1
|
Torii S, Gouttenoire J, Kumar K, Antanasijevic A, Kohn T. Influence of Amino Acid Substitutions in Capsid Proteins of Coxsackievirus B5 on Free Chlorine and Thermal Inactivation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:5279-5289. [PMID: 38488515 DOI: 10.1021/acs.est.3c10409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
The sensitivity of enteroviruses to disinfectants varies among genetically similar variants and coincides with amino acid changes in capsid proteins, although the effect of individual substitutions remains unknown. Here, we employed reverse genetics to investigate how amino acid substitutions in coxsackievirus B5 (CVB5) capsid proteins affect the virus' sensitivity to free chlorine and heat treatment. Of ten amino acid changes observed in CVB5 variants with free chlorine resistance, none significantly reduced the chlorine sensitivity, indicating a minor role of the capsid composition in chlorine sensitivity of CVB5. Conversely, a subset of these amino acid changes located at the C-terminal region of viral protein 1 led to reduced heat sensitivity. Cryo-electron microscopy revealed that these changes affect the assembly of intermediate viral states (altered and empty particles), suggesting that the mechanism for reduced heat sensitivity could be related to improved molecular packing of CVB5, resulting in greater stability or altered dynamics of virus uncoating during infection.
Collapse
Affiliation(s)
- Shotaro Torii
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Jérôme Gouttenoire
- Division of Gastroenterology and Hepatology, Lausanne University Hospital and University of Lausanne, CH-1011 Lausanne, Switzerland
| | - Kiruthika Kumar
- Virology and Structural Immunology Laboratory, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Aleksandar Antanasijevic
- Virology and Structural Immunology Laboratory, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Tamar Kohn
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| |
Collapse
|
2
|
Song J, Lu H, Ma L, Zhu S, Yan D, Han J, Zhang Y. Molecular Characteristics of Enterovirus B83 Strain Isolated from a Patient with Acute Viral Myocarditis and Global Transmission Dynamics. Viruses 2023; 15:1360. [PMID: 37376658 DOI: 10.3390/v15061360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 06/08/2023] [Accepted: 06/10/2023] [Indexed: 06/29/2023] Open
Abstract
This study determined the global genetic diversity and transmission dynamics of enterovirus B83 (EV-B83) and proposed future disease surveillance directions. Blood samples were collected from a patient with viral myocarditis, and viral isolation was performed. The complete genome sequence of the viral isolate was obtained using Sanger sequencing. A dataset of 15 sequences (from three continents) that had sufficient time signals for Bayesian phylogenetic analysis was set up, and the genetic diversity and transmission dynamics of global EV-B83 were analyzed using bioinformatics methods, including evolutionary dynamics, recombination event analysis, and phylogeographic analysis. Here, we report the complete genome sequence of an EV-B83 strain (S17/YN/CHN/2004) isolated from a patient with acute viral myocarditis in Yunnan Province, China. All 15 EV-B83 strains clustered together in a phylogenetic tree, confirming the classification of these isolates as a single EV type, and the predicted time for the most recent common ancestor appeared in 1998. Recombinant signals were detected in the 5'-untranslated region and 2A-3D coding regions of the S17 genome. The phylogeographic analysis revealed multiple intercontinental transmission routes of EV-B83. This study indicates that EV-B83 is globally distributed. Our findings add to the publicly available EV-B83 genomic sequence data and deepen our understanding of EV-B83 epidemiology.
Collapse
Affiliation(s)
- Juan Song
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Huanhuan Lu
- National Polio Laboratory and WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory of biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Lin Ma
- Yunnan Institute of Endemic Diseases Control and Prevention, No.5, Wenhua Road, Dali 671000, China
| | - Shuangli Zhu
- National Polio Laboratory and WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory of biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Dongmei Yan
- National Polio Laboratory and WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory of biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Jun Han
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Yong Zhang
- National Polio Laboratory and WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory of biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| |
Collapse
|
3
|
Tan M, Suo J, Zhang Z, He W, Tan L, Jiang H, Li M, He J, Pan Y, Xu B, Yan L, Bin S, Gan Z, Sun Y, Jiang H, Sun Q, Zhang Z. Molecular characterization of coxsackievirus B5 from the sputum of pneumonia children patients of Kunming, Southwest China. Virol J 2023; 20:74. [PMID: 37076847 PMCID: PMC10116704 DOI: 10.1186/s12985-023-02019-w] [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: 06/30/2022] [Accepted: 03/23/2023] [Indexed: 04/21/2023] Open
Abstract
BACKGROUND CVB5 can cause respiratory infections. However, the molecular epidemiological information about CVB5 in respiratory tract samples is still limited. Here, we report five cases in which CVB5 was detected in sputum sample of pneumonia children patients from Kunming, Southwest China. METHODS CVB5 isolates were obtained from sputum samples of patients with pneumonia. Whole-genome sequencing of CVB5 isolates was performed using segmented PCR, and phylogenetic, mutation and recombination analysis. The effect of mutations in the VP1 protein on hydration were analyzed by Protscale. The tertiary models of VP1 proteins were established by Colabfold, and the effect of mutations in VP1 protein on volume modifications and binding affinity were analyzed by Pymol software and PROVEAN. RESULTS A total of five CVB5 complete genome sequences were obtained. No obvious homologous recombination signals comparing with other coxsackie B viruses were observed in the five isolates. Phylogenetic analysis showed that the five CVB5 sputum isolates were from an independent branch in genogroup E. Due to the mutation, the structure and spatial of the VP1 protein N-terminus have changed significantly. Comparing to the Faulkner (CVB5 prototype strain), PROVEAN revealed three deleterious substitutions: Y75F, N166T (KM35), T140I (KM41). The last two of the three deleterious substitutions significantly increased the hydrophobicity of the residues. CONCLUSIONS We unexpectedly found five cases of CVB5 infection instead of rhinoviruses infection during our routine surveillance of rhinoviruses in respiratory tract samples. All five patients were hospitalized with pneumonia symptoms and were not tested for enterovirus during their hospitalization. This report suggests that enterovirus surveillance in patients with respiratory symptoms should be strengthened.
Collapse
Affiliation(s)
- Miao Tan
- Department of Clinical Pharmacy, Affiliated Hospital of Yunnan University, 176 Qing Nian Road, Kunming, 650118 Yunnan Province People’s Republic of China
- Kunming Medical University, Kunming, People’s Republic of China
| | - Jiale Suo
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), 935 Jiao Ling Road, Kunming, 650118 Yunnan Province People’s Republic of China
- Kunming Medical University, Kunming, People’s Republic of China
| | - Zhilei Zhang
- Kunming Children’s Hospital , The Affiliated Children’s Hospital of Kunming Medical University, 288 Qian Xin Road, Kunming, 650228 Yunnan Province People’s Republic of China
- Yunnan Key Laboratory of Children’s Major Disease Research, Kunming, People’s Republic of China
| | - Wenji He
- Kunming Children’s Hospital , The Affiliated Children’s Hospital of Kunming Medical University, 288 Qian Xin Road, Kunming, 650228 Yunnan Province People’s Republic of China
| | - Li Tan
- Kunming Children’s Hospital , The Affiliated Children’s Hospital of Kunming Medical University, 288 Qian Xin Road, Kunming, 650228 Yunnan Province People’s Republic of China
| | - Haiyan Jiang
- Kunming Children’s Hospital , The Affiliated Children’s Hospital of Kunming Medical University, 288 Qian Xin Road, Kunming, 650228 Yunnan Province People’s Republic of China
- Yunnan Key Laboratory of Children’s Major Disease Research, Kunming, People’s Republic of China
| | - Ming Li
- Kunming Children’s Hospital , The Affiliated Children’s Hospital of Kunming Medical University, 288 Qian Xin Road, Kunming, 650228 Yunnan Province People’s Republic of China
| | - Juan He
- Kunming Children’s Hospital , The Affiliated Children’s Hospital of Kunming Medical University, 288 Qian Xin Road, Kunming, 650228 Yunnan Province People’s Republic of China
| | - Yue Pan
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), 935 Jiao Ling Road, Kunming, 650118 Yunnan Province People’s Republic of China
- Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming, People’s Republic of China
| | - Bin Xu
