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. 2020 Sep 18;7(11):ofaa434.
doi: 10.1093/ofid/ofaa434. eCollection 2020 Nov.

A Distinct Phylogenetic Cluster of Indian Severe Acute Respiratory Syndrome Coronavirus 2 Isolates

Sofia Banu  1 , Bani Jolly  2   3 , Payel Mukherjee  1 , Priya Singh  1 , Shagufta Khan  1 , Lamuk Zaveri  1 , Sakshi Shambhavi  1   3 , Namami Gaur  1 , Shashikala Reddy  4 , K Kaveri  5 , Sivasubramanian Srinivasan  5 , Dhinakar Raj Gopal  6 , Archana Bharadwaj Siva  1 , Kumarasamy Thangaraj  1 , Karthik Bharadwaj Tallapaka  1 , Rakesh K Mishra  1 , Vinod Scaria  2 , Divya Tej Sowpati  1
Affiliations

A Distinct Phylogenetic Cluster of Indian Severe Acute Respiratory Syndrome Coronavirus 2 Isolates

Sofia Banu et al. Open Forum Infect Dis. .

Abstract

Background: From an isolated epidemic, coronavirus disease 2019 has now emerged as a global pandemic. The availability of genomes in the public domain after the epidemic provides a unique opportunity to understand the evolution and spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus across the globe.

Methods: We performed whole-genome sequencing of 303 Indian isolates, and we analyzed them in the context of publicly available data from India.

Results: We describe a distinct phylogenetic cluster (Clade I/A3i) of SARS-CoV-2 genomes from India, which encompasses 22% of all genomes deposited in the public domain from India. Globally, approximately 2% of genomes, which to date could not be mapped to any distinct known cluster, fall within this clade.

Conclusions: The cluster is characterized by a core set of 4 genetic variants and has a nucleotide substitution rate of 1.1 × 10-3 variants per site per year, which is lower than the prevalent A2a cluster. Epidemiological assessments suggest that the common ancestor emerged at the end of January 2020 and possibly resulted in an outbreak followed by countrywide spread. To the best of our knowledge, this is the first comprehensive study characterizing this cluster of SARS-CoV-2 in India.

Keywords: COVID-19; Clade I/A3i; India; genetic epidemiology; phylogenomics.

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Figures

Figure 1.
Figure 1.
Phylogenetic clusters and clades as generated by Nextstrain for the dataset of 1377 high-quality Indian severe acute respiratory syndrome coronavirus 2 genomes. Indian genomes were found to fall under 7 clusters with the majority of the genomes falling under clade A2a. The second largest cluster in India (purple) has been designated as clade I/A3i.
Figure 2.
Figure 2.
Shared variants among the variants that define the clusters of the Indian severe acute respiratory syndrome coronavirus 2 genomes. The size of the circle represents the allele frequencies of the respective variants, and clade-defining variants are marked with a red circle.
Figure 3.
Figure 3.
(A) Proportion of the I/A3i clade (purple) and A2a (teal) in the genomes sequenced from different states of India. The proportion of the A2a clade (teal) is also shown for comparison, whereas all other clades are shaded gray. (B) The short tree of the I/A3i clade diverging from a central point suggests a single point of introduction and spread across the different states. The 23 global genomes that were sampled before the first Indian genome from this cluster are highlighted in gray.
Figure 4.
Figure 4.
(A) A week-wise stacked bar displaying the proportion of clades across India, starting from the week of March 1, 2020. (B) A bubble plot depicting the change in the predominant clades with time in various states. X-axis indicates the date on which the sample was collected, and color indicates the clade. Only those states with collection data across at least 2 months are plotted.
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