Scholarly Publications
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This community showcases the academic contributions of faculty and researchers at Banaras Hindu University (BHU) and provides a year-wise compilation of publications across disciplines. Institutional Repository BHU
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PublicationBook Chapter Inferring Recombination Events in SARS-CoV-2 Variants In Silico(Springer, 2023) Nihal Najeeb; Aparna B. Murukan; Anagha Renjitha; Malavika Jayaram; Ayisha A. Jabbar; Haripriya Haridasan; Akshara Prijikumar; Sneha Baiju; Adrial Ann Nixon; Ponnambil Anantha Krishnan; Sunu Rodriguez; Somesh Kumar; Sunil K. Polipalli; Keshav K. Singh; Bipin G. Nair; Sudeep D. Ghate; R. Shyama Prasad Rao; Polavarapu Bilhan Kavi Kishor; Arya Aloor; Renuka Suravajhala; Gyaneshwer Chaubey; Prashanth SuravajhalaOver the last 34 months, at least 10 severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) distinct variants have evolved. Among these, some were more infectious while others were not. These variants may serve as candidates for identification of the signature sequences linked to infectivity and viral transgressions. Based on our previous hijacking and transgression hypothesis, we aimed to investigate whether SARS-CoV-2 sequences associated with infectivity and trespassing of long noncoding RNAs (lncRNAs) provide a possible recombination mechanism to drive the formation of new variants. This work involved a sequence and structure-based approach to screen SARS-CoV-2 variants in silico, taking into account effects of glycosylation and links to known lncRNAs. Taken together, the findings suggest that transgressions involving lncRNAs may be linked with changes in SARS-CoV-2–host interactions driven by glycosylation events. © 2023, The Author(s), under exclusive license to Springer Nature Switzerland AG.PublicationArticle Genetic association of TMPRSS2 rs2070788 polymorphism with COVID-19 case fatality rate among Indian populations(Elsevier B.V., 2022) Rudra Kumar Pandey; Anshika Srivastava; Prajjval Pratap Singh; Gyaneshwer ChaubeySARS-CoV-2, the causative agent for COVID-19, an ongoing pandemic, engages the ACE2 receptor to enter the host cell through S protein priming by a serine protease, TMPRSS2. Variation in the TMPRSS2 gene may account for the disparity in disease susceptibility between populations. Therefore, in the present study, we have used next-generation sequencing (NGS) data of world populations from 393 individuals and analyzed the TMPRSS2 gene using a haplotype-based approach with a major focus on South Asia to study its phylogenetic structure and their haplotype sharing among various populations worldwide. Our analysis of phylogenetic relatedness showed a closer affinity of South Asians with the West Eurasian populations therefore, host disease susceptibility and severity particularly in the context of TMPRSS2 will be more akin to West Eurasian instead of East Eurasian. This is in contrast to our prior study on the ACE2 gene which shows South Asian haplotypes have a strong affinity towards West Eurasians. Thus ACE2 and TMPRSS2 have an antagonistic genetic relatedness among South Asians. Considering the significance of the TMPRSS2 gene in the SARS-CoV-2 pathogenicity, COVID-19 infection and intensity trends could be directly associated with increased expression therefore, we have also tested the SNPs frequencies of this gene among various Indian state populations with respect to the case fatality rate (CFR). Interestingly, we found a significant positive association between the rs2070788 SNP (G Allele) and the CFR among Indian populations. Further our cis eQTL analysis of rs2070788 shows that the GG genotype of the rs2070788 tends to have a significantly higher expression of TMPRSS2 gene in the lung compared to the AG and AA genotypes thus validating the previous observation and therefore it might play a vital part in determining differential disease vulnerability. We trust that this information will be useful in understanding the role of the TMPRSS2 variant in COVID-19 susceptibility and using it as a biomarker may help to predict populations at risk. © 2022PublicationArticle Studying C-reactive protein and D-dimer levels in blood may