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Detection of Parechovirus and Enterovirus Among Infants Evaluated for Late-onset Sepsis in the Neonatal Intensive Care Unit: The Viral Respiratory Infections in the Neonatal Intensive Care Unit-Parechovirus-Enterovirus Study. Pediatr Infect Dis J 2022; 41:1017-1019. [PMID: 36102733 DOI: 10.1097/inf.0000000000003700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In a prospective cohort study of 65 inborn infants who were evaluated for late-onset sepsis at >72 hours of age in 2 academic neonatal intensive care units, none had parechovirus or enterovirus RNA detected by polymerase chain reaction performed on nasopharyngeal specimens during the first or subsequent sepsis evaluations (n = 80).
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Human pathogenic RNA viruses establish noncompeting lineages by occupying independent niches. Proc Natl Acad Sci U S A 2022; 119:e2121335119. [PMID: 35639694 PMCID: PMC9191635 DOI: 10.1073/pnas.2121335119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Numerous pathogenic viruses are endemic in humans and cause a broad variety of diseases, but what is their potential for causing new pandemics? We show that most human pathogenic RNA viruses form multiple, cocirculating lineages with low turnover rates. These lineages appear to be largely noncompeting and occupy distinct epidemiological niches that are not regionally or seasonally defined, and their persistence appears to stem from limited outbreaks in small communities so that only a small fraction of the global susceptible population is infected at any time. However, due to globalization, interaction and competition between lineages might increase, potentially leading to increased diversification and pathogenicity. Thus, endemic viruses appear to merit global attention with respect to the prevention of future pandemics. Many pathogenic viruses are endemic among human populations and can cause a broad variety of diseases, some potentially leading to devastating pandemics. How virus populations maintain diversity and what selective pressures drive population turnover is not thoroughly understood. We conducted a large-scale phylodynamic analysis of 27 human pathogenic RNA viruses spanning diverse life history traits, in search of unifying trends that shape virus evolution. For most virus species, we identify multiple, cocirculating lineages with low turnover rates. These lineages appear to be largely noncompeting and likely occupy semiindependent epidemiological niches that are not regionally or seasonally defined. Typically, intralineage mutational signatures are similar to interlineage signatures. The principal exception are members of the family Picornaviridae, for which mutations in capsid protein genes are primarily lineage defining. Interlineage turnover is slower than expected under a neutral model, whereas intralineage turnover is faster than the neutral expectation, further supporting the existence of independent niches. The persistence of virus lineages appears to stem from limited outbreaks within small communities, so that only a small fraction of the global susceptible population is infected at any time. As disparate communities become increasingly connected through globalization, interaction and competition between lineages might increase as well, which could result in changing selective pressures and increased diversification and/or pathogenicity. Thus, in addition to zoonotic events, ongoing surveillance of familiar, endemic viruses appears to merit global attention with respect to the prevention or mitigation of future pandemics.
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Chowdhury SR, Lee D. Atypical acral swelling and viral exanthem with parechovirus meningitis. J Paediatr Child Health 2020; 56:815-817. [PMID: 31833105 DOI: 10.1111/jpc.14713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 11/15/2019] [Accepted: 11/17/2019] [Indexed: 11/28/2022]
Affiliation(s)
| | - Dawn Lee
- Department of Pediatrics, KK Women's and Children's Hospital, Singapore
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Ioulia K, Vasiliki P, Stavroula L, Emmanouil A, Andreas M. A 5-year study of human parechoviruses in children living in bad sanitation conditions and non-polio acute flaccid paralysis children from Greece. Eur J Clin Microbiol Infect Dis 2019; 38:1907-1913. [DOI: 10.1007/s10096-019-03627-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 06/30/2019] [Indexed: 10/26/2022]
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Chien YS, Luo ST, Tsao KC, Huang YC, Chung WY, Liao YC, Tan Y, Das SR, Lee MS. Genomic analysis of serologically untypable human enteroviruses in Taiwan. J Biomed Sci 2019; 26:49. [PMID: 31266491 PMCID: PMC6607526 DOI: 10.1186/s12929-019-0541-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 06/11/2019] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Human enteroviruses contain over 100 serotypes. We have routinely conducted enterovirus surveillance in northern Taiwan; but about 10% of isolates could not be serotyped using traditional assays. Next-generation sequencing (NGS) is a powerful tool for genome sequencing. METHODS In this study, we established an NGS platform to conduct genome sequencing for the serologically untypable enterovirus isolates. RESULTS Among 130 serologically untypable isolates, 121 (93%) of them were classified into 29 serotypes using CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primer)-based RT-PCR to amplify VP1 genes (VP1-CODEHOP). We further selected 52 samples for NGS and identified 59 genome sequences from 51 samples, including 8 samples containing two virus genomes. We also detected 23 genome variants (nucleotide identity < 90% compared with genome sequences in the public domain) which were potential genetic recombination, including 9 inter-serotype recombinants and 14 strains with unknown sources of recombination. CONCLUSIONS We successfully integrated VP1-CODEHOP and NGS techniques to conduct genomic analysis of serologically untypable enteroviruses.
