The study, led by the Quadram Institute in partnership with the Norfolk and Norwich University Hospital and James Paget University Hospital, has shown how long the virus persists in the saliva and faeces of infected people.

By analysing samples provided by people from across Norfolk during waves of the pandemic, the researchers have shown how in this group RNA from the SARS-CoV-2 virus that caused COVID-19 is detected for longer in saliva than in faeces, with the duration dependent on the severity of the symptoms.

Taken alongside studies in North America and Asia, this research builds on our understanding of COVID-19 that will help prepare us for future pandemics.

Five years on from the first UK lockdown, we’ve learned more about the virus and it’s clear that COVID-19 affects more than just the lungs. The receptor the virus uses to infect the lungs is also found in cells in the gut. This could explain why the virus can colonise the gut and why around 10% of people with post-COVID syndrome experience gastrointestinal symptoms. Faecal material could also be a potential route of transmission; something seen with similar viruses.

To investigate this further, researchers from the Quadram Institute joined the global effort to study SARS-CoV-2. With expertise in microbial research and high-level containment labs, Quadram repurposed its facilities to safely receive, inactivate, and analyse patient samples.

This study, called the SARS-CoV-2 Prevalence and Persistence in Stool (CoPS), was part of that wider initiative, and was funded by the Biotechnology and Biological Science Research Council, part of UKRI.

The CoPS Study ran in partnership with the Norfolk and Norwich University Hospital along with the James Paget Hospital on Norfolk’s east coast, who were at the front line of treating patients with COVID-19.

Modeled estimates of SARS-C0V-2 prevalence in saliva and faeces, from Kellingray L, et al Microbiol Spectr0:e03195-24.

In total, 120 adults from Norfolk joined the study, who had recently tested positive for SARS-CoV-2, most of whom were recruited onto the study following a social media campaign, and researchers appearing in the local news media.

Participants were screened remotely to ensure they were eligible and taken through the study to ensure they were fully informed and able to give consent to take part.

They were asked to provide a weekly sample of their saliva and faeces, as well as provide information about their symptoms.

Positive samples for COVID-19 were sequenced at the Quadram Institute. As a key member of COVID-19 Genomics UK Consortium (COG-UK), Quadram contributed to national efforts that analysed and tracked the genetic variants that characterised the different waves during the pandemic.

The results of the CoPS Study have now been published in the journal Microbiology Spectrum. In this, the researchers show that while most participants had detectable virus in their saliva and faeces in the first week after infection, this declined over time. The virus appears to persist in saliva samples slightly longer than in faeces.

Compared with other studies carried out in other parts of the world, the CoPS study revealed that SARS-CoV-2 virus persists for less time in faeces than previously seen. This may reflect differences in population vaccination status, public health interventions, or the dominant viral variants in circulation at the time.

SARS-CoV-2 evolved rapidly during the pandemic, with each new “Variant of Concern”—such as Alpha, Delta, and Omicron—bringing changes in transmissibility, virulence, and symptom severity. The CoPS study found that the duration of viral shedding was linked to how severe participants’ symptoms were, reinforcing the need to consider variant characteristics in strategies to control viral spread.

In one case, a participant even had two different SARS-CoV-2 variants in their saliva and their faeces, emphasising the complexities of understanding the virus during a pandemic, and the value of genomic sequencing to track and fully understand the dynamics.

“This study shows how local research efforts, built on collaboration with the community, can offer critical insights into how a virus behaves” said Dr Lizbeth Sayavedra.

“By combining clinical sampling with genomic analysis, we were able to see how factors like symptom severity influence viral persistence in saliva and stool.”

“The study was conducted at the height of Covid epidemic when the virus was new, and we did not know the extent of faecal transmission” said Professor Arjan Narbad. “This research provides further insight into the dynamics of viral presence in the GI tract.”

Reference: Temporal dynamics of SARS-CoV-2 shedding in feces and saliva: a longitudinal study in Norfolk, United Kingdom during the 2021–2022 COVID-19 waves, Kellingray L, Savva GM, Garcia-Gutierrez E, Snell J, Romano S, Yara DA, Altera A, de Oliveira Martins L, Hutchins C, Baker D, Hayhoe A, Hacon C, Elumogo N, Narbad A, Sayavedra L. Microbiology Spectrum 0:e03195-24. DOI: 10.1128/spectrum.03195-24