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. 2021 Mar 17:12:630542.
doi: 10.3389/fgene.2021.630542. eCollection 2021.

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

Chandni Radhakrishnan  1 , Mohit Kumar Divakar  2   3 , Abhinav Jain  2   3 , Prasanth Viswanathan  1 , Rahul C Bhoyar  2 , Bani Jolly  2   3 , Mohamed Imran  2   3 , Disha Sharma  2 , Mercy Rophina  2   3 , Gyan Ranjan  2   3 , Paras Sehgal  2   3 , Beena Philomina Jose  1 , Rajendran Vadukkoot Raman  1 , Thulaseedharan Nallaveettil Kesavan  1 , Kalpana George  1 , Sheela Mathew  1 , Jayesh Kumar Poovullathil  1 , Sajeeth Kumar Keeriyatt Govindan  1 , Priyanka Raveendranadhan Nair  1 , Shameer Vadekkandiyil  1 , Vineeth Gladson  1 , Midhun Mohan  1 , Fairoz Cheriyalingal Parambath  1 , Mohit Mangla  2   3 , Afra Shamnath  2 ; Indian CoV2 Genomics & Genetic Epidemiology (IndiCovGEN) Consortium; Sridhar Sivasubbu  2   3 , Vinod Scaria  2   3
Affiliations

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

Chandni Radhakrishnan et al. Front Genet. .

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.

Keywords: COVID-19; COVIDSeq; Kerala; genetic epidemiology; variants.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
The mean coverage of the SARS-CoV-2 genomes across the amplicons of the COVIDSeq amplicon-based sequencing.
Figure 2
Figure 2
(A) Distribution of variants across genomes used in the study. (B) Comparison of the proportion of the variants represented with their allele frequency across the SARS-CoV-2 genome in datasets includes Kerala (present study), India, and global. (C) Distribution of the genetic context of variants and their functional classification.
Figure 3
Figure 3
(A) Phylogenetic map of the 113 genomes sequenced from Kerala (highlighted by blue dots) with respect to the other genomes from India. (B) Distribution of the clades and lineages in Kerala. All genomes clustered under the clade A2a (GISAID clade G and GH) while the dominant lineage was B.1. (C) Lineage distribution in Kerala compared to the distribution across India and global populations.
Figure 4
Figure 4
Haplotype network of 850 genomes of Indian isolates of SARS-CoV-2 belonging to the A2a clade. The three major haplogroups encompassing the genomes from Kerala are designated as K1, K2, and K3.
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