key: cord-0686128-ltess4n5
authors: Gupta, Abhishek; Karyakarte, Rajesh; Joshi, Suvarna; Das, Rashmita; Jani, Kunal; Shouche, Yogesh; Sharma, Avinash
title: Nasopharyngeal microbiome reveals the prevalence of opportunistic pathogens in SARS-CoV-2 infected individuals and their association with host types
date: 2021-08-21
journal: Microbes Infect
DOI: 10.1016/j.micinf.2021.104880
sha: 95a3d77eda8cef79ec3ecf3675b59a3f974b5d68
doc_id: 686128
cord_uid: ltess4n5

The novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is causing a severe global health emergency owing to its highly infectious nature. Although the symptoms of SARS-CoV-2 are well known but its impact on nasopharyngeal microbiome is poorly studied. The present cross-sectional study was intended to understand the perturbation in the nasopharyngeal microbiome composition within the infected (n=63) and non-infected (n=26) individuals using 16S rRNA gene based targeted amplicon sequencing and their association with host types and the prevalence of opportunistic pathogens at the stage of infection. The results confirmed that number of OTUs were significantly (p < 0.05) decreased in the SARS-CoV-2 infected individuals in comparison to non-infected individuals. Pairwise Wilcoxon test showed a significant (p<0.05) increase in the abundance of Proteobacteria in infected individuals compared to non-infected ones and vice-versa for Fusobacteria and Bacteroidetes. Similarity percentage (SIMPER) analysis showed the increment in the abundance of opportunistic pathogens (Haemophilus, Stenotrophomonas, Acineobacter, Moraxella, Corynebacterium I, Gemella, Ralstonia, and Pseudomonas) involved in secondary infection. Furthermore, this study highlighted the microbial community structure of individuals within and across the families. Further, we also assessed the microbiome associated with host types (age and genders) and COVID-19 conditions (symptomatic and asymptomatic). The data suggested that the host types/conditions during the COVID-19 infection are potential factors in enrichment of specific bacterial communities in upper respiratory tract.

Nasopharyngeal microbiome of SARS-CoV-2 infected (n=63) and non-infected individuals 152 (n=26) was ascertained through 16S rRNA gene based targeted amplicon sequencing. In total, 153 ~8.1 million usable reads were obtained after quality filtering. Detailed taxonomic and alpha 154 diversity analyses was performed on the rarefied reads (n=25000) and the number of OTUs 155 observed in the samples ranged from 919-2212 OTUs. Alpha diversity parameters such as 156 Simpson and Shannon indices did not show significant differences between the infected and 157 non-infected individuals (Fig. 1a) . In contrast, observed OTUs and chao1 values were found to 158 be significantly (p < 0.05) decreased in the infected individuals (Fig. 1a) . Goods coverage value 159 (>0.92) indicated the substantial coverage of the microbial diversity in both the conditions (Fig.   160 1a). 161 In total, 28 distinct bacterial phyla were observed in the nasal microbiome with a minimum of 162 ~10 phyla in each individual. Most of the reads (>90%) were assigned to the Proteobacteria, 163 Firmicutes, Bacteroidetes, Actinobacteria, and Fusobacteria in each of the infected and non- 164 infected individuals (Fig. 1b) . In case of non-infected individuals, Firmicutes (average: ~36%) 165 was found to be the dominant phyla followed by Proteobacteria (average: ~28%), and Fig. 2a) . Additionally, core microbiome (OTUs present in minimum 90% of the total samples) 178 between the infected and non-infected individuals was investigated (Fig. 2b) . Only 37 OTUs 179 were found to be the part of core microbiome (Fig. 2b) . In most of the samples, these core 180 OTUs accounted for more than 50% of the total microbial community. In order to understand 181 the difference between the shift in these core OTUs, pairwise Wilcoxcon test was performed. J o u r n a l P r e -p r o o f 

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