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Affiliation(s)
- Yeh-Sheng Chien
- Institute of Infectious Disease and Vaccinology, National Health Research Institutes, Zhunan, Miaoli County Taiwan
- Department of Life Sciences, National Central University, Taoyuan, Taiwan
| | - Shu-Ting Luo
- Institute of Infectious Disease and Vaccinology, National Health Research Institutes, Zhunan, Miaoli County Taiwan
| | - Kuo-Chien Tsao
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Guishan, Taoyuan County Taiwan
- Department of Pediatrics, Linkou Chang Gung Memorial Hospital, Guishan, Taoyuan County Taiwan
| | - Yhu-Chering Huang
- Department of Pediatrics, Linkou Chang Gung Memorial Hospital, Guishan, Taoyuan County Taiwan
| | - Wan-Yu Chung
- Institute of Infectious Disease and Vaccinology, National Health Research Institutes, Zhunan, Miaoli County Taiwan
| | - Yu-Chieh Liao
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli County Taiwan
| | - Yi Tan
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee USA
| | - Suman R. Das
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee USA
| | - Min-Shi Lee
- Institute of Infectious Disease and Vaccinology, National Health Research Institutes, Zhunan, Miaoli County Taiwan
- National Health Research Institutes, R1-7F, 35 Keyan Road, Zhunan, Miaoli County, 350 Taiwan
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Malasao R, Khamrin P, Kumthip K, Ushijima H, Maneekarn N. Molecular epidemiology and genetic diversity of human parechoviruses in children hospitalized with acute diarrhea in Thailand during 2011-2016. Arch Virol 2019; 164:1743-1752. [PMID: 30972593 DOI: 10.1007/s00705-019-04249-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 03/13/2019] [Indexed: 12/25/2022]
Abstract
Little is known about human parechovirus (HPeV) infection in Thailand. The genotype distribution of HPeV strains in children admitted to hospitals with acute gastroenteritis was investigated using polymerase chain reaction (PCR) and nucleotide sequencing of the VP1 region as the detection and genotype identification methods, respectively. Of a total of 2,002 stool samples, 49 (2.4%) were positive for HPeV. Of these, HPeV-1 was the most predominant genotype (40.8%), followed by HPeV-3 (16.3%) and HPeV-14 (16.3%), while HPeV-5, -6, -2, -4, and -8 strains were less frequently detected, at 10.2%, 8.2%, 2%, 2%, and 2%, respectively. HPeV infections were detected throughout the year with the biannual peaks of infection in the rainy (Jun-Jul-Aug) and winter (Nov-Dec-Jan) months in Thailand. Based on VP1 amino acid sequence alignment, the arginyl-glycyl-aspartic acid (RGD) motif was found in HPeV-1, -2, -4, and -6 strains. Additionally, an amino acid insertion at the N-terminus of VP1 was observed in HPeV-4 and HPeV-5 strains. Phylogenetic analysis revealed that small clades of HPeV-1 and HPeV-3 strains emerged in 2016 and 2015, respectively, and dominated in the year of their emergence. The HPeV strains detected in Thailand in this study were most closely related to reference strains from Asia and Europe. The evolutionary rate of HPeV strains was 2.87 × 10-4 (95% highest posterior density (HPD) 0.10-6.14 × 10-4) substitutions/site/year. These findings provide information about the genetic diversity and evolutionary dynamics of HPeV genotypes circulating in pediatric patients with acute gastroenteritis in Thailand.
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Affiliation(s)
- Rungnapa Malasao
- Department of Community Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
| | - Pattara Khamrin
- Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Suthep Rd, Si Phum, Amphoe Muang, Chiang Mai, 50200, Thailand
| | - Kattareeya Kumthip
- Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Suthep Rd, Si Phum, Amphoe Muang, Chiang Mai, 50200, Thailand
| | - Hiroshi Ushijima
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Niwat Maneekarn
- Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand.
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Suthep Rd, Si Phum, Amphoe Muang, Chiang Mai, 50200, Thailand.
