Socio-demographic and drug use factors associated with HIV-1 recombinants and dual infections in Northern Thai drug users: associations of risk with genetic complexity.

BACKGROUND: Dual infection with diverse HIV strains can foster the emergence of recombinants. The resulting increase in viral genetic diversity is a major challenge for vaccine development HIV treatment. In this study we aim to investigate the socio demographic factors associated with an increasing level of genetic diversity among HIV strains in a population of drug-users in Northern Thailand. METHODS: From 1999 through 2000, 2231 volunteers were enrolled in the Opiate-Users Research in Chiang Mai, Thailand. HIV subtype analysis was conducted among those HIV-1 seropositive (n=347) using a multi-region hybridization assay. Social and demographic variables were assessed using a structured questionnaire. RESULTS: Overall, 336/347 (96.8%) of the samples could be typed. 81.8% were CRF01_AE, 3.9% were subtype B, 9.2% were recombinants (mostly between CRF01_AE and B) and 5.1% were dual infections. Dual infections were more frequent among those with a lower education level (AOR: 5.2; 95% CI 1.4-20.3), those who have initiated injecting in the last 3 years (AOR: 3.9; 95% CI 1.1-14.6), and those reporting frequent needle sharing in the last 3 months (AOR: 7.0; 95% CI 1.5-34.1). Both recombinant strains and dual infection were more frequent among those reporting frequent needle sharing in the last 3 months (AOR: 5.3; 95% CI 1.6-17.1). CONCLUSION: To limit the expanding complexity of HIV-1 strains, early intervention should be aimed at reduction in needle sharing, especially among new intravenous drug users.

High-throughput genotyping of KIR2DL2/L3, KIR3DL1/S1, and their HLA class I ligands using real-time PCR.

Killer immunoglobulin-like receptors (KIRs) expressed on natural killer cells are critical components of innate immunity. Interactions between KIRs and their human leukocyte antigen (HLA) ligands have been shown to influence autoimmune and infectious disease course in defined populations. However, the low throughput and high cost of current methods impede confirmation of the universality of these findings. To support large epidemiology surveys, we developed a high-throughput real-time polymerase chain reaction-based assay to identify carriers of KIR3DL1, KIR3DS1, KIR2DL2, and KIR2DL3 and their HLA ligands. The platform performed with 100% sensitivity and specificity in detection of carrier and non-carrier on reference samples. The application of this platform will further clarify the nature and impact of the KIR-HLA epistatic interaction on disease course in large global population-based studies.

HLA class I allele and haplotype diversity in Ugandans supports the presence of a major east African genetic cluster.

The objective of this study was to characterize the class I human leukocyte antigen (HLA) genetic composition of the Ugandan population to better define its relationship with other African groups. Samples from 175 individuals from Kampala (Uganda) were subjected to class I HLA-A, -B, and -C sequence-based typing. The high concordance between the major alleles and haplotypes found in the current and Kenyan populations and interpopulation genetic distance analysis strongly supported the presence of an East African cluster that contained the current Ugandan population along with Kenyan Luo and Nandi populations. The congruence of major alleles in different populations would permit consideration of East Africa as an integrated setting when designing and evaluating much needed malaria, tuberculosis, and AIDS vaccines.

Discrepant results in the interpretation of HIV-1 drug-resistance genotypic data among widely used algorithms.

OBJECTIVES: The aim of this study was to assess the concordance on the interpretation of HIV-1 drug-resistance genotypic data by three widely used algorithms: Stanford University Database (SU), TruGene (Visible Genetics, Canada) (VG) and VirtualPhenotype (Virco, Belgium) (VP). METHODS: Genotypic data from 293 HIV-1-infected individuals with treatment failure was interpreted for 14 antiretroviral drugs by the three algorithms. RESULTS: Complete concordant results among the three systems for all the drugs studied were found in 40/293 (13.7%) samples. Low concordance in the interpretation was observed for most nucleoside reverse transcriptase inhibitors (NRTIs), while results agreed highly for all nonnucleoside reverse transcriptase inhibitors (NNRTIs) and most protease inhibitors (PIs). In pair-wise comparisons, discordant interpretations between SU and VP were found in over 50% of the samples for didanosine, zalcitabine, stavudine and abacavir, and the level of disagreement between VG and VP exceeded 40% for the same drugs. Major discrepancies (high-level resistance interpretation by one algorithm with sensitive interpretation by another) were observed between VG and VP in over 10% of the cases for didanosine, zalcitabine, stavudine and abacavir. On the other hand, the three algorithms had concordant results for lamivudine in over 90% of the cases. CONCLUSIONS: This work demonstrates the great level of discordance in the interpretation of genotyping results among algorithms, clearly showing the necessity for clinical validation. Moreover, these results suggest that a joint effort from the scientific community as well as national and international HIV societies is needed to achieve a consensus for the interpretation of genotypic data.

