Co-infection with SARS-CoV-2 Omicron and Delta variants revealed by genomic surveillance

Rebecca 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 and Vitali Sintchenko ()
Additional contact information
Rebecca J. Rockett: University of Sydney
Jenny Draper: University of Sydney
Mailie Gall: University of Sydney
Eby M. Sim: University of Sydney
Alicia Arnott: University of Sydney
Jessica E. Agius: University of Sydney
Jessica Johnson-Mackinnon: University of Sydney
Winkie Fong: University of Sydney
Elena Martinez: University of Sydney
Alexander P. Drew: Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology
Clement Lee: Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology
Christine Ngo: Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology
Marc Ramsperger: Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology
Andrew N. Ginn: University of Sydney
Qinning Wang: University of Sydney
Michael Fennell: Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology
Danny Ko: Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology
Linda Hueston: Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology
Lukas Kairaitis: Renal Services Blacktown Hospital, Western Sydney Local Health District
Edward C. Holmes: University of Sydney
Matthew N. O’Sullivan: University of Sydney
Sharon C.-A. Chen: University of Sydney
Jen Kok: University of Sydney
Dominic E. Dwyer: University of Sydney
Vitali Sintchenko: University of Sydney

Nature Communications, 2022, vol. 13, issue 1, 1-7

Abstract: 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.

Date: 2022
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Citations: View citations in EconPapers (4)

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DOI: 10.1038/s41467-022-30518-x

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