Targeted sequencing approach for Usutu virus (Orthoflavivirus usutuense)

The emergence and spread of Usutu virus (USUV), a mosquito-borne flavivirus closely related to West Nile virus, have raised significant public and veterinary health concerns in Europe and Africa. Since its first detection in Austria in 2001, USUV has caused recurrent outbreaks in birds and occasional infections in humans, some of which have led to neuroinvasive disease. Accurate and scalable genomic surveillance is crucial to monitor viral evolution, transmission dynamics, and the emergence of pathogenic variants.This project aims to develop a targeted, amplicon-based sequencing approach for USUV, optimized for high-throughput and cost-effective genome recovery directly from clinical and field samples. Amplicon sequencing already proven successful for other RNA viruses such as SARS-CoV-2 and Zika enables high sensitivity, even from low-titer or degraded RNA, and provides robust genomic data for molecular epidemiology, lineage tracking, and mutation monitoring. By designing overlapping primer sets covering the full USUV genome and validating them across representative strains, this method will support efficient and scalable USUV surveillance efforts and improve preparedness for future outbreaks.