Confirming genes influencing risk to cleft lip with/without cleft palate in a case-parent trio study

A collection of 1,108 case-parent trios ascertained through an isolated, nonsyndromic cleft lip with or without cleft palate (CL/P) was used to replicate the findings from a genome-wide association study (GWAS) conducted by Beaty et al. (Nat Genet 42:525-529, 2010), where four different genes/regions were identified as influencing risk to CL/P. Tagging SNPs for 33 different genes were genotyped (1,269 SNPs). All four of the genes originally identified as showing genome-wide significance (IRF6, ABCA4 and MAF, plus the 8q24 region) were confirmed in this independent sample of trios (who were primarily of European and Southeast Asian ancestry). In addition, eight genes classified as 'second tier' hits in the original study (PAX7, THADA, COL8A1/FILIP1L, DCAF4L2, GADD45G, NTN1, RBFOX3 and FOXE1) showed evidence of linkage and association in this replication sample. Meta-analysis between the original GWAS trios and these replication trios showed PAX7, COL8A1/FILIP1L and NTN1 achieved genome-wide significance. Tests for gene-environment interaction between these 33 genes and maternal smoking found evidence for interaction with two additional genes: GRID2 and ELAVL2 among European mothers (who had a higher rate of smoking than Asian mothers). Formal tests for gene-gene interaction (epistasis) failed to show evidence of statistical interaction in any simple fashion. This study confirms that many different genes influence risk to CL/P.

Evaluation of two indigenous rapid and two ELISA assays for the diagnosis of HIV infection India

PURPOSE

Human immunodeficiency virus (HIV) diagnostic tests are being used extensively in India. However, the evaluation data on these assays are very limited. The present study evaluates indigenous HIV test kits manufactured in India.

MATERIALS AND METHODS

A total of 200 characterised specimens were assayed with Comb AIDS - RS Advantage HIV 1+2 Immunodot Test, Enzaids HIV 1+2 ELISA test, Enzaids Duet HIV Antigen+antibody ELISA test and Signal HIV Flow Through HIV 1+2 test kits. Performance characteristics of these assays were calculated.

RESULTS

Sensitivity, specificity, positive predictive value, negative predictive value and efficiency of all the assays were 100% except for Signal HIV Flow Through HIV 1+2 test kit. The specificity, positive predictive value and efficiency of the Signal HIV Flow Through HIV 1+2 test kit were 98.9%, 98.9% and 99.4%, respectively. The Enzaids Duet HIV kit was found to be extremely sensitive in detecting p24 Ag with the sensitivity of 1.5 pg/mL.

CONCLUSIONS

To conclude, selection of better diagnostic assay is very much important to resolve discrepancies in HIV diagnosis. All these assays under evaluation in this report have got excellent performance characteristics and much suitable to use in serial testing algorithms in use for resources limited settings.

Impact of international laboratory partnerships on the performance of HIV/sexually transmitted infection testing in five resource-constrained countries

To review a quality control and quality assurance (QC/QA) model established to ensure the validity and reliability of collection, storage and analysis of biological outcome data, and to promote good laboratory practices (GLPs) and sustained operational improvements in international clinical laboratories, we conducted a two-arm randomized community-level HIV behavioural intervention trial in five countries: China, India, Peru, Russia and Zimbabwe. The trial was based on diffusion theory utilizing a Community Popular Opinion Leaders (CPOLs) intervention model with behavioural and biological outcomes. The QC/QA model was established by the Biological Outcome Workgroup, which collaborated with the Data Coordinating Center and John Hopkins University Reference Laboratory. Five international laboratories conducted chlamydia/gonorrhoea polymerase chain reaction (PRC)-based assays, herpes simplex virus type 2 enzyme immunoassay (EIA), syphilis serology (rapid plasma regain and Treponema pallidum particle agglutination assay, HIV serology (EIA/Western blot) and Trichomonas vaginalis culture. Data were collected at baseline, 12 and 24 months. Laboratory performance and infrastructure improved throughout the trial. Recommendations for improvement were consistently followed. Quality laboratories in resource-poor settings can be established, operating standards can be improved and certification can be obtained with consistent training, monitoring and technical support. Building collaborative partnership relations can establish a sustainable network for clinical trials, and can lead to accreditation and international laboratory development.

