1
|
Lin Y, Pascall DJ. Characterisation of putative novel tick viruses and zoonotic risk prediction. Ecol Evol 2024; 14:e10814. [PMID: 38259958 PMCID: PMC10800298 DOI: 10.1002/ece3.10814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 11/02/2023] [Accepted: 11/24/2023] [Indexed: 01/24/2024] Open
Abstract
Tick-associated viruses remain a substantial zoonotic risk worldwide, so knowledge of the diversity of tick viruses has potential health consequences. Despite their importance, large amounts of sequences in public data sets from tick meta-genomic and -transcriptomic projects remain unannotated, sequence data that could contain undocumented viruses. Through data mining and bioinformatic analysis of more than 37,800 public meta-genomic and -transcriptomic data sets, we found 83 unannotated contigs exhibiting high identity with known tick viruses. These putative viral contigs were classified into three RNA viral families (Alphatetraviridae, Orthomyxoviridae and Chuviridae) and one DNA viral family (Asfarviridae). After manual checking of quality and dissimilarity towards other sequences in the data set, these 83 contigs were reduced to five contigs in the Alphatetraviridae from four putative viruses, four in the Orthomyxoviridae from two putative viruses and one in the Chuviridae which clustered with known tick-associated viruses, forming a separate clade within the viral families. We further attempted to assess which previously known tick viruses likely represent zoonotic risks and thus deserve further investigation. We ranked the human infection potential of 133 known tick-associated viruses using a genome composition-based machine learning model. We found five high-risk tick-associated viruses (Langat virus, Lonestar tick chuvirus 1, Grotenhout virus, Taggert virus and Johnston Atoll virus) that have not been known to infect human and two viral families (Nairoviridae and Phenuiviridae) that contain a large proportion of potential zoonotic tick-associated viruses. This adds to the knowledge of tick virus diversity and highlights the importance of surveillance of newly emerging tick-associated diseases.
Collapse
Affiliation(s)
- Yuting Lin
- MRC Biostatistics UnitUniversity of CambridgeCambridgeUK
- Royal Veterinary CollegeUniversity of LondonLondonUK
| | | |
Collapse
|
2
|
Luo DS, Zhou ZJ, Ge XY, Bourhy H, Shi ZL, Grandadam M, Dacheux L. Genome Characterization of Bird-Related Rhabdoviruses Circulating in Africa. Viruses 2021; 13:v13112168. [PMID: 34834974 PMCID: PMC8622386 DOI: 10.3390/v13112168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 11/16/2022] Open
Abstract
Rhabdoviridae is the most diverse family of the negative, single-stranded RNA viruses, which includes 40 ecologically different genera that infect plants, insects, reptiles, fishes, and mammals, including humans, and birds. To date, only a few bird-related rhabdoviruses among the genera Sunrhavirus, Hapavirus, and Tupavirus have been described and analyzed at the molecular level. In this study, we characterized seven additional and previously unclassified rhabdoviruses, which were isolated from various bird species collected in Africa during the 1960s and 1970s. Based on the analysis of their genome sequences obtained by next generation sequencing, we observed a classical genomic structure, with the presence of the five canonical rhabdovirus genes, i.e., nucleoprotein (N), phosphoprotein (P), matrix protein (M), glycoprotein (G), and polymerase (L). In addition, different additional open reading frames which code putative proteins of unknown function were identified, with the common presence of the C and the SH proteins, within the P gene and between the M and G genes, respectively. Genetic comparisons and phylogenetic analysis demonstrated that these seven bird-related rhabdoviruses could be considered as putative new species within the genus Sunrhavirus, where they clustered into a single group (named Clade III), a companion to two other groups that encompass mainly insect-related viruses. The results of this study shed light on the high diversity of the rhabdoviruses circulating in birds, mainly in Africa. Their close relationship with other insect-related sunrhaviruses raise questions about their potential role and impact as arboviruses that affect bird communities.
Collapse
Affiliation(s)
- Dong-Sheng Luo
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (D.-S.L.); (Z.-L.S.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Lyssavirus Epidemiology and Neuropathology Unit, Institut Pasteur, Université de Paris, 75015 Paris, France;
| | - Zhi-Jian Zhou
- Hunan Provincial Key Laboratory of Medical Virology, College of Biology, Hunan University, Changsha 410082, China; (Z.-J.Z.); (X.-Y.G.)
| | - Xing-Yi Ge
- Hunan Provincial Key Laboratory of Medical Virology, College of Biology, Hunan University, Changsha 410082, China; (Z.-J.Z.); (X.-Y.G.)
| | - Hervé Bourhy
- Lyssavirus Epidemiology and Neuropathology Unit, Institut Pasteur, Université de Paris, 75015 Paris, France;
| | - Zheng-Li Shi
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (D.-S.L.); (Z.-L.S.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Marc Grandadam
- Institut de Recherche Biomédicale des Armées, 91220 Bretigny-sur-Orge, France;
- National Reference Center for Arboviruses, Institut Pasteur, Université de Paris, 75015 Paris, France
| | - Laurent Dacheux
- Lyssavirus Epidemiology and Neuropathology Unit, Institut Pasteur, Université de Paris, 75015 Paris, France;
- Correspondence: ; Tel.: +33-140613303
| |
Collapse
|
3
|
Update on Potentially Zoonotic Viruses of European Bats. Vaccines (Basel) 2021; 9:vaccines9070690. [PMID: 34201666 PMCID: PMC8310327 DOI: 10.3390/vaccines9070690] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/10/2021] [Accepted: 06/21/2021] [Indexed: 12/13/2022] Open
Abstract
Bats have been increasingly gaining attention as potential reservoir hosts of some of the most virulent viruses known. Numerous review articles summarize bats as potential reservoir hosts of human-pathogenic zoonotic viruses. For European bats, just one review article is available that we published in 2014. The present review provides an update on the earlier article and summarizes the most important viruses found in European bats and their possible implications for Public Health. We identify the research gaps and recommend monitoring of these viruses.
Collapse
|
4
|
Mohsin H, Asif A, Fatima M, Rehman Y. Potential role of viral metagenomics as a surveillance tool for the early detection of emerging novel pathogens. Arch Microbiol 2020; 203:865-872. [PMID: 33175192 PMCID: PMC7656497 DOI: 10.1007/s00203-020-02105-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 10/01/2020] [Accepted: 10/19/2020] [Indexed: 12/28/2022]
Abstract
Since the early times, human beings have always been faced with deadly microbial infections, both bacterial and viral. Pathogens such as viruses are always evolving owing to the processes of antigenic shift and drift. Such viral evolution results in the emergence of new types and serovars that prove deadly for humans-like influenza pandemics, severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS). The pandemic of novel coronavirus SARS-CoV-2 is the recent example. It has resulted in a great loss of human lives and a serious burden on economy across the globe. To counter such situations, a system should exist for the early detection of emerging viral pathogens. This will help prevent possible outbreaks and save human lives. Most of such deadly novel viruses and viral outbreaks are known to be originated from animal hosts. Regular monitoring of potential hot spots of such emerging microbes, such as zoos and animal markets, through metagenomics could help assess the presence of new viruses and pathogens. In this review, we focus on the potential of viral metagenomics and propose a surveillance system based on it for the early detection and hence prevention of such emerging viral infections.
Collapse
Affiliation(s)
- Hareem Mohsin
- Department of Allied Health Sciences, Superior University, Lahore, Pakistan
| | - Azka Asif
- Schoool of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Minhaj Fatima
- Learning Resource Center, University of Management and Technology, Lahore, Pakistan
| | - Yasir Rehman
- Department of Life Sciences, School of Science, University of Management and Technology, Lahore, Pakistan.
| |
Collapse
|
5
|
Filippone C, Castel G, Murri S, Ermonval M, Korva M, Avšič-Županc T, Sironen T, Vapalahati O, McElhinney LM, Ulrich RG, Groschup MH, Caro V, Sauvage F, van der Werf S, Manuguerra JC, Gessain A, Marianneau P, Tordo N. Revisiting the genetic diversity of emerging hantaviruses circulating in Europe using a pan-viral resequencing microarray. Sci Rep 2019; 9:12404. [PMID: 31455867 PMCID: PMC6712034 DOI: 10.1038/s41598-019-47508-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 06/21/2019] [Indexed: 11/09/2022] Open
Abstract
Hantaviruses are zoonotic agents transmitted from small mammals, mainly rodents, to humans, where they provoke diseases such as Hemorrhagic fever with Renal Syndrome (HFRS) and its mild form, Nephropathia Epidemica (NE), or Hantavirus Cardio-Pulmonary Syndrome (HCPS). Hantaviruses are spread worldwide and monitoring animal reservoirs is of primary importance to control the zoonotic risk. Here, we describe the development of a pan-viral resequencing microarray (PathogenID v3.0) able to explore the genetic diversity of rodent-borne hantaviruses endemic in Europe. Among about 800 sequences tiled on the microarray, 52 correspond to a tight molecular sieve of hantavirus probes covering a large genetic landscape. RNAs from infected animal tissues or from laboratory strains have been reverse transcribed, amplified, then hybridized to the microarray. A classical BLASTN analysis applied to the sequence delivered through the microarray allows to identify the hantavirus species up to the exact geographical variant present in the tested samples. Geographical variants of the most common European hantaviruses from France, Germany, Slovenia and Finland, such as Puumala virus, Dobrava virus and Tula virus, were genetically discriminated. Furthermore, we precisely characterized geographical variants still unknown when the chip was conceived, such as Seoul virus isolates, recently emerged in France and the United Kingdom.
