Introduction: Metatranscriptomic analyses provide critical insights into differentially expressed genes (DEGs) and their clinical implications. By leveraging wastewater-based epidemiology (WBE) and high-throughput sequencing, we can monitor viral pathogens cost-effectively, offering a robust approach to public health surveillance. Materials and methods: Our study utilized short-read Illumina whole transcriptome shotgun sequencing (WTSS) and long-read Oxford Nanopore Technologies (ONT) to identify DEGs associated with SARS-CoV-2 pathogenesis and viral–host interactions. We processed 10 samples via an Illumina metatranscriptomic approach and 48 samples using the ONT midnight protocol, followed by downstream statistical and pathway analyses. Results: The merged assembly between Illumina and ONT yielded 381,524 transcripts mapped to 340,439 unigenes, with a total transcript length of 287,252,541 and an average unigene length of 752.9 bases. Our research reveals distinct transcriptional and microbial diversity patterns across sample types, likely reflecting both environmental and host-specific factors. We identified distinct alpha diversity clades between WBE and clinical microbiomes, suggesting concurrent infections. Conclusions: Host transcriptional signatures, such as methyl-accepting chemotaxis proteins (MCP) signals and ATP-binding cassette (ABC) transporters, clarify the role of DEGs in the infectious cycle. This analysis advances our understanding of the molecular basis of SARS-CoV-2 and underscores the importance of WBE in combating infectious diseases.
Nag et al. (Tue,) studied this question.