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Evolutionary Relationships of Ljungan Virus Variants Circulating in Multi-Host Systems across Europe. Viruses 2021; 13:v13071317. [PMID: 34372523 PMCID: PMC8310206 DOI: 10.3390/v13071317] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 07/01/2021] [Accepted: 07/02/2021] [Indexed: 12/12/2022] Open
Abstract
The picornavirus named 'Ljungan virus' (LV, species Parechovirus B) has been detected in a dozen small mammal species from across Europe, but detailed information on its genetic diversity and host specificity is lacking. Here, we analyze the evolutionary relationships of LV variants circulating in free-living mammal populations by comparing the phylogenetics of the VP1 region (encoding the capsid protein and associated with LV serotype) and the 3Dpol region (encoding the RNA polymerase) from 24 LV RNA-positive animals and a fragment of the 5' untranslated region (UTR) sequence (used for defining strains) in sympatric small mammals. We define three new VP1 genotypes: two in bank voles (Myodes glareolus) (genotype 8 from Finland, Sweden, France, and Italy, and genotype 9 from France and Italy) and one in field voles (Microtus arvalis) (genotype 7 from Finland). There are several other indications that LV variants are host-specific, at least in parts of their range. Our results suggest that LV evolution is rapid, ongoing and affected by genetic drift, purifying selection, spillover and host evolutionary history. Although recent studies suggest that LV does not have zoonotic potential, its widespread geographical and host distribution in natural populations of well-characterized small mammals could make it useful as a model for studying RNA virus evolution and transmission.
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Phylogenetic molecular evolution and recombination analysis of complete genome of human parechovirus in Thailand. Sci Rep 2021; 11:8572. [PMID: 33883644 PMCID: PMC8060412 DOI: 10.1038/s41598-021-88124-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 04/08/2021] [Indexed: 12/24/2022] Open
Abstract
Human parechovirus (HPeV), which is a member of the Picornavirus group of viruses, is a pathogen that is reported to be associated with manifestations that include respiratory tract involvement, gastroenteritis, sepsis-like symptom, and central nervous system complication. Until now, nineteen genotypes have been identified. The lack of proofreading property of viral RNA-dependent RNA polymerase (RdRp) together with recombination among the intra- and inter-genotypes of the virus results in high diversity. However, data specific to the molecular evolutionary perspective of the complete genome of HPeV remains limited. This study aimed to analyze the phylogenetic, molecular evolution, and recombination characteristics of the complete genome of HPeV strains isolated in Thailand during 2009–2012. Fifty-eight samples that were previously confirmed to be HPeV positive and then evaluated for genotyping were subjected to complete genome amplification to generate ten overlapping PCR fragments using a set of in-house designed primers. The same position of the viral genome was read in triplicate using direct Sanger sequencing. All samples were classified into the same previously defined genotypes in both whole-genome and VP1 phylogenic tree. However, sample B1091/HPeV14/2011 exhibited discordant grouping between whole-genome and VP1 on the phylogenetic tree. Bootscan analysis revealed that B1091/HPeV14/2011 inherited from two genotypic viruses, including VP1 from HPeV14, and the rest of the genome from HPeV1B. The results of this study provide important insights into the molecular evolution of and recombination in the viral genome of HPeV that will improve and accelerate our ability to develop treatment and prophylactic strategies in the future.
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Molecular characterization of the complete genome sequence of human Parechovirus 1 in Pakistan. Virus Res 2020; 290:198178. [PMID: 33010373 DOI: 10.1016/j.virusres.2020.198178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/19/2020] [Accepted: 09/21/2020] [Indexed: 11/22/2022]
Abstract
Human parechoviruses (HPeVs) are highly common pathogens in children under 2 years of age. Of the 19 distinct HPeV genotypes identified worldwide, HPeV1 is still the most prevalent type associated with respiratory and gastrointestinal symptoms in infants and young children. Pakistan's previous studies have focused only on the detection and partial sequencing of HPeV genotypes. In the present study, we have obtained the complete genomes of 2 HPeV1 strains (PAK419 and PAK663) from children using NGS method on Illumina Hiseq Platform. These samples were collected from children suffering from acute gastroenteritis in Rawalpindi, Pakistan during 2016. The near complete genome sequences obtained for two HPeV1 strains (PAK419 and PAK663) consist of total 6877 nucleotides with a single, large open reading frame (ORF) encoding a polyprotein gene. Phylogenetic analysis showed that both HPeV1 strains exhibited maximum amino acid similarity (97 %) to HPeV1 strains from The Nederlands (2007-863, GQ183034) and clustered closely with this and with other HPeV1 strains isolated from other countries in the world (Ethiopia, Taiwan, Russia and Brazil). A motif of arginine-glycine-aspartic acid (RGD) in the VP1 (Outer capsid protein) C-terminus region that is suggested to help virus entry into the host cell also identified in PAK419 and PAK663. SimPlot analysis revealed that intergenotypic recombination events may have take place in the non-structural region between both HPeV1 strains (PAK419, PAK663), two major strains of HPeV1 (GQ183034 and MG873157) and four minor strains of HPeV4 (AM235750), HPeV7 (EU556224), HPeV15 (MN265386) and HPeV18 (KT879915). The full genome of HPeV1 strains characterized in the current study will provide complete information on these newly isolated strains for further preventive or treatment measures.
