Semi-quantitative duplex RT-PCR reveals the low occurrence of Porcine Pegivirus and Atypical Porcine Pestivirus in diagnostic samples from the United States.

Fangzhou Chen,Stephanie Rossow,Douglas G Marthaler,Todd P Knutson,Yin Jiang,Eli Braun

doi:10.1111/tbed.13154

Abstract

SummaryPorcine Pegivirus (PPgV) and Atypical Porcine Pestivirus (APPV) are two recently identified porcine viruses. In this study, the identification of two viruses by metagenomic sequencing, and a duplex semi‐quantitative RT‐PCR was developed to detect these pathogens simultaneously. The PPgV strain Minnesota‐1/2016 had a 95.5%–96.3% nucleotide identity and clustered with the recently identified US PPgV strains, which is a distant clade from the German PPgV strains. The APPV strain Minnesota‐1/2016 shared an 87.3%–92.0% nucleotide identity with the other global APPV strains identity but only shared an 82.8%–83.0% nucleotide identity with clade II consisting of strain identified in China. Detection of both PPgV and APPV was 9.0% of the diagnostic cases. Co‐infection of PPgV and APPV was identified in 7.5% of the diagnostic cases. The occurrence and genetic characterization of PPgV and APPV further enhance our knowledge regarding these new pathogens in the United States.

Highlights

The Pegivirus genus, together with Flavivirus, Hepacivirus and Pestivirus genera, are members of the family Flaviviridae (Lindenbach, Murray, Thiel, & Rice, 2013)
Pegiviruses have been detected in North and South America, Africa, Asia and Europe, indicating global presence of this virus (Bailey et al, 2016; de Souza et al, 2015; N'Guessan et al, 2018; Thézé et al, 2015; Van Nguyen et al, 2018)
Porcine Pegiviruses (PPgV) was identified in the US, and 15.1% of the screened samples were positive for PPgV (Yang et al, 2018)

Summary

Introduction

The Pegivirus genus, together with Flavivirus, Hepacivirus and Pestivirus genera, are members of the family Flaviviridae (Lindenbach, Murray, Thiel, & Rice, 2013). Pegiviruses are divided into 11 species (Pegivirus A-K) (Smith et al, 2016) and have been identified from a variety of mammalian species including human, baboons, chimpanzees, monkeys, tamarins, bats, camels, horses, rodents and pigs (Tang et al, 2018; Thézé, Lowes, Parker, & Pybus, 2015). In 2016, Porcine Pegiviruses (PPgV) were discovered in pigs from Germany using Generation Sequencing (NGS) of serum from asymptomatic animals, and subsequent PCR testing detected PPgV in 2.2% of serum samples (Baechlein et al, 2016). PPgV was identified in the US, and 15.1% of the screened samples were positive for PPgV (Yang et al, 2018). In 2015, a novel genetically distinct pestivirus, designated as Atypical Porcine Pestivirus (APPV), was identified via NGS in US

Methods

Findings

Discussion

Conclusion