AUTHOR=Radhakrishnan Chandni , Divakar Mohit Kumar , Jain Abhinav , Viswanathan Prasanth , Bhoyar Rahul C. , Jolly Bani , Imran Mohamed , Sharma Disha , Rophina Mercy , Ranjan Gyan , Sehgal Paras , Jose Beena Philomina , Raman Rajendran Vadukkoot , Kesavan Thulaseedharan Nallaveettil , George Kalpana , Mathew Sheela , Poovullathil Jayesh Kumar , Keeriyatt Govindan Sajeeth Kumar , Nair Priyanka Raveendranadhan , Vadekkandiyil Shameer , Gladson Vineeth , Mohan Midhun , Parambath Fairoz Cheriyalingal , Mangla Mohit , Shamnath Afra , Indian CoV2 Genomics & Genetic Epidemiology (IndiCovGEN) Consortium , Sivasubbu Sridhar , Scaria Vinod TITLE=Initial Insights Into the Genetic Epidemiology of SARS-CoV-2 Isolates From Kerala Suggest Local Spread From Limited Introductions JOURNAL=Frontiers in Genetics VOLUME=12 YEAR=2021 URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2021.630542 DOI=10.3389/fgene.2021.630542 ISSN=1664-8021 ABSTRACT=

Coronavirus disease 2019 (COVID-19) rapidly spread from a city in China to almost every country in the world, affecting millions of individuals. The rapid increase in the COVID-19 cases in the state of Kerala in India has necessitated the understanding of SARS-CoV-2 genetic epidemiology. We sequenced 200 samples from patients in Kerala using COVIDSeq protocol amplicon-based sequencing. The analysis identified 166 high-quality single-nucleotide variants encompassing four novel variants and 89 new variants in the Indian isolated SARS-CoV-2. Phylogenetic and haplotype analysis revealed that the virus was dominated by three distinct introductions followed by local spread suggesting recent outbreaks and that it belongs to the A2a clade. Further analysis of the functional variants revealed that two variants in the S gene associated with increased infectivity and five variants mapped in primer binding sites affect the efficacy of RT-PCR. To the best of our knowledge, this is the first and most comprehensive report of SARS-CoV-2 genetic epidemiology from Kerala.