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Wang Y, Shah PT, Liu Y, Bahoussi AN, Xing L. Genetic Characteristics and Phylogeographic Dynamics of Echovirus. J Microbiol 2023; 61:865-877. [PMID: 37713068 DOI: 10.1007/s12275-023-00078-w] [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: 06/16/2023] [Revised: 08/20/2023] [Accepted: 08/22/2023] [Indexed: 09/16/2023]
Abstract
Echoviruses belong to the genus Enterovirus in the Picornaviridae family, forming a large group of Enterovirus B (EV-B) within the Enteroviruses. Previously, Echoviruses were classified based on the coding sequence of VP1. In this study, we performed a reliable phylogenetic classification of 277 sequences isolated from 1992 to 2019 based on the full-length genomes of Echovirus. In this report, phylogenetic, phylogeographic, recombination, and amino acid variability landscape analyses were performed to reveal the evolutional characteristics of Echovirus worldwide. Echoviruses were clustered into nine major clades, e.g., G1-G9. Phylogeographic analysis showed that branches G2-G9 were linked to common strains, while the branch G1 was only linked to G5. In contrast, strains E12, E14, and E16 clustered separately from their G3 and G7 clades respectively, and became a separate branch. In addition, we identified a total of 93 recombination events, where most of the events occurred within the VP1-VP4 coding regions. Analysis of amino acid variation showed high variability in the a positions of VP2, VP1, and VP3. This study updates the phylogenetic and phylogeographic information of Echovirus and indicates that extensive recombination and significant amino acid variation in the capsid proteins drove the emergence of new strains.
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Affiliation(s)
- Yan Wang
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, 030006, Shanxi, People's Republic of China
| | - Pir Tariq Shah
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, 030006, Shanxi, People's Republic of China
| | - Yue Liu
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, 030006, Shanxi, People's Republic of China
| | - Amina Nawal Bahoussi
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, 030006, Shanxi, People's Republic of China
| | - Li Xing
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, 030006, Shanxi, People's Republic of China.
- Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Shanxi University, Taiyuan, 030006, People's Republic of China.
- Shanxi Provincial Key Laboratory for Prevention and Treatment of Major Infectious Diseases, Taiyuan, 030006, People's Republic of China.
- The Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, 030006, People's Republic of China.
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2
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Teutsch SM, Nunez CA, Morris A, Eslick GD, Khandaker G, Berkhout A, Novakovic D, Brotherton JML, McGregor S, King J, Egilmezer E, Booy R, Jones CA, Rawlinson W, Thorley BR, Elliott EJ. Australian Paediatric Surveillance Unit (APSU) Annual Surveillance Report 2020. ACTA ACUST UNITED AC 2021; 45. [PMID: 34711146 DOI: 10.33321/cdi.2021.45.59] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract For 27 years, national prospective data on selected rare childhood diseases have been collected monthly by the Australian Paediatric Surveillance Unit (APSU) from paediatricians and other clinical specialists who report cases in children aged up to 16 years. We report here the annual results of APSU surveillance in 2020 for ten rare communicable diseases and complications of communicable diseases, namely: acute flaccid paralysis (AFP); congenital cytomegalovirus (CMV) infection; neonatal herpes simplex virus (HSV) infection; perinatal exposure to human immunodeficiency virus (HIV); paediatric HIV infection; severe complications of seasonal influenza; juvenile onset recurrent respiratory papillomatosis (JoRRP); congenital rubella syndrome; congenital varicella syndrome; and neonatal varicella infection. We describe the results for each disease in the context of the total period of study, including demographics, clinical characteristics, treatment and short-term outcomes. Despite challenges presented by the coronavirus disease 2019 (COVID-19) pandemic in 2020, more than 1,400 paediatricians reported regularly to the APSU and an overall monthly reporting rate of > 90% was achieved. The minimum AFP target of 1 case per 100,000 children aged less than 15 years was achieved and there were few cases of vaccine-preventable diseases (JoRRP, rubella, varicella). However, high cases of congenital CMV, neonatal HSV and perinatal exposure to HIV persist. There were no severe complications of seasonal influenza reported for the first time in 13 years. This is consistent with other surveillance data reporting a decline of influenza and other communicable diseases in 2020, and likely reflects the wider effects of public health measures to reduce transmission of SARS-CoV-2 in the Australian community.