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Arhab Y, Bulakhov AG, Pestova TV, Hellen CU. Dissemination of Internal Ribosomal Entry Sites (IRES) Between Viruses by Horizontal Gene Transfer. Viruses 2020; 12:v12060612. [PMID: 32512856 PMCID: PMC7354566 DOI: 10.3390/v12060612] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/01/2020] [Accepted: 06/02/2020] [Indexed: 12/19/2022] Open
Abstract
Members of Picornaviridae and of the Hepacivirus, Pegivirus and Pestivirus genera of Flaviviridae all contain an internal ribosomal entry site (IRES) in the 5'-untranslated region (5'UTR) of their genomes. Each class of IRES has a conserved structure and promotes 5'-end-independent initiation of translation by a different mechanism. Picornavirus 5'UTRs, including the IRES, evolve independently of other parts of the genome and can move between genomes, most commonly by intratypic recombination. We review accumulating evidence that IRESs are genetic entities that can also move between members of different genera and even between families. Type IV IRESs, first identified in the Hepacivirus genus, have subsequently been identified in over 25 genera of Picornaviridae, juxtaposed against diverse coding sequences. In several genera, members have either type IV IRES or an IRES of type I, II or III. Similarly, in the genus Pegivirus, members contain either a type IV IRES or an unrelated type; both classes of IRES also occur in members of the genus Hepacivirus. IRESs utilize different mechanisms, have different factor requirements and contain determinants of viral growth, pathogenesis and cell type specificity. Their dissemination between viruses by horizontal gene transfer has unexpectedly emerged as an important facet of viral evolution.
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Zhirakovskaia E, Tikunov A, Babkin I, Tikunova N. Complete genome sequences of the first parechoviruses A associated with sporadic pediatric acute gastroenteritis in Russia. INFECTION GENETICS AND EVOLUTION 2020; 80:104214. [DOI: 10.1016/j.meegid.2020.104214] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 12/24/2019] [Accepted: 01/28/2020] [Indexed: 01/12/2023]
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Fernandez-Garcia MD, Simon-Loriere E, Kebe O, Sakuntabhai A, Ndiaye K. Identification and molecular characterization of the first complete genome sequence of Human Parechovirus type 15. Sci Rep 2020; 10:6759. [PMID: 32317760 PMCID: PMC7174385 DOI: 10.1038/s41598-020-63467-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 03/26/2020] [Indexed: 12/29/2022] Open
Abstract
Using a metagenomics approach, we have determined the first full-length genome sequence of a human parechovirus type 15 (HPeV15) strain, isolated from a child with acute flaccid paralysis and co-infected with EV-A71. HPeV15 is a rarely reported type. To date, no full-length genome sequence of HPeV15 is available in the GenBank database, where only limited VP1 sequences of this virus are available. Pairwise comparisons of the complete VP1 nucleotide and deduced amino acid sequences revealed that the study strain belongs to type 15 as it displayed 79.6% nucleotide and 93.4% amino acid identity with the HPeV15 prototype strain. Comparative analysis of available genomic regions and phylogenetic analysis using the P2 and P3 coding regions revealed low nucleotide identity to HPeV reference genomes. Phylogenetic and similarity plot analyses showed that genomic recombination events might have occurred in the UTRs and nonstructural region during HPeV15 evolution. The study strain has high similarity features with different variants of HPeV3 suggesting intertypic recombination. Our data contributes to the scarce data available on HPeVs in Africa and provides valuable information for future studies that aim to understand the evolutionary history, molecular epidemiology or biological and pathogenic properties of HPeV15.
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Recombinant Strains of Human Parechovirus in Rural Areas in the North of Brazil. Viruses 2019; 11:v11060488. [PMID: 31146371 PMCID: PMC6630568 DOI: 10.3390/v11060488] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 04/30/2019] [Accepted: 05/03/2019] [Indexed: 02/07/2023] Open
Abstract
We characterized the 24 nearly full-length genomes of human parechoviruses (PeV) from children in the north of Brazil. The initial phylogenetic analysis indicated that 17 strains belonged to genotype 1, 5 to genotype 4, and 1 to genotype 17. A more detailed analysis revealed a high frequency of recombinant strains (58%): A total of 14 of our PeV-As were chimeric, with four distinct recombination patterns identified. Five strains were composed of genotypes 1 and 5 (Rec1/5); five strains shared a complex mosaic pattern formed by genotypes 4, 5, and 17 (Rec4/17/5); two strains were composed of genotypes 1 and 17 (Rec1/17); and two strains were composed of genotype 1 and an undetermined strain (Rec1/und). Coalescent analysis based on the Vp1 gene, which is free of recombination, indicated that the recombinant strains most likely arose in this region approximately 30 years ago. They are present in high frequencies and are circulating in different small and isolated cities in the state of Tocantins. Further studies will be needed to establish whether the detected recombinant strains have been replacing parental strains or if they are co-circulating in distinct frequencies in Tocantins.
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Evolutionary and network analysis of virus sequences from infants infected with an Australian recombinant strain of human parechovirus type 3. Sci Rep 2017. [PMID: 28634337 PMCID: PMC5478645 DOI: 10.1038/s41598-017-04145-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
We present the near complete virus genome sequences with phylogenetic and network analyses of potential transmission networks of a total of 18 Australian cases of human parechovirus type 3 (HPeV3) infection in infants in the period from 2012–2015. Overall the results support our previous finding that the Australian outbreak strain/lineage is a result of a major recombination event that took place between March 2012 and November 2013 followed by further virus evolution and possibly recombination. While the nonstructural coding region of unknown provenance appears to evolve significantly both at the nucleotide and amino acid level, the capsid encoding region derived from the Yamagata 2011 lineage of HPeV3 appears to be very stable, particularly at the amino acid level. The phylogenetic and network analyses performed support a temporal evolution from the first Australian recombinant virus sequence from November 2013 to March/April 2014, onto the 2015 outbreak. The 2015 outbreak samples fall into two separate clusters with a possible common ancestor between March/April 2014 and September 2015, with each cluster further evolving in the period from September to November/December 2015.
