RT Journal Article
SR Electronic
T1 Initial insights into the genetic epidemiology of SARS-CoV-2 isolates from Kerala suggest local spread from limited introductions
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.09.09.289892
DO 10.1101/2020.09.09.289892
A1 Chandni Radhakrishnan
A1 Mohit Kumar Divakar
A1 Abhinav Jain
A1 Prasanth Viswanathan
A1 Rahul C. Bhoyar
A1 Bani Jolly
A1 Mohamed Imran
A1 Disha Sharma
A1 Mercy Rophina
A1 Gyan Ranjan
A1 Beena Philomina Jose
A1 Rajendran Vadukkoot Raman
A1 Thulaseedharan Nallaveettil Kesavan
A1 Kalpana George
A1 Sheela Mathew
A1 Jayesh Kumar Poovullathil
A1 Sajeeth Kumar Keeriyatt Govindan
A1 Priyanka Raveendranadhan Nair
A1 Shameer Vadekkandiyil
A1 Vineeth Gladson
A1 Midhun Mohan
A1 Fairoz Cheriyalingal Parambath
A1 Mohit Mangla
A1 Afra Shamnath
A1 Indian CoV2 Genomics & Genetic Epidemiology (IndiCovGEN) Consortium
A1 Sridhar Sivasubbu
A1 Vinod Scaria
YR 2020
UL http://biorxiv.org/content/early/2020/09/09/2020.09.09.289892.abstract
AB Coronavirus disease 2019 (COVID-19) rapidly spread from a city in China to almost every country in the world, affecting millions of individuals. Genomic approaches have been extensively used to understand the evolution and epidemiology of SARS-CoV-2 across the world. Kerala is a unique state in India well connected with the rest of the world through a large number of expatriates, trade, and tourism. The first case of COVID-19 in India was reported in Kerala in January 2020, during the initial days of the pandemic. The rapid increase in the COVID-19 cases in the state of Kerala has necessitated the understanding of the genetic epidemiology of circulating virus, evolution, and mutations in SARS-CoV-2. We sequenced a total of 200 samples from patients at a tertiary hospital in Kerala using COVIDSeq protocol at a mean coverage of 7,755X. The analysis identified 166 unique high-quality variants encompassing 4 novel variants and 89 new variants identified for the first time in SARS-CoV-2 samples isolated from India. Phylogenetic and haplotype analysis revealed that the circulating population of the virus was dominated (94.6% of genomes) by three distinct introductions followed by local spread, apart from identifying polytomies suggesting recent outbreaks. The genomes formed a monophyletic distribution exclusively mapping to the A2a clade. Further analysis of the functional variants revealed two variants in the S gene of the virus reportedly associated with increased infectivity and 5 variants that mapped to five primer/probe binding sites that could potentially compromise the efficacy of RT-PCR detection. To the best of our knowledge, this is the first and most comprehensive report of genetic epidemiology and evolution of SARS-CoV-2 isolates from Kerala.Competing Interest StatementThe authors have declared no competing interest.