Introduction
Respiratory infection caused by SARS-CoV-2 may lead to prolonged symptoms, a condition called post COVID-19 condition or long COVID1. The World Health Organization defines long COVID as persistent symptoms or new symptoms three months after the initial infection, and these symptoms should last at least two months with no other diagnosis explaining them. Patients suffer from several symptoms, such as fatigue, difficulties in breathing, muscle pain and gastrointestinal symptoms. Since studies have reported differences in microbiota composition and its function between COVID-19 patients and long COVID patients as compared to healthy controls2-4, there is a need to evaluate the association of microbiome with long COVID.
Aims & Methods
We shotgun sequenced stool DNA from long COVID patients (LC, n=65), patients with PCR-confirmed SARS-CoV-2 infection with no persistent symptoms (LC-CNT, n=66), and pre-pandemic healthy controls (preC-CNT, n=64). One stool sample from each patient was used. Taxonomical analysis was done with Kraken2 and Bracken pipeline, and metabolic pathways were profiled with HUManN 3.0 pipeline. MaAsLin 3 was used for differential abundance testing. The aim of this study was to investigate the composition and functional characteristics of the microbiome among the study groups to identify potential disease-specific variations.
Results
First, we compared the bacterial richness and diversity between the study groups. Patients in LC-CNT group had a significantly lower Shannon diversity than patients in LC and preC-CNT groups (p < 0.05, Wilcoxon signed rank test). In Principal Coordinates Analysis, patients in preC-CNT group grouped away from patients from both LC and LC-CNT group (p < 0.01, PERMANOVA with 999 permutations, both comparisons). At phylum level, the average relative abundance of Bacillota was higher in preC-CNT groups as compared to both LC and LC-CNT groups (q < 0.05, Linear model). Moreover, the average relative abundance of phylum Bacteroidota was significantly higher in LC-CNT group as compared to preC-CNT group (q < 0.05, Linear model). The relative abundance of several potential short-chain fatty acid producing taxa, such as members of genera Ruminococcus and Blautia, were decreased in LC and LC-CNT groups as compared to preC-CNT group (q < 0.05, Linear model).
At functional level, we found differences exclusively between preC-CNT groups compared to LC and LC-CNT groups. Especially, some pathways related to tryptophan biosynthesis and fermentation were decreased in both LC and LC-CNT groups as compared to preC-CNT group (q < 0.1, Linear model). We did not find differences in the metabolic pathways between LC and LC-CNT groups.
Conclusion
As we could not detect differences in microbiome composition or its function between LC and LC-CNT groups, persistent symptoms may not be explained alone with differences in microbiome. Differences were found between both LC and LC-CNT group when compared to preC-CNT group, highlighting the possibility that lifestyle changes, such as changes in diet, exercise and social interactions, may explain the differences found in this study.
References
1https://www.who.int/europe/news-room/fact-sheets/item/post-covid-19-condition, 2 PMID: 33431578, 3 PMID: 35082169, 4 PMID: 37069814
Disclosure
This project has received funding from the European Union's Horizon Europe research and innovation programme under grant agreement No 101057553.