to initial strain, or replacement of initial strain. Four subjects were dually-infected with HIV-1 strains of the same subtype, while 6 were infected with different subtypes.

CONCLUSIONS

The high prevalence of recombinant HIV-1 strains in Cameroon may in part be explained by the high frequency of dual infection. In this genetically-diverse HIV-1 milieu, dual infections and the recombinant viruses they generate are strongly driving viral evolution, complicating vaccine strategies.

The changing trend of HIV type 1 subtypes in Nairobi

Monitoring the distribution of HIV-1 subtypes and recombinants among infected individuals has become a priority in HIV therapy. A laboratory analysis of samples collected from HIV-positive patients attending an STI clinic in Nairobi was done between March and May 2004. PCR was carried out on pol (intergrase) and env (C2V3) regions and resulting data on the 54 samples successfully analyzed revealed the following as circulating subtypes: 35/54(65%) were A1/A1, 5/54(9%) were A/C, 4/54 (7%) were A1/D, 1/54 (2%) was C/D, 1/54 (2%) was D/D, 1/54 (2%) was A1/A2, 1/54 (2%)was G/G, 1/54 (2%) was A2/D, 1/54 (2%) was C/C, and 4/54 (7%) were CRF02_ AG. The results show an increase in HIV-1 recombinants with the emergence of A1/A2 and an increase in CRF02_AG recombinants. Subtype diversity in the advent of ARV use will impact negatively on treatment outcomes. As such, increased viral evolution and recombination will call for continuous evaluation of available anti-HIV regimens for better management of those infected with HIV-1.

Genetic variability of human immunodeficiency virus-1 in Bahia state, Northeast, Brazil: high diversity of HIV genotypes

The HIV-1 genetic variability in Bahia state, Brazil, was investigated. DNA samples from 229 and 213 HIV-1-infected individuals were analyzed using the heteroduplex mobility assay (HMA) in gag and env fragments, respectively. One hundred seventy-five samples were characterized in both genes. Thirty-two subtype F and BF recombinant viruses were sequenced and analyzed by phylogenetic methods. The combination of HMA and sequencing results showed that seven different HIV-1 genotypes comprised this sample: 147 (84%) B/B, 4 (2.3%) F/F, 3 (1.7%) B/F, 1 (0.6%) F/B, 1 (0.6%) F/D, 1 (0.6%) BF/F, and 18 (10.3%) BF/B. A significant divergence was observed between these two techniques results (84.4%). This is explained by the low accuracy of the HMA for detecting recombinant viruses. These recombinants were unrelated to CRF12, while two sequences were related to CRF28 and CRF29. Nineteen BF mosaics shared the same gag breakpoint. In conclusion, the use of HMA may be inappropriate in regions where different subtypes are co-circulating. Subtype B is the most common genotype, however, an increased prevalence (13.1%) of different BF variants and a potentially new CRF suggest that recombination is occurring frequently in Bahia. These viruses were associated with women infected heterosexually. Finally, this study identified the presence of an F/D recombinant HIV-1 in Brazil.

Polymorphism, recombination, and mutations in HIV type 1 gag-infecting Peruvian male sex workers

HIV genetic diversity in female sex workers (FSW) has been previously described in Peru; however this information is not yet available for male sex workers (MSW). Therefore, purified peripheral blood mononuclear cell DNA from 147 HIV-infected subjects identified as MSW and FSW was used to amplify a 460-bp fragment corresponding to the p24-p7 region of the gag gene. The PCR product was digested with restriction enzymes to identify genetic polymorphism. Later, a random group of samples (n = 19) was sequenced to perform phylogenetic analysis, intragenic recombination analysis, and deleterious mutations leading to a nonfunctional protein in conservative regions of the Gag protein. RFLP analysis revealed 11 genetic variants for AluI and five for MspI. A group of nonsex workers (NSW) used for comparison showed different RFLP genetic variant distributions. Of interest, nine cases of mixed genetic variants were observed for MSW, one case for FSW, and none for NSW. Phylogenetic analysis revealed that all HIV-1 species were subtype B. Intragenic recombination analysis showed a B/C recombination case from an FSW (boostrap = 1000; p value < 0.05). Of interest, deleterious mutations were observed in three cases of conservative D2 zinc domains for Gag 3/19 and one case of the high homology region (1/19). This study shows that gag of HIV circulating from MSW has high genetic polymorphism involving deleterious mutations in conserved domains from the p24-p7 gag region.

