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Wang X, Cun J, Li S, Shi Y, Liu Y, Wei H, Zhang Y, Cong R, Yang T, Wang W, Xiao J, Song Y, Yan D, Yang Q, Sun Q, Ji T. Genotype F of Echovirus 25 with multiple recombination pattern have been persistently and extensively circulating in Chinese mainland. Sci Rep 2024; 14:3212. [PMID: 38332009 PMCID: PMC10853551 DOI: 10.1038/s41598-024-53513-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 02/01/2024] [Indexed: 02/10/2024] Open
Abstract
Echovirus 25 (E25), a member of the Enterovirus B (EV-B) species, can cause aseptic meningitis (AM), viral meningitis (VM), and acute flaccid paralysis (AFP). However, systematic studies on the molecular epidemiology of E25, especially those concerning its evolution and recombination, are lacking. In this study, 18 strains of E25, isolated from seven provinces of China between 2009 and 2018, were collected based on the Chinese hand, foot, and mouth disease (HFMD) surveillance network, and 95 sequences downloaded from GenBank were also screened. Based on the phylogenetic analysis of 113 full-length VP1 sequences worldwide, globally occurring E25 strains were classified into 9 genotypes (A-I), and genotype F was the dominant genotype in the Chinese mainland. The average nucleotide substitution rate of E25 was 6.08 × 10-3 substitutions/site/year, and six important transmission routes were identified worldwide. Seventeen recombination patterns were determined, of which genotype F can be divided into 9 recombination patterns. A positive selector site was found in the capsid protein region of genotype F. Recombination analysis and pressure selection analysis for genotype F showed multiple recombination patterns and evolution characteristics, which may be responsible for it being the dominant genotype in the Chinese mainland. This study provides a theoretical basis for the subsequent prevention and control of E25.
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Affiliation(s)
- Xiaoyi Wang
- Medical School, Anhui University of Science and Technology, Huainan, 232001, China
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Jianping Cun
- Yunnan Center for Disease Control and Prevention, Kunming, 650100, China
| | - Shikang Li
- Hunan Center for Disease Control and Prevention, Changsha, 410005, China
| | - Yong Shi
- Jiangxi Center for Disease Control and Prevention, Nanchang, 330006, China
| | - Yingying Liu
- Hebei Center for Disease Control and Prevention, Shijiazhuang, 050000, China
| | - Haiyan Wei
- Henan Center for Disease Control and Prevention, Zhengzhou, 450000, China
| | - Yong Zhang
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Ruyi Cong
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
- Shandong First Medical University (Shandong Academy of Medical Sciences) School of Public Health and Health Management, Jinan, 250117, China
| | - Tingting Yang
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
- Shandong First Medical University (Shandong Academy of Medical Sciences) School of Public Health and Health Management, Jinan, 250117, China
| | - Wenhui Wang
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
- Shandong First Medical University (Shandong Academy of Medical Sciences) School of Public Health and Health Management, Jinan, 250117, China
| | - Jinbo Xiao
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Yang Song
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Dongmei Yan
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Qian Yang
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Qiang Sun
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Tianjiao Ji
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
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Fang C, Fu W, Liu N, Zhao H, Zhao C, Yu K, Liu C, Yin Z, Xu L, Xia N, Wang W, Cheng T. Investigating the virulence of coxsackievirus B6 strains and antiviral treatments in a neonatal murine model. Antiviral Res 2024; 221:105781. [PMID: 38097049 DOI: 10.1016/j.antiviral.2023.105781] [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: 10/17/2023] [Revised: 12/05/2023] [Accepted: 12/08/2023] [Indexed: 12/19/2023]
Abstract
Coxsackievirus B6 (CVB6), a member of the human enterovirus family, is associated with severe diseases such as myocarditis in children. However, to date, only a limited number of CVB6 strains have been identified, and their characterization in animal models has been lacking. To address this gap, in this study, a neonatal murine model of CVB6 infection was established to compare the replication and virulence of three infectious-clone-derived CVB6 strains in vivo. The results showed that following challenge with a lethal dose of CVB6 strains, the neonatal mice rapidly exhibited a series of clinical signs, such as weight loss, limb paralysis, and death. For the two high-virulence CVB6 strains, histological examination revealed myocyte necrosis in skeletal and cardiac muscle, and immunohistochemistry confirmed the expression of CVB6 viral protein in these tissues. Real-time PCR assay also revealed higher viral loads in the skeletal and cardiac muscle than in other tissues at different time points post infection. Furthermore, the protective effect of passive immunization with antisera and a neutralizing monoclonal antibody against CVB6 infection was evaluated in the neonatal mouse model. This study should provide insights into the pathogenesis of CVB6 and facilitate further research in the development of vaccines and antivirals against CVBs.
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Affiliation(s)
- Changjian Fang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, 361102, PR China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, 361102, PR China
| | - Wenkun Fu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, 361102, PR China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, 361102, PR China
| | - Nanyi Liu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, 361102, PR China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, 361102, PR China
| | - Huan Zhao
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, 361102, PR China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, 361102, PR China
| | - Canyang Zhao
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, 361102, PR China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, 361102, PR China
| | - Kang Yu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, 361102, PR China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, 361102, PR China
| | - Che Liu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, 361102, PR China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, 361102, PR China
| | - Zhichao Yin
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, 361102, PR China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, 361102, PR China
| | - Longfa Xu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, 361102, PR China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, 361102, PR China
| | - Ningshao Xia
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, 361102, PR China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, 361102, PR China
| | - Wei Wang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, 361102, PR China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, 361102, PR China.
| | - Tong Cheng
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, 361102, PR China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, 361102, PR China.
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Han Z, Wang F, Xiao J, Fu H, Song Y, Jiang M, Lu H, Li J, Xu Y, Zhu R, Zhang Y, Zhao L. Synergetic association between coxsackievirus A16 genotype evolution and recombinant form shifts. Virus Evol 2023; 10:vead080. [PMID: 38361814 PMCID: PMC10868544 DOI: 10.1093/ve/vead080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 11/05/2023] [Accepted: 12/17/2023] [Indexed: 02/17/2024] Open
Abstract
Coxsackievirus A16 (CVA16) is a major pathogen that causes hand, foot, and mouth disease (HFMD). The recombination form (RF) shifts and global transmission dynamics of CVA16 remain unknown. In this retrospective study, global sequences of CVA16 were retrieved from the GenBank database and analyzed using comprehensive phylogenetic inference, RF surveys, and population structure. A total of 1,663 sequences were collected, forming a 442-sequences dataset for VP1 coding region analysis and a 345-sequences dataset for RF identification. Based on the VP1 coding region used for serotyping, three genotypes (A, B, and D), two subgenotypes of genotype B (B1 and B2), and three clusters of subgenotype B1 (B1a, B1b, and B1c) were identified. Cluster B1b has dominated the global epidemics, B2 disappeared in 2000, and D is an emerging genotype dating back to August 2002. Globally, four oscillation phases of CVA16 evolution, with a peak in 2013, and three migration pathways were identified. Europe, China, and Japan have served as the seeds for the global transmission of CVA16. Based on the 3D coding region of the RFs, five clusters of RFs (RF-A to -E) were identified. The shift in RFs from RF-B and RF-C to RF-D was accompanied by a change in genotype from B2 to B1a and B1c and then to B1b. In conclusion, the evolution and population dynamics of CVA16, especially the coevolution of 3D and VP1 genes, revealed that genotype evolution and RF replacement were synergistic rather than stochastic.
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Affiliation(s)
| | - Fangming Wang
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, Yabao Road, Chaoyang District, Beijing 100020, China
| | - Jinbo Xiao
- WHO WPRO Regional Polio Reference Laboratory, NHC Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No.155 Changbai Road, Changping District, Beijing 102206, People’s Republic of China
| | - Hanhaoyu Fu
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, Yabao Road, Chaoyang District, Beijing 100020, China
| | - Yang Song
- WHO WPRO Regional Polio Reference Laboratory, NHC Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No.155 Changbai Road, Changping District, Beijing 102206, People’s Republic of China
| | - Mingli Jiang
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, Yabao Road, Chaoyang District, Beijing 100020, China
| | - Huanhuan Lu
- WHO WPRO Regional Polio Reference Laboratory, NHC Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No.155 Changbai Road, Changping District, Beijing 102206, People’s Republic of China
| | - Jichen Li
- WHO WPRO Regional Polio Reference Laboratory, NHC Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No.155 Changbai Road, Changping District, Beijing 102206, People’s Republic of China
| | - Yanpeng Xu
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, Yabao Road, Chaoyang District, Beijing 100020, China
| | - Runan Zhu
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, Yabao Road, Chaoyang District, Beijing 100020, China
| | - Yong Zhang
- WHO WPRO Regional Polio Reference Laboratory, NHC Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No.155 Changbai Road, Changping District, Beijing 102206, People’s Republic of China
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, Yabao Road, Chaoyang District, Beijing 100020, China
| | - Linqing Zhao
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, Yabao Road, Chaoyang District, Beijing 100020, China
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Ibrahim YM, Zhang W, Wang X, Werid GM, Fu L, Yu H, Wang Y. Molecular characterization and pathogenicity evaluation of enterovirus G isolated from diarrheic piglets. Microbiol Spectr 2023; 11:e0264323. [PMID: 37830808 PMCID: PMC10715025 DOI: 10.1128/spectrum.02643-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 09/03/2023] [Indexed: 10/14/2023] Open
Abstract
IMPORTANCE Enterovirus G is a species of positive-sense single-stranded RNA viruses associated with several mammalian diseases. The porcine enterovirus strains isolated here were chimeric viruses with the PLCP gene of porcine torovirus, which grouped together with global EV-G1 strains. The isolated EV-G strain could infect various cell types from different species, suggesting its potential cross-species infection risk. Animal experiment showed the pathogenic ability of the isolated EV-G to piglets. Additionally, the EV-Gs were widely distributed in the swine herds. Our findings suggest that EV-G may have evolved a novel mechanism for broad tropism, which has important implications for disease control and prevention.
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Affiliation(s)
- Yassein M. Ibrahim
- College of Veterinary Medicine, Southwest University, Chongqing, China
- Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Wenli Zhang
- Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Xinrong Wang
- College of Veterinary Medicine, Southwest University, Chongqing, China
| | - Gebremeskel Mamu Werid
- Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Lizhi Fu
- Chongqing Academy of Animal Science, Chongqing, China
- National Center of Technology Innovation for Pigs, Chongqing, China
| | - Haidong Yu
- Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yue Wang
- College of Veterinary Medicine, Southwest University, Chongqing, China
- Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
- National Center of Technology Innovation for Pigs, Chongqing, China
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Foronda JLM, Jiao MMAD, Climacosa FMM, Oshitani H, Apostol LNG. Epidemiological and molecular characterization of Coxsackievirus A6 causing hand, foot, and mouth disease in the Philippines, 2012-2017. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 114:105498. [PMID: 37657679 DOI: 10.1016/j.meegid.2023.105498] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/27/2023] [Accepted: 08/30/2023] [Indexed: 09/03/2023]
Abstract
Coxsackievirus A6 (CVA6) is emerging as the dominant serotype among enteroviruses (EVs) responsible for hand, foot, and mouth disease (HFMD) outbreaks in multiple countries. However, details regarding this serotype in the Philippines are limited. In this study, we investigated the epidemiological and molecular characteristics of laboratory-confirmed CVA6 HFMD cases in the Philippines between 2012 and 2017. Data collected from case report forms submitted to the National Reference Laboratory for Poliovirus and other Enteroviruses were used to determine the distribution and clinical findings of laboratory-confirmed CVA6 HFMD. Phylogenetic analyses of the complete viral protein 1 (VP1) and partial 3D polymerase (3Dpol) gene sequences were performed to determine the genotype and recombinant (RF) form of the selected samples. An increase in the detection rate of CVA6 among enterovirus-positive HFMD cases was observed from 61.9% (140/226) in 2012 to 88.1% (482/587) in 2017, with most cases coming from the Luzon island group. Among the detected cases, the majority were children, with a median age of 2 years old (interquartile range: 1.17-3.40). Respiratory-related morbidities were the commonly reported complications (7.9%; 72/907). Based on the VP1 and 3Dpol gene sequence analysis, the CVA6 strains in this study were classified as genotype D3b and RF-A group, respectively. This study elucidated that CVA6 was the most prevalent enterovirus serotype causing HFMD in the Philippines in 2012-2017, with genotype D3b/RF-A circulating within this period. This study highlights the importance of viral surveillance and molecular epidemiological analysis to broaden our understanding of HFMD in the Philippines.
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Affiliation(s)
- Janiza Lianne M Foronda
- Department of Virology, Research Institute for Tropical Medicine, Muntinlupa City, Philippines; Department of Medical Microbiology, College of Public Health, University of the Philippines, Manila City, Philippines
| | | | - Fresthel Monica M Climacosa
- Department of Medical Microbiology, College of Public Health, University of the Philippines, Manila City, Philippines
| | - Hitoshi Oshitani
- Department of Virology, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Lea Necitas G Apostol
- Department of Virology, Research Institute for Tropical Medicine, Muntinlupa City, Philippines.
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Li ZH, Li ZR, Zhu P, Zhang ZX, Song JL. First Identification and Pathogenicity Evaluation of an EV-G17 Strain Carrying a Torovirus Papain-like Cysteine Protease (PLCP) Gene in China. Viruses 2023; 15:1747. [PMID: 37632087 PMCID: PMC10459844 DOI: 10.3390/v15081747] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 08/09/2023] [Accepted: 08/12/2023] [Indexed: 08/27/2023] Open
Abstract
Enterovirus G (EV-G) is prevalent in pig populations worldwide, and a total of 20 genotypes (G1 to G20) have been confirmed. Recently, recombinant EV-Gs carrying the papain-like cysteine protease (PLCP) gene of porcine torovirus have been isolated or detected, while their pathogenicity is poorly understood. In this study, an EV-G17-PLCP strain, 'EV-G/YN23/2022', was isolated from the feces of pigs with diarrhea, and the virus replicated robustly in numerous cell lines. The isolate showed the highest complete genome nucleotide (87.5%) and polyprotein amino acid (96.6%) identity in relation to the G17 strain 'IShi-Ya4' (LC549655), and a possible recombination event was detected at the 708 and 3383 positions in the EV-G/YN23/2022 genome. EV-G/YN23/2022 was nonlethal to piglets, but mild diarrhea, transient fever, typical skin lesions, and weight gain deceleration were observed. The virus replicated efficiently in multiple organs, and the pathological lesions were mainly located in the small intestine. All the challenged piglets showed seroconversion for EV-G/YN23/2022 at 6 to 9 days post-inoculation (dpi), and the neutralization antibody peaked at 15 dpi. The mRNA expression levels of IL-6, IL-18, IFN-α, IFN-β, and ISG-15 in the peripheral blood mononuclear cells (PBMCs) were significantly up-regulated during viral infection. This is the first documentation of the isolation and pathogenicity evaluation of the EV-G17-PLCP strain in China. The results may advance our understanding of the evolution characteristics and pathogenesis of EV-G-PLCP.
