Genotyping and Molecular Characterization of Classical Swine Fever Virus Isolated in China during 2016–2018

Madiha Fatima,Hua-Ji Qiu,Yongfeng Li,Yuzi Luo,Peng-Ying Wang,Hao Song,Yanhui Fu,Li Zhang,Su Li,Yun-Juan Bao,Yuan Sun

doi:10.3390/v13040664

Abstract

Classical swine fever (CSF) is a highly contagious disease of swine caused by classical swine fever virus (CSFV). For decades the disease has been controlled in China by a modified live vaccine (C-strain) of genotype 1. The emergent genotype 2 strains have become predominant in China in the past years that are genetically distant from the vaccine strain. Here, we aimed to evaluate the current infectious status of CSF, and for this purpose 24 isolates of CSFV were identified from different areas of China during 2016–2018. Phylogenetic analysis of NS5B, E2 and full genome revealed that the new isolates were clustered into subgenotype 2.1d and 2.1b, while subgenotype 2.1d was predominant. Moreover, E2 and Erns displayed multiple variations in neutralizing epitope regions. Furthermore, the new isolates exhibited capacity to escape C-strain-derived antibody neutralization compared with the Shimen strain (genotype 1). Potential positive selection sites were identified in antigenic regions of E2 and Erns, which are related with antibody binding affinity. Recombination events were predicted in the new isolates with vaccine strains in the E2 gene region. In conclusion, the new isolates showed molecular variations and antigenic alterations, which provide evidence for the emergence of vaccine-escaping mutants and emphasize the need of updated strategies for CSF control.

Highlights

Introduction published maps and institutional affilClassical swine fever (CSF) is a highly infectious viral disease of swine notifiable to the World Organization of Animal Health (OIE) due to its devastating impact on the swine industry [1,2]
Tissue samples that were collected from CSF-suspected pig farms in different provinces of China were analyzed and 24 samples tested positive for classical swine fever virus (CSFV) by reversetranscription-polymerase chain reaction (RT-PCR)
The phylogenetic analysis revealed that isolates and isolates were clustered into subgenotype 2.1d based on NS5B and E2 genes, respectively, but four isolates (HL18-490, HL18-462, SD18-461 and NM16-333) were clustered into subgenotype 2.1b (Figure 2)

Summary

Introduction

Classical swine fever (CSF) is a highly infectious viral disease of swine notifiable to the World Organization of Animal Health (OIE) due to its devastating impact on the swine industry [1,2]. CSF can run acute, chronic, or subclinical courses depending on the age of the infected animals and the virulence of the virus [4,5]. CSF is caused by classical swine fever virus (CSFV), a member of the genus Pestivirus within the family Flaviviridae [6,7]. RNA genome of 12.3 kb that contains one open reading frame (ORF) surrounded by 50 and 30 un-translated regions (UTRs) [8]. The ORF is translated into a 3898-AA polyprotein that is later cleaved into individual proteins, including four structural (C, Erns , E1, and E2)

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