Genetic analysis of HIV-1 subtypes in Nairobi, Kenya

Background

Genetic analysis of a viral infection helps in following its spread in a given population, in tracking the routes of infection and, where applicable, in vaccine design. Additionally, sequence analysis of the viral genome provides information about patterns of genetic divergence that may have occurred during viral evolution.

Objective

In this study we have analyzed the subtypes of Human Immunodeficiency Virus -1 (HIV-1) circulating in a diverse sample population of Nairobi, Kenya.

Methodology

69 blood samples were collected from a diverse subject population attending the Aga Khan University Hospital in Nairobi, Kenya. Total DNA was extracted from peripheral blood mononuclear cells (PBMCs), and used in a Polymerase Chain Reaction (PCR) to amplify the HIV gag gene. The PCR amplimers were partially sequenced, and alignment and phylogenetic analysis of these sequences was performed using the Los Alamos HIV Database.

Results

Blood samples from 69 HIV-1 infected subjects from varying ethnic backgrounds were analyzed. Sequence alignment and phylogenetic analysis showed 39 isolates to be subtype A, 13 subtype D, 7 subtype C, 3 subtype AD and CRF01_AE, 2 subtype G and 1 subtype AC and 1 AG. Deeper phylogenetic analysis revealed HIV subtype A sequences to be highly divergent as compared to subtypes D and C.

Conclusion

Our analysis indicates that HIV-1 subtypes in the Nairobi province of Kenya are dominated by a genetically diverse clade A. Additionally, the prevalence of highly divergent, complex subtypes, intersubtypes, and the recombinant forms indicates viral mixing in Kenyan population, possibly as a result of dual infections.

Optimization of the oligonucleotide ligation assay, a rapid and inexpensive test for detection of HIV-1 drug resistance mutations, for non-North American variants

OBJECTIVE

We evaluated the feasibility of the oligonucleotide ligation assay (OLA), a specific, sensitive, and economical ligase-based point mutation assay designed to detect HIV-1 drug-resistance mutations at 12 codons of HIV-1 subtype B pol, for potential use in resource-poor settings.

METHODS

Specimens from HIV-1-infected individuals collected by 7 international laboratories, including subtypes A, B, C, D, F, G, J, and recombinants AE and AG, were tested by the OLA developed for HIV-1 subtype B. Common polymorphisms that interfered with reactivity of the OLA were identified and modified probes designed and evaluated.

RESULTS

92.5% (2,410) of 2,604 codons in specimens from 217 individuals were successfully genotyped by the subtype B OLA. A high rate (range 8.3%-31.2%) of indeterminate results (negative OLA reaction for both mutant and wild type) was observed for 5 codons. Modified probes at reverse transcriptase codons 151 and 184 and protease codon 90 increased the rate of valid OLA to 96.1%.

CONCLUSIONS

The OLA designed for HIV-1 subtype B genotyped most pol codons in non-B subtypes from Asia and Africa but was improved by addition of several modified probes. International laboratories experienced in molecular techniques were able to perform the OLA.

An optimized nested polymerase chain reaction (PCR) approach allows detection and characterization of human immunodeficiency virus type 1 (HIV-1) env and gag genes from clinical samples

The needs for development and/or improvement of molecular approaches for microorganism detection and characterization such as polymerase chain reaction (PCR) are of high interest due their sensitivity and specificity when compared to traditional microbiological techniques. Considering the worldwide importance of human immunodeficiency virus type 1 (HIV-1) infection, it is essential that such approaches consider the genetic variability of the virus, the heterogeneous nature of the clinical samples, the existence of contaminants and inhibitors, and the consequent needs for standardization in order to guarantee the reproducibility of the methods. In this work we describe a nested PCR assay targeting HIV-1 virus gag and env genes, allowing specific and sensitive diagnosis and further direct characterization of clinical samples. The method described herein was tested on clinical samples and allowed the detection of HIV-1 presence in all samples tested for the gag gene and 90.9% for the env gene, revealing sensitivities of 1 fg and 100 fg, respectively. Also, no cross-reactions were observed with DNA from infected and noninfected patients and the method allowed detection of the env and gag genes on an excess of 10(8) and 10(4) of human deoxyribonucleic acid (DNA), respectively. Furthermore, it was possible to direct sequence all amplified products, which allowed the sub typing of the virus in clinical samples.