Couples at risk for HIV infection in Southern India: characteristics of HIV-infected patients in concordant and discordant heterosexual relationships

The aim of the article is to compare the clinical and behavioural characteristics of HIV-infected South Indian patients in concordant and discordant heterosexual relationships. A cross-sectional analysis of married couples in concordant and discordant relationships was carried out. Demographic and clinical characteristics, sexual behaviours, CD4 cell count and plasma HIV-1 RNA loads were assessed. A total of 839 concordant patients and 996 discordant patients were included in this analysis. Significantly more men were in discordant than concordant relationships (97% versus 59%; P = 0.002). More discordant patients had never initiated highly active antiretroviral treatment (HAART) than concordant patients (14.1% versus 8.5%; P = 0.004). Concordant patients had significantly higher CD4 cell counts than discordant patients at the time of enrolling to care (205 versus 139 cells/μL; P = 0.001). Discordant patients had significantly higher plasma viral loads than concordant patients (100,000 copies/mL versus 89,154 copies/mL; P = 0.002). Discordant patients were more likely to use condoms with their spouses than concordant patients (49% versus 28.8%; P = 0.01).

In conclusion, couples-based interventions and the provision of HAART could substantially decrease behavioural and clinical correlates of HIV transmission among discordant South Indian married couples. The spouses of HIV-infected index patients are at increased risk for HIV infection, and further preventive measures are needed.

Risk factors for HIV transmission among heterosexual discordant couples in South India

OBJECTIVE

To assess the risk factors associated with heterosexual HIV transmission among South Indian discordant couples enrolled in clinical care.

METHODS

A nested matched case-control study of serodiscordant couples in which the HIV-infected partner (index case) was enrolled in care. Demographic and clinical characteristics, sexual behaviours, CD4 cell count and plasma HIV-1 RNA loads were measured at enrollment and longitudinally over 12 months of follow-up. The study included 70 cases who seroconverted during study follow-up and 167 matched controls who remained persistently serodiscordant.

RESULTS

The incidence of HIV infection among the initially seronegative partners was 6.52 per 100 person-years. Persistently discordant patients were more likely to have initiated highly active antiretroviral therapy (HAART) than patients in seroconverting relationships (62.9%vs. 42.9%) (P=0.001). Patients in seroconverting relationships had significantly higher plasma viral loads (PVLs) than patients in discordant relationships at enrolment, at 6 months and at 12 months (P<0.05). Patients in seroconverting relationships were less likely to use condoms with their primary partners than patients in discordant relationships (P<0.05). Patients in relationships that seroconverted between 6 and 12 months were diagnosed more often with genital Herpes simplex than patients in discordant relationships (P=0.001). In the univariate and multivariate logistic regression, the following variables were associated with seroconversion: PVL >100,000 [odds ratio (OR): 1.82; 95% confidence interval (CI): 1.1-2.8], non-disclosure of HIV status (OR: 5.5; 95% CI: 4.3-6.2) and not using condoms (OR: 2.8; 95% CI: 2.4-3.6).

CONCLUSIONS

Couples-based intervention models are crucial in preventing HIV transmission to seronegative spouses. Providing early treatment for sexually transmitted infections, HAART and enhancing condom use and disclosure could potentially decrease the risk of HIV transmission within Indian married couples.

Primary HIV-1 drug resistance and polymorphic patterns among injecting drug users (IDUs) in Chennai, Southern India

BACKGROUND AND OBJECTIVE

India has 1.1 million injecting drug users (IDUs) with an HIV prevalence rate as high as 64%. Drug resistance screening before therapy is beneficial to the individual. Here, we have studied primary drug resistance among IDUs in Chennai.

METHODS

Specimens (n = 55) collected between March 2005 and April 2006 were subjected to genotyping assay. The mutations for the drug resistance were interpreted using the Stanford HIV Drug Resistance Database.

