Prevalence of persistent SARS-CoV-2 in a large community surveillance study, 2024, Ghafari et al

[EndME]

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

Abstract
Persistent SARS-CoV-2 infections may act as viral reservoirs that could seed future outbreaks1,2,3,4,5, give rise to highly divergent lineages6,7,8 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 people11,12,13,14.

This work has profound implications for understanding and characterizing SARS-CoV-2 infection, epidemiology and evolution.

https://www.nature.com/articles/s41586-024-07029-4

 

[EndME]

The data is probably very interesting to a virologist or epidemiologist.

Unfortunately, the Long-Covid section is more mundane.

From February 2021, as well as reporting symptoms, participants were asked whether they describe themselves as having long COVID and if they were still experiencing symptoms more than 4 weeks after they first had COVID-19 (see Methods).

Correcting for confounders, we found strong evidence for a 55% higher odds of reporting long COVID at 12 weeks or more post-infection among individuals with persistent infection than individuals with non-persistent infection (P = 0.004 for the unadjusted model; P = 0.021 for the adjusted model), but no evidence of a difference for long COVID at 26 weeks or more post-infection (P = 0.127 for the unadjusted model; P = 0.367 for the adjusted model) (Table 3). The lower probability of reporting long COVID 26 weeks post-infection than at 12 weeks post-infection could be because the majority of the persistent infections that we identified lasted for less than 3 months, and hence persistence of an infection may no longer be a contributing factor to long COVID beyond 3 months.