1
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Georgieva I, Stoyanova A, Stoitsova S, Nikolaeva-Glomb L. Echovirus 30 in Bulgaria during the European Upsurge of the Virus, 2017-2018. Pathogens 2024; 13:143. [PMID: 38392881 PMCID: PMC10893257 DOI: 10.3390/pathogens13020143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 02/02/2024] [Accepted: 02/03/2024] [Indexed: 02/25/2024] Open
Abstract
In 2018, an increase in echovirus 30 (E30) detections was reported in some European countries. To assess the circulation and phylogenetic relationships of E30 in Bulgaria, E30 samples identified at the National Reference Laboratory for Enteroviruses, National Centre of Infectious and Parasitic Diseases, Bulgaria (NRL for Enteroviruses) in 2017 and 2018 were subjected to sequencing and phylogenetic analysis. The present study revealed that sample positivity did not significantly increase in Bulgaria during the European upsurge. E30 was identified in six patients, two of whom were epidemiologically linked. The maximum-likelihood phylogenetic tree showed that sequences from five patients belonged to the G1 lineage (clades G1a and G1b). The sequence from one patient belonged to the G2 lineage and was grouped closer to sequences from the last E30 outbreak in Bulgaria in 2012. No recombination events were detected. The European E30 upsurge in 2018 was caused by two clades, and one of them was G1. The fact that the majority of the Bulgarian samples belonged to G1 indicated that the virus was present in the country but did not cause a local upsurge. Phylogenetic and epidemiological data indicated sporadic E30 cases and a possible shift towards G1 lineage in 2017 and 2018.
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Affiliation(s)
- Irina Georgieva
- National Reference Laboratory for Enteroviruses, Department of Virology, National Centre of Infectious and Parasitic Diseases, 1233 Sofia, Bulgaria (L.N.-G.)
| | - Asya Stoyanova
- National Reference Laboratory for Enteroviruses, Department of Virology, National Centre of Infectious and Parasitic Diseases, 1233 Sofia, Bulgaria (L.N.-G.)
| | - Savina Stoitsova
- Department of Epidemiology, National Centre of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria
| | - Lubomira Nikolaeva-Glomb
- National Reference Laboratory for Enteroviruses, Department of Virology, National Centre of Infectious and Parasitic Diseases, 1233 Sofia, Bulgaria (L.N.-G.)
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2
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Gong YN, Yang SL, Chen YC, Liu YC, Huang YC, Tsao KC. Novel intertypic recombination of Echovirus 11 in the Enterovirus species B. J Med Virol 2024; 96:e29323. [PMID: 38164047 DOI: 10.1002/jmv.29323] [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: 08/12/2023] [Revised: 11/27/2023] [Accepted: 12/02/2023] [Indexed: 01/03/2024]
Abstract
Enteroviruses (EVs), single-stranded, positive-sense RNA viruses, can be classified into four species (A-D), which have previously been linked to a diverse range of disease manifestations and infections affecting the central nervous system. In the Enterovirus species B (EV-B), Echovirus type 11 (E11) has been observed to occasionally circulate in Taiwan, which was responsible for an epidemic of enterovirus infections in 2018. Here, 48 clinical specimens isolated in 2003, 2004, 2009, and 2018 were collected for the high-throughput sequencing. Notably, we identified 2018 Taiwanese strains having potential recombinations in the 3D gene, as well as one 2003 strain having a double recombination with E6 and Coxsackievirus B5 in the P2 and P3 regions, respectively. Additionally, one amino acid signature mutated from the Histidine (H) in throat swab specimens to the Tyrosine (Y) in cerebral spinal fluid specimens was detected at position 1496 (or 57) of the genomic coordinate (or 3A gene) to further demonstrate intra-host evolution in different organs. In conclusion, this study identifies potential intertypic recombination events and an intra-host signature mutation in E11 strains, isolated during a 2018 neurological disease outbreak in Taiwan, contributing to our understanding of its evolution and pathogenesis.
