Targeted Sequencing of West Nile virus (Lineage 2)

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.West Nile virus (WNV, Orthoflavivirus nilense) is widespread arbovirus which is mainly transmitted to humans via mosquito bites. In the natural circulation of WNV multiple hosts are involved which raise the need for sufficient sequencing method.There are already available, established targeted sequencing methods for WNV lineage-2, 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.