Whole Genome Sequencing of Porcine Epidemic Diarrhea Virus and Porcine Deltacoronavirus

Swine enteric coronaviruses, such as porcine epidemic diarrhea virus (PEDV) and porcine deltacoronavirus (PDCoV), are among the most important pathogens in the swine industry. The diseases due to infection of enteric coronaviruses cause significant losses within the pork industry in the United States. Whole genome sequencing of both viruses is becoming increasingly important for not only the molecular epidemiology and evolutionary genomic research but also the diagnostic tool and vaccine development. With current next-generation sequencing (NGS) method based on the Illumina TrueSeq RNA library preparation kit with random primers, near-complete genome sequences of PEDV and PDCoV can be determined from cell culture isolates, intestine tissue, and fecal samples with high viral titers (low Ct values). However, this approach doesn’t work for clinical samples such as fecal swab and intestine tissue samples with relative lower viral amounts (higher Ct values). In this chapter, we describe a NGS protocol using PEDV and PDCoV-specific primers for cDNA synthesis and then using Illumina Nextera XT DNA Library Preparation kit for DNA sequencing library preparation.