prevent severe complications: A study in Bangladeshi COVID-19 patients(Frontiers Media S.A., 2022) Gazi Nurun Nahar Sultana; Anshika Srivastava; Khalida Akhtaar; Prajjval Pratap Singh; Md. Anarul Islam; Rahul Kumar Mishra; Gyaneshwer ChaubeyThe ongoing COVID-19 pandemic has been a scientific, medical and social challenge. Since clinical course of this disease is largely unpredictable and can develop rapidly causing severe complications, it is important to identify laboratory biomarkers, which may help to classify patient’s severity during initial stage. Previous studies have suggested C—reactive protein (inflammatory) and D-dimer (biochemical) as an effective biomarker. The differential severity in patients across the world and our limited understanding in the progression of the disease calls for a multi-country analysis for biomarkers. Therefore, we have analyzed these biomarkers among 228 Bangladeshi COVID-19 patients. We observed significant association of COVID-19 severity with these two biomarkers. Thus, we suggest to use these biomarkers for Bangladeshi COVID-19 patients for better disease monitoring. Such validated preventive measures may decrease the case fatality ratio substantially. Copyright © 2022 Sultana, Srivastava, Akhtaar, Singh, Islam, Mishra and Chaubey.PublicationLetter Can alcohol kill harmful microbes from our skin?(Elsevier Inc., 2021) Pankaj Shrivastava; Toshi Jain; Vijay Nema; Mahendra K. Gupta; Naveen Kango; Pradeep K. Singhal; Gyaneshwer Chaubey; R.K. Kumawat[No abstract available]PublicationReview The Omic Insights on Unfolding Saga of COVID-19(Frontiers Media S.A., 2021) Arvinpreet Kaur; Mehak Chopra; Mahak Bhushan; Sonal Gupta; Hima Kumari P; Narmadhaa Sivagurunathan; Nidhi Shukla; Shalini Rajagopal; Purva Bhalothia; Purnima Sharma; Jalaja Naravula; Renuka Suravajhala; Ayam Gupta; Bilal Ahmed Abbasi; Prittam Goswami; Harpreet Singh; Rahul Narang; Rathnagiri Polavarapu; Krishna Mohan Medicherla; Jayaraman Valadi; Anil Kumar S; Gyaneshwer Chaubey; Keshav K. Singh; Obul Reddy Bandapalli; Polavarapu Bilhan Kavi Kishor; Prashanth SuravajhalaThe year 2019 has seen an emergence of the novel coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing coronavirus disease of 2019 (COVID-19). Since the onset of the pandemic, biological and interdisciplinary research is being carried out across the world at a rapid pace to beat the pandemic. There is an increased need to comprehensively understand various aspects of the virus from detection to treatment options including drugs and vaccines for effective global management of the disease. In this review, we summarize the salient findings pertaining to SARS-CoV-2 biology, including symptoms, hosts, epidemiology, SARS-CoV-2 genome, and its emerging variants, viral diagnostics, host-pathogen interactions, alternative antiviral strategies and application of machine learning heuristics and artificial intelligence for effective management of COVID-19 and future pandemics. © Copyright © 2021 Kaur, Chopra, Bhushan, Gupta, Kumari P, Sivagurunathan, Shukla, Rajagopal, Bhalothia, Sharma, Naravula, Suravajhala, Gupta, Abbasi, Goswami, Singh, Narang, Polavarapu, Medicherla, Valadi, Kumar S, Chaubey, Singh, Bandapalli, Kavi Kishor and Suravajhala.PublicationArticle The association of ABO blood group with the asymptomatic COVID-19 cases in India(Elsevier Ltd, 2021) Prajjval Pratap Singh; Abhishek K. Srivastava; Sudhir K. Upadhyay; Ashish Singh; Shashank Upadhyay; Pradeep Kumar; Vandana Rai; Pankaj Shrivastava; Gyaneshwer ChaubeyThe COVID-19 pandemic resulted in multiple waves of infection worldwide. The large variations in case fatality rate among different geographical regions suggest that the human susceptibility against this virus varies substantially. Several studies from different parts of the world showed a significant association of ABO blood group and COVID-19 susceptibility. It was demonstrated that individuals with blood group O are at the lower risk of coronavirus infection. To establish the association of ABO blood group in SARS-CoV-2 susceptibility, we for the first time analysed SARS-CoV-2 neutralising antibodies among 509 individuals, collected from three major districts of Eastern Uttar Pradesh region of India. Interestingly, we