SARS-CoV-2 Genomic Surveillance Enables the Identification of Delta/Omicron Co-Infections in Argentina

Frontiers in Virology

María Belén Pisano¹  Viviana E. Ré¹  Franco Fernandez²  Gonzalo M. Castro⁵  Paola Sicilia⁵  Andrea Lucca⁶  Maximiliano Zeballos⁶  Stephanie Goya⁷  Mariana Viegas⁷  María Gabriela Barbás⁸  Laura López⁹ 

[1] Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina;Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Unidad de Fitopatología y Modelización Agrícola (UFYMA), Córdoba, Argentina;Instituto Nacional de Tecnología Agropecuaria (INTA), Centro de Investigaciones Agropecuarias (CIAP), Instituto de Patología Vegetal (IPAVE), Córdoba, Argentina;Instituto de Virología “Dr. J. M. Vanella”, Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Córdoba, Argentina;Laboratorio Central de la Provincia de Córdoba, Ministerio de Salud de la Provincia de Córdoba, Córdoba, Argentina;Laboratorio de Biología Molecular, Fundación para el Progreso de la Medicina, Córdoba, Argentina;Laboratorio de Virología, Hospital de Niños Dr. Ricardo Gutiérrez, Buenos Aires, Argentina;Secretaría de prevención y promoción de la salud, Ministerio de Salud de la Provincia de Córdoba, Córdoba, Argentina;Área de Epidemiología, Ministerio de Salud de la Provincia de Córdoba, Córdoba, Argentina;

关键词: SARS-CoV-2;    co-infection;    Delta;    Omicron;    Argentina;    molecular surveillance;   

DOI  :  10.3389/fviro.2022.910839

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown