Entropy based analysis of SARS-CoV-2 spread in India using informative subtype markers

Area of Science:

• Virology
• Epidemiology
• Genomics

Background:

• India faced a severe COVID-19 outbreak by September 2020.
• Understanding SARS-CoV-2 transmission dynamics and genetic variations is crucial.

Purpose of the Study:

• To analyze the temporal and geographic spread of SARS-CoV-2 subtypes in India.
• To investigate the RGD motif and D614G mutation in the spike protein.
• To identify viral origins and transmission routes within India.

Main Methods:

• Utilized a viral subtyping method based on informative subtype markers (ISMs).
• Analyzed 94,515 SARS-CoV-2 genome sequences from GISAID.
• Identified 798 unique ISMs from 11 distinct genomic positions.

Main Results:

• The most common ISM in India originated from Europe; the second most common arrived via Australia.
• Eastern India showed infection patterns linked to Chinese ISMs due to proximity.
• The S-G614 variant, associated with increased transmissibility, was more prevalent than S-D614 nationwide, with exceptions in specific regions.

Conclusions:

• SARS-CoV-2 spread in India involved multiple international introductions and geographic transmission patterns.
• The D614G mutation, particularly the G614 variant, likely contributed to the pandemic's progression in India.
• Subtyping based on ISMs provides a valuable tool for tracking viral evolution and spread.