found neutralising antibodies in a significantly higher percentage of people with blood group AB (0.36) followed by B (0.31), A (0.22) and lowest in people with blood group O (0.11). We further estimated that people with blood group AB are at comparatively higher risk of infection than other blood groups. Thus, among the asymptomatic SARS-CoV-2 recovered people blood group AB has highest, whilst individuals with blood group O has lowest risk of infection. © 2021 Elsevier LtdPublicationArticle Coronavirus (SARS-CoV-2) and Mortality Rate in India: The Winning Edge(Frontiers Media S.A., 2020) Gyaneshwer Chaubey[No abstract available]PublicationReview Decoding sars-cov-2 hijacking of host mitochondria in covid-19 pathogenesis(American Physiological Society, 2020) Keshav K. Singh; Gyaneshwer Chaubey; Jake Y. Chen; Prashanth SuravajhalaDecoding SARS-CoV-2 hijacking of host mitochondria in COVID-19 pathogenesis. Am J Physiol Cell Physiol 319: C258–C267, 2020. First published June 8, 2020; doi:10.1152/ajpcell.00224.2020.—Because of the ongoing pandemic around the world, the mechanisms underlying the SARS-CoV-2-induced COVID-19 are subject to intense investigation. Based on available data for the SARS-CoV-1 virus, we suggest how CoV-2 localization of RNA transcripts in mitochondria hijacks the host cell’s mitochondrial function to viral advantage. Besides viral RNA transcripts, RNA also localizes to mitochondria. SARS-CoV-2 may manipulate mitochondrial function indirectly, first by ACE2 regulation of mitochondrial function, and once it enters the host cell, open-reading frames (ORFs) such as ORF-9b can directly manipulate mitochondrial function to evade host cell immunity and facilitate virus replication and COVID-19 disease. Manipulations of host mitochondria by viral ORFs can release mitochondrial DNA (mtDNA) in the cytoplasm and activate mtDNA-induced inflammasome and suppress innate and adaptive immunity. We argue that a decline in ACE2 function in aged individuals, coupled with the age-associated decline in mitochondrial functions resulting in chronic metabolic disorders like diabetes or cancer, may make the host more vulnerable to infection and health complications to mortality. These observations suggest that distinct localization of viral RNA and proteins in mitochondria must play essential roles in SARS-CoV-2 pathogenesis. Understanding the mechanisms underlying virus communication with host mitochondria may provide critical insights into COVID-19 pathologies. An investigation into the SARS-CoV-2 hijacking of mitochondria should lead to novel approaches to prevent and treat COVID-19. © 2020 the American Physiological SocietyPublicationArticle Genetic Association of ACE2 rs2285666 Polymorphism With COVID-19 Spatial Distribution in India(Frontiers Media S.A., 2020) Anshika Srivastava; Audditiya Bandopadhyay; Debashurti Das; Rudra Kumar Pandey; Vanya Singh; Nargis Khanam; Nikhil Srivastava; Prajjval Pratap Singh; Pavan Kumar Dubey; Abhishek Pathak; Pranav Gupta; Niraj Rai; Gazi Nurun Nahar Sultana; Gyaneshwer ChaubeyStudies on host-pathogen interaction have identified human ACE2 as a host cell receptor responsible for mediating infection by coronavirus (COVID-19). Subsequent studies have shown striking difference of allele frequency among Europeans and Asians for a polymorphism rs2285666, present in ACE2. It has been revealed that the alternate allele (TT-plus strand or AA-minus strand) of rs2285666 elevate the expression level of this gene upto 50%, hence may play a significant role in SARS-CoV-2 susceptibility. Therefore, we have first looked the phylogenetic structure of rs2285666 derived haplotypes in worldwide populations and compared the spatial frequency of this particular allele with respect to the COVID-19 infection as well as case-fatality rate in India. For the first time, we ascertained a significant positive correlation for alternate allele (T or A) of rs2285666, with the lower infection as well as case-fatality rate among Indian populations. We trust that this information will be useful to understand the role of ACE2 in COVID-19 susceptibility. © Copyright © 2020 Srivastava, Bandopadhyay, Das, Pandey, Singh, Khanam, Srivastava, Singh, Dubey, Pathak, Gupta, Rai, Sultana and Chaubey.