Initial Insights Into the Genetic Epidemiology of SARS-CoV-2 Isolates From Kerala Suggest Local Spread From Limited Introductions

• Main Authors: Chandni Radhakrishnan, Mohit Kumar Divakar, Abhinav Jain, Prasanth Viswanathan, Rahul C. Bhoyar, Bani Jolly, Mohamed Imran, Disha Sharma, Mercy Rophina, Gyan Ranjan, Paras Sehgal, Beena Philomina Jose, Rajendran Vadukkoot Raman, Thulaseedharan Nallaveettil Kesavan, Kalpana George, Sheela Mathew, Jayesh Kumar Poovullathil, Sajeeth Kumar Keeriyatt Govindan, Priyanka Raveendranadhan Nair, Shameer Vadekkandiyil, Vineeth Gladson, Midhun Mohan, Fairoz Cheriyalingal Parambath, Mohit Mangla, Afra Shamnath, Indian CoV2 Genomics & Genetic Epidemiology (IndiCovGEN) Consortium, Sridhar Sivasubbu, Vinod Scaria
• Format: Article
• Language: English
• Published: Frontiers Media S.A. 2021-03-01
• Series: Frontiers in Genetics
• Subjects: COVID-19; COVIDSeq; Kerala; genetic epidemiology; variants
• Online Access: https://www.frontiersin.org/articles/10.3389/fgene.2021.630542/full

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.