Genomics for Arbovirus Surveillance: Considerations for Routine Use in Public Health Laboratories

The emergence and re-emergence of arthropod-borne viruses is a public health threat. For routine surveillance in public health laboratories, cost-effective and reproducible methods are essential. In this review, we address the technical considerations of high-throughput sequencing methods (HTS) for arbovirus surveillance in national health laboratories, focusing on pre-sequencing, sequencing, and post-sequencing approaches, underlining the importance of robust wet and dry laboratory workflows for reproducible analysis. We aim to provide insights for researchers and clinicians interested in arbovirus, diagnosis, and surveillance by discussing current advances in sequencing methods and bioinformatics pipelines applied to arboviruses.