Prevalence of persistent SARS-CoV-2 in a large community surveillance study

Mahan Ghafari (), Matthew Hall, Tanya Golubchik, Daniel Ayoubkhani, Thomas House, George MacIntyre-Cockett, Helen R. Fryer, Laura Thomson, Anel Nurtay, Steven A. Kemp, Luca Ferretti, David Buck, Angie Green, Amy Trebes, Paolo Piazza, Lorne J. Lonie, Ruth Studley, Emma Rourke, Darren L. Smith, Matthew Bashton, Andrew Nelson, Matthew Crown, Clare McCann, Gregory R. Young, Rui Andre Nunes dos Santos, Zack Richards, Mohammad Adnan Tariq, Roberto Cahuantzi, Jeff Barrett, Christophe Fraser, David Bonsall, Ann Sarah Walker and Katrina Lythgoe ()
Additional contact information
Mahan Ghafari: University of Oxford
Matthew Hall: University of Oxford
Tanya Golubchik: University of Oxford
Daniel Ayoubkhani: Office for National Statistics
Thomas House: University of Manchester
George MacIntyre-Cockett: University of Oxford
Helen R. Fryer: University of Oxford
Laura Thomson: University of Oxford
Anel Nurtay: University of Oxford
Steven A. Kemp: University of Oxford
Luca Ferretti: University of Oxford
David Buck: University of Oxford
Angie Green: University of Oxford
Amy Trebes: University of Oxford
Paolo Piazza: University of Oxford
Lorne J. Lonie: University of Oxford
Ruth Studley: Office for National Statistics
Emma Rourke: Office for National Statistics
Darren L. Smith: Northumbria University
Matthew Bashton: Northumbria University
Andrew Nelson: Northumbria University
Matthew Crown: Northumbria University
Clare McCann: Northumbria University
Gregory R. Young: Northumbria University
Rui Andre Nunes dos Santos: Northumbria University
Zack Richards: Northumbria University
Mohammad Adnan Tariq: Northumbria University
Roberto Cahuantzi: Office for National Statistics
Jeff Barrett: Wellcome Sanger Institute
Christophe Fraser: University of Oxford
David Bonsall: University of Oxford
Ann Sarah Walker: University of Oxford
Katrina Lythgoe: University of Oxford

Nature, 2024, vol. 626, issue 8001, 1094-1101

Abstract: Abstract Persistent SARS-CoV-2 infections may act as viral reservoirs that could seed future outbreaks1–5, give rise to highly divergent lineages6–8 and contribute to cases with post-acute COVID-19 sequelae (long COVID)9,10. However, the population prevalence of persistent infections, their viral load kinetics and evolutionary dynamics over the course of infections remain largely unknown. Here, using viral sequence data collected as part of a national infection survey, we identified 381 individuals with SARS-CoV-2 RNA at high titre persisting for at least 30 days, of which 54 had viral RNA persisting at least 60 days. We refer to these as ‘persistent infections’ as available evidence suggests that they represent ongoing viral replication, although the persistence of non-replicating RNA cannot be ruled out in all. Individuals with persistent infection had more than 50% higher odds of self-reporting long COVID than individuals with non-persistent infection. We estimate that 0.1–0.5% of infections may become persistent with typically rebounding high viral loads and last for at least 60 days. In some individuals, we identified many viral amino acid substitutions, indicating periods of strong positive selection, whereas others had no consensus change in the sequences for prolonged periods, consistent with weak selection. Substitutions included mutations that are lineage defining for SARS-CoV-2 variants, at target sites for monoclonal antibodies and/or are commonly found in immunocompromised people11–14. This work has profound implications for understanding and characterizing SARS-CoV-2 infection, epidemiology and evolution.

Date: 2024
References: Add references at CitEc
Citations: View citations in EconPapers (1)

Downloads: (external link)
https://www.nature.com/articles/s41586-024-07029-4 Abstract (text/html)
Access to the full text of the articles in this series is restricted.

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:nature:v:626:y:2024:i:8001:d:10.1038_s41586-024-07029-4

Ordering information: This journal article can be ordered from
https://www.nature.com/

DOI: 10.1038/s41586-024-07029-4

Access Statistics for this article

Nature is currently edited by Magdalena Skipper

More articles in Nature from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().