SARS-CoV-2 genomic surveillance in the third wave of COVID-19 in Córdoba, Argentina: phylogenetic analysis of Omicron and identification of Delta/Omicron co-infections
During the COVID-19 pandemic, a SARS-CoV-2 molecular surveillance strategy was implemented in Córdoba based on the detection of point mutations by real-time RT-PCR. This, together with the whole genome sequencing (WGS), allowed the first detection of the variant of concern (VOC) Omicron in Dece...
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| Formato: | Artículo revista |
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Universidad Nacional Córdoba. Facultad de Ciencias Médicas. Secretaria de Ciencia y Tecnología
2022
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| Acceso en línea: | https://revistas.unc.edu.ar/index.php/med/article/view/39105 |
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I10-R327-article-39105 |
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| record_format |
ojs |
| institution |
Universidad Nacional de Córdoba |
| institution_str |
I-10 |
| repository_str |
R-327 |
| container_title_str |
Revista de la Facultad de Ciencias Médicas de Córdoba |
| format |
Artículo revista |
| topic |
SARS-CoV-2 infection covid-19 next generation sequencing viral RNA coinfection infección por SARS-CoV-2 covid-19 secuenciación de nueva generación RNA viral coinfección |
| spellingShingle |
SARS-CoV-2 infection covid-19 next generation sequencing viral RNA coinfection infección por SARS-CoV-2 covid-19 secuenciación de nueva generación RNA viral coinfección Sicilia, PE Castro, GM Torres, C Fernandez, F Viegas, M Barbas, MG Re, VE Pisano, MB SARS-CoV-2 genomic surveillance in the third wave of COVID-19 in Córdoba, Argentina: phylogenetic analysis of Omicron and identification of Delta/Omicron co-infections |
| topic_facet |
SARS-CoV-2 infection covid-19 next generation sequencing viral RNA coinfection infección por SARS-CoV-2 covid-19 secuenciación de nueva generación RNA viral coinfección |
| author |
Sicilia, PE Castro, GM Torres, C Fernandez, F Viegas, M Barbas, MG Re, VE Pisano, MB |
| author_facet |
Sicilia, PE Castro, GM Torres, C Fernandez, F Viegas, M Barbas, MG Re, VE Pisano, MB |
| author_sort |
Sicilia, PE |
| title |
SARS-CoV-2 genomic surveillance in the third wave of COVID-19 in Córdoba, Argentina: phylogenetic analysis of Omicron and identification of Delta/Omicron co-infections |
| title_short |
SARS-CoV-2 genomic surveillance in the third wave of COVID-19 in Córdoba, Argentina: phylogenetic analysis of Omicron and identification of Delta/Omicron co-infections |
| title_full |
SARS-CoV-2 genomic surveillance in the third wave of COVID-19 in Córdoba, Argentina: phylogenetic analysis of Omicron and identification of Delta/Omicron co-infections |
| title_fullStr |
SARS-CoV-2 genomic surveillance in the third wave of COVID-19 in Córdoba, Argentina: phylogenetic analysis of Omicron and identification of Delta/Omicron co-infections |
| title_full_unstemmed |
SARS-CoV-2 genomic surveillance in the third wave of COVID-19 in Córdoba, Argentina: phylogenetic analysis of Omicron and identification of Delta/Omicron co-infections |
| title_sort |
sars-cov-2 genomic surveillance in the third wave of covid-19 in córdoba, argentina: phylogenetic analysis of omicron and identification of delta/omicron co-infections |
| description |
During the COVID-19 pandemic, a SARS-CoV-2 molecular surveillance strategy was implemented in Córdoba based on the detection of point mutations by real-time RT-PCR. This, together with the whole genome sequencing (WGS), allowed the first detection of the variant of concern (VOC) Omicron in December 2021. The aim of this study was to perform phylogenetic analyzes of the first Omicron sequences detected in Córdoba and to determine the SARS-CoV-2 variants circulating in our region during December 2021 and January 2022.