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Affiliation(s)
- Suzy M Teutsch
- The Australian Paediatric Surveillance Unit.,The University of Sydney, Faculty of Medicine and Health, Discipline of Child and Adolescent Health, Sydney, New South Wales, AUSTRALIA.,The Sydney Children's Hospitals Network, Westmead, Sydney, New South Wales, AUSTRALIA
| | - Carlos A Nunez
- The Australian Paediatric Surveillance Unit.,The University of Sydney, Faculty of Medicine and Health, Discipline of Child and Adolescent Health, Sydney, New South Wales, AUSTRALIA.,The Sydney Children's Hospitals Network, Westmead, Sydney, New South Wales, AUSTRALIA
| | - Anne Morris
- The Australian Paediatric Surveillance Unit.,The University of Sydney, Faculty of Medicine and Health, Discipline of Child and Adolescent Health, Sydney, New South Wales, AUSTRALIA.,The Sydney Children's Hospitals Network, Westmead, Sydney, New South Wales, AUSTRALIA
| | - Guy D Eslick
- The Australian Paediatric Surveillance Unit.,The University of Sydney, Faculty of Medicine and Health, Discipline of Child and Adolescent Health, Sydney, New South Wales, AUSTRALIA.,The Sydney Children's Hospitals Network, Westmead, Sydney, New South Wales, AUSTRALIA
| | - Gulam Khandaker
- Director of Public Health/Public Health Physician and Director of Medical Research, Central Queensland Hospital and Health Service, Rockhampton, Queensland, AUSTRALIA
| | - Angela Berkhout
- Microbiology Registrar, Microbiology and laboratory services, The Royal Children's Hospital, Melbourne, Victoria, AUSTRALIA
| | - Daniel Novakovic
- ENT, Head and Neck Surgeon, Laryngologist, and Director, Dr Liang Voice Program, The University of Sydney, Faculty of Medicine and Health, Central Clinical School, Sydney, New South Wales, AUSTRALIA
| | - Julia M L Brotherton
- Medical Director, VCS Population Health, VCS Foundation, Melbourne, Victoria, AUSTRALIA.,Honorary Principal Fellow, Melbourne School of Population and Global Health, University of Melbourne, Victoria, AUSTRALIA
| | - Skye McGregor
- Epidemiologist, The Kirby Institute, UNSW Sydney, New South Wales, AUSTRALIA
| | - Jonathan King
- Epidemiologist, The Kirby Institute, UNSW Sydney, New South Wales, AUSTRALIA
| | - Ece Egilmezer
- Virology Research Laboratory, Prince of Wales Hospital, Randwick, Sydney, New South Wales, AUSTRALIA.,UNSW Sydney, New South Wales, AUSTRALIA
| | - Robert Booy
- Senior Professorial Fellow, National Centre for Immunisation Research and Surveillance, Sydney, New South Wales, AUSTRALIA
| | - Cheryl A Jones
- Dean and Head of Sydney Medical School, The University of Sydney, Faculty of Medicine and Health, Sydney, New South Wales, AUSTRALIA
| | - William Rawlinson
- Senior Medical Virologist, Director of Serology, Virology and OTDS Laboratories, NSW Health Pathology Randwick, Sydney, New South Wales, AUSTRALIA.,UNSW Sydney, New South Wales, AUSTRALIA
| | - Bruce R Thorley
- Head, National Enterovirus Reference Laboratory and WHO Polio Regional Reference Laboratory, Victorian Infectious Disease Reference Laboratory, Melbourne, Victoria, AUSTRALIA.,The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, AUSTRALIA
| | - Elizabeth J Elliott
- The University of Sydney, Faculty of Medicine and Health, Discipline of Child and Adolescent Health, Sydney, New South Wales, AUSTRALIA.,The Sydney Children's Hospitals Network, Westmead, Sydney, New South Wales, AUSTRALIA
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Dinsmore N. Paediatric Active Enhanced Disease Surveillance (PAEDS) 2019: Prospective hospital-based surveillance for serious paediatric conditions. COMMUNICABLE DISEASES INTELLIGENCE (2018) 2021; 45. [PMID: 34587877 DOI: 10.33321/cdi.2021.45.53] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Introduction The Paediatric Active Enhanced Disease Surveillance (PAEDS) network is an Australian hospital-based active surveillance system employing prospective case ascertainment for selected serious childhood conditions, particularly vaccine preventable diseases and potential adverse events following immunisation (AEFI). This report presents surveillance data for 2019. Methods Specialist nurses