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Emergence and expansion of highly infectious spike protein D614G mutant SARS-CoV-2 in central India.
Sci Rep. 2021 09 13; 11(1):18126.SR

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.

Authors+Show Affiliations

Virology Division, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, 474002, India. COVID-19 Diagnosis Task Force, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, 474002, India.Virology Division, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, 474002, India. pabandash@drde.drdo.in. COVID-19 Diagnosis Task Force, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, 474002, India. pabandash@drde.drdo.in.Virology Division, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, 474002, India. COVID-19 Diagnosis Task Force, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, 474002, India.Virology Division, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, 474002, India. COVID-19 Diagnosis Task Force, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, 474002, India.Virology Division, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, 474002, India. COVID-19 Diagnosis Task Force, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, 474002, India.COVID-19 Diagnosis Task Force, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, 474002, India.COVID-19 Diagnosis Task Force, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, 474002, India.COVID-19 Diagnosis Task Force, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, 474002, India.COVID-19 Diagnosis Task Force, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, 474002, India.Virology Division, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, 474002, India. COVID-19 Diagnosis Task Force, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, 474002, India.COVID-19 Diagnosis Task Force, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, 474002, India.COVID-19 Diagnosis Task Force, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, 474002, India.COVID-19 Diagnosis Task Force, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, 474002, India.COVID-19 Diagnosis Task Force, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, 474002, India.COVID-19 Diagnosis Task Force, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, 474002, India.COVID-19 Diagnosis Task Force, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, 474002, India.COVID-19 Diagnosis Task Force, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, 474002, India. subodh@drde.drdo.in.COVID-19 Diagnosis Task Force, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, 474002, India.COVID-19 Diagnosis Task Force, Defence Research and Development Establishment, Gwalior, Madhya Pradesh, 474002, India.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

34518554

Citation

Sharma, Shashi, et al. "Emergence and Expansion of Highly Infectious Spike Protein D614G Mutant SARS-CoV-2 in Central India." Scientific Reports, vol. 11, no. 1, 2021, p. 18126.
Sharma S, Dash PK, Sharma SK, et al. Emergence and expansion of highly infectious spike protein D614G mutant SARS-CoV-2 in central India. Sci Rep. 2021;11(1):18126.
Sharma, S., Dash, P. K., Sharma, S. K., Srivastava, A., Kumar, J. S., Karothia, B. S., Chelvam, K. T., Singh, S., Gupta, A., Yadav, R. G., Yadav, R., Greeshma, T. S., Kushwaha, P. K., Kumar, R. B., Nagar, D. P., Nandan, M., Kumar, S., Thavaselvam, D., & Dubey, D. K. (2021). Emergence and expansion of highly infectious spike protein D614G mutant SARS-CoV-2 in central India. Scientific Reports, 11(1), 18126. https://doi.org/10.1038/s41598-021-95822-w
Sharma S, et al. Emergence and Expansion of Highly Infectious Spike Protein D614G Mutant SARS-CoV-2 in Central India. Sci Rep. 2021 09 13;11(1):18126. PubMed PMID: 34518554.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Emergence and expansion of highly infectious spike protein D614G mutant SARS-CoV-2 in central India. AU - Sharma,Shashi, AU - Dash,Paban Kumar, AU - Sharma,Sushil Kumar, AU - Srivastava,Ambuj, AU - Kumar,Jyoti S, AU - Karothia,B S, AU - Chelvam,K T, AU - Singh,Sandeep, AU - Gupta,Abhaydeep, AU - Yadav,Ram Govind, AU - Yadav,Ruchi, AU - Greeshma,T S, AU - Kushwaha,Pramod Kumar, AU - Kumar,Ravi Bhushan, AU - Nagar,D P, AU - Nandan,Manvendra, AU - Kumar,Subodh, AU - Thavaselvam,Duraipandian, AU - Dubey,Devendra Kumar, Y1 - 2021/09/13/ PY - 2020/10/23/received PY - 2021/07/23/accepted PY - 2021/9/14/entrez PY - 2021/9/15/pubmed PY - 2021/9/28/medline SP - 18126 EP - 18126 JF - Scientific reports JO - Sci Rep VL - 11 IS - 1 N2 - 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. SN - 2045-2322 UR - https://www.unboundmedicine.com/medline/citation/34518554/Emergence_and_expansion_of_highly_infectious_spike_protein_D614G_mutant_SARS_CoV_2_in_central_India_ L2 - https://doi.org/10.1038/s41598-021-95822-w DB - PRIME DP - Unbound Medicine ER -