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. 2021;153(1 & 2):166-174.
doi: 10.4103/ijmr.IJMR_3418_20.

Phylogenetic classification of the whole-genome sequences of SARS-CoV-2 from India & evolutionary trends

Varsha Potdar  1 , Veena Vipat  1 , Ashwini Ramdasi  2 , Santosh Jadhav  3 , Jayashri Pawar-Patil  2 , Atul Walimbe  3 , Sucheta S Patil  3 , Manohar L Choudhury  1 , Jayanthi Shastri  4 , Sachee Agrawal  4 , Shailesh Pawar  5 , Kavita Lole  6 , Priya Abraham  2 , Sarah Cherian  3 ; ICMR-NIV NIC Team
Affiliations

Phylogenetic classification of the whole-genome sequences of SARS-CoV-2 from India & evolutionary trends

Varsha Potdar et al. Indian J Med Res. 2021.

Erratum in

Abstract

Background & objectives: Several phylogenetic classification systems have been devised to trace the viral lineages of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, inconsistency in the nomenclature limits uniformity in its epidemiological understanding. This study provides an integration of existing classifications and describes evolutionary trends of the SARS-CoV-2 strains circulating in India.

Methods: The whole genomes of 330 SARS-CoV-2 samples were sequenced using next-generation sequencing (NGS). Phylogenetic and sequence analysis of a total of 3014 Indian SARS-CoV-2 sequences from 20 different States/Union Territories (January to September 2020) from the Global Initiative on Sharing All Influenza Data (GISAID) database was performed to observe the clustering of Nextstrain and Phylogenetic Assignment of Named Global Outbreak LINeages (Pangolin) lineages with the GISAID clades. The identification of mutational sites under selection pressure was performed using Mixed Effects Model of Evolution and Single-Likelihood Ancestor Counting methods available in the Datamonkey server.

Results: Temporal data of the Indian SARS-CoV-2 genomes revealed that except for Uttarakhand, West Bengal and Haryana that showed the circulation of GISAID clade O even after July 2020, the rest of the States showed a complete switch to GR/GH clades. Pangolin lineages B.1.1.8 and B.1.113 identified within GR and GH clades, respectively, were noted to be indigenous evolutions. Sites identified to be under positive selection pressure within these clades were found to occur majorly in the non-structural proteins coded by ORF1a and ORF1b.

Interpretation & conclusions: This study interpreted the geographical and temporal dominance of SARS-CoV-2 strains in India over a period of nine months based on the GISAID classification. An integration of the GISAID, Nextstrain and Pangolin classifications is also provided. The emergence of new lineages B.1.1.8 and B.1.113 was indicative of host-specific evolution of the SARS-CoV-2 strains in India. The hotspot mutations such as those driven by positive selection need to be further characterized.

Keywords: COVID-19- nucleotide substitution; Clades; India; SARS-CoV-2; selection pressure; whole genomes.

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Conflict of interest statement

None

Figures

Fig. 1
Fig. 1
Workflow for SARS-CoV-2 data analysis.
Fig. 2
Fig. 2
Sunburst diagrams coloured according to Global Initiative on Sharing All Influenza Data (GISAID) clades showing relationship between GISAID and Phylogenetic Assignment of Named Global Outbreak LINeages (Pangolin) annotations on the inner and outer circles, respectively for the Indian SARS-CoV-2 genomes (n=3014). (A) The proportionate chart showing dominant Pangolin corresponding to each of the GISAID clades (The count for individual clades/lineages is shown in Supplementary Table II). (B) The schematic representation of association between the GISAID clades and the Pangolin lineages.
Fig. 3
Fig. 3
State-wise distribution of total number of SARS-CoV-2 sequences deposited from India to Global Initiative on Sharing All Influenza Data (GISAID) from January to September 2020. The colours on the graph denote the GISAID clades.
Fig. 4
Fig. 4
Temporal distribution of SARS-CoV-2 sequences from different States of India. The number of SARS-CoV-2 sequences belonging to distinct GISAID clades is represented as a percentage plot of the clades for each month.
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