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Global Viral Epidemics: a Challenging Threat’’, During 12–14 November, 2018, at PGIMER, Chandigarh, India

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Global Viral Epidemics: a Challenging Threat’’, During 12–14 November, 2018, at PGIMER, Chandigarh, India VirusDis. (January–March 2019) 30(1):112–169 https://doi.org/10.1007/s13337-019-00523-8 ABSTRACT Abstracts of the papers presented in the international conference of Indian virological society, ‘‘Global viral epidemics: a challenging threat’’, during 12–14 November, 2018, at PGIMER, Chandigarh, India Ó Indian Virological Society 2019 Medical Virology of Indian MuVs is not expected to alter the antigenicity and structural stability. Analysis of Indian and global MeV isolates indicates that the circulating strains during 2009-17 in India belong to genotypes D4 Complete Genome Sequencing of Measles Virus Isolates and D8, which have limited divergence with no potential impact on Obtained during 2009-2017 from different parts antigenicity and efficacy of the current vaccine strains in controlling of India MeV infection to meet elimination target by 2020. Sunil R. Vaidya1, Sunitha M. Kasibhatla2,3, Divya R. Bhattad1, Mukund R. Ramtirthkar4, Mohan M. Kale4, 5 2 Denovo assembly of Hepatitis C virus full-length Chandrashekhar G. Raut and Urmila Kulkarni-Kale genome following next generation sequencing 1ICMR-National Institute of Virology, Pune; 2Bioinformatics Centre, and genetic variations of strains circulating in north Savitribai Phule Pune University; 3HPC-Medical & Bioinformatics and north-east India Applications Group, Centre for Development of Advanced 4 Computing, Pune; Department of Statistics, Savitribai Phule Pune Sonu Kumar1, Renu Yadav1, Yogesh Kumar1, 5 University; ICMR-National Institute for Research in Tribal Health, Chandreswar Prasad1, Jyotish Kumar Jha1, Kekungu Puro4, Nagpur Road, Jabalpur, India Sachin Kumar3, Anoop Saraya1, Shalimar1, 2 1 Measles is a highly contagious viral disease of major public health Suraj Nongthombam , Baibaswata Nayak concern. Measles virus (MeV) is enveloped, single stranded negative RNA genome (15,894 nucleotides) belong to Pramyxoviridae family Email ID for Correspondence: [email protected] 1 (genus Morbillivirus). MeV is serologically monotypic virus and Department of Gastroenterology, All India Institute of Medical 2 genetically divided into 24 genotypes i.e. A, B1-B3, C1-C2, D1-D11, Sciences, Ansari Nagar, New Delhi; Jawaharlal Nehru Institute of 3 E, F, G1-G3 and H1-H2. World Health Organization has a target for Medical Sciences, Imphal; Department of Biosciences and 4 elimination of measles and rubella control by 2020. Government of Bioengineering, IIT Guwahati; ICAR Research Complex for NEH India is committed on ‘Measles Elimination’ in a phased manner. Region, Meghalaya Hence, a second dose of measles introduced in year 2010 through Introduction: Hepatitis C virus (HCV) infection is silent and infected Universal Immunization Program. As per policy, suspected measles patient develop chronic hepatitis with increased risk of cirrhosis, cases (fever with skin rash, cough, coryza and conjunctivitis) was hepatocellular carcinoma and end stage live disease. Current treat- monitored and laboratory confirmed by serological/molecular tests by ment with direct acting antivirals (DAAs) is very effective in the WHO accredited laboratory. Complete genome sequencing of achieving sustained virological response (SVR). However, expected thirty MeV isolates obtained during 2009-17 from six states of India drug resistance and suboptimal activity against diverse HCV geno- were performed using standard RT-PCR and sequencing protocols. types are major drawback. Next generation sequencing (NGS) with All these MeV isolates were grown on Vero hSLAM cells. Consensus more coverage will be effective in studying genetic variations in both MeV genomes/genes were subjected to phylogenetic and bioiformatic wild type and resistance associated variants (RAV) and immune analysis. Phylogeny with global isolates revealed genotype-based response. HCV genotyping by commercial real time PCR assays spatio-temporal clustering. Estimated genome/gene-wide nucleotide escapes subtypic variations within genotype that need to be evaluated substitution rates of Indian MeV are comparable with global isolates. by direct sequencing for unusual subtype that may evade SVR. The Selection pressure analysis indicated modest role of positive selection serum samples from treatment naı¨ve consecutive chronic hepatitis C in MeV evolution corroborating with its serologically monotypic patients at AIIMS (North India) and JNIMS, Imphal were obtained to nature. Though selection was found to be operational across all MeV study genetic variation of HCV. Real time PCR for HCV quantitation genes except L-gene in global isolates, no positively selected sites and genotyping was carried out. The next generation