Collapse
Affiliation(s)
- Claudia Filippone
- Institut Pasteur, Antiviral Strategies Unit, Department of Virology, Paris, France.,Institut Pasteur, Unit of Epidemiology and Physiopathology of Oncogenic Viruses, CNRS, UMR 3569, Department of Virology, Paris, France.,Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Guillaume Castel
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France, Montpellier, France
| | | | - Myriam Ermonval
- Institut Pasteur, Antiviral Strategies Unit, Department of Virology, Paris, France
| | - Misa Korva
- University of Ljubljana, Microbiology and Immunology Institute, Faculty of Medicine, Ljubljana, Slovenia
| | - Tatjana Avšič-Županc
- University of Ljubljana, Microbiology and Immunology Institute, Faculty of Medicine, Ljubljana, Slovenia
| | - Tarja Sironen
- Haartman Institute, Department of Virology, Helsinki, Finland
| | - Olli Vapalahati
- Haartman Institute, Department of Virology, Helsinki, Finland
| | - Lorraine M McElhinney
- Animal and Plant Health Agency (APHA), Surrey, UK. University of Liverpool, South Wirral, United Kingdom
| | - Rainer G Ulrich
- Friedrich-Loeffler-Institut, Institute for Novel and Emerging Infectious Diseases, Greifswald, Insel Riems, Germany
| | - Martin H Groschup
- Friedrich-Loeffler-Institut, Institute for Novel and Emerging Infectious Diseases, Greifswald, Insel Riems, Germany
| | - Valérie Caro
- Institut Pasteur, Laboratory for Urgent Response to Biological Threats - CIBU Unit, Paris, France
| | - Frank Sauvage
- University of Lyon, UMR- CNRS, 5558, Villeurbanne, France
| | - Sylvie van der Werf
- Institut Pasteur, Unit of Molecular Genetics of RNA viruses, Department of Virology, Paris, France
| | - Jean-Claude Manuguerra
- Institut Pasteur, Laboratory for Urgent Response to Biological Threats - CIBU Unit, Paris, France
| | - Antoine Gessain
- Institut Pasteur, Unit of Epidemiology and Physiopathology of Oncogenic Viruses, CNRS, UMR 3569, Department of Virology, Paris, France
| | | | - Noël Tordo
- Institut Pasteur, Antiviral Strategies Unit, Department of Virology, Paris, France. .,Institut Pasteur de Guinée, Conakry, Guinea.
| |
Collapse
|
6
|
Development and Validation of Heminested RT-PCR and qRT-PCR Assays for Comprehensive Detection of Rabies Virus in the Suspected Rabid Brain and Saliva Samples. ARCHIVES OF CLINICAL INFECTIOUS DISEASES 2019. [DOI: 10.5812/archcid.85790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
7
|
Troupin C, Picard-Meyer E, Dellicour S, Casademont I, Kergoat L, Lepelletier A, Dacheux L, Baele G, Monchâtre-Leroy E, Cliquet F, Lemey P, Bourhy H. Host Genetic Variation Does Not Determine Spatio-Temporal Patterns of European Bat 1 Lyssavirus. Genome Biol Evol 2017; 9:3202-3213. [PMID: 29165566 PMCID: PMC5721339 DOI: 10.1093/gbe/evx236] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/17/2017] [Indexed: 12/22/2022] Open
Abstract
The majority of bat rabies cases in Europe are attributed to European bat 1 lyssavirus (EBLV-1), circulating mainly in serotine bats (Eptesicus serotinus). Two subtypes have been defined (EBLV-1a and EBLV-1b), each associated with a different geographical distribution. In this study, we undertake a comprehensive sequence analysis based on 80 newly obtained EBLV-1 nearly complete genome sequences from nine European countries over a 45-year period to infer selection pressures, rates of nucleotide substitution, and evolutionary time scale of these two subtypes in Europe. Our results suggest that the current lineage of EBLV-1 arose in Europe ∼600 years ago and the virus has evolved at an estimated average substitution rate of ∼4.19×10-5 subs/site/year, which is among the lowest recorded for RNA viruses. In parallel, we investigate the genetic structure of French serotine bats at both the nuclear and mitochondrial level and find that they constitute a single genetic cluster. Furthermore, Mantel tests based on interindividual distances reveal the absence of correlation between genetic distances estimated between viruses and between host individuals. Taken together, this indicates that the genetic diversity observed in our E. serotinus samples does not account for EBLV-1a and -1b segregation and dispersal in Europe.
Collapse
Affiliation(s)
- Cécile Troupin
- Institut Pasteur, Unit Lyssavirus Dynamics and Host Adaptation, WHO Collaborating Centre for Reference and Research on Rabies, Paris, France
| | - Evelyne Picard-Meyer
- Laboratory for Rabies and Wildlife ANSES, Nancy, OIE Reference Laboratory for Rabies, European Union Reference Laboratory for Rabies, European Union Reference Laboratory for Rabies Serology, WHO Collaborating Centre for Research and Management on Zoonoses, Malzeville, France
| | - Simon Dellicour
- Institut Pasteur, Laboratory for Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute, KU Leuven – University of Leuven, Belgium
| | - Isabelle Casademont
- Unité de la Génétique Fonctionnelle des Maladies Infectieuses, Paris, France
| | - Lauriane Kergoat
- Institut Pasteur, Unit Lyssavirus Dynamics and Host Adaptation, WHO Collaborating Centre for Reference and Research on Rabies, Paris, France
| | - Anthony Lepelletier
- Institut Pasteur, Unit Lyssavirus Dynamics and Host Adaptation, WHO Collaborating Centre for Reference and Research on Rabies, Paris, France
| | - Laurent Dacheux
- Institut Pasteur, Unit Lyssavirus Dynamics and Host Adaptation, WHO Collaborating Centre for Reference and Research on Rabies, Paris, France
| | - Guy Baele
- Institut Pasteur, Laboratory for Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute, KU Leuven – University of Leuven, Belgium
| | - Elodie Monchâtre-Leroy
- Laboratory for Rabies and Wildlife ANSES, Nancy, OIE Reference Laboratory for Rabies, European Union Reference Laboratory for Rabies, European Union Reference Laboratory for Rabies Serology, WHO Collaborating Centre for Research and Management on Zoonoses, Malzeville, France
| | - Florence Cliquet
- Laboratory for Rabies and Wildlife ANSES, Nancy, OIE Reference Laboratory for Rabies, European Union Reference Laboratory for Rabies, European Union Reference Laboratory for Rabies Serology, WHO Collaborating Centre for Research and Management on Zoonoses, Malzeville, France
| | - Philippe Lemey
- Institut Pasteur, Laboratory for Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute, KU Leuven – University of Leuven, Belgium
| | - Hervé Bourhy
- Institut Pasteur, Unit Lyssavirus Dynamics and Host Adaptation, WHO Collaborating Centre for Reference and Research on Rabies, Paris, France
| |
Collapse
|
8
|
Wang J, Yu P, Xie Z, Yan T, Chen C, Shen X, Chen X, Li L, Wang X, Sun S, Ma X. A resequencing pathogen microarray method for high-throughput molecular diagnosis of multiple etiologies associated with central nervous system infection. Arch Virol 2017; 162:3769-3778. [PMID: 28913577 PMCID: PMC7087039 DOI: 10.1007/s00705-017-3550-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 08/01/2017] [Indexed: 12/28/2022]
Abstract
Central nervous system infection (CNSI) results in significant health and economic burdens worldwide, but the diversity of causative pathogens makes differential diagnosis very difficult. Although PCR and real-time fluorescent quantitative PCR (q-PCR) assays are widely applied for pathogen detection, they are generally optimized for the detection of a single or limited number of targets and are not suitable for the diagnosis of numerous CNSI agents. In this study, we describe the development of a resequencing pathogen microarray (RPM-IVDC4) method for the simultaneous detection of viruses, bacteria, fungi and parasites that cause CNSI. The test panel of this assay included more than 100 microorganism species across 45 genera and 30 families. The analytical specificity and sensitivity were examined using a panel of positive reference strains, and the clinical performance was evaluated using 432 clinical samples by comparing the results with q-PCR assays. Our results demonstrated good performance of the RPM-IVDC4 assay in terms of sensitivity, specificity and detection range, suggesting that the platform can be further developed for high-throughput CNSI diagnosis.
Collapse
Affiliation(s)
- Ji Wang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Panhui Yu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Neurology Department, Children's Hospital of Hebei Province, Shijiazhuang, China
| | - Zhengde Xie
- MOE Key Laboratory of Major Diseases in Children, National Key Discipline of Pediatrics, National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Tengfei Yan
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,No. 1 Hospital of Shijiazhuang, Shijiazhuang, China
| | - Chen Chen
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xinxin Shen
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiangpeng Chen
- MOE Key Laboratory of Major Diseases in Children, National Key Discipline of Pediatrics, National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Lixin Li
- No. 1 Hospital of Shijiazhuang, Shijiazhuang, China
| | - Xiuxia Wang
- Department of Pediatrics, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Suzhen Sun
- Neurology Department, Children's Hospital of Hebei Province, Shijiazhuang, China.
| | - Xuejun Ma
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
| |
Collapse
|
9
|
Gubala A, Walsh S, McAllister J, Weir R, Davis S, Melville L, Mitchell I, Bulach D, Gauci P, Skvortsov A, Boyle D. Identification of very small open reading frames in the genomes of Holmes Jungle virus, Ord River virus, and Wongabel virus of the genus Hapavirus, family Rhabdoviridae. Evol Bioinform Online 2017; 13:1176934317713484. [PMID: 28747815 PMCID: PMC5510769 DOI: 10.1177/1176934317713484] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 05/05/2017] [Indexed: 12/11/2022] Open
Abstract
Viruses of the family Rhabdoviridae infect a broad range of hosts from a variety of ecological and geographical niches, including vertebrates, arthropods, and plants. The arthropod-transmitted members of this family display considerable genetic diversity and remarkable genomic flexibility that enable coding for various accessory proteins in different locations of the genome. Here, we describe the genome of Holmes Jungle virus, isolated from Culex annulirostris mosquitoes collected in northern Australia, and make detailed comparisons with the closely related Ord River and Wongabel viruses, with a focus on identifying very small open reading frames (smORFs) in their genomes. This is the first systematic prediction of smORFs in rhabdoviruses, emphasising the intricacy of the rhabdovirus genome and the knowledge gaps. We speculate that these smORFs may be of importance to the life cycle of the virus in the arthropod vector.
