Molecular surveillance of SARS-CoV-2 in the province of Córdoba: monitoring of variants
Abstract: The study of the SARS-CoV-2 genome allows to evaluate its evolutionary pattern, identify mutations, lineages and variants that may have an impact on public health. Variants of concern (VOC) and variants of interest (VOI), which have different biological characteristics, have...
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| Formato: | Artículo revista |
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Universidad Nacional Córdoba. Facultad de Ciencias Médicas. Secretaria de Ciencia y Tecnología
2021
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| Acceso en línea: | https://revistas.unc.edu.ar/index.php/med/article/view/34934 |
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I10-R327-article-34934 |
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ojs |
| institution |
Universidad Nacional de Córdoba |
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I-10 |
| repository_str |
R-327 |
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Revista de la Facultad de Ciencias Médicas de Córdoba |
| format |
Artículo revista |
| topic |
SARS-CoV-2 molecular epidemiology surveillance variants SARS-CoV-2 epidemiología molecular vigilancia variantes . |
| spellingShingle |
SARS-CoV-2 molecular epidemiology surveillance variants SARS-CoV-2 epidemiología molecular vigilancia variantes . Castro , G Sicilia, P Fernández, F Bolzón, ML Debat, H Marquez, N Mojsiejczuk , L Grupo de Trabajo Consorcio Proyecto PAIS , P Lopez , L Barbás , MG Torres, C Viegas, M Pisano , MB Re, V Molecular surveillance of SARS-CoV-2 in the province of Córdoba: monitoring of variants |
| topic_facet |
SARS-CoV-2 molecular epidemiology surveillance variants SARS-CoV-2 epidemiología molecular vigilancia variantes . |
| author |
Castro , G Sicilia, P Fernández, F Bolzón, ML Debat, H Marquez, N Mojsiejczuk , L Grupo de Trabajo Consorcio Proyecto PAIS , P Lopez , L Barbás , MG Torres, C Viegas, M Pisano , MB Re, V |
| author_facet |
Castro , G Sicilia, P Fernández, F Bolzón, ML Debat, H Marquez, N Mojsiejczuk , L Grupo de Trabajo Consorcio Proyecto PAIS , P Lopez , L Barbás , MG Torres, C Viegas, M Pisano , MB Re, V |
| author_sort |
Castro , G |
| title |
Molecular surveillance of SARS-CoV-2 in the province of Córdoba: monitoring of variants |
| title_short |
Molecular surveillance of SARS-CoV-2 in the province of Córdoba: monitoring of variants |
| title_full |
Molecular surveillance of SARS-CoV-2 in the province of Córdoba: monitoring of variants |
| title_fullStr |
Molecular surveillance of SARS-CoV-2 in the province of Córdoba: monitoring of variants |
| title_full_unstemmed |
Molecular surveillance of SARS-CoV-2 in the province of Córdoba: monitoring of variants |
| title_sort |
molecular surveillance of sars-cov-2 in the province of córdoba: monitoring of variants |
| description |
Abstract:
The study of the SARS-CoV-2 genome allows to evaluate its evolutionary pattern, identify mutations, lineages and variants that may have an impact on public health. Variants of concern (VOC) and variants of interest (VOI), which have different biological characteristics, have been identified worldwide. The objective of this work is to describe the lineages and variants of SARS-CoV-2 circulating in Córdoba using different strategies.
Three strategies were implemented from positive SARS-CoV-2 RNA samples (Cts<30): 1)-whole genome sequencing (WGS) (ONT-MinION): 203 samples analysed from March 2020 to June 2021; 2)-partial sequencing of the Spike protein gene (Sanger): 54 samples analysed between February and April 2021 of travellers from abroad; and 3)-real time RT-PCR for detection of relevant VOC mutations (TaqMan™ SARS-CoV-2 Mutation Panel, Applied Biosystems): 816 samples analysed between May and June 2021.
Results were the following: 1)-circulation of 7 lineages with a greater predominance of B.1.1.33.3 (N3) (40.5%) and B.1.499 (38.8%), between March 2020 and January 2021; and circulation of 12 lineages with presence of VOC [P.1 (Gamma, 28.4%), B.1.1.7 (Alpha, 6.9%)] and VOI [C.37 (Lambda, 20.6%), B.1.427 (Epsilon, 10.8%), P2 (Zeta, 2.9%), B.1.526 (Iota, 2%)], between February and June 2021; 2)-presence of VOC Alpha (26.4%) and Gamma (17%), and samples compatible with VOI Epsilon and Zeta; 3)-presence of VOC Gamma (56%) and Alpha (11%), and other variants which could not be typified by this methodology.
Results show the circulation of many SARS-CoV-2 lineages in Córdoba, which varied their distribution over time, according to the different introductions occurred, the population movement and the evolutionary advantages of some variants over others. In March 2021, the first VOC detections were realized in the province (Alpha and Gamma), being Gamma the one that mostly circulates at present. Although the WGS is the technique which provides more information, the other 2 strategies implemented were and are very useful tools for molecular epidemiological surveillance, obtaining the information in real time. Strategy 3 is a simpler, faster and more operative tool for molecular VOC screening.