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Nelson TM, Vuillermin P, Hodge J, Druce J, Williams DT, Jasrotia R, Alexandersen S. An outbreak of severe infections among Australian infants caused by a novel recombinant strain of human parechovirus type 3. Sci Rep 2017; 7:44423. [PMID: 28290509 PMCID: PMC5349594 DOI: 10.1038/srep44423] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 02/07/2017] [Indexed: 12/27/2022] Open
Abstract
Human parechovirus types 1–16 (HPeV1–16) are positive strand RNA viruses in the family Picornaviridae. We investigated a 2015 outbreak of HPeV3 causing illness in infants in Victoria, Australia. Virus genome was extracted from clinical material and isolates and sequenced using a combination of next generation and Sanger sequencing. The HPeV3 outbreak genome was 98.7% similar to the HPeV3 Yamagata 2011 lineage for the region encoding the structural proteins up to nucleotide position 3115, but downstream of that the genome varied from known HPeV sequences with a similarity of 85% or less. Analysis indicated that recombination had occurred, may have involved multiple types of HPeV and that the recombination event/s occurred between March 2012 and November 2013. However the origin of the genome downstream of the recombination site is unknown. Overall, the capsid of this virus is highly conserved, but recombination provided a different non-structural protein coding region that may convey an evolutionary advantage. The indication that the capsid encoding region is highly conserved at the amino acid level may be helpful in directing energy towards the development of a preventive vaccine for expecting mothers or antibody treatment of young infants with severe disease.
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Affiliation(s)
- Tiffanie M Nelson
- Geelong Center for Emerging Infectious Diseases, Geelong, Victoria 3220, Australia.,Deakin University, School of Medicine, Geelong, Victoria 3220, Australia
| | - Peter Vuillermin
- Deakin University, School of Medicine, Geelong, Victoria 3220, Australia.,Barwon Health, University Hospital Geelong, Geelong, Victoria 3220, Australia
| | - Jason Hodge
- Geelong Center for Emerging Infectious Diseases, Geelong, Victoria 3220, Australia.,Barwon Health, University Hospital Geelong, Geelong, Victoria 3220, Australia
| | - Julian Druce
- Victorian Infectious Diseases Reference Laboratory (VIDRL), Doherty Institute, Melbourne, Victoria 3000, Australia
| | - David T Williams
- CSIRO, Australian Animal Health Laboratory, Geelong, Victoria 3220, Australia
| | - Rekha Jasrotia
- Barwon Health, University Hospital Geelong, Geelong, Victoria 3220, Australia
| | - Soren Alexandersen
- Geelong Center for Emerging Infectious Diseases, Geelong, Victoria 3220, Australia.,Deakin University, School of Medicine, Geelong, Victoria 3220, Australia.,Barwon Health, University Hospital Geelong, Geelong, Victoria 3220, Australia
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Intertypic recombination of human parechovirus 4 isolated from infants with sepsis-like disease. J Clin Virol 2017; 88:1-7. [PMID: 28081453 DOI: 10.1016/j.jcv.2017.01.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 12/30/2016] [Accepted: 01/02/2017] [Indexed: 11/24/2022]
Abstract
BACKGROUND Human parechoviruses (HPeVs) (family Picornaviridae), are common pathogens in young children. Despite their high prevalence, research on their genetic identity, diversity and evolution have remained scarce. OBJECTIVES Complete coding regions of three previously reported HPeV-4 isolates from Finnish children with sepsis-like disease were sequenced in order to elucidate the phylogenetic relationships and potential recombination events during the evolution of these isolates. STUDY DESIGN The isolated viruses were sequenced and aligned with all HPeV complete genome sequences available in GenBank. Phylogenetic trees were constructed and similarity plot and bootscanning methods were used for recombination analysis. RESULTS The three HPeV-4 isolates had 99.8% nucleotide sequence similarity. The phylogenetic analysis indicated that capsid-encoding sequences of these HPeV-4 isolates were closely related to other HPeV-4 strains (80.7-94.7% nucleotide similarity), whereas their non-structural region genes 2A to 3C clustered together with several HPeV-1 and HPeV-3 strains, in addition to the HPeV-4 strain K251176-02 (isolated 2002 in the Netherlands), but not with other HPeV-4 strains. However, in 3D-encoding sequence the Finnish HPeV-4 isolates did not cluster with the strain HPeV-4/K251176-02, but instead, formed a distinct group together with several HPeV-1 and HPeV-3 strains. Similarity plot and Bootscan analyses further confirmed intertypic recombination events in the evolution of the Finnish HPeV-4 isolates. CONCLUSION Intertypic recombination event(s) have occurred during the evolution of HPeV-4 isolates from children with sepsis-like disease. However, due to the low number of parechovirus complete genomes available, the precise recombination partners could not be detected. The results suggest frequent intratypic recombination among parechoviruses.
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Zhao X, Shi Y, Xia Y. Genome analysis revealed novel genotypes and recombination of the human parechoviruses prevalent in children in Eastern China. Gut Pathog 2016; 8:52. [PMID: 27826360 PMCID: PMC5100207 DOI: 10.1186/s13099-016-0135-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 10/19/2016] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Human parechovirus (HPeV) is a genus of virus in the family Picornaviridae, having two species A and B. HPeVs are common infectious agents, usually causing mild diarrhea and respiratory disease in young children. RESULTS Here, we collected and sequenced the near complete genome sequences of 17 novel HPeVs from children with diarrhea in eastern China, which showed significant nucleotide sequence divergence. Phylogenetic analysis based on the complete genomes of these HPeV strains revealed that they belonged to seven different genotypes (including three putative novel genotypes), suggesting that HPeVs showed genotype diversity in this area. Recombination analysis indicated that one of the HPeVs, belonging to HPeV-1 with strain name 146Chzj02, was a recombinant generated by inter-genotype recombination among three HPeV strains belonging to three different genotypes, respectively. CONCLUSION Our data revealed the property of the genotype diversity of HPeVs prevalent in children with diarrhea in eastern China, which will be helpful in the future study of the viral evolution of HPeVs and the identification and typing of HPeVs in the clinical laboratory.