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Affiliation(s)
- Zhan-Hong Li
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Fengyu Road, Jindian, Panlong District, Kunming 650224, China; (Z.-H.L.); (Z.-R.L.); (P.Z.); (Z.-X.Z.)
- Key Laboratory of Transboundary Animal Diseases Prevention and Control (Co-Construction by Ministry and Province), Yunnan Animal Science and Veterinary Institute, Fengyu Road, Jindian, Panlong District, Kunming 650224, China
| | - Zhuo-Ran Li
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Fengyu Road, Jindian, Panlong District, Kunming 650224, China; (Z.-H.L.); (Z.-R.L.); (P.Z.); (Z.-X.Z.)
- Key Laboratory of Transboundary Animal Diseases Prevention and Control (Co-Construction by Ministry and Province), Yunnan Animal Science and Veterinary Institute, Fengyu Road, Jindian, Panlong District, Kunming 650224, China
| | - Pei Zhu
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Fengyu Road, Jindian, Panlong District, Kunming 650224, China; (Z.-H.L.); (Z.-R.L.); (P.Z.); (Z.-X.Z.)
- Key Laboratory of Transboundary Animal Diseases Prevention and Control (Co-Construction by Ministry and Province), Yunnan Animal Science and Veterinary Institute, Fengyu Road, Jindian, Panlong District, Kunming 650224, China
| | - Zhen-Xing Zhang
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Fengyu Road, Jindian, Panlong District, Kunming 650224, China; (Z.-H.L.); (Z.-R.L.); (P.Z.); (Z.-X.Z.)
- Key Laboratory of Transboundary Animal Diseases Prevention and Control (Co-Construction by Ministry and Province), Yunnan Animal Science and Veterinary Institute, Fengyu Road, Jindian, Panlong District, Kunming 650224, China
| | - Jian-Ling Song
- Yunnan Tropical and Subtropical Animal Virus Diseases Laboratory, Yunnan Animal Science and Veterinary Institute, Fengyu Road, Jindian, Panlong District, Kunming 650224, China; (Z.-H.L.); (Z.-R.L.); (P.Z.); (Z.-X.Z.)
- Key Laboratory of Transboundary Animal Diseases Prevention and Control (Co-Construction by Ministry and Province), Yunnan Animal Science and Veterinary Institute, Fengyu Road, Jindian, Panlong District, Kunming 650224, China
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Imai R, Rongduo W, Kaixin L, Borjigin S, Matsumura H, Masuda T, Ozawa T, Oba M, Makino S, Nagai M, Mizutani T. Novel recombinant porcine enterovirus G viruses lacking structural proteins are maintained in pig farms in Japan. J Vet Med Sci 2023; 85:252-265. [PMID: 36543238 PMCID: PMC10017297 DOI: 10.1292/jvms.22-0505] [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] [Indexed: 12/24/2022] Open
Abstract
Type 1 recombinant enterovirus G (EV-G), which carries the papain-like cysteine protease (PLCP) gene of torovirus between its 2C/3A regions, and type 2 recombinant EV-G, which carries the torovirus PLCP gene with its flanking regions having non-EV-G sequences in place of the viral structural genes, have been detected in pig farms in several countries. In a previous study, we collected 222 fecal samples from 77 pig farms from 2104 to 2016 and detected one type 2 recombinant EV-G genome by metagenomics sequencing. In this study, we reanalyzed the metagenomic data and detected 11 type 2 recombinant EV-G genomes. In addition, we discovered new type 2 recombinant EV-G genomes of the two strains from two pig farms samples in 2018 and 2019. Thus, we identified the genomes of 13 novel type 2 recombinant EV-Gs isolated from several pig farms in Japan. Type 2 recombinant EV-G has previously been detected only in neonatal piglets. The present findings suggest that type 2 recombinant EV-G replicates in weaning piglets and sows. The detection of type 1 recombinant EV-Gs and type 2 recombinant EV-Gs at 3-year and 2-year intervals, respectively, from the same pig farm suggests that the viruses were persistently infecting or circulating in these farms.
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Affiliation(s)
- Ryo Imai
- Center for Infectious Disease Epidemiology and Prevention Research, Tokyo University of Agriculture and Technology, Tokyo, Japan.,Graduate School of Agriculture Cooperative Division of Veterinary Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Wen Rongduo
- Center for Infectious Disease Epidemiology and Prevention Research, Tokyo University of Agriculture and Technology, Tokyo, Japan.,Graduate School of Agriculture Cooperative Division of Veterinary Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Li Kaixin
- Center for Infectious Disease Epidemiology and Prevention Research, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Sumiya Borjigin
- Center for Infectious Disease Epidemiology and Prevention Research, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Hirofumi Matsumura
- Center for Infectious Disease Epidemiology and Prevention Research, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | | | - Takuji Ozawa
- Japanese Animal Hospital Association, Tokyo, Japan
| | - Mami Oba
- Center for Infectious Disease Epidemiology and Prevention Research, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Shinji Makino
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Makoto Nagai
- Laboratory of Infectious Diseases, Department of Veterinary Medicine, Faculty of Veterinary Medicine, Azabu University, Kanagawa, Japan
| | - Tetsuya Mizutani
- Center for Infectious Disease Epidemiology and Prevention Research, Tokyo University of Agriculture and Technology, Tokyo, Japan.,Graduate School of Agriculture Cooperative Division of Veterinary Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
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Oba M, Obinata S, Takemae H, Kazama K, Oguro M, Ito K, Kakinuma S, Ishida H, Murakami H, Sakaguchi S, Mizutani T, Nagai M. Prevalence and genetic diversity in bovine parechovirus infecting Japanese cattle. Arch Virol 2023; 168:91. [PMID: 36786868 DOI: 10.1007/s00705-023-05712-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 01/02/2023] [Indexed: 02/15/2023]
Abstract
The first bovine parechovirus (Bo_ParV) was reported in 2021, and currently, only two nearly complete genome sequences of Bo_ParV are available. In this study, we detected Bo_ParVs in 10 out of 158 bovine fecal samples tested using real-time RT-PCR, and Bo_ParVs were isolated from three of these samples using MA104 cells. Analysis of the P1 region revealed that Bo_ParVs shared high pairwise amino acid sequence similarity (≥ 95.7% identity), suggesting antigenic similarity among Bo_ParVs, whereas nucleotide sequence identity values (≥ 84.8%) indicated more variability. A recombination breakpoint was identified in the 2B region, which may influence the evolution of this virus.
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Affiliation(s)
- Mami Oba
- Center for infectious Disease Epidemiology and Prevention Research, Tokyo University of Agriculture and Technology, 183-8509, Fuchu, Tokyo, Japan.,School of Veterinary Medicine, Azabu University, 252-5201, Sagamihara, Kanagawa, Japan
| | - Shiho Obinata
- School of Veterinary Medicine, Azabu University, 252-5201, Sagamihara, Kanagawa, Japan
| | - Hitoshi Takemae
- Center for infectious Disease Epidemiology and Prevention Research, Tokyo University of Agriculture and Technology, 183-8509, Fuchu, Tokyo, Japan
| | - Kei Kazama
- School of Veterinary Medicine, Azabu University, 252-5201, Sagamihara, Kanagawa, Japan
| | | | - Kazuki Ito
- Veterinary Clinic, Saitama Agricultural Mutual Aid Association, 360-0843, Kumagaya, Saitama, Japan
| | - Seiichi Kakinuma
- Kakinuma Veterinary Hospital, Kodama-chou, 367-0212, Kodama, Honjou, Saitama, Japan
| | - Hiroho Ishida
- School of Veterinary Medicine, Azabu University, 252-5201, Sagamihara, Kanagawa, Japan
| | - Hironobu Murakami
- School of Veterinary Medicine, Azabu University, 252-5201, Sagamihara, Kanagawa, Japan
| | - Shoichi Sakaguchi
- Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University, 569-8686, Osaka, Japan
| | - Tetsuya Mizutani
- Center for infectious Disease Epidemiology and Prevention Research, Tokyo University of Agriculture and Technology, 183-8509, Fuchu, Tokyo, Japan
| | - Makoto Nagai
- Center for infectious Disease Epidemiology and Prevention Research, Tokyo University of Agriculture and Technology, 183-8509, Fuchu, Tokyo, Japan. .,School of Veterinary Medicine, Azabu University, 252-5201, Sagamihara, Kanagawa, Japan.
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He Y, Wei H, Wei L, Fan H, Yan D, Zhao H, Zhu S, Ji T, Xiao J, Lu H, Wang W, Guo Q, Yang Q, Xing W, Zhang Y. Molecular Epidemiology Reveals the Co-Circulation of Two Genotypes of Coxsackievirus B5 in China. Viruses 2022; 14:v14122693. [PMID: 36560696 PMCID: PMC9785520 DOI: 10.3390/v14122693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 11/22/2022] [Accepted: 11/22/2022] [Indexed: 12/02/2022] Open
Abstract
Coxsackievirus B5 (CVB5) is an important enterovirus B species (EV-Bs) type. We used the full-length genomic sequences of 53 viral sequences from the national hand, foot, and mouth disease surveillance network in the Chinese mainland (2001-2021). Among them, 69 entire VP1 coding region nucleotide sequences were used for CVB5 genotyping and genetic evolution analysis. Phylogenetic analysis based on a data set of 448 complete VP1 sequences showed that CVB5 could be divided into four genotypes (A-D) worldwide. Sequences from this study belonged to genotypes B and D, which dominated transmission in the Chinese mainland. Two transmission lineages of CVB5 have been discovered in the Chinese mainland, lineage 2 was predominant. Markov chain Monte Carlo analysis indicated that the tMRCA of CVB5 in the Chinese mainland could be traced to 1955, while the global trend could be traced to 1862, 93 years earlier than China. The evolution rate of CVB5 was higher in the Chinese mainland than worldwide. The spatiotemporal dynamics analysis of CVB5 assessed that virus transportation events were relatively active in Central, Northeast, North and Northwest China. Recombination analysis revealed frequent intertypic recombination in the non-structural region of CVB5 genotypes B and D with the other EV-Bs, revealing eight recombination lineages. Our study showed the molecular evolution and phylogeography of CVB5 that could provide valuable information for disease prevention.
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Affiliation(s)
- Yun He
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
- School of Public Health and Management, Shandong First Medical University, Shandong Academy of Medical Sciences, 6699 Qindao Road, Jinan 250117, China
| | - Haiyan Wei
- Henan Center for Disease Control and Prevention, Zhengzhou 450016, China
| | - Leilei Wei
- Jilin Center for Disease Control and Prevention, Jilin Institute of Public Health, Changchun 130062, China
| | - Huan Fan
- Jiangsu Center for Disease Control and Prevention, Nanjing 210009, China
| | - Dongmei Yan
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Hua Zhao
- Chongqing Center for Disease Control and Prevention, Chongqing 400042, China
| | - Shuangli Zhu
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Tianjiao Ji
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Jinbo Xiao
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Huanhuan Lu
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Wenhui Wang
- School of Public Health and Management, Shandong First Medical University, Shandong Academy of Medical Sciences, 6699 Qindao Road, Jinan 250117, China
| | - Qin Guo
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Qian Yang
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
- Correspondence: (Q.Y.); (W.X.); (Y.Z.); Tel.: +86-10-58900185 (Q.Y.); +86-531-59567833 (W.X.); +86-10-58900183 (Y.Z.)
| | - Weijia Xing
- School of Public Health and Management, Shandong First Medical University, Shandong Academy of Medical Sciences, 6699 Qindao Road, Jinan 250117, China
- Correspondence: (Q.Y.); (W.X.); (Y.Z.); Tel.: +86-10-58900185 (Q.Y.); +86-531-59567833 (W.X.); +86-10-58900183 (Y.Z.)
| | - Yong Zhang
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
- Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China
- Correspondence: (Q.Y.); (W.X.); (Y.Z.); Tel.: +86-10-58900185 (Q.Y.); +86-531-59567833 (W.X.); +86-10-58900183 (Y.Z.)
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10
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Molecular Characteristics and Genetic Evolution of Echovirus 33 in Mainland of China. Pathogens 2022; 11:pathogens11111379. [PMID: 36422630 PMCID: PMC9697921 DOI: 10.3390/pathogens11111379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/01/2022] [Accepted: 11/08/2022] [Indexed: 11/22/2022] Open
Abstract
Echovirus, a member of the Enterovirus B (EV-B) family, has led to numerous outbreaks and pandemics, causing a broad spectrum of diseases. Based on the national hand, foot, and mouth disease (HFMD) surveillance system, seven strains of echovirus 33 (E33) were isolated from Mainland of China between 2010 and 2018. The whole genomes of these strains were isolated and sequenced, and phylogenetic trees were constructed based on the gene sequences in different regions of the EV-B prototype strains. It was found that E33 may be recombined in the P2 and P3 regions. Five genotypes (A–E) were defined based on the entire VP1 region of E33, of which the C gene subtype was the dominant gene subtype at present. Recombinant analysis showed that genotype C strains likely recombined with EV-B80, EV-B85, E13, and CVA9 in the P2 and P3 regions, while genotype E had the possibility of recombination with CVB3, E3, E6, and E4. Results of Bayesian analysis indicated that E33 may have appeared around 1955 (95% confidence interval: 1945–1959), with a high evolutionary rate of 1.11 × 10−2 substitution/site/year (95% highest posterior density (HPD): 8.17 × 10−3 to 1.4 × 10−2 substitution/site/year). According to spatial transmission route analysis, two significant transmission routes were identified: from Australia to India and from Oman to Thailand, which the E33 strain in Mainland of China likely introduced from Mexico and India. In conclusion, our study fills the gaps in the evolutionary analysis of E33 and can provide important data for enterovirus surveillance.