sequencing and were observed in Indian isolates. The mutation noted in the H-protein NS5b region Sanger sequencing of HCV genome was carried out 123 113 Denovo assembly and phylogenetic analysis of strains were done The etiological role of infection with high-risk Human papillomavirus using web based bioinformatics software. (HPV) types and cervical cancer is well established, while HPV type Out of 90 HCV samples collected at AIIMS, Genotype 1 was 21% 16 is most prevalent globally and in India. In a given HPV type, the and genotype 3a was 78% (n = 71) whereas among 142 north east genome is further classified into ‘variants’ if presence of nucleotide sample, genotype 1 was 29% (n = 42), 3 was 60.5% (n = 86), 4 was variations is \ 2% in coding regions. Major capsid or L1 protein is 1.5% (n = 2) and genotype 6 was 8.5% (n = 12). HCV complete corner stone in HPV structure. L1 variants can affect viral assembly genome cDNA and library preparation was carried out for NGS. The and restrict immunological recognition. Developing information on sequence data were subjected for filtration and exclusion of human L1 variants is imperative for rational design of newer diagnostics and sequence by mapping with HG19 sequence. The remaining reads vaccine. The present study was carried out to characterize HPV16 L1 were used for denovo genome assembly. Three north-east strains from variants by cervical intraepithelial neoplastic status, evaluate their genotype 1 and 3 were sequenced and analyzed. Phylogenetic analysis impact on epitopes and determine their phylogeny. HPV16 L1 open of NS5b region of north Indian HCV strain have shown 3a, 3b, 3 g reading frame was analyzed in 152 well characterized archival and 3i subtypes within genotype 3 HCV. HPV16 positive cervical samples (48 with normal, 51 with low-grade and 53 with high-grade cervical status). Intratype variants were ana- Delineating the role of DNA damage response lyzed using PCR-directed sequencing, impact on experimentally validated epitopes was predicted in silico, while phylogenetic analysis during Rotavirus replication was carried out using MEGA software with maximum likelihood method. A total of 58 nucleotide polymorphisms were detected, of Sarkar R, Chawla-Sarkar M which 26 were novel and 20 non-synonymous. Commonest L1 vari- ants were A6432G (73.7%), G7058T (17.8%) and C6852T (16.4%). Email ID for Correspondence: [email protected] L1 variants C5862T (H102Y), C6163 (T202N), A6178C (N207T), Division of Virology, National Institute of Cholera and Enteric A6693C (T379P) and A6801T (T415S) showed significant associa- Diseases, Kolkata, India tion with high-grade cervical disease and an increasing trend with cervical disease progression. Predominance of European lineage Cellular DNA damage response (DDR) machinery is present in all (84.2%) was observed, while non-European lineages were associated eukaryotic cells to monitor and repair DNA in response to cellular with high grade cervical intraepithelial neoplasia, p = 0.012. Ten DNA damage. Induction of cellular DDR results in the activation of variants were part of experimentally validated B cell and three of T cell cycle arrest, DNA repair pathway or apoptosis. Several studies cell epitopes respectively. Five variants were located in the immuno- have shown that both DNA and RNA viruses can activate the cellular genetic FG and HI capsid loops and could potentially impact anti- DDR pathway and hijack this pathway to facilate their own replica- HPV vaccine efficacy. Results suggest association of specific L1 tion. This study was conducted to check the activation of DDR variants and non-European lineages with cervical intraepithelial following Rotavirus infection and find out its role in Rotavirus neoplasia. replication. Western blotting was performed to check the expressions of cellular and viral proteins following Rotavirus infection. Expres- sions of viral RNAs were quantified by qRT-PCR. Cellular DNA damage was measured by comet assay. Localization of cellular pro- Development and evaluation of rapid field compatible teins were visualized by immunofluorescence technique. Infective sample to answer detection technique for rapid on-site virion particles formation was measured by plaque assay. Results have shown that Rotavirus infection induces the activation of the detection of Chikungunya virus ATM branch of DDR pathway. ATM activation was found to be independent of cellular DNA damagebut dependent on double Shashi Sharma1, Paban Kumar Dash1, M.M.Parida1, stranded break sensor MRN complex as knockdown of MRE11 and Deepak Pardasani2, D.K. Dubey2 RAD50 by lentivirus prevented ATM activation. Activated form of ATM, CHK2 and MRN complex components, MRE11 and RAD50 Virology Division1 DRDE, Gwalior,Vertox Division2 DRDE, were found to localize within the viroplasm. Inhibition of ATM and Gwalior,Defence food research laboratory, Mysore CHK2 proteins by chemical
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