Metatranscriptomic analyses of SARS-CoV-2 and humans reveal distinct differentially expressed genes. Wastewater Based Epidemiology (WBE) samples

Metatranscriptomic analyses offer unprecedented insights into the interplay between SARS-CoV-2 and human hosts, shedding light on distinct differentially expressed genes (DEGs) and their implications. The global significance of wastewater as a resource underscores its potential for disease surveillance and public health. Leveraging wastewater-based epidemiology (WBE) and advanced sequencing technologies, this study aims to elucidate DEGs between SARS-CoV-2 and human hosts. The introduction of high-throughput sequencing techniques has revolutionized our ability to detect and monitor viral pathogens in wastewater, presenting a cost-effective and comprehensive approach to epidemiological surveillance. By employing both, short-read Illumina whole transcriptome shotgun sequencing (WTSS) and long-read Oxford Nanopore Technologies (ONT), this study reveals DEGs associated with SARS-CoV-2 pathogenesis, providing valuable insights into viral-host interactions. The analysis identifies distinct alpha diversity clades between WBE and clinical microbiomes, offering potential clues to concurrent infections and underlying pathways. Host transcriptional signatures associated with COVID-19, such as those observed in MCP signal and ABC transporters, hold promise for elucidating the role of DEGs in the infectious cycle. This pioneering metatranscriptome analysis represents a significant step towards understanding the molecular basis of SARS-CoV-2 pathogenesis and highlights the potential of wastewater-based surveillance in combating infectious diseases.