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van den Braak WJP, Monica B, Limpens D, Rockx-Brouwer D, de Boer M, Oosterhoff D. Construction of a Vero Cell Line Expressing Human ICAM1 for the Development of Rhinovirus Vaccines. Viruses 2022; 14:v14102235. [PMID: 36298792 PMCID: PMC9607643 DOI: 10.3390/v14102235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/04/2022] [Accepted: 10/07/2022] [Indexed: 11/16/2022] Open
Abstract
Human rhinoviruses (HRVs) are small non-enveloped RNA viruses that belong to the Enterovirus genus within the Picornaviridae family and are known for causing the common cold. Though symptoms are generally mild in healthy individuals, the economic burden associated with HRV infection is significant. A vaccine could prevent disease. The Vero-cell-based viral vaccine platform technology was considered for such vaccine development. Unfortunately, most HRV strains are unable to propagate on Vero cells due to a lack of the major receptor of HRV group A and B, intercellular adhesion molecule (ICAM1, also known as CD54). Therefore, stable human ICAM1 expressing Vero cell clones were generated by transfecting the ICAM1 gene in Vero cells and selecting clones that overexpressed ICAM1 on the cell surface. Cell banks were made and expression of ICAM1 was stable for at least 30 passages. The Vero_ICAM1 cells and parental Vero cells were infected with four HRV prototypes, B14, A16, B37 and A57. Replication of all four viruses was detected in Vero_ICAM1, but not in the parental Vero cells. Altogether, Vero cells expressing ICAM1 could efficiently propagate the tested HRV strains. Therefore, ICAM1-expressing cells could be a useful tool for the development and future production of polyvalent HRV vaccines or other viruses that use ICAM1 as a receptor.
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12
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Hu L, Zhou L, Wang P, Maimaiti H, Lu Y. Molecular characteristics of a coxsackievirus A12 strain in Zhejiang of China, 2019. Virol J 2022; 19:160. [PMID: 36224635 PMCID: PMC9555000 DOI: 10.1186/s12985-022-01892-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 09/30/2022] [Indexed: 11/29/2022] Open
Abstract
Background Enterovirus A (EV-A), such as enterovirus A71 (EV-A71), generally causes hand, foot, and mouth disease (HFMD). However, limited studies focused on uncommon enterovirus serotypes such as coxsackievirus A12 (CV-A12). This study aimed to provide evidence to determine the molecular characteristics of a CV-A12 strain isolated in Zhejiang province, China. Methods In routine surveillance of HFMD, we identified a child case with CV-A12 infection in 2019 in Zhejiang province, China. Enterovirus was examined by using real-time reverse transcription-PCR (qRT-PCR). A partial VP1 sequence was amplified to determine the serotype, and then a full-length CV-A12 genome was sequenced. Nucleotide and amino acid similarity was calculated with those CV-A12 strains available in GenBank. Recombination was detected using RDP 4 and SimPlot. Furthermore, phylogenetic analysis was conducted by using BEAST 1.10, and protein modeling was performed with I-TASSER webserver. Results A full-length CV-A12 genome PJ201984 was isolated in a Chinese child with HFMD. The similarities with complete coding sequences of the CV-A12 strains in GenBank ranged between 79.3–100% (nucleotide) and 94.4–100% (amino acid), whereas it was 88.7–100.0% (nucleotide) and 97.2–100% (amino acid) when excluding the CV-A12 prototype strain Texas-12. In PJ201984, amino acid variations were more divergent in P2 and P3 regions than those in P1; the majority of those variations in VP1 (13/15) and VP4 (7/8) were similar to those documented in recently isolated CV-A12 strains in China. Furthermore, recombination was identified in P2 region, which involved a CV-A5 strain collected in China. Phylogenetic analysis revealed that PJ201984 clustered together with multiple CV-A12 strains isolated in China and the Netherlands during 2013–2018, as compared to another cluster consisting of CV-A12 strains in China and France during 2009–2015. Additionally, protein models of VP1 and VP4 in PJ201984 were well predicted to be similar to VP1 protein of EV-A71 and VP4 protein of coxsackievirus A21, respectively. Conclusions The full-length CV-A12 genome was characterized to have common recombination in P2 region and be phylogenetically related to those CV-A12 strains isolated in recent years, suggesting a continual spread in China. It warrants strengthening the routine surveillance for uncommon enterovirus serotypes, particularly on possible recombination and variation. Supplementary Information The online version contains supplementary material available at 10.1186/s12985-022-01892-1.
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Affiliation(s)
- Linjie Hu
- Department of Epidemiology, Ministry of Education Key Laboratory of Public Health Safety, School of Public Health, Fudan University, Fosun Tower, 131 Dong An Road, Shanghai, 200032, China
| | - Lu Zhou
- Department of Epidemiology, Ministry of Education Key Laboratory of Public Health Safety, School of Public Health, Fudan University, Fosun Tower, 131 Dong An Road, Shanghai, 200032, China
| | - Pingping Wang
- Pujiang Center for Disease Control and Prevention, Jinhua, 321000, Zhejiang, China
| | - Hairenguli Maimaiti
- Department of Epidemiology, Ministry of Education Key Laboratory of Public Health Safety, School of Public Health, Fudan University, Fosun Tower, 131 Dong An Road, Shanghai, 200032, China
| | - Yihan Lu
- Department of Epidemiology, Ministry of Education Key Laboratory of Public Health Safety, School of Public Health, Fudan University, Fosun Tower, 131 Dong An Road, Shanghai, 200032, China.
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13
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Robust AAV Genotyping Based on Genetic Distances in Rep Gene That Are Maintained by Ubiquitous Recombination. Viruses 2022; 14:v14051038. [PMID: 35632781 PMCID: PMC9143360 DOI: 10.3390/v14051038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/04/2022] [Accepted: 05/09/2022] [Indexed: 02/01/2023] Open
Abstract
Adeno-associated viruses (AAVs) are a convenient tool for gene therapy delivery. According to the current classification, they are divided into the species AAV A and AAV B within the genus Dependoparvovirus. Historically AAVs were also subdivided on the intraspecies level into 13 serotypes, which differ in tissue tropism and targeted gene delivery capacity. Serotype, however, is not a universal taxonomic category, and their assignment is not always robust. Cross-reactivity has been shown, indicating that classification could not rely on the results of serological tests alone. Moreover, since the isolation of AAV4, all subsequent AAVs were subdivided into serotypes based primarily on genetic differences and phylogenetic reconstructions. An increased interest in the use of AAV as a gene delivery tool justifies the need to improve the existing classification. Here, we suggest genotype-based AAV classification below the species level based on the rep gene. A robust threshold was established as 10% nt differences within the 1248 nt genome fragment, with 4 distinct AAV genotypes identified. This distinct sub-species structure is maintained by ubiquitous recombination within, but not between, rep genes of the suggested genotypes.
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14
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Yang Q, Yan D, Song Y, Zhu S, He Y, Han Z, Wang D, Ji T, Zhang Y, Xu W. Whole-genome analysis of coxsackievirus B3 reflects its genetic diversity in China and worldwide. Virol J 2022; 19:69. [PMID: 35436962 PMCID: PMC9014606 DOI: 10.1186/s12985-022-01796-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 04/03/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Coxsackievirus B3 (CVB3) has emerged as an active pathogen in myocarditis, aseptic meningitis, hand, foot, and mouth disease (HFMD), and pancreatitis, and is a heavy burden on public health. However, CVB3 has not been systematically analyzed with regard to whole-genome diversity and recombination. Therefore, this study was undertaken to systematically examine the genetic characteristics of CVB3 based on its whole genome.
Methods
We combined CVB3 isolates from our national HFMD surveillance and global sequences retrieved from GenBank. Phylogenetic analysis was performed to examine the whole genome variety and recombination forms of CVB3 in China and worldwide.
Results
Phylogenetic analysis showed that CVB3 strains isolated worldwide could be classified into clusters A–E based on the sequence of the entire VP1 region. The predominant CVB3 strains in China belonged to cluster D, whereas cluster E CVB3 might be circulated globally compared to other clusters. The average nucleotide substitution rate in the P1 region of CVB3 was 4.82 × 10–3 substitutions/site/year. Myocarditis was more common with cluster A. Clusters C and D presented more cases of acute flaccid paralysis, and cluster D may be more likely to cause HFMD. Multiple recombination events were detected among CVB3 variants, and there were twenty-three recombinant lineages of CVB3 circulating worldwide.
Conclusions
Overall, this study provides full-length genomic sequences of CVB3 isolates with a wide geographic distribution over a long-term time scale in China, which will be helpful for understanding the evolution of this pathogen. Simultaneously, continuous surveillance of CVB3 is indispensable to determine its genetic diversity in China as well as worldwide.
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15
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Piot N, Smagghe G. Critical View on the Importance of Host Defense Strategies on Virus Distribution of Bee Viruses: What Can We Learn from SARS-CoV-2 Variants? Viruses 2022; 14:503. [PMID: 35336909 PMCID: PMC8951442 DOI: 10.3390/v14030503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/22/2022] [Accepted: 02/26/2022] [Indexed: 02/05/2023] Open
Abstract
Bees, both wild and domesticated ones, are hosts to a plethora of viruses, with most of them infecting a wide range of bee species and genera. Although viral discovery and research on bee viruses date back over 50 years, the last decade is marked by a surge of new studies, new virus discoveries, and reports on viral transmission in and between bee species. This steep increase in research on bee viruses was mainly initiated by the global reports on honeybee colony losses and the worldwide wild bee decline, where viruses are regarded as one of the main drivers. While the knowledge gained on bee viruses has significantly progressed in a short amount of time, we believe that integration of host defense strategies and their effect on viral dynamics in the multi-host viral landscape are important aspects that are currently still missing. With the large epidemiological dataset generated over the last two years on the SARS-CoV-2 pandemic, the role of these defense mechanisms in shaping viral dynamics has become eminent. Integration of these dynamics in a multi-host system would not only greatly aid the understanding of viral dynamics as a driver of wild bee decline, but we believe bee pollinators and their viruses provide an ideal system to study the multi-host viruses and their epidemiology.
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Affiliation(s)
- Niels Piot
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Guy Smagghe
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
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16
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Oki H, Masuda T, Hayashi-Miyamoto M, Kawai M, Ito M, Madarame H, Fukase Y, Takemae H, Sakaguchi S, Furuya T, Mizutani T, Oba M, Nagai M. Genomic diversity and intragenic recombination of species C rotaviruses. J Gen Virol 2022; 103. [PMID: 35175914 DOI: 10.1099/jgv.0.001703] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Rotavirus C (RVC) is a major cause of diarrhoea in swine, cattle, and humans worldwide. RVC exhibits sequence diversity in all 11 genes, especially in VP4 and VP7, and all segment-based genotyping has been performed similar to rotavirus A. To date, recombination events have been reported in rotavirus A and B. However, there are no reports describing gene recombination of RVC, except for recombination in NSP3 between RVC and rotavirus H. In this study, nine porcine RVC strains identified in Japanese pigs were completely sequenced and analysed together with RVC sequences from the GenBank database. The analyses showed that sequences of the VP4, VP2, and NSP1 of several porcine RVC strains did not branch with any of those of the RVC strains in the GenBank database, suggesting new genotypes. Several homologous recombination events, between or within genotypes, were identified in the VP4, VP7, VP2, NSP1, and NSP3 genes. Of these, nine, one, and one intergenotypic recombination events in the VP4, VP2, and NSP3 genes, respectively, were supported with sufficient statistical values. Although these findings suggest occurrences of the intragenic recombination events in the RVC genome, potential sequence errors and poor sequence assemblies in the databases should be watched with care. The results in this study present data about the important recombination events of the RVCs, which influence evolution of the virus by aiding them to gain genetic diversity and plasticity, although further sequence data will be necessary to obtain more comprehensive understanding of such mechanisms.
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Affiliation(s)
- Hisako Oki
- Ishikawa Nanbu Livestock Hygiene Service Center, Kanazawa, Ishikawa 920-3101, Japan
| | - Tsuneyuki Masuda
- Seibu Livestock Hygiene Service Center, Houki, Tottori 689-4213, Japan
| | | | - Megumi Kawai
- Ishikawa Nanbu Livestock Hygiene Service Center, Kanazawa, Ishikawa 920-3101, Japan
| | - Mika Ito
- Ishikawa Nanbu Livestock Hygiene Service Center, Kanazawa, Ishikawa 920-3101, Japan
| | - Hiroo Madarame
- School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa 252-5201, Japan
| | - Yuka Fukase
- School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa 252-5201, Japan
| | - Hitoshi Takemae
- Center for Infectious Diseases of Epidemiology and Prevention Research, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Shoichi Sakaguchi
- Department of Microbiology and Infection Control, Osaka Medical College, Osaka 569-8686, Japan
| | - Tetsuya Furuya
- Cooperative Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Tetsuya Mizutani
- Center for Infectious Diseases of Epidemiology and Prevention Research, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Mami Oba
- School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa 252-5201, Japan
- Center for Infectious Diseases of Epidemiology and Prevention Research, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Makoto Nagai
- School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa 252-5201, Japan
- Center for Infectious Diseases of Epidemiology and Prevention Research, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
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WGS- versus ORF5-Based Typing of PRRSV: A Belgian Case Study. Viruses 2021; 13:v13122419. [PMID: 34960688 PMCID: PMC8707199 DOI: 10.3390/v13122419] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/17/2021] [Accepted: 11/24/2021] [Indexed: 12/18/2022] Open
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) is the causative agent of one of the most widespread and economically devastating diseases in the swine industry. Typing circulating PRRSV strains by means of sequencing is crucial for developing adequate control strategies. Most genetic studies only target the highly variable open reading frame (ORF) 5, for which an extensive database is available. In this study, we performed whole-genome sequencing (WGS) on a collection of 124 PRRSV-1 positive serum samples that were collected over a 5-year period (2015–2019) in Belgium. Our results show that (nearly) complete PRRSV genomes can be obtained directly from serum samples with a high success rate. Analysis of the coding regions confirmed the exceptionally high genetic diversity, even among Belgian PRRSV-1 strains. To gain more insight into the added value of WGS, we performed phylogenetic cluster analyses on separate ORF datasets as well as on a single, concatenated dataset (CDS) containing all ORFs. A comparison between the CDS and ORF clustering schemes revealed numerous discrepancies. To explain these differences, we performed a large-scale recombination analysis, which allowed us to identify a large number of potential recombination events that were scattered across the genome. As PRRSV does not contain typical recombination hot-spots, typing PRRSV strains based on a single ORF is not recommended. Although the typing accuracy can be improved by including multiple regions, our results show that the full genetic diversity among PRRSV strains can only be captured by analysing (nearly) complete genomes. Finally, we also identified several vaccine-derived recombinant strains, which once more raises the question of the safety of these vaccines.
