# SARS-CoV-2 Persistence and the Gut Microbiota: New Insights into Long COVID Pathogenesis

**Authors:** Sofia De Stefanis, Francesca Colavita, Fabrizio Maggi, Manuela Antonioli

PMC · DOI: 10.3390/v18020247 · Viruses · 2026-02-14

## TL;DR

This paper explores how SARS-CoV-2 can persist in the gut, leading to chronic inflammation and gut microbiota changes that may cause long-term conditions like Long COVID and inflammatory bowel diseases.

## Contribution

The paper introduces new insights into the role of gut microbiota and persistent SARS-CoV-2 infection in the development of Long COVID and enteric disorders.

## Key findings

- SARS-CoV-2 persistence in the gastrointestinal tract is linked to Long COVID and chronic inflammation.
- Persistent infection may contribute to the development of Crohn’s disease and ulcerative colitis.
- Gut microbiota dysbiosis is a key factor in antiviral defense and gastrointestinal conditions.

## Abstract

In December 2019, the world experienced the emergence of a new virus, SARS-CoV-2, which caused the 2020 pandemic. SARS-CoV-2 causes COVID-19, primarily affecting the respiratory system, as well as the gastrointestinal tract. Remarkably, one in eight COVID-19 patients develops Long COVID, which is linked to SARS-CoV-2 persistence in the gastrointestinal tract, resulting in chronic inflammation and microbiota dysregulation. Given that gut microbiota dysbiosis plays a pivotal role in antiviral defense and gastrointestinal conditions, here we examine emerging evidence on how persistent SARS-CoV-2 infection may contribute to the aetiology of enteric disorders. In particular, we emphasise the intricate connection between chronic inflammation caused by persistent SARS-CoV-2 infection (e.g., irritable bowel syndrome and inflammatory bowel disease) and the possible development of diseases such as Crohn’s disease and ulcerative colitis.

## Linked entities

- **Diseases:** irritable bowel syndrome (MONDO:0005052), inflammatory bowel disease (MONDO:0005265), Crohn’s disease (MONDO:0005011), ulcerative colitis (MONDO:0005101)

## Full-text entities

- **Genes:** mucin [NCBI Gene 100508689], ACE2 (angiotensin converting enzyme 2) [NCBI Gene 59272] {aka ACEH}, S (surface glycoprotein) [NCBI Gene 43740568] {aka spike glycoprotein}, NFKB1 (nuclear factor kappa B subunit 1) [NCBI Gene 4790] {aka CVID12, EBP-1, KBF1, NF-kB, NF-kB1, NF-kappa-B1}, IL10 (interleukin 10) [NCBI Gene 3586] {aka CSIF, GVHDS, IL-10, IL10A, TGIF}, TNF (tumor necrosis factor) [NCBI Gene 7124] {aka DIF, IMD127, TNF-alpha, TNFA, TNFSF2, TNLG1F}, SLC6A19 (solute carrier family 6 member 19) [NCBI Gene 340024] {aka B0AT1, HND}
- **Diseases:** vomiting (MESH:D014839), fever (MESH:D005334), enteric viral infections (MESH:D053489), ARDS (MESH:D012128), bloody diarrhoea (MESH:D003967), cognitive symptoms (MESH:D019954), fatigue (MESH:D005221), nausea (MESH:D009325), multiple organ failure (MESH:D009102), abdominal pain (MESH:D015746), dysbiosis (MESH:D064806), IBS (MESH:D053560), cancer (MESH:D009369), pain (MESH:D010146), injury to (MESH:D014947), gastrointestinal symptoms (MESH:D012817), chronic intestinal inflammation (MESH:D007249), chronic inflammatory diseases (MESH:D002908), Long COVID (MESH:D000094024), cognitive deficits (MESH:D003072), brain fog (MESH:D005222), ulcerative colitis (MESH:D003093), immune dysregulation (OMIM:614878), dyspepsia (MESH:D004415), CAC (MESH:D000083023), IBD (MESH:D015212), mucosal damage (MESH:D052016), irritable bowel syndrome (MESH:D043183), enteric disorders (MESH:D004751), ulcers (MESH:D014456), cough (MESH:D003371), COVID-19 (MESH:D000086382), gastrointestinal alterations (MESH:D005767), chronic colitis (MESH:D003092), Crohn's disease (MESH:D003424), cardiovascular complications (MESH:D002318), Infection (MESH:D007239), CRC (MESH:D015179), viral (MESH:D014777), death (MESH:D003643)
- **Chemicals:** oxygen (MESH:D010100), SCFA (MESH:D005232), Tryptophan (MESH:D014364), acetate (MESH:D000085), LPS (MESH:D008070), propionate (MESH:D011422), amino acid (MESH:D000596), butyrate (MESH:D002087), Na+ (MESH:D012964), bile acids (MESH:D001647)
- **Species:** Actinomycetota (actinobacteria, phylum) [taxon 201174], Severe acute respiratory syndrome-related coronavirus (no rank) [taxon 694009], Coprobacillus (genus) [taxon 100883], Agathobacter rectalis (species) [taxon 39491], Severe acute respiratory syndrome coronavirus 2 (no rank) [taxon 2697049], Mus musculus (house mouse, species) [taxon 10090], Middle East respiratory syndrome-related coronavirus (no rank) [taxon 1335626], Adeno-associated virus (species) [taxon 272636], Rotavirus (genus) [taxon 10912], Betacoronavirus (genus) [taxon 694002], Homo sapiens (human, species) [taxon 9606], Enterovirus C (no rank) [taxon 138950], Faecalibacterium prausnitzii (species) [taxon 853], Bacteroides (genus) [taxon 816], Bacteria Latreille et al. 1825 (Bacteria stick insect, genus) [taxon 629395], Hungatella hathewayi (species) [taxon 154046], Streptococcus (genus) [taxon 1301], Thomasclavelia ramosa (species) [taxon 1547]

## Full text

_Full body text omitted from this summary view._ Fetch the complete paper as Markdown: https://tomesphere.com/paper/PMC12945300/full.md

## Figures

1 figure with captions in the complete paper: https://tomesphere.com/paper/PMC12945300/full.md

## References

60 references — full list in the complete paper: https://tomesphere.com/paper/PMC12945300/full.md

---
Source: https://tomesphere.com/paper/PMC12945300