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Affiliation(s)
- Xiangyang Zhao
- Nanjing Lishui People's Hospital, Lishui, Jiangsu 211200 China
| | - Yongqiang Shi
- Nanjing Lishui People's Hospital, Lishui, Jiangsu 211200 China
| | - Yu Xia
- Nanjing Lishui People's Hospital, Lishui, Jiangsu 211200 China
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Guo WP, Lin XD, Chen YP, Liu Q, Wang W, Wang CQ, Li MH, Sun XY, Shi M, Holmes EC, Zhang YZ. Fourteen types of co-circulating recombinant enterovirus were associated with hand, foot, and mouth disease in children from Wenzhou, China. J Clin Virol 2015; 70:29-38. [PMID: 26305816 DOI: 10.1016/j.jcv.2015.06.093] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 06/03/2015] [Accepted: 06/07/2015] [Indexed: 10/23/2022]
Abstract
BACKGROUND Although hand, foot, and mouth disease (HFMD) is a major public concern in China, the prevalence and clinical symptoms associated with the different agents of HFMD in this country remain poorly understood. OBJECTIVES We investigated the clinical and molecular characteristics of enteroviruses in patients with HFMD from Wenzhou, China. STUDY DESIGN Patients with laboratory-confirmed HFMD admitted to the Yuying Children's Hospital in Wenzhou, China during 2013 were included in this study. Viral RNA sequences were amplified using RT-PCR, determined by sequencing, and compared by phylogenetic analysis. RESULTS A total of 955 clinically diagnosed HFMD cases were determined using PCR, with whole viral genomes obtained for each enterovirus type. 14 types of enterovirus belonging to two viral species were identified. Notably, Coxsackievirus A6 (CV-A6) was the most common species detected (77.8%), followed by EV-A71 (8.2%) and CV-A10 (8.1%). Phylogenetic analysis revealed multiple independent introductions of these viruses into Wenzhou. In addition, the enterovirus observed in Wenzhou had a recombinant history, with two or three recombination breakpoints. Although the illness associated with CV-A6 was milder than that of EV-A71, CV-A6 infection caused more widespread rash, larger blisters, and subsequent skin peeling and/or nail shedding. CONCLUSION Our study revealed the co-circulation of 14 types of enteroviruses in a single location - Wenzhou, China - with CV-A6 virus the predominant agent of HFMD. This work highlights the need to perform larger-scale surveillance to fully understand the epidemiology of enteroviruses in China and the wider Asia-Pacific region.
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Affiliation(s)
- Wen-Ping Guo
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping Liuzi 5, 102206 Beijing, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Xian-Dan Lin
- Wenzhou Center for Disease Control and Prevention, Wenzhou 325001, Zhejiang Province, China
| | - Yi-Ping Chen
- The Second Affiliated Hospital & Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325027, Zhejiang Province, China
| | - Qi Liu
- The Second Affiliated Hospital & Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325027, Zhejiang Province, China
| | - Wen Wang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping Liuzi 5, 102206 Beijing, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Cai-Qiao Wang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping Liuzi 5, 102206 Beijing, China
| | - Ming-Hui Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping Liuzi 5, 102206 Beijing, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Xiao-Yu Sun
- Wenzhou Center for Disease Control and Prevention, Wenzhou 325001, Zhejiang Province, China
| | - Mang Shi
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping Liuzi 5, 102206 Beijing, China; Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
| | - Edward C Holmes
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping Liuzi 5, 102206 Beijing, China; Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
| | - Yong-Zhen Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping Liuzi 5, 102206 Beijing, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China.
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Asnani M, Kumar P, Hellen CUT. Widespread distribution and structural diversity of Type IV IRESs in members of Picornaviridae. Virology 2015; 478:61-74. [PMID: 25726971 DOI: 10.1016/j.virol.2015.02.016] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 02/05/2015] [Accepted: 02/09/2015] [Indexed: 01/13/2023]
Abstract
Picornavirus genomes contain internal ribosomal entry sites (IRESs) that promote end-independent translation initiation. Five structural classes of picornavirus IRES have been identified, but numerous IRESs remain unclassified. Here, previously unrecognized Type IV IRESs were identified in members of three proposed picornavirus genera (Limnipivirus, Pasivirus, Rafivirus) and four recognized genera (Kobuvirus, Megrivirus, Sapelovirus, Parechovirus). These IRESs are ~230-420 nucleotides long, reflecting heterogeneity outside a common structural core. Closer analysis yielded insights into evolutionary processes that have shaped contemporary IRESs. The presence of related IRESs in diverse genera supports the hypothesis that they are heritable genetic elements that spread by horizontal gene transfer. Recombination likely also accounts for the exchange of some peripheral subdomains, suggesting that IRES evolution involves incremental addition of elements to a pre-existing core. Nucleotide conservation is concentrated in ribosome-binding sites, and at the junction of helical domains, likely to ensure orientation of subdomains in an active conformation.
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Affiliation(s)
- Mukta Asnani
- Department of Cell Biology, State University of New York Downstate Medical Center, Brooklyn, NY 11203, USA
| | - Parimal Kumar
- Department of Cell Biology, State University of New York Downstate Medical Center, Brooklyn, NY 11203, USA
| | - Christopher U T Hellen
- Department of Cell Biology, State University of New York Downstate Medical Center, Brooklyn, NY 11203, USA.
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Chang JT, Yang CS, Chen YS, Chen BC, Chiang AJ, Chang YH, Tsai WL, Lin YS, Chao D, Chang TH. Genome and infection characteristics of human parechovirus type 1: the interplay between viral infection and type I interferon antiviral system. PLoS One 2015; 10:e0116158. [PMID: 25646764 PMCID: PMC4380134 DOI: 10.1371/journal.pone.0116158] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 12/02/2014] [Indexed: 01/05/2023] Open
Abstract
Human parechoviruses (HPeVs), members of the family
Picornaviridae, are associated with severe human clinical
conditions such as gastrointestinal disease, encephalitis, meningitis,
respiratory disease and neonatal sepsis. A new contemporary strain of HPeV1,
KVP6 (accession no. KC769584), was isolated from a clinical specimen.