Collapse
Affiliation(s)
- Aneta Gubala
- Land Division, Defence Science and Technology Group, Fishermans Bend, VIC, Australia
| | - Susan Walsh
- Berrimah Veterinary Laboratories, Department of Primary Industry and Fisheries, Northern Territory Government, Berrimah, NT, Australia
| | - Jane McAllister
- Land Division, Defence Science and Technology Group, Fishermans Bend, VIC, Australia
| | - Richard Weir
- Berrimah Veterinary Laboratories, Department of Primary Industry and Fisheries, Northern Territory Government, Berrimah, NT, Australia
| | - Steven Davis
- Berrimah Veterinary Laboratories, Department of Primary Industry and Fisheries, Northern Territory Government, Berrimah, NT, Australia
| | - Lorna Melville
- Berrimah Veterinary Laboratories, Department of Primary Industry and Fisheries, Northern Territory Government, Berrimah, NT, Australia
| | - Ian Mitchell
- Land Division, Defence Science and Technology Group, Fishermans Bend, VIC, Australia
| | - Dieter Bulach
- Australian Animal Health Laboratory, Commonwealth Scientific and Industrial Research Organisation, Geelong, VIC, Australia
| | - Penny Gauci
- Land Division, Defence Science and Technology Group, Fishermans Bend, VIC, Australia
| | - Alex Skvortsov
- Land Division, Defence Science and Technology Group, Fishermans Bend, VIC, Australia
| | - David Boyle
- Australian Animal Health Laboratory, Commonwealth Scientific and Industrial Research Organisation, Geelong, VIC, Australia
| |
Collapse
|
10
|
Simo Tchetgna HD, Nakoune E, Selekon B, Gessain A, Manuguerra JC, Kazanji M, Berthet N. Molecular Characterization of the Kamese Virus, an Unassigned Rhabdovirus, Isolated from Culex pruina in the Central African Republic. Vector Borne Zoonotic Dis 2017; 17:447-451. [PMID: 28350284 DOI: 10.1089/vbz.2016.2068] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Rhabdoviridae is one of the most diversified families of RNA viruses whose members infect a wide range of plants, animals, and arthropods. The members of this family are classified into 13 genera and >150 unassigned viruses. Here, we sequenced the complete genome of a rhabdovirus belonging to the Hart Park serogroup, the Kamese virus (KAMV), isolated in 1977 from Culex pruina in the Central African Republic. The genomic sequence showed an organization typical of rhabdoviruses with additional genes in the P-M and G-L intergenic regions, as already reported for the Hart Park serogroup. Our Kamese strain (ArB9074) had 98% and 78.8% nucleotide sequence similarity with the prototypes of the KAMV and Mossuril virus isolated in Uganda and Mozambique in two different Culex species, respectively. Moreover, the protein sequences had 98-100% amino acid similarity with the prototype of the KAMV, except for an additional gene (U3) that showed a divergence of 6%. These molecular data show that our strain of the KAMV is genetically close to the Culex annuliorus strain that was circulating in Uganda in 1967. However, this study suggests the need to improve our knowledge of the KAMV to better understand its behavior, its life cycle, and its potential reservoirs.
Collapse
Affiliation(s)
| | - Emmanuel Nakoune
- 2 Virology Department, Institut Pasteur de Bangui , Bangui, Central African Republic
| | - Benjamin Selekon
- 2 Virology Department, Institut Pasteur de Bangui , Bangui, Central African Republic
| | - Antoine Gessain
- 3 Epidemiology and Physiopathology of Oncogenic Viruses, Institut Pasteur , Paris, France .,4 Centre National de Recherche Scientifique (CNRS) UMR3569 , Paris, France
| | - Jean-Claude Manuguerra
- 5 Unité Environnement et Risques Infectieux, Cellule d'Intervention Biologique d'Urgence, Institut Pasteur , Paris, France
| | - Mirdad Kazanji
- 2 Virology Department, Institut Pasteur de Bangui , Bangui, Central African Republic
| | - Nicolas Berthet
- 1 Centre International de Recherches Médicales de Franceville (CIRMF) , Franceville, Gabon .,4 Centre National de Recherche Scientifique (CNRS) UMR3569 , Paris, France .,5 Unité Environnement et Risques Infectieux, Cellule d'Intervention Biologique d'Urgence, Institut Pasteur , Paris, France
| |
Collapse
|
11
|
Troupin C, Dacheux L, Tanguy M, Sabeta C, Blanc H, Bouchier C, Vignuzzi M, Duchene S, Holmes EC, Bourhy H. Large-Scale Phylogenomic Analysis Reveals the Complex Evolutionary History of Rabies Virus in Multiple Carnivore Hosts. PLoS Pathog 2016; 12:e1006041. [PMID: 27977811 PMCID: PMC5158080 DOI: 10.1371/journal.ppat.1006041] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 11/03/2016] [Indexed: 12/25/2022] Open
Abstract
The natural evolution of rabies virus (RABV) provides a potent example of multiple host shifts and an important opportunity to determine the mechanisms that underpin viral emergence. Using 321 genome sequences spanning an unprecedented diversity of RABV, we compared evolutionary rates and selection pressures in viruses sampled from multiple primary host shifts that occurred on various continents. Two major phylogenetic groups, bat-related RABV and dog-related RABV, experiencing markedly different evolutionary dynamics were identified. While no correlation between time and genetic divergence was found in bat-related RABV, the evolution of dog-related RABV followed a generally clock-like structure, although with a relatively low evolutionary rate. Subsequent molecular clock dating indicated that dog-related RABV likely underwent a rapid global spread following the intensification of intercontinental trade starting in the 15th century. Strikingly, although dog RABV has jumped to various wildlife species from the order Carnivora, we found no clear evidence that these host-jumping events involved adaptive evolution, with RABV instead characterized by strong purifying selection, suggesting that ecological processes also play an important role in shaping patterns of emergence. However, specific amino acid changes were associated with the parallel emergence of RABV in ferret-badgers in Asia, and some host shifts were associated with increases in evolutionary rate, particularly in the ferret-badger and mongoose, implying that changes in host species can have important impacts on evolutionary dynamics. Zoonoses account for most recently emerged infectious diseases of humans, although little is known about the evolutionary mechanisms involved in cross-species virus transmission. Understanding the evolutionary patterns and processes that underpin such cross-species transmission is of importance for predicting the spread of zoonotic infections, and hence to their ultimate control. We present a large-scale and detailed reconstruction of the evolutionary history of rabies virus (RABV) in domestic and wildlife animal species. RABV is of particular interest as it is capable of infecting many mammals but, paradoxically, is only maintained in distinct epidemiological cycles associated with animal species from the orders Carnivora and Chiroptera. We show that bat-related RABV and dog-related RABV have experienced very different evolutionary dynamics, and that host jumps are sometimes characterized by significant increases in evolutionary rate. Among Carnivora, the association between RABV and particular host species most likely arose from a combination of the historical human-mediated spread of the virus and jumps into new primary host species. In addition, we show that changes in host species are associated with multiple evolutionary pathways including the occurrence of host-specific parallel evolution. Overall, our data indicate that the establishment of dog-related RABV in new carnivore hosts may only require subtle adaptive evolution.
Collapse
Affiliation(s)
- Cécile Troupin
- Institut Pasteur, Unit Lyssavirus Dynamics and Host Adaptation, WHO Collaborating Centre for Reference and Research on Rabies, Paris, France
| | - Laurent Dacheux
- Institut Pasteur, Unit Lyssavirus Dynamics and Host Adaptation, WHO Collaborating Centre for Reference and Research on Rabies, Paris, France
| | - Marion Tanguy
- Institut Pasteur, Unit Lyssavirus Dynamics and Host Adaptation, WHO Collaborating Centre for Reference and Research on Rabies, Paris, France
- Institut Pasteur, Genomics Platform, Paris, France
| | - Claude Sabeta
- Agricultural Research Council, Onderstepoort Veterinary Institute, OIE Rabies Reference Laboratory, Pretoria, South Africa
| | - Hervé Blanc
- Institut Pasteur, Centre National de la Recherche Scientifique UMR 3569, Viral Populations and Pathogenesis Unit, Paris, France
| | | | - Marco Vignuzzi
- Institut Pasteur, Centre National de la Recherche Scientifique UMR 3569, Viral Populations and Pathogenesis Unit, Paris, France
| | - Sebastián Duchene
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia
- Centre for Systems Genomics, University of Melbourne, Parkville, Victoria, Australia
| | - Edward C. Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Hervé Bourhy
- Institut Pasteur, Unit Lyssavirus Dynamics and Host Adaptation, WHO Collaborating Centre for Reference and Research on Rabies, Paris, France
- * E-mail:
| |
Collapse
|
12
|
Berthet N, Falguières M, Filippone C, Bertolus C, Bole-Feysot C, Brisse S, Gessain A, Heard I, Favre M. Resequencing microarray technology for genotyping human papillomavirus in cervical smears. PLoS One 2014; 9:e109301. [PMID: 25383888 PMCID: PMC4226468 DOI: 10.1371/journal.pone.0109301] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 09/10/2014] [Indexed: 11/19/2022] Open
Abstract
There are more than 40 human papillomaviruses (HPVs) belonging to the alpha genus that cause sexually transmitted infections; these infections are among the most frequent and can lead to condylomas and anogenital intra-epithelial neoplasia. At least 18 of these viruses are causative agents of anogenital carcinomas. We evaluated the performance of a resequencing microarray for the detection and genotyping of alpha HPV of clinical significance using cloned HPV DNA. To reduce the number of HPV genotypes tiled on microarray, we used reconstructed ancestral sequences (RASs) as they are more closely related to the various genotypes than the current genotypes are among themselves. The performance of this approach was tested by genotyping with a set of 40 cervical smears already genotyped using the commercial PapilloCheck kit. The results of the two tests were concordant for 70% (28/40) of the samples and compatible for 30% (12/40). Our findings indicate that RASs were able to detect and identify one or several HPV in clinical samples. Associating RASs with homonym sequences improved the genotyping of HPV present in cases of multiple infection. In conclusion, we demonstrate the diagnostic potential of resequencing technology for genotyping of HPV, and illustrate its value both for epidemiological studies and for monitoring the distribution of HPV in the post-vaccination era.