RESULTS

M41LM (1.8%), K65KN (1.8%), and G73GS (2.7%) were found to be associated with low-level resistance to zidovudine (ZDV), stavudine (d4T), abacavir (ABC), didanosine (ddI), emtricitabine (FTC), tenofovir (TDF), and saquinavir (SQV) in each specimen. The rate of polymorphisms is significantly different from universally established subtype ''C''-specific polymorphisms (P < .0001).

CONCLUSION

The presence of drug resistance mutations, though minimal, is alarming as it could spread easily between IDUs and from them to their sexual partners. The genetic variation is of importance in vaccine design.

Evaluation of two human immunodeficiency virus-1 genotyping systems: ViroSeq 2.0 and an in-house method

Commercial HIV-1 genotypic resistance assays are very expensive, particularly for use in resource-constrained settings like India. Hence a cost effective in-house assay for drug resistance was validated against the standard ViroSeq HIV-1 Genotyping System 2.0 (Celera Diagnostics, CA, USA). A total of 50 samples were used for this evaluation (21 proficiency panels and 29 clinical isolates). Known resistance positions within HIV-1 protease (PR) region (1-99 codons) and HIV-1 reverse-transcriptase (RT) region (1-240 codons) were included. The results were analysed for each codon as follows: (i) concordant; (ii) partially concordant; (iii) indeterminate and (iv) discordant. A total of 2750 codons (55 codons per patient samplex50 samples) associated with drug resistance (1050 PR and 1700 RT) were analysed. For PR, 99% of the codon results were concordant and 1% were partially concordant. For RT, 99% of the codon results were concordant, 0.9% were partially concordant and 0.1% were discordant. No indeterminate results were observed and the results were reproducible. Overall, the in-house assay provided comparable results to those of US FDA approved ViroSeq, which costs about a half of the commercial assay ($ 100 vs. $ 230), making it suitable for resource-limited settings.

Cofactors for Low Serum Albumin Levels Among HIV-Infected Individuals in Southern India

Background and aims. Malnutrition and low serum albumin among human immunodeficiency virus (HIV)-infected individuals are cofactors for HIV disease progression. The present study aimed to identify the proportion of HIV-infected individuals with low serum albumin and the possible cofactors among highly active antiretroviral therapy (HAART) experienced and HAART naïve individuals. Methods. A total of 835 HIV-infected individuals (HAART-experienced, HAART-naïve) were included in the study. Results. Of the 835 individuals, 44.6% had normal (4.2-5.2 g/dL) and 55.4% had abnormal (<4.2 g/dL) albumin levels. The abnormal group had significantly lower body mass index (BMI) compared with the normal group (P = .02). Among those with abnormal albumin, 388 (84%) were HAART experienced compared with 239 (64%) with normal albumin (P < .001). Among the abnormal group, 259 (55.9%) had CD4 count <200 cells/mL as compared with 124 (33.3%) in the normal group (P < .001). Conclusions. CD4 count and lower were the major cofactors for low serum albumin among HIV-infected individuals. Therefore, serum albumin would be a useful biochemical test for HIV disease in resource-limited settings.

Establishment of T-lymphocyte subset reference intervals in a healthy adult population in Chennai, India

Estimation of CD4+ T-lymphocytes continues to be an important aspect for monitoring HIV disease progression and response to antiretroviral therapy. Most of the diagnostic laboratories often rely on western text books for CD4+ T-lymphocyte reference values, which could, often be unreliable for usage in local settings. Therefore, we attempted to establish the reference values for T-lymphocyte subsets among healthy adults in a cross-sectional study carried out at the YRG Centre for AIDS Research and Education (YRG CARE) in Chennai, south India, in 213 (84 female and 129 male) healthy, HIV-1/2 seronegative adults as volunteers. Whole blood specimens were processed for CD4+, CD8+ T-lymphocyte estimation and haematological parameters. The established range of CD4+ T-lymphocyte counts for men and women were 383-1347 cells/microl (mean 865 and median 845 cells/microl) and 448-1593 cells/microl (mean 1021 and median 954 cells/microl), respectively. Women had significantly higher absolute CD4+ Tlymphocyte counts (P<0.001) and CD4+:CD8+ T-lymphocyte ratio as compared to men. The established normal range of CD4+ T-lymphocyte % was 21-59 (mean 40.2 and median 40.1). The influence of age was not observed in any of the parameters except CD4+/CD8+ T-lymphocyte ratio with the >45 yr age group. Further studies with greater sample size may be required to define the staging of HIV disease in relation to the normal CD4 T-lymphocyte count in the general population.