- Kunming Children’s Hospital , The Affiliated Children’s Hospital of Kunming Medical University, 288 Qian Xin Road, Kunming, 650228 Yunnan Province People’s Republic of China
| | - Lingmei Yan
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), 935 Jiao Ling Road, Kunming, 650118 Yunnan Province People’s Republic of China
- Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming, People’s Republic of China
| | - Songtao Bin
- Kunming Children’s Hospital , The Affiliated Children’s Hospital of Kunming Medical University, 288 Qian Xin Road, Kunming, 650228 Yunnan Province People’s Republic of China
| | - Zhengyan Gan
- Kunming Children’s Hospital , The Affiliated Children’s Hospital of Kunming Medical University, 288 Qian Xin Road, Kunming, 650228 Yunnan Province People’s Republic of China
| | - Yuxing Sun
- Kunming Children’s Hospital , The Affiliated Children’s Hospital of Kunming Medical University, 288 Qian Xin Road, Kunming, 650228 Yunnan Province People’s Republic of China
| | - Hongchao Jiang
- Kunming Children’s Hospital , The Affiliated Children’s Hospital of Kunming Medical University, 288 Qian Xin Road, Kunming, 650228 Yunnan Province People’s Republic of China
- Yunnan Key Laboratory of Children’s Major Disease Research, Kunming, People’s Republic of China
| | - Qiangming Sun
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), 935 Jiao Ling Road, Kunming, 650118 Yunnan Province People’s Republic of China
- Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming, People’s Republic of China
| | - Zhen Zhang
- Department of Clinical Pharmacy, Affiliated Hospital of Yunnan University, 176 Qing Nian Road, Kunming, 650118 Yunnan Province People’s Republic of China
| |
Collapse
|
4
|
Razafindratsimandresy R, Joffret ML, Andriamandimby SF, Andriamamonjy S, Rabemanantsoa S, Richard V, Delpeyroux F, Heraud JM, Bessaud M. Enterovirus detection in different regions of Madagascar reveals a higher abundance of enteroviruses of species C in areas where several outbreaks of vaccine-derived polioviruses occurred. BMC Infect Dis 2022; 22:821. [PMID: 36348312 PMCID: PMC9641760 DOI: 10.1186/s12879-022-07826-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 10/31/2022] [Indexed: 11/11/2022] Open
Abstract
Background Poliomyelitis outbreaks due to pathogenic vaccine-derived polioviruses (VDPVs) are threatening and complicating the global polio eradication initiative. Most of these VDPVs are genetic recombinants with non-polio enteroviruses (NPEVs) of species C. Little is known about factors favoring this genetic macroevolution process. Since 2001, Madagascar has experienced several outbreaks of poliomyelitis due to VDPVs, and most of VDPVs were isolated in the south of the island. The current study explored some of the viral factors that can promote and explain the emergence of recombinant VDPVs in Madagascar. Methods Between May to August 2011, we collected stools from healthy children living in two southern and two northern regions of Madagascar. Virus isolation was done in RD, HEp-2c, and L20B cell lines, and enteroviruses were detected using a wide-spectrum 5ʹ-untranslated region RT-PCR assay. NPEVs were then sequenced for the VP1 gene used for viral genotyping. Results Overall, we collected 1309 stools, of which 351 NPEVs (26.8%) were identified. Sequencing revealed 33 types of viruses belonging to three different species: Enterovirus A (8.5%), Enterovirus B (EV-B, 40.2%), and Enterovirus C (EV-C, 51.3%). EV-C species included coxsackievirus A13, A17, and A20 previously described as putative recombination partners for poliovirus vaccine strains. Interestingly, the isolation rate was higher among stools originating from the South (30.3% vs. 23.6%, p-value = 0.009). EV-C were predominant in southern sites (65.7%) while EV-B predominated in northern sites (54.9%). The factors that explain the relative abundance of EV-C in the South are still unknown. Conclusions Whatever its causes, the relative abundance of EV-C in the South of Madagascar may have promoted the infections of children by EV-C, including the PV vaccine strains, and have favored the recombination events between PVs and NPEVs in co-infected children, thus leading to the recurrent emergence of recombinant VDPVs in this region of Madagascar. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-022-07826-0.
Collapse
|
5
|
Cheng D, Chiu YW, Huang SW, Lien YY, Chang CL, Tsai HP, Wang YF, Wang JR. Genetic and Cross Neutralization Analyses of Coxsackievirus A16 Circulating in Taiwan from 1998 to 2021 Suggest Dominant Genotype B1 can Serve as Vaccine Candidate. Viruses 2022; 14:2306. [PMID: 36298861 PMCID: PMC9608817 DOI: 10.3390/v14102306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 10/15/2022] [Accepted: 10/18/2022] [Indexed: 07/30/2023] Open
Abstract
Coxsackievirus A16 (CVA16) is well known for causing hand-foot-and-mouth disease (HFMD) and outbreaks were frequently reported in Taiwan in the past twenty years. The epidemiology and genetic variations of CVA16 in Taiwan from 1998 to 2021 were analyzed in this study. CVA16 infections usually occurred in early summer and early winter, and showed increased incidence in 1998, 2000-2003, 2005, 2007-2008, and 2010 in Taiwan. Little or no CVA16 was detected from 2017 to 2021. CVA16 infection was prevalent in patients between 1 to 3 years old. A total of 69 isolates were sequenced. Phylogenetic analysis based on the VP1 region showed that CVA16 subgenotype B1 was dominantly isolated in Taiwan from 1998 to 2019, and B2 was identified only from isolates collected in 1999 and 2000. There was a high frequency of synonymous mutations in the amino acid sequences of the VP1 region among CVA16 isolates, with the exception of position 145 which showed positive selection. The recombination analysis of the whole genome of CVA16 isolates indicated that the 5'-untranslated region and the non-structural protein region of CVA16 subgenotype B1 were recombined with Coxsackievirus A4 (CVA4) and enterovirus A71 (EVA71) genotype A, respectively. The recombination pattern of subgenotype B2 was similar to B1, however, the 3D region was similar to EVA71 genotype B. Cross-neutralization among CVA16 showed that mouse antisera from various subgenotypes viruses can cross-neutralize different genotype with high neutralizing antibody titers. These results suggest that the dominant CVA16 genotype B1 can serve as a vaccine candidate for CVA16.
Collapse
Affiliation(s)
- Dayna Cheng
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
| | - Yo-Wei Chiu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Tainan 70101, Taiwan
| | - Sheng-Wen Huang
- National Mosquito-Borne Diseases Control Research Center, National Health Research Institutes, Tainan 70101, Taiwan
| | - Yun-Yin Lien
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Tainan 70101, Taiwan
| | - Chia-Lun Chang
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Tainan 70101, Taiwan
| | - Huey-Pin Tsai
- Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
| | - Ya-Fang Wang
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Tainan 70101, Taiwan
- National Mosquito-Borne Diseases Control Research Center, National Health Research Institutes, Tainan 70101, Taiwan
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
| | - Jen-Ren Wang
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Tainan 70101, Taiwan
- Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
| |
Collapse
|
6
|
Chakraborty C, Bhattacharya M, Sharma AR, Dhama K, Lee SS. Continent-wide evolutionary trends of emerging SARS-CoV-2 variants: dynamic profiles from Alpha to Omicron. GeroScience 2022; 44:2371-2392. [PMID: 35831773 PMCID: PMC9281186 DOI: 10.1007/s11357-022-00619-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 06/27/2022] [Indexed: 01/06/2023] Open
Abstract
The ongoing SARS-CoV-2 evolution process has generated several variants due to its continuous mutations, making pandemics more critical. The present study illustrates SARS-CoV-2 evolution and its emerging mutations in five directions. First, the significant mutations in the genome and S-glycoprotein were analyzed in different variants. Three linear models were developed with the regression line to depict the mutational load for S-glycoprotein, total genome excluding S-glycoprotein, and whole genome. Second, the continent-wide evolution of SARS-CoV-2 and its variants with their clades and divergence were evaluated. It showed the region-wise evolution of the SARS-CoV-2 variants and their clustering event. The major clades for each variant were identified. One example is clade 21K, a major clade of the Omicron variant. Third, lineage dynamics and comparison between SARS-CoV-2 lineages across different countries are also illustrated, demonstrating dominant variants in various countries over time. Fourth, gene-wise mutation patterns and genetic variability of SARS-CoV-2 variants across various countries are illustrated. High mutation patterns were found in the ORF10, ORF6, S, and low mutation pattern E genes. Finally, emerging AA point mutations (T478K, L452R, N501Y, S477N, E484A, Q498R, and Y505H), their frequencies, and country-wise occurrence were identified, and the highest event of two mutations (T478K and L452R) was observed.