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Affiliation(s)
- Yu-Nong Gong
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- International Master Degree Program for Molecular Medicine in Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Taiwan
| | - Shu-Li Yang
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Yi-Ching Chen
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
- School of Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Yi-Chun Liu
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Yhu-Chering Huang
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
- School of Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Kuo-Chien Tsao
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
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3
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Peterson CJ, Hurst BL, Evans WJ, Van Wettere AJ, Gibson SA, Smee DF, Tarbet EB. Human IVIG treatment in a neurological disease model for Enterovirus A71 infection in 28-day-old AG129 mice. Virology 2023; 580:62-72. [PMID: 36780728 DOI: 10.1016/j.virol.2023.02.002] [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: 11/15/2022] [Revised: 01/27/2023] [Accepted: 02/02/2023] [Indexed: 02/07/2023]
Abstract
Enterovirus A71 can cause serious neurological disease in young children. Animal models for EV-A71 are needed to evaluate potential antiviral therapies. Existing models have limitations, including lack of lethality or crucial disease signs. Here we report the development of an EV-A71 model in 28-day-old mice. Virus was serially passaged until it produced consistent lethality and rear-limb paralysis. Onset of disease occurred between days 6-9 post-infection, with mortality following weight loss and neurological signs on days 9-14. In addition, a single administration of human intravenous immunoglobulin at doses of 200, 400 and 800 mg/kg at 4h post-infection was evaluated in the model. Protection from weight loss, neurological signs, and mortality (between 50 and 89%) were observed at doses of 400 mg/kg or greater. Based on these results, IVIG was selected for use as a positive control in this acute model, and suggest that IVIG is a potential therapeutic for EV-A71 infections.
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Affiliation(s)
- Christopher J Peterson
- Institute for Antiviral Research, Department of Animal, Dairy, and Veterinary Sciences, 5600 Old Main Hill, Utah State University, Logan, UT, 84322, USA; Department of Animal, Dairy, and Veterinary Sciences, Utah State University, 5600 Old Main Hill, Logan, UT, 84322, USA; Carilion Clinic-Virginia Tech Carilion School of Medicine, 2 Riverside Circle, Roanoke, VA, 24016, USA
| | - Brett L Hurst
- Institute for Antiviral Research, Department of Animal, Dairy, and Veterinary Sciences, 5600 Old Main Hill, Utah State University, Logan, UT, 84322, USA; Department of Animal, Dairy, and Veterinary Sciences, Utah State University, 5600 Old Main Hill, Logan, UT, 84322, USA
| | - W Joseph Evans
- Institute for Antiviral Research, Department of Animal, Dairy, and Veterinary Sciences, 5600 Old Main Hill, Utah State University, Logan, UT, 84322, USA; Department of Animal, Dairy, and Veterinary Sciences, Utah State University, 5600 Old Main Hill, Logan, UT, 84322, USA
| | - Arnaud J Van Wettere
- Department of Animal, Dairy, and Veterinary Sciences, Utah State University, 5600 Old Main Hill, Logan, UT, 84322, USA; Utah Veterinary Diagnostic Laboratory, Department of Animal, Dairy, and Veterinary Sciences, 950 East 1400 North, Utah State University, Logan, UT, 84341, USA
| | - Scott A Gibson
- Institute for Antiviral Research, Department of Animal, Dairy, and Veterinary Sciences, 5600 Old Main Hill, Utah State University, Logan, UT, 84322, USA; Department of Animal, Dairy, and Veterinary Sciences, Utah State University, 5600 Old Main Hill, Logan, UT, 84322, USA
| | - Donald F Smee
- Institute for Antiviral Research, Department of Animal, Dairy, and Veterinary Sciences, 5600 Old Main Hill, Utah State University, Logan, UT, 84322, USA; Department of Animal, Dairy, and Veterinary Sciences, Utah State University, 5600 Old Main Hill, Logan, UT, 84322, USA
| | - E Bart Tarbet
- Institute for Antiviral Research, Department of Animal, Dairy, and Veterinary Sciences, 5600 Old Main Hill, Utah State University, Logan, UT, 84322, USA; Department of Animal, Dairy, and Veterinary Sciences, Utah State University, 5600 Old Main Hill, Logan, UT, 84322, USA; Utah Veterinary Diagnostic Laboratory, Department of Animal, Dairy, and Veterinary Sciences, 950 East 1400 North, Utah State University, Logan, UT, 84341, USA.
