HIV-1 Genetic Diversity Research Articles

Molecular diversity and polymerase gene genotypes of HIV-1 among treatment-naïve Cameroonian subjects with advanced disease

Background The progress of antiretroviral treatment roll-out programs in developing countries requires extensive monitoring of primary drug resistance prior to initiation of therapy. This is particularly relevant for Cameroon where a high HIV diversity has been reported. Objectives To determine HIV diversity in Yaoundé, Cameroon, in a cohort of HIV-infected subjects with advanced disease. To characterize HIV-1 mutations conferring primary drug resistance and to assess primary resistance patterns in the RNase H domain of the reverse transcriptase of these viruses. Study design HIV-1 RNA was extracted from plasma of 59 HIV-1 infected, drug-naïve subjects with CD4 + T-cell counts < 200/μl. HIV-1 pol (PR, RT and RNase H) regions were sequenced for subtyping and for identifying drug resistance mutations in pol (PR, RT and RNase H). Results A complex HIV-1 diversity was seen, with multiple subtypes (A1, A2, C, D, F2, H, group O), CRFs (02_AG, 09_cpx, 11_cpx, 13_cpx, 22_01A1, 30_0206, 43_02G) and URFs. Primary drug resistance was low in PR (2%) and in RT regions (4%). RNase H mutations Q509L and Q547K were found in non-CRF02_AG strains. Conclusions A high HIV-1 diversity was already present in Cameroon in the early 90s, when the subjects were likely infected. Primary HIV-1 drug resistance was low. Occurrence of RNase H mutations with proven phenotypic effect on susceptibility to antiretrovirals encourages further assessment of their impact in treatment outcome in the context of complex HIV genetic diversity and in a subtype-specific fashion.

HIV-1 recombinants with multiple parental strains in low-prevalence, remote regions of Cameroon: Evolutionary relics?

BackgroundThe HIV pandemic disseminated globally from Central West Africa, beginning in the second half of the twentieth century. To elucidate the virologic origins of the pandemic, a cross-sectional study was conducted of the genetic diversity of HIV-1 strains in villagers in 14 remote locations in Cameroon and in hospitalized and STI patients. DNA extracted from PBMC was PCR amplified from HIV(+) subjects. Partial pol amplicons (N = 164) and nearly full virus genomes (N = 78) were sequenced. Among the 3956 rural villagers studied, the prevalence of HIV infection was 4.9%; among the hospitalized and clinic patients, it was 8.6%.ResultsVirus genotypes fell into two distinctive groups. A majority of the genotyped strains (109/164) were the circulating recombinant form (CRF) known to be endemic in West Africa and Central West Africa, CRF02_AG. The second most common genetic form (9/164) was the recently described CRF22_01A1, and the rest were a collection of 4 different subtypes (A2, D, F2, G) and 6 different CRFs (-01, -11, -13, -18, -25, -37). Remarkably, 10.4% of HIV-1 genomes detected (17/164) were heretofore undescribed unique recombinant forms (URF) present in only a single person. Nearly full genome sequencing was completed for 78 of the viruses of interest. HIV genetic diversity was commonplace in rural villages: 12 villages each had at least one newly detected URF, and 9 villages had two or more.ConclusionsThese results show that while CRF02_AG dominated the HIV strains in the rural villages, the remainder of the viruses had tremendous genetic diversity. Between the trans-species transmission of SIVcpz and the dispersal of pandemic HIV-1, there was a time when we hypothesize that nascent HIV-1 was spreading, but only to a limited extent, recombining with other local HIV-1, creating a large variety of recombinants. When one of those recombinants began to spread widely (i.e. became epidemic), it was recognized as a subtype. We hypothesize that the viruses in these remote Cameroon villages may represent that pre-epidemic stage of viral evolution.

Impact of extensive HIV-1 variability on molecular diagnosis in the Congo basin

Background Previous studies have shown a high HIV-1 genetic variability in the Republic of Congo. This can greatly influence the performance of molecular assays for HIV-1 diagnosis. Objectives To define a reliable test for detection of HIV-1 DNA in this area. Study design We compared a commercial nested PCR (C-PCR) assay and an in house nested PCR (H-PCR) assay for the detection of HIV-1 DNA in the first 30 seropositive pregnant women enrolled into the ongoing “Kento-Mwana” project, for the prevention of HIV mother-to-child transmission in the city of Pointe Noire, Republic of Congo, Africa. Sequencing and phylogenetic analysis of partial HIV-1 pol sequences were also performed. Results C-PCR detected HIV-1 DNA in only 15/30 samples from seropositive women (50.0%), as opposed to 29/30 (96.6%) by H-PCR ( P < 0.0001). Phylogenetic analysis and bootscanning showed that only 10 sequences could be assigned to known clades (seven pure subtypes and three circulating recombinant forms), whereas the other 20 sequences were unique recombinant forms. Conclusions The great genetic variability of HIV-1 in this area strongly advises to for using molecular methods only after local validation to avoid false negative results.