HIV type 1 genetic diversity is a major obstacle for antiretroviral drug resistance hybridization-based assays.

Human immunodeficiency virus type 1 (HIV-1) is characterized by high genetic diversity. Current antiretroviral (ARV) drug resistance genotyping assays have been designed on the basis of the most prevalent sequence patterns circulating in the United States and Europe, which belong to the B subtype. However, little is known about their performance on non-B subtype samples. In Argentina, circulating forms have been characterized as subtypes B, C, F, and B/F recombinant forms. Our aim was to analyze the association between the genetic diversity of HIV-1 forms circulating in Argentina and the lack of reactivity at codon 74 in an ARV drug resistance hybridization-based assay. Samples taken from 93 HIV-1-infected individuals of Buenos Aires, Argentina were studied. The reverse transcriptase (RT) region of HIV-1 was genotypically assessed by a line probe assay (INNO-LiPA HIV-1 RT; Innogenetics, Ghent, Belgium) and automatic sequencing (TruGene and OpenGene; Visible Genetics, Toronto, Canada). Phylogenetic and intersubtype recombination analyses were carried out, showing that 52 of 93 (55.9%) samples belonged to subtype B, whereas 41 of 93 (44.1%) showed a (5') F1/B (3') subtype recombinant genomic structure. For codon 74 in the LiPA test, 4 of 52 (7.7%) B-subtype samples were nonreactive, whereas 27 of 41 (65.9 %) F1/B recombinant samples showed a nonreacting result, indicating a significant difference in the subtype distribution of the nonreacting samples. The presence of a synonymous polymorphism at codon 72 of RT (AGA --> AGG) associated with the lack of reaction at codon 74 in LiPA, was more prevalent in F1/B subtype recombinant samples (p < 0.001). The present data indicate that HIV-1 genetic diversity is a major obstacle for ARV drug resistance hybridization-based assays.

Mother-to-child transmission of drug-resistant HIV.

Mother-to-child transmission of HIV-I is responsible for the infection of hundreds of thousands of infants every year. The use of prophylactic antiretroviral treatments has brought about a dramatic decrease in the risk of transmission. Nevertheless, vertical transmission can still occur. In some cases, the presence of drug-resistant HIV-I strains in the mother has been responsible for the failure of the prophylactic scheme. Moreover, these strains have also been detected in the newborn. The aim of this review is to provide updated information on mother-to-child transmission of drug-resistant HIV strains and to help guide treatment decisions during pregnancy.

Resistance profiles to antiretroviral drugs in HIV-1 drug-naive patients in Argentina.

The drug resistance profile of treatment-naive HIV-infected individuals living in Buenos Aires, Argentina, was studied. Samples taken from 94 drug-naive individuals with established HIV infection and 13 patients with primary HIV infection were assessed by nucleotide sequencing and LIPA. The prevalence of drug-associated primary mutations in individuals with established infection was very low. In the viral protease region, 1/86 (1.2%) individuals carried the D30N mutation, whereas 1/85 (1.2%) had the M41L mutation in the reverse transcriptase (RT) region. Secondary mutations in both the protease and RT regions were found in almost 90% of the individuals. In individuals with primary infection, primary mutations were detected in 2/13 (15.4%) patients, one of them carrying M461 mutation in the protease while the other patient had a mutation at codon 184 of the RT. In accordance with current drug resistance testing guidelines, the results of this study suggest that susceptibility tests need not be performed at this time prior to initiation of antiretroviral therapy in HIV-1-infected people in Argentina. However, the public health implications of this subject warrant follow-up studies that will examine a larger number of drug-naive patients, not only in Buenos Aires but also in other major Argentinian cities and in rural areas.

A highly prevalent polymorphism at codon 72 of HIV-1 reverse transcriptase in Argentina prevents hybridization reaction at codon 74 in the LiPA genotyping test.

The aim of this study was to compare the performance of two commercial drug-resistance HIV-1genotyping kits: LiPA (Innogenetics, Belgium) and TruGene (Visible Genetics, Canada). Samples from 103 HIV-1 infected individuals from Argentina were studied. The average correlation between the two methods was 92.81%. More codons could be analysed by TruGene than by LiPA (610/618 and 541/618 codons, respectively). The sequences of the samples and the LiPA probes were aligned showing that a silent mutation at codon 72 (AGA-->AGG) of the HIV-1 reverse transcriptase, which was not recognised by the LiPA probes, was present in 35/36 non-reactive samples for position 74. The overall prevalence of this polymorphism in the population studied was 39.81%. When sequences from different parts of the world were analysed 189/3395 (5.63%) carried the mutation at codon 72, while 23/133 (17.29%) of the sequences from Latin America (excluding Argentina) had this mutation. In both cases, the prevalence of this polymorphism in the Argentinean population was significantly higher. This highlights the importance of carrying out studies on the performance of genotyping kits outside the United States and Europe, especially in areas where non-B HIV-1 subtypes are prevalent.