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

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 i...

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Autores principales:	Shashi Sharma, Paban Kumar Dash, Sushil Kumar Sharma, Ambuj Srivastava, Jyoti S. Kumar, B. S. Karothia, K. T. Chelvam, Sandeep Singh, Abhaydeep Gupta, Ram Govind Yadav, Ruchi Yadav, T. S. Greeshma, Pramod Kumar Kushwaha, Ravi Bhushan Kumar, D. P. Nagar, Manvendra Nandan, Subodh Kumar, Duraipandian Thavaselvam, Devendra Kumar Dubey
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/012d70e5f07e4181aabbdfe16e5bf55f
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spelling	oai:doaj.org-article:012d70e5f07e4181aabbdfe16e5bf55f2021-12-02T18:02:06ZEmergence and expansion of highly infectious spike protein D614G mutant SARS-CoV-2 in central India10.1038/s41598-021-95822-w2045-2322https://doaj.org/article/012d70e5f07e4181aabbdfe16e5bf55f2021-09-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-95822-whttps://doaj.org/toc/2045-2322Abstract 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.Shashi SharmaPaban Kumar DashSushil Kumar SharmaAmbuj SrivastavaJyoti S. KumarB. S. KarothiaK. T. ChelvamSandeep SinghAbhaydeep GuptaRam Govind YadavRuchi YadavT. S. GreeshmaPramod Kumar KushwahaRavi Bhushan KumarD. P. NagarManvendra NandanSubodh KumarDuraipandian ThavaselvamDevendra Kumar DubeyNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-8 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Shashi Sharma Paban Kumar Dash Sushil Kumar Sharma Ambuj Srivastava Jyoti S. Kumar B. S. Karothia K. T. Chelvam Sandeep Singh Abhaydeep Gupta Ram Govind Yadav Ruchi Yadav T. S. Greeshma Pramod Kumar Kushwaha Ravi Bhushan Kumar D. P. Nagar Manvendra Nandan Subodh Kumar Duraipandian Thavaselvam Devendra Kumar Dubey Emergence and expansion of highly infectious spike protein D614G mutant SARS-CoV-2 in central India
description	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.
format	article
author	Shashi Sharma Paban Kumar Dash Sushil Kumar Sharma Ambuj Srivastava Jyoti S. Kumar B. S. Karothia K. T. Chelvam Sandeep Singh Abhaydeep Gupta Ram Govind Yadav Ruchi Yadav T. S. Greeshma Pramod Kumar Kushwaha Ravi Bhushan Kumar D. P. Nagar Manvendra Nandan Subodh Kumar Duraipandian Thavaselvam Devendra Kumar Dubey
author_facet	Shashi Sharma Paban Kumar Dash Sushil Kumar Sharma Ambuj Srivastava Jyoti S. Kumar B. S. Karothia K. T. Chelvam Sandeep Singh Abhaydeep Gupta Ram Govind Yadav Ruchi Yadav T. S. Greeshma Pramod Kumar Kushwaha Ravi Bhushan Kumar D. P. Nagar Manvendra Nandan Subodh Kumar Duraipandian Thavaselvam Devendra Kumar Dubey
author_sort	Shashi Sharma
title	Emergence and expansion of highly infectious spike protein D614G mutant SARS-CoV-2 in central India
title_short	Emergence and expansion of highly infectious spike protein D614G mutant SARS-CoV-2 in central India
title_full	Emergence and expansion of highly infectious spike protein D614G mutant SARS-CoV-2 in central India
title_fullStr	Emergence and expansion of highly infectious spike protein D614G mutant SARS-CoV-2 in central India
title_full_unstemmed	Emergence and expansion of highly infectious spike protein D614G mutant SARS-CoV-2 in central India
title_sort	emergence and expansion of highly infectious spike protein d614g mutant sars-cov-2 in central india
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/012d70e5f07e4181aabbdfe16e5bf55f
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Emergence and expansion of highly infectious spike protein D614G mutant SARS-CoV-2 in central India

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