Collapse
Affiliation(s)
- Nicolas Berthet
- Institut Pasteur, Epidémiologie et Physiopathologie des Virus Oncogènes, 75724 Paris Cedex 15, France
- Centre National de la Recherche Scientifique, UMR 3569, 75724 Paris Cedex 15, France
- * E-mail:
| | - Michael Falguières
- Institut Pasteur, Centre National de Référence des Papillomavirus, 75724 Paris Cedex 15, France
| | - Claudia Filippone
- Institut Pasteur, Epidémiologie et Physiopathologie des Virus Oncogènes, 75724 Paris Cedex 15, France
- Centre National de la Recherche Scientifique, UMR 3569, 75724 Paris Cedex 15, France
| | - Chloé Bertolus
- AP-HP, Hôpital Pitié-Salpêtrière, Service de Chirurgie Maxillo-Faciale et Stomatologie, 75013 Paris, France
- UPMC, Université Paris 06, CIMI-Paris, UMRS CR7, INSERM U1135, 75005, Paris, France
| | - Christine Bole-Feysot
- Imagine, Institut des maladies génétiques - Plateforme Génomique, Hôpital Necker - Enfants Malades, 75743 Paris cedex 15, France
| | - Sylvain Brisse
- Institut Pasteur, Plate-forme Génotypage des Pathogènes et Santé Publique, 75724 Paris Cedex 15, France
| | - Antoine Gessain
- Institut Pasteur, Epidémiologie et Physiopathologie des Virus Oncogènes, 75724 Paris Cedex 15, France
- Centre National de la Recherche Scientifique, UMR 3569, 75724 Paris Cedex 15, France
| | - Isabelle Heard
- Institut Pasteur, Centre National de Référence des Papillomavirus, 75724 Paris Cedex 15, France
- UPMC Université Paris 06, Groupe hospitalier Pitié-Salpêtrière, Paris Cedex 13, France
| | - Michel Favre
- Institut Pasteur, Centre National de Référence des Papillomavirus, 75724 Paris Cedex 15, France
- Institut Pasteur, Unité de Génétique, Papillomavirus et Cancer humain, 75724 Paris Cedex 15, France
| |
Collapse
|
13
|
Kohl C, Kurth A. European bats as carriers of viruses with zoonotic potential. Viruses 2014; 6:3110-28. [PMID: 25123684 PMCID: PMC4147689 DOI: 10.3390/v6083110] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 07/29/2014] [Accepted: 07/30/2014] [Indexed: 12/23/2022] Open
Abstract
Bats are being increasingly recognized as reservoir hosts of highly pathogenic and zoonotic emerging viruses (Marburg virus, Nipah virus, Hendra virus, Rabies virus, and coronaviruses). While numerous studies have focused on the mentioned highly human-pathogenic bat viruses in tropical regions, little is known on similar human-pathogenic viruses that may be present in European bats. Although novel viruses are being detected, their zoonotic potential remains unclear unless further studies are conducted. At present, it is assumed that the risk posed by bats to the general public is rather low. In this review, selected viruses detected and isolated in Europe are discussed from our point of view in regard to their human-pathogenic potential. All European bat species and their roosts are legally protected and some European species are even endangered. Nevertheless, the increasing public fear of bats and their viruses is an obstacle to their protection. Educating the public regarding bat lyssaviruses might result in reduced threats to both the public and the bats.
Collapse
Affiliation(s)
- Claudia Kohl
- Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Nordufer 20, 13353 Berlin, Germany.
| | - Andreas Kurth
- Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Nordufer 20, 13353 Berlin, Germany.
| |
Collapse
|
14
|
Ledermann JP, Zeidner N, Borland EM, Mutebi JP, Lanciotti RS, Miller BR, Lutwama JJ, Tendo JM, Andama V, Powers AM. Sunguru virus: a novel virus in the family Rhabdoviridae isolated from a chicken in north-western Uganda. J Gen Virol 2014; 95:1436-1443. [PMID: 24718834 DOI: 10.1099/vir.0.060764-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Sunguru virus (SUNV), a novel virus belonging to the highly diverse Rhabdoviridae family, was isolated from a domestic chicken in the district of Arua, Uganda, in 2011. This is the first documented isolation of a rhabdovirus from a chicken. SUNV is related to, but distinct from, Boteke virus and other members of the unclassified Sandjimba group. The genome is 11056 nt in length and contains the five core rhabdovirus genes plus an additional C gene (within the ORF of a phosphoprotein gene) and a small hydrophobic protein (between the matrix and glycoprotein genes). Inoculation of vertebrate cells with SUNV resulted in significant viral growth, with a peak titre of 7.8 log10 p.f.u. ml(-1) observed in baby hamster kidney (BHK) cells. Little to no growth was observed in invertebrate cells and in live mosquitoes, with Anopheles gambiae mosquitoes having a 47.4% infection rate in the body but no dissemination of the virus to the salivary glands; this suggests that this novel virus is not arthropod borne as some other members of the family Rhabdoviridae.
Collapse
Affiliation(s)
- Jeremy P Ledermann
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, 3156 Rampart Rd, Fort Collins, CO 80521, USA
| | - Nord Zeidner
- International Centre for Diarrheal Diseases Research, Bangladesh, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka 1212, Bangladesh
| | - Erin M Borland
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, 3156 Rampart Rd, Fort Collins, CO 80521, USA
| | - John-Paul Mutebi
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, 3156 Rampart Rd, Fort Collins, CO 80521, USA
| | - Robert S Lanciotti
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, 3156 Rampart Rd, Fort Collins, CO 80521, USA
| | - Barry R Miller
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, 3156 Rampart Rd, Fort Collins, CO 80521, USA
| | - Julius J Lutwama
- Department of Arbovirology, Uganda Virus Research Institute (UVRI), PO Box 49, Entebbe, Uganda
| | - Joseph M Tendo
- CDC Uganda Plaque Laboratory, Uganda Virus Research Institute (UVRI), Arua, Uganda
| | | | - Ann M Powers
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, 3156 Rampart Rd, Fort Collins, CO 80521, USA
| |
Collapse
|
15
|
A preliminary study of viral metagenomics of French bat species in contact with humans: identification of new mammalian viruses. PLoS One 2014; 9:e87194. [PMID: 24489870 PMCID: PMC3906132 DOI: 10.1371/journal.pone.0087194] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 12/18/2013] [Indexed: 02/07/2023] Open
Abstract
The prediction of viral zoonosis epidemics has become a major public health issue. A profound understanding of the viral population in key animal species acting as reservoirs represents an important step towards this goal. Bats harbor diverse viruses, some of which are of particular interest because they cause severe human diseases. However, little is known about the diversity of the global population of viruses found in bats (virome). We determined the viral diversity of five different French insectivorous bat species (nine specimens in total) in close contact with humans. Sequence-independent amplification, high-throughput sequencing with Illumina technology and a dedicated bioinformatics analysis pipeline were used on pooled tissues (brain, liver and lungs). Comparisons of the sequences of contigs and unassembled reads provided a global taxonomic distribution of virus-related sequences for each sample, highlighting differences both within and between bat species. Many viral families were present in these viromes, including viruses known to infect bacteria, plants/fungi, insects or vertebrates, the most relevant being those infecting mammals (Retroviridae, Herpesviridae, Bunyaviridae, Poxviridae, Flaviviridae, Reoviridae, Bornaviridae, Picobirnaviridae). In particular, we detected several new mammalian viruses, including rotaviruses, gammaretroviruses, bornaviruses and bunyaviruses with the identification of the first bat nairovirus. These observations demonstrate that bats naturally harbor viruses from many different families, most of which infect mammals. They may therefore constitute a major reservoir of viral diversity that should be analyzed carefully, to determine the role played by bats in the spread of zoonotic viral infections.
Collapse
|
16
|
Allison AB, Mead DG, Palacios GF, Tesh RB, Holmes EC. Gene duplication and phylogeography of North American members of the Hart Park serogroup of avian rhabdoviruses. Virology 2013; 448:284-92. [PMID: 24314659 PMCID: PMC3873333 DOI: 10.1016/j.virol.2013.10.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2013] [Revised: 06/11/2013] [Accepted: 10/17/2013] [Indexed: 12/28/2022]
Abstract
Flanders virus (FLAV) and Hart Park virus (HPV) are rhabdoviruses that circulate in mosquito–bird cycles in the eastern and western United States, respectively, and constitute the only two North American representatives of the Hart Park serogroup. Previously, it was suggested that FLAV is unique among the rhabdoviruses in that it contains two pseudogenes located between the P and M genes, while the cognate sequence for HPV has been lacking. Herein, we demonstrate that FLAV and HPV do not contain pseudogenes in this region, but encode three small functional proteins designated as U1–U3 that apparently arose by gene duplication. To further investigate the U1–U3 region, we conducted the first large-scale evolutionary analysis of a member of the Hart Park serogroup by analyzing over 100 spatially and temporally distinct FLAV isolates. Our phylogeographic analysis demonstrates that although FLAV appears to be slowly evolving, phylogenetically divergent lineages co-circulate sympatrically. Flanders virus (FLAV) does not contain pseudogenes as previously reported. The FLAV U1–U3 proteins arose by gene duplication. The SH protein of FLAV is tentatively expressed by coupled translation. Distinct lineages of FLAV circulate sympatrically in the United States. Histone H4 and cyclophilin A are apparently incorporated into FLAV particles.
