Ontology type: schema:ScholarlyArticle Open Access: True
2022-05-18
AUTHORSRebecca J. Rockett, Jenny Draper, Mailie Gall, Eby M. Sim, Alicia Arnott, Jessica E. Agius, Jessica Johnson-Mackinnon, Winkie Fong, Elena Martinez, Alexander P. Drew, Clement Lee, Christine Ngo, Marc Ramsperger, Andrew N. Ginn, Qinning Wang, Michael Fennell, Danny Ko, Linda Hueston, Lukas Kairaitis, Edward C. Holmes, Matthew N. O’Sullivan, Sharon C.-A. Chen, Jen Kok, Dominic E. Dwyer, Vitali Sintchenko
ABSTRACTCo-infections with different variants of SARS-CoV-2 are a key precursor to recombination events that are likely to drive SARS-CoV-2 evolution. Rapid identification of such co-infections is required to determine their frequency in the community, particularly in populations at-risk of severe COVID-19, which have already been identified as incubators for punctuated evolutionary events. However, limited data and tools are currently available to detect and characterise the SARS-CoV-2 co-infections associated with recognised variants of concern. Here we describe co-infection with the SARS-CoV-2 variants of concern Omicron and Delta in two epidemiologically unrelated adult patients with chronic kidney disease requiring maintenance haemodialysis. Both variants were co-circulating in the community at the time of detection. Genomic surveillance based on amplicon- and probe-based sequencing using short- and long-read technologies identified and quantified subpopulations of Delta and Omicron viruses in respiratory samples. These findings highlight the importance of integrated genomic surveillance in vulnerable populations and provide diagnostic pathways to recognise SARS-CoV-2 co-infection using genomic data. More... »
PAGES2745
http://scigraph.springernature.com/pub.10.1038/s41467-022-30518-x
DOIhttp://dx.doi.org/10.1038/s41467-022-30518-x
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PUBMEDhttps://www.ncbi.nlm.nih.gov/pubmed/35585202
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"description": "Co-infections with different variants of SARS-CoV-2 are a key precursor to recombination events that are likely to drive SARS-CoV-2 evolution. Rapid identification of such co-infections is required to determine their frequency in the community, particularly in populations at-risk of severe COVID-19, which have already been identified as incubators for punctuated evolutionary events. However, limited data and tools are currently available to detect and characterise the SARS-CoV-2 co-infections associated with recognised variants of concern. Here we describe co-infection\u00a0with the SARS-CoV-2 variants of concern Omicron and Delta in two epidemiologically unrelated adult patients with chronic kidney disease requiring maintenance haemodialysis. Both variants were co-circulating in the community at the time of detection. Genomic surveillance based on amplicon- and probe-based sequencing using short- and long-read technologies identified and quantified subpopulations of Delta and Omicron viruses in respiratory samples. These findings highlight the importance of integrated genomic surveillance in vulnerable populations and provide diagnostic pathways to recognise SARS-CoV-2 co-infection using genomic data.",
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"name": "Co-infection with SARS-CoV-2 Omicron and Delta variants revealed by genomic surveillance",
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