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Randall RE, Young DF, Hughes DJ, Goodbourn S. Persistent paramyxovirus infections: in co-infections the parainfluenza virus type 5 persistent phenotype is dominant over the lytic phenotype. J Gen Virol 2023; 104:001916. [PMID: 37962188 PMCID: PMC10768688 DOI: 10.1099/jgv.0.001916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 10/20/2023] [Indexed: 11/15/2023] Open
Abstract
Parainfluenza virus type 5 (PIV5) can either have a persistent or a lytic phenotype in cultured cells. We have previously shown that the phenotype is determined by the phosphorylation status of the phosphoprotein (P). Single amino acid substitutions at critical residues, including a serine-to-phenylalanine substitution at position 157 on P, result in a switch between persistent and lytic phenotypes. Here, using PIV5 vectors expressing either mCherry or GFP with persistent or lytic phenotypes, we show that in co-infections the persistent phenotype is dominant. Thus, in contrast to the cell death observed with cells infected solely with the lytic variant, in co-infected cells persistence is immediately established and both lytic and persistent genotypes persist. Furthermore, 10-20 % of virus released from dually infected cells contains both genotypes, indicating that PIV5 particles can package more than one genome. Co-infected cells continue to maintain both genotypes/phenotypes during cell passage, as do individual colonies of cells derived from a culture of persistently infected cells. A refinement of our model on how the dynamics of virus selection may occur in vivo is presented.
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Affiliation(s)
- Richard E. Randall
- School of Biology, Centre for Biomolecular Sciences, BMS Building, North Haugh, University of St Andrews, St Andrews, Fife, KY16 9ST, UK
| | - Dan F. Young
- School of Biology, Centre for Biomolecular Sciences, BMS Building, North Haugh, University of St Andrews, St Andrews, Fife, KY16 9ST, UK
| | - David J. Hughes
- School of Biology, Centre for Biomolecular Sciences, BMS Building, North Haugh, University of St Andrews, St Andrews, Fife, KY16 9ST, UK
| | - Steve Goodbourn
- Section for Pathogen Research, Institute for Infection and Immunity, St George’s, University of London, London SW17 0RE, UK
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Truong HT, Nguyen VG, Pham LBH, Huynh TML, Lee J, Hwang SJ, Lee JM, Chung HC. PCR-Based Detection and Genetic Characterization of Parainfluenza Virus 5 Detected in Pigs in Korea from 2016 to 2018. Vet Sci 2023; 10:414. [PMID: 37505820 PMCID: PMC10384901 DOI: 10.3390/vetsci10070414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/22/2023] [Accepted: 06/24/2023] [Indexed: 07/29/2023] Open
Abstract
This study applied a molecular-based method to detect parainfluenza virus 5 (PIV5) collected from 2016 to 2018 in nine provinces of Republic of Korea. We demonstrated that PIV5 was detectable in both serum and pooled organs at an average positive rate of 1.78% (99/5566). Among these, the complete genome sequence of 15,246 nucleotides was obtained for 12 field strains. Three out of the 12 strains had the lowest genetic identity (96.20-96.68%) among the 21 porcine PIV5 genomes collected in Germany, China, India, and Republic of Korea from 1998 to 2017. By analyzing a large collection of complete genome sequences of the structural protein-coding F and HN genes, this study proposed a classification of PIV5 into two lineages, 1 and 2, and identified that group 2.2.2 within sub-lineage 2.2 was substantially divergent. The evolution of two structural protein-coding genes was largely under purifying selection. A few codons (6/9 for the F gene, 7/8 for the HN gene) had elevated dN/dS values, which were loaded on internal branches and were predicted to be related to beneficial trait(s) of the virus.
