Abstract
An unbiased metagenomics approach to virus identification can be essential in the initial phase of a pandemic. Better molecular surveillance strategies are needed for the detection of SARS-CoV-2 variants of concern and potential co-pathogens triggering respiratory symptoms. Here, a metagenomics workflow was developed to identify the metagenome diversity by SARS-CoV-2 diagnosis (n positive = 65; n negative = 60), symptomatology status (n symptomatic = 71; n asymptomatic = 54) and anatomical swabbing site (n nasopharyngeal = 96; n throat = 29) in 125 individuals. Furthermore, the workflow was able to identify putative respiratory co-pathogens, and the SARS-CoV-2 lineage across 29 samples. The diversity analysis showed a significant shift in the DNA-metagenome by symptomatology status and anatomical swabbing site. Additionally, metagenomic diversity differed between SARS-CoV-2 infected and uninfected asymptomatic individuals. While 31 co-pathogens were identified in SARS-CoV-2 infected patients, no significant increase in pathogen or associated reads were noted when compared to SARS-CoV-2 negative patients. The Alpha SARS-CoV-2 VOC and 2 variants of interest (Zeta) were successfully identified for the first time using a clinical metagenomics approach. The metagenomics pipeline showed a sensitivity of 86% and a specificity of 72% for the detection of SARS-CoV-2. Clinical metagenomics can be employed to identify SARS-CoV-2 variants and respiratory co-pathogens potentially contributing to COVID-19 symptoms. The overall diversity analysis suggests a complex set of microorganisms with different genomic abundance profiles in SARS-CoV-2 infected patients compared to healthy controls. More studies are needed to correlate severity of COVID-19 disease in relation to potential disbyosis in the upper respiratory tract. A metagenomics approach is particularly useful when novel pandemic pathogens emerge.
Keywords: COVID-19; Metagenomics; SARS-CoV-2; Variants of Concern; Variants of Interest.
【저자키워드】 COVID-19, SARS-CoV-2, variants of concern, metagenomics, variants of interest., 【초록키워드】 pandemic, VoC, SARS-CoV-2 variant, Diagnosis, virus, variants, COVID-19 disease, sensitivity, specificity, Asymptomatic individuals, Asymptomatic, pathogen, Surveillance, SARS-CoV-2 variants, nasopharyngeal, severity of COVID-19, symptomatic, clinical, Lineage, Alpha, variants of interest, microorganisms, Pathogens, metagenomics, molecular, respiratory, swabbing, genomic, disease, COVID-19 symptoms, upper respiratory tract, patients, microorganism, Analysis, respiratory symptoms, negative patients, profile, SARS-CoV-2 infected patients, significant increase, complex, healthy controls, Zeta, positive, while, triggering, SARS-CoV-2 lineage, uninfected, metagenome, approach, interest, initial, identify, anatomical, contributing to, individuals, Better, metagenomic, SARS-CoV-2 infected patient, the SARS-CoV-2,