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Abstract: Background: Human immunodeficiency virus type-1 (HIV-1) has developed marked genomic sequence differences over the course of an epidemic because of an error prone reverse transcriptase (RT), which rapidly incorporates mutations resulting in genomic diversity, altered cell tropism, immune escape and variable resistance to antiretroviral drugs. The best preventive strategy for HIV control is development of an efficacious prophylactic vaccine using the most appropriate (antigenically related) subtypes. On the basis of phylogenetic analysis, HIV strains can be separated into major group “M” consisting of genetic subtypes A–K, “N”, the new group and “O”, the outlier group. Methods: Heteroduplex mobility assay (HMA) is a rapid, economical and reliable technique of subtyping HIV-1. It is based on the principle of determining the genomic relatedness and divergence of the unknown sample with the known reference plasmid HIV-1 subtypes by studying the mobility patterns of the resulting heteroduplexes formed on the polyacrylamide gel. Result: A total of 70 HIV-1 seropositive samples obtained from service personnel, their families and civilians from service hospitals were analyzed and their subtype distribution studied. 66 (94.28%) were HIV-1 subtype C and two (2.85%) subtype B. In two (2.85%) samples, the subtype distribution was homotypic recombinant, one each of subtype C1 & C2 and C2 & C4 respectively. Conclusion: Service personnel and their families represent a divergent population from different regions of India. An analysis of subtypes in these HIV-1 seropositive individuals will help in understanding the geographical distribution and evolution of the virus. Determination of HIV-1 subtypes has significant implications for development of candidate vaccine for India. [Copyright &y& Elsevier]

Abstract: Background: Rapidly evolving viruses such as human immunodeficiency virus (HIV-1) develop marked sequence differences in their genome over the course of an epidemic and in individuals infected for longer duration. This is because of the error prone reverse transcriptase (RT), which rapidly incorporates mutations resulting in genomic diversity, altered cell tropism, immune escape, and variable resistance to antiretroviral drugs. As a result, radically different genomic combinations may be generated in individuals infected by genetically diverse viruses that have mosaic genomes. Methods: Whole blood sample was collected from 25 HIV-1 infected patients. Chromosomal DNA was isolated from the patient''s peripheral blood mononuclear cells (PBMCs). Full-length gag gene (∼1.5 kb) was amplified. PCR products were subjected to direct automated sequencing. For identification of recombinants Simplot version 2.5 was used. Results: Out of 25 gag genes that were sequenced, the gene amplified from a 29 years old HIV-1 seropositive male revealed a putative recombinant sequence. This sequence showed maximum homology with HIV-1 subtype A. Simplot analysis revealed the sequence to be a likely recombinant with the following composition: Initial stretch of 1 to 200 nucleotides representing AE circulating recombinant form (CRF), 201 to 440 nucleotides representing HIV-1 subtype A, 441 to 660 nucleotides representing AE CRF again, 661 to 700 nucleotides representing HIV-1 subtype A and the remaining stretch of the nucleotides from 701 to 1076 representing AE CRF. Conclusion: We document a putative HIV-1 subtype A/ AE CRF. It is important to monitor various CRFs that are being generated and horizontally spread in the community. This has significant implications for development of candidate vaccine for India. [Copyright &y& Elsevier]