HIV Genetic Diversity and Drug Resistance

Most of the current knowledge on antiretroviral (ARV) drug development and resistance is based on the study of subtype B of HIV-1, which only accounts for 10% of the worldwide HIV infections. Cumulative evidence has emerged that different HIV types, groups and subtypes harbor distinct biological properties, including the response and susceptibility to ARV. Recent laboratory and clinical data highlighting such disparities are summarized in this review. Variations in drug susceptibility, in the emergence and selection of specific drug resistance mutations, in viral replicative capacity and in the dynamics of resistance acquisition under ARV selective pressure are discussed. Clinical responses to ARV therapy and associated confounding factors are also analyzed in the context of infections by distinct HIV genetic variants.

HIV‐1 primary and secondary antiretroviral drug resistance and genetic diversity among pregnant women from central Brazil

Antiretroviral (ARV) resistance mutations in HIV-1 may reduce the efficacy of prophylactic therapy to mother-to-child transmission and impact future treatment options. ARV resistance mutations and HIV-1 phylogenetic diversity in protease (PR) and reverse transcriptase (RT) genes were assessed among 77 pregnant women (35 naïve, 42 treated with ARV) from Goiânia/Goiás, central west Brazil. ARV mutations in PR/RT genes were analyzed against the Stanford Database, PR/RT HIV-1 subtypes were assigned by phylogenetic analysis and env/gag subtypes were identified by heteroduplex mobility analysis (HMA). Naïve patients had accessory mutations in the PR gene [A71T (1/6), L10V (2/6), L10I (3/6)] and in the RT gene [V118I (2/6), V179D (1/6), V106I (1/6), K101Q (1/6), H221Y (1/6)]. Seven patients (16.7%) under ARV presented drug resistance mutations, one of them to three ARV classes. Most isolates (67.5%) were subtype B, 11.7% subtype F1 and 3.9% subtype C. Recombinant B(PR)/F1(RT) viruses represented 10.4% while F1(PR)/B(RT) viruses made up 6.5%. HIV-1 envgag/PRRT genes were identified as 66.2% subtype B, 3.9% subtype C, 6.5% subtype F1 and approximately 25% B and F1 viruses. HIV-1 genetic diversity in envgag/PRRT genes indicates the spread and dissemination of BF1 recombinant viruses among a significant proportion of patients from central west Brazil. Moreover, discovery of HIV-1 secondary resistance among a considerable number of pregnant women under ARV therapy indicates the importance of genotypic testing during pregnancy for optimal prophylactic intervention. J. Med. Virol. 82:351-357, 2010. (c) 2010 Wiley-Liss, Inc.

The Challenge of HIV-1 Genetic Diversity: Discordant CD4+ T-Cell Count and Viral Load in an Untreated Patient Infected With a Subtype F Strain

The Challenge of HIV-1 Genetic Diversity: Discordant CD4+ T-Cell Count and Viral Load in an Untreated Patient Infected With a Subtype F Strain

HIV Type 1 Subtype Diversity and Drug Resistance among HIV Type 1-Infected Kenyan Patients Initiating Antiretroviral Therapy

The treatment of HIV-1 infection with antiretroviral drugs has greatly improved the survival of those who are infected. However, HIV-1 diversity and drug resistance are major challenges in patient management, especially in resource-poor countries. To evaluate HIV-1 genetic diversity and drug resistance-associated mutations among drug-naive patients in Kenya prior to antiretroviral therapy (ART), a genetic analysis of HIV-1 pol-RT and env-gp41 was performed on samples collected from 53 (18 males and 35 females) consenting patients between April and June 2005. The average age, baseline CD4(+) T cell counts, and viral loads were 38 (range, 24-62) years, 475 (range, 203-799) cells/mm(3), and 4.7 (range, 3.4-5.9) log(10) copies/ml, respectively. Phylogenetic analysis revealed that 40 samples (75.5%) were concordant subtypes for the two genes and 13 (24.5%) were discordant, suggesting possible recombination and/or dual infections. Prevalent subtypes included A1/A1(pol-RT/env-gp41), 31 (58.5%); D/D, 9 (16.9%); A1/C, 2 (3.8%); A1/D, 4 (7.5%); G/A1, 2 (3.8%); A1/A2, 1 (1.9%); C/A1, 2 (3.8%); D/A1, 1(1.9%); and D/A2, 1 (1.9%). Major reverse transcriptase inhibitor (RTI) resistance-associated mutations were found in four patients (7.5%). Of these patients, three had nucleoside RTI resistance mutations, such as M184V, K65R, D67N, K70R, and K219Q. Nonnucleoside RTI resistance-associated mutations K103N and Y181C were detected in three patients and one patient, respectively. Multiple drug resistance mutations were observed in this drug-naive population. With increasing numbers of patients that require treatment and the rapid upscaling of ART in Kenya, HIV-1 drug resistance testing is recommended before starting treatment in order to achieve better clinical outcomes.

