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- Title
Co-infection with SARS-CoV-2 Omicron and Delta variants revealed by genomic surveillance.
- Authors
Rockett, Rebecca J.; Draper, Jenny; Gall, Mailie; Sim, Eby M.; Arnott, Alicia; Agius, Jessica E.; Johnson-Mackinnon, Jessica; Fong, Winkie; Martinez, Elena; Drew, Alexander P.; Lee, Clement; Ngo, Christine; Ramsperger, Marc; Ginn, Andrew N.; Wang, Qinning; Fennell, Michael; Ko, Danny; Hueston, Linda; Kairaitis, Lukas; Holmes, Edward C.
- Abstract
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 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. Here, using genomic approaches, Rockett et al. identify Omicron and Delta SARS-CoV-2 co-infections in two adults, highlighting the usefulness of genomic surveillance for the timely recognition of co-infections in situations when different variants of the virus are circulating in the community.
- Subjects
SARS-CoV-2 Omicron variant; SARS-CoV-2 Delta variant; SARS-CoV-2; MIXED infections; CHRONIC kidney failure
- Publication
Nature Communications, 2022, Vol 13, Issue 1, p1
- ISSN
2041-1723
- Publication type
Article
- DOI
10.1038/s41467-022-30518-x