Molecular confirmation of human immunodeficiency virus (HIV) type 2 in HIV-seropositive subjects in south India

The development, evaluation, performance, and validation of micro-PCR and extractor for the quantification of HIV-1 &-2 RNA

HIV infection has been a global public health threat and overall reported ~ 40 million deaths. Acquired immunodeficiency syndrome (AIDS) is attributed to the retroviruses (HIV-1/2), disseminated through various body fluids. The temporal progression of AIDS is in context to the rate of HIV-1 infection, which is twice as protracted in HIV-2 transmission. Q-PCR is the only available method that requires a well-developed lab infrastructure and trained personnel. Micro-PCR, a portable Q-PCR device, was developed by Bigtec Labs, Bangalore, India. It is simple, accurate, fast, and operationalised in remote places where diagnostic services are inaccessible in developing countries. This novel micro-PCR determines HIV-1 and HIV-2 viral load using a TruePrep™ extractor device for RNA isolation. Five ml blood samples were collected at the blood collection centre at AIIMS, New Delhi, India. Samples were screened for serology, and a comparison of HIV-1/2 RNA was done between qPCR and micro-PCR in the samples. The micro-PCR assay of HIV-RNA has compared well with those from real-time PCR (r = 0.99, i < 0.002). Micro-PCR has good inter and intra-assay reproducibility over a wide dynamic range (1.0 × 102-1.0 × 108 IU/ml). The linear dynamic range was 102-108 IU/ml. The clinical and analytical specificity of the assay was comparable, i.e., 100%. Intra-assay and inter-assay coefficients of variation ranged from 1.17% to 3.15% and from 0.02% to 0.46%, respectively. Moreover, due to the robust, simple, and empirical method, the Probit analysis has also been done for qPCR LODs to avoid uncertainties in target recoveries. The micro-PCR is reliable, accurate, and reproducible for early detection of HIV-1 and HIV-2 viral loads simultaneously. Thus, it can easily be used in the field and in remote places where quantification of both HIV-1/2 is not reachable.

HIV-1/2 differentiation in a South African public laboratory

Background

The human immunodeficiency virus type-2 (HIV-2) prevalence in South Africa (SA) is unknown, however, sporadic cases have been reported. Human immunodeficiency virus -1 and 2 differentiation is not part of most South African public laboratories’ testing algorithm. Human immunodeficiency virus -2 diagnosis using serology assays may be complicated by HIV-1 and HIV-2 antibody cross-reactivity.

Objectives

To determine the proportion of HIV-2 infections in specimens that tested HIV-1/2 positive at a public laboratory in Tshwane.

Method

A total of 480 specimens that were previously tested with fourth generation ELISA platforms (Modular E170 [Roche, Switzerland] and Architect i2000 [Abbott, Germany]) were randomly selected. Human immunodeficiency virus -1 and 2 antibody differentiation testing was carried out using the Multispot HIV-1/2 rapid assay (Bio-Rad Laboratories, USA). An in-house nested HIV-2 PCR assay targeting the 5′-long terminal repeats (5′-LTR) region was evaluated and used as a confirmatory test.

Results

The study tested 480 HIV-1/2 seropositive patients and their mean age was 36.7 years (range 3–82 years). Of the 480 patients, 292 (60.8%) were female, 182 (37.9%) were male and 6 (1.3%) were not specified. Human immunodeficiency virus differentiation results were as follows: 466 (97.1%) were positive for only HIV-1 antibodies, 11 (2.3%) [95%CI: (0.98%; 3.74%)] were positive for both HIV-1 and HIV-2 antibodies, 3 (0.6%) were negative for both antibodies and none were positive for only HIV-2 antibodies. Of the 11 specimens with both HIV-1 and HIV-2 antibodies, seven had sufficient volume for confirmatory testing and were all negative on the in-house HIV-2 PCR assay.