screened hospital admissions, emergency department records, laboratory and other data on a daily basis in seven paediatric tertiary referral hospitals across Australia, to identify children with the conditions under surveillance. Standardised protocols and case definitions were used across all sites. In 2019, the conditions under surveillance comprised: acute flaccid paralysis (AFP; a syndrome associated with poliovirus infection), acute childhood encephalitis (ACE), influenza, intussusception (IS; a potential AEFI with rotavirus vaccines), pertussis, varicella-zoster virus infection (varicella and herpes zoster), invasive meningococcal and invasive Group A streptococcus diseases and two new conditions, Kawasaki disease and gram-negative bloodstream infections. An additional social research component continued to evaluate parental attitudes to influenza vaccination. Results PAEDS captured 2,701 cases for 2019 across all conditions under surveillance. Key outcomes of PAEDS included: contribution to national AFP surveillance to reach the World Health Organization reporting targets for detection of poliomyelitis cases; demonstration of high influenza activity in 2019 and influenza-associated deaths in ACE cases; identification of key barriers to influenza vaccination of children hospitalised for acute respiratory illness; reporting of all IS cases associated with vaccine receipt to relevant state health department; and showing a further reduction nationally in varicella cases. Enhanced pertussis surveillance continued to capture controls to support vaccine efficacy estimation. Invasive meningococcal disease surveillance showed predominance of serotype B and a reduction in cases nationally. Surveillance for invasive group A streptococcus captured severe cases in children. Monitoring of Kawasaki disease incidence and gram-negative bloodstream infections commenced. Conclusions PAEDS continues to provide unique policy-relevant data on serious paediatric conditions using sentinel hospital-based enhanced surveillance. Keywords: paediatric, surveillance, child, hospital, vaccine preventable diseases, adverse event following immunisation, acute flaccid paralysis, encephalitis, influenza, intussusception, pertussis, varicella zoster virus, meningococcal, group A streptococcus, Kawasaki, bloodstream infections.
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Affiliation(s)
- Nicole Dinsmore
- National Centre for Immunisation Research and Surveillance (NCIRS), Kids Research Institute, The Children's Hospital at Westmead
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Keeren K, Böttcher S, Diedrich S. Enterovirus Surveillance (EVSurv) in Germany. Microorganisms 2021; 9:2005. [PMID: 34683328 PMCID: PMC8538599 DOI: 10.3390/microorganisms9102005] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/17/2021] [Accepted: 09/17/2021] [Indexed: 01/22/2023] Open
Abstract
The major aim of the enterovirus surveillance (EVSurv) in Germany is to prove the absence of poliovirus circulation in the framework of the Global Polio Eradication Program (GPEI). Therefore, a free-of-charge enterovirus diagnostic is offered to all hospitals for patients with symptoms compatible with a polio infection. Within the quality proven laboratory network for enterovirus diagnostic (LaNED), stool and cerebrospinal fluid (CSF) samples from patients with suspected aseptic meningitis/encephalitis or acute flaccid paralysis (AFP) are screened for enterovirus (EV), typing is performed in all EV positive sample to exclude poliovirus infections. Since 2006, ≈200 hospitals from all 16 German federal states have participated annually. On average, 2500 samples (70% stool, 28% CSF) were tested every year. Overall, the majority of the patients studied are children <15 years. During the 15-year period, 53 different EV serotypes were detected. While EV-A71 was most frequently detected in infants, E30 dominated in older children and adults. Polioviruses were not detected. The German enterovirus surveillance allows monitoring of the circulation of clinically relevant serotypes resulting in continuous data about non-polio enterovirus epidemiology.