Collapse
Affiliation(s)
- Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, West Bengal 700126 India
| | - Manojit Bhattacharya
- Department of Zoology, Fakir Mohan University, Vyasa Vihar, Balasore, 756020 Odisha India
| | - Ashish Ranjan Sharma
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si, 24252 Gangwon-do Republic of Korea
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122 Uttar Pradesh India
| | - Sang-Soo Lee
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si, 24252 Gangwon-do Republic of Korea
| |
Collapse
|
7
|
Machado RS, Gomes-Neto F, Aguiar-Oliveira ML, Burlandy FM, Tavares FN, da Silva EE, Sousa IP. Analysis of Coxsackievirus B5 Infections in the Central Nervous System in Brazil: Insights into Molecular Epidemiology and Genetic Diversity. Viruses 2022; 14:v14050899. [PMID: 35632640 PMCID: PMC9146130 DOI: 10.3390/v14050899] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/17/2022] [Accepted: 04/19/2022] [Indexed: 11/16/2022] Open
Abstract
Coxsackievirus B5 (CVB5) is one of the most prevalent enteroviruses types in humans and causes annual epidemics worldwide. In the present study, we explored viral genetic diversity, molecular and epidemiological aspects of CVB5 obtained from cerebrospinal fluid and stool samples of patients with aseptic meningitis or acute flaccid paralysis, information that is still scarce in Brazil. From 2005 to 2018, 57 isolates of CVB5 were identified in the scope of the Brazilian Poliomyelitis Surveillance Program. Phylogenetic analyses of VP1 sequences revealed the circulation of two CVB5 genogroups, with genogroup B circulating until 2017, further replaced by genogroup A. Network analysis based on deduced amino acid sequences showed important substitutions in residues known to play critical roles in viral host tropism, cell entry, and viral antigenicity. Amino acid substitutions were investigated by the Protein Variation Effect Analyzer (PROVEAN) tool, which revealed two deleterious substitutions: T130N and T130A. To the best of our knowledge, this is the first report to use in silico approaches to determine the putative impact of amino acid substitutions on the CVB5 capsid structure. This work provides valuable information on CVB5 diversity associated with central nervous system (CNS) infections, highlighting the importance of evaluating the biological impact of certain amino acids substitutions associated with epidemiological and structural analyses.
Collapse
Affiliation(s)
- Raiana S. Machado
- Laboratório de Enterovírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil; (R.S.M.); (F.M.B.); (E.E.d.S.)
- Programa de Pós-Graduação em Medicina Tropical, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil
| | - Francisco Gomes-Neto
- Laboratório de Toxinologia, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil;
| | - Maria L. Aguiar-Oliveira
- Laboratório de Vírus Respiratórios e do Sarampo, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil;
| | - Fernanda M. Burlandy
- Laboratório de Enterovírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil; (R.S.M.); (F.M.B.); (E.E.d.S.)
| | - Fernando N. Tavares
- Laboratório de Referência Regional em Enteroviroses, Seção de Virologia, Instituto Evandro Chagas/Serviço de Vigilância Saúde/Ministério de SaúdeS, Ananindeua 67030-000, Brazil;
| | - Edson E. da Silva
- Laboratório de Enterovírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil; (R.S.M.); (F.M.B.); (E.E.d.S.)
| | - Ivanildo P. Sousa
- Laboratório de Enterovírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil; (R.S.M.); (F.M.B.); (E.E.d.S.)
- Correspondence: ; Tel.: +55-21-2562-1781
| |
Collapse
|
8
|
Torii S, Miura F, Itamochi M, Haga K, Katayama K, Katayama H. Impact of the Heterogeneity in Free Chlorine, UV 254, and Ozone Susceptibilities Among Coxsackievirus B5 on the Prediction of the Overall Inactivation Efficiency. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:3156-3164. [PMID: 33583178 DOI: 10.1021/acs.est.0c07796] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The disinfection susceptibilities of viruses vary even among variants, yet the inactivation efficiency of a certain virus genotype, species, or genus was determined based on the susceptibility of its laboratory strain. The objectives were to evaluate the variability in susceptibilities to free chlorine, UV254, and ozone among 13 variants of coxsackievirus B5 (CVB5) and develop the model allowing for predicting the overall inactivation of heterogeneous CVB5. Our results showed that the susceptibilities differed by up to 3.4-fold, 1.3-fold, and 1.8-fold in free chlorine, UV254, and ozone, respectively. CVB5 in genogroup B exhibited significantly lower susceptibility to free chlorine and ozone than genogroup A, where the laboratory strain, Faulkner, belongs. The capsid protein in genogroup B contained a lower number of sulfur-containing amino acids, readily reactive to oxidants. We reformulated the Chick-Watson model by incorporating the probability distributions of inactivation rate constants to capture the heterogeneity. This expanded Chick-Watson model indicated that up to 4.2-fold larger free chlorine CT is required to achieve 6-log inactivation of CVB5 than the prediction by the Faulkner strain. Therefore, it is recommended to incorporate the variation in disinfection susceptibilities for predicting the overall inactivation of a certain type of viruses.
Collapse
Affiliation(s)
- Shotaro Torii
- Department of Urban Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Fuminari Miura
- Center for Marine Environmental Studies (CMES), Ehime University, Bunkyo-cho 3, Matsuyama-shi, Ehime 790-8577, Japan
| | - Masae Itamochi
- Department of Virology, Toyama Institute of Health, 17-1 Nakataikoyama, Imizu-shi, Toyama 939-0363, Japan
| | - Kei Haga
- Laboratory of Viral Infection I, Department of Infection Control and Immunology, O̅mura Satoshi Memorial Institute & Graduate School of Infection Control Sciences, Kitasato University, Tokyo 108-8641, Japan
| | - Kazuhiko Katayama
- Laboratory of Viral Infection I, Department of Infection Control and Immunology, O̅mura Satoshi Memorial Institute & Graduate School of Infection Control Sciences, Kitasato University, Tokyo 108-8641, Japan
| | - Hiroyuki Katayama
- Department of Urban Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| |
Collapse
|
9
|
Torii S, Itamochi M, Katayama H. Inactivation kinetics of waterborne virus by ozone determined by a continuous quench flow system. WATER RESEARCH 2020; 186:116291. [PMID: 32836147 DOI: 10.1016/j.watres.2020.116291] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/07/2020] [Accepted: 08/09/2020] [Indexed: 05/22/2023]
Abstract
Ozone has a strong oxidation power that allows effective inactivation of waterborne viruses. Few studies have accurately measured the kinetic relationship between virus inactivation and ozone exposure, because the high reactivity of ozone makes it difficult to measure them simultaneously. A continuous quench flow system (CQFS) is a possible solution for analyzing such a fast reaction; however, previous studies reported that CQFS provided different results of inactivation rate constants from the batch system. The objectives of this study were (1) to develop a CQFS to evaluate the kinetics of microbial inactivation accurately, (2) to evaluate the inactivation rate constants of waterborne virus by ozone, and (3) to compare the results with previous studies. The results indicated that the simple plug flow assumption in the reaction tube of CQFS led to underestimation of the rate constants. The accurate measurement of rate constants was achieved by the pseudo-first-order reaction model that takes the residence time distribution (RTD; i.e., the laminar flow assumption) into account. The results of inactivation experiments suggested that the resistance of viruses were getting higher in the following order: Qβ < MS2, fr, GA < CVB5 Faulkner, φX-174, PV1 Sabin, CVB3 Nancy. The environmental isolates of CVB3 and CVB5 had a 2-fold higher resistance compared with their lab strains. Predicted CT values for 4-log inactivation ranged from 0.018 mg sec L-1 (Qβ) to 0.31 mg sec L-1 (CVB3 Environmental strain). The required CT values for 4-log PV1 inactivation was 0.15 mg sec L-1, which was 166-fold smaller than those reported in the United States Environmental Protection Agency guidance manuals. The overestimation in previous studies was due to the sparse assumption of RTD in the reactor. Consequently, the required ozone CT values for virus inactivation should be reconsidered to minimize the health risks and environmental costs in water treatment.
Collapse
Affiliation(s)
- Shotaro Torii
- Department of Urban Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan.
| | - Masae Itamochi
- Department of Virology, Toyama Institute of Health, 17-1 Nakataikoyama, Imizu-shi, Toyama, Japan
| | - Hiroyuki Katayama
- Department of Urban Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan
| |
Collapse
|
10
|
Toczylowski K, Wieczorek M, Bojkiewicz E, Wietlicka-Piszcz M, Gad B, Sulik A. Pediatric Enteroviral Central Nervous System Infections in Bialystok, Poland: Epidemiology, Viral Types, and Drivers of Seasonal Variation. Viruses 2020; 12:v12080893. [PMID: 32824117 PMCID: PMC7472221 DOI: 10.3390/v12080893] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/09/2020] [Accepted: 08/11/2020] [Indexed: 12/15/2022] Open
Abstract
Enteroviruses are common causes of infections of the central nervous system (CNS) that in temperate climates tend to peak in the summer. The aim of the study was to describe epidemiology, drivers of seasonality, and types of enteroviruses causing infections of the CNS in children in Northeastern Poland. We prospectively collected data on children hospitalized with infection of the CNS attributed to enteroviruses in Bialystok, Poland, from January 2015 to December 2019. In total, 224 children were included. Nineteen different enterovirus types were identified in isolates collected from 188 children. Coxsackie B5 (32%), echovirus 30 (20%), and echovirus 6 (14%) were the three most common types. Enteroviruses were more prevalent during the summer–fall season. Infections caused by echovirus 30 peaked early in June and coxsackievirus B5 in July, whereas echovirus 6 peaked late in October. Phylogenetic analyses of these three enterovirus types showed multiple lineages co-circulating in this region. Mean air temperatures and precipitation rates were independently associated with monthly number of cases. Considering lack of effective treatment or vaccine, easy transmission of enteroviruses between susceptible individuals, their high mutation rate and prolonged time of viral shedding, continued monitoring and surveillance are imperative to recognize enteroviral infections of the CNS and the changes in circulation of enteroviruses in Poland.