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18
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Liu M, Yang Q, Han J. Transcriptomic analysis reveals that coxsackievirus B3 Woodruff and GD strains use similar key genes to induce FoxO signaling pathway activation in HeLa cells. Arch Virol 2021; 167:131-140. [PMID: 34773511 DOI: 10.1007/s00705-021-05292-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 09/16/2021] [Indexed: 11/28/2022]
Abstract
Coxsackievirus B3 (CVB3) is a major cause of viral myocarditis in humans. Although there have been studies on CVB3 infection and pathogenesis, the precise disease mechanism is still not clear. In this study, we used RNA-seq technology to compare the transcriptomic profile of virus-infected HeLa cells to that of uninfected cells to identify key genes involved in host-virus interaction. For this, two CVB3 strains, CVB3 Woodruff, an experimental strain, and GD16-69/GD/CHN/2016, a clinical strain, were selected to examine the common mechanisms underlying their infection. Transcriptomic profiles revealed increased expression of the cell cycle genes CCNG2, GADD45B, PIM1, RBM15, KLF10, and RIOK3 and decreased expression of CYBA. The autophagy-related genes ATG12 and YOD1 were found to be upregulated, while the expression of SOD2 and XPO1 increased slightly in infected cells, and only a minor change was observed in GABARAP expression. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed the FoxO signaling pathway to be enriched and showed a close interaction with differentially expressed genes (DEGs) in the protein-protein interaction network. DEGs associated with related pathways such as cell cycle, autophagy, and oxidative stress resistance were also confirmed by qRT-PCR. In summary, the FoxO signaling pathway was activated during infection with both CVB3 strains and was found to have a regulatory role in downstream pathways such as cell cycle, autophagy, oxidative stress resistance, and the antiviral immune response.
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Affiliation(s)
- Mi Liu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Rd, Beijing, 102206, China
| | - Qian Yang
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Beijing, 102206, China
| | - Jun Han
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Rd, Beijing, 102206, China.
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19
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Khan H, Khan A. Genome-wide population structure inferences of human coxsackievirus-A; insights the genotypes diversity and evolution. INFECTION GENETICS AND EVOLUTION 2021; 95:105068. [PMID: 34492386 DOI: 10.1016/j.meegid.2021.105068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 08/25/2021] [Accepted: 09/01/2021] [Indexed: 11/24/2022]
Abstract
Coxsackievirus-A (CV-A) is a causative agent of Hand Foot Mouth Disease (HFMD) worldwide. It belongs to the Human Enterovirus genus of the family Picornaviridae. The genomics data availability of CV-A samples, isolated from human host across different continental regions, provide an excellent opportunity to study its genetic composition, diversity, and evolutionary events. The complete genome sequences of 424 CV-A isolates were analyzed through a model-based population genetic approach implemented in the STRUCTURE program. Twelve genetically distinct sub-populations were identified for CV-A isolates with a marked Fst distinction of 0.76991 (P-value = 0.00000). Besides, genetically admixed strains were characterized in the G-Id, G-IIIb clusters constituted by the CV-A12 and CV-A6 enterovirus serotypes. The serotypes depicted inter/intra-genotype recombination and episodic positive selection signatures in the structural and non-structural protein-coding regions. The observed genetic composition of CV-A samples was also deduced by the phylogenetic tree analyses, where a uniform genetic structure was inferred for most of the CV-A genotypes. However, the CV-A6 serotype samples genetically stratified into three sub-populations that may lead to the emergence of new lineages in future. These informations may implicate in planning the effective strategies to combat the coxsackievirus-A-mediated infection.
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Affiliation(s)
- Hizbullah Khan
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan 23200, Khyber Pakhtunkhwa, Pakistan
| | - Asifullah Khan
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan 23200, Khyber Pakhtunkhwa, Pakistan.
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20
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Mi X, Yang C, Lu Y, Wang H, Qin Q, Chen R, Chen Z, Luo Y, Chen Y, Wei Z, Huang W, Ouyang K. Isolation, Identification, and Evaluation of the Pathogenicity of a Porcine Enterovirus G Isolated From China. Front Vet Sci 2021; 8:712679. [PMID: 34368288 PMCID: PMC8339413 DOI: 10.3389/fvets.2021.712679] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 06/29/2021] [Indexed: 02/01/2023] Open
Abstract
Enterovirus G (EV-G) infects porcine populations worldwide and the infections are generally asymptomatic, with the insertion of the papain-like cysteine protease gene (PLCP) increasing the potential public health threats. However, the genetic and pathogenic characteristics of EV-G itself are not fully understood as yet. In the present study, one EV-G strain, named CH/17GXQZ/2017, was isolated and purified from piglets with diarrheic symptoms from the Guangxi Province, China. This strain produced stable cytopathic effects on Marc-145 cells with a titer of 5 × 106 PFU/mL. The spherical enterovirus particles with diameters of 25–30 nm were observed by using transmission electron microscopy. The whole genome sequence of the CH/17GXQZ/2017 strain consists of 7,364 nucleotides, and the phylogenetic tree based on the amino acid sequences of VP1 indicated this strain was clustered to the G1 genotype. Seven-day-old piglets were inoculated orally with the CH/17GXQZ/2017 strain in order to evaluate its pathogenicity. Although none of the infected piglets died during the experiment, clinical neurological symptoms were observed manifesting as mild hyperemia and Nissl bodies vacuolization in the cerebrum. In addition, the infection with the CH/17GXQZ/2017 strain decelerated the weight gain of suckling piglets significantly. This study demonstrates that CH/17GXQZ/2017 is pathogenic to neonatal piglets and advance knowledge on the biological characteristics, evolution and pathogenicity of EV-G.
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Affiliation(s)
- Xue Mi
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Chunjie Yang
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Ying Lu
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Hejie Wang
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Qiuying Qin
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Ronglin Chen
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Zhenkong Chen
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Yunyan Luo
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Ying Chen
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Zuzhang Wei
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Weijian Huang
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Kang Ouyang
- College of Animal Science and Technology, Guangxi University, Nanning, China
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21
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Tian X, Han Z, He Y, Sun Q, Wang W, Xu W, Li H, Zhang Y. Temporal phylogeny and molecular characterization of echovirus 30 associated with aseptic meningitis outbreaks in China. Virol J 2021; 18:118. [PMID: 34092258 PMCID: PMC8182919 DOI: 10.1186/s12985-021-01590-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/28/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND An outbreak of aseptic meningitis occurred from June to August 2016, in Inner Mongolia Autonomous Region, China. METHODS To determine its epidemiological characteristics, etiologic agent, and possible origin, specimens were collected for virus isolation and identification, followed by molecular epidemiological analysis. RESULTS A total of 363 patients were clinically diagnosed from June 1st to August 31st 2016, and most cases (63.1%, n = 229) were identified between June 22nd and July 17th, with children aged 6 to 12 years constituting the highest percentage (68.9%, n = 250). All viral isolates from this study belonged to genotype C of echovirus 30 (E30), which dominated transmission in China. To date, two E30 transmission lineages have been identified in China, of which Lineage 2 was predominant. We observed fluctuant progress of E30 genetic diversity, with Lineage 2 contributing to increased genetic diversity after 2002, whereas Lineage 1 was significant for the genetic diversity of E30 before 2002. CONCLUSIONS We identified the epidemiological and etiological causes of an aseptic meningitis outbreak in Inner Mongolia in 2016, and found that Lineage 2 played an important role in recent outbreaks. Moreover, we found that Gansu province could play an important role in E30 spread and might be a possible origin site. Furthermore, Fujian, Shandong, Taiwan, and Zhejiang provinces also demonstrated significant involvement in E30 evolution and persistence over time in China.
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Affiliation(s)
- Xiaoling Tian
- Inner Mongolia Center for Disease Control and Prevention, Huhhot, 010031, People's Republic of China
| | - Zhenzhi Han
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory of biosafety, National Health Commission Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People's Republic of China.,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China
| | - Yulong He
- Tongliao City Center for Disease Control and Prevention, Tongliao, 028000, People's Republic of China
| | - Qiang Sun
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory of biosafety, National Health Commission Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People's Republic of China.,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China
| | - Wenrui Wang
- Inner Mongolia Center for Disease Control and Prevention, Huhhot, 010031, People's Republic of China
| | - Wenbo Xu
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory of biosafety, National Health Commission Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People's Republic of China.,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China
| | - Hongying Li
- Tongliao City Hospital, Tongliao, 028000, People's Republic of China.
| | - Yong Zhang
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory of biosafety, National Health Commission Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People's Republic of China. .,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, People's Republic of China.
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22
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Cheng W, Ji T, Zhou S, Shi Y, Jiang L, Zhang Y, Yan D, Yang Q, Song Y, Cai R, Xu W. Molecular epidemiological characteristics of echovirus 6 in mainland China: extensive circulation of genotype F from 2007 to 2018. Arch Virol 2021; 166:1305-1312. [PMID: 33638089 PMCID: PMC8036204 DOI: 10.1007/s00705-020-04934-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 11/04/2020] [Indexed: 11/26/2022]
Abstract
Echovirus 6 (E6) is associated with various clinical diseases and is frequently detected in environmental sewage. Despite its high prevalence in humans and the environment, little is known about its molecular phylogeography in mainland China. In this study, 114 of 21,539 (0.53%) clinical specimens from hand, foot, and mouth disease (HFMD) cases collected between 2007 and 2018 were positive for E6. The complete VP1 sequences of 87 representative E6 strains, including 24 strains from this study, were used to investigate the evolutionary genetic characteristics and geographical spread of E6 strains. Phylogenetic analysis based on VP1 nucleotide sequence divergence showed that, globally, E6 strains can be grouped into six genotypes, designated A to F. Chinese E6 strains collected between 1988 and 2018 were found to belong to genotypes C, E, and F, with genotype F being predominant from 2007 to 2018. There was no significant difference in the geographical distribution of each genotype. The evolutionary rate of E6 was estimated to be 3.631 × 10-3 substitutions site-1 year-1 (95% highest posterior density [HPD]: 3.2406 × 10-3-4.031 × 10-3 substitutions site-1 year-1) by Bayesian MCMC analysis. The most recent common ancestor of the E6 genotypes was traced back to 1863, whereas their common ancestor in China was traced back to around 1962. A small genetic shift was detected in the Chinese E6 population size in 2009 according to Bayesian skyline analysis, which indicated that there might have been an epidemic around that year.
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Affiliation(s)
- Wenjun Cheng
- Medical School, Anhui University of Science and Technology, Huainan, 232001, Anhui, People's Republic of China
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Tianjiao Ji
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Shuaifeng Zhou
- Hunan Provincial Centers for Disease Control and Prevention, Changsha, People's Republic of China
| | - Yong Shi
- Jiangxi Provincial Centers for Disease Control and Prevention, Nanchang, People's Republic of China
| | - Lili Jiang
- Yunnan Provincial Centers for Disease Control and Prevention, Kunming, People's Republic of China
| | - Yong Zhang
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Dongmei Yan
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Qian Yang
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Yang Song
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Ru Cai
- Medical School, Anhui University of Science and Technology, Huainan, 232001, Anhui, People's Republic of China.
| | - Wenbo Xu
- Medical School, Anhui University of Science and Technology, Huainan, 232001, Anhui, People's Republic of China.
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China.
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23
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Majumdar M, Klapsa D, Wilton T, Bujaki E, Fernandez-Garcia MD, Faleye TOC, Oyero AO, Adewumi MO, Ndiaye K, Adeniji JA, Martin J. High Diversity of Human Non-Polio Enterovirus Serotypes Identified in Contaminated Water in Nigeria. Viruses 2021; 13:v13020249. [PMID: 33562806 PMCID: PMC7914538 DOI: 10.3390/v13020249] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 01/30/2021] [Accepted: 02/01/2021] [Indexed: 01/06/2023] Open
Abstract
Human enteroviruses (EVs) are highly prevalent in sewage and have been associated with human diseases with complications leading to severe neurological syndromes. We have used a recently developed molecular method to investigate the presence of EVs in eight samples collected in 2017–2018 from water streams contaminated by drainage channels in three different locations in Nigeria. A total of 93 human EV strains belonging to 45 different serotypes were identified, far exceeding the number of strains and serotypes found in similar samples in previous studies. Next generation sequencing analysis retrieved whole-capsid genomic nucleotide sequences of EV strains belonging to all four A, B, C, and D species. Our results further demonstrate the value of environmental surveillance for the detection of EV transmission of both serotypes commonly associated with clinical syndromes, such as EV-A71, and those that appear to circulate silently but could eventually cause outbreaks and disease. Several uncommon serotypes, rarely reported elsewhere, were detected such as EV-A119, EV-B87, EV-C116, and EV-D111. Ten EV serotypes were detected in Nigeria for the first time and two of them, CV-A12 and EV-B86, firstly described in Africa. This method can be expanded to generate whole-genome EV sequences as we show here for one EV-D111 strain. Our data revealed phylogenetic relationships of Nigerian sewage strains with EV strains reported elsewhere, mostly from African origin, and provided new insights into the whole-genome structure of emerging serotype EV-D111 and recombination events among EV-D serotypes.
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Affiliation(s)
- Manasi Majumdar
- Division of Virology, National Institute for Biological Standards and Control (NIBSC), Potters Bar EN6 3QG, Hertfordshire, UK; (M.M.); (D.K.); (T.W.); (E.B.)
| | - Dimitra Klapsa
- Division of Virology, National Institute for Biological Standards and Control (NIBSC), Potters Bar EN6 3QG, Hertfordshire, UK; (M.M.); (D.K.); (T.W.); (E.B.)
| | - Thomas Wilton
- Division of Virology, National Institute for Biological Standards and Control (NIBSC), Potters Bar EN6 3QG, Hertfordshire, UK; (M.M.); (D.K.); (T.W.); (E.B.)
| | - Erika Bujaki
- Division of Virology, National Institute for Biological Standards and Control (NIBSC), Potters Bar EN6 3QG, Hertfordshire, UK; (M.M.); (D.K.); (T.W.); (E.B.)
| | | | - Temitope Oluwasegun Cephas Faleye
- Department of Virology, Faculty of Basic Medical Sciences, College of Medicine, University of Ibadan, Ibadan, Oyo State, Nigeria; (T.O.C.F.); (M.O.A.); (J.A.A.)
| | | | - Moses Olubusuyi Adewumi
- Department of Virology, Faculty of Basic Medical Sciences, College of Medicine, University of Ibadan, Ibadan, Oyo State, Nigeria; (T.O.C.F.); (M.O.A.); (J.A.A.)
| | - Kader Ndiaye
- Department of Virology, Institute Pasteur, Dakar, Senegal; (M.D.F.-G.); (K.N.)
| | - Johnson Adekunle Adeniji
- Department of Virology, Faculty of Basic Medical Sciences, College of Medicine, University of Ibadan, Ibadan, Oyo State, Nigeria; (T.O.C.F.); (M.O.A.); (J.A.A.)
- World Health Organization National Polio Laboratory, Ibadan, Oyo State, Nigeria;
| | - Javier Martin
- Division of Virology, National Institute for Biological Standards and Control (NIBSC), Potters Bar EN6 3QG, Hertfordshire, UK; (M.M.); (D.K.); (T.W.); (E.B.)