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4
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Isaacs SR, Foskett DB, Maxwell AJ, Ward EJ, Faulkner CL, Luo JYX, Rawlinson WD, Craig ME, Kim KW. Viruses and Type 1 Diabetes: From Enteroviruses to the Virome. Microorganisms 2021; 9:microorganisms9071519. [PMID: 34361954 PMCID: PMC8306446 DOI: 10.3390/microorganisms9071519] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 07/12/2021] [Accepted: 07/14/2021] [Indexed: 12/15/2022] Open
Abstract
For over a century, viruses have left a long trail of evidence implicating them as frequent suspects in the development of type 1 diabetes. Through vigorous interrogation of viral infections in individuals with islet autoimmunity and type 1 diabetes using serological and molecular virus detection methods, as well as mechanistic studies of virus-infected human pancreatic β-cells, the prime suspects have been narrowed down to predominantly human enteroviruses. Here, we provide a comprehensive overview of evidence supporting the hypothesised role of enteroviruses in the development of islet autoimmunity and type 1 diabetes. We also discuss concerns over the historical focus and investigation bias toward enteroviruses and summarise current unbiased efforts aimed at characterising the complete population of viruses (the “virome”) contributing early in life to the development of islet autoimmunity and type 1 diabetes. Finally, we review the range of vaccine and antiviral drug candidates currently being evaluated in clinical trials for the prevention and potential treatment of type 1 diabetes.
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Affiliation(s)
- Sonia R. Isaacs
- Faculty of Medicine and Health, School of Women’s and Children’s Health, University of New South Wales, Sydney, NSW 2031, Australia; (S.R.I.); (D.B.F.); (A.J.M.); (E.J.W.); (C.L.F.); (J.Y.X.L.); (W.D.R.); (M.E.C.)
- Virology Research Laboratory, Serology and Virology Division, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia
| | - Dylan B. Foskett
- Faculty of Medicine and Health, School of Women’s and Children’s Health, University of New South Wales, Sydney, NSW 2031, Australia; (S.R.I.); (D.B.F.); (A.J.M.); (E.J.W.); (C.L.F.); (J.Y.X.L.); (W.D.R.); (M.E.C.)
- Virology Research Laboratory, Serology and Virology Division, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia
| | - Anna J. Maxwell
- Faculty of Medicine and Health, School of Women’s and Children’s Health, University of New South Wales, Sydney, NSW 2031, Australia; (S.R.I.); (D.B.F.); (A.J.M.); (E.J.W.); (C.L.F.); (J.Y.X.L.); (W.D.R.); (M.E.C.)
- Virology Research Laboratory, Serology and Virology Division, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia
| | - Emily J. Ward
- Faculty of Medicine and Health, School of Women’s and Children’s Health, University of New South Wales, Sydney, NSW 2031, Australia; (S.R.I.); (D.B.F.); (A.J.M.); (E.J.W.); (C.L.F.); (J.Y.X.L.); (W.D.R.); (M.E.C.)
- Faculty of Medicine and Health, School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Clare L. Faulkner
- Faculty of Medicine and Health, School of Women’s and Children’s Health, University of New South Wales, Sydney, NSW 2031, Australia; (S.R.I.); (D.B.F.); (A.J.M.); (E.J.W.); (C.L.F.); (J.Y.X.L.); (W.D.R.); (M.E.C.)