Full-genome alignment revealed that HPeV1 KVP6 shares high genome homology with
the German strain of HPeV1, 7555312 (accession no. FM178558) and could be
classified in the clade 1B group. An intertypic recombination was shown within
the P2-P3 genome regions of HPeV1. Cell-type tropism test showed that T84 cells
(colon carcinoma cells), A549 cells (lung carcinoma cells) and DBTRG-5MG cells
(glioblastoma cells) were susceptible to HPeV1 infection, which might be
relevant clinically. A facilitated cytopathic effect and increased viral titers
were reached after serial viral passages in Vero cells, with viral genome
mutation found in later passages. HPeV1 is sensitive to elevated temperature
because 39°C incubation impaired virion production. HPeV1 induced innate
immunity with phosphorylation of interferon (IFN) regulatory transcription
factor 3 and production of type I IFN in A549 but not T84 cells. Furthermore,
type I IFN inhibited HPeV1 production in A549 cells but not T84 cells; T84 cells
may be less responsive to type I IFN stimulation. Moreover, HPeV1-infected cells
showed downregulated type I IFN activation, which indicated a type I IFN evasion
mechanism. The characterization of the complete genome and infection features of
HPeV1 provide comprehensive information about this newly isolated HPeV1 for
further diagnosis, prevention or treatment strategies.
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Affiliation(s)
- Jenn-Tzong Chang
- Department of Biological Sciences, National Sun Yat-Sen University,
Kaohsiung, Taiwan
- Department of Medical Education and Research, Kaohsiung Veterans General
Hospital, Kaohsiung, Taiwan
- Department of Pediatrics; Kaohsiung Veterans General Hospital, Kaohsiung,
Taiwan
| | - Chih-Shiang Yang
- Department of Medical Education and Research, Kaohsiung Veterans General
Hospital, Kaohsiung, Taiwan
| | - Yao-Shen Chen
- Department of Infectious Diseases, Kaohsiung Veterans General Hospital,
Kaohsiung, Taiwan
| | - Bao-Chen Chen
- Department of Microbiology, Kaohsiung Veterans General Hospital,
Kaohsiung, Taiwan
| | - An-Jen Chiang
- Department of Biological Sciences, National Sun Yat-Sen University,
Kaohsiung, Taiwan
- Department of Obstetrics and Gynecology, Kaohsiung Veterans General
Hospital, Kaohsiung, Taiwan
| | - Yu-Hsiang Chang
- Department of Pediatrics; Kaohsiung Veterans General Hospital, Kaohsiung,
Taiwan
| | - Wei-Lun Tsai
- Division of Gastroenterology, Department of Internal Medicine, Kaohsiung
Veterans General Hospital, Kaohsiung, Taiwan
| | - You-Sheng Lin
- Department of Medical Education and Research, Kaohsiung Veterans General
Hospital, Kaohsiung, Taiwan
| | - David Chao
- Department of Biological Sciences, National Sun Yat-Sen University,
Kaohsiung, Taiwan
| | - Tsung-Hsien Chang
- Department of Medical Education and Research, Kaohsiung Veterans General
Hospital, Kaohsiung, Taiwan
- Department of Pharmacy and Graduate Institute of Pharmaceutical
Technology, Tajen University, Pingtung, Taiwan
- * E-mail:
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15
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Characteristics of the mosaic genome of a human parechovirus type 1 strain isolated from an infant with pneumonia in China. INFECTION GENETICS AND EVOLUTION 2014; 29:91-8. [PMID: 25461260 DOI: 10.1016/j.meegid.2014.11.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 11/02/2014] [Accepted: 11/05/2014] [Indexed: 12/22/2022]
Abstract
Human parechoviruses (HPeVs) belong to the Parechovirus genus of the large and growing family of Picornaviridae with a non-enveloped, single-stranded and positive-sense RNA. An HPeV strain was isolated from the nasopharyngeal aspirate specimen of a 2 months old infant hospitalized with pneumonia in Beijing, China and nominated as BJ-37359 followed the code of the specimen. Strain BJ-37359 was identified as HPeV1 by whole genome sequencing. The full genome of strain BJ-37359 consisted of 7336 nucleotides (nt), excluding a poly (A) tail and contained an ORF of 6537 nt flanked by 5'UTR of 709 nt and 3'UTR of 90 nt. Phylogenetic analyses revealed that strain BJ-37359 were clustered together with HPeV1 strains in the structural capsid protein region, while uncoupling in the non-structural gene regions. Analyses with Simplot and Bootscan indicated that multiple recombination events occurred in the non-structural region and VP0 region of strain BJ-37359 with other HPeV1, and other types might have contributed to the recombination, especially HPeV6 and HPeV7 strains. Recombination analyses indicated that strain BJ-37359 may have a mosaic genome with new genomic recombination breakpoints.
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16
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Thoi TC, Than VT, Kim W. Whole genomic characterization of a Korean human parechovirus type 1 (HPeV1) identifies recombination events. J Med Virol 2014; 86:2084-91. [PMID: 24634137 DOI: 10.1002/jmv.23921] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/11/2014] [Indexed: 11/07/2022]
Abstract
A human parechovirus (HPeV) strain CAU10-NN was detected from a stool sample of a 2-year-old healthy female infant in South Korea using a metagenomic approach. The CAU10-NN virus was isolated using a cell culture system and its whole genome was analyzed. The RNA genome of the CAU10-NN strain consists of 7,348 nucleotides (nt), excluding a poly(A) tail. A large open reading frame of 6,540 nt that encodes a putative polyprotein precursor of 2,180 amino acids is flanked by a 5'-untranslated region (UTR) of 708 nt and 3'-UTR of 88 nt followed by a poly(A) tail. Phylogenetic analysis shows that the CAU10-NN strain belongs to HPeV1. SimPlot and Bootscan analyses reveal that the virus genome is composed of regions related to corresponding genomic regions of other HPeVs. Recombination analysis indicates that the CAU10-NN strain might be a product of more than one genomic recombination event that occurred among HPeV1, HPeV3, and HPeV4 strains.