Collapse
Affiliation(s)
- Andrew B Allison
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA; Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA.
| | | | | | | | | |
Collapse
|
17
|
Ghedin E, Rogers MB, Widen SG, Guzman H, Travassos da Rosa APA, Wood TG, Fitch A, Popov V, Holmes EC, Walker PJ, Vasilakis N, Tesh RB. Kolente virus, a rhabdovirus species isolated from ticks and bats in the Republic of Guinea. J Gen Virol 2013; 94:2609-2615. [PMID: 24062532 DOI: 10.1099/vir.0.055939-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Kolente virus (KOLEV) is a rhabdovirus originally isolated from ticks and a bat in Guinea, West Africa, in 1985. Although tests at the time of isolation suggested that KOLEV is a novel rhabdovirus, it has remained largely uncharacterized. We assembled the complete genome sequence of the prototype strain DakAr K7292, which was found to encode the five canonical rhabdovirus structural proteins (N, P, M, G and L) with alternative ORFs (>180 nt) in the P and L genes. Serologically, KOLEV exhibited a weak antigenic relationship with Barur and Fukuoka viruses in the Kern Canyon group. Phylogenetic analysis revealed that KOLEV represents a distinct and divergent lineage that shows no clear relationship to any rhabdovirus except Oita virus, although with limited phylogenetic resolution. In summary, KOLEV represents a novel species in the family Rhabdoviridae.
Collapse
Affiliation(s)
- Elodie Ghedin
- Center for Vaccine Research, Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Matthew B Rogers
- Center for Vaccine Research, Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Steven G Widen
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Hilda Guzman
- Center for Biodefense and Emerging Infectious Diseases and Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Amelia P A Travassos da Rosa
- Center for Biodefense and Emerging Infectious Diseases and Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Thomas G Wood
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Adam Fitch
- Center for Vaccine Research, Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Vsevolod Popov
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA.,Center for Tropical Diseases, University of Texas Medical Branch, Galveston, TX, USA.,Center for Biodefense and Emerging Infectious Diseases and Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Edward C Holmes
- Fogarty International Center, National Institutes of Health, Bethesda, MD, USA.,Sydney Emerging Infections & Biosecurity Institute, School of Biological Sciences and Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia
| | - Peter J Walker
- CSIRO Animal, Food and Health Sciences, Australian Animal Health Laboratory, Geelong, VIC 3220, Australia
| | - Nikos Vasilakis
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA.,Center for Tropical Diseases, University of Texas Medical Branch, Galveston, TX, USA.,Center for Biodefense and Emerging Infectious Diseases and Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Robert B Tesh
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA.,Center for Tropical Diseases, University of Texas Medical Branch, Galveston, TX, USA.,Center for Biodefense and Emerging Infectious Diseases and Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| |
Collapse
|
18
|
Joffret ML, Bouchier C, Grandadam M, Zeller H, Maufrais C, Bourhy H, Despres P, Delpeyroux F, Dacheux L. Genomic characterization of Sebokele virus 1 (SEBV1) reveals a new candidate species among the genus Parechovirus. J Gen Virol 2013; 94:1547-1553. [DOI: 10.1099/vir.0.053157-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
We determined the genomic features and the taxonomic classification of Sebokele virus 1 (SEBV1), a previously unclassified arbovirus isolated in 1972 from rodents collected in Botambi, Central African Republic. The complete genome sequence was obtained using a deep sequencing approach (Illumina technology) and dedicated bioinformatics workflows for data analysis. Molecular analysis identified SEBV1 as a picornavirus, most closely related to Ljungan viruses of the genus Parechovirus. The genome has a typical Ljungan virus-like organization, including the presence of two unrelated 2A protein motifs. Phylogenetic analysis confirmed that SEBV1 belongs to the parechovirus phylogroup and was most closely related to the Ljungan virus species. However, it appeared clearly distinct from all members of this phylogroup, suggesting that it represents a novel species of the genus Parechovirus.
Collapse
Affiliation(s)
- M. L. Joffret
- INSERM, U994, Paris, France
- Institut Pasteur, Unité de Biologie des Virus Entériques, Paris, France
| | - C. Bouchier
- Institut Pasteur, Plate-forme Génomique, Paris, France
| | - M. Grandadam
- Institut Pasteur, Centre National de Reference des Arbovirus, Unité des Interactions Moléculaires Flavivirus-Hôtes, Paris, France
| | - H. Zeller
- Institut Pasteur, Unité de Biologie des Infections Emergentes, Lyon, France
| | - C. Maufrais
- Institut Pasteur, Centre d’Informatique pour les Biologistes, Paris, France
| | - H. Bourhy
- Institut Pasteur, Unité de Dynamique des Lyssavirus et Adaptation à l’Hôte, Paris, France
| | - P. Despres
- Institut Pasteur, Unité des Interactions Moléculaires Flavivirus-Hôtes, Paris, France
| | - F. Delpeyroux
- INSERM, U994, Paris, France
- Institut Pasteur, Unité de Biologie des Virus Entériques, Paris, France
| | - L. Dacheux
- Institut Pasteur, Unité de Dynamique des Lyssavirus et Adaptation à l’Hôte, Paris, France
| |
Collapse
|
19
|
Vanhomwegen J, Berthet N, Mazuet C, Guigon G, Vallaeys T, Stamboliyska R, Dubois P, Kennedy GC, Cole ST, Caro V, Manuguerra JC, Popoff MR. Application of high-density DNA resequencing microarray for detection and characterization of botulinum neurotoxin-producing clostridia. PLoS One 2013; 8:e67510. [PMID: 23818983 PMCID: PMC3688605 DOI: 10.1371/journal.pone.0067510] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Accepted: 05/22/2013] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Clostridium botulinum and related clostridia express extremely potent toxins known as botulinum neurotoxins (BoNTs) that cause severe, potentially lethal intoxications in humans. These BoNT-producing bacteria are categorized in seven major toxinotypes (A through G) and several subtypes. The high diversity in nucleotide sequence and genetic organization of the gene cluster encoding the BoNT components poses a great challenge for the screening and characterization of BoNT-producing strains. METHODOLOGY/PRINCIPAL FINDINGS In the present study, we designed and evaluated the performances of a resequencing microarray (RMA), the PathogenId v2.0, combined with an automated data approach for the simultaneous detection and characterization of BoNT-producing clostridia. The unique design of the PathogenID v2.0 array allows the simultaneous detection and characterization of 48 sequences targeting the BoNT gene cluster components. This approach allowed successful identification and typing of representative strains of the different toxinotypes and subtypes, as well as the neurotoxin-producing C. botulinum strain in a naturally contaminated food sample. Moreover, the method allowed fine characterization of the different neurotoxin gene cluster components of all studied strains, including genomic regions exhibiting up to 24.65% divergence with the sequences tiled on the arrays. CONCLUSIONS/SIGNIFICANCE The severity of the disease demands rapid and accurate means for performing risk assessments of BoNT-producing clostridia and for tracing potentials sources of contamination in outbreak situations. The RMA approach constitutes an essential higher echelon component in a diagnostics and surveillance pipeline. In addition, it is an important asset to characterise potential outbreak related strains, but also environment isolates, in order to obtain a better picture of the molecular epidemiology of BoNT-producing clostridia.
Collapse
Affiliation(s)
- Jessica Vanhomwegen
- Institut Pasteur, Laboratory for Urgent Responses to Biological Threats, Paris, France
| | - Nicolas Berthet
- Institut Pasteur, Epidemiology and Pathophysiology of Oncogenic Viruses, Paris, France
- CNRS, UMR3569, Paris, France
| | | | - Ghislaine Guigon
- Institut Pasteur, Genotyping of Pathogens and Public Health, Paris, France
| | - Tatiana Vallaeys
- CNRS – CC093 Université Montpellier II, UMR5119 Ecosystèmes lagunaires, Montpellier, France
| | - Rayna Stamboliyska
- Department of Biology II, University of Munich (LMU), Planegg-Martinsried, Germany
| | - Philippe Dubois
- Institut Pasteur, Laboratory for Urgent Responses to Biological Threats, Paris, France
| | - Giulia C. Kennedy
- Department of Research and Development, Veracyte, Inc., South San Francisco, California, United States of America
| | - Stewart T. Cole
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Valérie Caro
- Institut Pasteur, Genotyping of Pathogens and Public Health, Paris, France
| | | | | |
Collapse
|
20
|
Abstract
Determining the viral etiology of respiratory tract infections (RTI) has been limited for the most part to specific primer PCR-based methods due to their increased sensitivity and specificity compared to other methods, such as tissue culture. However, specific primer approaches have limited the ability to fully understand the diversity of infecting pathogens. A pathogen chip system (PathChip), developed at the Genome Institute of Singapore (GIS), using a random-tagged PCR coupled to a chip with over 170,000 probes, has the potential to recognize all known human viral pathogens. We tested 290 nasal wash specimens from Filipino children <2 years of age with respiratory tract infections using culture and 3 PCR methods-EraGen, Luminex, and the GIS PathChip. The PathChip had good diagnostic accuracy, ranging from 85.9% (95% confidence interval [CI], 81.3 to 89.7%) for rhinovirus/enteroviruses to 98.6% (95% CI, 96.5 to 99.6%) for PIV 2, compared to the other methods and additionally identified a number of viruses not detected by these methods.
