Evolution of SARS-CoV-2 during the first year of the COVID-19 pandemic in Northwestern Argentina
Studies about the evolution of SARS-CoV-2 lineages in different backgrounds such as naive populations are still scarce, especially from South America. This work aimed to study the introduction and diversification pattern of SARS-CoV-2 during the first year of the COVID-19 pandemic in the Northwestern Argentina (NWA) region and to analyze the evolutionary dynamics of the main lineages found. In this study, we analyzed a total of 260 SARS-CoV-2 whole-genome sequences from Argentina, belonging to the Provinces of Jujuy, Salta, and Tucumán, from March 31st, 2020, to May 22nd, 2021, which covered the full first wave and the early second wave of the COVID-19 pandemic in Argentina. In the first wave, eight lineages were identified: B.1.499 (76.9%), followed by N.5 (10.2%), B.1.1.274 (3.7%), B.1.1.348 (3.7%), B.1 (2.8%), B.1.600 (0.9%), B.1.1.33 (0.9%) and N.3 (0.9%). During the early second wave, the first-wave lineages were displaced by the introduction of variants of concern (VOC) (Alpha, Gamma), or variants of interest (VOI) (Lambda, Zeta, Epsilon) and other lineages with more limited distribution. Phylodynamic analyses of the B.1.499 and N.5, the two most prevalent lineages in the NWA, revealed that the rate of evolution of lineage N.5 (7.9 × 10−4 substitutions per site per year, s/s/y) was a ∼40% faster than that of lineage B.1.499 (5.6 × 10−4 s/s/y), although both are in the same order of magnitude than other non-VOC lineages. No mutations associated with a biological characteristic of importance were observed as signatures markers of the phylogenetic groups established in Northwestern Argentina, however, single sequences in non-VOC lineages did present mutations of biological importance or associated with VOCs as sporadic events, showing that many of these mutations could emerge from circulation in the general population. This study contributed to the knowledge about the evolution of SARS-CoV-2 in a pre-vaccination and without post-exposure immunization period.
Main Authors: | , , , , , , , , , , , , , , , , , , , , , , |
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Format: | info:ar-repo/semantics/artículo biblioteca |
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Elsevier
2022-10-06T10:36:02Z
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Subjects: | Severe Acute Respiratory Syndrome Coronavirus 2, COVID-19, Argentina, Coronavirus del Síndrome Respiratorio Agudo Grave 2, SARS-CoV-2, Rate Of Evolution, First-Wave Lineages, |
Online Access: | http://hdl.handle.net/20.500.12123/13067 https://www.sciencedirect.com/science/article/pii/S0168170222002647 https://doi.org/10.1016/j.virusres.2022.198936 |
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Severe Acute Respiratory Syndrome Coronavirus 2 COVID-19 Argentina Coronavirus del Síndrome Respiratorio Agudo Grave 2 SARS-CoV-2 Rate Of Evolution First-Wave Lineages Severe Acute Respiratory Syndrome Coronavirus 2 COVID-19 Argentina Coronavirus del Síndrome Respiratorio Agudo Grave 2 SARS-CoV-2 Rate Of Evolution First-Wave Lineages |
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Severe Acute Respiratory Syndrome Coronavirus 2 COVID-19 Argentina Coronavirus del Síndrome Respiratorio Agudo Grave 2 SARS-CoV-2 Rate Of Evolution First-Wave Lineages Severe Acute Respiratory Syndrome Coronavirus 2 COVID-19 Argentina Coronavirus del Síndrome Respiratorio Agudo Grave 2 SARS-CoV-2 Rate Of Evolution First-Wave Lineages Zambrana Montaño, Romina Culasso, Andrés Carlos Alberto Fernandez, Franco Daniel Marquez, Nathalie Debat, Humberto Julio Salmerón, Mariana Zamora, Ana María Ruíz de Huidobro, Gustavo Costas, Dardo Alabarse, Graciela Charre, Miguel Alejandro Fridman, Ariel David Mamani, Claudia Vaca, Fabiana Maza Diaz, Claudia Raskovsky, Viviana Lavaque, Esteban Lesser, Veronica Cajal, Pamela Agüero, Fernanda Calvente, Cintia Torres, Carolina Viegas, Mariana Evolution of SARS-CoV-2 during the first year of the COVID-19 pandemic in Northwestern Argentina |
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Studies about the evolution of SARS-CoV-2 lineages in different backgrounds such as naive populations are still scarce, especially from South America. This work aimed to study the introduction and diversification pattern of SARS-CoV-2 during the first year of the COVID-19 pandemic in the Northwestern Argentina (NWA) region and to analyze the evolutionary dynamics of the main lineages found. In this study, we analyzed a total of 260 SARS-CoV-2 whole-genome sequences from Argentina, belonging to the Provinces of Jujuy, Salta, and Tucumán, from March 31st, 2020, to May 22nd, 2021, which covered the full first wave and the early second wave of the COVID-19 pandemic in Argentina. In the first wave, eight