Introduction: Enteric-fever is a major public-health problem in developing countries emerging as multidrug-resistant, Nalidixic-acid resistant and extremely drug-resistant Salmonella (Pakistan, 2016), has intensified the use of WHO watch/reserve group antimicrobials such as azithromycin and meropenem., Methods: This ambispective-study was conducted on 782 non-repeat blood-culture isolates of S. Typhi, S. Paratyphi A and S. Paratyphi B obtained from 29,184 blood cultures received at a 1000-bedded tertiary-care hospital of North-India from 2011-2017. Identification and antibiograms were obtained by Vitek-2 compact and Kirby-Bauer's disc diffusion with resistance to ampicillin, chloramphenicol and cotrimoxazole being labeled as multidrug-resistant. Decreased ciprofloxacin-susceptibility and ciprofloxacin-resistance were defined as MIC 0.125-0.5 and >1 μg/ml., Results: S. Typhi and S. Paratyphi A in a ratio of 3.9:1 were seen between July-September predominantly distributed between 6-45 year age group. Resistance to co-trimoxazole, chloramphenicol, ceftriaxone and azithromycin was 6.1%, 13.8%, 16.1 and 5.78% respectively. Multidrug-resistant S. typhi and S. paratyphi A were 2.73% and 1.91% respectively., Conclusion: Enteric-fever is a major public-health problem in India. Emergence of multidrug-resistant, Nalidixic-acid resistant and extremely-drug resistant Salmonella mandates ongoing surveillance for targeted empirical therapy and containment of spread. Repeated epidemics call for water, sanitation, hygiene and vaccination strategies to sustain herd-immunity.

Since the introduction of varicella vaccination in India, surveillance of circulating VZV strains has gained significance. Differentiating wild-type VZV strains from the Oka vaccine strain can be achieved only by molecular genotyping methods. The development of PCR methods for VZV strain differentiation has been hampered by the fact that the VZV genome is highly conserved. We used VZV ORF 62 PCR-RFLP analysis to identify and differentiate wild-type VZV strains in India from the Oka vaccine strain. Digestion of VZV ORF 62 amplicons with SmaI, enabled accurate strain differentiation; the Oka strain was positive for three SmaI sites, compared to two SmaI sites in the wild-type VZV strains that we tested.

Genomic variations in HIV-1 represent a major problem in understanding disease progression, studying drug resistance and developing effective vaccines. Heteroduplex Mobility Assay (HMA) was used for analyzing HIV-1 subtypes resulting from genetic similarity or divergence of C2 -V3 -V5 region of envelope gene between HIV-1 strains obtained from clinical samples in a tertiary care center at Pune. DNA from the PBMCs of infected individuals was amplified by nested PCR. Heteroduplexes were then formed by denaturing DNA from the unknowns with DNA from the reference strains. The results were analyzed by polyacrylamide gel electrophoresis. Out of 177 samples analyzed, 170 were of subtype C (96%). Four samples were found to be of subtype B (2.2%); in three samples, no definitive assignment of subtype was possible by HMA and these perhaps could be circulating recombinant forms (CRFs) of HIV-1. These findings may have significant implications toward development of a candidate vaccine for India.

The majority of the HIV drug resistance (HIVDR) testing studies have focused on subtype B virus. The predominance of subtype C in the Indian subcontinent along with greater access to antiretroviral therapy (ART) necessitates studies on HIVDR genotyping. We determined the prevalence of mutations associated with protease inhibitors (PI), nucleoside reverse transcriptase inhibitors (NRTI), and nonnucleoside reverse transcriptase inhibitors (NNRTI) from plasma of 40 antiretroviral drug-naive study participants in Indian HIV-1 pol gene sequences. Of these, 36 sequences belonged to subtype C, two to subtype A1, and two were subtype A1C recombinants. The heterosexual route was the most common route of transmission. Drug resistance-associated mutations were observed in 10% (4/40) of the study participants. The resistance mutation observed in the protease gene was V82A, whereas in the RT gene, M41L, D67N, M184V, and A98G were documented. This is the first study reporting major protease mutations by genotyping in ART-naive individuals from western India.