Phylodynamics of HIV-1 from a Phase-III AIDS Vaccine Trial in North America

In 2003, a phase III placebo-controlled trial (VAX004) of a candidate HIV-1 vaccine (AIDSVAX B/B) was completed in 5,403 volunteers at high risk for HIV-1 infection from North America and the Netherlands. A total of 368 individuals became infected with HIV-1 during the trial. The envelope glycoprotein gene (gp120) from the HIV-1 subtype B viruses infecting 349 patients was sequenced from clinical samples taken as close as possible to the time of diagnosis, rendering a final data set of 1,047 sequences (1,032 from North America and 15 from the Netherlands). Here, we used these data in combination with other sequences available in public databases to assess HIV-1 variation as a function of vaccination treatment, geographic region, race, risk behavior, and viral load. Viral samples did not show any phylogenetic structure for any of these factors, but individuals with different viral loads showed significant differences (P = 0.009) in genetic diversity. The estimated time of emergence of HIV-1 subtype B was 1966–1970. Despite the fact that the number of AIDS cases has decreased in North America since the early 90s, HIV-1 genetic diversity seems to have remained almost constant over time. This study represents one of the largest molecular epidemiologic surveys of viruses responsible for new HIV-1 infections in North America and could help the selection of epidemiologically representative vaccine antigens to include in the next generation of candidate HIV-1 vaccines.

P20-01. HIV-1 genetic diversity among HIV drug naive populations of Nairobi, Kenya

P20-01. HIV-1 genetic diversity among HIV drug naive populations of Nairobi, Kenya

P16-44. Investigating T cell immune responses in Cameroon, a country with broad HIV-1 genetic diversity

Background HIV-1 diversity presents a challenge for the development of an effective HIV vaccine. Cameroon in central Africa, exhibits very broad HIV-1 genetic diversity. That makes it one of the few places in the world where vaccine efficacy can be tested against a broad range of subtypes and recombinants. The aim of the study is to assess cross-clade T cell responses in HIV-infected Cameroonians.

PV-14 CMV and HCV infection in children born to HIV infected mothers

Quantitation of HIV-1 RNA levels in plasma has significant prognostic value since high viral load concentrations in plasma are associated with a faster disease progression. Viral load testing became one the most important tools for monitoring HIV patients. New real time methodologies to quantify HIV viral load had arisen in the last decade. HIV is a virus with a high genetic variability, with the potential to negatively affect the performance of the viral load assays. Consequently, any new assay should be challenged against, at least, the most prevalent HIV-1 genetic variants. In the present study, the new version of NucliSENS EasyQ® HIV-1 (Version 2.0) quantitative assay was compared with another ultra-sensitive test – Abbott RealTime HIV-1 – using 175 plasma samples from patients infected with several HIV-1 subtypes and recombinant forms: subtype B (41, 23%), subtype C (19, 11%), subtype G (76, 44%), and CRF02_AG (39, 22%). Overall, there was agreement between the assays in 95.43% of the samples. Both assays have a very good dynamic range [1.4–6.9] and [1.60–7.0] log10 copies/mL and excellent correlation in samples with various subtypes. Based on the fact that no clinically significant differences were observed in the viral load measurements by these two assays, HIV-1 subtypes are quantified equally by both assays. However due to HIV diversity, mainly in regions were non B subtypes are predominant more evaluations are needed, so we do not recommend to switch platform during longitudinal viral load monitoring.

