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Co-infection with SARS-CoV-2 Omicron and Delta variants revealed by genomic surveillance. 2022
Rebecca J Rockett, and
Jenny Draper, and
Mailie Gall, and
Eby M Sim, and
Alicia Arnott, and
Jessica E Agius, and
Jessica Johnson-Mackinnon, and
Winkie Fong, and
Elena Martinez, and
Alexander P Drew, and
Clement Lee, and
Christine Ngo, and
Marc Ramsperger, and
Andrew N Ginn, and
Qinning Wang, and
Michael Fennell, and
Danny Ko, and
Linda Hueston, and
Lukas Kairaitis, and
Edward C Holmes, and
Matthew N O'Sullivan, and
Sharon C-A Chen, and
Jen Kok, and
Dominic E Dwyer, and
Vitali Sintchenko
Sydney Institute for Infectious Diseases, University of Sydney, Sydney, NSW, Australia.
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.
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