- Correspondence:
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24
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Woodford L, Evans DJ. Deformed wing virus: using reverse genetics to tackle unanswered questions about the most important viral pathogen of honey bees. FEMS Microbiol Rev 2020; 45:6035241. [PMID: 33320949 DOI: 10.1093/femsre/fuaa070] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 12/11/2020] [Indexed: 12/31/2022] Open
Abstract
Deformed wing virus (DWV) is the most important viral pathogen of honey bees. It usually causes asymptomatic infections but, when vectored by the ectoparasitic mite Varroa destructor, it is responsible for the majority of overwintering colony losses globally. Although DWV was discovered four decades ago, research has been hampered by the absence of an in vitro cell culture system or the ability to culture pure stocks of the virus. The recent developments of reverse genetic systems for DWV go some way to addressing these limitations. They will allow the investigation of specific questions about strain variation, host tropism and pathogenesis to be answered, and are already being exploited to study tissue tropism and replication in Varroa and non-Apis pollinators. Three areas neatly illustrate the advances possible with reverse genetic approaches: (i) strain variation and recombination, in which reverse genetics has highlighted similarities rather than differences between virus strains; (ii) analysis of replication kinetics in both honey bees and Varroa, in studies that likely explain the near clonality of virus populations often reported; and (iii) pathogen spillover to non-Apis pollinators, using genetically tagged viruses to accurately monitor replication and infection.
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Affiliation(s)
- Luke Woodford
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, UK
| | - David J Evans
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, UK
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25
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Multiple genotypes of enterovirus G carrying a papain-like cysteine protease (PL-CP) sequence circulating on two pig farms in Japan: first identification of enterovirus G10 carrying a PL-CP sequence. Arch Virol 2020; 165:2909-2914. [PMID: 32951133 DOI: 10.1007/s00705-020-04816-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 08/18/2020] [Indexed: 10/23/2022]
Abstract
Two and three genotypes of enterovirus G (EV-G) carrying a papain-like cysteine protease (PL-CP) sequence were detected on two pig farms and classified into genotypes G1 and G10, and G1, G8, and G17, respectively, based on VP1 sequences. A G10 EV-G virus bearing a PL-CP sequence was detected for the first time. Phylogenetic analysis of the P2 and P3 regions grouped the viruses by farm with high sequence similarity. Furthermore, clear recombination break points were detected in the 2A region, suggesting that PL-CP EV-G-containing strains gained sequence diversity through recombination events among the multiple circulating EV-G genotypes on the farms.
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26
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Arhab Y, Bulakhov AG, Pestova TV, Hellen CU. Dissemination of Internal Ribosomal Entry Sites (IRES) Between Viruses by Horizontal Gene Transfer. Viruses 2020; 12:E612. [PMID: 32512856 PMCID: PMC7354566 DOI: 10.3390/v12060612] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/01/2020] [Accepted: 06/02/2020] [Indexed: 12/19/2022] Open
Abstract
Members of Picornaviridae and of the Hepacivirus, Pegivirus and Pestivirus genera of Flaviviridae all contain an internal ribosomal entry site (IRES) in the 5'-untranslated region (5'UTR) of their genomes. Each class of IRES has a conserved structure and promotes 5'-end-independent initiation of translation by a different mechanism. Picornavirus 5'UTRs, including the IRES, evolve independently of other parts of the genome and can move between genomes, most commonly by intratypic recombination. We review accumulating evidence that IRESs are genetic entities that can also move between members of different genera and even between families. Type IV IRESs, first identified in the Hepacivirus genus, have subsequently been identified in over 25 genera of Picornaviridae, juxtaposed against diverse coding sequences. In several genera, members have either type IV IRES or an IRES of type I, II or III. Similarly, in the genus Pegivirus, members contain either a type IV IRES or an unrelated type; both classes of IRES also occur in members of the genus Hepacivirus. IRESs utilize different mechanisms, have different factor requirements and contain determinants of viral growth, pathogenesis and cell type specificity. Their dissemination between viruses by horizontal gene transfer has unexpectedly emerged as an important facet of viral evolution.
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Affiliation(s)
| | | | | | - Christopher U.T. Hellen
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, NY 11203, USA; (Y.A.); (A.G.B.); (T.V.P.)
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27
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Abstract
Because of their replication mode and segmented dsRNA genome, homologous recombination is assumed to be rare in the rotaviruses. We analyzed 23,627 complete rotavirus genome sequences available in the NCBI Virus Variation database, and found 109 instances of homologous recombination, at least eleven of which prevailed across multiple sequenced isolates. In one case, recombination may have generated a novel rotavirus VP1 lineage. We also found strong evidence for intergenotypic recombination in which more than one sequence strongly supported the same event, particularly between different genotypes of segment 9, which encodes the glycoprotein, VP7. The recombined regions of many putative recombinants showed amino acid substitutions differentiating them from their major and minor parents. This finding suggests that these recombination events were not overly deleterious, since presumably these recombinants proliferated long enough to acquire adaptive mutations in their recombined regions. Protein structural predictions indicated that, despite the sometimes substantial amino acid replacements resulting from recombination, the overall protein structures remained relatively unaffected. Notably, recombination junctions appear to occur nonrandomly with hot spots corresponding to secondary RNA structures, a pattern seen consistently across segments. In total, we found strong evidence for recombination in nine of eleven rotavirus A segments. Only segments 7 (NSP3) and 11 (NSP5) did not show strong evidence of recombination. Collectively, the results of our computational analyses suggest that, contrary to the prevailing sentiment, recombination may be a significant driver of rotavirus evolution and may influence circulating strain diversity.
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Affiliation(s)
- Irene Hoxie
- Biology Department, Queens College of The City University of New York, 65-30 Kissena Blvd, Queens, NY 11367, USA.,The Graduate Center of The City University of New York, Biology Program, 365 5th Ave, New York, NY 10016, USA
| | - John J Dennehy
- Biology Department, Queens College of The City University of New York, 65-30 Kissena Blvd, Queens, NY 11367, USA.,The Graduate Center of The City University of New York, Biology Program, 365 5th Ave, New York, NY 10016, USA
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28
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Coutinho CRM, Siqueira JAM, Machado RS, Bandeira RDS, Ferreira JL, Alves JCDS, Gabbay YB, Tavares FN. Enterovirus detection and serotyping of fecal material collected from three children living on the outskirts of Belém city, Amazon region, Brazil, during the first 3 years of life (1983-1986). J Med Virol 2020; 92:1075-1084. [PMID: 31840822 DOI: 10.1002/jmv.25656] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 12/12/2019] [Indexed: 12/17/2022]
Abstract
In the current investigation, fecal material was obtained during a community-based longitudinal study conducted from 1983 to 1986. This study consisted of 71 children aged newborn to 3 years. A total of 216 samples from three of these children were screened by real-time quantitative polymerase chain reaction (RT-qPCR) for the presence of enteroviruses, and positive samples were serotyped by VP1 and VP3 sequencing of the viral genome. Of these, 12 (5.6%) came from symptomatic cases, and the remaining asymptomatic cases were collected fortnightly during the 3 years of study. A positivity of 63.4% (137/216) was obtained by RT-qPCR, with 58.3% (7/12) in relation to the symptomatic group and 63.7% (130/204) in relation to the asymptomatic group. The 137 positive samples were inoculated into the RD, HEp2C, and L20B cell lines, and the cytopathic effect was observed in 37.2% (51/137) samples. It was also possible to identify 40.9% (56/137), between isolated (n = 46) and nonisolated (n = 10). Enterovirus serotype diversity (n = 25) was identified in this study, with the predominant species being B (80.3%), followed by C (16.1%) and A (3.6%). Cases of reinfection by different serotypes were also observed in the three children studied. Analyses involving different age groups of these minors confirmed that the most affected age was between 12 to 24 months, with a prevalence of 77.6% (52/67). The enterovirus (EV) circulated in the 3 years of research, showed peaks in some months, without defined seasonality. This study demonstrated a high circulation and serotype diversity of EV in fecal samples, collected over 30 years ago. This endorsed the evaluation of important points of the epidemiology of these viruses, such as the presence of coinfection and reinfection of the same individual by different circulating serotypes. Understanding the frequency and duration of EV infections is important in determining their association with persistent diarrhea.
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Affiliation(s)
- Carla Rafaela Monteiro Coutinho
- Programa de Pós-graduação em Biologia Parasitária na Amazônia (PPGBPA), Universidade do Estado do Pará - UEPA, Belém, Pará, Brazil
| | - Jones Anderson Monteiro Siqueira
- Laboratório de Norovírus e outros Vírus Gastroentéricos-LNOV, Seção de Virologia-SAVIR, Instituto Evandro Chagas-IEC, Secretaria de Vigilância em Saúde, Ministério da Saúde, Ananindeua, Pará, Brazil
| | - Raiana Scerni Machado
- Laboratório de Enterovírus-LEV, Seção de Virologia-SAVIR, Instituto Evandro Chagas-IEC, Secretaria de Vigilância em Saúde, Ministério da Saúde, Ananindeua, Pará, Brazil
| | - Renato Da Silva Bandeira
- Laboratório de Rotavírus, Seção de Virologia-SAVIR, Instituto Evandro Chagas-IEC, Secretaria de Vigilância em Saúde, Ministério da Saúde, Ananindeua, Pará, Brazil
| | - James Lima Ferreira
- Laboratório de Enterovírus-LEV, Seção de Virologia-SAVIR, Instituto Evandro Chagas-IEC, Secretaria de Vigilância em Saúde, Ministério da Saúde, Ananindeua, Pará, Brazil
| | - Jainara Cristina Dos Santos Alves
- Laboratório de Enterovírus-LEV, Seção de Virologia-SAVIR, Instituto Evandro Chagas-IEC, Secretaria de Vigilância em Saúde, Ministério da Saúde, Ananindeua, Pará, Brazil
| | - Yvone Benchimol Gabbay
- Laboratório de Norovírus e outros Vírus Gastroentéricos-LNOV, Seção de Virologia-SAVIR, Instituto Evandro Chagas-IEC, Secretaria de Vigilância em Saúde, Ministério da Saúde, Ananindeua, Pará, Brazil
| | - Fernando Neto Tavares
- Laboratório de Enterovírus-LEV, Seção de Virologia-SAVIR, Instituto Evandro Chagas-IEC, Secretaria de Vigilância em Saúde, Ministério da Saúde, Ananindeua, Pará, Brazil
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Ryabov EV, Childers AK, Lopez D, Grubbs K, Posada-Florez F, Weaver D, Girten W, vanEngelsdorp D, Chen Y, Evans JD. Dynamic evolution in the key honey bee pathogen deformed wing virus: Novel insights into virulence and competition using reverse genetics. PLoS Biol 2019; 17:e3000502. [PMID: 31600204 PMCID: PMC6805011 DOI: 10.1371/journal.pbio.3000502] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 10/22/2019] [Accepted: 09/20/2019] [Indexed: 12/23/2022] Open
Abstract
The impacts of invertebrate RNA virus population dynamics on virulence and infection outcomes are poorly understood. Deformed wing virus (DWV), the main viral pathogen of honey bees, negatively impacts bee health, which can lead to colony death. Despite previous reports on the reduction of DWV diversity following the arrival of the parasitic mite Varroa destructor, the key DWV vector, we found high genetic diversity of DWV in infested United States honey bee colonies. Phylogenetic analysis showed that divergent US DWV genotypes are of monophyletic origin and were likely generated as a result of diversification after a genetic bottleneck. To investigate the population dynamics of this divergent DWV, we designed a series of novel infectious cDNA clones corresponding to coexisting DWV genotypes, thereby devising a reverse-genetics system for an invertebrate RNA virus quasispecies. Equal replication rates were observed for all clone-derived DWV variants in single infections. Surprisingly, individual clones replicated to the same high levels as their mixtures and even the parental highly diverse natural DWV population, suggesting that complementation between genotypes was not required to replicate to high levels. Mixed clone–derived infections showed a lack of strong competitive exclusion, suggesting that the DWV genotypes were adapted to coexist. Mutational and recombination events were observed across clone progeny, providing new insights into the forces that drive and constrain virus diversification. Accordingly, our results suggest that Varroa influences DWV dynamics by causing an initial selective sweep, which is followed by virus diversification fueled by negative frequency-dependent selection for new genotypes. We suggest that this selection might reflect the ability of rare lineages to evade host defenses, specifically antiviral RNA interference (RNAi). In support of this hypothesis, we show that RNAi induced against one DWV strain is less effective against an alternate strain from the same population. Deformed wing virus, a key pathogen of honey bees, shows rapid diversification after genetic bottlenecks; a novel reverse-genetic system provides insights into the forces that shape virus diversity, suggesting that virus quasi-species diversification may be driven by selection of genotypes capable of evading host RNAi defences.
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Affiliation(s)
- Eugene V. Ryabov
- Bee Research Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland, United States of America
- * E-mail: ,
| | - Anna K. Childers
- Bee Research Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland, United States of America
| | - Dawn Lopez
- Bee Research Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland, United States of America
| | - Kyle Grubbs
- Bee Research Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland, United States of America
| | - Francisco Posada-Florez
- Bee Research Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland, United States of America
| | - Daniel Weaver
- Bee Research Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland, United States of America
- Beeweaver Apiaries, Navasota, Texas, United States of America
| | - William Girten
- Bee Research Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland, United States of America
- Department of Chemistry, Fort Lewis College, Durango, Colorado, United States of America
| | - Dennis vanEngelsdorp
- Department of Entomology, University of Maryland, College Park, Maryland, United States of America
| | - Yanping Chen
- Bee Research Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland, United States of America
| | - Jay D. Evans
- Bee Research Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, Maryland, United States of America
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Muslin C, Mac Kain A, Bessaud M, Blondel B, Delpeyroux F. Recombination in Enteroviruses, a Multi-Step Modular Evolutionary Process. Viruses 2019; 11:E859. [PMID: 31540135 PMCID: PMC6784155 DOI: 10.3390/v11090859] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 09/05/2019] [Accepted: 09/06/2019] [Indexed: 01/15/2023] Open
Abstract
RNA recombination is a major driving force in the evolution and genetic architecture shaping of enteroviruses. In particular, intertypic recombination is implicated in the emergence of most pathogenic circulating vaccine-derived polioviruses, which have caused numerous outbreaks of paralytic poliomyelitis worldwide. Recent experimental studies that relied on recombination cellular systems mimicking natural genetic exchanges between enteroviruses provided new insights into the molecular mechanisms of enterovirus recombination and enabled to define a new model of genetic plasticity for enteroviruses. Homologous intertypic recombinant enteroviruses that were observed in nature would be the final products of a multi-step process, during which precursor nonhomologous recombinant genomes are generated through an initial inter-genomic RNA recombination event and can then evolve into a diversity of fitter homologous recombinant genomes over subsequent intra-genomic rearrangements. Moreover, these experimental studies demonstrated that the enterovirus genome could be defined as a combination of genomic modules that can be preferentially exchanged through recombination, and enabled defining the boundaries of these recombination modules. These results provided the first experimental evidence supporting the theoretical model of enterovirus modular evolution previously elaborated from phylogenetic studies of circulating enterovirus strains. This review summarizes our current knowledge regarding the mechanisms of recombination in enteroviruses and presents a new evolutionary process that may apply to other RNA viruses.