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Affiliation(s)
- Kathrin Keeren
- Secretary of the National Commission for Polio Eradication in Germany, Robert Koch Institute, 13353 Berlin, Germany;
| | - Sindy Böttcher
- National Reference Centre for Poliomyelitis and Enteroviruses, Robert Koch Institute, 13353 Berlin, Germany;
| | | | - Sabine Diedrich
- National Reference Centre for Poliomyelitis and Enteroviruses, Robert Koch Institute, 13353 Berlin, Germany;
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Bruggink LD, Garcia-Clapes A, Tran T, Druce JD, Thorley BR. Decreased incidence of enterovirus and norovirus infections during the COVID-19 pandemic, Victoria, Australia, 2020. ACTA ACUST UNITED AC 2021; 45. [PMID: 33573536 DOI: 10.33321/cdi.2021.45.5] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Abstract Significant reductions in the incidence of enteroviruses and noroviruses, both transmitted primarily by the faecal-oral route, were noted in 2020 compared to the previous decade, in Victoria, Australia. The enterovirus specimen positivity rate was reduced by 84.2% in 2020, while the norovirus outbreak positivity rate declined by 49.0%. The most likely explanation for these reductions is the concurrence of social restrictions, physical distancing, personal hygiene awareness and international and domestic border closures in response to the COVID-19 pandemic.
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Affiliation(s)
- Leesa D Bruggink
- Enteric Virus Laboratory, Victorian Infectious Diseases Reference Laboratory (VIDRL), Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity
| | - Arnau Garcia-Clapes
- Enteric Virus Laboratory, Victorian Infectious Diseases Reference Laboratory (VIDRL), Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity
| | - Thomas Tran
- Viral Identification Laboratory, Victorian Infectious Diseases Reference Laboratory (VIDRL), Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity
| | - Julian D Druce
- Viral Identification Laboratory, Victorian Infectious Diseases Reference Laboratory (VIDRL), Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity
| | - Bruce R Thorley
- Enteric Virus Laboratory, Victorian Infectious Diseases Reference Laboratory (VIDRL), Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity
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Baicus A, Joffret ML, Bessaud M, Delpeyroux F, Oprisan G. Reinforced poliovirus and enterovirus surveillance in Romania, 2015-2016. Arch Virol 2020; 165:2627-2632. [PMID: 32776175 DOI: 10.1007/s00705-020-04772-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 07/13/2020] [Indexed: 10/23/2022]
Abstract
Due to the risk of poliovirus importation from Ukraine in 2015, a combined surveillance program monitoring the circulation of enteroviruses (EVs) in healthy children from at-risk areas and in the environment was conducted in Romania. Virological testing of stool samples collected from 155 healthy children aged from two months to six years and of 186 sewage water samples collected from different areas was performed. A total of 58 (37.42%) stool samples and 50 (26.88%) sewage water samples were positive for non-polio EVs, but no poliovirus was detected. A high level of circulation of echovirus (E) types 6 and 7 and coxsackievirus (CV) type B5 was observed.
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Affiliation(s)
- Anda Baicus
- Cantacuzino Medico Military National Institute of Research and Development, Bucharest, Romania. .,Carol Davila University of Medicine and Pharmacy, Bucharest, Romania.
| | | | | | | | - Gabriela Oprisan
- Cantacuzino Medico Military National Institute of Research and Development, Bucharest, Romania.,Faculty of Pharmacy, Titu Maiorescu University, Bucharest, Romania
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