Viral Epidemiology and Diagnosis: Public Health and Clinical Implications

Genomic sequencing technologies and bioinformatic developments provide powerful means of real-time tracking viral pathogens, uncovering difficult-to-identify variants, identifying new and emerging viruses, and surveying for antimicrobial resistance. The COVID-19 pandemic demonstrated the value of rapidly generated sequence data while also exposing operational challenges involving sampling bias, uneven infrastructure, data sharing, computational latency, and the interpretation of incomplete genomic observations. Portable sequencing platforms, cloud computing, and automated analytical pipelines are now enabling increasingly rapid characterization of viral populations. Recent studies have supported lineage tracking, transmission cluster inference, estimation of effective reproduction numbers, and integration of genomic data with epidemiological and mobility information. Further research and implementation cases are needed to establish showcase how genomic platforms can be translated into timely public-health and clinical decisions across diverse settings.This Research Topic aims to advance computational frameworks and operational strategies for viral epidemiology and diagnosis. It will address how sequence data can be processed, analysed, integrated, and communicated with minimal delay while accounting for sampling bias and uncertainty. The topic will also explore how genomic information can improve outbreak response, variant assessment, clinical diagnosis, antimicrobial resistance and preparedness for future epidemics.To gather further insights in viral surveillance, clinical diagnosis and bioinformatic development, we welcome articles addressing, but not limited to, the following themes:o Bioinformatic pipelines related to genomic surveillance, identification of viruses, and diagnosis of viral infections including metagenomic next-generation sequencing (mNGS) for rare or novel viral infections.o Outbreak lineage tracking and transmission cluster detection including cluster identification in healthcare and community settings.o Wastewater and environmental genomic surveillanceo Automated Clinical Decision-Support & Early Warning Systems: Integrating viral genomic, epidemiological, mobility, and patient clinical data to generate actionable, real-time diagnostic and outbreak responses.o Case studies related to portable sequencing and field-deployable analysiso Case studies involving influenza, SARS-CoV-2, mpox, arboviruses, and other emerging pathogenso Standards for data sharing, validation, reproducibility, and uncertainty reportingAppendix: We invite Original Research, Methods, Case Report and Data Report articles. Topic editors: Yuan Chao Xue, Saina Beitari, Matthew Surette Source: https://www.frontiersin.org/research-topics/85047/viral-epidemiology-and-diagnosis-public-health-and-clinical-implications