Collapse
|
21
|
Aznar-Lopez C, Vazquez-Moron S, Marston DA, Juste J, Ibáñez C, Berciano JM, Salsamendi E, Aihartza J, Banyard AC, McElhinney L, Fooks AR, Echevarria J. Detection of rhabdovirus viral RNA in oropharyngeal swabs and ectoparasites of Spanish bats. J Gen Virol 2013; 94:69-75. [DOI: 10.1099/vir.0.046490-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Rhabdoviruses infect a variety of hosts, including mammals, birds, reptiles, fish, insects and plants. As bats are the natural host for most members of the genus Lyssavirus, the specificity of the amplification methods used for active surveillance is usually restricted to lyssaviruses. However, the presence of other rhabdoviruses in bats has also been reported. In order to broaden the scope of such methods, a new RT-PCR, able to detect a diverse range of rhabdoviruses, was designed. The method detected 81 of 86 different rhabdoviruses. In total, 1488 oropharyngeal bat swabs and 38 nycteribiid samples were analysed, and 17 unique rhabdovirus-related sequences were detected. Phylogenetic analysis suggested that those sequences detected in bats did not constitute a monophyletic group, even when originating from the same bat species. However, all of the sequences detected in nycteribiids and one sequence obtained from a bat did constitute a monophyletic group with Drosophila melanogaster sigma rhabdovirus.
Collapse
Affiliation(s)
- Carolina Aznar-Lopez
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid 28220, Spain
- Centro de Investigación Biomédica de Epidemiología y Salud Pública, CIBERESP, Spain
| | - Sonia Vazquez-Moron
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid 28220, Spain
- Centro de Investigación Biomédica de Epidemiología y Salud Pública, CIBERESP, Spain
| | - Denise A. Marston
- Wildlife Zoonoses and Vector-borne Diseases Research Group (OIE Reference Laboratory/WHO Collaborating Centre), Animal Health and Veterinary Laboratories Agency (AHVLA, Weybridge), New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Javier Juste
- Estación Biológica de Doñana, CSIC, Seville 41092, Andalusia, Spain
| | - Carlos Ibáñez
- Estación Biológica de Doñana, CSIC, Seville 41092, Andalusia, Spain
| | - Jose Miguel Berciano
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid 28220, Spain
- Centro de Investigación Biomédica de Epidemiología y Salud Pública, CIBERESP, Spain
| | - Egoitz Salsamendi
- Department of Zoology and Animal Cell Biology, University of the Basque Country (UPV/EHU), Leioa 48940, The Basque Country, Spain
| | - Joxerra Aihartza
- Department of Zoology and Animal Cell Biology, University of the Basque Country (UPV/EHU), Leioa 48940, The Basque Country, Spain
| | - Ashley C. Banyard
- Wildlife Zoonoses and Vector-borne Diseases Research Group (OIE Reference Laboratory/WHO Collaborating Centre), Animal Health and Veterinary Laboratories Agency (AHVLA, Weybridge), New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Lorraine McElhinney
- Wildlife Zoonoses and Vector-borne Diseases Research Group (OIE Reference Laboratory/WHO Collaborating Centre), Animal Health and Veterinary Laboratories Agency (AHVLA, Weybridge), New Haw, Addlestone, Surrey KT15 3NB, UK
- University of Liverpool, National Consortium for Zoonosis Research, Leahurst, Neston, South Wirral CH64 7TE, UK
| | - Anthony R. Fooks
- Wildlife Zoonoses and Vector-borne Diseases Research Group (OIE Reference Laboratory/WHO Collaborating Centre), Animal Health and Veterinary Laboratories Agency (AHVLA, Weybridge), New Haw, Addlestone, Surrey KT15 3NB, UK
- University of Liverpool, National Consortium for Zoonosis Research, Leahurst, Neston, South Wirral CH64 7TE, UK
| | - Juan Echevarria
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid 28220, Spain
- Centro de Investigación Biomédica de Epidemiología y Salud Pública, CIBERESP, Spain
| |
Collapse
|
22
|
Filippone C, Marianneau P, Murri S, Mollard N, Avsic-Zupanc T, Chinikar S, Desprès P, Caro V, Gessain A, Berthet N, Tordo N. Molecular diagnostic and genetic characterization of highly pathogenic viruses: application during Crimean-Congo haemorrhagic fever virus outbreaks in Eastern Europe and the Middle East. Clin Microbiol Infect 2012; 19:E118-28. [PMID: 23240764 PMCID: PMC3663000 DOI: 10.1111/1469-0691.12075] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Revised: 08/24/2012] [Accepted: 09/03/2012] [Indexed: 01/15/2023]
Abstract
Several haemorrhagic fevers are caused by highly pathogenic viruses that must be handled in Biosafety level 4 (BSL–4) containment. These zoonotic infections have an important impact on public health and the development of a rapid and differential diagnosis in case of outbreak in risk areas represents a critical priority. We have demonstrated the potential of a DNA resequencing microarray (PathogenID v2.0) for this purpose. The microarray was first validated in vitro using supernatants of cells infected with prototype strains from five different families of BSL-4 viruses (e.g. families Arenaviridae, Bunyaviridae, Filoviridae, Flaviviridae and Paramyxoviridae). RNA was amplified based on isothermal amplification by Phi29 polymerase before hybridization. We were able to detect and characterize Nipah virus and Crimean–Congo haemorrhagic fever virus (CCHFV) in the brains of experimentally infected animals. CCHFV was finally used as a paradigm for epidemics because of recent outbreaks in Turkey, Kosovo and Iran. Viral variants present in human sera were characterized by BLASTN analysis. Sensitivity was estimated to be 105–106 PFU/mL of hybridized cDNA. Detection specificity was limited to viral sequences having ∼13–14% of global divergence with the tiled sequence, or stretches of ∼20 identical nucleotides. These results highlight the benefits of using the PathogenID v2.0 resequencing microarray to characterize geographical variants in the follow-up of haemorrhagic fever epidemics; to manage patients and protect communities; and in cases of bioterrorism.
Collapse
Affiliation(s)
- C Filippone
- Institut Pasteur, Unit of Epidemiology and Pathophysiology of Oncogenic Viruses, Paris, France
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
23
|
Berthet N, Paulous S, Coffey LL, Frenkiel MP, Moltini I, Tran C, Matheus S, Ottone C, Ungeheuer MN, Renaudat C, Caro V, Dussart P, Gessain A, Desprès P. Resequencing microarray method for molecular diagnosis of human arboviral diseases. J Clin Virol 2012; 56:238-43. [PMID: 23219893 DOI: 10.1016/j.jcv.2012.10.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Accepted: 10/31/2012] [Indexed: 12/29/2022]
Abstract
BACKGROUND Resequencing DNA microarray (RMA) technology uses probes designed to identify a panel of viral sequences. It can be used for detecting emerging viruses by revealing the nucleotide polymorphisms within the target of interest. OBJECTIVES/STUDY DESIGN As a new tool for molecular diagnosis of arbovirus infection, high density PathogenID v2.0 RMA (PID2-RMA) was assessed for the detection and genetic analysis of dengue, West Nile, and Chikungunya viruses in spiked blood samples or sera from individuals infected with dengue virus. Viral RNAs extracted from biological samples were retrotranscribed into cDNA and amplified using the Phi 29 polymerase-based method. This amplified cDNA was used for hybridization on PID2-RMA. RESULTS A good specificity of RMA-based detection was demonstrated using a panel of arboviruses including Dengue, West Nile and Chikungunya viruses. This technology was also efficient for the detection and genetic analysis of the different serotypes of dengue virus in sera of infected patients. Furthermore, the mixing of dengue, West Nile and Chikungunya prototype viruses within a single sample of human blood did not interfere with the sensitivity of PID2-RMA. CONCLUSIONS Our data show that high density PID2-RMA was suitable for the identification of medically important arboviruses. It appears to be particularly adapted to the genetic analysis of dengue, West Nile, and Chikungunya viruses in urgent clinical situations where the rapid identification and characterization of the pathogen is essential.
Collapse
Affiliation(s)
- N Berthet
- Institut Pasteur, Epidemiology and Physiopathology of Oncogenic Viruses Unit, 28 rue du Docteur Roux, F75015 Paris, France
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Peng DW, Zheng GH, Zheng ZZ, Tong QX, Ming YL. Orchid fleck virus: an unclassified bipartite, negative-sense RNA plant virus. Arch Virol 2012; 158:313-23. [DOI: 10.1007/s00705-012-1506-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2012] [Accepted: 09/02/2012] [Indexed: 12/27/2022]
|
25
|
Recurrent Breast Abscesses due to Corynebacterium kroppenstedtii, a Human Pathogen Uncommon in Caucasian Women. Case Rep Infect Dis 2012; 2012:120968. [PMID: 23008788 PMCID: PMC3449112 DOI: 10.1155/2012/120968] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Accepted: 07/08/2012] [Indexed: 12/03/2022] Open
Abstract
Background. Corynebacterium kroppenstedtii (Ck) was first described in 1998 from human sputum. Contrary to what is observed in ethnic groups such as Maori, Ck is rarely isolated from breast abscesses and granulomatous mastitis in Caucasian women. Case Presentation. We herein report a case of recurrent breast abscesses in a 46-year-old Caucasian woman. Conclusion. In the case of recurrent breast abscesses, even in Caucasian women, the possible involvement of Ck should be investigated. The current lack of such investigations, probably due to the difficulty to detect Ck, may cause the underestimation of such an aetiology.