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Affiliation(s)
- Claire Muslin
- One Health Research Group, Faculty of Health Sciences, Universidad de las Américas, Quito EC170125, Pichincha, Ecuador.
| | - Alice Mac Kain
- Institut Pasteur, Viral Populations and Pathogenesis Unit, CNRS UMR 3569, 75015 Paris, France.
| | - Maël Bessaud
- Institut Pasteur, Viral Populations and Pathogenesis Unit, CNRS UMR 3569, 75015 Paris, France.
| | - Bruno Blondel
- Institut Pasteur, Biology of Enteric Viruses Unit, 75015 Paris, France.
- INSERM U994, Institut National de la Santé et de la Recherche Médicale, 75015 Paris, France.
| | - Francis Delpeyroux
- Institut Pasteur, Biology of Enteric Viruses Unit, 75015 Paris, France.
- INSERM U994, Institut National de la Santé et de la Recherche Médicale, 75015 Paris, France.
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High Permissiveness for Genetic Exchanges between Enteroviruses of Species A, including Enterovirus 71, Favors Evolution through Intertypic Recombination in Madagascar. J Virol 2019; 93:JVI.01667-18. [PMID: 30602612 DOI: 10.1128/jvi.01667-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Accepted: 12/18/2018] [Indexed: 12/30/2022] Open
Abstract
Human enteroviruses of species A (EV-A) are the leading cause of hand-foot-and-mouth disease (HFMD). EV-A71 is frequently implicated in HFMD outbreaks and can also cause severe neurological manifestations. We investigated the molecular epidemiological processes at work and the contribution of genetic recombination to the evolutionary history of EV-A in Madagascar, focusing on the recently described EV-A71 genogroup F in particular. Twenty-three EV-A isolates, collected mostly in 2011 from healthy children living in various districts of Madagascar, were characterized by whole-genome sequencing. Eight different types were identified, highlighting the local circulation and diversity of EV-A. Comparative genome analysis revealed evidence of frequent recent intra- and intertypic genetic exchanges between the noncapsid sequences of Madagascan EV-A isolates. The three EV-A71 isolates had different evolutionary histories in terms of recombination, with one isolate displaying a mosaic genome resulting from recent genetic exchanges with Madagascan coxsackieviruses A7 and possibly A5 and A10 or common ancestors. The engineering and characterization of recombinants generated from progenitors belonging to different EV-A types or EV-A71 genogroups with distantly related nonstructural sequences indicated a high level of permissiveness for intertypic genetic exchange in EV-A. This permissiveness suggests that the primary viral functions associated with the nonstructural sequences have been highly conserved through the diversification and evolution of the EV-A species. No outbreak of disease due to EV-A has yet been reported in Madagascar, but the diversity, circulation, and evolution of these viruses justify surveillance of EV-A circulation and HFMD cases to prevent possible outbreaks due to emerging strains.IMPORTANCE Human enteroviruses of species A (EV-A), including EV-A71, are the leading cause of hand-foot-and-mouth disease (HFMD) and may also cause severe neurological manifestations. We investigated the circulation and molecular evolution of EV-A in Madagascar, focusing particularly on the recently described EV-A71 genogroup F. Eight different types, collected mostly in 2011, were identified, highlighting the local circulation and diversity of EV-A. Comparative genome analysis revealed evidence of frequent genetic exchanges between the different types of isolates. The three EV-A71 isolates had different evolutionary histories in terms of recombination. The engineering and characterization of recombinants involving progenitors belonging to different EV-A types indicated a high degree of permissiveness for genetic exchange in EV-A. No outbreak of disease due to EV-A has yet been reported in Madagascar, but the diversity, circulation, and evolution of these viruses justify the surveillance of EV-A circulation to prevent possible HFMD outbreaks due to emerging strains.
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Molecular Epidemiology of Echovirus 18 Circulating in Mainland China from 2015 to 2016. Virol Sin 2019; 34:50-58. [PMID: 30790201 DOI: 10.1007/s12250-018-0080-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 11/26/2018] [Indexed: 10/27/2022] Open
Abstract
Echovirus 18 (E18), a serotype of Enterovirus B (EV-B) species, is an important pathogen in aseptic meningitis. E18 had rarely been detected in mainland China, but became the predominant pathogen associated with viral encephalitis (VE) and meningitis in Hebei province for the first time in 2015. To investigate the molecular epidemiology and genetic characteristics of E18 in mainland China, sixteen E18 strains from patient throat swabs with hand, foot, and mouth disease (HFMD) in six provinces in China collected between 2015 and 2016, and four E18 strains isolated from 18 patient cerebrospinal fluid specimens with VE in Hebei Province in 2015 were obtained and sequenced. Combined with the sequences from the GenBank database, we performed an extensive genetic analysis. Phylogenetic analysis of VP1 gene sequences revealed that all E18 strains from mainland China after 2015 belonged to subgenotype C2. There were no obvious specific differences in phylogenetic and variation analyses of E18 genome sequences between HFMD and VE/meningitis strains. Potential multiple recombination may have occurred in the 5'-untranslated region and in the P2 and P3 nonstructural protein-encoding regions of E18 strains from China. The current E18 strains were potential multiple-recombinant viruses. Overall, these findings supported that E18 caused HFMD, VE, and meningitis, although there were no significant associations between clinical features and viral genomic characteristics.
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Lamari A, Triki H, Driss N, Touzi H, Meddeb Z, Ben Yahia A, Barbouche MR, Rezig D. Iterative Excretion of Human Cosaviruses from Different Genotypes Associated with Combined Immunodeficiency Disorder. Intervirology 2019; 61:247-254. [PMID: 30726837 DOI: 10.1159/000495182] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 10/15/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Human cosaviruses (HCoSVs) are newly discovered enteric viruses in the Picornaviridae family. They have been described in non-polio acute flaccid paralysis, diarrheal patients, and healthy individuals. They remain rarely documented in immunodeficient patients. OBJECTIVES This study reports iterative excretion of HCoSVs in a patient with major histocompatibility complex (MHC) class II combined immunodeficiency, a relatively common primary immunodeficiency in consanguineous settings. METHODS A total of 35 samples were collected from a patient followed for oral polio vaccine strains detection in stool samples during a 57-month period. Detection of HCoSVs in stools was performed by nested RT-PCR in the 5' noncoding region. The genotype identification and screening for recombinant strains was performed by sequencing in the VP1 and 3D genomic regions followed by phylogenetic analysis. RESULTS The patient was infected with HCoSVs twice at a 3-year interval. The excreted viruses belonged to 2 different genotypes with 2 probable recombinant viruses. During HCoSV infections, the patient was also excreting Sabin-related polioviruses. CONCLUSIONS This study describes excretion kinetics and genetic characteristics of HCoSVs in a patient with combined immunodeficiency due to MHC class II expression defect. The patient did not have concomitant symptoms related to the HCoSV infection.
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Affiliation(s)
- Asma Lamari
- Faculty of Sciences, University of Tunis El Manar, Tunis, Tunisia.,WHO Regional Reference Laboratory for Poliomyelitis and Measles, Laboratory of Clinical Virology, Pasteur Institute of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Henda Triki
- WHO Regional Reference Laboratory for Poliomyelitis and Measles, Laboratory of Clinical Virology, Pasteur Institute of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Nadia Driss
- WHO Regional Reference Laboratory for Poliomyelitis and Measles, Laboratory of Clinical Virology, Pasteur Institute of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Henda Touzi
- WHO Regional Reference Laboratory for Poliomyelitis and Measles, Laboratory of Clinical Virology, Pasteur Institute of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Zina Meddeb
- WHO Regional Reference Laboratory for Poliomyelitis and Measles, Laboratory of Clinical Virology, Pasteur Institute of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Ahlem Ben Yahia
- WHO Regional Reference Laboratory for Poliomyelitis and Measles, Laboratory of Clinical Virology, Pasteur Institute of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Mohamed-Ridha Barbouche
- Laboratory of Immunology, Pasteur Institute of Tunis and Faculty of Medicine, University of Tunis El Manar, Tunis, Tunisia
| | - Dorra Rezig
- WHO Regional Reference Laboratory for Poliomyelitis and Measles, Laboratory of Clinical Virology, Pasteur Institute of Tunis, University of Tunis El Manar, Tunis, Tunisia,
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34
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Nikolaidis M, Mimouli K, Kyriakopoulou Z, Tsimpidis M, Tsakogiannis D, Markoulatos P, Amoutzias GD. Large-scale genomic analysis reveals recurrent patterns of intertypic recombination in human enteroviruses. Virology 2019; 526:72-80. [DOI: 10.1016/j.virol.2018.10.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 10/04/2018] [Accepted: 10/04/2018] [Indexed: 12/21/2022]
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Genetic diversity of the enteroviruses detected from cerebrospinal fluid (CSF) samples of patients with suspected aseptic meningitis in northern West Bank, Palestine in 2017. PLoS One 2018; 13:e0202243. [PMID: 30532168 PMCID: PMC6287809 DOI: 10.1371/journal.pone.0202243] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 11/21/2018] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Human enterovirus genus showed a wide range of genetic diversity. OBJECTIVES To investigate the genetic diversity of the enteroviruses isolated in 2017 in northern West Bank, Palestine. STUDY DESIGN 249 CSF samples from aseptic meningitis cases were investigated for HEV using two RT-PCR protocols targeting the 5' NCR and the VP1 region of the HEV genome. The phylogenetic characterization of the sequenced VP1 region of Echovirus18 (E18) and Coxsackievirus B5 (CVB5) isolated in Palestine along with 27 E18 and 27 CVB5 sequences available from the Genbank were described. RESULTS E18 and CVB5 account for 50% and 35% of the successfully HEV types, respectively. Phylogenetic tree of E18 and CVB5 showed three main clusters, with all Palestinian isolates uniquely clustering together with those from China and from different countries, respectively. Cluster I of E18, with 13 Palestinian and 6 Chinese isolates, showed the lowest haplotype-to-sequence ratio (0.6:1), haplotype diversity (Hd), nucleotide diversity (π), and number of segregating sites (S) compared to clusters II and III. Furthermore, cluster I showed negative Tajima's D and Fu-Li'sF tests with statistically significant departure from neutrality (P<0.01). In both E18 and CVB5 populations, high haplotype diversity, but low genetic diversity was evident. Inter-population pairwise genetic distance (Fst) and gene flow (Nm) showed that the Palestinian E18 and CVB5 clusters were highly differentiated from the other clusters. CONCLUSIONS The study divulged close genetic relationship between Palestinian HEV strains as confirmed by population genetics and phylogenetic analyses.
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Cinek O, Kramna L, Mazankova K, Kunteová K, Chudá K, C J Claas E, Stene LC, Tapia G. Virus genotyping by massive parallel amplicon sequencing: adenovirus and enterovirus in the Norwegian MIDIA study. J Med Virol 2018; 91:606-614. [PMID: 30537228 DOI: 10.1002/jmv.25361] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 11/04/2018] [Indexed: 01/30/2023]
Abstract
OBJECTIVES Direct genotyping of adenovirus or enterovirus from clinical material using polymerase chain reaction (PCR) followed by Sanger sequencing is often difficult due to the presence of multiple virus types in a sample, or due to varying efficacy of PCR amplifying the capsid gene on the background of foreign nucleic acids. Here we present a simple protocol for virus genotyping using massive parallel amplicon sequencing. METHODS The protocol utilized a set of 16 tailed degenerate primers flanking the seventh hypervariable region of the adenovirus hexon gene and 9 tailed degenerate primers targeted to the proximal portion of the enterovirus VP1 gene. Subsequent addition of dual indices enabled simultaneous sequencing of 384 different samples on an Illumina MiSeq instrument. Downstream bioinformatic analysis was based on remapping to a set of references representative of the presently known repertoire of virus types. RESULTS After validation with known virus types, the sequencing method was applied on 301 adenovirus-positive samples and 350 enterovirus-positive samples from a longitudinally collected series of stools from 83 children aged 3 to 36 months. We detected 7 different adenovirus types and 27 different enterovirus types. There were 37 (6.2%) samples containing more than one genotype of the same viral genus. At least one dual infection was experienced by 23 of 83 (28%) of the children observed over the 3 years' observation period. CONCLUSIONS Amplicon sequencing with a multiplex set of degenerate primers seems to be a rapid and reliable technical solution for genotyping of large collections of samples where simultaneous infections with multiple strains can be expected.
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Affiliation(s)
- Ondrej Cinek
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University in Prague and University Hospital Motol, Prague, Czech Republic
| | - Lenka Kramna
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University in Prague and University Hospital Motol, Prague, Czech Republic
| | - Karla Mazankova
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University in Prague and University Hospital Motol, Prague, Czech Republic
| | - Kateřina Kunteová
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University in Prague and University Hospital Motol, Prague, Czech Republic
| | - Kateřina Chudá
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University in Prague and University Hospital Motol, Prague, Czech Republic
| | - Eric C J Claas
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Lars C Stene
- Division of Mental and Physical Health, Department of Chronic Diseases and Ageing, Norwegian Institute of Public Health, Oslo, Norway
| | - German Tapia
- Division of Mental and Physical Health, Department of Chronic Diseases and Ageing, Norwegian Institute of Public Health, Oslo, Norway
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Lee S, Lee C. First detection of novel enterovirus G recombining a torovirus papain-like protease gene associated with diarrhoea in swine in South Korea. Transbound Emerg Dis 2018; 66:1023-1028. [PMID: 30431236 PMCID: PMC7168547 DOI: 10.1111/tbed.13073] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 10/17/2018] [Accepted: 11/08/2018] [Indexed: 01/02/2023]
Abstract
Enterovirus species G (EV-G) comprises a highly diversity of 20 genotypes that is prevalent in pig populations, with or without diarrhoea. In the present study, a novel EV-G strain (KOR/KNU-1811/2018) that resulted from cross-order recombination was discovered in diagnostic faecal samples from neonatal pigs with diarrhoea that were negative for swine enteric coronaviruses and rotavirus. The recombinant EV-G genome possessed an exogenous 594-nucleotide (198-amino acid) sequence, flanked by two viral 3Cpro cleavage sites at the 5' and 3' ends in its 2C/3A junction region. This insertion encoded a predicted protease similar to the porcine torovirus papain-like cysteine protease (PLCP), which was recently found in the EV-G1, -G2, and -G17 genomes. The complete KNU-1811 genome shared 73.7% nucleotide identity with a prototype EV-G1 strain, but had 83.9%-86.7% sequence homology with the global EV-G1-PLCP strains. Genetic and phylogenetic analyses demonstrated that the Korean recombinant EV-G's own VP1 and inserted foreign PLCP genes are most closely related independently to contemporary chimeric G1-PLCP and G17-PLCP strains respectively. These results implied that the torovirus-derived PLCP gene might have undergone continuous nucleotide mutations in the respective EV-G genome following its independent acquisition through naturally occurring recombination. Our results advance the understanding of the genetic evolution of EV-G driven by infrequent viral recombination events, by which EV-G populations laterally gain an exotic gene encoding a virulence factor from heterogeneous virus families, thereby causing clinical disease in swine.
