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Introduction: HBV can evolve under selection pressure exerted by drugs and/or host immunity, resulting in accumulation of escape mutations that can affect the drug or the immune activity. Hepatitis delta virus (HDV) coinfection is also known to exert selection pressure on HBV, which leads to selective amplification of certain mutations, especially in genes that are required for HDV pathogenesis, such as HBsAg. However, little is known about the function of these mutations on HBV or HDV life cycle. The purpose of this study is to determine mutations selectively amplified in the backdrop of HDV, and how these mutations affect processing of CD4‐ and CD8‐T cell epitopes. Methods: HBsAg was successfully amplified from 49/50 HBV mono‐ and 36/50 coinfected samples. The sequences were used to identify mutations specific to each study group, followed by an in silico analysis to determine the effect of these mutations on (1) proteasomal degradation, (2) MHC‐I and MHC‐II biding, and (3) processing of T‐cell epitopes. Results: HBV‐HDV coinfected sequences exhibited certain unique mutations in HBsAg genes. Some of these mutations affected the generation of proteasomal sites, binding of HBsAg epitopes to MHC‐I and ‐II ligands, and subsequent generation of T‐ cell epitopes. Conclusion: These observations suggest that HBV selectively amplifies certain mutations in the backdrop of HDV coinfection. Selective amplification of these mutations at certain strategic locations might not only enable HBV to counteract the inhibitory effects of HDV on HBV replication but also facilitate its survival by escaping the immune response. [ABSTRACT FROM AUTHOR]

Worldwide antiretroviral therapy (ART) has reduced the mortality and morbidity rates in individuals with HIV infection. However, the increasing occurrence of drug resistance is limiting treatment options. In recent years, Pakistan has witnessed a concentrated epidemic of HIV. It is very important to identify geographical linkages and mutations that generate selective pressure and drive resistance of HIV in our population. The aim of this work was to identify genetic diversity and drug resistance patterns of HIV in Pakistan, using available sequences and bioinformatics tools, which may help in selecting effective combination of available drugs. A total of 755 Pakistani HIV gag, pol and env sequences were retrieved from the Los Alamos HIV database. Sequences were aligned with reference sequences of different subtypes. For geographical linkages, sequences of predominant subtypes were aligned with sequences of the same subtypes from different countries. Phylogenetic trees were constructed using the maximum-likelihood method in MEGA 7 software. For drug resistance analysis, sequences were entered into the Stanford University HIV Drug Resistance Database. Phylogenetic trees for studying genetic diversity showed that 82% of the sequences were of subtype A, while the rest of the sequences were of subtypes B (9.5%), K (2%), D (2%) and AE (1%). Moreover, trees that were constructed to examine geographical linkages showed close clustering of strains with those of the neighboring countries Afghanistan and India, as well as some African countries. A search for drug resistance mutations showed that 93% of the sequences had no major or minor mutations. The remaining 7% of the sequences contained a major mutation, Y115F, which causes the virus to exhibit low to intermediate resistance against lamivudine and emtricitabine. Our data indicate that HIV subtype A is the major subtype, while subtypes K, D and AE are also present in our country, suggesting gradual viral evolution and possible entry of different subtypes from neighboring countries. These data suggest that HIV is still sensitive to most of the antiretroviral drugs used in Pakistan. [ABSTRACT FROM AUTHOR]

Objective: To study the ratio of false negativity in sputum samples in diagnostic smears received for acid fast bacilli smear microscopy., Methods: The retrospective cross-sectional study was conducted at the Ojha Institute of Chest Diseases, Karachi, and comprised specimens for microscopy and culture from presumptive tuberculosis patients for 38 months starting from November 2010.All laboratory investigations had been done as per the National Tuberculosis Control Programme guidelines. Statistical analyses were performed on MedCalc and Social statistics calculators, and Open Epi software., Results: TOf the 2,158 specimens, 1,316(60.98%) were of men and 842(39.02%) of women (male-to-female ratio: 1.56:1). Besides, 843(39.06%) were smear-negative, of which 99(11.74%) were false negative. Of the 1,275(96.88%) men whose age was reported, 808(63.37%) were aged 19-45 years, whereas out of the 792(94.06) women whose age was known, 517(65.28%) were in that age group. Microscopic outcomes were significantly related to gender (p<0.001)., Conclusions: Smear microscopy cannot be solely relied upon for diagnosis and its results must be correlated with additional clinical information and other diagnostics due to considerable amount of false negativity, especially in female population.