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; Vitali Sintchenko

doi:10.1038/s41467-022-30518-x

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

Nat Commun. 2022 May 18;13(1):2745. doi: 10.1038/s41467-022-30518-x.

Authors

Rebecca J Rockett^#^{1

2}, Jenny Draper^#^{1

3}, Mailie Gall^#^{1

3}, Eby M Sim^#^{1

2

3}, Alicia Arnott^{1

2

3}, Jessica E Agius¹, Jessica Johnson-Mackinnon^{1

2}, Winkie Fong^{1

2}, Elena Martinez^{1

2

3}, Alexander P Drew³, Clement Lee³, Christine Ngo³, Marc Ramsperger³, Andrew N Ginn^{1

3}, Qinning Wang^{1

2

3}, Michael Fennell³, Danny Ko³, Linda Hueston³, Lukas Kairaitis⁴, Edward C Holmes^{1

5

6}, Matthew N O'Sullivan^{1

2

3}, Sharon C-A Chen^{1

2

3}, Jen Kok^{1

2

3}, Dominic E Dwyer^{1

2

3}, Vitali Sintchenko^{7

8

9

10}

Affiliations

¹ Sydney Institute for Infectious Diseases, University of Sydney, Sydney, NSW, Australia.
² Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, NSW, Australia.
³ Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead, NSW, Australia.
⁴ Renal Services Blacktown Hospital, Western Sydney Local Health District, Sydney, NSW, Australia.
⁵ School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia.
⁶ School of Medical Sciences, University of Sydney, Sydney, NSW, Australia.
⁷ Sydney Institute for Infectious Diseases, University of Sydney, Sydney, NSW, Australia. [email protected].
⁸ Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, NSW, Australia. [email protected].
⁹ Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead, NSW, Australia. [email protected].
¹⁰ School of Medical Sciences, University of Sydney, Sydney, NSW, Australia. [email protected].

^# Contributed equally.

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

COVID-19*
Coinfection*
Genomics
Humans
SARS-CoV-2 / genetics

Supplementary concepts

SARS-CoV-2 variants