Emergence and expansion of highly infectious spike protein D614G mutant SARS-CoV-2 in central India

Shashi Sharma,Sandeep Singh,Abhaydeep Gupta,Subodh Kumar,Ram Govind Yadav,Ravi Bhushan Kumar,Paban Kumar Dash,Devendra Kumar Dubey,Ambuj Srivastava,B S Karothia,Ruchi Yadav,Manvendra Nandan,Pramod Kumar Kushwaha,D P Nagar,K T Chelvam,Jyoti S Kumar,T S Greeshma,Duraipandian Thavaselvam,Sushil Kumar Sharma

doi:10.1038/s41598-021-95822-w

Shashi Sharma, Sandeep Singh + Show 17 more

Open Access

https://doi.org/10.1038/s41598-021-95822-w

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Abstract

COVID-19 has emerged as global pandemic with largest damage to the public health, economy and human psyche.The genome sequence data obtained during the ongoing pandemic are valuable to understand the virus evolutionary patterns and spread across the globe. Increased availability of genome information of circulating SARS-CoV-2 strains in India will enable the scientific community to understand the emergence of new variants and their impact on human health. The first case of COVID-19 was detected in Chambal region of Madhya Pradesh state in mid of March 2020 followed by multiple introduction events and expansion of cases within next three months. More than 5000 COVID-19 suspected samples referred to Defence Research and Development Establishment, Gwalior, Madhya Pradesh were analyzed during the nation -wide lockdown and unlock period. A total of 136 cases were found positive over a span of three months that included virus introduction to the region and its further spread. Whole genome sequences employing Oxford nanopore technology were generated for 26 SARS-CoV-2 circulating in 10 different districts in Madhya Pradesh state of India. This period witnessed index cases with multiple travel histories responsible for introduction of COVID-19 followed by remarkable expansion of virus. The genome wide substitutions including in important viral proteins were identified. The detailed phylogenetic analysis revealed the circulating SARS-CoV-2 clustered in multiple clades including A2a, A4 and B. The cluster-wise segregation was observed, suggesting multiple introduction links and subsequent evolution of virus in the region. This is the first comprehensive whole genome sequence analysis from central India, which revealed the emergence and evolution of SARS-CoV-2 during thenation-wide lockdown and unlock.

Highlights

Emergence of novel virus is always considered as a major challenge to humanity
The rapid transmission of SARS-CoV-2 and its expansion into geographical territories has led to devastating effect on global health and economy
There is a renewed interest to understand the evolutionary path being followed by SARS-CoV-2 to undertake effective control and mitigation m easures[10]

Summary

Introduction

Emergence of novel virus is always considered as a major challenge to humanity. SARS-CoV-2, the etiological agent of “coronavirus disease 2019” (COVID-19) pandemic has been causing devastating damage to global public health and economy since its emergence in December 2 0191,2. In March, impositions of nationwide lockdown successfully contained the epidemic curve Despite these measurements, the exodus of individual from their place of work to native places during later part of lockdown led to rapid transmission of virus to remote corners of the country. Generation sequencing (NGS), an emerging technology has aided in understanding the evolution of SARS-CoV-2 genomes and its transmission patterns after it enters a new population[8,9]. This technology has been proven to be an important tool towards formulating strategies for management of this pandemic.

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