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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| Autores principales: | , , , , , , , |
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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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| Sumario: | 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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