- Virology Research Laboratory, Serology and Virology Division, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia
| | - Jessica Y. X. Luo
- Faculty of Medicine and Health, School of Women’s and Children’s Health, University of New South Wales, Sydney, NSW 2031, Australia; (S.R.I.); (D.B.F.); (A.J.M.); (E.J.W.); (C.L.F.); (J.Y.X.L.); (W.D.R.); (M.E.C.)
- Virology Research Laboratory, Serology and Virology Division, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia
| | - William D. Rawlinson
- Faculty of Medicine and Health, School of Women’s and Children’s Health, University of New South Wales, Sydney, NSW 2031, Australia; (S.R.I.); (D.B.F.); (A.J.M.); (E.J.W.); (C.L.F.); (J.Y.X.L.); (W.D.R.); (M.E.C.)
- Virology Research Laboratory, Serology and Virology Division, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia
- Faculty of Medicine and Health, School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
- Faculty of Science, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Maria E. Craig
- Faculty of Medicine and Health, School of Women’s and Children’s Health, University of New South Wales, Sydney, NSW 2031, Australia; (S.R.I.); (D.B.F.); (A.J.M.); (E.J.W.); (C.L.F.); (J.Y.X.L.); (W.D.R.); (M.E.C.)
- Virology Research Laboratory, Serology and Virology Division, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia
- Institute of Endocrinology and Diabetes, Children’s Hospital at Westmead, Sydney, NSW 2145, Australia
- Faculty of Medicine and Health, Discipline of Child and Adolescent Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Ki Wook Kim
- Faculty of Medicine and Health, School of Women’s and Children’s Health, University of New South Wales, Sydney, NSW 2031, Australia; (S.R.I.); (D.B.F.); (A.J.M.); (E.J.W.); (C.L.F.); (J.Y.X.L.); (W.D.R.); (M.E.C.)
- Virology Research Laboratory, Serology and Virology Division, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia
- Correspondence: ; Tel.: +61-2-9382-9096
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5
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Liu H, Cong S, Xu D, Lin K, Huang X, Sun H, Yang Z, Ma S. Characterization of a novel echovirus 21 strain isolated from a healthy child in China in 2013. Arch Virol 2020; 165:757-760. [PMID: 31912293 DOI: 10.1007/s00705-019-04506-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 11/20/2019] [Indexed: 11/29/2022]
Abstract
Echovirus 21 (E21) belongs to the species Enterovirus B, whose members are frequently associated with acute flaccid paralysis. E21 strain 553/YN/CHN/2013 was isolated from a healthy child in Yunnan, China, in 2013. This is the first report of the complete genome sequence of E21 in China. This strain shared 81.7% nucleotide sequence identity and 96.8% amino acid sequence identity with the E21 prototype strain Farina. Although strain 553/YN/CHN/2013 belongs to the E21 serotype, the only similarity to the E21 strain was in the VP1 region, as other genomic regions, including VP2-VP4, were more similar to other EV-B members. Recombination analysis showed evidence of recombination events between E21 and other EV-B viruses. E21 strain 553/YN/CHN/2013 failed to infect suckling mice via intracerebral injection. Surveillance of E21 is very important to help forecast the potential of emerging E21 outbreaks and related diseases.