A heteroduplex assay for the rapid detection of dual Human Immunodeficiency Virus Type 1 infections

The predominance of circulating and unique recombinant forms (URFs) of Human Immunodeficiency Virus Type 1 (HIV-1) in Cameroon suggests that dual infection occurs frequently in this region. Despite the potential impact of these infections on the evolution of HIV diversity, relatively few have been detected. The failure to detect dual infections may be attributable to the laborious and costly sequence analysis involved in their identification. As such, there is a need for a cost-effective, more rapid method to efficiently distinguish this subset of HIV-positive individuals, particularly in regions where HIV diversity is broad. In the present study, the heteroduplex assay (HDA) was developed to detect dual HIV-1 infection. This assay was validated on sequential specimens obtained from 20 HIV+ study subjects, whose single or dual infection status was determined by standard sequence analysis. By mixing gag fragments amplified from the sequential specimens from each study subject in HDA reactions, it was shown that single and dual infection status correlated with the absence and presence, respectively, of heteroduplex bands upon gel electrophoresis. Therefore, this novel assay is capable of identifying dual infections with a sensitivity and specificity equivalent to that of sequence analysis. Given the impact of dual infection on viral recombination and diversity, this simple technique will be beneficial to understanding HIV-1 evolution within an individual, as well as at a population level, in West-Central Africa and globally.

Utility of the heteroduplex assay (HDA) as a simple and cost-effective tool for the identification of HIV type 1 dual infections in resource-limited settings

The predominance of unique recombinant forms (URFs) of HIV-1 in Cameroon suggests that dual infection, the concomitant or sequential infection with genetically distinct HIV-1 strains, occurs frequently in this region; yet, identifying dual infection among large HIV cohorts in local, resource-limited settings is uncommon, since this generally relies on labor-intensive and costly sequencing methods. Consequently, there is a need to develop an effective, cost-efficient method appropriate to the developing world to identify these infections. In the present study, the heteroduplex assay (HDA) was used to verify dual or single infection status, as shown by traditional sequence analysis, for 15 longitudinally sampled study subjects from Cameroon. Heteroduplex formation, indicative of a dual infection, was identified for all five study subjects shown by sequence analysis to be dually infected. Conversely, heteroduplex formation was not detectable for all 10 HDA reactions of the singly infected study subjects. These results suggest that the HDA is a simple yet powerful and inexpensive tool for the detection of both intersubtype and intrasubtype dual infections, and that the HDA harbors significant potential for reliable, high-throughput screening for dual infection. As these infections and the recombinants they generate facilitate leaps in HIV-1 evolution, and may present major challenges for treatment and vaccine design, this assay will be critical for monitoring the continuing pandemic in regions of the world where HIV-1 viral diversity is broad.

Molecular epidemiology of HIV-1 in Santa Catarina State confirms increases of subtype C in Southern Brazil

Recent studies have demonstrated an increased prevalence of human immunodeficiency virus type 1 (HIV-1) subtype C in southern Brazil. Although Santa Catarina State (SC) is located in this area and presents one of the country's highest incidences of HIV/AIDS, knowledge on the molecular epidemiology of HIV-1 in such State is lacking. The aim of this study was to investigate the HIV-1 molecular diversity and epidemiological profile of HIV-1-infected patients from SC. DNA samples were PCR amplified and HIV-1 subtypes were determined using both env and gag genes by direct sequencing. Phylogenetic analyses revealed that 48% were subtype C and 23% were subtype B. Possible recombinant forms were observed for both B/C (23%) and B/F (6%) subtypes. Our results, for the first time, identifies HIV-1 subtype C as a major clade circulating in SC and contributes to the understanding of HIV epidemics in the country by confirming the epidemic spread of the HIV-1 subtype C in southern Brazil.

