Abstract
BackgroundSARS-CoV-2 is an RNA virus causing COVID-19. The clinical characteristics and epidemiology of COVID-19 have been extensively investigated, however, only one study so far focused on the patient’s nasopharynx microbiota. In this study we investigated the nasopharynx microbial community of patients that developed different severity levels of COVID-19. We performed 16S ribosomal DNA sequencing from nasopharyngeal swab samples obtained from SARS-CoV-2 positive (56) and negative (18) patients in the province of Alicante (Spain) in their first visit to the hospital. Positive SARS-CoV-2 patients were observed and later categorized in mild (symptomatic without hospitalization), moderate (hospitalization), and severe (admission to ICU). We compared the microbiota diversity and OTU composition among severity groups and built bacterial co-abundance networks for each group.ResultsStatistical analysis indicated differences in the nasopharyngeal microbiome of COVID19 patients. 62 OTUs were found exclusively in SARS-CoV-2 positive patients, mostly classified as members of the phylum Bacteroidota (18) and Firmicutes (25). OTUs classified as Prevotella were found to be significantly more abundant in patients that developed more severe COVID-19. Furthermore, co-abundance analysis indicated a loss of network complexity among samples from patients that later developed more severe symptoms.ConclusionOur study shows that the nasopharyngeal microbiome of COVID-19 patients showed differences in the composition of specific OTUs and complexity of co-abundance networks. Taxa with differential abundances among groups could serve as biomarkers for COVID-19 severity. Nevertheless, further studies with larger sample sizes should be conducted to validate these results.
Highlights
SARS-CoV-2 is an RNA virus causing COVID-19
Four groups were established: group 0: SARS-CoV-2 negative patients (n = 18); group 1: mild COVID-19 symptoms but no later hospital admission (n = 19); group 2: severe COVID-19 symptoms followed by hospital admission (n = 18); and group 3: patients with severe COVID-19 symptoms which were eventually admitted into intensive care units (ICU) (n = 19)
Sixteen patients belonged to the negative control, whereas the remaining patients were classified into three groups according to the severity
Summary
SARS-CoV-2 is an RNA virus causing COVID-19. The clinical characteristics and epidemiology of COVID-19 have been extensively investigated, only one study so far focused on the patient’s nasopharynx microbiota. In this study we investigated the nasopharynx microbial community of patients that developed different severity levels of COVID-19. Positive SARS-CoV-2 patients were observed and later categorized in mild (symptomatic without hospitalization), moderate (hospitalization), and severe (admission to ICU). Severe Acute Respiratory Syndrome Coronavirus-2 (SARSCoV-2) is a positive-sense single-stranded RNA virus causing Coronavirus Disease 2019 (COVID-19) (Andersen et al, 2020). In diseased individuals, the lung microbiota composition undergoes a decrease in diversity (Kalantar et al, 2019) accompanied by a shift in the dominant taxa: from Bacteroidota to Gammaproteobacteria, a class that includes many respiratory pathogens
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