Gender-based differences in treatment and outcome among HIV patients in South India

OBJECTIVE

To describe gender-based differences in disease progression, treatment, and outcome among patients receiving highly active antiretroviral therapy (HAART) in South India.

METHODS

Therapy-naïve patients initiating HAART between February 1996 and June 2006 at a tertiary HIV referral center in Chennai, South India, were analyzed using the YRG CARE HIV Observational Database. Patients with 1 year of follow-up after initiating HAART were examined to investigate immunological and clinical outcomes, including the development of adverse events to therapy and opportunistic infections.

RESULTS

All previously therapy-naïve patients who initiated HAART with at least 1 year of follow-up (n = 1972) were analyzed. At enrollment into care, women had higher CD4 counts, lower hemoglobin, and higher body mass index (BMI) than their male counterparts (p < 0.05). At the time of initiating therapy, women had higher CD4 counts and lower hemoglobin (p < 0.05); women continued to have higher CD4 counts at 12 months (p < 0.05). After 1 year following HAART initiation, significantly more men developed tuberculosis and Pneumocystis jiroveci pneumonia (p < 0.05), more women experienced lactic acidosis and nausea, and more men developed immune reconstitution syndrome (p < 0.05).

CONCLUSIONS

Significant physiological, immunological, and clinical differences exist between men and women initiating HAART in a resource-limited setting in South India. Future studies should examine whether clinical management strategies should be different for men and women in resource-limited settings.

Prevalence and incidence of sexually transmitted infections among South Indians at increased risk of HIV infection

Sexually transmitted infections (STIs) have been identified as cofactors of HIV transmission. Greater understanding of local STI burdens can assist in the development of more effective STI and HIV prevention strategies. The aim of this study is to determine the prevalence and incidence of STIs among South Indian men and women identified to be at increased risk for HIV infection. Individuals at increased risk for HIV infection were enrolled in a prospective longitudinal study in Chennai, India (n = 480) between August 2002 and December 2003. Participants were enrolled from patients seeking services at an sexually transmitted disease (STD) clinic and a confidential HIV testing and counseling program. The most common prevalent STIs were herpes simplex virus (HSV)-2 (50% of women, 29% of men), syphilis (11% of women, 8% of men), and Trichomonas vaginalis (6% of women). At enrollment, women, participants with no schooling, participants with greater than four sex partners, and single participants were found to be at increased risk for HSV-2 infection (p < 0.05). The two most common incident STIs at 12 months were HSV-2 with 12% of men and 8% of women testing positive and hepatitis B with 2% of men and 5% of women testing hepatitis B surface antigen (HBsAg) positive. In this cohort of South Indian men and women with a high background prevalence of HSV-2, suppressive therapy against herpes replication may have a substantial impact in reducing both HSV-2 transmission and HIV acquisition. With the high incidence of STIs, targeted prevention and clinical management strategies among individuals practicing high risk behaviors may help to slow the continued spread of HIV in India.

Performance characteristics of a new rapid immunochromatographic test for the detection of antibodies to human immunodeficiency virus (HIV) types 1 and 2