Production of human immunodeficiency virus type 1 (HIV-1) pseudoviruses using linear HIV-1 envelope expression cassettes

HIV-1 pseudoviruses constitute an important tool in HIV-1 vaccine and entry inhibitor research. Single-cycle pseudoviruses carrying functional envelopes are generated by co-transfecting HEK293T cells with pNL4-3.LucR(-)E(-) and Env expression plasmids. However, cloning of Env genes is time consuming and single Env clones are not representative of the diversity of HIV-1 in a patient's blood sample. A new method to construct Env expression cassettes is proposed which can be used for the rapid generation of heterogeneous HIV-1 pseudoviruses without a cloning step. The linear Env expression cassettes are constructed by ligating PCR amplified Env genes between a 5' CMV promoter and 3' SV40 polyadenylation element. The resulting cassettes generate pseudoviruses carrying heterogeneous Env variants of a primary HIV-1 isolate derived from viral RNA or proviral DNA. The influence of cis-acting sequences upstream of the Env gene on infectivity was compared between pseudoviruses generated from plasmids and linear expression cassettes. The results suggest that the presence of these upstream sequences tends to result in higher infectivity of pseudoviruses when present in heterogeneous Env expression cassettes, but they do not enhance infectivity of pseudoviruses generated with homogeneous Env expression constructs. Using linear expression cassettes allows for the rapid production of heterogeneous patient-derived functional Env genes.

Molecular screening shows extensive HIV-1 genetic diversity in Central West Brazil

BACKGROUND

Information is limited about HIV-1 subtypes circulating in less populated Brazilian areas where the AIDS epidemic is expanding, such as in the Central West region.

OBJECTIVE

To describe HIV-1 subtypes in patients from the States of Goias, Mato Grosso do Sul and Mato Grosso in Central West Brazil.

STUDY DESIGN

Heteroduplex mobility analysis of nested-PCR products from env (primers: ED5/ED12, ES7/ES8) and gag regions (primers: H1P202/H1G777, H1Gag1584/g17) of 406 HIV-1 isolates from Goias (n=271), Mato Grosso do Sul (n=85) and Mato Grosso (n=50) collected from 2001 to 2004.

RESULTS

Median age of patients was 26 years (1-79 range), 68.7% (279/406) females, 69.9% (269/385) sexual exposure, 14.3% parenteral risk, 15.8% vertical cases. Overall 69.9% (284/406) of HIV-1 subtypes were concordant B(env)/B(gag), 1.7% F(env)/F(gag) and 1% C(env)/C(gag). Discordant HIV-1 isolates were 14.5% (59/406), mainly B(env)/F(gag) and F(env)/B(gag) (49/59); five were B(env)/D(gag), four B(env)/C(gag) and one C(env)/D(gag). B/B and discordant B/F isolates were detected among all risk categories and among children and adults.

CONCLUSION

Extensive genetic diversity of HIV-1 was observed in Central West Brazil. Continued molecular studies should monitor the changing dynamics of HIV-1 over time especially in areas where the epidemic is growing.

HIV-1 seroprevalence in the general population of Salvador, Bahia State, Northeast Brazil

To estimate HIV-1 seroprevalence in the general population of Salvador, Bahia, Brazil, we conducted a cross-sectional survey of 3,437 residents from 1998 to 2000. Subjects were drawn from 30 sentinel areas representing a wide range of living conditions. Plasma samples were screened for HIV-1 antibodies by ELISA and confirmed by immunofluorescent assay. Subtype determination by HMA was performed after proviral DNA amplification. Phylogenetic analysis using parsimony was performed with the neighbor-joining method. Overall HIV-1 seroprevalence was 0.55% (19/3,446): 0.8% for men and 0.36% for women. Seroprevalence was higher in the 31-45-year age group (1%) and among persons with family income less than twice the minimum wage (0.78%) as compared to 0.33% for the higher income group. Syphilis was detected in 37% of HIV seropositive individuals. Phylogenetic inferences identified 10 samples as subtype B in the env region and 2 samples with Benv/Fgag/Fpol and Fenv/Bgag. Age > or = 30 years, male gender, and income < or = 2 times the minimum wage were identified as risk factors for HIV-1 infection. Extrapolating the proportion of seropositive individuals to Salvador, the number of HIV-1 infected individuals was estimated at 13,750.

