Nanopore sequencing revealed unique nasopharyngeal microbial communities associated with different SARS-CoV-2 variants.

New variants arising from mutations within the SARS-CoV-2 genome could subsequently lead to increased mortality and morbidity in COVID-19 patients. Microbiota within the human respiratory tract is part of the immune system that can provide protection from infection, including from SARS-CoV-2. Unfortunately, the pathogenesis of various SARS-CoV-2 variants can interfere with the homeostasis of microbial community in the respiratory tract. It is therefore imperative to study the bacterial community profile within the respiratory tract of COVID-19 patients having different SARS-CoV-2 variants. In this study, we identified SARS-CoV-2 variants using whole genome sequencing of naso/oropharyngeal swabs of confirmed COVID-19 patients with Oxford Nanopore Technologies (ONT), followed by 16S rRNA gene amplicon sequencing to assess the bacterial community diversity. Sequencing of 23 selected isolates yielded six SARS-CoV-2 variants, with the majority being B.1.617.2 (Delta), B.1.1.7 (Alpha), and B.1.466.2 (Indonesian). Bacterial community of samples identified as having the Alpha and Delta variants was dominated by Streptococcus, Prevotella. Corynebacterium, and Veillonella, whereas within the Indonesian variant samples Staphylococcus, Salmonella, Enterococcus, and Corynebacterium were predominant. Overall, the bacterial community found in the naso/oropharyngeal swabs of COVID-19 patients has a significant degree of diversity between different SARS-CoV-2 variants, with Prevotella being the overall predominant genus detected (16.2 %).