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Background and Objectives: A virus population often exists as a complex mixture of genetic populations. Antiviral-resistant mutants could be circulating as minority variants in the mixed virus population that are not detected by standard sequencing methods. The role of minor drug-resistant variants and clinical outcome is slowly evolving and there is a need to employ sensitive methods for detection of minority variants that emerge as dominant species and subsequently affect the antiviral efficacy. This study was intended to develop a technique called the ligation amplification assay (LigAmp) to identify minor drug-resistant variants of hepatitis B virus (HBV). Methods: A LigAmp HBV assay was developed and clinical samples were tested from chronic hepatitis B subjects on antiviral treatment. Nucleotide sequencing of HBV reverse transcriptase (rt) region was performed and the results were compared with LigAmp assay. The performance of LigAmp assay was validated by clonal sequencing. Virological response was measured using HBV DNA levels and the results were correlated with antiviral-resistant mutations detected by sequencing and LigAmp assays. Results: A total of 80 reactions of LigAmp assay were performed for rtM204V and rtM204I (ATT) mutant detection. Samples were obtained from 40 chronic hepatitis B subjects. Among these subjects, rtM204V and rtM204I (ATT) mutations were identified by standard sequencing in 10 (25 %) and 12 (30 %) subjects, respectively. LigAmp detected both rtM204V and rtM204I (ATT) mutations in 13 (32.5 %) subjects, rtM204I mutation in 12 (30 %) subjects and rtM204V mutation in 1 (2.5 %) subject, respectively. LigAmp detected primary resistant mutants in 69.4 % of lamivudine non-responders while sequencing detected resistant mutations in only 55.6 % subjects ( p < 0.001). Conclusions: This data shows significantly higher sensitivity of LigAmp for detection of minority rtM204V and rtM204I (ATT) mutations over standard sequencing. Therefore, LigAmp has potential clinical utility for appropriate monitoring and tailoring of HBV therapy. [ABSTRACT FROM AUTHOR]

Background and objective: Management of chronic hepatitis B is a global public health challenge. There are several updated guidelines proposed based on treatment outcome data from the respective study populations. In this study, we aim to characterize the antiviral resistance mutations to lamivudine monotherapy in patients diagnosed with chronic hepatitis B from the Indian subcontinent. Methods: A total of 147 lamivudine-treated patients with a median treatment duration of 13 (interquartile range 8-24) months were studied. Virological response was measured by hepatitis B virus (HBV) DNA levels. Antiviral resistance mutations were identified by sequencing HBV reverse transcriptase domains. Factors associated with virological response and antiviral resistance mutations were analyzed. Results: Virological response was observed in 50 (35 %) patients while 84 (57 %) were non-responders. The virological response for the remaining 13 (9 %) patients was undetermined. Forty patients (27 %) developed lamivudine-resistant mutations. HBV genotypes, subgenotypes and hepatitis B surface antigen subtypes did not show significant association with virological response or lamivudine-resistant mutations. High HBV DNA levels and increased treatment duration were strongly associated with the development of lamivudine-resistant mutations ( p = 0.002 and p < 0.001). Patients who continued to be positive for hepatitis B e antigen have an increased risk for treatment failure ( p = 0.010). High baseline aspartate transaminase levels were significantly associated with subsequent lamivudine response ( p = 0.037). Conclusion: Considering the limited potency and high resistance rates to lamivudine therapy, our study emphasizes the use of more potent drugs in the management of chronic hepatitis B in the Indian subcontinent. [ABSTRACT FROM AUTHOR]

Background and objective: HIV-1 uses co-receptors CCR5 and CXCR4 in addition to CD4 for viral entry into cells. CCR5 is used in the early stages of HIV-1 infection, but viruses that utilize CXCR4 for viral entry emerge in the later stages. This is not common among clade Cstrains, with previous data from India showing the absence of the emergence of CXCR4-using strains. Sequence analysis has demonstrated that the V3 loop plays a very important role in determining the syncytium-inducing (SI) phenotype. The V3 region of the SI variants were observed to have positively charged amino acids at positions 11 and/or 25 and also a overall higher charge. This study looked at co-receptor usage among HIV-1 strains in India from individuals who were antiretroviral therapy (ART) naïve and those not responding to ART. Methods: Amplification and sequencing of the HIV-1 env gp120 V3 region was done on 40 ART-naïve individuals, who were selected for the study based on their CD4 counts, and eight patients who had not responded to ART. The sequences were submitted to Geno2Pheno and Web PSSM. The pol gene sequences of these strains were submitted to the REGA HIV-1 subtyping tool. Results: Forty-seven strains were identified as clade C and one strain as clade A1. Geno2Pheno identified three CXCR4-using strains, and the Web PSSM clade C matrix identified two. Conclusion: We report, for the first time, CXCR4-using strains among HIV-1 clade C strains circulating in India. [ABSTRACT FROM AUTHOR]

Introduction: Morbidity and mortality among HIV-1-infected individuals has been dramatically reduced by the implementation of combinational antiretroviral therapy (ART). However, the efficiency of these therapies is compromised due to HIV-1 transmitted drug resistance mutations (TDRMs). Methods: We collected a total of 127 samples from ART-naïve HIV-infected individuals and sequenced the pol gene and analysed for drug resistance mutations using the Calibrated Population Resistance (CPR) tool in the Stanford database. Results: All the 127 clinical samples (100 %) were identified as HIV-1 subtype C. Based on the CPR tool, three strains (2.4 %) had TDRMs, and these were K101E, Y181C and G190A. Our findings correlated well with the WHO surveys conducted in Asia, including India, which consistently reported <5 % TDRM among the specific populations assessed. Conclusion: In countries like India, regular monitoring of TDRMs will provide better information for clinical practice improvement and policy making. [ABSTRACT FROM AUTHOR]