HIV-1 Genetic Diversity and Transmitted Drug Resistance in Health Care Settings in Maputo, Mozambique

To characterize HIV-1 diversity and transmitted drug resistance in persons with access to care and treatment in Maputo, Mozambique. Samples were collected in 2002-2004 from 144 drug-naive patients attending public hospitals and private clinics. Plasma viremia, CD4, and CD8 cell counts were determined for each patient. The Stanford Algorithm was used for resistance genotyping on pol sequences. Subtyping was done by phylogenetic analysis. Most patients had high viral load (mean, 5.0 log copies/mL) and low CD4 cell counts (median, 260 CD4 cells/microL). Protease and/or reverse transcriptase sequences were obtained from 104 (72%) samples. Patients harbored subtypes C (80.8%), G (3.8%), CRF37_cpx (6.7%), untypable (U) (1.0%), and recombinant strains (7.7%) comprising the A, C, D, F, and U clades. There were no major protease inhibitor resistance mutations. Mutations conferring resistance to the nucleoside/nucleotide reverse transcriptase inhibitors and/or nonnucleoside reverse transcriptase inhibitors were found in 4 (4/68; 5.9%) patients. Phylogenetic analysis suggested an imported origin for 2 resistant variants. The HIV-1 epidemic in Maputo is evolving rapidly in genetic complexity due to the recent introduction of all major subtypes and recombinant forms. Continued surveillance of drug resistance in treated and untreated populations is needed to prevent further transmission of HIV drug-resistant variants and maximize the efficacy of antiretroviral therapy in Maputo.

Molecular Epidemiology of HIV-1 in St Petersburg, Russia: Predominance of Subtype A, Former Soviet Union Variant, and Identification of Intrasubtype Subclusters

To examine HIV-1 genetic diversity in St. Petersburg. Partial HIV-1 pol sequences from 102 plasma samples collected in 2006 were analyzed with a Bayesian phylogeny inference method. Subtype A, former Soviet Union (FSU) variant (AFSU), was the predominant clade (89.3%); other clades were subtypes B (9.7%) and F1 (1%). AFSU was predominant both among injecting drug users (98.2%) and heterosexually infected individuals (91.4%), whereas subtype B was more prevalent among homosexual men (75%). Within the AFSU variant, most sequences (93.5%) branched within 1 of 4 strongly supported subclusters. The largest comprised 63% AFSU viruses and was uncommon outside St Petersburg. A second subcluster (17.4% AFSU viruses) corresponds to the variant with the V77I substitution in protease, which is widely circulating in different FSU countries. Two minor subclusters comprised 8.7% and 6.5% AFSU viruses, respectively. There was no correlation between risk exposure and AFSU subclusters. Six of 8 subtype B sequences, 4 of them from homosexual men, grouped in a monophyletic subcluster. The results of this study show a great predominance of AFSU viruses in St Petersburg and point to a few phylogenetically identifiable introductions as the origin of most current HIV-1 AFSU infections in the city.

Genetic characterization of HIV-1 strains in Togo reveals a high genetic complexity and genotypic drug-resistance mutations in ARV naive patients

In this study, the genetic diversity of HIV-1 and the presence of genotypic drug-resistance mutations in ARV naive patients in Lomé, the capital city of Togo, was documented for the first time. Between June 2006 and January 2007, 83 plasma samples were collected in Lomé from HIV-1 positive and antiretroviral (ARV) naive individuals. Pol (protease + RT) and env (V3–V5) regions were amplified and sequenced. Phylogenetic and recombination analyses were done to identify the HIV-1 variants. Pol sequences were then inspected to identify presence of drug-resistance mutations based on the WHO list recommended for epidemiological studies. A total of 75 plasma samples were amplified and sequenced in both genomic regions. The phylogenetic analysis showed that CRF02 (48.7% and 51.2%) and G (12.8% and 16.2%) were predominant, followed by A3 (6.4% and 6.2%) and CRF06 (3.8% and 12.5%) in pol and env, respectively. One strain was identified as CRF05 in pol and env. Two divergent subtype A strains in env were undetermined (U) in pol but clustered with a previously described complex recombinant strain, 99GR303. Overall, at least 23/83 (27.7%) strains were recombinant, 19 had a unique recombinant structure in pol, and 4 had discordant subtype/CRF designations between pol and env. The subtypes/CRFs involved in the recombination events corresponded to those already circulating as non-recombinant strains in the country. A total of 8 patients harbored strains with mutations associated to drug resistance: L90M ( n = 1), K103N ( n = 1), T69N ( n = 1), T215S ( n = 1), M41L ( n = 4). In this study we showed the complexity of the HIV-1 strains circulating in Togo and documented a relative high proportion of ARV naive patients with drug-resistance mutations. The high number of resistant strains observed in Togo needs further attention and additional studies are needed to confirm this trend especially because the national ART program experienced major problems to provide drugs on a regular base.

