AUTHOR=Raghav Sunil , Ghosh Arup , Turuk Jyotirmayee , Kumar Sugandh , Jha Atimukta , Madhulika Swati , Priyadarshini Manasi , Biswas Viplov K. , Shyamli P. Sushree , Singh Bharati , Singh Neha , Singh Deepika , Datey Ankita , Avula Kiran , Smita Shuchi , Sabat Jyotsnamayee , Bhattacharya Debdutta , Kshatri Jaya Singh , Vasudevan Dileep , Suryawanshi Amol , Dash Rupesh , Senapati Shantibhushan , Beuria Tushar K. , Swain Rajeeb , Chattopadhyay Soma , Syed Gulam Hussain , Dixit Anshuman , Prasad Punit , Odisha COVID-19 Study Group , ILS COVID-19 Team , Pati Sanghamitra , Parida Ajay , Singh Arvind Kumar , Mishra Baijayantimala , Parida Banajini , Patro Binod Kumar , Dogra D. P. , Das Dasarathi , Prasad Deepa , Jena Dhaneswari , Mohapatra Dharitri , Sahu Dinesh Prasad , Satapathy Durga Madhab , Sahoo Durgesh Prasad , Panda Jayanta , Khatri Jaya Singh , Mishra Kaushik , Satpathy Manoranjan , Chaini Nirupama , Rattan Roma , Panda Sadhu , Das Sangeeta , Pradhan Somen Kumar , Kanungo Srikanta , Mohanty Sriprasad , Palo Subrata Kumar , Chatterjee Aditi , Mishra Adyasha , Singh Ajit Kumar , Ray Amrita , Datey Ankita , Minz Aliva , Yadav Ashish , Khuntia Auromira , Dixit Anshuman , Barik Debyashreeta , Singh Deepak , Laha Eshna , Dodia Hiren G. , Chawla Jeky , Jena Kautilya , Sen Kaushik , Das Niyati , Shriwas Omprakash , Vaishali P. M. , Nath Parej , Nath Paritosh , Mamidi Prabhudutta , Mohapatra Priyanka , Das Rahul , Yadav Rina , Rout Sachikanta , De Saikat , Chatterjee Sanchari , Suranjika Sandhya , Sahoo Satyaranjan , Ansari Shamima , Aggarwal Shifu , Pradhan Shiva , Krishna Sivaram , Dutta Sneha , Mahapatra Soumendu , Gosh Soumyajit , Barik Subhabrata , Boral Sudhir , Keshry Supriya Suman , Priyadarshini Swatismita , Sherpa Tsheten TITLE=Analysis of Indian SARS-CoV-2 Genomes Reveals Prevalence of D614G Mutation in Spike Protein Predicting an Increase in Interaction With TMPRSS2 and Virus Infectivity JOURNAL=Frontiers in Microbiology VOLUME=11 YEAR=2020 URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2020.594928 DOI=10.3389/fmicb.2020.594928 ISSN=1664-302X ABSTRACT=

Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, has emerged as a global pandemic worldwide. In this study, we used ARTIC primers–based amplicon sequencing to profile 225 SARS-CoV-2 genomes from India. Phylogenetic analysis of 202 high-quality assemblies identified the presence of all the five reported clades 19A, 19B, 20A, 20B, and 20C in the population. The analyses revealed Europe and Southeast Asia as two major routes for introduction of the disease in India followed by local transmission. Interestingly, the19B clade was found to be more prevalent in our sequenced genomes (17%) compared to other genomes reported so far from India. Haplotype network analysis showed evolution of 19A and 19B clades in parallel from predominantly Gujarat state in India, suggesting it to be one of the major routes of disease transmission in India during the months of March and April, whereas 20B and 20C appeared to evolve from 20A. At the same time, 20A and 20B clades depicted prevalence of four common mutations 241 C > T in 5′ UTR, P4715L, F942F along with D614G in the Spike protein. D614G mutation has been reported to increase virus shedding and infectivity. Our molecular modeling and docking analysis identified that D614G mutation resulted in enhanced affinity of Spike S1–S2 hinge region with TMPRSS2 protease, possibly the reason for increased shedding of S1 domain in G614 as compared to D614. Moreover, we also observed an increased concordance of G614 mutation with the viral load, as evident from decreased Ct value of Spike and the ORF1ab gene.