Molecular Evolution of Infectious Pancreatic Necrosis Virus in China.

Kaiyue Duan,Liming Xu,Guangming Ren,Tongyan Lu,Lipu Xu,Wenwen Zhao,Yizhi Shao,Xin Tang,Jingzhuang Zhao

doi:10.3390/v13030488

Abstract

Passive virus surveillance was performed in twenty-nine salmon and trout farms from seven provinces and districts in China during the period 2017–2020. A total of 25 infectious pancreatic necrosis virus (IPNV) isolates were obtained, mainly from rainbow trout (Oncorhynchus mykiss). The molecular evolution of these Chinese IPNV isolates and the previously reported Chinese IPNV strains ChRtm213 and WZ2016 was analyzed, based on their VP2 gene coding region sequences (CDS). All 27 Chinese IPNV isolates clustered within genogroups I and V, with 24 of the IPNV isolates belonging to genogroup I (including ChRtm213 and WZ2016), and only three isolates clustering in genogroup V. The Chinese genogroup I IPNV isolates lacked diversity, composing six haplotypes with 41 polymorphic sites, and the identity of nucleotide and amino acid sequences among the entire VP2 gene CDS from these isolates was 97.44%–100% and 98.19%–100%, respectively. Divergence time analyses revealed that the Chinese genogroup I IPNV isolates likely diverged from Japanese IPNV isolates in 1985 (95% highest posterior density (HPD), 1965–1997), and diverged again in 2006 (95% HPD, 1996–2013) in China. Each of the three Chinese genogroup V IPNV isolates has a unique VP2 gene CDS, with a total of 21 polymorphic sites; the identity of nucleotide and amino acid sequences among all VP2 gene CDS from these isolates was 98.5%–99.5% and 98.6%–99.0%, respectively. The data demonstrate that genogroups I and V are more likely the currently prevalent Chinese IPNV genotypes.

Highlights

Infectious pancreatic necrosis (IPN), a severe viral aquatic disease, was first recorded in salmonids in the Canada in the 1941 [1]
Atotal of 108 samples from 29 fish farms in seven provinces and districts in China were tested during the period from 2017 to 2020 in our passive surveillance, and a total of twenty-five IPN virus (IPNV) isolates were isolated from nine farms located across the seven provinces and districts (Table 1, Figure 1)
Co-infection of infectious hematopoietic necrosis virus (IHNV) and IPNV were observed from three rainbow trout samples from farm A in Gansu province and one rainbow trout sample from farm D (Table 3)

Summary

Introduction

Infectious pancreatic necrosis (IPN), a severe viral aquatic disease, was first recorded in salmonids in the Canada in the 1941 [1]. IPN virus (IPNV), which belongs to the genus Aquabirnavirus, is an unenveloped virus of about 60–65 nm in diameter [14,15]. The IPNV genome is composed of two linear double-stranded RNA segments (segment A and segment B). Segment A contains two open reading frames (ORFs), which encode a polyprotein composed of VP2, VP4, and VP3 [17] and the non-structural protein VP5, respectively. Segment B encodes the RNA polymerase VP1 [18,19]. Aquabirnavirus can be divided into seven genotypes based on the VP2 gene; these include six genotypes (genogroups I–VI) of IPNV [2] and one genotype (genogroup VII) comprising Japanese aquabirnavirus [10]. Ten Aquabirnavirus serotypes have been identified: nine serotypes from serogroup A (A1–A9) and one serotype from serogroup B (B1)

Methods

Results

Conclusion