1
|
Duan K, Zhao J, Ren G, Shao Y, Lu T, Xu L, Tang X, Zhao W, Xu L. Molecular Evolution of Infectious Pancreatic Necrosis Virus in China. Viruses 2021; 13:v13030488. [PMID: 33809489 PMCID: PMC7998647 DOI: 10.3390/v13030488] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/11/2021] [Accepted: 03/13/2021] [Indexed: 11/16/2022] Open
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.
Collapse
Affiliation(s)
- Kaiyue Duan
- Key Laboratory of Aquatic Animal Diseases and Immune Technology of Heilongjiang Province, Department of Aquatic Animal Diseases and Control, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, China; (K.D.); (J.Z.); (G.R.); (Y.S.); (T.L.); (X.T.); (W.Z.)
| | - Jingzhuang Zhao
- Key Laboratory of Aquatic Animal Diseases and Immune Technology of Heilongjiang Province, Department of Aquatic Animal Diseases and Control, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, China; (K.D.); (J.Z.); (G.R.); (Y.S.); (T.L.); (X.T.); (W.Z.)
| | - Guangming Ren
- Key Laboratory of Aquatic Animal Diseases and Immune Technology of Heilongjiang Province, Department of Aquatic Animal Diseases and Control, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, China; (K.D.); (J.Z.); (G.R.); (Y.S.); (T.L.); (X.T.); (W.Z.)
| | - Yizhi Shao
- Key Laboratory of Aquatic Animal Diseases and Immune Technology of Heilongjiang Province, Department of Aquatic Animal Diseases and Control, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, China; (K.D.); (J.Z.); (G.R.); (Y.S.); (T.L.); (X.T.); (W.Z.)
| | - Tongyan Lu
- Key Laboratory of Aquatic Animal Diseases and Immune Technology of Heilongjiang Province, Department of Aquatic Animal Diseases and Control, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, China; (K.D.); (J.Z.); (G.R.); (Y.S.); (T.L.); (X.T.); (W.Z.)
| | - Lipu Xu
- Fish Disease Department of Beijing Fisheries Technical Extension Station, Beijing 100176, China;
| | - Xin Tang
- Key Laboratory of Aquatic Animal Diseases and Immune Technology of Heilongjiang Province, Department of Aquatic Animal Diseases and Control, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, China; (K.D.); (J.Z.); (G.R.); (Y.S.); (T.L.); (X.T.); (W.Z.)
| | - Wenwen Zhao
- Key Laboratory of Aquatic Animal Diseases and Immune Technology of Heilongjiang Province, Department of Aquatic Animal Diseases and Control, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, China; (K.D.); (J.Z.); (G.R.); (Y.S.); (T.L.); (X.T.); (W.Z.)
| | - Liming Xu
- Key Laboratory of Aquatic Animal Diseases and Immune Technology of Heilongjiang Province, Department of Aquatic Animal Diseases and Control, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, China; (K.D.); (J.Z.); (G.R.); (Y.S.); (T.L.); (X.T.); (W.Z.)
- Key Laboratory of Aquatic Animal Immune Technology, Key Laboratory of Fishery Drug Development, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Ministry of Agriculture and Rural Affairs, Guangzhou 510380, China
- Correspondence: ; Tel.: +86-0451-87930965
| |
Collapse
|
2
|
Ke F, Zhang QY. Aquatic animal viruses mediated immune evasion in their host. FISH & SHELLFISH IMMUNOLOGY 2019; 86:1096-1105. [PMID: 30557608 DOI: 10.1016/j.fsi.2018.12.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 12/09/2018] [Accepted: 12/13/2018] [Indexed: 06/09/2023]
Abstract
Viruses are important and lethal pathogens that hamper aquatic animals. The result of the battle between host and virus would determine the occurrence of diseases. The host will fight against virus infection with various responses such as innate immunity, adaptive immunity, apoptosis, and so on. On the other hand, the virus also develops numerous strategies such as immune evasion to antagonize host antiviral responses. Here, We review the research advances on virus mediated immune evasions to host responses containing interferon response, NF-κB signaling, apoptosis, and adaptive response, which are executed by viral genes, proteins, and miRNAs from different aquatic animal viruses including Alloherpesviridae, Iridoviridae, Nimaviridae, Birnaviridae, Reoviridae, and Rhabdoviridae. Thus, it will facilitate the understanding of aquatic animal virus mediated immune evasion and potentially benefit the development of novel antiviral applications.
