SARS-CoV-2 Genomic Surveillance Enables the Identification of Delta/Omicron Co-Infections in Argentina
- Autores
- Pisano, María Belén; Sicilia, Paola; Zeballos, Maximiliano; Andrea, Luca; Fernandez, Franco Daniel; Castro, Gonzalo Manuel; Goya, Stephanie; Viegas, Mariana; Laura, Lopez; Barbas, Maria Gabriela; Ré, Viviana Elizabeth
- Año de publicación
- 2022
- Idioma
- inglés
- Tipo de recurso
- artículo
- Estado
- versión publicada
- Descripción
- Molecular surveillance of SARS-CoV-2 is crucial for the early detection of new variants and lineages. In addition, detection of co-infections with more than one SARS-CoV-2 lineage has been sporadically reported. In this work, surveillance of SARS-CoV-2 variants was performed on 2,067 RNA samples (Ct > 30) obtained during December 2021 and January 2022 from Córdoba province, Argentina, by real-time RT-PCR specific for variants of concern (VOCs) and variants of interest (VOIs) relevant mutations (TaqMan™ SARS-CoV-2 Mutation Panel, Applied Biosystems). The following distribution of variants was obtained: Omicron (54.9%), Delta (44.2%), and Lambda (0.8%). Three samples (0.1%), from the last week of December, were compatible with a Delta/Omicron co-infection. One of them was sequenced by NGS-Illumina, obtaining reads for both VOCs. One of the co-infected patients presented with severe symptoms, was not vaccinated, and had risk factors (older than 60 years and arterial hypertension). We describe for the first time in Argentina the identification of cases of co-infection with two SARS-CoV-2 lineages, VOCs Delta and Omicron, during the third COVID-19 wave in the country (a high viral circulation period), when Delta and Omicron co-circulated. Our findings highlight the importance of continuing molecular surveillance, in order to elucidate possible recombination events and the emergence of new variants.
Fil: Pisano, María Belén. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Córdoba. Facultad de Medicina. Instituto de Virología Dr. J. M. Vanella; Argentina
Fil: Sicilia, Paola. Gobierno de la Provincia de Córdoba. Ministerio de Salud. Laboratorio Central de la Provincia; Argentina
Fil: Zeballos, Maximiliano. Fundación para el Progreso de la Medicina; Argentina
Fil: Andrea, Luca. Fundación Para El Progreso de la Medicina; Argentina
Fil: Fernandez, Franco Daniel. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigaciones Agropecuarias. Instituto de Patología Vegetal; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigaciones Agropecuarias. Unidad de Fitopatología y Modelización Agrícola - Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Unidad de Fitopatología y Modelización Agrícola; Argentina
Fil: Castro, Gonzalo Manuel. Gobierno de la Provincia de Córdoba. Ministerio de Salud. Laboratorio Central de la Provincia; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba; Argentina
Fil: Goya, Stephanie. Gobierno de la Ciudad de Buenos Aires. Hospital General de Niños "Ricardo Gutiérrez"; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Viegas, Mariana. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Gobierno de la Ciudad de Buenos Aires. Hospital General de Niños "Ricardo Gutiérrez"; Argentina
Fil: Laura, Lopez. Provincia de Córdoba. Ministerio de Salud; Argentina
Fil: Barbas, Maria Gabriela. Provincia de Córdoba. Ministerio de Salud; Argentina
Fil: Ré, Viviana Elizabeth. Universidad Nacional de Córdoba. Facultad de Medicina. Instituto de Virología Dr. J. M. Vanella; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba; Argentina - Materia
-
SARS-COV-2
CO-INFECTION
DELTA
OMICRON
ARGENTINA
MOLECULAR SURVEILLANCE
COVID-19 - Nivel de accesibilidad
- acceso abierto
- Condiciones de uso
- https://creativecommons.org/licenses/by/2.5/ar/
- Repositorio
- Institución
- Consejo Nacional de Investigaciones Científicas y Técnicas
- OAI Identificador
- oai:ri.conicet.gov.ar:11336/235259