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Affiliation(s)
- Sunhee Lee
- Animal Virology Laboratory, School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu, Korea
| | - Changhee Lee
- Animal Virology Laboratory, School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu, Korea
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Lukashev AN, Vakulenko YA, Turbabina NA, Deviatkin AA, Drexler JF. Molecular epidemiology and phylogenetics of human enteroviruses: Is there a forest behind the trees? Rev Med Virol 2018; 28:e2002. [PMID: 30069956 DOI: 10.1002/rmv.2002] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 06/28/2018] [Accepted: 07/01/2018] [Indexed: 11/05/2022]
Abstract
Enteroviruses are among the best studied small non-enveloped enteric RNA viruses. Most enteroviruses are easy to isolate in cell culture, and many non-polio enterovirus strains were archived worldwide as a byproduct of the WHO poliovirus surveillance system. Common outbreaks and epidemics, most prominently the epidemic of hand-foot-and-mouth disease with severe neurological complications in East and South-East Asia, justify practical interest of non-polio enteroviruses. As a result, there are over 50 000 enterovirus nucleotide sequences available in GenBank. Technical possibilities have been also improving, as Bayesian phylogenetic methods with an integrated molecular clock were introduced a decade ago and provided unprecedented opportunities for phylogenetic analysis. As a result, hundreds of papers were published on the molecular epidemiology of enteroviruses. This review covers the modern methodology, structure, and biases of the sequence dataset available in GenBank. The relevance of the subtype classification, findings of co-circulation of multiple genetic variants, previously unappreciated complexity of viral populations, and global evolutionary patterns are addressed. The most relevant conclusions and prospects for further studies on outbreak emergence mechanisms are discussed.
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Affiliation(s)
- Alexander N Lukashev
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, Moscow, Russia.,Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Preparations, Moscow, Russia
| | - Yulia A Vakulenko
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, Moscow, Russia.,Virology Department, Biological Faculty, Lomonosov Moscow State University, Moscow, Russia
| | - Natalia A Turbabina
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, Moscow, Russia
| | | | - Jan Felix Drexler
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin, Germany
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39
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Cobbin JCA, Britton PN, Burrell R, Thosar D, Selvakumar K, Eden JS, Jones CA, Holmes EC. A complex mosaic of enteroviruses shapes community-acquired hand, foot and mouth disease transmission and evolution within a single hospital. Virus Evol 2018; 4:vey020. [PMID: 30026965 PMCID: PMC6047454 DOI: 10.1093/ve/vey020] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Human enteroviruses (EV) pose a major risk to public health. This is especially so in the Asia-Pacific region where increasing numbers of hand, foot and mouth disease (HFMD) cases and large outbreaks of severe neurological disease associated with EV-A71 have occurred. Despite their importance, key aspects of the emergence, epidemiology and evolution of EVs remain unclear, and most studies of EV evolution have focused on a limited number of genes. Here, we describe the genomic-scale evolution of EV-A viruses sampled from pediatric patients with mild disease attending a single hospital in western Sydney, Australia, over an 18-month period. This analysis revealed the presence of eight viral serotypes-Coxsackievirus (CV) A2, A4, A5, A6, A8, A10, A16 and EV-A71-with up to four different serotypes circulating in any 1 month. Despite an absence of large-scale outbreaks, high levels of geographical and temporal mixing of serotypes were identified. Phylogenetic analysis revealed that multiple strains of the same serotype were present in the community, and that this diversity was shaped by multiple introductions into the Sydney population, with only a single lineage of CV-A6 exhibiting in situ transmission over the entire study period. Genomic-scale analyses also revealed the presence of novel and historical EV recombinants. Notably, our analysis revealed no association between viral phylogeny, including serotype, and patient age, sex, nor disease severity (for uncomplicated disease). This study emphasizes the contribution of EV-A viruses other than EV-A71 to mild EV disease including HFMD in Australia and highlights the need for greater surveillance of these viruses to improve strategies for outbreak preparedness and vaccine design.
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Affiliation(s)
- Joanna C A Cobbin
- School of Life and Environmental Sciences, Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
| | - Philip N Britton
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School, The University of Sydney, Sydney, NSW, Australia.,The Children's Hospital at Westmead, Westmead, NSW, Australia.,Kids Research, Sydney Children's Hospitals Network (Westmead), Westmead, NSW, Australia
| | - Rebecca Burrell
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School, The University of Sydney, Sydney, NSW, Australia.,Kids Research, Sydney Children's Hospitals Network (Westmead), Westmead, NSW, Australia
| | - Deepali Thosar
- Kids Research, Sydney Children's Hospitals Network (Westmead), Westmead, NSW, Australia
| | - Kierrtana Selvakumar
- Kids Research, Sydney Children's Hospitals Network (Westmead), Westmead, NSW, Australia
| | - John-Sebastian Eden
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School, The University of Sydney, Sydney, NSW, Australia.,The Westmead Institute for Medical Research, Westmead, NSW, Australia
| | - Cheryl A Jones
- The Westmead Institute for Medical Research, Westmead, NSW, Australia.,Royal Children's Hospital, Melbourne, VIC, Australia.,Murdoch Children's Research Institute and University of Melbourne, Melbourne, VIC, Australia
| | - Edward C Holmes
- School of Life and Environmental Sciences, Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
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40
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Lewandowska DW, Capaul R, Prader S, Zagordi O, Geissberger FD, Kügler M, Knorr M, Berger C, Güngör T, Reichenbach J, Shah C, Böni J, Zbinden A, Trkola A, Pachlopnik Schmid J, Huber M. Persistent mammalian orthoreovirus, coxsackievirus and adenovirus co-infection in a child with a primary immunodeficiency detected by metagenomic sequencing: a case report. BMC Infect Dis 2018; 18:33. [PMID: 29325543 PMCID: PMC5765704 DOI: 10.1186/s12879-018-2946-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 01/04/2018] [Indexed: 12/19/2022] Open
Abstract
Background We report a rare case of Mammalian orthoreovirus (MRV) infection in a child with a primary immunodeficiency (PID). Infections with Mammalian orthoreovirus are very rare and probably of zoonotic origin. Only a few cases have been described so far, including one with similar pathogenesis as in our case. Case presentation The patient, age 11, presented with flu-like symptoms and persistent severe diarrhea. Enterovirus has been detected over several months, however, exact typing of a positive cell culture remained inconclusive. Unbiased metagenomic sequencing then detected MRV in stool samples from several time points. The sequencing approach further revealed co-infection with a recombinant Coxsackievirus and Adenovirus. MRV-specific antibodies detected by immunofluorescence proved that the patient seroconverted. Conclusion This case highlights the potential of unbiased metagenomic sequencing in supplementing routine diagnostic methods, especially in situations of chronic infection with multiple viruses as seen here in an immunocompromised host. The origin, transmission routes and implications of MRV infection in humans merit further investigation. Electronic supplementary material The online version of this article (10.1186/s12879-018-2946-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dagmara W Lewandowska
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Riccarda Capaul
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Seraina Prader
- Division of Immunology, University Children's Hospital Zurich, Steinwiesstrasse 75, 8032, Zurich, Switzerland
| | - Osvaldo Zagordi
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | | | - Martin Kügler
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.,Present address: Unilabs, Ringstrasse 12, 8600, Dübendorf, Switzerland
| | - Marcus Knorr
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Christoph Berger
- Division of Infectious Diseases and Hospital Epidemiology, University Children's Hospital Zurich, Steinwiesstrasse 75, 8032, Zurich, Switzerland
| | - Tayfun Güngör
- Division of Stem Cell Transplantation, University Children's Hospital Zurich, Rämistrasse 100, 8091, Zurich, Switzerland
| | - Janine Reichenbach
- Division of Immunology, University Children's Hospital Zurich, Steinwiesstrasse 75, 8032, Zurich, Switzerland
| | - Cyril Shah
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Jürg Böni
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Andrea Zbinden
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Jana Pachlopnik Schmid
- Division of Immunology, University Children's Hospital Zurich, Steinwiesstrasse 75, 8032, Zurich, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
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41
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Tsuchiaka S, Naoi Y, Imai R, Masuda T, Ito M, Akagami M, Ouchi Y, Ishii K, Sakaguchi S, Omatsu T, Katayama Y, Oba M, Shirai J, Satani Y, Takashima Y, Taniguchi Y, Takasu M, Madarame H, Sunaga F, Aoki H, Makino S, Mizutani T, Nagai M. Genetic diversity and recombination of enterovirus G strains in Japanese pigs: High prevalence of strains carrying a papain-like cysteine protease sequence in the enterovirus G population. PLoS One 2018; 13:e0190819. [PMID: 29324778 PMCID: PMC5764308 DOI: 10.1371/journal.pone.0190819] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 12/20/2017] [Indexed: 11/18/2022] Open
Abstract
To study the genetic diversity of enterovirus G (EV-G) among Japanese pigs, metagenomics sequencing was performed on fecal samples from pigs with or without diarrhea, collected between 2014 and 2016. Fifty-nine EV-G sequences, which were >5,000 nucleotides long, were obtained. By complete VP1 sequence analysis, Japanese EV-G isolates were classified into G1 (17 strains), G2 (four strains), G3 (22 strains), G4 (two strains), G6 (two strains), G9 (six strains), G10 (five strains), and a new genotype (one strain). Remarkably, 16 G1 and one G2 strain identified in diarrheic (23.5%; four strains) or normal (76.5%; 13 strains) fecal samples possessed a papain-like cysteine protease (PL-CP) sequence, which was recently found in the USA and Belgium in the EV-G genome, at the 2C–3A junction site. This paper presents the first report of the high prevalence of viruses carrying PL-CP in the EV-G population. Furthermore, possible inter- and intragenotype recombination events were found among EV-G strains, including G1-PL-CP strains. Our findings may advance the understanding of the molecular epidemiology and genetic evolution of EV-Gs.
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Affiliation(s)
- Shinobu Tsuchiaka
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Yuki Naoi
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Ryo Imai
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Tsuneyuki Masuda
- Kurayoshi Livestock Hygiene Service Center, Kurayoshi, Tottori, Japan
| | - Mika Ito
- Ishikawa Nanbu Livestock Hygiene Service Center, Kanazawa, Ishikawa, Japan
| | | | - Yoshinao Ouchi
- Kenpoku Livestock Hygiene Service Center, Mito, Ibaraki, Japan
| | - Kazuo Ishii
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Shoichi Sakaguchi
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Tsutomu Omatsu
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Yukie Katayama
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Mami Oba
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Junsuke Shirai
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Yuki Satani
- Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Yanagido, Gifu, Japan
| | - Yasuhiro Takashima
- Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Yanagido, Gifu, Japan
- Education and Research Center for Food Animal Health, Gifu University (GeFAH), Gifu, Japan
- Center for Highly Advanced Integration of Nano and Life Sciences, Gifu University (G-CHAIN), Gifu, Japan
| | - Yuji Taniguchi
- Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Yanagido, Gifu, Japan
| | - Masaki Takasu
- Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Yanagido, Gifu, Japan
| | - Hiroo Madarame
- Laboratory of Small Animal Clinics, School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa, Japan
| | - Fujiko Sunaga
- Department of Veterinary Medicine, School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa, Japan
| | - Hiroshi Aoki
- Faculty of Veterinary Science, Nippon Veterinary and Life Science University, Musashino, Tokyo, Japan
| | - Shinji Makino
- Department of Microbiology and Immunology, The University of Texas Medical Branch at Galveston, Galveston, Texas, United States of America
| | - Tetsuya Mizutani
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
- * E-mail: (TM); (MN)
| | - Makoto Nagai
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
- Department of Bioproduction Science, Ishikawa Prefectural University, Nonoichi, Ishikawa, Japan
- * E-mail: (TM); (MN)
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42
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Lukashev AN, Vakulenko YA. Molecular evolution of types in non-polio enteroviruses. J Gen Virol 2017; 98:2968-2981. [PMID: 29095688 DOI: 10.1099/jgv.0.000966] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Non-polio enteroviruses are a ubiquitous and divergent group of non-enveloped RNA viruses. Novel types are reported regularly in addition to over 100 known types; however, mechanisms of emergence of novel types remain obscure. Here, the 33 most common types represented by 35-629 non-redundant partial VP1 sequences in GenBank were studied in parallel using Bayesian coalescent molecular clock analysis to investigate common evolutionary trends among enterovirus types. Inferred substitution rates were in the range of 0.41×10-2 to 3.07×10-2 substitutions per site per year. The most recent common ancestors of known isolates of each type presumably existed between 55 and 200 years ago. Phylogenetic analysis results suggested that global type populations underwent bottlenecks that could repeatedly reset the common ancestor dates. Nevertheless, species-level analysis suggested that the contemporary enterovirus types emerged within the last millennium. Analysis of 2657 complete VP1 sequences of the 24 most common types indicated that the type criterion based upon 75 % nucleotide sequence identity remains generally valid, despite exponential growth of the number of known sequences and a high rate of mutation fixation. However, in few types there was evidence that enteroviruses can drift slightly beyond the type threshold, up to 73 % identity, and both amino acid and nucleotide sequences should be considered for type identification. Analysis of sequence distances within types implied that sequence-identity-based identification of genotypes is rational within some, but not all, types and distinct genotype cut-offs (9-20 %) may be useful for different types.
