Evolution of SARS-CoV-2 during the first year of the COVID-19 pandemic in Northwestern Argentina
- Autores
- Zambrana Montaño, Romina Micaela; 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
- Año de publicación
- 2022
- Idioma
- inglés
- Tipo de recurso
- artículo
- Estado
- versión aceptada
- Descripción
- 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 - Fuente
- Virus Research : 198936 (28 September 2022)
- Materia
-
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 - Nivel de accesibilidad
- acceso abierto
- Condiciones de uso
- Repositorio
.jpg)
- Institución
- Instituto Nacional de Tecnología Agropecuaria
- OAI Identificador
- oai:localhost:20.500.12123/13067
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Evolution of SARS-CoV-2 during the first year of the COVID-19 pandemic in Northwestern ArgentinaZambrana Montaño, Romina MicaelaCulasso, Andrés Carlos AlbertoFernandez, Franco DanielMarquez, NathalieDebat, Humberto JulioSalmerón, MarianaZamora, Ana MaríaRuíz de Huidobro, GustavoCostas, DardoAlabarse, GracielaCharre, Miguel AlejandroFridman, Ariel DavidMamani, ClaudiaVaca, FabianaMaza Diaz, ClaudiaRaskovsky, VivianaLavaque, EstebanLesser, VeronicaCajal, PamelaAgüero, FernandaCalvente, CintiaTorres, CarolinaViegas, MarianaSevere Acute Respiratory Syndrome Coronavirus 2COVID-19ArgentinaCoronavirus del Síndrome Respiratorio Agudo Grave 2SARS-CoV-2Rate Of EvolutionFirst-Wave LineagesStudies 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 VegetalFil: Zambrana Montaño, Romina. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Investigaciones en Bacteriología y Virología Molecular; ArgentinaFil: Zambrana Montaño, Romina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Culasso, Andrés Carlos Alberto. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Investigaciones en Bacteriología y Virología Molecular; ArgentinaFil: Culasso, Andrés Carlos Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Fernandez, Franco Daniel. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; ArgentinaFil: Fernandez, Franco Daniel. Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Fitopatología y Modelización Agrícola (UFyMA); ArgentinaFil: Marquez, Nathalie. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; ArgentinaFil: Marquez, Nathalie. Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Fitopatología y Modelización Agrícola (UFyMA); ArgentinaFil: Debat, Humberto Julio. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; ArgentinaFil: Debat, Humberto Julio. Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Fitopatología y Modelización Agrícola (UFyMA); ArgentinaFil: Salmerón, Mariana. Laboratorio de Salud Pública; ArgentinaFil: Zamora, Ana María. Laboratorio de Salud Pública; ArgentinaFil: Ruíz de Huidobro, Gustavo. Laboratorio de Salud Pública; ArgentinaFil: Costas, Dardo. Laboratorio de Salud Pública; ArgentinaFil: Alabarse, Graciela. Laboratorio de Salud Pública; ArgentinaFil: Charre, Miguel Alejandro. Laboratorio Central de Salud Pública, San Salvador de Jujuy; ArgentinaFil: Fridman, Ariel David. Laboratorio Central de Salud Pública. San Salvador de Jujuy; ArgentinaFil: Mamani, Claudia. Laboratorio Central de Salud Pública. San Salvador de Jujuy; ArgentinaFil: Vaca, Fabiana. Laboratorio Central de Salud Pública. San Salvador de Jujuy; ArgentinaFil: Maza Diaz, Claudia. Laboratorio Central de Salud Pública. San Salvador de Jujuy; ArgentinaFil: Raskovsky, Viviana. Hospital Señor del Milagro. Laboratorio de Virus Respiratorios y Neurovirosis; ArgentinaFil: Lavaque, Esteban. Hospital Señor del Milagro. Laboratorio de Virus Respiratorios y Neurovirosis; ArgentinaFil: Lesser, Veronica. Hospital Señor del Milagro. Laboratorio de Virus Respiratorios y Neurovirosis; ArgentinaFil: Cajal, Pamela. Hospital Señor del Milagro. Laboratorio de Virus Respiratorios y Neurovirosis; ArgentinaFil: Agüero, Fernanda. Hospital Señor del Milagro. Laboratorio de Virus Respiratorios y Neurovirosis; ArgentinaFil: Calvente, Cintia. Hospital Señor del Milagro. Laboratorio de Virus Respiratorios y Neurovirosis; ArgentinaFil: Torres, Carolina. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Investigaciones en Bacteriología y Virología Molecular; ArgentinaFil: Torres, Carolina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Viegas, Mariana. Hospital de Niños Dr. Ricardo Gutiérrez. Laboratorio de Virología; ArgentinaElsevierinfo:eu-repo/date/embargoEnd/2023-10-062022-10-06T10:36:02Z2022-10-06T10:36:02Z2022-09-28info:eu-repo/semantics/articleinfo:eu-repo/semantics/acceptedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfhttp://hdl.handle.net/20.500.12123/13067https://www.sciencedirect.com/science/article/pii/S01681702220026470168-17021872-7492 (online)https://doi.org/10.1016/j.virusres.2022.198936Virus Research : 198936 (28 September 2022)reponame:INTA Digital (INTA)instname:Instituto Nacional de Tecnología Agropecuariaenginfo:eu-repo/semantics/openAccess2025-09-04T09:49:35Zoai:localhost:20.500.12123/13067instacron:INTAInstitucionalhttp://repositorio.inta.gob.ar/Organismo científico-tecnológicoNo correspondehttp://repositorio.inta.gob.ar/oai/requesttripaldi.nicolas@inta.gob.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:l2025-09-04 09:49:35.467INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuariafalse |
| dc.title.none.fl_str_mv |
Evolution of SARS-CoV-2 during the first year of the COVID-19 pandemic in Northwestern Argentina |
| title |
Evolution of SARS-CoV-2 during the first year of the COVID-19 pandemic in Northwestern Argentina |
| spellingShingle |
Evolution of SARS-CoV-2 during the first year of the COVID-19 pandemic in Northwestern Argentina Zambrana Montaño, Romina Micaela 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 |
| 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 |
| dc.creator.none.fl_str_mv |
Zambrana Montaño, Romina Micaela 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 |
Zambrana Montaño, Romina Micaela |
| author_facet |
Zambrana Montaño, Romina Micaela 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_role |
author |
| author2 |
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 |
| author2_role |
author author author author author author author author author author author author author author author author author author author author author author |
| dc.subject.none.fl_str_mv |
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 |
| topic |
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 |
| dc.description.none.fl_txt_mv |
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 |
| description |
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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2022 |
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article |
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acceptedVersion |
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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 |
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