lineages were identified: B.1.499 (76.9%), followed by N.5 (10.2%), B.1.1.274 (3.7%), B.1.1.348 (3.7%), B.1 (2.8%), B.1.600 (0.9%), B.1.1.33 (0.9%) and N.3 (0.9%). During the early second wave, the first-wave lineages were displaced by the introduction of variants of concern (VOC) (Alpha, Gamma), or variants of interest (VOI) (Lambda, Zeta, Epsilon) and other lineages with more limited distribution. Phylodynamic analyses of the B.1.499 and N.5, the two most prevalent lineages in the NWA, revealed that the rate of evolution of lineage N.5 (7.9 × 10−4 substitutions per site per year, s/s/y) was a ∼40% faster than that of lineage B.1.499 (5.6 × 10−4 s/s/y), although both are in the same order of magnitude than other non-VOC lineages. No mutations associated with a biological characteristic of importance were observed as signatures markers of the phylogenetic groups established in Northwestern Argentina, however, single sequences in non-VOC lineages did present mutations of biological importance or associated with VOCs as sporadic events, showing that many of these mutations could emerge from circulation in the general population. This study contributed to the knowledge about the evolution of SARS-CoV-2 in a pre-vaccination and without post-exposure immunization period. |
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info:ar-repo/semantics/artículo |
topic_facet |
Severe Acute Respiratory Syndrome Coronavirus 2 COVID-19 Argentina Coronavirus del Síndrome Respiratorio Agudo Grave 2 SARS-CoV-2 Rate Of Evolution First-Wave Lineages |
author |
Zambrana Montaño, Romina Culasso, Andrés Carlos Alberto Fernandez, Franco Daniel Marquez, Nathalie Debat, Humberto Julio Salmerón, Mariana Zamora, Ana María Ruíz de Huidobro, Gustavo Costas, Dardo Alabarse, Graciela Charre, Miguel Alejandro Fridman, Ariel David Mamani, Claudia Vaca, Fabiana Maza Diaz, Claudia Raskovsky, Viviana Lavaque, Esteban Lesser, Veronica Cajal, Pamela Agüero, Fernanda Calvente, Cintia Torres, Carolina Viegas, Mariana |
author_facet |
Zambrana Montaño, Romina Culasso, Andrés Carlos Alberto Fernandez, Franco Daniel Marquez, Nathalie Debat, Humberto Julio Salmerón, Mariana Zamora, Ana María Ruíz de Huidobro, Gustavo Costas, Dardo Alabarse, Graciela Charre, Miguel Alejandro Fridman, Ariel David Mamani, Claudia Vaca, Fabiana Maza Diaz, Claudia Raskovsky, Viviana Lavaque, Esteban Lesser, Veronica Cajal, Pamela Agüero, Fernanda Calvente, Cintia Torres, Carolina Viegas, Mariana |
author_sort |
Zambrana Montaño, Romina |
title |
Evolution of SARS-CoV-2 during the first year of the COVID-19 pandemic in Northwestern Argentina |
title_short |
Evolution of SARS-CoV-2 during the first year of the COVID-19 pandemic in Northwestern Argentina |
title_full |
Evolution of SARS-CoV-2 during the first year of the COVID-19 pandemic in Northwestern Argentina |
title_fullStr |
Evolution of SARS-CoV-2 during the first year of the COVID-19 pandemic in Northwestern Argentina |
title_full_unstemmed |
Evolution of SARS-CoV-2 during the first year of the COVID-19 pandemic in Northwestern Argentina |
title_sort |
evolution of sars-cov-2 during the first year of the covid-19 pandemic in northwestern argentina |
publisher |
Elsevier |
publishDate |
2022-10-06T10:36:02Z |
url |
http://hdl.handle.net/20.500.12123/13067 https://www.sciencedirect.com/science/article/pii/S0168170222002647 https://doi.org/10.1016/j.virusres.2022.198936 |
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oai:localhost:20.500.12123-130672022-10-06T10:53:51Z Evolution of SARS-CoV-2 during the first year of the COVID-19 pandemic in Northwestern Argentina Zambrana Montaño, Romina Culasso, Andrés Carlos Alberto Fernandez, Franco Daniel Marquez, Nathalie Debat, Humberto Julio Salmerón, Mariana Zamora, Ana María Ruíz de Huidobro, Gustavo Costas, Dardo Alabarse, Graciela Charre, Miguel Alejandro Fridman, Ariel David Mamani, Claudia Vaca, Fabiana Maza Diaz, Claudia Raskovsky, Viviana Lavaque, Esteban Lesser, Veronica Cajal, Pamela Agüero, Fernanda Calvente, Cintia Torres, Carolina Viegas, Mariana Severe Acute Respiratory Syndrome Coronavirus 2 COVID-19 Argentina Coronavirus del Síndrome Respiratorio Agudo Grave 2 SARS-CoV-2 Rate Of Evolution First-Wave Lineages Studies about the evolution of SARS-CoV-2 lineages in different backgrounds such as naive populations are still scarce, especially from South America. This work aimed to study the introduction and diversification pattern of SARS-CoV-2 during the first year of the COVID-19 pandemic in the Northwestern Argentina (NWA) region and to analyze the evolutionary dynamics of the main lineages found. In this study, we analyzed a total of 260 SARS-CoV-2 whole-genome sequences from Argentina, belonging to the Provinces of Jujuy, Salta, and Tucumán, from March 31st, 2020, to May 22nd, 2021, which covered