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Affiliation(s)
- Truong Cong Thoi
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, South Korea
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17
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Feng Q, Hato SV, Langereis MA, Zoll J, Virgen-Slane R, Peisley A, Hur S, Semler BL, van Rij RP, van Kuppeveld FJM. MDA5 detects the double-stranded RNA replicative form in picornavirus-infected cells. Cell Rep 2012; 2:1187-96. [PMID: 23142662 PMCID: PMC7103987 DOI: 10.1016/j.celrep.2012.10.005] [Citation(s) in RCA: 179] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Revised: 06/26/2012] [Accepted: 10/08/2012] [Indexed: 12/24/2022] Open
Abstract
RIG-I and MDA5 are cytosolic RNA sensors that play a critical role in innate antiviral responses. Major advances have been made in identifying RIG-I ligands, but our knowledge of the ligands for MDA5 remains restricted to data from transfection experiments mostly using poly(I:C), a synthetic dsRNA mimic. Here, we dissected the IFN-α/β-stimulatory activity of different viral RNA species produced during picornavirus infection, both by RNA transfection and in infected cells in which specific steps of viral RNA replication were inhibited. Our results show that the incoming genomic plus-strand RNA does not activate MDA5, but minus-strand RNA synthesis and production of the 7.5 kbp replicative form trigger a strong IFN-α/β response. IFN-α/β production does not rely on plus-strand RNA synthesis and thus generation of the partially double-stranded replicative intermediate. This study reports MDA5 activation by a natural RNA ligand under physiological conditions.
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Affiliation(s)
- Qian Feng
- Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, Nijmegen, PO Box 9101, 6500 HB, The Netherlands
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New genotypes of Orientia tsutsugamushi isolated from humans in Eastern Taiwan. PLoS One 2012; 7:e46997. [PMID: 23071693 PMCID: PMC3468442 DOI: 10.1371/journal.pone.0046997] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Accepted: 09/11/2012] [Indexed: 01/17/2023] Open
Abstract
Scrub typhus, an acute febrile illness, is caused by the obligate intracellular bacterium Orientia tsutsugamushi. In our study, O. tsutsugamushi was rapidly detected and typed by polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) analysis of the 56-kDa type-specific antigen (TSA) gene. To investigate the genotypes of clinical variants of O. tsutsugamushi, we collected 3223 blood samples from eastern Taiwanese patients with suspected scrub typhus from 2002 to 2008. In total, 505 samples were found to be positive for scrub typhus infection by PCR, and bacteria were isolated from 282 of them. Four prototype genotype strains (Karp, Kato, Kawasaki and Gilliam) and eleven different Taiwanese genotype isolates (Taiwan-A, -B, -C, -D, -E, -G, -H, -J, -N, -O and -P) were identified by RPLF analysis. Taiwan-H, the major genotype in eastern Taiwan, exhibited prevalence and isolation rates of 47.3% (239/505) and 42.6% (120/282), respectively. We also assessed the genetic relatedness of the 56-kDa TSA gene among eight Taiwan-H isolates, thirteen other Taiwanese isolates and 104 DNA sequences deposited in the GenBank database using MEGA version 5.0 and PHYLIP version 3.66. We found that the Taiwan-H isolates formed into a new cluster, which was designated the Taiwan Gilliam-variant (TG-v) cluster to distinguish it from the Japanese Gilliam-variant (JG-v) cluster. According to Simplot analysis, TG-v is a new recombinant strain among Gilliam, Ikeda and Kato. Moreover, the Gilliam-Kawasaki cluster had the highest percentage of RFLP cases and was the most frequently isolated type in eastern Taiwan (50.1%, 253/505; 44.0%, 124/282). These findings shed light on the genetic evolution of O. tsutsugamushi into different strains and may be useful in vaccine development and epidemic disease control in the future.
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Diemer GS, Stedman KM. A novel virus genome discovered in an extreme environment suggests recombination between unrelated groups of RNA and DNA viruses. Biol Direct 2012; 7:13. [PMID: 22515485 PMCID: PMC3372434 DOI: 10.1186/1745-6150-7-13] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Accepted: 04/19/2012] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Viruses are known to be the most abundant organisms on earth, yet little is known about their collective origin and evolutionary history. With exceptionally high rates of genetic mutation and mosaicism, it is not currently possible to resolve deep evolutionary histories of the known major virus groups. Metagenomics offers a potential means of establishing a more comprehensive view of viral evolution as vast amounts of new sequence data becomes available for comparative analysis. RESULTS Bioinformatic analysis of viral metagenomic sequences derived from a hot, acidic lake revealed a circular, putatively single-stranded DNA virus encoding a major capsid protein similar to those found only in single-stranded RNA viruses. The presence and circular configuration of the complete virus genome was confirmed by inverse PCR amplification from native DNA extracted from lake sediment. The virus genome appears to be the result of a RNA-DNA recombination event between two ostensibly unrelated virus groups. Environmental sequence databases were examined for homologous genes arranged in similar configurations and three similar putative virus genomes from marine environments were identified. This result indicates the existence of a widespread but previously undetected group of viruses. CONCLUSIONS This unique viral genome carries implications for theories of virus emergence and evolution, as no mechanism for interviral RNA-DNA recombination has yet been identified, and only scant evidence exists that genetic exchange occurs between such distinct virus lineages. REVIEWERS This article was reviewed by EK, MK (nominated by PF) and AM. For the full reviews, please go to the Reviewers' comments section.