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SARS-CoV-2 Genomic Surveillance Enables the Identification of Delta/Omicron Co-Infections in ArgentinaPisano, María BelénSicilia, PaolaZeballos, MaximilianoAndrea, LucaFernandez, Franco DanielCastro, Gonzalo ManuelGoya, StephanieViegas, MarianaLaura, LopezBarbas, Maria GabrielaRé, Viviana ElizabethSARS-COV-2CO-INFECTIONDELTAOMICRONARGENTINAMOLECULAR SURVEILLANCECOVID-19https://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Molecular surveillance of SARS-CoV-2 is crucial for the early detection of new variants and lineages. In addition, detection of co-infections with more than one SARS-CoV-2 lineage has been sporadically reported. In this work, surveillance of SARS-CoV-2 variants was performed on 2,067 RNA samples (Ct > 30) obtained during December 2021 and January 2022 from Córdoba province, Argentina, by real-time RT-PCR specific for variants of concern (VOCs) and variants of interest (VOIs) relevant mutations (TaqMan™ SARS-CoV-2 Mutation Panel, Applied Biosystems). The following distribution of variants was obtained: Omicron (54.9%), Delta (44.2%), and Lambda (0.8%). Three samples (0.1%), from the last week of December, were compatible with a Delta/Omicron co-infection. One of them was sequenced by NGS-Illumina, obtaining reads for both VOCs. One of the co-infected patients presented with severe symptoms, was not vaccinated, and had risk factors (older than 60 years and arterial hypertension). We describe for the first time in Argentina the identification of cases of co-infection with two SARS-CoV-2 lineages, VOCs Delta and Omicron, during the third COVID-19 wave in the country (a high viral circulation period), when Delta and Omicron co-circulated. Our findings highlight the importance of continuing molecular surveillance, in order to elucidate possible recombination events and the emergence of new variants.Fil: Pisano, María Belén. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Córdoba. Facultad de Medicina. Instituto de Virología Dr. J. M. Vanella; ArgentinaFil: Sicilia, Paola. Gobierno de la Provincia de Córdoba. Ministerio de Salud. Laboratorio Central de la Provincia; ArgentinaFil: Zeballos, Maximiliano. Fundación para el Progreso de la Medicina; ArgentinaFil: Andrea, Luca. Fundación Para El Progreso de la Medicina; ArgentinaFil: Fernandez, Franco Daniel. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigaciones Agropecuarias. Instituto de Patología Vegetal; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigaciones Agropecuarias. Unidad de Fitopatología y Modelización Agrícola - Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Unidad de Fitopatología y Modelización Agrícola; ArgentinaFil: Castro, Gonzalo Manuel. Gobierno de la Provincia de Córdoba. Ministerio de Salud. Laboratorio Central de la Provincia; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba; ArgentinaFil: Goya, Stephanie. Gobierno de la Ciudad de Buenos Aires. Hospital General de Niños "Ricardo Gutiérrez"; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Viegas, Mariana. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Gobierno de la Ciudad de Buenos Aires. Hospital General de Niños "Ricardo Gutiérrez"; ArgentinaFil: Laura, Lopez. Provincia de Córdoba. Ministerio de Salud; ArgentinaFil: Barbas, Maria Gabriela. Provincia de Córdoba. Ministerio de Salud; ArgentinaFil: Ré, Viviana Elizabeth. Universidad Nacional de Córdoba. Facultad de Medicina. Instituto de Virología Dr. J. M. Vanella; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba; ArgentinaFrontiers Media2022-06info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfapplication/pdfapplication/pdfapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/235259Pisano, María Belén; Sicilia, Paola; Zeballos, Maximiliano ; Andrea, Luca; Fernandez, Franco Daniel; et al.; SARS-CoV-2 Genomic Surveillance Enables the Identification of Delta/Omicron Co-Infections in Argentina; Frontiers Media; Frontiers in Virology; 2; 910839; 6-2022; 1-52673-818XCONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://www.frontiersin.org/articles/10.3389/fviro.2022.910839/fullinfo:eu-repo/semantics/altIdentifier/doi/10.3389/fviro.2022.910839info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T10:43:21Zoai:ri.conicet.gov.ar:11336/235259instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-29 10:43:21.822CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse |
