Correlation of SARS-CoV-2 fecal negative with gastrointestinal eubiosis in asymptomatic, mild and moderate cases of COVID-19 in Lagos, Nigeria

Abstract

Abstract Background: The severe acute respiratory syndrome, coronavirus 2 (SARS-CoV-2) when disseminated to the gastrointestinal (GI) tract through the bidirectional gut-lung crosstalk can cause alterations in GI microbiota composition and diversity. There is, however, paucity of data linking SARS-CoV-2 fecal negative with GI microbial balance. This study investigated the association of the GI bacterial composition with clinically defined asymptomatic, mild/moderate COVID-19 fecal negative individuals. A total of twelve (12) fecal samples comprising COVID-19 nasopharyngeal (NP) positive (P) (n=7) and negative (N) (n=5) consenting participants were collected and analyzed. The extracted RNA from the stool samples of NP positive were used as templates for the RT-qPCR detection of SARS-CoV-2 nucleocapsid (N) and open reading frame (ORF1ab) genes, while DNA from all samples (n=12) was used for the 16S bacterial rRNA metagenomics analysis. The Pielou index and Shannon index were used to assess the alpha diversity of the two groups (P and N) using the Kruskal-Wallis significance test, while the beta taxonomic diversity was assessed with the Bray-Curtis diversity index using the Permutational Multivariate Analysis of Variance (PERMANOVA) for the significance test. Taxonomic classification was performed using the Greengenes database trained for the hyper variable 4 of the 16S rRNA (gg_2022_10_backbone. v4. nb). Results: Participants positive for nasopharyngeal COVID-19 RT-PCR (ages 17-74 years) reported none (n=2, 28.5%), mild (n=4, 57.1%) and moderate (n=1, 14.3%) clinical symptoms. The viral genes were not detected with uniformity and richness of bacterial species in stool samples from positive and negative COVID-19 without significant differences in alpha diversity, Pielou (p=0.223), Shannon index (p = 0.062), and beta taxonomic diversity (PERMANOVA p=0.357). The taxonomic classification showed 14 phyla, 276 genera and 448 species in the samples, with Firmicutes, Bacteroidota, and Proteobacteria as the most abundant phyla. The most dominant species were beneficial microbes such as Prevotella copri, Phocaeicola vulgatus, and the immunomodulatory, anti-inflammatory bacterium Faecalibacterium prausnitzii. Conclusions: This study did not reveal any differences in the gut bacterial community of SARS-CoV-2 fecal negative, asymptomatic, mild and moderate COVID-19 compared to the apparently healthy control.