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.

新型冠状病毒，即严重急性呼吸综合征冠状病毒 2 (SARS-CoV-2)，由于其高度传染性，正在造成严重的全球卫生紧急情况。尽管 SARS-CoV-2 的症状众所周知，但其对鼻咽微生物组的影响却鲜有研究。本横断面研究旨在使用基于 16S rRNA 基因的靶向扩增子测序来了解感染者 (n=63) 和未感染者 (n=26) 个体中鼻咽微生物组组成的扰动及其与宿主类型和宿主的关系。感染阶段机会性病原体的流行情况。结果证实，与未感染个体相比，SARS-CoV-2 感染个体的 OTU 数量显着减少 (p < 0.05)。成对 Wilcoxon 检验显示，与未感染个体相比，感染个体中变形杆菌丰度显着增加（p<0.05），梭杆菌和拟杆菌门反之亦然。相似百分比 (SIMPER) 分析显示，参与继发感染的机会性病原体（嗜血杆菌、寡养单胞菌、不动杆菌、莫拉氏菌、I 型棒状杆菌、双球菌、罗尔斯通氏菌和假单胞菌）的丰度有所增加。此外，这项研究强调了家庭内部和家庭之间个体的微生物群落结构。此外，我们还评估了与宿主类型（年龄和性别）和 COVID-19 状况（有症状和无症状）相关的微生物组。数据表明，COVID-19 感染期间的宿主类型/条件是上呼吸道特定细菌群落富集的潜在因素。