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

Kamran Zaman; Anita M Shete; Shailendra Kumar Mishra; Abhinendra Kumar; Mahendra M Reddy; Rima R Sahay; Shailendra Yadav; Triparna Majumdar; Ashok K Pandey; Gaurav Raj Dwivedi; Hirawati Deval; Rajeev Singh; Sthita Pragnya Behera; 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

doi:10.3389/fmed.2022.955930

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

Front Med (Lausanne). 2022 Nov 2:9:955930. doi: 10.3389/fmed.2022.955930. eCollection 2022.

Authors

Kamran Zaman¹, Anita M Shete², Shailendra Kumar Mishra¹, Abhinendra Kumar², Mahendra M Reddy¹, Rima R Sahay², Shailendra Yadav¹, Triparna Majumdar², Ashok K Pandey¹, Gaurav Raj Dwivedi¹, Hirawati Deval¹, Rajeev Singh¹, Sthita Pragnya Behera¹, Niraj Kumar¹, Savita Patil², Ashish Kumar¹, Manisha Dudhmal², Yash Joshi², Aishwarya Shukla¹, Pranita Gawande², Asif Kavathekar¹, Nalin Kumar¹, Vijay Kumar¹, Kamlesh Kumar¹, Ravi Shankar Singh¹, Manoj Kumar¹, Shashikant Tiwari¹, Ajay Verma², Pragya D Yadav², Rajni Kant¹

Affiliations

¹ Indian Council of Medical Research-Regional Medical Research Centre Gorakhpur (ICMR-RMRC Gorakhpur), Gorakhpur, India.
² Maximum Containment Facility, Indian Council of Medical Research-National Institute of Virology Pune (ICMR-NIV Pune), Pune, India.

Abstract

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 and vaccine-induced immunity. The present study aims to analyze the clinical profile and genome characterization of the SARS-CoV-2 variant in eastern Uttar Pradesh (UP), North India.

Methods: Whole-genome sequencing (WGS) was conducted for 146 SARS-CoV-2 samples obtained from individuals who tested coronavirus disease 2019 (COVID-19) positive between the period of 1 January 2022 and 24 February 2022, from three districts of eastern UP. The details regarding clinical and hospitalized status were captured through telephonic interviews after obtaining verbal informed consent. A maximum-likelihood phylogenetic tree was created for evolutionary analysis using MEGA7.

Results: The mean age of study participants was 33.9 ± 13.1 years, with 73.5% accounting for male patients. Of the 98 cases contacted by telephone, 30 (30.6%) had a travel history (domestic/international), 16 (16.3%) reported having been infected with COVID-19 in past, 79 (80.6%) had symptoms, and seven had at least one comorbidity. Most of the sequences belonged to the Omicron variant, with BA.1 (6.2%), BA.1.1 (2.7%), BA.1.1.1 (0.7%), BA.1.1.7 (5.5%), BA.1.17.2 (0.7%), BA.1.18 (0.7%), BA.2 (30.8%), BA.2.10 (50.7%), BA.2.12 (0.7%), and B.1.617.2 (1.3%) lineages. BA.1 and BA.1.1 strains possess signature spike mutations S:A67V, S:T95I, S:R346K, S:S371L, S:G446S, S:G496S, S:T547K, S:N856K, and S:L981F, and BA.2 contains S:V213G, S:T376A, and S:D405N. Notably, ins214EPE (S1- N-Terminal domain) mutation was found in a significant number of Omicron BA.1 and sub-lineages. The overall Omicron BA.2 lineage was observed in 79.5% of women and 83.2% of men.

Conclusion: The current study showed a predominance of the Omicron BA.2 variant outcompeting the BA.1 over a period in eastern UP. Most of the cases had a breakthrough infection following the recommended two doses of vaccine with four in five cases being symptomatic. There is a need to further explore the immune evasion properties of the Omicron variant.

Keywords: COVID-19; SARS-CoV-2; omicron; third wave; variant of concern (VOC); whole-genome sequencing (WGS).

Copyright © 2022 Zaman, Shete, Mishra, Kumar, Reddy, Sahay, Yadav, Majumdar, Pandey, Dwivedi, Deval, Singh, Behera, Kumar, Patil, Kumar, Dudhmal, Joshi, Shukla, Gawande, Kavathekar, Kumar, Kumar, Kumar, Singh, Kumar, Tiwari, Verma, Yadav and Kant.