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Affiliation(s)
- Alexander N Lukashev
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, Moscow, Russia.,Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products, Moscow, Russia
| | - Yulia A Vakulenko
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products, Moscow, Russia.,Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
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43
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Kyriakopoulou Z, Amoutzias GD, Dimitriou TG, Tsakogiannis D, Mossialos D, Markoulatos P. Intra- and inter-serotypic recombinations in the 5΄ UTR-VP4 region of Echovirus 30 strains. Arch Virol 2017; 163:365-375. [DOI: 10.1007/s00705-017-3600-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 09/06/2017] [Indexed: 12/23/2022]
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44
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A Naturally Occurring Recombinant Enterovirus Expresses a Torovirus Deubiquitinase. J Virol 2017; 91:JVI.00450-17. [PMID: 28490584 DOI: 10.1128/jvi.00450-17] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 04/26/2017] [Indexed: 11/20/2022] Open
Abstract
Enteroviruses (EVs) are implicated in a wide range of diseases in humans and animals. In this study, a novel enterovirus (enterovirus species G [EVG]) (EVG 08/NC_USA/2015) was isolated from a diagnostic sample from a neonatal pig diarrhea case and identified by using metagenomics and complete genome sequencing. The viral genome shares 75.4% nucleotide identity with a prototypic EVG strain (PEV9 UKG/410/73). Remarkably, a 582-nucleotide insertion, flanked by 3Cpro cleavage sites at the 5' and 3' ends, was found in the 2C/3A junction region of the viral genome. This insertion encodes a predicted protease with 54 to 68% amino acid identity to torovirus (ToV) papain-like protease (PLP) (ToV-PLP). Structural homology modeling predicts that this protease adopts a fold and a catalytic site characteristic of minimal PLP catalytic domains. This structure is similar to those of core catalytic domains of the foot-and-mouth disease virus leader protease and coronavirus PLPs, which act as deubiquitinating and deISGylating (interferon [IFN]-stimulated gene 15 [ISG15]-removing) enzymes on host cell substrates. Importantly, the recombinant ToV-PLP protein derived from this novel enterovirus also showed strong deubiquitination and deISGylation activities and demonstrated the ability to suppress IFN-β expression. Using reverse genetics, we generated a ToV-PLP knockout recombinant virus. Compared to the wild-type virus, the ToV-PLP knockout mutant virus showed impaired growth and induced higher expression levels of innate immune genes in infected cells. These results suggest that ToV-PLP functions as an innate immune antagonist; enterovirus G may therefore gain fitness through the acquisition of ToV-PLP from a recombination event.IMPORTANCE Enteroviruses comprise a highly diversified group of viruses. Genetic recombination has been considered a driving force for viral evolution; however, recombination between viruses from two different orders is a rare event. In this study, we identified a special case of cross-order recombination between enterovirus G (order Picornavirales) and torovirus (order Nidovirales). This naturally occurring recombination event may have broad implications for other picornaviral and/or nidoviral species. Importantly, we demonstrated that the exogenous ToV-PLP gene that was inserted into the EVG genome encodes a deubiquitinase/deISGylase and potentially suppresses host cellular innate immune responses. Our results provide insights into how a gain of function through genetic recombination, in particular cross-order recombination, may improve the ability of a virus to evade host immunity.
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45
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Benschop KSM, Rahamat-Langendoen JC, van der Avoort HGAM, Claas ECJ, Pas SD, Schuurman R, Verweij JJ, Wolthers KC, Niesters HGM, Koopmans MPG. VIRO-TypeNed, systematic molecular surveillance of enteroviruses in the Netherlands between 2010 and 2014. ACTA ACUST UNITED AC 2017; 21:30352. [PMID: 27719752 PMCID: PMC5069426 DOI: 10.2807/1560-7917.es.2016.21.39.30352] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 05/23/2016] [Indexed: 12/29/2022]
Abstract
VIRO-TypeNed is a collaborative molecular surveillance platform facilitated through a web-based database. Genetic data in combination with epidemiological, clinical and patient data are shared between clinical and public health laboratories, as part of the surveillance underpinning poliovirus eradication. We analysed the combination of data submitted from 2010 to 2014 to understand circulation patterns of non-polio enteroviruses (NPEV) of public health relevance. Two epidemiological patterns were observed based on VIRO-TypeNed data and classical surveillance data dating back to 1996: (i) endemic cyclic, characterised by predictable upsurges/outbreaks every two to four years, and (ii) epidemic, where rare virus types caused upsurges/outbreaks. Genetic analysis suggests continuous temporal displacement of virus lineages due to the accumulation of (silent) genetic changes. Non-synonymous changes in the antigenic B/C loop suggest antigenic diversification, which may affect population susceptibility. Infections were frequently detected at an age under three months and at an older, parenting age (25–49 years) pointing to a distinct role of immunity in the circulation patterns. Upsurges were detected in the summer and winter which can promote increased transmissibility underlying new (cyclic) upsurges and requires close monitoring. The combination of data provide a better understanding of NPEV circulation required to control and curtail upsurges and outbreaks.
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Affiliation(s)
- Kimberley S M Benschop
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
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46
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Abstract
Enteroviruses (EVs) belong to the family Picornaviridae and are responsible for mild to severe diseases in mammals including humans and non-human primates (NHP). Simian EVs were first discovered in the 1950s in the Old World Monkeys and recently in wild chimpanzee, gorilla and mandrill in Cameroon. In the present study, we screened by PCR EVs in 600 fecal samples of wild apes and monkeys that were collected at four sites in Gabon. A total of 32 samples were positive for EVs (25 from mandrills, 7 from chimpanzees, none from gorillas). The phylogenetic analysis of VP1 and VP2 genes showed that EVs identified in chimpanzees were members of two human EV species, EV-A and EV-B, and those identified in mandrills were members of the human species EV-B and the simian species EV-J. The identification of two novel enterovirus types, EV-B112 in a chimpanzee and EV-B113 in a mandrill, suggests these NHPs could be potential sources of new EV types. The identification of EV-B107 and EV90 that were previously found in humans indicates cross-species transfers. Also the identification of chimpanzee-derived EV110 in a mandrill demonstrated a wide host range of this EV. Further research of EVs in NHPs would help understanding emergence of new types or variants, and evaluating the real risk of cross-species transmission for humans as well for NHPs populations.
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47
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The Transcriptome of Rhabdomyosarcoma Cells Infected with Cytolytic and Non-Cytolytic Variants of Coxsackievirus B2 Ohio-1. PLoS One 2016; 11:e0164548. [PMID: 27760161 PMCID: PMC5070843 DOI: 10.1371/journal.pone.0164548] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 09/07/2016] [Indexed: 11/19/2022] Open
Abstract
The transcriptomes of cells infected with lytic and non-lytic variants of coxsackievirus B2 Ohio-1 (CVB2O) were analyzed using next generation sequencing. This approach was selected with the purpose of elucidating the effects of lytic and non-lytic viruses on host cell transcription. Total RNA was extracted from infected cells and sequenced. The resulting reads were subsequently mapped against the human and CVB2O genomes. The amount of intracellular RNA was measured, indicating lower proportions of human RNA in the cells infected with the lytic virus compared to the non-lytic virus after 48 hours. This may be explained by reduced activity of the cellular transcription/translation machinery in lytic enteroviral replication due to activities of the enteroviral proteases 2A and/or 3C. Furthermore, differential expression in the cells infected with the two virus variants was identified and a number of transcripts were singled out as possible answers to the question of how the viruses interact with the host cells, resulting in lytic or non-lytic infections.
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48
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Kempf BJ, Peersen OB, Barton DJ. Poliovirus Polymerase Leu420 Facilitates RNA Recombination and Ribavirin Resistance. J Virol 2016; 90:8410-21. [PMID: 27412593 PMCID: PMC5021434 DOI: 10.1128/jvi.00078-16] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 06/29/2016] [Indexed: 01/23/2023] Open
Abstract
UNLABELLED RNA recombination is important in the formation of picornavirus species groups and the ongoing evolution of viruses within species groups. In this study, we examined the structure and function of poliovirus polymerase, 3D(pol), as it relates to RNA recombination. Recombination occurs when nascent RNA products exchange one viral RNA template for another during RNA replication. Because recombination is a natural aspect of picornavirus replication, we hypothesized that some features of 3D(pol) may exist, in part, to facilitate RNA recombination. Furthermore, we reasoned that alanine substitution mutations that disrupt 3D(pol)-RNA interactions within the polymerase elongation complex might increase and/or decrease the magnitudes of recombination. We found that an L420A mutation in 3D(pol) decreased the frequency of RNA recombination, whereas alanine substitutions at other sites in 3D(pol) increased the frequency of recombination. The 3D(pol) Leu420 side chain interacts with a ribose in the nascent RNA product 3 nucleotides from the active site of the polymerase. Notably, the L420A mutation that reduced recombination also rendered the virus more susceptible to inhibition by ribavirin, coincident with the accumulation of ribavirin-induced G→A and C→U mutations in viral RNA. We conclude that 3D(pol) Leu420 is critically important for RNA recombination and that RNA recombination contributes to ribavirin resistance. IMPORTANCE Recombination contributes to the formation of picornavirus species groups and the emergence of circulating vaccine-derived polioviruses (cVDPVs). The recombinant viruses that arise in nature are occasionally more fit than either parental strain, especially when the two partners in recombination are closely related, i.e., members of characteristic species groups, such as enterovirus species groups A to H or rhinovirus species groups A to C. Our study shows that RNA recombination requires conserved features of the viral polymerase. Furthermore, a polymerase mutation that disables recombination renders the virus more susceptible to the antiviral drug ribavirin, suggesting that recombination contributes to ribavirin resistance. Elucidating the molecular mechanisms of RNA replication and recombination may help mankind achieve and maintain poliovirus eradication.
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Affiliation(s)
- Brian J Kempf
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Olve B Peersen
- Department of Biochemistry, Colorado State University, Fort Collins, Colorado, USA
| | - David J Barton
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
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49
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Ecale Zhou CL. S2M: A Stochastic Simulation Model of Poliovirus Genetic State Transition. Bioinform Biol Insights 2016; 10:81-95. [PMID: 27385911 PMCID: PMC4924885 DOI: 10.4137/bbi.s38194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 06/01/2016] [Accepted: 06/05/2016] [Indexed: 12/11/2022] Open
Abstract
Modeling the molecular mechanisms that govern genetic variation can be useful in understanding the dynamics that drive genetic state transition in quasispecies viruses. For example, there is considerable interest in understanding how the relatively benign vaccine strains of poliovirus eventually revert to forms that confer neurovirulence and cause disease (ie, vaccine-derived poliovirus). This report describes a stochastic simulation model, S2M, which can be used to generate hypothetical outcomes based on known mechanisms of genetic diversity. S2M begins with predefined genotypes based on the Sabin-1 and Mahoney wild-type sequences, constructs a set of independent cell-based populations, and performs in-cell replication and cell-to-cell infection cycles while quantifying genetic changes that track the transition from Sabin-1 toward Mahoney. Realism is incorporated into the model by assigning defaults for variables that constrain mechanisms of genetic variability based roughly on metrics reported in the literature, yet these values can be modified at the command line in order to generate hypothetical outcomes driven by these parameters. To demonstrate the utility of S2M, simulations were performed to examine the effects of the rates of replication error and recombination and the presence or absence of defective interfering particles, upon reaching the end states of Mahoney resemblance (semblance of a vaccine-derived state), neurovirulence, genome fitness, and cloud diversity. Simulations provide insight into how modeled biological features may drive hypothetical outcomes, independently or in combination, in ways that are not always intuitively obvious.
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Affiliation(s)
- Carol L Ecale Zhou
- Computation Applications and Research Department, Lawrence Livermore National Laboratory, Livermore, CA, USA
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50
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Zhang W, Lin X, Jiang P, Tao Z, Liu X, Ji F, Wang T, Wang S, Lv H, Xu A, Wang H. Complete genome sequence of a coxsackievirus B3 recombinant isolated from an aseptic meningitis outbreak in eastern China. Arch Virol 2016; 161:2335-42. [PMID: 27236460 DOI: 10.1007/s00705-016-2893-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 05/11/2016] [Indexed: 11/29/2022]
Abstract
Coxsackievirus B3 (CV-B3) has frequently been associated with aseptic meningitis outbreaks in China. To identify sequence motifs related to aseptic meningitis and to construct an infectious clone, the genome sequence of 08TC170, a representative strain isolated from cerebrospinal fluid (CSF) samples from an outbreak in Shandong in 2008, was determined, and the coding regions for P1-P3 and VP1 were aligned. The first 21 and last 20 residues were "TTAAAACAGCCTGTGGGTTGT" and "ATTCTCCGCATTCGGTGCGG", respectively. The whole genome consisted of 7401 nucleotides, sharing 80.8 % identity with the prototype strain Nancy and low sequence similarity with members of clusters A-C. In contrast, 08TC170 showed high sequence similarity to members of cluster D. An especially high level of sequence identity (≥97.7 %) was found within a branch constituted by 08TC170 and four Chinese strains that clustered together in all of the P1-P3 phylogenic trees. In addition, 08TC170 also possessed a close relationship to the Hong Kong strain 26362/08 in VP1. Similarity plot analysis showed that 08TC170 was most similar to the Chinese CV-B3 strain SSM in P1 and the partial P2 coding region but to the CV-B5 or E-6 strain in 2C and following regions. A T277A mutation was found in 08TC170 and other strains isolated in 2008-2010, but not in strains isolated before 2008, which had high sequence similarity and formed the cluster A277. The results suggested that 08TC170 was the product of both intertypic recombination and point mutation, whose effects on viral neurovirulence will be investigated in a further study. The high homology between 08TC170 and other strains revealed their co-circulation in mainland China and Hong Kong and indicates that further surveillance is needed.
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Affiliation(s)
- Wenqiang Zhang
- Academy of Preventive Medicine, Shandong University, Jinan, People's Republic of China.,Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, People's Republic of China
| | - Xiaojuan Lin
- Academy of Preventive Medicine, Shandong University, Jinan, People's Republic of China.,Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, People's Republic of China
| | - Ping Jiang
- Department of Molecular Genetics and Microbiology, School of Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Zexin Tao
- Academy of Preventive Medicine, Shandong University, Jinan, People's Republic of China.,Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, People's Republic of China
| | - Xiaolin Liu
- Academy of Preventive Medicine, Shandong University, Jinan, People's Republic of China.,Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, People's Republic of China
| | - Feng Ji
- Academy of Preventive Medicine, Shandong University, Jinan, People's Republic of China.,Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, People's Republic of China
| | - Tongzhan Wang
- Academy of Preventive Medicine, Shandong University, Jinan, People's Republic of China.,Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, People's Republic of China
| | - Suting Wang
- Academy of Preventive Medicine, Shandong University, Jinan, People's Republic of China.,Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, People's Republic of China
| | - Hui Lv
- Academy of Preventive Medicine, Shandong University, Jinan, People's Republic of China.,Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, People's Republic of China
| | - Aiqiang Xu
- Academy of Preventive Medicine, Shandong University, Jinan, People's Republic of China.,Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, People's Republic of China
| | - Haiyan Wang
- Academy of Preventive Medicine, Shandong University, Jinan, People's Republic of China. .,Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, People's Republic of China.
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