COVID-19 Surveillance through Wastewater Microbiome Analysis

5 October 2022by Barış Özdinç

Nasal swabs and saliva are conventional methods for detection of SARS-CoV-2, but the virus is also present in feces. Therefore, fecal material in wastewater samples could be used to track community dynamics of the virus. To do that, Brumfield et al. (2022) collected wastewater samples from manholes and then processed them for microbial genome sequencing and metatranscriptomic RNA sequencing. The CosmosID-HUB pipeline was used for microbiome profiling of viruses, bacteria, archaea, fungi, protozoa and antimicrobial resistance, and virulence factors in their genomes. SARS-CoV2 N protein copy number was calculated from the data and compared with epidemiological data. Using this method, the study identified that N protein copy number/mL followed the increased trend of COVID-19 cases in winter and a decrease in warmer months, but identified no significant associations. Regarding the microbiome, the study identified a strong positive correlation of SARS-CoV-2 RNA associated with Bifidobacterium, Leclercia, Pyramidobacter, Tannerella, Massilimaliae, and Erythrobacter relative abundance. The sole virus that correlated with SARS-CoV-2 was JC polyomavirus. Link to the paper.

Barış Özdinç

Barış Özdinç analyzes microbiome research with his educational background in genetics and evolution. As a research analyst for CosmosID, he combines metagenomics and data analyses to identify microbial biomarkers in disease cohorts and evaluate microbiome research tools. His work involves curating microbiome data and creating interesting microbiome content for newsletters and blog posts. Barış Özdinç received his bachelor’s degree in genetics and master’s degree in biodiversity, evolution, and conservation from University College London (UCL). Currently, he lives in Istanbul, Turkey, where he lives with his cat, Delight, and mentors female students in their STEM career pursuits.