Collapse
Affiliation(s)
- Kacper Toczylowski
- Department of Pediatric Infectious Diseases, Medical University of Bialystok, Waszyngtona 17, 15-274 Bialystok, Poland; (E.B.); (A.S.)
- Correspondence: ; Tel.: +48-857-450-680
| | - Magdalena Wieczorek
- Department of Virology, National Institute of Public Health—National Institute of Hygiene, Chocimska 24, 00-791 Warsaw, Poland; (M.W.); (B.G.)
| | - Ewa Bojkiewicz
- Department of Pediatric Infectious Diseases, Medical University of Bialystok, Waszyngtona 17, 15-274 Bialystok, Poland; (E.B.); (A.S.)
| | - Magdalena Wietlicka-Piszcz
- Department of Theoretical Foundations of Biomedical Sciences and Medical Computer Science, Nicolaus Copernicus University in Torun, L. Rydygier Collegium Medicum in Bydgoszcz, 9 M. Skłodowska-Curie St., 85-094 Bydgoszcz, Poland;
| | - Beata Gad
- Department of Virology, National Institute of Public Health—National Institute of Hygiene, Chocimska 24, 00-791 Warsaw, Poland; (M.W.); (B.G.)
| | - Artur Sulik
- Department of Pediatric Infectious Diseases, Medical University of Bialystok, Waszyngtona 17, 15-274 Bialystok, Poland; (E.B.); (A.S.)
| |
Collapse
|
11
|
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.
Collapse
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
| |
Collapse
|
12
|
Bondaryuk AN, Sidorova EA, Adelshin RV, Andaev EI, Balakhonov SV. Reporting of New tick-borne encephalitis virus strains isolated in Eastern Siberia (Russia) in 1960-2011 and explaining them in an evolutionary context using Bayesian phylogenetic inference. Ticks Tick Borne Dis 2020; 11:101496. [PMID: 32723652 DOI: 10.1016/j.ttbdis.2020.101496] [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: 10/13/2019] [Revised: 06/03/2020] [Accepted: 06/12/2020] [Indexed: 12/11/2022]
Abstract
Tick-borne encephalitis virus (TBEV) is one of the main tick-borne viral pathogens of humans. Infection may induce signs of meningitis, encephalitis, paralysis and high fever. TBEV is well studied by molecular phylogenetic methods. The present-day implementation of Bayesian phylogenetic models allows population dynamics to be tracked, providing changes in population size that were not directly observed. However, the description of the past population dynamics of TBEV is rare in the literature. In our investigation, we provide data on the dynamics of viral genetic diversity of TBEV in Zabaikalsky Krai (Eastern Siberia, Russia) revealed by the Bayesian coalescent inference in a BEAST program. As a data set, we used the envelope (E) protein partial gene sequences (1308 nt) of 38 TBEV strains (including six "886-84-like" or Baikalian subtype strains (TBEV-B)), isolated in Zabaikalsky Krai (Eastern Siberia, Russia) in 1960-1963 and 1995-2011. To increase estimations reliability, we compared 9 model combinations by Path sampling and Stepping-stone sampling methods. It has been shown that the genetic diversity decline in the population history of TBEV in the 1950s coincides with the date of the beginning of wide dichlorodiphenyltrichloroethane forest dusting in Siberia. We assumed that the TBEV population on the territory of Siberia went through a genetic bottleneck. Also, we provide data estimating the divergence time of TBEV-B strains and indicate the specific evolution rate of an ancestor lineage of the Baikalian subtype, illustrated on a phylogenetic tree, and reconstructed under a relaxed clock model.
Collapse
Affiliation(s)
- Artem N Bondaryuk
- Irkutsk Antiplague Research Institute of Siberia and Far East, Trilisser 78, 664047, Irkutsk, Russia.
| | - Elena A Sidorova
- Irkutsk Antiplague Research Institute of Siberia and Far East, Trilisser 78, 664047, Irkutsk, Russia.
| | - Renat V Adelshin
- Irkutsk Antiplague Research Institute of Siberia and Far East, Trilisser 78, 664047, Irkutsk, Russia; Irkutsk State University, Irkutsk, Russia.
| | - Evgeny I Andaev
- Irkutsk Antiplague Research Institute of Siberia and Far East, Trilisser 78, 664047, Irkutsk, Russia.
| | - Sergey V Balakhonov
- Irkutsk Antiplague Research Institute of Siberia and Far East, Trilisser 78, 664047, Irkutsk, Russia.
| |
Collapse
|
13
|
Bisseux M, Debroas D, Mirand A, Archimbaud C, Peigue-Lafeuille H, Bailly JL, Henquell C. Monitoring of enterovirus diversity in wastewater by ultra-deep sequencing: An effective complementary tool for clinical enterovirus surveillance. WATER RESEARCH 2020; 169:115246. [PMID: 31710918 DOI: 10.1016/j.watres.2019.115246] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 10/07/2019] [Accepted: 10/26/2019] [Indexed: 05/28/2023]
Abstract
In a one-year (October 2014-October 2015) pilot study, we assessed wastewater monitoring with sustained sampling for analysis of global enterovirus (EV) infections in an urban community. Wastewater was analysed by ultra-deep sequencing (UDS) after PCR amplification of the partial VP1 capsid protein gene. The nucleotide sequence analysis showed an unprecedented diversity of 48 EV types within the community, which were assigned to the taxonomic species A (n = 13), B (n = 23), and C (n = 12). During the same period, 26 EV types, of which 22 were detected in wastewater, were identified in patients referred to the teaching hospital serving the same urban population. Wastewater surveillance detected a silent circulation of 26 EV types including viruses reported in clinically rare respiratory diseases. Wastewater monitoring as a supplementary procedure can complement clinical surveillance of severe diseases related to non-polio EVs and contribute to the final stages of poliomyelitis eradication.
Collapse
Affiliation(s)
- Maxime Bisseux
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Genome et Environnement, F-63000, Clermont-Ferrand, France; CHU Clermont-Ferrand, 3 IHP, Centre National de Référence des entérovirus et parechovirus - Laboratoire Associé, Laboratoire de Virologie, F-63000, Clermont-Ferrand, France.
| | - Didier Debroas
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Genome et Environnement, F-63000, Clermont-Ferrand, France
| | - Audrey Mirand
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Genome et Environnement, F-63000, Clermont-Ferrand, France; CHU Clermont-Ferrand, 3 IHP, Centre National de Référence des entérovirus et parechovirus - Laboratoire Associé, Laboratoire de Virologie, F-63000, Clermont-Ferrand, France
| | - Christine Archimbaud
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Genome et Environnement, F-63000, Clermont-Ferrand, France; CHU Clermont-Ferrand, 3 IHP, Centre National de Référence des entérovirus et parechovirus - Laboratoire Associé, Laboratoire de Virologie, F-63000, Clermont-Ferrand, France
| | - Hélène Peigue-Lafeuille
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Genome et Environnement, F-63000, Clermont-Ferrand, France; CHU Clermont-Ferrand, 3 IHP, Centre National de Référence des entérovirus et parechovirus - Laboratoire Associé, Laboratoire de Virologie, F-63000, Clermont-Ferrand, France
| | - Jean-Luc Bailly
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Genome et Environnement, F-63000, Clermont-Ferrand, France; CHU Clermont-Ferrand, 3 IHP, Centre National de Référence des entérovirus et parechovirus - Laboratoire Associé, Laboratoire de Virologie, F-63000, Clermont-Ferrand, France
| | - Cécile Henquell
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Genome et Environnement, F-63000, Clermont-Ferrand, France; CHU Clermont-Ferrand, 3 IHP, Centre National de Référence des entérovirus et parechovirus - Laboratoire Associé, Laboratoire de Virologie, F-63000, Clermont-Ferrand, France
| |
Collapse
|
14
|
Genetic characterization of a novel recombinant echovirus 30 strain causing a regional epidemic of aseptic meningitis in Hokkaido, Japan, 2017. Arch Virol 2019; 165:433-438. [PMID: 31828510 PMCID: PMC7223842 DOI: 10.1007/s00705-019-04484-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 10/26/2019] [Indexed: 12/27/2022]
Abstract
A regional epidemic of aseptic meningitis caused by echovirus 30 (E30) occurred in Hokkaido, Japan, during the period of August-December 2017. To investigate their phylogenetic relationship to other human enteroviruses, we determined the complete genomic nucleotide sequences of isolates from this outbreak. Phylogenetic analysis of the viral capsid protein 1 gene showed that the strains were most closely related to E30 strains detected in Germany, France, and Russia in 2013. In contrast, the region encoding the viral protease and the RNA-dependent RNA polymerase had a close phylogenetic relationship to non-E30 enteroviruses detected in the United Kingdom and Switzerland in 2015-2017, suggesting that a recombination event had occurred.
