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

Chandni Radhakrishnan,Shameer Vadekkandiyil,Mohamed Imran,Vinod Scaria,Afra Shamnath,Fairoz Cheriyalingal Parambath,Rahul C Bhoyar,Kalpana George,Mohit Kumar Divakar,Midhun Mohan,Sridhar Sivasubbu,Abhinav Jain,Priyanka Raveendranadhan Nair,Beena Philomina Jose,Gyan Ranjan,Mercy Rophina,Mohit Mangla,Vineeth Gladson,Disha Sharma,Bani Jolly,Thulaseedharan Nallaveettil Kesavan,Jayesh Kumar Poovullathil,Paras Sehgal,Sheela Mathew,Prasanth Viswanathan,Sajeev Chakanalil Govindan ,R Raman

doi:10.3389/fgene.2021.630542

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.

Highlights

The coronavirus disease 2019 (COVID-19) pandemic has seen a widespread application of genomic approaches to understand the epidemiology and evolution of SARS-CoV-2
trade and tourism is uniquely poised in this pandemic
that it originated from China

Summary

Introduction

The coronavirus disease 2019 (COVID-19) pandemic has seen a widespread application of genomic approaches to understand the epidemiology and evolution of SARS-CoV-2. A number of approaches have emerged for rapid and scalable sequencing of SARS-CoV-2 from clinical isolates. This includes direct shotgun approaches, targeted amplicon-based, and targeted capture-based approaches (Meredith et al, 2020; Yángüez et al, 2020). Sequencing based approaches provide a unique opportunity for high fidelity of detection and for understanding the genetic epidemiology of SARS-CoV-2 (Bhoyar et al, 2020). The genetic variants could offer insights into the mutational spectrum, evolution, infectivity, and attenuation of the virus (Muth et al, 2018; Korber et al, 2020). Additional analyses on genomic variants have provided useful insights into the efficacy of primer/probe-based diagnostic assays as well as immune epitopes and resistance to antisera (Grifoni et al, 2020; Jain et al, 2020)

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