Molecular Analysis and Genome Sequencing of SARS-CoV-2 during Second Wave 2021 Revealed Variant Diversity in India

Rupinder Bakshi,Palika Sharma,Jaspreet Kaur Boparai,Amritpal Kaur,Kulwinder Singh,Akshdeep Singh,Paramjeet Kaur,Savita Rani,Tanveer Kaur,Satinder Kaur,Kajal Verma,Navdeep Kaur,Vikram Thakur,Sukhvir Kaur,Jaspreet Kaur,Ramanpreet Kaur,Gagandeep Singh,Sweety Sweety,Ritika Ghai,Balwant Singh,Dhavni Singla,Harbhajan Singh,Karashdeep Kaur,Kuljeet Kaur,Naina Rai ,Suman ,Shiv Kumar Singh

doi:10.22207/jpam.15.4.07

Abstract

SARS-CoV-2 variants rapid emergence has posed critical challenge of higher transmission and immune escape causing serious threats to control the pandemic. The present study was carried out in confirmed cases of SARS-CoV-2 patients to elucidate the prevalence of SARS-CoV-2 variant strain. We performed RT-PCR using extracted RNA from the nasopharyngeal swabs of suspected Covid-19 patients. Confirmed positive cases with CT<25 were subjected to whole-genome sequencing to track the prevalence of the virus in the Malwa region of Punjab. The presence of B.1, B.1.1.7, B.1.351, B.1.617.1, B.1.617.2, AY.1 and other unidentified variants of SARS-CoV-2 was found in the studied population. Among all the variants, B.1.1.7 (UK variant) and B.1.617.2 (delta-Indian variant) was found to be the most dominant variant in the population and was found majorly in Patiala followed by Ludhiana, SBS Nagar, Mansa and Sangrur. In addition to this, sequencing results also observed that the dominant trait was more prevalent in male population and age group 21-40 years. The B.1.1.7 and B.1.617.2 variant of SARS-CoV-2 is replacing the wild type (Wuhan Strain) and emerging as the dominant variant in Punjab.

Highlights

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), earlier known as novel CoV/ nCoV lead to coronavirus pandemic in 2019
As India is the second largest infected country of SARS-CoV-2, the current study focused on Indian isolates (Punjab) to explore the variations occurring in the population.[9]
Covid-19 cases have continued to surge in India during second wave as new records have been made by current outbreak of SARS-CoV-2 in India

Summary

Introduction

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), earlier known as novel CoV/ nCoV lead to coronavirus pandemic in 2019. SARS-CoV-2 belongs to Coronaviridae family having single stranded ‘+’ sense RNA causing infection in mainly humans and animals resulting in respiratory congestions. The first reported case of this virus was identified in Wuhan Hubei, China during December 2019 and spread hastily all around the world. The beginning of the outbreak in India began in January 2020, one of the medical student carrying Wuhan strain returned from Wuhan University reported positive in Kerala on 30th January 20201. In Punjab it appeared during the month of March 2020 with 42 active cases.[2] Later Indian health ministry initiated the surveillance of SARS-CoV-2 with ICMR (Indian Council of Medical Research) through VRDL (Viral Research Diagnostics Laboratories)

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Discussion

Conclusion