dc.title.none.fl_str_mv |
SARS-CoV-2 Genomic Surveillance Enables the Identification of Delta/Omicron Co-Infections in Argentina |
title |
SARS-CoV-2 Genomic Surveillance Enables the Identification of Delta/Omicron Co-Infections in Argentina |
spellingShingle |
SARS-CoV-2 Genomic Surveillance Enables the Identification of Delta/Omicron Co-Infections in Argentina Pisano, María Belén SARS-COV-2 CO-INFECTION DELTA OMICRON ARGENTINA MOLECULAR SURVEILLANCE COVID-19 |
title_short |
SARS-CoV-2 Genomic Surveillance Enables the Identification of Delta/Omicron Co-Infections in Argentina |
title_full |
SARS-CoV-2 Genomic Surveillance Enables the Identification of Delta/Omicron Co-Infections in Argentina |
title_fullStr |
SARS-CoV-2 Genomic Surveillance Enables the Identification of Delta/Omicron Co-Infections in Argentina |
title_full_unstemmed |
SARS-CoV-2 Genomic Surveillance Enables the Identification of Delta/Omicron Co-Infections in Argentina |
title_sort |
SARS-CoV-2 Genomic Surveillance Enables the Identification of Delta/Omicron Co-Infections in Argentina |
dc.creator.none.fl_str_mv |
Pisano, María Belén Sicilia, Paola Zeballos, Maximiliano Andrea, Luca Fernandez, Franco Daniel Castro, Gonzalo Manuel Goya, Stephanie Viegas, Mariana Laura, Lopez Barbas, Maria Gabriela Ré, Viviana Elizabeth |
author |
Pisano, María Belén |
author_facet |
Pisano, María Belén Sicilia, Paola Zeballos, Maximiliano Andrea, Luca Fernandez, Franco Daniel Castro, Gonzalo Manuel Goya, Stephanie Viegas, Mariana Laura, Lopez Barbas, Maria Gabriela Ré, Viviana Elizabeth |
author_role |
author |
author2 |
Sicilia, Paola Zeballos, Maximiliano Andrea, Luca Fernandez, Franco Daniel Castro, Gonzalo Manuel Goya, Stephanie Viegas, Mariana Laura, Lopez Barbas, Maria Gabriela Ré, Viviana Elizabeth |
author2_role |
author author author author author author author author author author |
dc.subject.none.fl_str_mv |
SARS-COV-2 CO-INFECTION DELTA OMICRON ARGENTINA MOLECULAR SURVEILLANCE COVID-19 |
topic |
SARS-COV-2 CO-INFECTION DELTA OMICRON ARGENTINA MOLECULAR SURVEILLANCE COVID-19 |
purl_subject.fl_str_mv |
https://purl.org/becyt/ford/1.6 https://purl.org/becyt/ford/1 |
dc.description.none.fl_txt_mv |
Molecular surveillance of SARS-CoV-2 is crucial for the early detection of new variants and lineages. In addition, detection of co-infections with more than one SARS-CoV-2 lineage has been sporadically reported. In this work, surveillance of SARS-CoV-2 variants was performed on 2,067 RNA samples (Ct > 30) obtained during December 2021 and January 2022 from Córdoba province, Argentina, by real-time RT-PCR specific for variants of concern (VOCs) and variants of interest (VOIs) relevant mutations (TaqMan™ SARS-CoV-2 Mutation Panel, Applied Biosystems). The following distribution of variants was obtained: Omicron (54.9%), Delta (44.2%), and Lambda (0.8%). Three samples (0.1%), from the last week of December, were compatible with a Delta/Omicron co-infection. One of them was sequenced by NGS-Illumina, obtaining reads for both VOCs. One of the co-infected patients presented with severe symptoms, was not vaccinated, and had risk factors (older than 60 years and arterial hypertension). We describe for the first time in Argentina the identification of cases of co-infection with two SARS-CoV-2 lineages, VOCs Delta and Omicron, during the third COVID-19 wave in the country (a high viral circulation period), when Delta and Omicron co-circulated. Our findings highlight the importance of continuing molecular surveillance, in order to elucidate possible recombination events and the emergence of new variants. Fil: Pisano, María Belén. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Córdoba. Facultad de Medicina. Instituto de Virología Dr. J. M. Vanella; Argentina Fil: Sicilia, Paola. Gobierno de la Provincia de Córdoba. Ministerio de Salud. Laboratorio Central de la Provincia; Argentina Fil: Zeballos, Maximiliano. Fundación para el Progreso de la Medicina; Argentina Fil: Andrea, Luca. Fundación Para El Progreso de la Medicina; Argentina Fil: Fernandez, Franco Daniel. