Towards high quality real-time whole genome sequencing during outbreaks using Usutu virus as example

Area of Science:

• Virology
• Genomics
• Bioinformatics

Background:

• Nanopore sequencing offers potential for viral outbreak surveillance but its reliability is debated.
• Accurate whole genome sequencing is crucial for tracking viral lineages, transmission, and genetic markers.
• Limited data exists on the necessary read coverage to overcome Nanopore's error profile.

Purpose of the Study:

• To validate a Nanopore sequencing protocol for Usutu virus (USUV) whole genome sequencing.
• To compare Nanopore sequencing data with established Illumina sequencing methods.
• To assess the reliability of Nanopore sequencing for epidemiological applications.

Main Methods:

• Developed and validated an amplicon-based whole genome sequencing protocol using Nanopore technology for USUV.
• Compared Nanopore sequencing results with Illumina sequencing data.
• Utilized brain tissue samples from birds infected with high viral loads of USUV.

Main Results:

• The Nanopore sequencing protocol demonstrated reliability when compared to Illumina sequencing.
• High viral loads in avian brain tissue samples were suitable for Nanopore sequencing.
• The study provides insights into the required read coverage for accurate USUV genome assembly.

Conclusions:

• The low-cost MinION Nanopore sequencing platform is suitable for characterizing and tracking Usutu virus outbreaks.
• Nanopore sequencing can be a valuable tool for real-time epidemiological surveillance of USUV.
• Further studies are needed to define optimal read coverage for Nanopore-based viral sequencing.