Analysis of SARS-CoV-2 viral loads in stool samples and nasopharyngeal swabs from COVID-19 patients in the United Arab Emirates

Coronavirus disease 2019 (COVID-19) was first identified in respiratory samples and was found to commonly cause cough and pneumonia. However, non-respiratory symptoms including gastrointestinal disorders are also present and a big proportion of patients test positive for the virus in stools for a prolonged period. In this cross-sectional study, we investigated viral load trends in stools and nasopharyngeal swabs and their correlation with multiple demographic and clinical factors. The study included 211 laboratory-confirmed cases suffering from a mild form of the disease and completing their isolation period at a non-hospital center in the United Arab Emirates. Demographic and clinical information was collected by standardized questionnaire and from the medical records of the patient. Of the 211 participants, 25 % tested negative in both sample types at the time of this study and 53 % of the remaining patients had detectable viral RNA in their stools. A positive fecal viral test was associated with male gender, diarrhea as a symptom, and hospitalization during infection. A positive correlation was also observed between a delayed onset of symptoms and a positive stool test. Viral load in stools positively correlated with, being overweight, exercising, taking antibiotics in the last 3 months and blood type O. The viral load in nasopharyngeal swabs, on the other hand, was higher for blood type A, and rhesus positive (Rh factor). Regression analysis showed no correlation between the viral loads measured in stool and nasopharyngeal samples in any given patient. The results of this work highlight the factors associated with a higher viral count in each sample. It also shows the importance of stool sample analysis for the follow-up and diagnosis of recovering COVID-19 patients

Gut microbiota interplay with COVID-19 reveals links to host lipid metabolism among Middle Eastern populations

The interplay between the compositional changes in the gastrointestinal microbiome, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) susceptibility and severity, and host functions is complex and yet to be fully understood. This study performed 16S rRNA gene-based microbial profiling of 143 subjects. We observed structural and compositional alterations in the gut microbiota of the SARS-CoV-2-infected group in comparison to non-infected controls. The gut microbiota composition of the SARS-CoV-2-infected individuals showed an increase in anti-inflammatory bacteria such as Faecalibacterium (p-value = 1.72 × 10–6) and Bacteroides (p-value = 5.67 × 10–8). We also revealed a higher relative abundance of the highly beneficial butyrate producers such as Anaerostipes (p-value = 1.75 × 10–230), Lachnospiraceae (p-value = 7.14 × 10–65), and Blautia (p-value = 9.22 × 10–18) in the SARS-CoV-2-infected group in comparison to the control group. Moreover, phylogenetic investigation of communities by reconstructing unobserved state (PICRUSt) functional prediction analysis of the 16S rRNA gene abundance data showed substantial differences in the enrichment of metabolic pathways such as lipid, amino acid, carbohydrate, and xenobiotic metabolism, in comparison between both groups. We discovered an enrichment of linoleic acid, ether lipid, glycerolipid, and glycerophospholipid metabolism in the SARS-CoV-2-infected group, suggesting a link to SARS-CoV-2 entry and replication in host cells. We estimate the major contributing genera to the four pathways to be Parabacteroides, Streptococcus, Dorea, and Blautia, respectively. The identified differences provide a new insight to enrich our understanding of SARS-CoV-2-related changes in gut microbiota, their metabolic capabilities, and potential screening biomarkers linked to COVID-19 disease severity

The distribution of SARS-CoV-2 S protein mutations detected in samples collected during four different periods between 2020 and 2021.

The distribution of SARS-CoV-2 S protein mutations detected in samples collected during four different periods between 2020 and 2021.</p

Viral load in stools and nasopharyngeal swabs of unvaccinated and vaccinated (at least 1 dose) participants.

The graph presents the median and the minimal to the maximal range of viral load in log10 copies/mL. The significance of the pairwise two-sided t-tests is indicated on top.</p

Comparing viral loads in stools and nasopharyngeal swabs of patients infected by different SARS-CoV-2 variants.

(a) negative for S protein mutations (b) N501Y mutation, (c) N501Y+K417N+E484K mutations, and (d) L452R mutation. The graph presents the median and the minimal to the maximal range of viral load in log10 copies/mL. The significance of the pairwise two-sided t-tests is indicated on top.</p

Minimal data set.

(XLSX)</p

Factors associated with changes in viral load in stools.

Factors associated with changes in viral load in stools.</p

Factors associated with changes in viral load in nasopharyngeal swabs.

Factors associated with changes in viral load in nasopharyngeal swabs.</p

Baseline characteristics of the participants categorized by sample positivity.

Baseline characteristics of the participants categorized by sample positivity.</p

SARS-CoV-2 PCR test results among COVID-19 participants.

SARS-CoV-2 PCR test results among COVID-19 participants.</p