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigaciones Agropecuarias. Instituto de Patología Vegetal; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigaciones Agropecuarias. Unidad de Fitopatología y Modelización Agrícola - Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Unidad de Fitopatología y Modelización Agrícola; Argentina Fil: Castro, Gonzalo Manuel. Gobierno de la Provincia de Córdoba. Ministerio de Salud. Laboratorio Central de la Provincia; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba; Argentina Fil: Goya, Stephanie. Gobierno de la Ciudad de Buenos Aires. Hospital General de Niños "Ricardo Gutiérrez"; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Viegas, Mariana. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Gobierno de la Ciudad de Buenos Aires. Hospital General de Niños "Ricardo Gutiérrez"; Argentina Fil: Laura, Lopez. Provincia de Córdoba. Ministerio de Salud; Argentina Fil: Barbas, Maria Gabriela. Provincia de Córdoba. Ministerio de Salud; Argentina Fil: Ré, Viviana Elizabeth. Universidad Nacional de Córdoba. Facultad de Medicina. Instituto de Virología Dr. J. M. Vanella; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba; Argentina |
description |
Molecular surveillance of SARS-CoV-2 is crucial for the early detection of new variants and lineages. In addition, detection of co-infections with more than one SARS-CoV-2 lineage has been sporadically reported. In this work, surveillance of SARS-CoV-2 variants was performed on 2,067 RNA samples (Ct > 30) obtained during December 2021 and January 2022 from Córdoba province, Argentina, by real-time RT-PCR specific for variants of concern (VOCs) and variants of interest (VOIs) relevant mutations (TaqMan™ SARS-CoV-2 Mutation Panel, Applied Biosystems). The following distribution of variants was obtained: Omicron (54.9%), Delta (44.2%), and Lambda (0.8%). Three samples (0.1%), from the last week of December, were compatible with a Delta/Omicron co-infection. One of them was sequenced by NGS-Illumina, obtaining reads for both VOCs. One of the co-infected patients presented with severe symptoms, was not vaccinated, and had risk factors (older than 60 years and arterial hypertension). We describe for the first time in Argentina the identification of cases of co-infection with two SARS-CoV-2 lineages, VOCs Delta and Omicron, during the third COVID-19 wave in the country (a high viral circulation period), when Delta and Omicron co-circulated. Our findings highlight the importance of continuing molecular surveillance, in order to elucidate possible recombination events and the emergence of new variants. |
publishDate |
2022 |
dc.date.none.fl_str_mv |
2022-06 |
dc.type.none.fl_str_mv |
info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion http://purl.org/coar/resource_type/c_6501 info:ar-repo/semantics/articulo |
format |
article |
status_str |
publishedVersion |
dc.identifier.none.fl_str_mv |
http://hdl.handle.net/11336/235259 Pisano, María Belén; Sicilia, Paola; Zeballos, Maximiliano ; Andrea, Luca; Fernandez, Franco Daniel; et al.; SARS-CoV-2 Genomic Surveillance Enables the Identification of Delta/Omicron Co-Infections in Argentina; Frontiers Media; Frontiers in Virology; 2; 910839; 6-2022; 1-5 2673-818X CONICET Digital CONICET |
url |
http://hdl.handle.net/11336/235259 |
identifier_str_mv |
Pisano, María Belén; Sicilia, Paola; Zeballos, Maximiliano ; Andrea, Luca; Fernandez, Franco Daniel; et al.; SARS-CoV-2 Genomic Surveillance Enables the Identification of Delta/Omicron Co-Infections in Argentina; Frontiers Media; Frontiers in Virology; 2; 910839; 6-2022; 1-5 2673-818X CONICET Digital CONICET |
dc.language.none.fl_str_mv |
eng |
language |
eng |
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Frontiers Media |
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Frontiers Media |
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dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar |
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