Collapse
|
15
|
Fontana S, Fiore S, Buttinelli G, Amato C, Veronesi L, Zoni R, Triassi M, Pennino F, Giammanco GM, De Grazia S, Cicala A, Siragusa A, Gamper S, Spertini S, Castiglia P, Cossu A, Germinario C, Larocca AMV, Stefanelli P. Molecular Characterization of Coxsackievirus B5 Isolates from Sewage, Italy 2016-2017. FOOD AND ENVIRONMENTAL VIROLOGY 2019; 11:440-445. [PMID: 31346976 PMCID: PMC6848032 DOI: 10.1007/s12560-019-09395-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 07/19/2019] [Indexed: 06/10/2023]
Abstract
Hereby, the partial Viral Protein 1 sequences of Coxsackievirus B5 (CV-B5) from sewage samples, collected in Italy from 2016 to 2017, were compared with those available in GenBank from clinical samples. Phylogenetic analysis highlighted: (I) the predominant circulation of CV-B5 genogroup B in Italy, and (II) the presence of two new sub-genogroups.
Collapse
Affiliation(s)
- Stefano Fontana
- Department of Infectious Diseases, Italian National Institute of Health (Istituto Superiore di Sanità, ISS), Viale Regina Elena 299, 00161, Rome, Italy
| | - Stefano Fiore
- Department of Infectious Diseases, Italian National Institute of Health (Istituto Superiore di Sanità, ISS), Viale Regina Elena 299, 00161, Rome, Italy
| | - Gabriele Buttinelli
- Department of Infectious Diseases, Italian National Institute of Health (Istituto Superiore di Sanità, ISS), Viale Regina Elena 299, 00161, Rome, Italy
| | - Concetta Amato
- Department of Infectious Diseases, Italian National Institute of Health (Istituto Superiore di Sanità, ISS), Viale Regina Elena 299, 00161, Rome, Italy
| | - Licia Veronesi
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Roberta Zoni
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Maria Triassi
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Francesca Pennino
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Giovanni Maurizio Giammanco
- Department of Health Promotion, Mother and Child Care and Internal Medicine 'G. D'Alessandro', University of Palermo, Palermo, Italy
| | - Simona De Grazia
- Department of Health Promotion, Mother and Child Care and Internal Medicine 'G. D'Alessandro', University of Palermo, Palermo, Italy
| | | | | | - Sabine Gamper
- Comprensorio Sanitario di Bolzano, Servizio Igiene e Sanità Pubblica, Bolzano, Italy
| | - Silvia Spertini
- Comprensorio Sanitario di Bolzano, Servizio Igiene e Sanità Pubblica, Bolzano, Italy
| | - Paolo Castiglia
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Sassari, Italy
| | - Andrea Cossu
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Sassari, Italy
| | - Cinzia Germinario
- Department of Biomedical Science and Human Oncology, University of Bari "Aldo Moro", Bari, Italy
| | | | - Paola Stefanelli
- Department of Infectious Diseases, Italian National Institute of Health (Istituto Superiore di Sanità, ISS), Viale Regina Elena 299, 00161, Rome, Italy.
| |
Collapse
|
16
|
Environmental Surveillance Can Dynamically Track Ecological Changes in Enteroviruses. Appl Environ Microbiol 2019; 85:AEM.01604-19. [PMID: 31585989 DOI: 10.1128/aem.01604-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 09/26/2019] [Indexed: 11/20/2022] Open
Abstract
Environmental surveillance can be used to trace enteroviruses shed from human stool using a sewer network that is independent of symptomatic or asymptomatic infection. In this study, the local transmission of enteroviruses was analyzed using two wastewater treatment plants, which were relatively close to each other (15 km), designated as sentinels. Influent was collected at both sentinels once a month from 2013 to 2016, and viruses were isolated. Using neutralizing tests with type-specific polyclonal antisera and molecular typing, 933 isolates were identified as enteroviruses. Our results showed that the frequency of virus isolation varied for each serotype at the two sentinels in a time-dependent manner. Because echovirus 11 (Echo11) and coxsackievirus B5 isolates showed a high frequency and were difficult to distinguish, they were further grouped into various lineages based on the VP1 amino acid sequences. The prevalence of each lineage was visualized using multidimensional scaling. The results showed that Echo11 isolates of the same lineage were isolated continuously, similar to coxsackievirus B5 isolates of three lineages. Conversely, Echo1, Echo13, Echo18, Echo19, Echo20, Echo29, and Echo33 were isolated only once each. Our findings suggested that if an enterovirus is imported into the population, it may result in small-scale transmission, whereas if there are initially many infected individuals, it may be possible for the virus to spread to a wide area, beyond the local community, over time. In addition, our findings could provide insights into risk assessment of transmission for importation of poliovirus in polio-free countries and regions.IMPORTANCE In this study, we showed that environmental enterovirus surveillance can be used to monitor the propagation of nonpolio enteroviruses in addition to poliovirus detection. Since epidemiological studies of virus transmission based on the past were performed using specimens from humans, there were limitations to research design, such as specimen collection for implementation on a large-scale target population. However, environmental monitoring can dynamically track the ecological changes in enteroviruses in the region by monitoring viruses in chronological order and targeting the population within the area by monitoring viruses over time. We observed differences in the transmission of echovirus 11 and coxsackievirus B5 in the region according to lineage in a time-dependent manner and with a multidimensional scaling pattern.
Collapse
|
17
|
Richter J, Tryfonos C, Christodoulou C. Molecular epidemiology of enteroviruses in Cyprus 2008-2017. PLoS One 2019; 14:e0220938. [PMID: 31393960 PMCID: PMC6687182 DOI: 10.1371/journal.pone.0220938] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 07/26/2019] [Indexed: 12/28/2022] Open
Abstract
Enteroviruses (EVs) are associated with a broad spectrum of disease manifestations, including aseptic meningitis, encephalitis, hand, foot and mouth disease, acute flaccid paralysis and acute flaccid myelitis with outbreaks being reported frequently world-wide. The aim of this study was the molecular characterization of all enteroviruses detected in Cyprus in the ten-year period from January 2008 and December 2017 as well as a description of the circulation patterns associated with the most frequently encountered genotypes. For this purpose, serum, cerebrospinal fluid, nasal swab, skin swab and/or stool samples from 2666 patients with a suspected EV infection were analysed between January 2008 and December 2017. Enteroviruses were detected in 295 (11.1%) patients, which were then investigated further for epidemiological analysis by VP1 genotyping. Overall, 24 different enterovirus types belonging to three different species were identified. The predominant species was EV-B (209/295, 71%), followed by species EV-A (77/295, 26.1%). Only one virus belonged to species EV-D, whereas EV-C enteroviruses were not identified at all. The most frequent genotypes identified were echovirus 30 (26.1%), echovirus 6 (14.2%) and coxsackievirus A6 (10.9%). While Echovirus 30 and echovirus 6 frequency was significantly higher in patients older than 3 years of age, the opposite was observed for CV-A16 and EV-A71, which dominated in young children less than 3 years. Importantly, for the current study period a significant increase of previously only sporadically observed EV-A types, such as EV-A71 and CV-A16 was noted. A phylogenetic analysis of EV-A71 showed that the majority of the EV-A71 strains from Cyprus belonged to sub-genogroup C1 and C2, with the exception of one C4 strain that was observed in 2011. The data presented provide a comprehensive picture of enteroviruses circulating in Cyprus over the last decade and will be helpful to clinicians and researchers involved in the treatment, prevention and control of enteroviral infections by helping interpret trends in enteroviral diseases by associating them with circulating serotypes, for studying the association of enteroviruses with clinical manifestations and develop strategies for designing future EV vaccines.