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Affiliation(s)
- Geoffrey S Diemer
- Department of Biology, and the Center for Life in Extreme Environments, Portland State University, 1719 SW 10th Avenue, SRTC room 246, Portland, OR 97201, USA
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Partitioning the genetic diversity of a virus family: approach and evaluation through a case study of picornaviruses. J Virol 2012; 86:3890-904. [PMID: 22278230 DOI: 10.1128/jvi.07173-11] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The recent advent of genome sequences as the only source available to classify many newly discovered viruses challenges the development of virus taxonomy by expert virologists who traditionally rely on extensive virus characterization. In this proof-of-principle study, we address this issue by presenting a computational approach (DEmARC) to classify viruses of a family into groups at hierarchical levels using a sole criterion-intervirus genetic divergence. To quantify genetic divergence, we used pairwise evolutionary distances (PEDs) estimated by maximum likelihood inference on a multiple alignment of family-wide conserved proteins. PEDs were calculated for all virus pairs, and the resulting distribution was modeled via a mixture of probability density functions. The model enables the quantitative inference of regions of distance discontinuity in the family-wide PED distribution, which define the levels of hierarchy. For each level, a limit on genetic divergence, below which two viruses join the same group, was objectively selected among a set of candidates by minimizing violations of intragroup PEDs to the limit. In a case study, we applied the procedure to hundreds of genome sequences of picornaviruses and extensively evaluated it by modulating four key parameters. It was found that the genetics-based classification largely tolerates variations in virus sampling and multiple alignment construction but is affected by the choice of protein and the measure of genetic divergence. In an accompanying paper (C. Lauber and A. E. Gorbalenya, J. Virol. 86:3905-3915, 2012), we analyze the substantial insight gained with the genetics-based classification approach by comparing it with the expert-based picornavirus taxonomy.
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The association of recombination events in the founding and emergence of subgenogroup evolutionary lineages of human enterovirus 71. J Virol 2011; 86:2676-85. [PMID: 22205739 DOI: 10.1128/jvi.06065-11] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Enterovirus 71 (EV71) is responsible for frequent large-scale outbreaks of hand, foot, and mouth disease worldwide and represent a major etiological agent of severe, sometimes fatal neurological disease. EV71 variants have been classified into three genogroups (GgA, GgB, and GgC), and the latter two are further subdivided into subgenogroups B1 to B5 and C1 to C5. To investigate the dual roles of recombination and evolution in the epidemiology and transmission of EV71 worldwide, we performed a large-scale genetic analysis of isolates (n = 308) collected from 19 countries worldwide over a 40-year period. A series of recombination events occurred over this period, which have been identified through incongruities in sequence grouping between the VP1 and 3Dpol regions. Eleven 3Dpol clades were identified, each specific to EV71 and associated with specific subgenogroups but interspersed phylogenetically with clades of coxsackievirus A16 and other EV species A serotypes. The likelihood of recombination increased with VP1 sequence divergence; mean half-lives for EV71 recombinant forms (RFs) of 6 and 9 years for GgB and GgC overlapped with those observed for the EV-B serotypes, echovirus 9 (E9), E30, and E11, respectively (1.3 to 9.8 years). Furthermore, within genogroups, sporadic recombination events occurred, such as the linkage of two B4 variants to RF-W instead of RF-A and of two C4 variants to RF-H. Intriguingly, recombination events occurred as a founding event of most subgenogroups immediately preceding their lineage expansion and global emergence. The possibility that recombination contributed to their subsequent spread through improved fitness requires further biological and immunological characterization.
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Chieochansin T, Vichiwattana P, Korkong S, Theamboonlers A, Poovorawan Y. Molecular epidemiology, genome characterization, and recombination event of human parechovirus. Virology 2011; 421:159-66. [PMID: 22018784 DOI: 10.1016/j.virol.2011.09.021] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Revised: 09/22/2011] [Accepted: 09/24/2011] [Indexed: 11/18/2022]
Abstract
Human Parechovirus (HPeV), a member of the Picornaviridae family, is an infectious agent mostly affecting children. There are 16 recognized genotypes which have globally spread. This study incorporated a total of 2957 nasopharyngeal (NP) swab and 759 fecal samples that were collected from different parts of Thailand. The NP of HPeV was detected in 0.4% of NP swab and 6.1% of fecal samples. The majority of HPeV infections occur in infants below the age of 2 years, while infections were detected in children above the age of 10 years as well. Various genotypes comprising 1A, 1B, 2, 3, 4, 5, 6, 10 and 14 have been characterized. This study revealed recombination events in 16 samples in which HPeV1B was shown as the highest frequency. In conclusion, HPeV can be detected in both the respiratory and GI tract. Moreover, HPeV which circulates in Thailand is highly diverse and subject to recombination.
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Affiliation(s)
- Thaweesak Chieochansin
- Center of Excellence in Clinical Virology, Department of Pediatrics, Chulalongkorng University, Bangkok, Thailand
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23
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Han TH, Kim CH, Park SH, Chung JY, Hwang ES. Detection of human parechoviruses in children with gastroenteritis in South Korea. Arch Virol 2011; 156:1471-5. [DOI: 10.1007/s00705-011-0995-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2011] [Accepted: 03/29/2011] [Indexed: 10/18/2022]
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24
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Azoulay E. Emerging Viral Infections. PULMONARY INVOLVEMENT IN PATIENTS WITH HEMATOLOGICAL MALIGNANCIES 2011. [PMCID: PMC7123354 DOI: 10.1007/978-3-642-15742-4_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Elie Azoulay
- Service de Réanimation Médicale, Hôpital Saint Louis, Avenue Claude Vellefaux 1, Paris, 75010 France
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Abstract
Picornaviruses are small non-enveloped positive strand RNA viruses that can cause a wide range of clinical manifestations in humans and animals. Many of these viruses are highly diversified and globally prevalent. Natural recombination has been reported in most picornavirus genera and is a key genetic feature of these infectious agents. In several socially relevant picornavirus genera, such as enteroviruses, aphthoviruses, parechoviruses and cardioviruses, recombination, combined with dynamic global epidemiology, maintains virus species as a worldwide pool of genetic information. It can be suggested that on a short time scale recombination acts to promote virus diversity, and new recombinant forms of picornaviruses emerge frequently as 'snapshots' of this global pool. On a longer time scale, recombination maintains stability of a gene pool of a species by shuffling sequences and thus limiting divergence and speciation. This review covers existing evidence of recombination in most genera of the family Picornaviridae and possible implications for diagnostics, epidemiology and classification.