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Affiliation(s)
- Hongbo Liu
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Peking Union Medical College (CAMS and PUMC), 935 Jiao Ling Road, Kunming, 650118, Yunnan, People's Republic of China.,Yunnan Key Laboratory of Vaccine Research Development on Severe Infectious Disease, Kunming, 650118, People's Republic of China
| | - Shanri Cong
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Peking Union Medical College (CAMS and PUMC), 935 Jiao Ling Road, Kunming, 650118, Yunnan, People's Republic of China.,Yunnan Key Laboratory of Vaccine Research Development on Severe Infectious Disease, Kunming, 650118, People's Republic of China
| | - Danhan Xu
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Peking Union Medical College (CAMS and PUMC), 935 Jiao Ling Road, Kunming, 650118, Yunnan, People's Republic of China.,Yunnan Key Laboratory of Vaccine Research Development on Severe Infectious Disease, Kunming, 650118, People's Republic of China
| | - Keqin Lin
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Peking Union Medical College (CAMS and PUMC), 935 Jiao Ling Road, Kunming, 650118, Yunnan, People's Republic of China.,Yunnan Key Laboratory of Vaccine Research Development on Severe Infectious Disease, Kunming, 650118, People's Republic of China
| | - Xiaoqin Huang
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Peking Union Medical College (CAMS and PUMC), 935 Jiao Ling Road, Kunming, 650118, Yunnan, People's Republic of China.,Yunnan Key Laboratory of Vaccine Research Development on Severe Infectious Disease, Kunming, 650118, People's Republic of China
| | - Hao Sun
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Peking Union Medical College (CAMS and PUMC), 935 Jiao Ling Road, Kunming, 650118, Yunnan, People's Republic of China.,Yunnan Key Laboratory of Vaccine Research Development on Severe Infectious Disease, Kunming, 650118, People's Republic of China
| | - Zhaoqing Yang
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Peking Union Medical College (CAMS and PUMC), 935 Jiao Ling Road, Kunming, 650118, Yunnan, People's Republic of China. .,Yunnan Key Laboratory of Vaccine Research Development on Severe Infectious Disease, Kunming, 650118, People's Republic of China.
| | - Shaohui Ma
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Peking Union Medical College (CAMS and PUMC), 935 Jiao Ling Road, Kunming, 650118, Yunnan, People's Republic of China. .,Yunnan Key Laboratory of Vaccine Research Development on Severe Infectious Disease, Kunming, 650118, People's Republic of China.
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6
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Isaacs SR, Kim KW, Cheng JX, Bull RA, Stelzer-Braid S, Luciani F, Rawlinson WD, Craig ME. Amplification and next generation sequencing of near full-length human enteroviruses for identification and characterisation from clinical samples. Sci Rep 2018; 8:11889. [PMID: 30089864 PMCID: PMC6082906 DOI: 10.1038/s41598-018-30322-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 07/19/2018] [Indexed: 12/16/2022] Open
Abstract
More than 100 different enterovirus (EV) genotypes infect humans and contribute to substantial morbidity. However, current methods for characterisation of full-length genomes are based on Sanger sequencing of short genomic regions, which are labour-intensive and do not enable comprehensive characterisation of viral populations. Here, we describe a simple and sensitive protocol for the amplification and sequencing of near full-length genomes of human EV species using next generation sequencing. EV genomes were amplified from 89% of samples tested, with Ct values ranging between 15.7 and 39.3. These samples included 7 EV-A genotypes (CVA2, 5–7, 10, 16 and EV71), 19 EV-B genotypes (CVA9, CVB1-6, ECHO3, 4, 6, 7, 9, 11, 16, 18, 25, 29, 30, and EV69), 3 EV-C genotypes (CVA19 and PV2, 3) and 1 EV-D genotype (EV70). We characterised 70 EVs from 58 clinical stool samples and eight reference strains, with a minimum of 100X depth. We found evidence of co-infection in four clinical specimens, each containing two distinct EV genotypes (CVB3/ECHO7, CVB3/ECHO18 and ECHO9/30). Characterisation of the complete genome provided conclusive genotyping of EVs, which can be applied to investigate the intra-host virus evolution of EVs, and allows further identification and investigation of EV outbreaks.