Collapse
Affiliation(s)
- Jan Richter
- Department of Molecular Virology, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- * E-mail:
| | - Christina Tryfonos
- Department of Molecular Virology, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Christina Christodoulou
- Department of Molecular Virology, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| |
Collapse
|
18
|
Evolutionary histories of coxsackievirus B5 and swine vesicular disease virus reconstructed by phylodynamic and sequence variation analyses. Sci Rep 2018; 8:8821. [PMID: 29891869 PMCID: PMC5995886 DOI: 10.1038/s41598-018-27254-y] [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: 02/03/2017] [Accepted: 05/21/2018] [Indexed: 01/15/2023] Open
Abstract
Coxsackievirus (CV)-B5 is a common human enterovirus reported worldwide; swine vesicular disease virus (SVDV) is a porcine variant of CV-B5. To clarify the transmission dynamics and molecular basis of host switching between CV-B5 and SVDV, we analysed and compared the VP1 and partial 3Dpol gene regions of these two viruses. Spatiotemporal dynamics of viral transmission were estimated using a Bayesian statistical inference framework. The detected selection events were used to analyse the key molecules associated with host switching. Analyses of VP1 sequences revealed six CV-B5 genotypes (A1–A4 and B1–B2) and three SVDV genotypes (I–III). Analyses of partial 3Dpol revealed five clusters (A–E). The genotypes evolved sequentially over different periods, albeit with some overlap. The major hub of CV-B5 transmission was in China whereas the major hubs of SVDV transmission were in Italy. Network analysis based on deduced amino acid sequences showed a diverse extension of the VP1 structural protein, whereas most sequences were clustered into two haplotypes in the partial 3Dpol region. Residue 178 of VP1 showed four epistatic interactions with residues known to play essential roles in viral host tropism, cell entry, and viral decoating.
Collapse
|
19
|
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.
Collapse
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
| |
Collapse
|
20
|
Hellferscee O, Tempia S, Walaza S, Variava E, Dawood H, Wolter N, Madhi SA, du Plessis M, Cohen C, Treurnicht FK. Enterovirus genotypes among patients with severe acute respiratory illness, influenza-like illness, and asymptomatic individuals in South Africa, 2012-2014. J Med Virol 2017; 89:1759-1767. [PMID: 28574589 PMCID: PMC5714810 DOI: 10.1002/jmv.24869] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 05/14/2017] [Indexed: 01/26/2023]
Abstract
Enteroviruses can cause outbreaks of severe acute respiratory illness (SARI) and EV-A, -B, -C, and -D species have different pathogenic profiles and circulation patterns. We aimed to characterize and determine the prevalence of enterovirus genotypes among South African patients with respiratory illness and controls during June 2012 to July 2014. Syndromic SARI and influenza-like illness (ILI) surveillance was performed at two sentinel sites. At each site nasopharyngeal/oropharyngeal specimens were collected from SARI and ILI patients as well as controls. Specimens were tested for enterovirus by real-time PCR. Positive specimens were further genotyped by sequencing a region of the VP1 gene. The prevalence of enterovirus was 5.8% (87/1494), 3.4% (103/3079), and 3.4% (46/1367) among SARI, ILI, and controls, respectively (SARI/controls, P = 0.002 and ILI/control, P = 0.973). Among the 101/236 (42.8%) enterovirus-positive specimens that could be genotyped, we observed a high diversity of circulating enterovirus genotypes (a total of 33 genotypes) from all four human enterovirus species with high prevalence of Enterovirus-B (60.4%; 61/101) and Enterovirus-A (21.8%; 22/101) compared to Enterovirus-C (10.9%; 11/101) and Enterovirus-D (6.9%; 7/101) (P = 0.477). Of the enterovirus genotypes identified, Echovirus 30 (9.9%, 10/101), Coxsackie virus B5 (7.9%, 8/101) and Enterovirus-D68 (6.9%, 7/101) were most prevalent. There was no difference in disease severity (SARI or ILI compared to controls) between the different enterovirus species (P = 0.167). We observed a high number of enterovirus genotypes in patients with respiratory illness and in controls from South Africa with no disease association of EV species with disease severity.
Collapse
Affiliation(s)
- Orienka Hellferscee
- National Institute for Communicable Diseases of the National Health Laboratory ServiceJohannesburgSouth Africa
- University of the WitwatersrandJohannesburgSouth Africa
| | - Stefano Tempia
- National Institute for Communicable Diseases of the National Health Laboratory ServiceJohannesburgSouth Africa
- Centres for Disease Control and PreventionAtlantaGeorgia
| | - Sibongile Walaza
- National Institute for Communicable Diseases of the National Health Laboratory ServiceJohannesburgSouth Africa
- University of the WitwatersrandJohannesburgSouth Africa
| | - Ebrahim Variava
- University of the WitwatersrandJohannesburgSouth Africa
- Department of MedicineKlerksdorp‐Tshepong Hospital ComplexKlerksdorpSouth Africa
| | - Halima Dawood
- Pietermaritzburg Metropolitan HospitalPietermaritzburgSouth Africa
- CaprisaUniversity of KwaZulu‐NatalSouth Africa
| | - Nicole Wolter
- National Institute for Communicable Diseases of the National Health Laboratory ServiceJohannesburgSouth Africa
- University of the WitwatersrandJohannesburgSouth Africa
| | - Shabir A. Madhi
- National Institute for Communicable Diseases of the National Health Laboratory ServiceJohannesburgSouth Africa
- University of the WitwatersrandJohannesburgSouth Africa
| | - Mignon du Plessis
- National Institute for Communicable Diseases of the National Health Laboratory ServiceJohannesburgSouth Africa
- University of the WitwatersrandJohannesburgSouth Africa
| | - Cheryl Cohen
- National Institute for Communicable Diseases of the National Health Laboratory ServiceJohannesburgSouth Africa
- University of the WitwatersrandJohannesburgSouth Africa
| | - Florette K. Treurnicht
- National Institute for Communicable Diseases of the National Health Laboratory ServiceJohannesburgSouth Africa
| |
Collapse
|
21
|
Tang J, Li Q, Tian B, Zhang J, Li K, Ding Z, Lu L. Complete Genome Analysis of an Enterovirus EV-B83 Isolated in China. Sci Rep 2016; 6:29432. [PMID: 27405393 PMCID: PMC4942604 DOI: 10.1038/srep29432] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 06/16/2016] [Indexed: 11/09/2022] Open
Abstract
Enterovirus B83 (EV-B83) is a recently identified member of enterovirus species B. It is a rarely reported serotype and up to date, only the complete genome sequence of the prototype strain from the United States is available. In this study, we describe the complete genomic characterization of an EV-B83 strain 246/YN/CHN/08HC isolated from a healthy child living in border region of Yunnan Province, China in 2008. Compared with the prototype strain, it had 79.6% similarity in the complete genome and 78.9% similarity in the VP1 coding region, reflecting the great genetic divergence among them. VP1-coding region alignment revealed it had 77.2–91.3% with other EV-B83 sequences available in GenBank. Similarity plot analysis revealed it had higher identity with several other EV-B serotypes than the EV-B83 prototype strain in the P2 and P3 coding region, suggesting multiple recombination events might have occurred. The great genetic divergence with previously isolated strains and the extremely rare isolation suggest this serotype has circulated at a low epidemic strength for many years. This is the first report of complete genome of EV-B83 in China.
Collapse
Affiliation(s)
- Jingjing Tang
- Yunnan Center for Disease Control and Prevention, Kunming, Yunnan Province, People's Republic of China
| | - Qiongfen Li
- Yunnan Center for Disease Control and Prevention, Kunming, Yunnan Province, People's Republic of China
| | - Bingjun Tian
- Yunnan Center for Disease Control and Prevention, Kunming, Yunnan Province, People's Republic of China
| | - Jie Zhang
- Yunnan Center for Disease Control and Prevention, Kunming, Yunnan Province, People's Republic of China
| | - Kai Li
- Yunnan Center for Disease Control and Prevention, Kunming, Yunnan Province, People's Republic of China
| | - Zhengrong Ding
- Yunnan Center for Disease Control and Prevention, Kunming, Yunnan Province, People's Republic of China
| | - Lin Lu
- Yunnan Center for Disease Control and Prevention, Kunming, Yunnan Province, People's Republic of China
| |
Collapse
|
22
|
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.
Collapse
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
| |
Collapse
|
23
|
Abstract
PURPOSE OF REVIEW There are over 100 serotypes of human enteroviruses, which cause a spectrum of illnesses, including meningitis, encephalitis, paralysis, myocarditis and rash. Increasing incidence of hand-foot-and-mouth disease in the Asia-Pacific region and recent outbreaks of enterovirus-associated disease, such as severe respiratory illness in the United States in 2014, highlight the threat of these viruses to human health. RECENT FINDINGS We describe recent outbreaks of human enteroviruses and summarize knowledge gaps regarding their burden, spectrum of diseases and epidemiology. SUMMARY Reported outbreaks of respiratory, neurological, skin and eye diseases associated with human enteroviruses have increased in frequency and size in recent years. Improved molecular diagnostics and genetic sequence analysis are beginning to reveal the complex dynamics of individual serotypes and genotypes, and their contribution to these outbreaks. However, the biological mechanisms underlying their emergence and transmission dynamics remain elusive. They are likely to involve changes in the virus, such as fitness, antigenicity, virulence or tropism, and in the human population, such as levels of sanitation and of homotypic and heterotypic immunity. Improvements in surveillance, serological surveys and detailed genetic and antigenic characterization of viral populations would help to elucidate these mechanisms. This will be important for the design of outbreak control and vaccine development strategies.