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Fortuna D, Cárdenas AM, Graf EH, Harshyne LA, Hooper DC, Prosniak M, Shields J, Curtis MT. Human parechovirus and enterovirus initiate distinct CNS innate immune responses: Pathogenic and diagnostic implications. J Clin Virol 2016; 86:39-45. [PMID: 27914285 DOI: 10.1016/j.jcv.2016.11.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Revised: 11/14/2016] [Accepted: 11/19/2016] [Indexed: 12/26/2022]
Abstract
BACKGROUND Human parechovirus (HPeV) and enterovirus (EV) cause a range of human diseases including serious CNS infections. Little is known regarding the immune response to HPeV meningitis compared to EV meningitis or how the immune response to HPeV reflects its pathogenesis. OBJECTIVE To characterize the innate immune response to HPeV CNS infection in order to increase our understanding of HPeV pathogenesis and possibly help identify HPeV in the clinical setting. STUDY DESIGN CSF samples from 13 patients with HPeV meningitis, 7 patients with EV meningitis, and 11 patients negative for CNS infections were analyzed for chemokines/cytokines using multiplex ELISA assays. RESULTS CSF levels of the majority of cytokines/chemokines analyzed were significantly higher in patients with EV meningitis (EV group) compared to patients with HPeV meningitis (HPeV group) and controls. In the HPeV group, a small number of cytokine/chemokine levels were higher than controls; however, these levels were either significantly lower or not significantly different compared to the EV group. IL-6 levels were lower in HPeV than in both EV and controls. CONCLUSIONS The immune response to HPeV CNS infection differs from that of EV. Distinct patterns of cytokine/chemokine expression in HPeV infections suggest HPeV-mediated modulation of the immune response. HPeV disrupts the interferon cascade and seems to interfere with early inflammatory signaling. Although HPeV elicits a predominantly muted immune reaction, a partial, general infectious-type cytokine/chemokine response does occur. Beyond providing insight into HPeV pathogenesis, the identified cytokine/chemokine profile may aid in early detection of HPeV infection.
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Affiliation(s)
- Danielle Fortuna
- Thomas Jefferson University Hospital, Pathology, Philadelphia, PA, United States
| | - Ana María Cárdenas
- Children's Hospital of Philadelphia, Pathology and Laboratory Medicine, Philadelphia, PA, United States; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Erin H Graf
- Children's Hospital of Philadelphia, Pathology and Laboratory Medicine, Philadelphia, PA, United States; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Larry A Harshyne
- Thomas Jefferson University Hospital, Neurosurgery, Philadelphia, PA, United States
| | - D Craig Hooper
- Thomas Jefferson University Hospital, Neurosurgery, Philadelphia, PA, United States; Thomas Jefferson University Hospital, Cancer Biology, Philadelphia, PA, United States
| | - Michael Prosniak
- Thomas Jefferson University Hospital, Cancer Biology, Philadelphia, PA, United States
| | - John Shields
- Thomas Jefferson University Hospital, Pathology, Philadelphia, PA, United States
| | - Mark T Curtis
- Thomas Jefferson University Hospital, Pathology, Philadelphia, PA, United States.
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Gong YN, Chen GW, Yang SL, Lee CJ, Shih SR, Tsao KC. A Next-Generation Sequencing Data Analysis Pipeline for Detecting Unknown Pathogens from Mixed Clinical Samples and Revealing Their Genetic Diversity. PLoS One 2016; 11:e0151495. [PMID: 26986479 PMCID: PMC4795770 DOI: 10.1371/journal.pone.0151495] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 02/29/2016] [Indexed: 12/02/2022] Open
Abstract
Forty-two cytopathic effect (CPE)-positive isolates were collected from 2008 to 2012. All isolates could not be identified for known viral pathogens by routine diagnostic assays. They were pooled into 8 groups of 5–6 isolates to reduce the sequencing cost. Next-generation sequencing (NGS) was conducted for each group of mixed samples, and the proposed data analysis pipeline was used to identify viral pathogens in these mixed samples. Polymerase chain reaction (PCR) or enzyme-linked immunosorbent assay (ELISA) was individually conducted for each of these 42 isolates depending on the predicted viral types in each group. Two isolates remained unknown after these tests. Moreover, iteration mapping was implemented for each of these 2 isolates, and predicted human parechovirus (HPeV) in both. In summary, our NGS pipeline detected the following viruses among the 42 isolates: 29 human rhinoviruses (HRVs), 10 HPeVs, 1 human adenovirus (HAdV), 1 echovirus and 1 rotavirus. We then focused on the 10 identified Taiwanese HPeVs because of their reported clinical significance over HRVs. Their genomes were assembled and their genetic diversity was explored. One novel 6-bp deletion was found in one HPeV-1 virus. In terms of nucleotide heterogeneity, 64 genetic variants were detected from these HPeVs using the mapped NGS reads. Most importantly, a recombination event was found between our HPeV-3 and a known HPeV-4 strain in the database. Similar event was detected in the other HPeV-3 strains in the same clade of the phylogenetic tree. These findings demonstrated that the proposed NGS data analysis pipeline identified unknown viruses from the mixed clinical samples, revealed their genetic identity and variants, and characterized their genetic features in terms of viral evolution.