Conclusion

The multispot HIV-1/2 rapid assay demonstrated cross-reactivity between HIV-1 and HIV-2 antibodies. Human immunodeficiency virus -2 infections were not detected.

Genetic Characterization of Full-Length HIV-2 Long Terminal Repeat Sequences: Identification of Rare Promoter Variants

In this study, we sequenced the full-length HIV type 2 (HIV-2) long terminal repeat region from the proviral DNA of 23 HIV-2-infected individuals from the southern parts of India. We identified two different promoter variant strains circulating in this region along with the globally circulating common promoter variant. Seven sequences had an additional nuclear factor kappa-light chain enhancer of activated B cells (NF-κB) binding motif and the sequence from another subject showed one NF-κB and one RBE-III binding site. Phylogenetic and subtyping analyses revealed that the circulating strains comprised HIV-2 subtype A. The occurrence of two NF-κB binding sites in ∼30% of the sequences analyzed in our study prompts us to hypothesize that as in the case of HIV-1 subtype C viruses that possess additional κB sites, the two NF-κB HIV-2 variants might possess superior replication fitness because of the increased magnitude of transcription, thus leading to the expansion of these variants in the country.

Male Circumcision and the Epidemic Emergence of HIV-2 in West Africa

BACKGROUND

Epidemic HIV-2 (groups A and B) emerged in humans circa 1930-40. Its closest ancestors are SIVsmm infecting sooty mangabeys from southwestern Côte d'Ivoire. The earliest large-scale serological surveys of HIV-2 in West Africa (1985-91) show a patchy spread. Côte d'Ivoire and Guinea-Bissau had the highest prevalence rates by then, and phylogeographical analysis suggests they were the earliest epicenters. Wars and parenteral transmission have been hypothesized to have promoted HIV-2 spread. Male circumcision (MC) is known to correlate negatively with HIV-1 prevalence in Africa, but studies examining this issue for HIV-2 are lacking.

METHODS

We reviewed published HIV-2 serosurveys for 30 cities of all West African countries and obtained credible estimates of real prevalence through Bayesian estimation. We estimated past MC rates of 218 West African ethnic groups, based on ethnographic literature and fieldwork. We collected demographic tables specifying the ethnic partition in cities. Uncertainty was incorporated by defining plausible ranges of parameters (e.g. timing of introduction, proportion circumcised). We generated 1,000 sets of past MC rates per city using Latin Hypercube Sampling with different parameter combinations, and explored the correlation between HIV-2 prevalence and estimated MC rate (both logit-transformed) in the 1,000 replicates.

RESULTS AND CONCLUSIONS

Our survey reveals that, in the early 20th century, MC was far less common and geographically more variable than nowadays. HIV-2 prevalence in 1985-91 and MC rates in 1950 were negatively correlated (Spearman rho = -0.546, IQR: -0.553--0.546, p≤0.0021). Guinea-Bissau and Côte d'Ivoire cities had markedly lower MC rates. In addition, MC was uncommon in rural southwestern Côte d'Ivoire in 1930.The differential HIV-2 spread in West Africa correlates with different historical MC rates. We suggest HIV-2 only formed early substantial foci in cities with substantial uncircumcised populations. Lack of MC in rural areas exposed to bushmeat may have had a role in successful HIV-2 emergence.

HIV-2 Infection: Where Are We Today?

Context:

The choice of antiretroviral therapy for HIV-2 differs from that for HIV-1, underscoring the importance of differentiating between the two.

Aims:

The current study was planned to find out the prevalence of HIV-2 infection at our center and to find out the utility of the current diagnostic algorithm in identifying the type of HIV infection.

Setting and Design:

Retrospective analysis in a tertiary care teaching institute over a period of three years.

Materials and Methods:

All patients diagnosed as HIV infected using NACO/WHO HIV testing strategy III were included in the study. They were classified as HIV-1 infected, HIV-2 infected and HIV-1 and HIV-2 co-infected based on their test results. For discordant samples, immunoblotting result from National Reference Laboratory was considered as final.