Collapse
|
24
|
Bruhn CAW, Nielsen SCA, Samaniego JA, Wadsworth J, Knowles NJ, Gilbert MTP. Viral meningitis epidemics and a single, recent, recombinant and anthroponotic origin of swine vesicular disease virus. EVOLUTION MEDICINE AND PUBLIC HEALTH 2015; 2015:289-303. [PMID: 26508717 PMCID: PMC4661520 DOI: 10.1093/emph/eov026] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 10/13/2015] [Indexed: 01/23/2023]
Abstract
Swine vesicular disease, an important viral disease affecting domestic pigs, is shown to have a single and recent origin in humans, leading us closer to a full understanding of the sudden emergence of this enigmatic veterinary disease, and exemplifying the sometimes overlooked risk of human to animal disease transfers. Background and objectives: Swine vesicular disease virus (SVDV) is a close relative of the human Enterovirus B serotype, coxsackievirus B5. As the etiological agent of a significant emergent veterinary disease, several studies have attempted to explain its origin. However, several key questions remain, including the full biological ancestry of the virus, and its geographical and temporal origin. Methodology: We sequenced near-complete genomes of 27 SVDV and 13 coxsackievirus B5 samples, all originally isolated between 1966 and 2006, and analysed these in conjunction with existing sequences and historical information. Results: While analyses incorporating 24 additional near-complete SVDV genomic sequences indicate clear signs of within-SVDV recombination, all 51 SVDV isolates remain monophyletic. This supports a hypothesis of a single anthroponotic transfer origin. Analysis of individual coding and non-coding regions supports that SVDV has a recombinant origin between coxsackievirus B5 and another Enterovirus B serotype, most likely coxsackievirus A9. Extensive Bayesian sequence-based analysis of the time of the most recent common ancestor of all analysed sequences places this within a few years around 1961. Epidemiological evidence points to China as an origin, but there are no available samples to test this conclusively. Conclusions and implications: Historical investigation and the clinical aspects of the involved Enterovirus B serotypes, makes the current results consistent with a hypothesis stating that SVDV originated through co-infection, recombination, and a single anthroponotic event, during large viral meningitis epidemics around 1960/1961 involving the ancestral serotypes. The exact geographical origin of SVDV may remain untestable due to historical aspects.
Collapse
Affiliation(s)
- Christian A W Bruhn
- Centre for GeoGenetics, Natural History Museum of Denmark, Soelvgade 83 S, Copenhagen K, DK-1307, Denmark; Present address: Weinberger Lab, Laboratory of Epidemiology and Public Health, Yale School of Medicine, 60 College Street, 06510 New Haven, CT and
| | - Sandra C Abel Nielsen
- Centre for GeoGenetics, Natural History Museum of Denmark, Soelvgade 83 S, Copenhagen K, DK-1307, Denmark; Stanford University, School of Medicine, 300 Pasteur Drive, CA 94305, USA
| | - Jose Alfredo Samaniego
- Centre for GeoGenetics, Natural History Museum of Denmark, Soelvgade 83 S, Copenhagen K, DK-1307, Denmark
| | - Jemma Wadsworth
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey, GU24 0NF, UK
| | - Nick J Knowles
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey, GU24 0NF, UK
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, Soelvgade 83 S, Copenhagen K, DK-1307, Denmark
| |
Collapse
|
25
|
Huang HW, Chen YS, Chen JYF, Lu PL, Lin YC, Chen BC, Chou LC, Wang CF, Su HJ, Huang YC, Shi YY, Chen HL, Sanno-Duanda B, Huang TS, Lin KH, Tyan YC, Chu PY. Phylodynamic reconstruction of the spatiotemporal transmission and demographic history of coxsackievirus B2. BMC Bioinformatics 2015; 16:302. [PMID: 26390997 PMCID: PMC4578604 DOI: 10.1186/s12859-015-0738-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 09/11/2015] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Studies regarding coxsackievirus (CV) tend to focus on epidemic outbreaks, an imbalanced topology is considered to be an indication of acute infection with partial cross-immunity. In enteroviruses, a clear understanding of the characteristics of tree topology, transmission, and its demographic dynamics in viral succession and circulation are essential for identifying prevalence trends in endemic pathogens such as coxsackievirus B2 (CV-B2). This study applied a novel Bayesian evolutionary approach to elucidate the phylodynamic characteristics of CV-B2. A dataset containing 51 VP1 sequences and a dataset containing 34 partial 3D(pol) sequencing were analyzed, where each dataset included Taiwan sequences isolated during 1988-2013. RESULTS Four and five genotypes were determined based on the 846-nucleotide VP1 and 441-nucleotide 3D(pol) (6641-7087) regions, respectively, with spatiotemporally structured topologies in both trees. Some strains with tree discordance indicated the occurrence of recombination in the region between the VP1 and 3D(pol) genes. The similarities of VP1 and 3D(pol) gene were 80.0%-96.8% and 74.7%-91.9%, respectively. Analyses of population dynamics using VP1 dataset indicated that the endemic CV-B2 has a small effective population size. The balance indices, high similarity, and low evolutionary rate in the VP1 region indicated mild herd immunity selection in the major capsid region. CONCLUSIONS Phylodynamic analysis can reveal demographic trends and herd immunity in endemic pathogens.
Collapse
Affiliation(s)
- Hui-Wen Huang
- Department of Anesthesiology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, ROC, Taiwan. .,Department of Biological Sciences, National Sun Yat-Sen University, Kaohsiung, ROC, Taiwan.
| | - Yao-Shen Chen
- Division of Infectious Diseases, Kaohsiung Veterans General Hospital, Kaohsiung, ROC, Taiwan. .,Division of Microbiology, Department of Pathology and Laboratory Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, ROC, Taiwan. .,Department of Internal Medicine, National Yang-Ming Medical University, Taipei, ROC, Taiwan.
| | - Jeff Yi-Fu Chen
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung, ROC, Taiwan.
| | - Po-Liang Lu
- School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, ROC, Taiwan. .,Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung, ROC, Taiwan.
| | - Yung-Cheng Lin
- Institute of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, ROC, Taiwan.
| | - Bao-Chen Chen
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, ROC, Taiwan.
| | - Li-Chiu Chou
- Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung, ROC, Taiwan.
| | - Chu-Feng Wang
- Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung, ROC, Taiwan.
| | - Hui-Ju Su
- Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung, ROC, Taiwan.
| | - Yi-Chien Huang
- Department of Medical Laboratory Science and Biotechnology, College of Health Sciences, Kaohsiung Medical University, Kaohsiung, ROC, Taiwan.
| | - Yong-Ying Shi
- Department of Medical Laboratory Science and Biotechnology, College of Health Sciences, Kaohsiung Medical University, Kaohsiung, ROC, Taiwan.
| | - Hsiu-Lin Chen
- Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung, ROC, Taiwan. .,Department of Respiratory Therapy, College of Medicine, Kaohsiung Medical University, Kaohsiung, ROC, Taiwan.
| | - Bintou Sanno-Duanda
- Department of Medical Laboratory Science and Biotechnology, College of Health Sciences, Kaohsiung Medical University, Kaohsiung, ROC, Taiwan. .,Department of laboratory medicine, Edward Francis Small Teaching Hospital, Banjul, Gambia.
| | - Tsi-Shu Huang
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, ROC, Taiwan.
| | - Kuei-Hsiang Lin
- School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, ROC, Taiwan.
| | - Yu-Chang Tyan
- Department of Medical Imaging and Radiological Sciences, Kaohsiung Medical University, Kaohsiung, Taiwan. .,Center for Infectious Disease and Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan.
| | - Pei-Yu Chu
- Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung, ROC, Taiwan. .,Department of Medical Laboratory Science and Biotechnology, College of Health Sciences, Kaohsiung Medical University, Kaohsiung, ROC, Taiwan.
| |
Collapse
|
26
|
Hassel C, Mirand A, Lukashev A, TerletskaiaLadwig E, Farkas A, Schuffenecker I, Diedrich S, Huemer HP, Archimbaud C, Peigue-Lafeuille H, Henquell C, Bailly JL. Transmission patterns of human enterovirus 71 to, from and among European countries, 2003 to 2013. Euro Surveill 2015; 20:30005. [DOI: 10.2807/1560-7917.es.2015.20.34.30005] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 01/21/2015] [Indexed: 11/20/2022] Open
Abstract
Enterovirus 71 (EV-71) is involved in epidemics of hand, foot, and mouth disease (HFMD) and has been reported to occur with severe neurological complications in eastern and south-east Asia. In other geographical areas, the transmission of this virus is poorly understood. We used large sequence datasets (of the gene encoding the viral protein 1, VP1) and a Bayesian phylogenetic approach to compare the molecular epidemiology and geographical spread patterns of EV-71 subgenogroups B4, B5, C1, C2, and C4 in Europe relative to other parts of the world. For the study, European countries considered were European Union (EU) Member States and Iceland, Norway and Switzerland. Viruses of the B4, B5, and C4 subgenogroups circulate mainly in eastern and south-east Asia. In Europe sporadic introductions of these subgenogroups are observed, however C1 and C2 viruses predominate. The phylogenies showed evidence of multiple events of spread involving C1 and C2 viruses within Europe since the mid-1990s. Two waves of sporadic C2 infections also occurred in 2010 and 2013. The 2007 Dutch outbreak caused by C2 and the occurrence of B5 and C4 infections in the EU between 2004 and 2013 arose while the circulation of C1 viruses was low. A transmission chain involving a C4 virus was traced from Japan to the EU and then further to Canada between 2001 and 2006. Recent events whereby spread of viruses have occurred from, to, and within Europe appear to be involved in the long term survival of EV-71, highlighting the need for enhanced surveillance of this virus.