With the introduction of varicella vaccination in India, surveillance of circulating varicella-zoster strains has gained significance. The aim of the present study was to achieve molecular characterization of circulating varicella-zoster virus (VZV) strains and differentiation from the Oka vaccine strain. In this study, the genotype of 100 clinical VZV strains was analyzed. Vesicle fluid was collected from patients with VZV infections (92 cases of varicella and 8 cases of herpes zoster). The PCR-RFLP analysis of two polymorphic loci--a PstI restriction site in ORF 38 and a BglI restriction site in ORF 54 was used to characterize and differentiate them from the vaccine strain. All the wild-type strains were positive for the PstI restriction site in ORF 38. This differentiated them from the Oka vaccine strain, which is PstI negative. The wild-type strains as well as the Oka vaccine strain were positive for the BglI restriction site in ORF 54. Thus, the genotype of all the VZV strains examined had the wild-type pattern represented as PstI(+) BglI(+). None of the strains had the PstI(-) BglI(+) genotype characteristic of the Oka strain or the PstI(+) BglI(-) wild-type pattern. To conclude, PstI and BglI serve as good reference markers in the genotyping of circulating varicella strains in India and serve to differentiate them from the vaccine strain as well as other wild-type strains.

Twenty-four HIV-1 gag genes from patients in India were sequenced and analyzed. All measured 1476-1491 nucleotides with an average of 1483 nucleotides in length. Phylogenetic analysis revealed a homogeneous epidemic of HIV-1 subtype C. Intragenotypic divergence of up to 6.6% was present. Fourteen novel conserved signature pattern residues were delineated for HIV-1 subtype C strains. Each of the 15 nucleocapsid (NC) basic residues was highly conserved p6 gag LXSLFG and PT/SAPP motifs were highly conserved except for PTVPT in three and PTAPT in two strains. Zinc finger motifs were conserved in all. Documented HIV-1 subtype C gag immunodominant CTL epitopes were conserved. The evolving predominance and the change in nature of the epidemic from Thai B to that of subtype C in the Northeastern regions of India were observed. Tracking the evolution of the Indian epidemic has implications for developing a vaccine.

One hundred four Rheumatoid factor (RF) positive Rheumatoid Arthritis (RA) patients fulfilling ARA criteria were screened for extraarticular manifestations. Rheumatoid nodules were present in 2.8% cases. Other extraarticular manifestations such as pulmonary, cardiac, occular, renal or GI involvement were absent in these cases. However, circulating immune complexes (CICs) were highly significantly raised in all the RA patients (P < 0.001). From amongst these cases a limited number (8 cases) have been subjected to qualitative and quantitative analysis of CICs to look for whether there could be any relationship between these and mild extraarticular manifestations that were being noticed in our groups of patients. Finding showed IgG-IgG CICs in five, IgG-IgM in two and IgG-IgA in one case. Quantitative analysis revealed mean IgG 4.97 +/- 1.7 IU/ml, IgM 14.58 +/- 5.53 IU/ml and IgA 5.08 +/- 1.53 IU/ml on LD Solugen plates. Serum concentration of C3 was not reduced (94.1 +/- 8.9 mg/dl). Low IgM contents of CICs and no reduction in complement level is the likely explanation for less severe inflammatory manifestations seen in our study. The conclusion and findings have been discussed in the light of observation reported by the Western workers.

Clinical presentation of rheumatoid arthritis (RA) and its severity differs in different races. Genetic factors play a significant role in its predeliction. The present study was undertaken to find out association of HLA class I and class II antigens with rheumatoid arthritis prevalent in Asian Indians residing at Varanasi. Ninety rheumatoid arthritis patients strictly fulfilling American Rheumatism Association criteria were screened for prevalent HLA class I and class II antigen by Terasaki Microlympho-cytotoxicity test. Results were compared with 100 healthy controls and 35 Seronegative Spondyloarthritides cases (SSA). Rheumatoid arthritis patients showed increased frequency of HLA-A2 and B40 antigens compared to healthy controls (p < .001). SSA patients showed significantly increased Phenotype frequency (PF) of HLA-B27 (p < .0001) and B40 (p < .001). Significant detection of HLA-A2 exclusively in RA patients suggests a more positive association of A2 in rheumatoid arthritis at Varanasi. HLA-B40 could not be attributed absolute significance of association with SSA or RA as it showed increased frequency in both diseases.