Towards tick virome and emerging tick-borne viruses: Protocols, challenges and perspectives.

Emerging tick-borne viruses are considered a significant public health threat. The understanding of the tick virome has been revolutionized by high-throughput meta-transcriptomic sequencing, and numerous novel pathogens have been unveiled. However, effective data integration and comparative analyses have been hindered by inconsistent research protocols. In response, standardized protocols are proposed, covering field surveys, sample processing, sequencing library construction, virus assembly, phylogenetic analysis, and classification, offering a unified framework for tick-virome research. Key challenges such as sampling representations, sequencing contamination, and classification discrepancies are also discussed. Furthermore, future perspectives on leveraging bioinformatics and machine learning to trace virus evolution, elucidate virus-tick-host interactions, and enhance surveillance in high-risk areas are outlined in our work. Ultimately, special emphasis is placed on the vital significance of worldwide cooperation and data sharing, which is essential for refining methodologies and guiding targeted interventions to mitigate emerging tick-borne diseases.