Collapse
Affiliation(s)
- Chervin Hassel
- Clermont Université, Université d’Auvergne, EPIE, EA 4843, Clermont-Ferrand, France
| | - Audrey Mirand
- Clermont Université, Université d’Auvergne, EPIE, EA 4843, Clermont-Ferrand, France
- CHU Clermont-Ferrand, Service de Virologie, Centre National de Référence des Entérovirus et Paréchovirus – Laboratoire associé, Clermont-Ferrand, France
| | - Alexander Lukashev
- Chumakov Institute of Poliomyelitis and Viral Encephalitides, Moscow, Russia
| | - Elena TerletskaiaLadwig
- Prof. Gisela Enders & Kollegen MVZ GbR and Institute of Virology, Infectious Diseases and Epidemiology, Stuttgart, Germany
| | - Agnes Farkas
- Division of Virology, National Center for Epidemiology, Budapest, Hungary
| | - Isabelle Schuffenecker
- Laboratoire de Virologie Est des Hospices Civils de Lyon, Centre National de Référence des Entérovirus et Paréchovirus, Bron, France
| | - Sabine Diedrich
- National Reference Center for Poliomyelitis and Enterovirus, Robert Koch Institute, Berlin, Germany
| | | | - Christine Archimbaud
- Clermont Université, Université d’Auvergne, EPIE, EA 4843, Clermont-Ferrand, France
- CHU Clermont-Ferrand, Service de Virologie, Centre National de Référence des Entérovirus et Paréchovirus – Laboratoire associé, Clermont-Ferrand, France
| | - Hélène Peigue-Lafeuille
- Clermont Université, Université d’Auvergne, EPIE, EA 4843, Clermont-Ferrand, France
- CHU Clermont-Ferrand, Service de Virologie, Centre National de Référence des Entérovirus et Paréchovirus – Laboratoire associé, Clermont-Ferrand, France
| | - Cécile Henquell
- Clermont Université, Université d’Auvergne, EPIE, EA 4843, Clermont-Ferrand, France
- CHU Clermont-Ferrand, Service de Virologie, Centre National de Référence des Entérovirus et Paréchovirus – Laboratoire associé, Clermont-Ferrand, France
| | - Jean-Luc Bailly
- Clermont Université, Université d’Auvergne, EPIE, EA 4843, Clermont-Ferrand, France
- CHU Clermont-Ferrand, Service de Virologie, Centre National de Référence des Entérovirus et Paréchovirus – Laboratoire associé, Clermont-Ferrand, France
| |
Collapse
|
27
|
Zhou F, Wang Q, Sintchenko V, Gilbert GL, O'Sullivan MVN, Iredell JR, Dwyer DE. Use of the 5' untranslated region and VP1 region to examine the molecular diversity in enterovirus B species. J Med Microbiol 2014; 63:1339-1355. [PMID: 25038138 DOI: 10.1099/jmm.0.074682-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Human enteroviruses evolve quickly. The 5' untranslated region (UTR) is fundamentally important for efficient viral replication and for virulence; the VP1 region correlates well with antigenic typing by neutralization, and can be used for virus identification and evolutionary studies. In order to investigate the molecular diversity in EV-B species, the 5' UTR and VP1 regions were analysed for 208 clinical isolates from a single public-health laboratory (serving New South Wales, Australia), representing 28 EV-B types. Sequences were compared with the 5' UTR and VP1 regions of 98 strains available in GenBank, representing the same 28 types. The genetic relationships were analysed using two types of software (mega and BioNumerics). The sequence analyses of the 5' UTR and VP1 regions of 306 EV-B strains demonstrated that: (i) comparing the two regions gives strong evidence of epidemiological linkage of strains in some serotypes; (ii) the intraserotypic genetic variation within each gene reveals that they evolve distinctly largely due to their different functions; and (iii) mutation and possible recombination in the two regions play significant roles in the molecular diversity of EV-B. Understanding the tempo and pattern of molecular diversity and evolution is of great importance in the pathogenesis of EV-B enteroviruses, information which will assist in disease prevention and control.
Collapse
Affiliation(s)
- Fei Zhou
- Centre for Infectious Diseases and Microbiology (CIDM), Institute of Clinical Pathology and Medical Research (ICPMR), Westmead Hospital, University of Sydney, Westmead, New South Wales, Australia
| | - Qinning Wang
- Centre for Infectious Diseases and Microbiology (CIDM), Institute of Clinical Pathology and Medical Research (ICPMR), Westmead Hospital, University of Sydney, Westmead, New South Wales, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology (CIDM), Institute of Clinical Pathology and Medical Research (ICPMR), Westmead Hospital, University of Sydney, Westmead, New South Wales, Australia
| | - Gwendolyn L Gilbert
- Centre for Infectious Diseases and Microbiology (CIDM), Institute of Clinical Pathology and Medical Research (ICPMR), Westmead Hospital, University of Sydney, Westmead, New South Wales, Australia
| | - Matthew V N O'Sullivan
- Centre for Infectious Diseases and Microbiology (CIDM), Institute of Clinical Pathology and Medical Research (ICPMR), Westmead Hospital, University of Sydney, Westmead, New South Wales, Australia
| | - Jonathan R Iredell
- Centre for Infectious Diseases and Microbiology (CIDM), Institute of Clinical Pathology and Medical Research (ICPMR), Westmead Hospital, University of Sydney, Westmead, New South Wales, Australia
| | - Dominic E Dwyer
- Centre for Infectious Diseases and Microbiology (CIDM), Institute of Clinical Pathology and Medical Research (ICPMR), Westmead Hospital, University of Sydney, Westmead, New South Wales, Australia
| |
Collapse
|
28
|
The evolution of Vp1 gene in enterovirus C species sub-group that contains types CVA-21, CVA-24, EV-C95, EV-C96 and EV-C99. PLoS One 2014; 9:e93737. [PMID: 24695547 PMCID: PMC3973639 DOI: 10.1371/journal.pone.0093737] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 03/07/2014] [Indexed: 12/17/2022] Open
Abstract
Genus Enterovirus (Family Picornaviridae,) consists of twelve species divided into genetically diverse types by their capsid protein VP1 coding sequences. Each enterovirus type can further be divided into intra-typic sub-clusters (genotypes). The aim of this study was to elucidate what leads to the emergence of novel enterovirus clades (types and genotypes). An evolutionary analysis was conducted for a sub-group of Enterovirus C species that contains types Coxsackievirus A21 (CVA-21), CVA-24, Enterovirus C95 (EV-C95), EV-C96 and EV-C99. VP1 gene datasets were collected and analysed to infer the phylogeny, rate of evolution, nucleotide and amino acid substitution patterns and signs of selection. In VP1 coding gene, high intra-typic sequence diversities and robust grouping into distinct genotypes within each type were detected. Within each type the majority of nucleotide substitutions were synonymous and the non-synonymous substitutions tended to cluster in distinct highly polymorphic sites. Signs of positive selection were detected in some of these highly polymorphic sites, while strong negative selection was indicated in most of the codons. Despite robust clustering to intra-typic genotypes, only few genotype-specific ‘signature’ amino acids were detected. In contrast, when different enterovirus types were compared, there was a clear tendency towards fixation of type-specific ‘signature’ amino acids. The results suggest that permanent fixation of type-specific amino acids is a hallmark associated with evolution of different enterovirus types, whereas neutral evolution and/or (frequency-dependent) positive selection in few highly polymorphic amino acid sites are the dominant forms of evolution when strains within an enterovirus type are compared.
Collapse
|
29
|
Volle R, Bailly JL, Mirand A, Pereira B, Marque-Juillet S, Chambon M, Regagnon C, Brebion A, Henquell C, Peigue-Lafeuille H, Archimbaud C. Variations in Cerebrospinal Fluid Viral Loads Among Enterovirus Genotypes in Patients Hospitalized With Laboratory-Confirmed Meningitis Due to Enterovirus. J Infect Dis 2014; 210:576-84. [DOI: 10.1093/infdis/jiu178] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|