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Mehl C, Adeyemi OA, Wylezich C, Höper D, Beer M, Triebenbacher C, Heckel G, Ulrich RG. Lymphocytic Choriomeningitis Virus Lineage V in Wood Mice, Germany. Emerg Infect Dis 2024; 30:399-401. [PMID: 38270110 PMCID: PMC10826776 DOI: 10.3201/eid3002.230868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024] Open
Abstract
We identified a novel lineage of lymphocytic choriomeningitis virus, tentatively named lineage V, in wood mice (Apodemus sylvaticus) from Germany. Wood mouse-derived lymphocytic choriomeningitis virus can be found across a substantially greater range than previously thought. Increased surveillance is needed to determine its geographic range and zoonotic potential.
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Joeres M, Maksimov P, Höper D, Calvelage S, Calero-Bernal R, Fernández-Escobar M, Koudela B, Blaga R, Vrhovec MG, Stollberg K, Bier N, Sotiraki S, Sroka J, Piotrowska W, Kodym P, Basso W, Conraths FJ, Mercier A, Galal L, Dardé ML, Balea A, Spano F, Schulze C, Peters M, Scuda N, Lundén A, Davidson RK, Terland R, Waap H, de Bruin E, Vatta P, Caccio S, Ortega-Mora LM, Jokelainen P, Schares G. Genotyping of European Toxoplasma gondii strains by a new high-resolution next-generation sequencing-based method. Eur J Clin Microbiol Infect Dis 2024; 43:355-371. [PMID: 38099986 PMCID: PMC10822014 DOI: 10.1007/s10096-023-04721-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 11/16/2023] [Indexed: 01/28/2024]
Abstract
PURPOSE A new high-resolution next-generation sequencing (NGS)-based method was established to type closely related European type II Toxoplasma gondii strains. METHODS T. gondii field isolates were collected from different parts of Europe and assessed by whole genome sequencing (WGS). In comparison to ME49 (a type II reference strain), highly polymorphic regions (HPRs) were identified, showing a considerable number of single nucleotide polymorphisms (SNPs). After confirmation by Sanger sequencing, 18 HPRs were used to design a primer panel for multiplex PCR to establish a multilocus Ion AmpliSeq typing method. Toxoplasma gondii isolates and T. gondii present in clinical samples were typed with the new method. The sensitivity of the method was tested with serially diluted reference DNA samples. RESULTS Among type II specimens, the method could differentiate the same number of haplotypes as the reference standard, microsatellite (MS) typing. Passages of the same isolates and specimens originating from abortion outbreaks were identified as identical. In addition, seven different genotypes, two atypical and two recombinant specimens were clearly distinguished from each other by the method. Furthermore, almost all SNPs detected by the Ion AmpliSeq method corresponded to those expected based on WGS. By testing serially diluted DNA samples, the method exhibited a similar analytical sensitivity as MS typing. CONCLUSION The new method can distinguish different T. gondii genotypes and detect intra-genotype variability among European type II T. gondii strains. Furthermore, with WGS data additional target regions can be added to the method to potentially increase typing resolution.
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Affiliation(s)
- M Joeres
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Epidemiology, Greifswald - Insel Riems, Germany
| | - P Maksimov
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Epidemiology, Greifswald - Insel Riems, Germany
| | - D Höper
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Diagnostic Virology, Greifswald - Insel Riems, Germany
| | - S Calvelage
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Diagnostic Virology, Greifswald - Insel Riems, Germany
| | - R Calero-Bernal
- SALUVET, Animal Health Department, Faculty of Veterinary Sciences, Complutense University of Madrid, Madrid, Spain
| | - M Fernández-Escobar
- SALUVET, Animal Health Department, Faculty of Veterinary Sciences, Complutense University of Madrid, Madrid, Spain
| | - B Koudela
- Central European Institute of Technology (CEITEC), University of Veterinary Sciences Brno, Brno, Czech Republic
- Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - R Blaga
- Anses, INRAE, Ecole Nationale Vétérinaire d'Alfort, Laboratoire de Santé Animale, BIPAR, Maisons-Alfort, France
- University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Romania
| | | | - K Stollberg
- German Federal Institute for Risk Assessment, Department for Biological Safety, Berlin, Germany
| | - N Bier
- German Federal Institute for Risk Assessment, Department for Biological Safety, Berlin, Germany
| | - S Sotiraki
- Veterinary Research Institute, Hellenic Agricultural Organisation-DIMITRA, Thessaloniki, Greece
| | - J Sroka
- Department of Parasitology and Invasive Diseases, National Veterinary Research Institute, Pulawy, Poland
| | - W Piotrowska