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Affiliation(s)
- Sonia R Isaacs
- School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, 2052, Australia.,Virology Research Laboratory, Prince of Wales Hospital, Sydney, NSW, 2031, Australia
| | - Ki Wook Kim
- School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, 2052, Australia.,Virology Research Laboratory, Prince of Wales Hospital, Sydney, NSW, 2031, Australia
| | - Junipearl X Cheng
- School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Rowena A Bull
- School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, 2052, Australia.,Systems Medicine, Inflammation and Infection Research Centre, School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Sacha Stelzer-Braid
- Virology Research Laboratory, Prince of Wales Hospital, Sydney, NSW, 2031, Australia.,School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Fabio Luciani
- School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, 2052, Australia.,Systems Medicine, Inflammation and Infection Research Centre, School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, 2052, Australia
| | - William D Rawlinson
- School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, 2052, Australia.,Virology Research Laboratory, Prince of Wales Hospital, Sydney, NSW, 2031, Australia.,School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, 2052, Australia.,Serology and Virology Division (SAViD), NSW Health Pathology East, Department of Microbiology, Prince of Wales Hospital, Sydney, NSW, 2031, Australia.,School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Maria E Craig
- School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, 2052, Australia. .,Virology Research Laboratory, Prince of Wales Hospital, Sydney, NSW, 2031, Australia. .,Institute of Endocrinology and Diabetes, The Children's Hospital at Westmead, Sydney, NSW, 2145, Australia. .,Discipline of Child and Adolescent Health, University of Sydney, Sydney, NSW, 2006, Australia.
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7
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Molecular characterization of echovirus 12 strains isolated from healthy children in China. Sci Rep 2018; 8:11716. [PMID: 30082917 PMCID: PMC6078983 DOI: 10.1038/s41598-018-30250-x] [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: 10/10/2017] [Accepted: 07/25/2018] [Indexed: 12/26/2022] Open
Abstract
Human echovirus 12 (E-12) belongs to the enterovirus B species. To date, only one full-length genome sequence of E-12 (prototype strain Travis) is available in the GenBank database. This study determined the complete sequence of three E-12 strains, which were isolated from the stools of three healthy children in Yunnan, China, in 2013. We revealed that the three Yunnan E-12 strains had only 80.8-80.9% nucleotide identity and 96.4-96.8% amino acid identity with the Travis strain based on pairwise comparisons of the complete genome nucleotide and amino acid sequences. The three Yunnan strains shared 99.7% nucleotide identity and 99.1-99.5% amino acid similarity. Phylogenetic and similarity plot analyses showed that intertypic recombination occurred in the non-structural regions of the three Yunnan E-12 strains. This is the first report of the complete genome sequence of E-12 in China and it enriches the complete genome sequences of E-12 in the GenBank database.
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8
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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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9
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Hao C, Hao C, Luo J, Li J. Genomic features of coxsackievirus A6 correlate with herpangina and hand, foot and mouth disease. Future Virol 2016. [DOI: 10.2217/fvl.15.110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aim: To study the genomic factors of coxsackievirus A6 (CVA6) correlated with herpangina and hand, foot and mouth disease (HFMD). Materials & methods: Complete genome of CVA6 strains and HFMD causing enteroviruses were enrolled for genomic comparisons. Results: Recombinations in the nonstructural P2-P3 region appeared to correlate with HFMD causing pathogenicity. Among nonrecombinant CVA6 strains, a markedly nucleotide diversity in 3C-3UTR was observed between herpangina and HFMD causing CVA6. Synonymous mutations take an important role in the evolution of CVA6 3C-3UTR region, as limited amino acid variations were resulted from the high nucleotide diversity. Key amino acid mutations at positions 168–170 of 3D protein were correlated with the differences in viral pathogenicities. Conclusion: These findings provide insights into viral genomic features correlated with CVA6 pathogenicities.
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Affiliation(s)
- Congjun Hao
- Department of Geriatrics, General Hospital of Beijing Military Command, Beijing 100700, PR China
| | - Chunyan Hao
- College of Chemical & Biological Engineering, Taiyuan University of Science & Technology, Taiyuan 030021, PR China
| | - Jizheng Luo
- Department of Geriatrics, General Hospital of Beijing Military Command, Beijing 100700, PR China
| | - Jianguo Li
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan 030006, PR China
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10
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Singh DV, Kumar A, Kumar P, Baluni M, Ghildiyal S, Kumar R, Misra UK, Dhole TN. An outbreak of encephalitis associated with echovirus 19 in Uttar Pradesh, India, in 2011. Arch Virol 2015; 161:967-70. [PMID: 26695770 DOI: 10.1007/s00705-015-2714-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 11/30/2015] [Indexed: 11/25/2022]
Abstract
A sequence-independent single-primer amplification method and a modified enterovirus VP1 gene typing primer were used for identification of echovirus 19 and enterovirus 101, which remained undiagnosed by standard enterovirus molecular typing methods. Six different serotypes were identified during this study, with the predominance of ECV 19 (n = 20) followed by echovirus 21 (n = 3), EV 69 and EV 101 (n = 2 each), coxsackievirus B5 and ECV 27 (n = 1 each). To our knowledge, this is the first report of enteroviruses 69 and 101 in encephalitis cases in India.