Statistical Analysis Used:

Comparison between HIV-1, HIV-2 and HIV-1+2 positive groups for age, gender, route of transmission was made using chi squared test. P value < 0.05 was considered as significant.

Results:

Of the total of 66,708 patients tested, 5,238 (7.9%) were positive for HIV antibodies. 7.62%, 0.14%, 0.08% and 0.004% were HIV-1, HIV-2, HIV-1 and HIV-2 co-infected and HIV type indeterminate (HIV-1 Indeterminate, 2+) respectively. The current algorithm could not differentiate between the types of HIV infection (as HIV-1 or HIV-2) in 63 (1.2%) cases.

Conclusion:

In areas like the Indian subcontinent, where epidemic of both HIV-1 and HIV-2 infections are ongoing, it is important to modify the current diagnostic algorithms to diagnose and confirm HIV-2 infections.

Molecular phylogenetics of nearly full-length HIV type 2 envelope gene sequences from West India

Abstract While infection with HIV-1 has become a pandemic, the presence of HIV-2 is also of concern in certain regions of the world. We have characterized the gp105 region of the envelope gene of HIV-2 isolates from Western India. Phylogenetic analysis of all 18 sequences revealed that these sequences were closely related to each other as well as to published African and European HIV-2 group A sequences, with an overall genetic divergence of 10.9% (range 2-14%). Our study sequences showed close relatedness with West African HIV-2 group A (CAM group) sequences from Guinea Bissau with 89% homology. This was further confirmed by SimPlot as well as RIP analysis. Accordingly, the sequences presented here demonstrate the predominance of HIV-2 group A infection and show no evidence of HIV-2 recombination in Western India.

Molecular investigation of human immunodeficiency virus type 2 subtype a cases in South Korea

We investigated the molecular characteristics of human immunodeficiency virus type 2 (HIV-2) subtype A isolates to clarify the transmission mode of HIV-2 within Korea. These findings indicated that the viruses from the six patients infected within Korea formed a distinct subcluster in the phylogenetic tree and might have been transmitted from one source.

Performance of a rapid immunochromatographic screening test for detection of antibodies to human immunodeficiency virus type 1 (HIV-1) and HIV-2: experience at a tertiary care hospital in South India

The performance characteristics of a rapid immunochromatographic-screening test, SD Bioline HIV-1/2 3.0 (Standard Diagnostics Inc., Kyonggi-do, South Korea) on 23,754 sera and 30 plasma samples are reported. The sensitivity and specificity for the assay on serum samples are 100% and 99.4%, respectively. The assay detected antibodies in individuals infected with human immunodeficiency virus type 1 (HIV-1) genotypes A and C and HIV-2. This straightforward assay is a reliable diagnostic tool for screening HIV in resource-poor settings.

HIV-2 subtype circulating in India (south)

The genetic types and subtypes of HIV vary from region to region. This study looked at the relative prevalence of HIV-2 subtypes in south India. Nucleotide sequencing of the HIV-2 envelope V3 region of strains from 11 individuals infected with HIV-2 and one individual who had dual infection with HIV-1 and HIV-2 was performed. Phylogenetic analysis showed that all individuals were infected with HIV-2 subtype A. These strains were from individuals who live in different regions of south India. In all, up to present, 17 strains inclusive of the authors' 12 have been sequenced, and subtype A of HIV-2 is seen in both monoinfections and dual infections with HIV-1 in India.

Introduction of human immunodeficiency virus type 2 infection in the Philippines

The aim of this study was to describe and document the first case of human immunodeficiency virus type 2 (HIV-2) in the Philippines by using serological and molecular techniques and to compare the diversity of this strain to that of strains from other countries. With the introduction of HIV-2 into the country and the presence of diversified strains of HIV-1, the use of highly sensitive assays to detect all these strains is recommended.

