Discovery of Diverse Rodent and Bat Pestiviruses With Distinct Genomic and Phylogenetic Characteristics in Several Chinese Provinces

Abstract

Bats and rodents are widely distributed worldwide and can be native or intermediate reservoirs of many important zoonotic viruses. Pestiviruses are a group of virus species of the genus Pestivirus under the family Flaviviridae that can infect a wide variety of artiodactylous hosts, including swine and ruminants. Two classic types of pestiviruses, bovine viral diarrhea virus and classical swine fever virus, are important causative agents of mild-to-severe disease in bovine and swine hosts, respectively, and cause tremendous economic losses in these industries. Recent reports revealed that bats and rodents could also act as natural hosts of pestiviruses and an atypical porcine pestivirus, which cause disease in piglets, showed a close genetic relationship with a specific bat pestivirus, RaPestV-1. This study aimed to describe the detection and characterization of novel pestiviruses from bats and rodents in different locations by analyzing the available bat and rodent virome data from throughout China. Two bat pestivirus species and four rodent pestivirus species that are distinct from other known viruses were identified and sequenced. These viruses were identified from two bat species and four rodent species in different Chinese provinces. There were two distinct lineages present in these viruses, that differ from artiodactylous pestivirus. These findings expand our understanding of the genetic diversity of pestiviruses in bats and rodents and suggest the presence of a diverse set of pestiviruses in non-artiodactylous hosts. This study may provide new insight for the prevention of future viral disease outbreaks originating from bats and rodents.

Keywords: bats; pestivirus; rodents; viral disease emergence; viral evolution.

FIGURE 1

Occurrence of pestivirus-related reads in bats and rodents from different locations. Provinces with pestivirus-related reads are labeled in green and aqua and the animal species from each province is noted in red to the right of the map.

FIGURE 2

Genomic analysis of BPVs. The genomic organization and 12 mature peptides of BPVs were predicted and shown in the upper diagram. The lengths of the predicted mature peptides and the pairwise amino acid identities (%) of those peptides compared to other Pestivirus members are shown in the lower table.

FIGURE 3

Genomic analysis of RPVs. The genomic organization and 12 mature peptides of RPVs were predicted and are shown in the upper diagram. The lengths of predicted mature peptides, and their pairwise amino acid identities (%) compared to other Pestivirus members are shown in the lower table.

FIGURE 4

Phylogenetic analysis. Phylogenetic trees based on pestivirus (A) partial polyprotein, (B) Erns, and (C) NS3 were constructed (left). All BPVs and RPVs are labeled in red font. The evolutionary lineages of involved artiodactylous hosts (right) were drawn from genus to family according to previous reports (Jansa and Weksler, 2004; Meredith et al., 2011), viruses of different hosts are labeled in different colors.