SARS-CoV-2 does not have a strong effect on the nasopharyngeal microbial composition

Tzipi Braun,Tzipi Braun,Sharon Amit,Sharon Amit,Natahan Keller,Natahan Keller,Efrat Glick Saar,Efrat Glick Saar,Amnon Amir,Gilate Efroni,Gilate Efroni,Shiraz Halevi,Shiraz Halevi,Yael Haberman,Yael Haberman,Yael Haberman,Yael Haberman,Rotem Hadar,Rotem Hadar

doi:10.1038/s41598-021-88536-6

Abstract

The coronavirus disease 2019 (COVID-19) has rapidly spread around the world, impacting the lives of many individuals. Growing evidence suggests that the nasopharyngeal and respiratory tract microbiome are influenced by various health and disease conditions, including the presence and the severity of different viral disease. To evaluate the potential interactions between Severe Acute Respiratory Syndrome Corona 2 (SARS-CoV-2) and the nasopharyngeal microbiome. Microbial composition of nasopharyngeal swab samples submitted to the clinical microbiology lab for suspected SARS-CoV-2 infections was assessed using 16S amplicon sequencing. The study included a total of 55 nasopharyngeal samples from 33 subjects, with longitudinal sampling available for 12 out of the 33 subjects. 21 of the 33 subjects had at least one positive COVID-19 PCR results as determined by the clinical microbiology lab. Inter-personal variation was the strongest factor explaining > 75% of the microbial variation, irrespective of the SARS-CoV-2 status. No significant effect of SARS-CoV-2 on the nasopharyngeal microbial community was observed using multiple analysis methods. These results indicate that unlike some other viruses, for which an effect on the microbial composition was noted, SARS-CoV-2 does not have a strong effect on the nasopharynx microbial habitants.

Highlights

The coronavirus disease 2019 (COVID-19) has rapidly spread around the world, impacting the lives of many individuals
19, were processed by 16S rRNA amplicon sequencing in parallel to SARS-CoV-2 testing by RT-PCR in the clinical microbiology lab
SARS-CoV-2 testing result does not seem to have a strong effect, as samples do not cluster by COVID-19 test results (Fig. 2A)

Summary

Introduction

The coronavirus disease 2019 (COVID-19) has rapidly spread around the world, impacting the lives of many individuals. Severe Acute Respiratory Syndrome Corona 2 (SARS-CoV-2)[1,2] is the coronavirus responsible for the 2019–2020 pandemic It infects the upper respiratory tract nasopharynx, and is transmitted mostly by tiny droplets and aerosols[2], with some evidence suggesting a fecal mode of transmission[3]. Due to low cross-protective immunity from related viral infections, SARS-CoV-2 transmissibility is high, facilitating widespread personto-person transmission[4,5] This SARS-CoV-2 has the highest transmissibility when compared to previous pandemics[6,7]. The second study used the direct Oxford Nanopore long-read third generation sequencing and included 50 patients suspected for COVID-19, and found some differences between those subjects that were positive and negative for SARS-CoV-212. We used 16S amplicon sequencing to define differences by using longitudinal samples, which supplement the other two previous studies that used cross-sectional sampling

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