Systematic surveillance of SARS-CoV-2 reveals dynamics of variant mutagenesis and transmission in a large urban population
Highly mutable pathogens generate viral diversity that impacts virulence, transmissibility, treatment, and thwarts acquired immunity. We previously described C19-SPAR-Seq, a high-throughput, next-generation sequencing platform to detect SARS-CoV-2 that we here deployed to systematically profile variant dynamics of SARS-CoV-2 for over 3 years in a large, North American urban environment (Toronto, Canada). Sequencing of the ACE2 receptor binding motif and polybasic furin cleavage site of the Spike gene in over 70,000 patients revealed that population sweeps of canonical variants of concern (VOCs) occurred in repeating wavelets. Furthermore, we found that VOC mutant derivatives and putative quasispecies that targeted functionally important residues and were found in future VOCs arose frequently, but were always extinguished. Systematic screening of functionally relevant domains in pathogens could thus provide a powerful tool for monitoring spread and mutational trajectories, particularly those with zoonotic potential.
Authors
- Jared T. Simpson (ORCID: https://orcid.org/0000-0002-2116-2602)
- Tony Mazzulli (ORCID: https://orcid.org/0000-0002-2682-8792)
- Seda Barutcu (ORCID: https://orcid.org/0000-0003-2739-4153)
- Min Jin (ORCID: https://orcid.org/0009-0009-1155-9890)
- Abiodun A. Ogunjimi (ORCID: https://orcid.org/0000-0002-2621-8070)
- Lucy Zhang (ORCID: https://orcid.org/0000-0002-8609-767X)
- Bradly G. Wouters (ORCID: https://orcid.org/0000-0002-8187-592X)
- James M. Rini (ORCID: https://orcid.org/0000-0002-0952-2409)
- Shyam Ajay Patel (ORCID: https://orcid.org/0000-0002-8208-1902)
- Marie-Ming Aynaud (ORCID: https://orcid.org/0000-0003-1788-3180)
- Paul M. Krzyzanowski (ORCID: https://orcid.org/0000-0001-6430-5995)
- Analiza Aquino
- Laurence Pelletier (ORCID: https://orcid.org/0000-0003-1171-4618)
- Jeffrey L. Wrana (ORCID: https://orcid.org/0000-0003-0932-0644)
- Kathleen-Rose Zakoor (ORCID: https://orcid.org/0000-0002-6874-5223)
- John Bartlett (ORCID: https://orcid.org/0000-0001-9529-6198)
- Andreea Obersterescu (ORCID: https://orcid.org/0000-0003-3285-0221)
- Lauren Caldwell (ORCID: https://orcid.org/0000-0001-9991-0757)
- Susan M. Poutanen (ORCID: https://orcid.org/0000-0003-4747-2550)
- Ilinca M. Lungu (ORCID: https://orcid.org/0000-0002-9996-5771)
- Khalid N. Al‐Zahrani (ORCID: https://orcid.org/0000-0001-5771-7537)
- Mark Jen
- Filiam Yonathan
- Amelia Ayson-Fortunato
- Nursrin Dewsi
- Princess Mae Veniegas
- Michael Gekas
- Ron Padilla
- Kin Chan
Institutions
- Ontario Institute for Cancer Research (CA)
- Mount Sinai Hospital (CA)
- University Health Network (CA)
- University of Toronto (CA)
- Lunenfeld-Tanenbaum Research Institute (CA)
- Toronto General Hospital (CA)
- Princess Margaret Cancer Centre (CA)
Publication Details
- Journal
- Nature Communications
- Published
- 2024-12-30
- DOI
- https://doi.org/10.1038/s41467-024-55031-1
- Primary Topic
- SARS-CoV-2 and COVID-19 Research
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- Government of Ontario
- Krembil Foundation
- Canadian Institutes of Health Research