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Affiliation(s)
- Yu-Nong Gong
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Department of Computer Science and Information Engineering, School of Electrical and Computer Engineering, College of Engineering, Chang Gung University, Taoyuan, Taiwan
| | - Guang-Wu Chen
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Department of Computer Science and Information Engineering, School of Electrical and Computer Engineering, College of Engineering, Chang Gung University, Taoyuan, Taiwan
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Shu-Li Yang
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Ching-Ju Lee
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Shin-Ru Shih
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Kuo-Chien Tsao
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- * E-mail:
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Cristanziano VD, Veronica DC, Böttcher S, Sindy B, Diedrich S, Sabine D, Timmen-Wego M, Monika TW, Knops E, Elena K, Lübke N, Nadine L, Kaiser R, Rolf K, Pfister H, Herbert P, Kaboré Y, Yolande K, D'Alfonso R, Rossella D. Detection and characterization of enteroviruses and parechoviruses in healthy people living in the South of Côte d'Ivoire. J Clin Virol 2015; 71:40-3. [PMID: 26370313 DOI: 10.1016/j.jcv.2015.08.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 08/01/2015] [Accepted: 08/03/2015] [Indexed: 11/25/2022]
Abstract
BACKGROUND Human enteroviruses (EVs) and parechoviruses (HPeVs) belong to the family Picornaviridae. Although most EV and HPeV infections remain asymptomatic, both pathogens can cause a wide spectrum of clinical manifestations ranging from respiratory or gastrointestinal symptoms to myocarditis, neonatal sepsis, and infections of the central nervous system. OBJECTIVES Aim of the present study was to investigate the spectrum of EVs and HPeVs in apparently healthy adults and children living in the South of Côte d'Ivoire. STUDY DESIGN The study included 105 stool samples obtained from healthy individuals aged 0-53 years between June 2013 and December 2014 in the Sud-Como region of Côte d'Ivoire. After collection and shipment to Germany, the samples were analyzed by real-time PCR for the presence of EVs and HPeVs RNA. Molecular typing and virus isolation of all samples were performed.''é RESULTS Out of 105 samples, 24 (22.8%) were EV positive and six (5.2%) were HPeV positive. Twenty-one EV positive samples could be characterized with serotypes belonging to EV group A-C, while three could not be further specified. Interestingly, several rarely described serotypes were identified, e.g., EV-C99, EV-B93, EV-C116, and EV-A119. Typing of HPeV positive samples resulted in HPeV-1 and -5 detections, while one isolate could not be assigned to the known HPeV types. CONCLUSIONS This study showed a large variety of EV strains in healthy people in the South of Côte d'Ivoire and provided the first available data about HPeV infections in a sub-Saharan African country.
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Affiliation(s)
| | | | | | - Böttcher Sindy
- National Reference Centre for Poliomyelitis and Enteroviruses, Robert Koch Institute, Berlin, Germany
| | | | - Diedrich Sabine
- National Reference Centre for Poliomyelitis and Enteroviruses, Robert Koch Institute, Berlin, Germany
| | | | | | | | - Knops Elena
- Institute of Virology, University of Cologne, Cologne, Germany
| | | | - Lübke Nadine
- Institute of Virology, University of Cologne, Cologne, Germany
| | | | - Kaiser Rolf
- Institute of Virology, University of Cologne, Cologne, Germany
| | | | - Pfister Herbert
- Institute of Virology, University of Cologne, Cologne, Germany
| | | | - Kaboré Yolande
- Centre Don Orione Pour Handicapés Physiques, Bonoua, Côte d'Ivoire
| | - Rossella D'Alfonso
- Centre Don Orione Pour Handicapés Physiques, Bonoua, Côte d'Ivoire; Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
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Human Parechovirus 3: The Most Common Viral Cause of Meningoencephalitis in Young Infants. Infect Dis Clin North Am 2015; 29:415-28. [PMID: 26188604 DOI: 10.1016/j.idc.2015.05.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Human parechoviruses (HPeVs) were initially classified as echoviruses. HPeVs occur worldwide, comprising up to 17 genotypes. HPeV1 and HPeV3 are most common. Clinical disease varies somewhat among genotypes. HPeV1 causes mostly gastrointestinal infections. HPeV3's prominence is due to its causing sepsis syndromes and central nervous system (CNS) infections in young infants. Currently, HPeV3 is the most common single cause of aseptic meningitis/meningoencephalitis in infants less than 90 days old in North America, usually with biannual summer-fall seasonality. HPeV3 CNS infections usually lack cerebrospinal fluid pleocytosis. Mortality and sequelae are uncommon, usually accompanying initially severe or neurologically complicated acute illnesses.
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