Whole Genome Sequencing of African Swine Fever

Methods Mol Biol. 2022:2503:205-215. doi: 10.1007/978-1-0716-2333-6_16.

Abstract

Next-generation sequencing (NGS) technologies have been powerfully applied in both research and clinical settings for the understanding and control of infectious disease. It enables high-resolution characterization of viral pathogens in terms of properties that include molecular epidemiology, genotype, serotype, and virulence. However, a beginner's NGS protocol for characterization of African swine fever virus (ASFV) is lacking. Here, we present detailed step-by-step methods for obtaining NGS data from ASF virus (ASFV) using the Illumina platform. The protocol has been performed with respect to ASFV DNA genome extraction, qualification of DNA, library preparation, quality control, de novo assembly, and data quality control. The protocol represents a step-by-step and reproducible method for producing high-quality sequencing data. The key advantages of this protocol include the protocol being very simple for users with no experience of genome sequencing and reproducibility of the protocol for other DNA genome viruses.

Keywords: African swine fever; DNA genome virus; Genome extraction; Next-generation sequencing; Whole genome sequencing.

MeSH terms

  • African Swine Fever Virus* / genetics
  • African Swine Fever* / epidemiology
  • African Swine Fever* / genetics
  • Animals
  • Genome, Viral
  • Reproducibility of Results
  • Swine
  • Whole Genome Sequencing / methods