First case of within-host co-infection of different SARS-CoV-2 variants in Ecuador. (July 2022)

• Record Type: Journal Article
• Authors: Fernandez-Cadena, J.C.; Carvajal, M.; Muñoz, E.; Prado-Vivar, B.; Marquez, S.; Proaño, S.; Bayas, R.; Guadalupe, J.J.; Becerra-Wong, M.; Gutierrez, B.; Morey-Leon, G.; Trueba, G.; Grunauer, M.; Barragán, V.; Rojas-Silva, P.; Andrade-Molina, D.; Cárdenas, P.
• Is Part Of: New microbes and new infections. Volume 48(2022)
• Publication Date: 2022-07
• Subjects: COVID19 -- co-infection -- genome sequencing -- NGS -- SARS-CoV-2; Medical microbiology -- Periodicals; Communicable diseases -- Periodicals; Infection -- Periodicals; Microbiology -- Periodicals; Communicable Diseases -- Periodicals; Infection -- Periodicals; 616.9041
• DOI: 10.1016/j.nmni.2022.101001
• Languages: English
• ISSNs: 2052-2975

Abstract

Abstract: Background: COVID-19 infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can cause mild symptoms to severe illness and death. Co-infections of SARS-CoV-2 with other respiratory viruses have been described. However, two SARS-CoV-2 lineage co-infection have been rarely reported. Methodology: A genotyping analysis and two different types of whole genome sequencing were performed (Illumina MiniSeq and ONT MinION). When examining the phylogenetic analysis in NextClade and Pangolin webservers, and considering the genotyping findings, conflicting results were obtained. Results: The raw data of the sequencing was analyzed, and nucleotide variants were identified between different reads of the virus genome. B.1 and P.1 lineages were identified within the same sample. Conclusions: We concluded that this is a co-infection case with two SARS-CoV-2 lineages, the first one reported in Ecuador.