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| publisher |
Universidad Nacional Córdoba. Facultad de Ciencias Médicas. Secretaria de Ciencia y Tecnología |
| publishDate |
2021 |
| url |
https://revistas.unc.edu.ar/index.php/med/article/view/34934 |
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I10-R327-article-349342024-04-15T16:19:09Z Molecular surveillance of SARS-CoV-2 in the province of Córdoba: monitoring of variants Vigilancia molecular de SARS-CoV-2 en la provincia de Córdoba: monitoreo de variantes A Castro , G Sicilia, P Fernández, F Bolzón, ML Debat, H Marquez, N Mojsiejczuk , L Grupo de Trabajo Consorcio Proyecto PAIS , P Lopez , L Barbás , MG Torres, C Viegas, M Pisano , MB Re, V SARS-CoV-2 molecular epidemiology surveillance variants SARS-CoV-2 epidemiología molecular vigilancia variantes . Abstract: The study of the SARS-CoV-2 genome allows to evaluate its evolutionary pattern, identify mutations, lineages and variants that may have an impact on public health. Variants of concern (VOC) and variants of interest (VOI), which have different biological characteristics, have been identified worldwide. The objective of this work is to describe the lineages and variants of SARS-CoV-2 circulating in Córdoba using different strategies. Three strategies were implemented from positive SARS-CoV-2 RNA samples (Cts<30): 1)-whole genome sequencing (WGS) (ONT-MinION): 203 samples analysed from March 2020 to June 2021; 2)-partial sequencing of the Spike protein gene (Sanger): 54 samples analysed between February and April 2021 of travellers from abroad; and 3)-real time RT-PCR for detection of relevant VOC mutations (TaqMan™ SARS-CoV-2 Mutation Panel, Applied Biosystems): 816 samples analysed between May and June 2021. Results were the following: 1)-circulation of 7 lineages with a greater predominance of B.1.1.33.3 (N3) (40.5%) and B.1.499 (38.8%), between March 2020 and January 2021; and circulation of 12 lineages with presence of VOC [P.1 (Gamma, 28.4%), B.1.1.7 (Alpha, 6.9%)] and VOI [C.37 (Lambda, 20.6%), B.1.427 (Epsilon, 10.8%), P2 (Zeta, 2.9%), B.1.526 (Iota, 2%)], between February and June 2021; 2)-presence of VOC Alpha (26.4%) and Gamma (17%), and samples compatible with VOI Epsilon and Zeta; 3)-presence of VOC Gamma (56%) and Alpha (11%), and other variants which could not be typified by this methodology. Results show the circulation of many SARS-CoV-2 lineages in Córdoba, which varied their distribution over time, according to the different introductions occurred, the population movement and the evolutionary advantages of some variants over others. In March 2021, the first VOC detections were realized in the province (Alpha and Gamma), being Gamma the one that mostly circulates at present. Although the WGS is the technique which provides more information, the other 2 strategies implemented were and are very useful tools for molecular epidemiological surveillance, obtaining the information in real time. Strategy 3 is a simpler, faster and more operative tool for molecular VOC screening. Resumen: El estudio del genoma de SARS-CoV-2 permite evaluar su dinámica evolutiva, identificar mutaciones, linajes y variantes que puedan impactar en la salud pública. A nivel mundial se identificaron variantes de preocupación (VOC) y variantes de interés (VOI), que presentan características biológicas diferentes. El objetivo del trabajo es describir los linajes y variantes de SARS-CoV-2 circulantes en Córdoba mediante tres estrategias. Se implementaron 3 estrategias, a partir de muestras de RNA positivas para el virus (Cts<30): 1)-secuenciación de genoma completo (ONT-MinION): 203 muestras analizadas desde marzo 2020 a junio 2021; 2)-secuenciación de un fragmento genómico de la proteína S (Sanger): 54 muestras analizadas entre febrero y abril 2021 en viajeros provenientes del exterior; y 3)-PCR en tiempo real para detección de VOC (TaqMan™ SARS-CoV-2 Mutation Panel, Applied Biosystems): 816 muestras analizadas entre mayo y junio de 2021. Los resultados fueron: 1)-circulación de siete linajes con mayor predominancia de B.1.1.33.3 (N3) (40,5%) y B.1.499 (38,8%), entre marzo 2020 y enero 2021; y circulación de 12 linajes con presencia de VOC [P.1 (Gamma, 28,4%), B.1.1.7 (Alpha, 6,9%)] y VOI [C.37 (Lambda, 20,6%), B.1.427 (Epsilon, 10,8%), P2 (Zeta, 2,9%), B.1.526 (Iota, 2%)], entre febrero y junio 2021; 2)-presencia de VOC Alpha (26,4%) y Gamma (17%), y muestras compatibles con las VOI Epsilon y Zeta (9,4%); 3)-presencia de VOC Gamma (56%) y Alpha (11%), y otras variantes no tipificables por esta metodología. Los resultados muestran circulación de diversos linajes de SARS-CoV-2 en Córdoba, que variaron su distribución a lo largo del tiempo, según las distintas introducciones ocurridas, el movimiento poblacional y las ventajas evolutivas de unos sobre otros. En marzo 2021 se realizaron las primeras detecciones de VOC en la provincia (Alpha y Gamma), siendo la variante Gamma la que circula mayoritariamente en la actualidad. Si bien la secuenciación del genoma completo es la técnica que mayor información brinda, las otras 2 estrategias implementadas fueron y son de gran utilidad para la vigilancia epidemiológica molecular, favoreciendo la obtención de información en tiempo real. La estrategia 3 resulta una herramienta más simple, rápida y con mayor capacidad operativa para el screening molecular de VOC. . Universidad Nacional Córdoba. Facultad de Ciencias Médicas. Secretaria de Ciencia y Tecnología 2021-10-12 info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion texto texto texto https://revistas.unc.edu.ar/index.php/med/article/view/34934 Revista de la Facultad de Ciencias Médicas de Córdoba.; Vol. 78 No. Suplemento (2021): Suplemento JIC XXII Revista de la Facultad de Ciencias Médicas de Córdoba; Vol. 78 Núm. Suplemento (2021): Suplemento JIC XXII Revista da Faculdade de Ciências Médicas de Córdoba; v. 78 n. Suplemento (2021): Suplemento JIC XXII 1853-0605 0014-6722 http://creativecommons.org/licenses/by-nc/4.0 |