Collapse
|
26
|
Leski TA, Lin B, Malanoski AP, Stenger DA. Application of resequencing microarrays in microbial detection and characterization. Future Microbiol 2012; 7:625-37. [PMID: 22568717 DOI: 10.2217/fmb.12.30] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Microarrays are powerful, highly parallel assays that are transforming microbiological diagnostics and research. The adaptation of microarray-based resequencing technology for microbial detection and characterization resulted in the development of a number assays that have unique advantages over other existing technologies. This technological platform seems to be especially useful for sensitive and high-resolution multiplexed diagnostics for clinical syndromes with similar symptoms, screening environmental samples for biothreat agents, as well as genotyping and whole-genome analysis of single pathogens.
Collapse
Affiliation(s)
- Tomasz A Leski
- Center for Bio/Molecular Science & Engineering, Naval Research Laboratory, SW, Washington, DC 20375, USA.
| | | | | | | |
Collapse
|
27
|
Singh DD, Jain A. Multipurpose instantaneous microarray detection of acute encephalitis causing viruses and their expression profiles. Curr Microbiol 2012; 65:290-303. [PMID: 22674173 PMCID: PMC7080014 DOI: 10.1007/s00284-012-0154-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Accepted: 05/14/2012] [Indexed: 01/15/2023]
Abstract
Detection of multiple viruses is important for global analysis of gene or protein content and expression, opening up new prospects in terms of molecular and physiological systems for pathogenic diagnosis. Early diagnosis is crucial for disease treatment and control as it reduces inappropriate use of antiviral therapy and focuses surveillance activity. This requires the ability to detect and accurately diagnose infection at or close to the source/outbreak with minimum delay and the need for specific, accessible point-of-care diagnosis able to distinguish causative viruses and their subtypes. None of the available viral diagnostic assays combine a point-of-care format with the complex capability to identify a large range of human and animal viruses. Microarray detection provides a useful, labor-saving tool for detection of multiple viruses with several advantages, such as convenience and prevention of cross-contamination of polymerase chain reaction (PCR) products, which is of foremost importance in such applications. Recently, real-time PCR assays with the ability to confirm the amplification product and quantitate the target concentration have been developed. Furthermore, nucleotide sequence analysis of amplification products has facilitated epidemiological studies of infectious disease outbreaks and monitoring of treatment outcomes for infections, in particular for viruses that mutate at high frequency. This review discusses applications of microarray technology as a potential new tool for detection and identification of acute encephalitis-causing viruses in human serum, plasma, and cell cultures.
Collapse
Affiliation(s)
- Desh Deepak Singh
- Virology Laboratory, Department of Microbiology, C S M Medical University, Lucknow, UP 226003, India.
| | | |
Collapse
|
28
|
Wellehan JFX, Pessier AP, Archer LL, Childress AL, Jacobson ER, Tesh RB. Initial sequence characterization of the rhabdoviruses of squamate reptiles, including a novel rhabdovirus from a caiman lizard (Dracaena guianensis). Vet Microbiol 2012; 158:274-9. [PMID: 22397930 DOI: 10.1016/j.vetmic.2012.02.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Revised: 01/25/2012] [Accepted: 02/13/2012] [Indexed: 11/25/2022]
Abstract
Rhabdoviruses infect a variety of hosts, including non-avian reptiles. Consensus PCR techniques were used to obtain partial RNA-dependent RNA polymerase gene sequence from five rhabdoviruses of South American lizards; Marco, Chaco, Timbo, Sena Madureira, and a rhabdovirus from a caiman lizard (Dracaena guianensis). The caiman lizard rhabdovirus formed inclusions in erythrocytes, which may be a route for infecting hematophagous insects. This is the first information on behavior of a rhabdovirus in squamates. We also obtained sequence from two rhabdoviruses of Australian lizards, confirming previous Charleville virus sequence and finding that, unlike a previous sequence report but in agreement with serologic reports, Almpiwar virus is clearly distinct from Charleville virus. Bayesian and maximum likelihood phylogenetic analysis revealed that most known rhabdoviruses of squamates cluster in the Almpiwar subgroup. The exception is Marco virus, which is found in the Hart Park group.
Collapse
Affiliation(s)
- James F X Wellehan
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL 32610, USA.
| | | | | | | | | | | |
Collapse
|
29
|
Differentiation of the seven major lyssavirus species by oligonucleotide microarray. J Clin Microbiol 2011; 50:619-25. [PMID: 22189108 DOI: 10.1128/jcm.00848-11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
An oligonucleotide microarray, LyssaChip, has been developed and verified as a highly specific diagnostic tool for differentiation of the 7 major lyssavirus species. As with conventional typing microarray methods, the LyssaChip relies on sequence differences in the 371-nucleotide region coding for the nucleoprotein. This region was amplified using nested reverse transcription-PCR primers that bind to the 7 major lyssaviruses. The LyssaChip includes 57 pairs of species typing and corresponding control oligonucleotide probes (oligoprobes) immobilized on glass slides, and it can analyze 12 samples on a single slide within 8 h. Analysis of 111 clinical brain specimens (65 from animals with suspected rabies submitted to the laboratory and 46 of butchered dog brain tissues collected from restaurants) showed that the chip method was 100% sensitive and highly consistent with the "gold standard," a fluorescent antibody test (FAT). The chip method could detect rabies virus in highly decayed brain tissues, whereas the FAT did not, and therefore the chip test may be more applicable to highly decayed brain tissues than the FAT. LyssaChip may provide a convenient and inexpensive alternative for diagnosis and differentiation of rabies and rabies-related diseases.
Collapse
|
30
|
Longdon B, Wilfert L, Osei-Poku J, Cagney H, Obbard DJ, Jiggins FM. Host-switching by a vertically transmitted rhabdovirus in Drosophila. Biol Lett 2011; 7:747-50. [PMID: 21450721 PMCID: PMC3169049 DOI: 10.1098/rsbl.2011.0160] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Accepted: 03/07/2011] [Indexed: 11/12/2022] Open
Abstract
A diverse range of endosymbionts are found within the cells of animals. As these endosymbionts are normally vertically transmitted, we might expect their evolutionary history to be dominated by host-fidelity and cospeciation with the host. However, studies of bacterial endosymbionts have shown that while this is true for some mutualists, parasites often move horizontally between host lineages over evolutionary timescales. For the first time, to our knowledge, we have investigated whether this is also the case for vertically transmitted viruses. Here, we describe four new sigma viruses, a group of vertically transmitted rhabdoviruses previously known in Drosophila. Using sequence data from these new viruses, and the previously described sigma viruses, we show that they have switched between hosts during their evolutionary history. Our results suggest that sigma virus infections may be short-lived in a given host lineage, so that their long-term persistence relies on rare horizontal transmission events between hosts.
Collapse
Affiliation(s)
- Ben Longdon
- Institute of Evolutionary Biology, Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3JT, UK.
| | | | | | | | | | | |
Collapse
|
31
|
Talbi C, Cabon J, Baud M, Bourjaily M, de Boisséson C, Castric J, Bigarré L. Genetic diversity of perch rhabdoviruses isolates based on the nucleoprotein and glycoprotein genes. Arch Virol 2011; 156:2133-44. [PMID: 21927897 DOI: 10.1007/s00705-011-1103-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2011] [Accepted: 09/02/2011] [Indexed: 11/30/2022]
Abstract
Despite the increasing impact of rhabdoviruses in European percid farming, the diversity of the viral populations is still poorly investigated. To address this issue, we sequenced the partial nucleoprotein (N) and complete glycoprotein (G) genes of nine rhabdoviruses isolated from perch (Perca fluviatilis) between 1999 and 2010, mostly from France, and analyzed six of them by immunofluorescence antibody test (IFAT). Using two rabbit antisera raised against either the reference perch rhabdovirus (PRhV) isolated in 1980 or the perch isolate R6146, two serogroups were distinguished. Meanwhile, based on partial N and complete G gene analysis, perch rhabdoviruses were divided into four genogroups, A-B-D and E, with a maximum of 32.9% divergence (G gene) between isolates. A comparison of the G amino acid sequences of isolates from the two identified serogroups revealed several variable regions that might account for antigenic differences. Comparative analysis of perch isolates with other rhabdoviruses isolated from black bass, pike-perch and pike showed some strong phylogenetic relationships, suggesting cross-host transmission. Similarly, striking genetic similarities were shown between perch rhabdoviruses and isolates from other European countries and various ecological niches, most likely reflecting the circulation of viruses through fish trade as well as putative transfers from marine to freshwater fish. Phylogenetic relationships of the newly characterized viruses were also determined within the family Rhabdoviridae. The analysis revealed a genetic cluster containing only fish viruses, including all rhabdoviruses from perch, as well as siniperca chuatsi rhabdovirus (SCRV) and eel virus X (EVEX). This cluster was distinct from the one represented by spring viraemia of carp vesiculovirus (SVCV), pike fry rhabdovirus (PFRV) and mammalian vesiculoviruses. The new genetic data provided in the present study shed light on the diversity of rhabdoviruses infecting perch in France and support the hypothesis of circulation of these viruses between other hosts and regions within Europe.