Human immunodeficiency virus type-1 subtypes of infected patients in Espírito Santo, Brazil

Genetic variability of human immunodeficiency virus type-1(HIV-1) is a potential threat for both diagnosis and treatment of HIV/AIDS, as well as the development of effective vaccines. Up to now, HIV subtypes circulating among HIV-positive patients in the state of Espírito Santo were not known. In the present study, blood samples from 100 therapy-naïve HIV-1 infected patients were collected and the HIV subtype was determined through the Heteroduplex Mobility Assay (HMA). Ninety-seven out of 100 studied samples were subtyped by HMA, 73 samples (75.2%) were from subtype B, 9 (9.3%) from subtype F, 3 (3.1%) from subtype C, 6 (6.2%) Benv/Fgag, and another 6 (6.2%) Fenv/Bgag, what suggests that recombinant viruses were present in the studied samples. Twenty-eight percent of the subtype B samples were represented by the Brazilian B" subtype, which were identified by RFLP with Fok I. Data presented here demonstrate that the epidemiological characteristics of the HIV epidemic in the state of Espírito Santo are similar to those from the other Southeastern states and helped to better understand the genetic polymorphism of HIV in Brazil.

HIV type 1 drug resistance among naive patients from Venezuela

In this study, we characterize proviral DNA of 20 HIV-1 asymptomatic antiretroviral-naive patients from Venezuela in env, gag, and pol genes regions. Results from both env/gag HMA subtyping and phylogenetic analysis of pol partial sequences led to the description of clade B in all cases. Nevertheless, the high prevalence of polymorphisms was particularly evident among the protease sequences. A 10% prevalence of major resistance mutations to RTIs was found. Our data also suggested that the protease polymorphisms I62T and V77T could be considered as molecular markers of the subtype B local epidemic. In addition, we show how proviral DNA can be used as a reliable tool to follow trends of resistance mutation transmission.

Genetic and biologic characterization of HIV type 1 subtype C isolates from south Brazil

The molecular and biological properties of HIV-1 subtype C strains from South Brazil were investigated. We sequenced gag and env fragments of viruses from 22 HIV-1-infected individuals from Porto Alegre City, which has the highest frequency of subtype C in the country. The sequences were then compared with other subtype B, C, and F strains isolated in Brazil and other countries using phylogenetic methods. Amino acid signatures were identified and correlated with phenotypic characteristics. We identified six strains with subtype C (27.3%), eight subtype B (36.4%), one subtype F (4.5%), six C/B recombinants (27.3%), and one B/F recombinant (4.5%). The Brazilian subtype C sequences formed a unique phylogenetic group and presented 6 and 18 specific amino acid signatures in gag and env, respectively. Three distinct patterns of C/B recombinants presented characteristic Brazilian amino acid substitutions. Subtype C viruses were predominantly R5 and non-syncytium-inducing, while C/B recombinants were R5/X4 and syncytium-inducing viruses. These findings suggest that subtype C viruses circulating in Brazil are the result of a unique introduction into the country. Recombination events between subtypes B and C have been occurring frequently for more than 10 years in South Brazil. Biological characterization confirms the hypothesis that subtype C is distinct from the others in the evolution of coreceptor utilization.

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.

HIV type 1 subtypes among STI patients in Nairobi: a genotypic study based on partial pol gene sequencing

Circulating strains of human immunodeficiency virus (HIV) exhibit an extraordinary degree of genetic diversity and have been classified on the basis of relationships into distinct lineages called groups, types, subtypes, and subsubtypes. Sexually transmitted infections (STIs) are known to be a risk factor for HIV infection. To establish HIV-1 subtype diversity among STI patients in Nairobi, 140 samples were collected and partial pol gene sequencing done. From the analysis it was established that subtype A1 was the major subtype (64%) followed by D (17%), C (9%), G (1%), and recombinants AD (4%), AC (3%), CRF02()AG (1%), and CRF16()A2D (1%). These results suggest that the HIV-1 epidemic may be evolving toward more virulent and complex subtypes through transmission of complex recombinants due to viral mixing. Any use of ARVs may therefore require initial testing for de novo resistance before commencement of treatment and/or management.

Detection of Human Immunodeficiency Virus Type 1 (HIV-1) A/AE Circulating Recombinant Form (CRF) in India: Possible Implications

BACKGROUND

Rapidly evolving viruses such as human immunodeficiency virus (HIV-1) develop marked sequence differences in their genome over the course of an epidemic and in individuals infected for longer duration. This is because of the error prone reverse transcriptase (RT), which rapidly incorporates mutations resulting in genomic diversity, altered cell tropism, immune escape, and variable resistance to antiretroviral drugs. As a result, radically different genomic combinations may be generated in individuals infected by genetically diverse viruses that have mosaic genomes.