Collapse
Affiliation(s)
- Fei Ke
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Qi-Ya Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
| |
Collapse
|
3
|
Ulrich K, Wehner S, Bekaert M, Di Paola N, Dilcher M, Muir KF, Taggart JB, Matejusova I, Weidmann M. Molecular epidemiological study on Infectious Pancreatic Necrosis Virus isolates from aquafarms in Scotland over three decades. J Gen Virol 2018; 99:1567-1581. [PMID: 30358526 DOI: 10.1099/jgv.0.001155] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
In order to obtain an insight into genomic changes and associated evolution and adaptation of Infectious Pancreatic Necrosis Virus (IPNV), the complete coding genomes of 57 IPNV isolates collected from Scottish aquafarms from 1982 to 2014 were sequenced and analysed. Phylogenetic analysis of the sequenced IPNV strains showed separate clustering of genogroups I, II, III and V. IPNV isolates with genetic reassortment of segment A/B of genogroup III/II were determined. About 59 % of the IPNV isolates belonged to the persistent type and 32 % to the low-virulent type, and only one highly pathogenic strain (1.79 %) was identified. Codon adaptation index calculations indicated that the IPNV major capsid protein VP2 has adapted to its salmonid host. Under-representation of CpG dinucleotides in the IPNV genome to minimize detection by the innate immunity receptors, and observed positive selection in the virulence determination sites of VP2 embedded in the variable region of the main antigenic region, suggest an immune escape mechanism driving virulence evolution. The prevalence of mostly persistent genotypes, together with the assumption of adaptation and immune escape, indicates that IPNV is evolving with the host.
Collapse
Affiliation(s)
- Kristina Ulrich
- 1Institute of Aquaculture, University of Stirling, Stirling, UK
| | | | - Michaël Bekaert
- 1Institute of Aquaculture, University of Stirling, Stirling, UK
| | - Nicholas Di Paola
- 3Biomedical Sciences Institute, University of Sao Paulo, Sao Paulo, Brazil
| | - Meik Dilcher
- 4Canterbury Health Laboratories, Christchurch, New-Zealand
| | | | - John B Taggart
- 1Institute of Aquaculture, University of Stirling, Stirling, UK
| | | | - Manfred Weidmann
- 1Institute of Aquaculture, University of Stirling, Stirling, UK
| |
Collapse
|
4
|
Ji F, Zhao JZ, Liu M, Lu TY, Liu HB, Yin J, Xu LM. Complete genomic sequence of an infectious pancreatic necrosis virus isolated from rainbow trout (Oncorhynchus mykiss) in China. Virus Genes 2016; 53:215-225. [PMID: 27858313 DOI: 10.1007/s11262-016-1408-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 11/08/2016] [Indexed: 10/20/2022]
Abstract
Infectious pancreatic necrosis (IPN) is a significant disease of farmed salmonids resulting in direct economic losses due to high mortality in China. However, no gene sequence of any Chinese infectious pancreatic necrosis virus (IPNV) isolates was available. In the study, moribund rainbow trout fry samples were collected during an outbreak of IPN in Yunnan province of southwest China in 2013. An IPNV was isolated and tentatively named ChRtm213. We determined the full genome sequence of the IPNV ChRtm213 and compared it with previously identified IPNV sequences worldwide. The sequences of different structural and non-structural protein genes were compared to those of other aquatic birnaviruses sequenced to date. The results indicated that the complete genome sequence of ChRtm213 strain contains a segment A (3099 nucleotides) coding a polyprotein VP2-VP4-VP3, and a segment B (2789 nucleotides) coding a RNA-dependent RNA polymerase VP1. The phylogenetic analyses showed that ChRtm213 strain fell within genogroup 1, serotype A9 (Jasper), having similarities of 96.3% (segment A) and 97.3% (segment B) with the IPNV strain AM98 from Japan. The results suggest that the Chinese IPNV isolate has relative closer relationship with Japanese IPNV strains. The sequence of ChRtm213 was the first gene sequence of IPNV isolates in China. This study provided a robust reference for diagnosis and/or control of IPNV prevalent in China.
Collapse
Affiliation(s)
- Feng Ji
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China.,College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Jing-Zhuang Zhao
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
| | - Miao Liu
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
| | - Tong-Yan Lu
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
| | - Hong-Bai Liu
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
| | - Jiasheng Yin
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China.
| | - Li-Ming Xu
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China.
