Ghafari, Mahan;
Hall, Matthew;
Golubchik, Tanya;
Ayoubkhani, Daniel;
House, Thomas;
MacIntyre-Cockett, George;
Fryer, Helen R;
... Lythgoe, Katrina; + view all
(2024)
Prevalence of persistent SARS-CoV-2 in
a large community surveillance study.
Nature
, 626
pp. 1094-1101.
10.1038/s41586-024-07029-4.
Preview |
Text
Walker_s41586-024-07029-4.pdf Download (10MB) | Preview |
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 identifed 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 identifed 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 defning 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.
| Type: | Article |
|---|---|
| Title: | Prevalence of persistent SARS-CoV-2 in a large community surveillance study |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.1038/s41586-024-07029-4 |
| Publisher version: | https://doi.org/10.1038/s41586-024-07029-4 |
| Language: | English |
| Additional information: | This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Population Health Sciences > Inst of Clinical Trials and Methodology UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Population Health Sciences > Inst of Clinical Trials and Methodology > MRC Clinical Trials Unit at UCL |
| URI: | https://discovery.ucl.ac.uk/id/eprint/10185249 |
Archive Staff Only
 |
View Item |