A total of 2067 SARS-CoV-2 RNA positive samples obtained from oropharyngeal swabs collected during December 2021 and January 2022 in the province of Córdoba were subjected VOC/variants of interest (VOI) detection as part of the surveillance program implemented by the Government of the Province. Typing was performed by detection of point mutations by real-time RT-PCR using the TaqMan™ SARS-CoV-2 Mutation Panel kit (Applied Biosystems). In order to study the first outbreak of Omicron, 85 samples were sequenced by NGS using the Illumina platform, with the Illumina COVIDSeq RUO kit. Phylogenetic analyzes were performed using the MAFFT v7.486 and IQ-Tree v2.1 programs.
From the 2067 samples, 913 (44.2%) belonged to VOC Delta, 1135 (54.9%) to VOC Omicron, 16 (0.8%) to VOI Lambda and 3 (0.1%) presented profiles compatible with co-infections. From all the complete genome sequences obtained, 1 confirmed the coinfection Delta/Omicron. Phylogenetic analysis showed that the Omicron sequences grouped within BA.1 lineage and formed 3 monophyletic groups: 1 of them confirmed an outbreak whose origin was traced back to a traveler, in Colonia Caroya; the other 2 groups included sequences obtained from individuals that had attended the same social event, inferring that at least two introductions would have occurred.
The Omicron outbreak that took place in Córdoba was probably due to multiple introductions. The rapid dissemination of this VOC originated the third wave in our region. Moreover, we describe for the first time in Argentina, cases of Delta/Omicron co-infection, during the third wave of COVID-19 in our province, when both variants co-circulated.
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| publisher |
Universidad Nacional Córdoba. Facultad de Ciencias Médicas. Secretaria de Ciencia y Tecnología |
| publishDate |
2022 |
| url |
https://revistas.unc.edu.ar/index.php/med/article/view/39105 |
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I10-R327-article-391052024-04-15T16:14:45Z SARS-CoV-2 genomic surveillance in the third wave of COVID-19 in Córdoba, Argentina: phylogenetic analysis of Omicron and identification of Delta/Omicron co-infections Vigilancia genómica de SARS-CoV-2 en la tercera ola de COVID-19 en Córdoba: análisis filogenético de Omicron, identificación de co-infecciones Delta/Omicron Sicilia, PE Castro, GM Torres, C Fernandez, F Viegas, M Barbas, MG Re, VE Pisano, MB SARS-CoV-2 infection covid-19 next generation sequencing viral RNA coinfection infección por SARS-CoV-2 covid-19 secuenciación de nueva generación RNA viral coinfección During the COVID-19 pandemic, a SARS-CoV-2 molecular surveillance strategy was implemented in Córdoba based on the detection of point mutations by real-time RT-PCR. This, together with the whole genome sequencing (WGS), allowed the first detection of the variant of concern (VOC) Omicron in December 2021. The aim of this study was to perform phylogenetic analyzes of the first Omicron sequences detected in Córdoba and to determine the SARS-CoV-2 variants circulating in our region during December 2021 and January 2022. A total of 2067 SARS-CoV-2 RNA positive samples obtained from oropharyngeal swabs collected during December 2021 and January 2022 in the province of Córdoba were subjected VOC/variants of interest (VOI) detection as part of the surveillance program implemented by the Government of the Province. Typing was performed by detection of point mutations by real-time RT-PCR using the TaqMan™ SARS-CoV-2 Mutation Panel kit (Applied Biosystems). In order to study the first outbreak of Omicron, 85 samples were sequenced by NGS using the Illumina platform, with the Illumina COVIDSeq RUO kit. Phylogenetic analyzes were performed using the MAFFT v7.486 and IQ-Tree v2.1 programs. From the 2067 samples, 913 (44.2%) belonged to VOC Delta, 1135 (54.9%) to VOC Omicron, 16 (0.8%) to