Phylogeny and evolution of SARS-CoV-2 during Delta and Omicron variant waves in India

Abstract

SARS-CoV-2 evolution has continued to generate variants, responsible for new pandemic waves locally and globally. Varying disease presentation and severity has been ascribed to inherent variant characteristics and vaccine immunity. This study analyzed genomic data from 305 whole genome sequences from SARS-CoV-2 patients before and through the third wave in India. Delta variant was reported in patients without comorbidity (97%), while Omicron BA.2 was reported in patients with comorbidity (77%). Tissue adaptation studies brought forth higher propensity of Omicron variants to bronchial tissue than lung, contrary to observation in Delta variants from Delhi. Study of codon usage pattern distinguished the prevalent variants, clustering them separately, Omicron BA.2 isolated in February grouped away from December strains, and all BA.2 after December acquired a new mutation S959P in ORF1b (44.3% of BA.2 in the study) indicating ongoing evolution. Loss of critical spike mutations in Omicron BA.2 and gain of immune evasion mutations including G142D, reported in Delta but absent in BA.1, and S371F instead of S371L in BA.1 could explain very brief period of BA.1 in December 2021, followed by complete replacement by BA.2. Higher propensity of Omicron variants to bronchial tissue, probably ensured increased transmission while Omicron BA.2 became the prevalent variant possibly due to evolutionary trade-off. Virus evolution continues to shape the epidemic and its culmination.

Communicated by Ramaswamy H. Sarma

Keywords:

• SARS-CoV-2
• COVID-19
• RT-PCR
• Omicron
• B.A.1
• B.A.2

Authors’ Contributions

UBS conceived and formulated the study, planned the work, and wrote the manuscript with SD, LR, SV, and DB. UBS, RC, KB, SS, RiG, MK, VA and RG contributed to diagnostics and laboratory management. JA, SG, SP, MN, AM, JSt conducted diagnostic tests, LR conducted Whole Genome Sequencing, SD conducted Bioinformatics. JN and PA provided clinical care. SD, DB, SV, LK and JS contributed to the data analysis.

Disclosure statement

Authors declare no conflicts of interest. The funding agency had no role in the analysis of data, preparation of manuscript or decision to publish.

Ethical Approval

Nasopharyngeal and oro-pharyngeal swabs were collected from individuals presenting to Emergency Department, AIIMS, New Delhi after informed consent.

Data availability statement

The sequence data is available in GISAID

Additional information

Funding

Authors acknowledge funding from All India Institute of Medical Sciences, New Delhi and support from Dr. N. Singhvi, Dev Bhoomi University, Uttarakhand for her assistance in molecular docking and simulations study. SS acknowledges the J C Bose Fellowship of the Department of Science and Technology, India.