the full first wave and the early second wave of the COVID-19 pandemic in Argentina. In the first wave, eight lineages were identified: B.1.499 (76.9%), followed by N.5 (10.2%), B.1.1.274 (3.7%), B.1.1.348 (3.7%), B.1 (2.8%), B.1.600 (0.9%), B.1.1.33 (0.9%) and N.3 (0.9%). During the early second wave, the first-wave lineages were displaced by the introduction of variants of concern (VOC) (Alpha, Gamma), or variants of interest (VOI) (Lambda, Zeta, Epsilon) and other lineages with more limited distribution. Phylodynamic analyses of the B.1.499 and N.5, the two most prevalent lineages in the NWA, revealed that the rate of evolution of lineage N.5 (7.9 × 10−4 substitutions per site per year, s/s/y) was a ∼40% faster than that of lineage B.1.499 (5.6 × 10−4 s/s/y), although both are in the same order of magnitude than other non-VOC lineages. No mutations associated with a biological characteristic of importance were observed as signatures markers of the phylogenetic groups established in Northwestern Argentina, however, single sequences in non-VOC lineages did present mutations of biological importance or associated with VOCs as sporadic events, showing that many of these mutations could emerge from circulation in the general population. This study contributed to the knowledge about the evolution of SARS-CoV-2 in a pre-vaccination and without post-exposure immunization period. Instituto de Patología Vegetal Fil: Zambrana Montaño, Romina. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Investigaciones en Bacteriología y Virología Molecular; Argentina Fil: Zambrana Montaño, Romina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Culasso, Andrés Carlos Alberto. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Investigaciones en Bacteriología y Virología Molecular; Argentina Fil: Culasso, Andrés Carlos Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Fernandez, Franco Daniel. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; Argentina Fil: Fernandez, Franco Daniel. Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Fitopatología y Modelización Agrícola (UFyMA); Argentina Fil: Marquez, Nathalie. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; Argentina Fil: Marquez, Nathalie. Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Fitopatología y Modelización Agrícola (UFyMA); Argentina Fil: Debat, Humberto Julio. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; Argentina Fil: Debat, Humberto Julio. Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Fitopatología y Modelización Agrícola (UFyMA); Argentina Fil: Salmerón, Mariana. Laboratorio de Salud Pública; Argentina Fil: Zamora, Ana María. Laboratorio de Salud Pública; Argentina Fil: Ruíz de Huidobro, Gustavo. Laboratorio de Salud Pública; Argentina Fil: Costas, Dardo. Laboratorio de Salud Pública; Argentina Fil: Alabarse, Graciela. Laboratorio de Salud Pública; Argentina Fil: Charre, Miguel Alejandro. Laboratorio Central de Salud Pública, San Salvador de Jujuy; Argentina Fil: Fridman, Ariel David. Laboratorio Central de Salud Pública. San Salvador de Jujuy; Argentina Fil: Mamani, Claudia. Laboratorio Central de Salud Pública. San Salvador de Jujuy; Argentina Fil: Vaca, Fabiana. Laboratorio Central de Salud Pública. San Salvador de Jujuy; Argentina Fil: Maza Diaz, Claudia. Laboratorio Central de Salud Pública. San Salvador de Jujuy; Argentina Fil: Raskovsky, Viviana. Hospital Señor del Milagro. Laboratorio de Virus Respiratorios y Neurovirosis; Argentina Fil: Lavaque, Esteban. Hospital Señor del Milagro. Laboratorio de Virus Respiratorios y Neurovirosis; Argentina Fil: Lesser, Veronica. Hospital Señor del Milagro. Laboratorio de Virus Respiratorios y Neurovirosis; Argentina Fil: Cajal, Pamela. Hospital Señor del Milagro. Laboratorio de Virus Respiratorios y Neurovirosis; Argentina Fil: Agüero, Fernanda. Hospital Señor del Milagro. Laboratorio de Virus Respiratorios y Neurovirosis; Argentina Fil: Calvente, Cintia. Hospital Señor del Milagro. Laboratorio de Virus Respiratorios y Neurovirosis; Argentina Fil: Torres, Carolina. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Investigaciones en Bacteriología y Virología Molecular; Argentina Fil: Torres, Carolina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Viegas, Mariana. Hospital de Niños Dr. Ricardo Gutiérrez. Laboratorio de Virología; Argentina info:eu-repo/date/embargoEnd/2023-10-06 2022-10-06T10:36:02Z 2022-10-06T10:36:02Z 2022-09-28 info:ar-repo/semantics/artículo info:eu-repo/semantics/article info:eu-repo/semantics/acceptedVersion http://hdl.handle.net/20.500.12123/13067 https://www.sciencedirect.com/science/article/pii/S0168170222002647 0168-1702 1872-7492 (online) https://doi.org/10.1016/j.virusres.2022.198936 eng info:eu-repo/semantics/embargoedAccess application/pdf Elsevier Virus Research : 198936 (28 September 2022) |