METHODS

Whole blood sample was collected from 25 HIV-1 infected patients. Chromosomal DNA was isolated from the patient's peripheral blood mononuclear cells (PBMCs). Full-length gag gene (~1.5 kb) was amplified. PCR products were subjected to direct automated sequencing. For identification of recombinants Simplot version 2.5 was used.

RESULTS

Out of 25 gag genes that were sequenced, the gene amplified from a 29 years old HIV-1 seropositive male revealed a putative recombinant sequence. This sequence showed maximum homology with HIV-1 subtype A. Simplot analysis revealed the sequence to be a likely recombinant with the following composition: Initial stretch of 1 to 200 nucleotides representing AE circulating recombinant form (CRF), 201 to 440 nucleotides representing HIV-1 subtype A, 441 to 660 nucleotides representing AE CRF again, 661 to 700 nucleotides representing HIV-1 subtype A and the remaining stretch of the nucleotides from 701 to 1076 representing AE CRF.

CONCLUSION

We document a putative HIV-1 subtype A/ AE CRF. It is important to monitor various CRFs that are being generated and horizontally spread in the community. This has significant implications for development of candidate vaccine for India.

Diversity of HIV in Rural Burkina Faso

SUMMARY

: On introduction of a program for prevention of mother-to-child transmission (PMTCT) of HIV in Nouna, rural Burkina Faso, we determined HIV prevalence in this region to be 3.6%, which is significantly lower than the 7% reported for 2 major cities of Burkina Faso. Forty-three samples from drug-naive pregnant women and patients before introduction of antiretroviral therapy (ART) were genotypically characterized in gag, pol, and env regions. One individual each was infected with HIV-2 or dually infected with HIV-1 and HIV-2. The most dominant HIV-1 subtypes were CRF02_AG and CRF06_cpx, similar to what has been observed in other West African countries. A discordant genotype was observed in almost half of the analyzed samples, with most putative recombinants deriving from CRF02_AG and CRF06_cpx. Recently reported strains like the CRF09_cpx and the sub-subtype A3 as well as some unique recombinant forms of HIV like D/D/CRF02_AG and CRF02_AG/CRF02.AG/CRF_09cpx were also detected. Analysis of drug resistance-associated polymorphisms detected the nonnucleoside reverse transcriptase inhibitor (NNRTI) resistance mutations K103N/E and V118I in 1 individual each, suggesting transmission of drug-resistant viruses or prior use of antiretroviral drugs. Resistance-associated polymorphisms (K20I and M36I) were prevalent in the complete protease (PR) region, but no primary drug resistance mutations were detected. Analysis of the HR1 and HR2 regions of gp41, important for T-20 sensitivity, revealed no known resistance mutations but several polymorphisms of unknown importance. Monitoring for drug resistance mutations among naive subjects is important in this area on introduction of antiretroviral drugs.

Genetic Analysis of HIV-1 Strains in Rural Eastern Cameroon Indicates the Evolution of Second-Generation Recombinants to Circulating Recombinant Forms

The HIV-1 genetic diversity in most parts of Cameroon is well described and shown to be very broad. However, little is known about the composition of the HIV-1 epidemic in the rural parts of eastern Cameroon. Therefore, we investigated 25 specimens from this region for their subtypes in gag, pol, and env gene fragments. Along with genetic material of subtypes A1, C, G, CRF01_AE, CRF02_AG, and CRF11_cpx, we also identified a large number (24%, 6/25) of distinct env sequences within the subtype A radiation. CRF02_AG was the predominant genetic form in all genes studied. Half of the specimens studied were considered "pure" based on concordant subtypes in the genes studied, whereas the other half were unique recombinant forms (URFs). Except for 1 URF, all were second-generation recombinants (SGRs), 90% of which contained genetic material of CRF02_AG in at least 1 gene. Notably, we identified individuals from 3 different villages infected with CRF01_AE(gag)CRF02_AG(pol)A(env) strains, which is indicative of the evolution of this URF to a circulating recombinant form (CRF). In addition, we identified a CRF02_AG(pol)C(env) recombinant infecting a man and a woman living in the same village, suggesting horizontal transmission of this recombinant. The current study emphasizes the power of HIV-1 recombination through the generation of SGRs and the evolution of URFs into CRFs. These findings suggest that, in a region where a predominant HIV-1 strain cocirculates among several subtypes, recombination could eventually decrease the proportion of this strain over time, such as CRF02_AG in Cameroon.