VOI Lambda and 3 (0.1%) presented profiles compatible with co-infections. From all the complete genome sequences obtained, 1 confirmed the coinfection Delta/Omicron. Phylogenetic analysis showed that the Omicron sequences grouped within BA.1 lineage and formed 3 monophyletic groups: 1 of them confirmed an outbreak whose origin was traced back to a traveler, in Colonia Caroya; the other 2 groups included sequences obtained from individuals that had attended the same social event, inferring that at least two introductions would have occurred. The Omicron outbreak that took place in Córdoba was probably due to multiple introductions. The rapid dissemination of this VOC originated the third wave in our region. Moreover, we describe for the first time in Argentina, cases of Delta/Omicron co-infection, during the third wave of COVID-19 in our province, when both variants co-circulated. En Córdoba, durante la pandemia de COVID-19, se implementó una estrategia de vigilancia molecular de SARS-CoV-2 basada en la detección de mutaciones puntuales por RT-PCR en tiempo real. Junto con la secuenciación de genomas completos, permitió la primera detección de la variante de preocupación (VOC) Omicron en diciembre 2021. El objetivo de este estudio fue realizar análisis filogenéticos a partir de las primeras secuencias de Omicron detectadas en Córdoba y determinar las variantes de SARS-CoV-2 circulantes en nuestra región durante diciembre 2021 y enero 2022. Se analizaron un total de 2067 muestras de RNA positivas para SARS-CoV-2 obtenidas de hisopados orofaríngeos colectados durante diciembre 2021 y enero 2022 en la provincia de Córdoba, para la detección de VOC y variantes de interés (VOI) como parte del programa de vigilancia molecular implementado por el Gobierno de la Provincia. La tipificación se realizó mediante la detección de mutaciones puntuales por RT-PCR en tiempo real usando el kit TaqMan™ SARS-CoV-2 Mutation Panel (Applied Biosystems). A fin de estudiar el primer brote de Omicron, 85 muestras fueron secuenciadas por NGS mediante plataforma Illumina, usando el kit Illumina COVIDSeq RUO. Los análisis filogenéticos fueron realizados mediante los programas MAFFT v7.486 e IQ-Tree v2.1. De las 2067 muestras analizadas, 913 (44,2%) correspondieron a VOC Delta, 1135 (54,9%) a VOC Omicron, 16 (0,8%) a VOI Lambda y 3 (0,1%) presentaron perfiles compatibles con co-infecciones. De los genomas completos secuenciados, 1 confirmó la co-infección Delta/Omicron. Los análisis filogenéticos mostraron que las secuencias de Omicron agruparon con el linaje BA.1, formando 3 grupos monofiléticos. Uno de ellos confirmó un brote cuyo origen fue un viajero, en Colonia Caroya; los otros 2 grupos incluyeron secuencias obtenidas de individuos que asistieron a una misma fiesta, señalando que habrían ocurrido al menos 2 introducciones de la variante. El brote de Omicron ocurrido en Córdoba durante diciembre 2021 y enero 2022 probablemente fue ocasionado por varias introducciones de esta variante, su rápida diseminación originó la tercera ola de COVID-19 en nuestra provincia. Además, durante este período se describieron por primera vez en Argentina casos de co-infección Delta/Omicron, cuando ambas VOC circularon simultáneamente Universidad Nacional Córdoba. Facultad de Ciencias Médicas. Secretaria de Ciencia y Tecnología 2022-10-26 info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion texto https://revistas.unc.edu.ar/index.php/med/article/view/39105 Revista de la Facultad de Ciencias Médicas de Córdoba.; Vol. 79 No. Suplemento JIC XXIII (2022): Suplemento JIC XXIII Revista de la Facultad de Ciencias Médicas de Córdoba; Vol. 79 Núm. Suplemento JIC XXIII (2022): Suplemento JIC XXIII Revista da Faculdade de Ciências Médicas de Córdoba; v. 79 n. Suplemento JIC XXIII (2022): Suplemento JIC XXIII 1853-0605 0014-6722 http://creativecommons.org/licenses/by-nc/4.0 |