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Affiliation(s)
- Ha-Thai Truong
- Department of Veterinary Microbiology and Infectious Diseases, Faculty of Veterinary Medicine, Vietnam National University of Agriculture (VNUA), Hanoi 100000, Vietnam
| | - Van-Giap Nguyen
- Department of Veterinary Microbiology and Infectious Diseases, Faculty of Veterinary Medicine, Vietnam National University of Agriculture (VNUA), Hanoi 100000, Vietnam
| | - Le-Bich-Hang Pham
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Vietnam
| | - Thi-My-Le Huynh
- Department of Veterinary Microbiology and Infectious Diseases, Faculty of Veterinary Medicine, Vietnam National University of Agriculture (VNUA), Hanoi 100000, Vietnam
| | - Jasper Lee
- Computational Neurobiology Laboratory, Salk Institute of Biological Sciences, La Jolla, CA 92037, USA
| | - Su-Jin Hwang
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Jae-Myun Lee
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Hee-Chun Chung
- Department of Microbiology and Immunology, Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
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Kawasaki J, Tomonaga K, Horie M. Large-scale investigation of zoonotic viruses in the era of high-throughput sequencing. Microbiol Immunol 2023; 67:1-13. [PMID: 36259224 DOI: 10.1111/1348-0421.13033] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 09/28/2022] [Accepted: 10/16/2022] [Indexed: 01/10/2023]
Abstract
Zoonotic diseases considerably impact public health and socioeconomics. RNA viruses reportedly caused approximately 94% of zoonotic diseases documented from 1990 to 2010, emphasizing the importance of investigating RNA viruses in animals. Furthermore, it has been estimated that hundreds of thousands of animal viruses capable of infecting humans are yet to be discovered, warning against the inadequacy of our understanding of viral diversity. High-throughput sequencing (HTS) has enabled the identification of viral infections with relatively little bias. Viral searches using both symptomatic and asymptomatic animal samples by HTS have revealed hidden viral infections. This review introduces the history of viral searches using HTS, current analytical limitations, and future potentials. We primarily summarize recent research on large-scale investigations on viral infections reusing HTS data from public databases. Furthermore, considering the accumulation of uncultivated viruses, we discuss current studies and challenges for connecting viral sequences to their phenotypes using various approaches: performing data analysis, developing predictive modeling, or implementing high-throughput platforms of virological experiments. We believe that this article provides a future direction in large-scale investigations of potential zoonotic viruses using the HTS technology.
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Affiliation(s)
- Junna Kawasaki
- Laboratory of RNA Viruses, Department of Virus Research, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan.,Laboratory of RNA Viruses, Department of Mammalian Regulatory Network, Graduate School of Biostudies, Kyoto University, Kyoto, Japan.,Faculty of Science and Engineering, Waseda University, Tokyo, Japan
| | - Keizo Tomonaga
- Laboratory of RNA Viruses, Department of Virus Research, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan.,Laboratory of RNA Viruses, Department of Mammalian Regulatory Network, Graduate School of Biostudies, Kyoto University, Kyoto, Japan.,Department of Molecular Virology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masayuki Horie
- Division of Veterinary Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, Japan.,Osaka International Research Center for Infectious Diseases, Osaka Prefecture University, Osaka, Japan
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Yang M, Ma Y, Jiang Q, Song M, Kang H, Liu J, Qu L. Isolation, identification and pathogenic characteristics of tick-derived parainfluenza virus 5 in northeast China. Transbound Emerg Dis 2022; 69:3300-3316. [PMID: 35964328 DOI: 10.1111/tbed.14681] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/19/2022] [Accepted: 08/04/2022] [Indexed: 02/07/2023]
Abstract
The number of parainfluenza virus 5 (PIV5) infection cases has increased worldwide over the past six decades; however, factors underlying this increase remain unclear. PIV5 has been emerging or re-emerging in humans and animal species. To date, no information is yet available regarding PIV5 infection in arthropod ticks. Here, we successfully isolated tick-derived PIV5 from the Ixodes persulcatus species designated as HLJ/Tick/2019 in Heilongjiang, China. Phylogenetic analysis revealed that the tick-derived PIV5 is closely related to subclade 2.2.6, which has become the dominant subtype prevalent in dogs, pigs and wildlife across China. Further experiments to understand the importance of this virus as an infectious vector revealed that a ferret animal model experimentally infected with Tick/HLJ/2019 via the oronasal and ocular inoculation routes developed moderate respiratory distress with pneumonia and neurologic tissue damage from inflammation for the first time. Further surveillance of PIV5 in vectors of viral transmission is necessary to enhance our knowledge of its ecology in reservoirs and facilitate the control of re-emerging diseases.
