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

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 GISMO chides. 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 Glade O even after July 2020, the rest of the States showed a complete stitch to GE/GH Glades. Pangolin lineages B.1.1.8 and B.1.113 identified within GR and GH Glades, respectively, were noted to be indigenous evolutions. Sites identified to be under positive selection pressure within these Glades 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.

Automated summary

This study integrated existing classifications to describe evolution trends of SARS-CoV-2 strains in India through phylogenetic and sequence analysis of 330 samples. It identified new lineages B.1.1.8 and B.1.113 as indigenous evolutions and hotspot mutations under positive selection pressure in non-structural proteins. Further characterization of these mutations is necessary for a comprehensive understanding.