Omicron BA.2 lineage predominance in severe acute respiratory syndrome coronavirus 2 positive cases during the third wave in North India

• DOI: 10.3389/fmed.2022.955930
• Publication Date: 2022-11-02T06:11:16Z
• Authors: Kamran Zaman; Anita M. Shete; Shailendra Kumar ...; Abhinendra Kumar; Mahendra M. Reddy; Rima R. Sahay; Shailendra Yadav; Triparna Majumdar; Ashok K. Pandey; Gaurav Raj Dwivedi; Hirawati Deval; Rajeev Singh; Sthita Pragnya Be...; Niraj Kumar; Savita Patil; Ashish Kumar; Manisha Dudhmal; Yash Joshi; Aishwarya Shukla; Pranita Gawande; Asif Kavathekar; Nalin Kumar; Vijay Kumar; Kamlesh Kumar; Ravi Shankar Singh; Manoj Kumar; Shashikant Tiwari; Ajay Verma; Pragya D. Yadav; Rajni Kant
• Keywords: Coronavirus; Lineage (genetic)

Background Recent studies on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reveal that Omicron variant BA.1 and sub-lineages have revived the concern over resistance to antiviral drugs vaccine-induced immunity. The present study aims analyze clinical profile genome characterization of SARS-CoV-2 in eastern Uttar Pradesh (UP), North India. Methods Whole-genome sequencing (WGS) was conducted for 146 samples obtained from individuals who tested disease 2019 (COVID-19) positive between period 1 January 2022 24 February 2022, three districts UP. details regarding hospitalized status were captured through telephonic interviews after obtaining verbal informed consent. A maximum-likelihood phylogenetic tree created evolutionary analysis using MEGA7. Results mean age participants 33.9 ± 13.1 years, with 73.5% accounting male patients. Of 98 cases contacted by telephone, 30 (30.6%) had a travel history (domestic/international), 16 (16.3%) reported having been infected COVID-19 past, 79 (80.6%) symptoms, seven at least one comorbidity. Most sequences belonged variant, (6.2%), BA.1.1 (2.7%), BA.1.1.1 (0.7%), BA.1.1.7 (5.5%), BA.1.17.2 BA.1.18 BA.2 (30.8%), BA.2.10 (50.7%), BA.2.12 B.1.617.2 (1.3%) lineages. strains possess signature spike mutations S:A67V, S:T95I, S:R346K, S:S371L, S:G446S, S:G496S, S:T547K, S:N856K, S:L981F, contains S:V213G, S:T376A, S:D405N. Notably, ins214EPE (S1- N-Terminal domain) mutation found significant number sub-lineages. overall lineage observed 79.5% women 83.2% men. Conclusion current showed predominance outcompeting breakthrough infection following recommended two doses vaccine four five being symptomatic. There is need further explore immune evasion properties variant.