Gut microbiota alterations in patients with persistent respiratory dysfunction three months after severe COVID-19 (preprint)

ObjectiveAlthough COVID-19 is primarily a respiratory infection, mounting evidence suggests that the GI tract is involved in the disease, with gut barrier dysfunction and gut microbiota alterations being related to disease severity. Whether these alterations persist and could be related to long-term respiratory dysfunction is unknown. DesignFrom the NOR-Solidarity trial (n=181), plasma was collected during hospital admission and after three months, and analyzed for markers of gut barrier dysfunction and inflammation. At the three-month follow-up, pulmonary function was assessed by measuring diffusing capacity of the lungs for carbon monoxide (DLCO), and rectal swabs for gut microbiota analyses were collected (n= 97) and analysed by sequencing of the 16S rRNA gene. ResultsGut microbiota diversity was reduced in COVID-19 patients with persistent respiratory dysfunction, defined as DLCO below lower limit of normal three months after hospitalization. These patients also had an altered global gut microbiota composition, with reduced abundance of Erysipelotrichaceae UCG-003 and increased abundance of Flavonifractor and Veillonella, the latter potentially being linked to fibrosis. During hospitalization, increased plasma levels of lipopolysaccharide-binding protein (LBP) were strongly associated with respiratory failure, defined as pO2/fiO2-(P/F-ratio)<26.6 kPa. LBP levels remained elevated during and after hospitalization, and was associated with low-grade inflammation and persistent respiratory dysfunction after three months. ConclusionPersistent respiratory dysfunction after COVID-19 is associated with reduced biodiversity and gut microbiota alterations, along with persistently elevated LBP levels. Our results point to a potential gut-lung axis that should be further investigated in relation to long-term pulmonary dysfunction and long COVID. Summary boxO_ST_ABSWhat is already known about this subject?C_ST_ABSO_LIMounting evidence suggests that the gastrointestinal tract is involved in the pathogenesis of COVID-19, with the putative SARS-CoV-2 receptor ACE 2 ubiquitously expressed in the gut. C_LIO_LIIn severe COVID-19, the gut-blood barrier is compromised, and leakage of microbial products, such as lipopolysaccharides (LPS), could affect the hosts response to COVID-19 infection. C_LIO_LICOVID-19 patients exhibit an altered gut microbiota composition, which has been related to disease severity. However, it is currently not known whether dysbiosis or gut barrier dysfunction persist long-term after hospitalization, or whether microbiota-related mechanisms could be related to persistent pulmonary dysfunction. C_LI What are the new findings?O_LICOVID-19 patients with persistent respiratory dysfunction after three months had a lower microbial diversity and an altered gut microbiota composition at the same time point. C_LIO_LIThe microbiota alterations included reduced abundance of Erysipelotrichaceae UCG-003 and increased abundance of Veillonella and Flavonifractor. C_LIO_LIDuring hospitalization, increased plasma levels of LBP were strongly associated with respiratory failure. C_LIO_LILBP levels remained elevated during and after hospitalization, and associated significantly with persistent respiratory dysfunction at three-month follow-up. C_LI How might it impact on clinical practice in the foreseeable future?Our findings point to a potential gut-lung axis in relation not only to respiratory failure during hospitalization, but also to long-term COVID-19 morbidity. Further studies on gut microbiota composition and gut barrier dysfunction as potential treatment targets and/or disease severity biomarkers in relation to long-term pulmonary dysfunction and long COVID are warranted.

Preexisting Cross-Reactive T Cells are Boosted and Comprise Significant Immunity in COVID-19 Recovered Patients (preprint)

Most SARS-CoV-2 infected individuals develop symptoms that do not require medical management. We hypothesized that pre-existing cross-reactive T cell responses could protect the majority from severe disease. Here we found that CTL and Th cells specific for seasonal human coronaviruses (HCoV) were significantly expanded in recovered COVID-19 donors and that CTL responses were significantly higher than responses to private SARS-CoV-2 peptides not shared with seasonal HCoV. A third of the SARS-CoV-2 peptide:HLA ligandome was matched by highly similar peptide mimics from seasonal HCoV, constituting a common HCoV peptide pool. CTL immunity was significantly skewed to the common HCoV peptide pool in age groups 20-70y, but not >70y-old donors. Over 40% of recovered donors lacked neutralizing antibodies, highlighting the role of T cell immunity in COVID-19. Results suggest a protective pre-acquired T cell immunity to SARS-CoV-2 and identify epitopes that may help boost vaccine responses and ensure broad protection against this family of viruses.Trial Registration: ClinicalTrials.gov: NCT04320732.Funding: This study was funded by The Health-South East Health Authority (Project 29286), the Research Council of Norway (Project 312693), the Oslo University Hospital, the KG Jebsen Foundation (grant 19), the University of Oslo, The Norwegian Cancer Society.Conflict of Interest: The authors declare that we have no competing interests.