Collapse
Affiliation(s)
- Chiraz Talbi
- Unité de Pathologie Virale des Poissons, ANSES, Technopôle Brest-Iroise, Plouzané, France.
| | | | | | | | | | | | | |
Collapse
|
32
|
Evaluation of high-throughput sequencing for identifying known and unknown viruses in biological samples. J Clin Microbiol 2011; 49:3268-75. [PMID: 21715589 DOI: 10.1128/jcm.00850-11] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
High-throughput sequencing furnishes a large number of short sequence reads from uncloned DNA and has rapidly become a major tool for identifying viruses in biological samples, and in particular when the target sequence is undefined. In this study, we assessed the analytical sensitivity of a pipeline for detection of viruses in biological samples based on either the Roche-454 genome sequencer or Illumina genome analyzer platforms. We sequenced biological samples artificially spiked with a wide range of viruses with genomes composed of single or double-stranded DNA or RNA, including linear or circular single-stranded DNA. Viruses were added at a very low concentration most often corresponding to 3 or 0.8 times the validated level of detection of quantitative reverse transcriptase PCRs (RT-PCRs). For the viruses represented, or resembling those represented, in public nucleotide sequence databases, we show that the higher output of Illumina is associated with a much greater sensitivity, approaching that of optimized quantitative (RT-)PCRs. In this blind study, identification of viruses was achieved without incorrect identification. Nevertheless, at these low concentrations, the number of reads generated by the Illumina platform was too small to facilitate assembly of contigs without the use of a reference sequence, thus precluding detection of unknown viruses. When the virus load was sufficiently high, de novo assembly permitted the generation of long contigs corresponding to nearly full-length genomes and thus should facilitate the identification of novel viruses.
Collapse
|
33
|
Quan PL, Williams DT, Johansen CA, Jain K, Petrosov A, Diviney SM, Tashmukhamedova A, Hutchison SK, Tesh RB, Mackenzie JS, Briese T, Lipkin WI. Genetic characterization of K13965, a strain of Oak Vale virus from Western Australia. Virus Res 2011; 160:206-13. [PMID: 21740935 DOI: 10.1016/j.virusres.2011.06.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Revised: 06/17/2011] [Accepted: 06/21/2011] [Indexed: 10/18/2022]
Abstract
K13965, an uncharacterized virus, was isolated in 1993 from Anopheles annulipes mosquitoes collected in the Kimberley region of northern Western Australia. Here, we report its genomic sequence, identify it as a rhabdovirus, and characterize its phylogenetic relationships. The genome comprises a P' (C) and SH protein similar to the recently characterized Tupaia and Durham viruses, and shows overlap between G and L genes. Comparison of K13965 genome sequence to other rhabdoviruses identified K13965 as a strain of the unclassified Australian Oak Vale rhabdovirus, whose complete genome sequence we also determined. Phylogenetic analysis of N and L sequences indicated genetic relationship to a recently proposed Sandjima virus clade, although the Oak Vale virus sequences form a branch separate from the African members of that group.
Collapse
Affiliation(s)
- Phenix-Lan Quan
- Center for Infection and Immunity, Columbia University, New York, NY 10032, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
34
|
Comparative detection of rabies RNA by NASBA, real-time PCR and conventional PCR. J Virol Methods 2011; 175:278-82. [PMID: 21600930 DOI: 10.1016/j.jviromet.2011.05.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Revised: 04/20/2011] [Accepted: 05/04/2011] [Indexed: 11/20/2022]
Abstract
Five methods for the RNA detection of rabies virus were directly compared in this study. These included conventional nucleic acid sequence-based amplification with electrochemiluminescence (NASBA-ECL) assay, reverse transcription (RT)-heminested (hn) polymerase chain reaction (PCR) and TaqMan real-time RT-PCR using protocols as described previously. The first two methods have been routinely utilised for ante-mortem diagnosis of human rabies in Thailand and other rabies-endemic Asian and African countries. In addition, two real-time NASBA assays based on the use of a NucliSens EasyQ analyser (NASBA-Beacon-EQ) and LightCycler real-time PCR machine (NASBA-Beacon-LC) were studied in parallel. All methods target the N gene, whereas the L gene is used for RT-hnPCR. Using serial dilutions of purified RNA from rabies-infected dog brain tissue to assess sensitivity, all five methods had comparable degrees of sensitivities of detection. However, both real-time NASBA assays had slightly lower sensitivities by 10-fold than the other three assays. This finding was also true (except for TaqMan real-time RT-PCR due to a mismatch between the target and probe sequences) when laboratory-adapted (challenge virus standard-11) virus was used in the assays. Testing on previously NASBA-ECL positive clinical samples from 10 rabies patients (saliva [6] and brain [4]) and 10 rabies-infected dog brain tissues, similar results were obtained among the five methods; real-time NASBA assays yielded false-negative results on 2 saliva samples. None of the assays showed positive results on cerebrospinal fluid specimens of 10 patients without rabies encephalitis. Due to the unavailability of the NASBA-ECL assay, the results show that TaqMan real-time RT-PCR and RT-hnPCR can be useful for ante- and post-mortem diagnosis of rabies.
Collapse
|
35
|
De Benedictis P, De Battisti C, Dacheux L, Marciano S, Ormelli S, Salomoni A, Caenazzo ST, Lepelletier A, Bourhy H, Capua I, Cattoli G. Lyssavirus detection and typing using pyrosequencing. J Clin Microbiol 2011; 49:1932-8. [PMID: 21389152 PMCID: PMC3122702 DOI: 10.1128/jcm.02015-10] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Accepted: 02/24/2011] [Indexed: 10/18/2022] Open
Abstract
Rabies is a fatal zoonosis caused by a nonsegmented negative-strand RNA virus, namely, rabies virus (RABV). Apart from RABV, at least 10 additional species are known as rabies-related lyssaviruses (RRVs), and some of them are responsible for occasional spillovers into humans. More lyssaviruses have also been detected recently in different bat ecosystems, thanks to the application of molecular diagnostic methods. Due to the variety of the members of the genus Lyssavirus, there is the necessity to develop a reliable molecular assay for rabies diagnosis able to detect and differentiate among the existing rabies and rabies-related viruses. In the present study, a pyrosequencing protocol targeting the 3' terminus of the nucleoprotein (N) gene was applied for the rapid characterization of lyssaviruses. Correct identification of species was achieved for each sample tested. Results from the pyrosequencing assay were also confirmed by those obtained using the Sanger sequencing method. A pan-lyssavirus one-step reverse transcription (RT)-PCR was developed within the framework of the pyrosequencing procedure. The sensitivity (Se) of the one-step RT-PCR assay was determined by using in vitro-transcribed RNA and serial dilutions of titrated viruses. The assay demonstrated high analytical and relative specificity (Sp) (98.94%) and sensitivity (99.71%). To date, this is the first case in which pyrosequencing has been applied for lyssavirus identification using a cheaper diagnostic approach than the one for all the other protocols for rapid typing that we are acquainted with. Results from this study indicate that this procedure is suitable for lyssavirus detection in samples of both human and animal origin.
Collapse
Affiliation(s)
- Paola De Benedictis
- OIE and National Collaborating Centre for Diseases at the Animal-Human Interface, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, 35020 Legnaro, Padova, Italy.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
36
|
Berthet N, Deletoile A, Passet V, Kennedy GC, Manuguerra JC, Cole ST, Brisse S. Reconstructed ancestral sequences improve pathogen identification using resequencing DNA microarrays. PLoS One 2010; 5:e15243. [PMID: 21187950 PMCID: PMC3004854 DOI: 10.1371/journal.pone.0015243] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Accepted: 11/09/2010] [Indexed: 11/19/2022] Open
Abstract
We describe the benefit of using reconstructed ancestral sequences (RAS) on resequencing microarrays for rapid pathogen identification, with Enterobacteriaceae rpoB sequences as a model. Our results demonstrate a sharp improvement of call rate and accuracy when using RASs as compared to extant sequences. This improvement was attributed to the lower sequence divergence of RASs, which also expanded the sequence space covered by the microarray. Extension of this novel microarray design strategy to viruses, antimicrobial resistance elements or toxins is straightforward.
Collapse
Affiliation(s)
- Nicolas Berthet
- Institut Pasteur, Genotyping of Pathogens and Public Health, Paris, France
- Institut Pasteur, Epidemiology and Pathophysiology Oncogenic Virus Unit, CNRS URA3015, Paris, France
| | - Alexis Deletoile
- Institut Pasteur, Genotyping of Pathogens and Public Health, Paris, France
| | - Virginie Passet
- Institut Pasteur, Genotyping of Pathogens and Public Health, Paris, France
| | | | | | - Stewart T. Cole
- Global Health Institute, Laboratory of Microbial Pathogenesis, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Sylvain Brisse
- Institut Pasteur, Genotyping of Pathogens and Public Health, Paris, France
- * E-mail:
| |
Collapse
|
37
|
Use of consensus sequences for the design of high density resequencing microarrays: the influenza virus paradigm. BMC Genomics 2010; 11:586. [PMID: 20961419 PMCID: PMC3091733 DOI: 10.1186/1471-2164-11-586] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2010] [Accepted: 10/20/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A resequencing microarray called PathogenID v2.0 has been developed and used to explore various strategies of sequence selection for its design. The part dedicated to influenza viruses was based on consensus sequences specific for one gene generated from global alignments of a large number of influenza virus sequences available in databanks. RESULTS For each HA (H1, H2, H3, H5, H7 and H9) and NA (N1, N2 and N7) molecular type chosen to be tested, 1 to 3 consensus sequences were computed and tiled on the microarray. A total of 12 influenza virus samples from different host origins (humans, pigs, horses and birds) and isolated over a period of about 50 years were used in this study. Influenza viruses were correctly identified, and in most cases with the accurate information of the time of their emergence. CONCLUSIONS PathogenID v2.0 microarray demonstrated its ability to type and subtype influenza viruses, often to the level of viral variants, with a minimum number of tiled sequences. This validated the strategy of using consensus sequences, which do not exist in nature, for our microarray design. The versatility, rapidity and high discriminatory power of the PathogenID v2.0 microarray could prove critical to detect and identify viral genome reassortment events resulting in a novel virus with epidemic or pandemic potential and therefore assist health authorities to make efficient decisions about patient treatment and outbreak management.
Collapse
|