| |
Collapse
|
5
|
Xu LM, Zhao JZ, Liu M, Cao YS, Yin JS, Liu HB, Lu T. Recombinant scFv antibodies against infectious pancreatic necrosis virus isolated by flow cytometry. J Virol Methods 2016; 237:204-209. [PMID: 27678027 DOI: 10.1016/j.jviromet.2016.07.029] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 07/29/2016] [Accepted: 07/31/2016] [Indexed: 11/28/2022]
Abstract
Infectious pancreatic necrosis is a significant disease of farmed salmonids in China. In this study, a single chain variable fragment (scFv) antibody library derived from rainbow trout (Oncorhynchus mykiss) and viral protein VP2 of a Chinese infectious pancreatic necrosis virus (IPNV) isolate ChRtm213 were co-expressed by a bacterial display technology. The library was subjected to three rounds of screening by flow cytometry (FCM) to select IPNV specific antibodies. Six antibody clones with different mean fluorescence intensities (MFI) were obtained by picking colonies at random. The antibody clones were expressed and purified. The purified IPNV-specific scFv antibodies were used successfully in Western blotting, enzyme linked immunosorbent assay (ELISA) and an immunofluorescence antibody test (IFAT). This method provides a high throughput means to screen an antibody library by flow cytometry, and isolate a panel of antibody that can be used as potential reagents for the detection and study of IPNV that are prevalent in China.
Collapse
Affiliation(s)
- Li-Ming Xu
- Heilongjiang River Fishery Research Institute Chinese Academy of Fishery Sciences, Harbin 150070, PR China.
| | - Jing-Zhuang Zhao
- Heilongjiang River Fishery Research Institute Chinese Academy of Fishery Sciences, Harbin 150070, PR China.
| | - Miao Liu
- Heilongjiang River Fishery Research Institute Chinese Academy of Fishery Sciences, Harbin 150070, PR China.
| | - Yong-Sheng Cao
- Heilongjiang River Fishery Research Institute Chinese Academy of Fishery Sciences, Harbin 150070, PR China.
| | - Jia-Sheng Yin
- Heilongjiang River Fishery Research Institute Chinese Academy of Fishery Sciences, Harbin 150070, PR China.
| | - Hong-Bai Liu
- Heilongjiang River Fishery Research Institute Chinese Academy of Fishery Sciences, Harbin 150070, PR China.
| | - Tongyan Lu
- Heilongjiang River Fishery Research Institute Chinese Academy of Fishery Sciences, Harbin 150070, PR China.
| |
Collapse
|
6
|
Zhu RL, Zhang QY. Determination and analysis of the complete genome sequence of Paralichthys olivaceus rhabdovirus (PORV). Arch Virol 2013; 159:817-20. [PMID: 24142268 DOI: 10.1007/s00705-013-1716-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 04/04/2013] [Indexed: 10/26/2022]
Abstract
Paralichthys olivaceus rhabdovirus (PORV), which is associated with high mortality rates in flounder, was isolated in China in 2005. Here, we provide an annotated sequence record of PORV, the genome of which comprises 11,182 nucleotides and contains six genes in the order 3'-N-P-M-G-NV-L-5'. Phylogenetic analysis based on glycoprotein sequences of PORV and other rhabdoviruses showed that PORV clusters with viral haemorrhagic septicemia virus (VHSV), genus Novirhabdovirus, family Rhabdoviridae. Further phylogenetic analysis of the combined amino acid sequences of six proteins of PORV and VHSV strains showed that PORV clusters with Korean strains and is closely related to Asian strains, all of which were isolated from flounder. In a comparison in which the sequences of the six proteins were combined, PORV shared the highest identity (98.3 %) with VHSV strain KJ2008 from Korea.
Collapse
Affiliation(s)
- Ruo-Lin Zhu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Graduate School of the Chinese Academy of Sciences, Chinese Academy of Sciences, WuHan, 430072, China
| | | |
Collapse
|
7
|
Abstract
Naturally occurring viral infections have the potential to introduce confounding variability that leads to invalid and misinterpreted data. Whereas the viral diseases of research rodents are well characterized and closely monitored, no naturally occurring viral infections have been characterized for the laboratory zebrafish (Danio rerio), an increasingly important biomedical research model. Despite the ignorance about naturally occurring zebrafish viruses, zebrafish models are rapidly expanding in areas of biomedical research where the confounding effects of unknown infectious agents present a serious concern. In addition, many zebrafish research colonies remain linked to the ornamental (pet) zebrafish trade, which can contribute to the introduction of new pathogens into research colonies, whereas mice used for research are purpose bred, with no introduction of new mice from the pet industry. Identification, characterization, and monitoring of naturally occurring viruses in zebrafish are crucial to the improvement of zebrafish health, the reduction of unwanted variability, and the continued development of the zebrafish as a model organism. This article addresses the importance of identifying and characterizing the viral diseases of zebrafish as the scope of zebrafish models expands into new research areas and also briefly addresses zebrafish susceptibility to experimental viral infection and the utility of the zebrafish as an infection and immunology model.
Collapse
Affiliation(s)
- Marcus J Crim
- Comparative Medicine Program, University of Missouri, Columbia, MO 65201, USA.
| | | |
Collapse
|