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Affiliation(s)
- A N Lukashev
- M.P. Chumakov Institute of Poliomyelitis and Viral Encephalitides, Russian Academy of Medical Sciences, Moscow Region, Russia.
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26
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Full genome sequence analysis of parechoviruses from Brazil reveals geographical patterns in the evolution of non-structural genes and intratypic recombination in the capsid region. J Gen Virol 2010; 92:564-71. [DOI: 10.1099/vir.0.022525-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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27
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Wang B, Tian ZJ, Gong DQ, Li DY, Wang Y, Chen JZ, An TQ, Peng JM, Tong GZ. Isolation of serotype 2 porcine teschovirus in China: Evidence of natural recombination. Vet Microbiol 2010; 146:138-43. [DOI: 10.1016/j.vetmic.2010.05.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2010] [Revised: 04/16/2010] [Accepted: 05/03/2010] [Indexed: 01/22/2023]
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Calvert J, Chieochansin T, Benschop KS, McWilliam Leitch EC, Drexler JF, Grywna K, da Costa Ribeiro H, Drosten C, Harvala H, Poovorawan Y, Wolthers KC, Simmonds P. Recombination dynamics of human parechoviruses: investigation of type-specific differences in frequency and epidemiological correlates. J Gen Virol 2010; 91:1229-38. [PMID: 20089803 DOI: 10.1099/vir.0.018747-0] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Human parechoviruses (HPeVs) are highly prevalent RNA viruses classified in the family Picornaviridae. Several antigenically distinct types circulate in human populations worldwide, whilst recombination additionally contributes to the genetic heterogeneity of the virus. To investigate factors influencing the likelihood of recombination and to compare its dynamics among types, 154 variants collected from four widely geographically separated referral centres (UK, The Netherlands, Thailand and Brazil) were typed by VP3/VP1 amplification/sequencing with recombination groups assigned by analysis of 3Dpol sequences. HPeV1B and HPeV3 were the most frequently detected types in each referral region, but with marked geographical differences in the frequencies of different recombinant forms (RFs) of types 1B, 5 and 6. HPeV1B showed more frequent recombination than HPeV3, in terms both of evolutionary divergence and of temporal/geographical indicators of population separation. HPeV1 variants showing between 10 and 20% divergence in VP3/VP1 almost invariably fell into different recombination groups, compared with only one-third of similarly divergent HPeV3 variants. Substitution rates calculated by beast in the VP3/VP1 region of HPeV1 and HPeV3 allowed half-lives of the RFs of 4 and 20 years, respectively, to be calculated, estimates fitting closely with their observed lifespans based on population sampling. The variability in recombination dynamics between HPeV1B and HPeV3 offers an intriguing link with their markedly different seasonal patterns of transmission, age distributions of infection and clinical outcomes. Future investigation of the epidemiological and biological opportunities and constraints on intertypic recombination will provide more information about its influence on the longer term evolution and pathogenicity of parechoviruses.
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Affiliation(s)
- J Calvert
- Centre for Infectious Diseases, University of Edinburgh, Summerhall, Edinburgh, UK
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Benschop KSM, de Vries M, Minnaar RP, Stanway G, van der Hoek L, Wolthers KC, Simmonds P. Comprehensive full-length sequence analyses of human parechoviruses: diversity and recombination. J Gen Virol 2009; 91:145-54. [DOI: 10.1099/vir.0.014670-0] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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30
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Williams ÇH, Panayiotou M, Girling GD, Peard CI, Oikarinen S, Hyöty H, Stanway G. Evolution and conservation in human parechovirus genomes. J Gen Virol 2009; 90:1702-1712. [DOI: 10.1099/vir.0.008813-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Human parechoviruses (HPeVs) are frequent pathogens with a seroprevalance of over 90 % in adults. Recent studies on these viruses have increased the number of HPeV types to eight. Here we analyse the complete genome of one clinical isolate, PicoBank/HPeV1/a, and VP1 and 3D protein sequences of PicoBank/HPeV6/a, isolated from the same individual 13 months later. PicoBank/HPeV1/a is closely related to other recent HPeV1 isolates but is distinct from the HPeV1 Harris prototype isolated 50 years ago. The availability of an increasing number of HPeV sequences has allowed a detailed analysis of these viruses. The results add weight to the observations that recombination plays a role in the generation of HPeV diversity. An important finding is the presence of unexpected conservation of codons utilized in part of the 3D-encoding region, some of which can be explained by the presence of a phylogenetically conserved predicted secondary structure domain. This suggests that in addition to the cis-acting replication element, RNA secondary structure domains in coding regions play a key role in picornavirus replication.
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Affiliation(s)
- Çiğdem H. Williams
- Department of Biological Sciences, University of Essex, Colchester CO4 3SQ, UK
| | - Maria Panayiotou
- Department of Biological Sciences, University of Essex, Colchester CO4 3SQ, UK
| | - Gareth D. Girling
- Department of Biological Sciences, University of Essex, Colchester CO4 3SQ, UK
| | - Curtis I. Peard
- Department of Biological Sciences, University of Essex, Colchester CO4 3SQ, UK
| | - Sami Oikarinen
- Department of Virology, University of Tampere, Medical School, Tampere, Finland
| | - Heikki Hyöty
- Center for Laboratory Medicine, Tampere University Hospital, Tampere, Finland
- Department of Virology, University of Tampere, Medical School, Tampere, Finland
| | - Glyn Stanway
- Department of Biological Sciences, University of Essex, Colchester CO4 3SQ, UK
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