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Affiliation(s)
- Dharam Veer Singh
- Department of Microbiology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Raebareli Road, Lucknow, 226014, Uttar Pradesh, India
| | - Arvind Kumar
- Department of Microbiology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Raebareli Road, Lucknow, 226014, Uttar Pradesh, India
| | - Pramesh Kumar
- Department of Microbiology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Raebareli Road, Lucknow, 226014, Uttar Pradesh, India
| | - Manjari Baluni
- Department of Microbiology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Raebareli Road, Lucknow, 226014, Uttar Pradesh, India
| | - Sneha Ghildiyal
- Department of Microbiology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Raebareli Road, Lucknow, 226014, Uttar Pradesh, India
| | - Rashmi Kumar
- Department of Paediatrics, King George's Medical University, Lucknow, 226003, Uttar Pradesh, India
| | - Usha Kant Misra
- Department of Neurology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, 226014, Uttar Pradesh, India
| | - Tapan N Dhole
- Department of Microbiology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Raebareli Road, Lucknow, 226014, Uttar Pradesh, India.
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Lin CH, Wang YB, Chen SH, Hsiung CA, Lin CY. Precise genotyping and recombination detection of Enterovirus. BMC Genomics 2015; 16 Suppl 12:S8. [PMID: 26678286 PMCID: PMC4682392 DOI: 10.1186/1471-2164-16-s12-s8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Enteroviruses (EV) with different genotypes cause diverse infectious diseases in humans and mammals. A correct EV typing result is crucial for effective medical treatment and disease control; however, the emergence of novel viral strains has impaired the performance of available diagnostic tools. Here, we present a web-based tool, named EVIDENCE (EnteroVirus In DEep conception, http://symbiont.iis.sinica.edu.tw/evidence), for EV genotyping and recombination detection. We introduce the idea of using mixed-ranking scores to evaluate the fitness of prototypes based on relatedness and on the genome regions of interest. Using phylogenetic methods, the most possible genotype is determined based on the closest neighbor among the selected references. To detect possible recombination events, EVIDENCE calculates the sequence distance and phylogenetic relationship among sequences of all sliding windows scanning over the whole genome. Detected recombination events are plotted in an interactive figure for viewing of fine details. In addition, all EV sequences available in GenBank were collected and revised using the latest classification and nomenclature of EV in EVIDENCE. These sequences are built into the database and are retrieved in an indexed catalog, or can be searched for by keywords or by sequence similarity. EVIDENCE is the first web-based tool containing pipelines for genotyping and recombination detection, with updated, built-in, and complete reference sequences to improve sensitivity and specificity. The use of EVIDENCE can accelerate genotype identification, aiding clinical diagnosis and enhancing our understanding of EV evolution.
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Abstract
The increasing availability of nucleic acid amplification tests since the 1980s has revolutionised our understanding of the pathogenesis, epidemiology, clinical and laboratory aspects of known and novel viral respiratory pathogens. High-throughput, multiplex polymerase chain reaction is the most commonly used qualitative detection method, but utilisation of newer techniques such as next-generation sequencing will become more common following significant cost reductions. Rapid and readily accessible isothermal amplification platforms have also allowed molecular diagnostics to be used in a ‘point-of-care’ format. This review focuses on the current applications and limitations of molecular diagnosis for respiratory viruses.
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