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.

Selection of HIV Variants in Heterosexual Transmission

Previous studies of HIV transmission in serodiscordant couples have shown a limited number of variants in newly infected individuals compared with their infecting partners. Over time, the genetic diversity of HIV in the newly infected partner expands, as expressed by a wider range …

Identificación de las diferentes variantes geneticas del VIH-1 en niños de procedencia no española

Introduction The prevalence of HIV-1 non-B subtypes (HIV-NBS) is increasing in Europe, beause of emigration from countries where genetic variants are endemic. Although HIV-NBS could have a different clinical evolution and could respond differently to antiretrovirals (AR) than B-subtypes, these variant's response remain undocumented. Aims To identify HIV-1 genetic variants and to determine clinical evolution in a non-Spaniard children infected with HIV-1. Patients and method Children with HIV-1 infection from endemic countries were tested for HIV-1 subtypes between 1-1-1988 and 31-12-2006. Twelve children less than 18 years old and born abroad were selected. Results HIV-NBS were isolated in 5 children (42%): CRF2_AG recombinant in 3 cases (Equatorial Guinea), Subtyoe C in one (Equatorial Guinea) and CRF13_cpx in last one (India). Discussion Because of the increasing frequency of patients with HIV-NBS and their unknown long-term evolution, all children from endemic countries should be tested for HIV subtypes. We believe new studies with more patients during longer times could reveal differences in these patient's clinical, immunological and virological evolution.

Current Status of HIV/AIDS in Cameroon: How Effective are Control Strategies?

Nearly three decades after its discovery, HIV infection remains the number one killer disease in Sub- Saharan Africa where up to 67% of the world's 33 million infected people live. In Cameroon, based on a Demographic Health Survey carried out in 2004, the national HIV prevalence is estimated at 5.5% with women and youths being predominantly infected. Orphans and vulnerable children (OVC) from the HIV and AIDS pandemic have increased steadily over the years; hospital occupancy is estimated at about 30%, hence stretching the health system; co-infections like HIV/tuberculosis have been reported to reach 40-50% of infected cases and 95% of teachers are said not to be productive on several counts. Thus, the impact is multi-sectorial. Furthermore, the HIV epidemic in Cameroon is peculiar because of the wide HIV-1 genetic diversity of HIV-1 Group M observed with several subtypes reported (A, B, C, D, F, G, H, J, K), predominantly subtype A. There are also circulating recombinant forms, mainly CRF02_AG. In addition, HIV-1 Groups O and N have all been noted in Cameroon. These findings have great implications not only for HIV diagnosis, but also for responsiveness to therapy as well as for vaccine development. In 1986, the initial response of the Cameroon government to the increasing trends in the HIV/AIDS infection was to create a National AIDS Control Committee to coordinate a national AIDS programme. By 2000, the first National Strategic Plan was drawn for 2000-2005. The second National Strategic Plan for 2006-2010 is currently being implemented and covers various axes. Some results obtained show that there has been significantly positive outcomes noted in the various arms of intervention by the Cameroon government.

A Study of HIV-1 Genetic Diversity in the Czech Republic: 1986-2007

The global HIV/AIDS epidemic consists of a number of regional epidemics caused by different HIV-1 subtypes prevailing in different regions. To study changes in genetic diversity of HIV-1 strains isolated in the Czech Republic (CR) over a more than twenty-year period (1986-2007). HIV-1 strains isolated in CR from 1986 to 2007 were subtyped by pol gene sequencing followed by phylogenetic analysis. The role of HIV-1 subtyping in molecular epidemiology was considered. Awide range of HIV-1 subtypes were found, with subtype B, into which 76.6% of 534 HIV-1 isolates were classified, being predominant during the whole study period. An increasing number of non-B subtypes A1, C, D, F1, G and some recombinant forms (CRF 01_AE, CRF 02_AG and CRF 06_cpx) were identified after 1990. The absolute predominance of subtype B among HIV-1 strains in the Czech Republic ended in 1991 when different non-B subtypes had been introduced into the country. The East-West migration is responsible for the introduction of HIV-1 subtypes prevalent in Eastern European and some Asian countries. Genetic analysis of HIV-1 isolates from a given region can be helpful in tracing the course of the HIV/AIDS epidemic.

Polymorphism, Recombination, and Mutations in HIV Type 1gag-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.