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
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/235259
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/235259
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repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling 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 Técnicas2025-10-15T15:41:31Zoai: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:34982025-10-15 15:41:31.845CONICET 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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info:eu-repo/semantics/altIdentifier/doi/10.3389/fviro.2022.910839
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
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eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
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dc.publisher.none.fl_str_mv Frontiers Media
publisher.none.fl_str_mv Frontiers Media
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
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repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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