Dynamics of SARS-CoV-2 mutations reveals regional-specificity and similar trends of N501 and high-frequency mutation N501Y in different levels of control measures

Abstract Coronavirus disease 2019 (COVID-19) is a contagious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This disease has spread globally, causing more than 161.5 million cases and 3.3 million deaths to date. Surveillance and monitoring of new mutations in the vir...

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Autores principales:	Santiago Justo Arevalo, Daniela Zapata Sifuentes, César J. Huallpa, Gianfranco Landa Bianchi, Adriana Castillo Chávez, Romina Garavito-Salini Casas, Carmen Sofia Uribe Calampa, Guillermo Uceda-Campos, Roberto Pineda Chavarría
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/97da6e6cb96446d0b212a5df9d7c7a40
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spelling	oai:doaj.org-article:97da6e6cb96446d0b212a5df9d7c7a402021-12-02T17:19:16ZDynamics of SARS-CoV-2 mutations reveals regional-specificity and similar trends of N501 and high-frequency mutation N501Y in different levels of control measures10.1038/s41598-021-97267-72045-2322https://doaj.org/article/97da6e6cb96446d0b212a5df9d7c7a402021-09-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-97267-7https://doaj.org/toc/2045-2322Abstract Coronavirus disease 2019 (COVID-19) is a contagious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This disease has spread globally, causing more than 161.5 million cases and 3.3 million deaths to date. Surveillance and monitoring of new mutations in the virus’ genome are crucial to our understanding of the adaptation of SARS-CoV-2. Moreover, how the temporal dynamics of these mutations is influenced by control measures and non-pharmaceutical interventions (NPIs) is poorly understood. Using 1,058,020 SARS-CoV-2 from sequenced COVID-19 cases from 98 countries (totaling 714 country-month combinations), we perform a normalization by COVID-19 cases to calculate the relative frequency of SARS-CoV-2 mutations and explore their dynamics over time. We found 115 mutations estimated to be present in more than 3% of global COVID-19 cases and determined three types of mutation dynamics: high-frequency, medium-frequency, and low-frequency. Classification of mutations based on temporal dynamics enable us to examine viral adaptation and evaluate the effects of implemented control measures in virus evolution during the pandemic. We showed that medium-frequency mutations are characterized by high prevalence in specific regions and/or in constant competition with other mutations in several regions. Finally, taking N501Y mutation as representative of high-frequency mutations, we showed that level of control measure stringency negatively correlates with the effective reproduction number of SARS-CoV-2 with high-frequency or not-high-frequency and both follows similar trends in different levels of stringency.Santiago Justo ArevaloDaniela Zapata SifuentesCésar J. HuallpaGianfranco Landa BianchiAdriana Castillo ChávezRomina Garavito-Salini CasasCarmen Sofia Uribe CalampaGuillermo Uceda-CamposRoberto Pineda ChavarríaNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-11 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Santiago Justo Arevalo Daniela Zapata Sifuentes César J. Huallpa Gianfranco Landa Bianchi Adriana Castillo Chávez Romina Garavito-Salini Casas Carmen Sofia Uribe Calampa Guillermo Uceda-Campos Roberto Pineda Chavarría Dynamics of SARS-CoV-2 mutations reveals regional-specificity and similar trends of N501 and high-frequency mutation N501Y in different levels of control measures
description	Abstract Coronavirus disease 2019 (COVID-19) is a contagious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This disease has spread globally, causing more than 161.5 million cases and 3.3 million deaths to date. Surveillance and monitoring of new mutations in the virus’ genome are crucial to our understanding of the adaptation of SARS-CoV-2. Moreover, how the temporal dynamics of these mutations is influenced by control measures and non-pharmaceutical interventions (NPIs) is poorly understood. Using 1,058,020 SARS-CoV-2 from sequenced COVID-19 cases from 98 countries (totaling 714 country-month combinations), we perform a normalization by COVID-19 cases to calculate the relative frequency of SARS-CoV-2 mutations and explore their dynamics over time. We found 115 mutations estimated to be present in more than 3% of global COVID-19 cases and determined three types of mutation dynamics: high-frequency, medium-frequency, and low-frequency. Classification of mutations based on temporal dynamics enable us to examine viral adaptation and evaluate the effects of implemented control measures in virus evolution during the pandemic. We showed that medium-frequency mutations are characterized by high prevalence in specific regions and/or in constant competition with other mutations in several regions. Finally, taking N501Y mutation as representative of high-frequency mutations, we showed that level of control measure stringency negatively correlates with the effective reproduction number of SARS-CoV-2 with high-frequency or not-high-frequency and both follows similar trends in different levels of stringency.
format	article
author	Santiago Justo Arevalo Daniela Zapata Sifuentes César J. Huallpa Gianfranco Landa Bianchi Adriana Castillo Chávez Romina Garavito-Salini Casas Carmen Sofia Uribe Calampa Guillermo Uceda-Campos Roberto Pineda Chavarría
author_facet	Santiago Justo Arevalo Daniela Zapata Sifuentes César J. Huallpa Gianfranco Landa Bianchi Adriana Castillo Chávez Romina Garavito-Salini Casas Carmen Sofia Uribe Calampa Guillermo Uceda-Campos Roberto Pineda Chavarría
author_sort	Santiago Justo Arevalo
title	Dynamics of SARS-CoV-2 mutations reveals regional-specificity and similar trends of N501 and high-frequency mutation N501Y in different levels of control measures
title_short	Dynamics of SARS-CoV-2 mutations reveals regional-specificity and similar trends of N501 and high-frequency mutation N501Y in different levels of control measures
title_full	Dynamics of SARS-CoV-2 mutations reveals regional-specificity and similar trends of N501 and high-frequency mutation N501Y in different levels of control measures
title_fullStr	Dynamics of SARS-CoV-2 mutations reveals regional-specificity and similar trends of N501 and high-frequency mutation N501Y in different levels of control measures
title_full_unstemmed	Dynamics of SARS-CoV-2 mutations reveals regional-specificity and similar trends of N501 and high-frequency mutation N501Y in different levels of control measures
title_sort	dynamics of sars-cov-2 mutations reveals regional-specificity and similar trends of n501 and high-frequency mutation n501y in different levels of control measures
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/97da6e6cb96446d0b212a5df9d7c7a40
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Dynamics of SARS-CoV-2 mutations reveals regional-specificity and similar trends of N501 and high-frequency mutation N501Y in different levels of control measures

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