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Affiliation(s)
- Mingfa Yang
- Division of Zoonosis of Natural Foci, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yunyun Ma
- Division of Zoonosis of Natural Foci, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Qian Jiang
- Division of Zoonosis of Natural Foci, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Mingxin Song
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Hongtao Kang
- Division of Zoonosis of Natural Foci, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Jiasen Liu
- Division of Zoonosis of Natural Foci, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Liandong Qu
- Division of Zoonosis of Natural Foci, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
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Kawasaki J, Kojima S, Tomonaga K, Horie M. Hidden Viral Sequences in Public Sequencing Data and Warning for Future Emerging Diseases. mBio 2021; 12:e0163821. [PMID: 34399612 PMCID: PMC8406186 DOI: 10.1128/mbio.01638-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 07/13/2021] [Indexed: 12/31/2022] Open
Abstract
RNA viruses cause numerous emerging diseases, mostly due to transmission from mammalian and avian reservoirs. Large-scale surveillance of RNA viral infections in these animals is a fundamental step for controlling viral infectious diseases. Metagenomic analysis is a powerful method for virus identification with low bias and has contributed substantially to the discovery of novel viruses. Deep-sequencing data have been collected from diverse animals and accumulated in public databases, which can be valuable resources for identifying unknown viral sequences. Here, we screened for infections of 33 RNA viral families in publicly available mammalian and avian sequencing data and found approximately 900 hidden viral infections. We also discovered six nearly complete viral genomes in livestock, wild, and experimental animals: hepatovirus in a goat, hepeviruses in blind mole-rats and a galago, astrovirus in macaque monkeys, parechovirus in a cow, and pegivirus in tree shrews. Some of these viruses were phylogenetically close to human-pathogenic viruses, suggesting the potential risk of causing disease in humans upon infection. Furthermore, infections of five novel viruses were identified in several different individuals, indicating that their infections may have already spread in the natural host population. Our findings demonstrate the reusability of public sequencing data for surveying viral infections and identifying novel viral sequences, presenting a warning about a new threat of viral infectious disease to public health. IMPORTANCE Monitoring the spread of viral infections and identifying novel viruses capable of infecting humans through animal reservoirs are necessary to control emerging viral diseases. Massive amounts of sequencing data collected from various animals are publicly available, and these data may contain sequences originating from a wide variety of viruses. Here, we analyzed more than 46,000 public sequencing data and identified approximately 900 hidden RNA viral infections in mammalian and avian samples. Some viruses discovered in this study were genetically similar to pathogens that cause hepatitis, diarrhea, or encephalitis in humans, suggesting the presence of new threats to public health. Our study demonstrates the effectiveness of reusing public sequencing data to identify known and unknown viral infections, indicating that future continuous monitoring of public sequencing data by metagenomic analyses would help prepare and mitigate future viral pandemics.
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Affiliation(s)
- Junna Kawasaki
- Laboratory of RNA Viruses, Department of Virus Research, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
- Laboratory of RNA Viruses, Department of Mammalian Regulatory Network, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Shohei Kojima
- Laboratory of RNA Viruses, Department of Virus Research, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Keizo Tomonaga
- Laboratory of RNA Viruses, Department of Virus Research, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
- Laboratory of RNA Viruses, Department of Mammalian Regulatory Network, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- Department of Molecular Virology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masayuki Horie
- Laboratory of RNA Viruses, Department of Virus Research, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
- Hakubi Center for Advanced Research, Kyoto University, Kyoto, Japan
- Division of Veterinary Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, Japan
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