Prevalence and origin of HIV-1 group M subtypes among patients attending a Belgian hospital in 1999

HIV-1 group M strains are usually subtyped based on gag and/or env gene sequences. In our lab, part of the pol gene sequence was available in order to determine the genotypic anti-HIV drug resistance profile. To estimate the prevalence of the different HIV-1 subtypes in patients visiting the University Hospitals in Leuven in 1999 and for whom a genotypic drug resistance test was needed, we tried to use the pol sequence for subtyping. Recombination was investigated by similarity plots and bootscanning and subtyping was performed by phylogenetic analysis. The overall region spanning the entire protease and 747 nucleotides of the reverse transcriptase proved very suitable for subtyping, although there was a low phylogenetic signal at the beginning of the reverse transcriptase (nucleotides 0-250), as we demonstrated by likelihood mapping. Of the 41 samples analyzed, 21 belonged to subtype B. Of the other 20 non-B strains, 9 belonged to subtype C, 2 to subtype D and 1 to subtype A, G, H and J, respectively, 3 were CRF_02 (Circulating Recombinant Form), 1 was recombinant with a novel breakpoint and 1 sample was untypable. Although subtype B is still the most prevalent subtype in Belgium, it seems to be responsible for only half of the infections in this study. We could also document that the prevalence of subtype C is high in the Belgian native patients, especially among the heterosexually infected population. This could possibly be an indication for an epidemic spread of HIV-1 subtype C in Belgium, as for one third of these patients, no link to an endemic region could be found. The other non-B subtypes and the recombinants are mainly introduced by immigrants or by Belgian citizens traveling abroad.

A peptide enzyme linked immunosorbent assay (ELISA) for the detection of human immunodeficiency virus type-2 (HIV-2) antibodies: an evaluation on polymerase chain reaction (PCR) confirmed samples

BACKGROUND

HIV-1 and HIV-2 infections differ in prognosis, and may also require different prevention and/or treatment approaches. Thus, estimating the true prevalence of HIV-1 and HIV-2 infections, as well as co-infections, is a critical step in controlling the disease. There are a few commercial ELISA and immunoblot kits, which can differentiate between HIV-1 and HIV-2 infections. However, some of these assays overestimate the prevalence of dual infection. Hence, it is necessary to develop assays capable of discriminating between the two infections.

OBJECTIVES

To develop a synthetic HIV-2 env based peptide ELISA for the detection of HIV-2 specific antibodies and evaluate its performance on samples from HIV positive individuals previously tested by HIV-1 and HIV-2 PCR and HIV seronegative individuals.

STUDY DESIGN

We studied 45 HIV seronegative and 63 HIV infected individuals, including 30 HIV-1 PCR and immunoblot positives, 19 HIV-2 PCR and immunoblot positives, five HIV-1 and two PCR and dual immunoblot positives, two PCR negative but positive for HIV-2 by immunoblot and seven dual immunoblot positives who were only positive for HIV-1 by PCR.

RESULTS

All 24 HIV-2 PCR positive samples tested were positive by the peptide assay. Among 30 HIV-1 PCR and immunoblot positive samples, only one (3.3%) showed an absorbance value above the cut off level. The seven dual positive samples by immunoblot (only positive for HIV-1 by PCR) were negative by the HIV-2 peptide ELISA. There was a 100% concordance between HIV-2 PCR and peptide ELISA. The sensitivity, specificity, and the likelihood ratio for the peptide ELISA were 100,94.9, and 19.5, respectively when compared against the PCR findings.

CONCLUSIONS

This ELISA, using a specific immunodominant epitope (11 amino acids) from the transmembrane (gp36) portion of the HIV-2 envelope glycoprotein showed a high concordance with PCR findings. This can be considered as a highly sensitive, specific and economically feasible assay for the discrimination of HIV-1 and HIV-2, and may serve as an alternative to HIV-2 PCR in epidemiological studies.