Usutu virus (Orthoflavivirus usutuense) amplicon sequencing for Illumina (LowCost) v2

Amplicon based targeted sequencing methods proved their importance in case of many human pathogenic viruses (e.g. Zika virus, Ebola virus, SARS-Cov 2). Application and development of this methods for other medically important viruses could be also beneficial as it ensure the possibility of molecular epidemiology. Usutu virus (USUV, Orthoflavivirus usutuense) is widespread arbovirus which is mainly transmitted to humans via mosquito bites. In the natural circulation of USUV multiple hosts are involved which raise the need for sufficient sequencing method. There are already available, established targeted sequencing methods for USUV, but we wanted to develop an additional one which uses shorter fragment length and optimised for Illumina iSeq 100. Shorter amplicon length works better on low quality samples and iSeq100 is the cheapest (most accessible) Illumina platform on the market.