Diagnostic kits for the detection of human immunodeficiency virus (HIV) antibodies have reached an unprecedented number. But choice of an ideal, cost-effective, and rapid test for HIV infection is of immense value for use in developing countries like India, where resources are limited. In this study we have evaluated the performance characteristics of the rapid immunochromatographic HIV test kit First Response HIV 1-2.O. First, the laboratory archived 450 characterized plasma/serum specimens, which were tested on First Response HIV 1-2.O. Second, a total of 134 consecutive voluntary counseling and testing (VCT) specimens were also tested and positive specimens were further confirmed with HIV TRI-DOT. All these VCT specimens were cross-checked with HIV double-enzyme-linked immunosorbent assay (ELISA) (Murex and Vironostika), and the results were matched. The sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and efficiency of First Response HIV 1-2.O with the 450 characterized specimens was 100% for HIV-1 with reference assay. The results in the VCT algorithm were correlating with double-ELISA. In the HIV-2 analysis, five HIV-2-positive specimens in First Response HIV 1-2.O were found to be HIV-2-indeterminate on Western blot. HIV TRI-DOT was unable to pick up two HIV-2 Western blot-positive specimens. First Response HIV 1-2.O has several advantages: low-cost (U.S. $0.70); only 10 microL of specimen; involves only two steps; room temperature storage; ability to differentiate HIV-1 and 2; and use of whole blood specimen. Hence this test kit could be suitable for initial screening in the HIV testing algorithm in resource-limited settings. J. Clin. Lab. Anal. 22:178-185, 2008. (c) 2008 Wiley-Liss, Inc.

Spectrum of adverse events after generic HAART in southern Indian HIV-infected patients

To determine the incidence of clinically significant adverse events after long-term, fixed-dose, generic highly active antiretroviral therapy (HAART) use among HIV-infected individuals in South India, we examined the experiences of 3154 HIV-infected individuals who received a minimum of 3 months of generic HAART between February 1996 and December 2006 at a tertiary HIV care referral center in South India. The most common regimens were 3TC + d4T + nevirapine (NVP) (54.8%), zidovudine (AZT) + 3TC + NVP (14.5%), 3TC + d4T + efavirenz (EFV) (20.1%), and AZT + 3TC + EFV (5.4%). The most common adverse events and median CD4 at time of event were rash (15.2%; CD4, 285 cells/microL) and peripheral neuropathy (9.0% and 348 cells/microL). Clinically significant anemia (hemoglobin <7 g/dL) was observed in 5.4% of patients (CD4, 165 cells/microL) and hepatitis (clinical jaundice with alanine aminotransferase > 5 times upper limits of normal) in 3.5% of patients (CD4, 260 cells/microL). Women were significantly more likely to experience lactic acidosis, while men were significantly more likely to experience immune reconstitution syndrome (p < 0.05). Among the patients with 1 year of follow-up, NVP therapy was significantly associated with developing rash and d4T therapy with developing peripheral neuropathy (p < 0.05). Anemia and hepatitis often occur within 12 weeks of initiating generic HAART. Frequent and early monitoring for these toxicities is warranted in developing countries where generic HAART is increasingly available.

Ethnic variation in certain hematological and biochemical reference intervals in a south Indian healthy adult population

BACKGROUND

We established the biochemical and hematological reference intervals among a south Indian healthy adult population attending an HIV referral centre in Chennai, southern India.

METHODS

In a cross sectional study, 213 study subjects (129 male and 84 female) were studied between March and August 2005. All of the parameters were analyzed using standard hematological and biochemical techniques.

RESULTS

Certain biochemical (viz. total bilirubin, alanine transaminase, albumin, creatinine, total protein, lipid profile, creatine phosphokinase, uric acid and lactate) and hematological (mean corpuscular hemoglobin, mean corpuscular hemoglobin concentration and lymphocyte levels) parameters presented higher upper limits. In addition, the upper limits of white blood cell count, platelet count, hematocrit, red blood cell count and hemoglobin level were low in comparison to the currently reported ranges.

CONCLUSION

Ethnic variation in reference intervals was observed in certain biochemical and hematological analytes in a south Indian adult population.

High proportion of isosporiasis among HIV-infected patients with diarrhea in southern India

We investigated 245 diarrheal stool specimens from HIV-positive subjects between January 2003 and December 2006 to determine the etiological role of coproparasites. Parasitic etiology was observed in 91 (37.1%) cases. Isospora belli (26.1%) was the most common parasite followed by Entameba histolytica/dispar (3.3%), Cryptosporidium spp. (2.9%), Giardia intestinalis (1.6%), and Strongyloides stercoralis (1.2%). Interesting trends of significant increase in the number of cases of I. belli and decline in Cryptosporidium spp. were observed during the study period.