Expedited retrieval of high-quality Usutu virus genomes via Nanopore sequencing with and without target enrichment

• DOI: 10.3389/fmicb.2022.1044316
• Publication Date: 2022-11-09T05:33:00Z
• Authors: Cora M. Holicki; Felicitas Bergmann; Franziska Stoek; Ansgar Schulz; Martin H. Groschup; Ute Ziegler; Balal Sadeghi
• Keywords: Minion; Viral quasispecies; Sanger sequencing; Illumina dye sequencing; Amplicon; Flavivirus

Usutu virus (USUV) is a mosquito-borne zoonotic and one of the causes flavivirus encephalitis in birds occasionally humans. USUV rapidly disperses susceptible host vector environment, as case South Central Europe. However, compared to other flaviviruses, has received less research attention there therefore limited access whole-genome sequences also in-depth phylogenetic phylodynamic analyses. To ease future molecular studies, this study compares first- (partial sequencing via Sanger), second- (Illumina), third-generation (MinION Nanopore) platforms for USUV. With emphasis on MinION Nanopore sequencing, cDNA-direct target-enrichment (amplicon-based) approaches were validated parallel. The was based four samples from succumbed commonly collected throughout Germany. isolated various sample matrices, organs well blood cruor, included three different lineages. We concluded that depending focus project, amplicon-based can be an ideal cost- time-effective alternative Illumina producing optimal genome coverage. It implemented array lab- or field-based objectives, including among others: studies analysis viral quasispecies.