- Department of Parasitology and Invasive Diseases, National Veterinary Research Institute, Pulawy, Poland
| | - P Kodym
- Centre of Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
| | - W Basso
- Institute of Parasitology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - F J Conraths
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Epidemiology, Greifswald - Insel Riems, Germany
| | - A Mercier
- Inserm U1094, IRD U270, Univ. Limoges, CHU Limoges, EpiMaCT - Epidemiology of chronic diseases in tropical zone, Institute of Epidemiology and Tropical Neurology, OmegaHealth, Limoges, France
- Centre National de Référence (CNR) Toxoplasmose Centre Hospitalier-Universitaire Dupuytren, Limoges, France
| | - L Galal
- Inserm U1094, IRD U270, Univ. Limoges, CHU Limoges, EpiMaCT - Epidemiology of chronic diseases in tropical zone, Institute of Epidemiology and Tropical Neurology, OmegaHealth, Limoges, France
| | - M L Dardé
- Inserm U1094, IRD U270, Univ. Limoges, CHU Limoges, EpiMaCT - Epidemiology of chronic diseases in tropical zone, Institute of Epidemiology and Tropical Neurology, OmegaHealth, Limoges, France
- Centre National de Référence (CNR) Toxoplasmose Centre Hospitalier-Universitaire Dupuytren, Limoges, France
| | - A Balea
- University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, Faculty of Veterinary Medicine, Department of Parasitology and Parasitic Diseases, Cluj-Napoca, Romania
| | - F Spano
- Italian National Institute of Health, Rome, Italy
| | - C Schulze
- Landeslabor Berlin-Brandenburg, Frankfurt (Oder), Germany
| | - M Peters
- Chemisches und Veterinäruntersuchungsamt Westfalen, Standort Arnsberg, Arnsberg, Germany
| | - N Scuda
- Bavarian Health and Food Safety Authority, Erlangen, Germany
| | - A Lundén
- Department of Microbiology, National Veterinary Institute, Uppsala, Sweden
| | - R K Davidson
- Department of Animal Health, Welfare and Food Safety, Norwegian Veterinary Institute, Tromsø, Norway
| | - R Terland
- Department of Analysis and Diagnostics, Norwegian Veterinary Institute, Ås, Norway
| | - H Waap
- Parasitology Laboratory, Instituto Nacional de Investigação Agrária e Veterinária, Oeiras, Portugal
| | - E de Bruin
- Dutch Wildlife Health Centre, Pathology Division, Department of Pathobiology, Faculty of Veterinary Medicine, University of Utrecht, Utrecht, The Netherlands
| | - P Vatta
- Italian National Institute of Health, Rome, Italy
| | - S Caccio
- Italian National Institute of Health, Rome, Italy
| | - L M Ortega-Mora
- SALUVET, Animal Health Department, Faculty of Veterinary Sciences, Complutense University of Madrid, Madrid, Spain
| | - P Jokelainen
- Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark
| | - G Schares
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Epidemiology, Greifswald - Insel Riems, Germany.
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Forth JH, Calvelage S, Fischer M, Hellert J, Sehl-Ewert J, Roszyk H, Deutschmann P, Reichold A, Lange M, Thulke HH, Sauter-Louis C, Höper D, Mandyhra S, Sapachova M, Beer M, Blome S. African swine fever virus - variants on the rise. Emerg Microbes Infect 2023; 12:2146537. [PMID: 36356059 PMCID: PMC9793911 DOI: 10.1080/22221751.2022.2146537] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
African swine fever virus (ASFV), a large and complex DNA-virus circulating between soft ticks and indigenous suids in sub-Saharan Africa, has made its way into swine populations from Europe to Asia. This virus, causing a severe haemorrhagic disease (African swine fever) with very high lethality rates in wild boar and domestic pigs, has demonstrated a remarkably high genetic stability for over 10 years. Consequently, analyses into virus evolution and molecular epidemiology often struggled to provide the genetic basis to trace outbreaks while few resources have been dedicated to genomic surveillance on whole-genome level. During its recent incursion into Germany in 2020, ASFV has unexpectedly diverged into five clearly distinguishable linages with at least ten different variants characterized by high-impact mutations never identified before. Noticeably, all new variants share a frameshift mutation in the 3' end of the DNA polymerase PolX gene O174L, suggesting a causative role as possible mutator gene. Although epidemiological modelling supported the influence of increased mutation rates, it remains unknown how fast virus evolution might progress under these circumstances. Moreover, a tailored Sanger sequencing approach allowed us, for the first time, to trace variants with genomic epidemiology to regional clusters. In conclusion, our findings suggest that this new factor has the potential to dramatically influence the course of the ASFV pandemic with unknown outcome. Therefore, our work highlights the importance of genomic surveillance of ASFV on whole-genome level, the need for high-quality sequences and calls for a closer monitoring of future phenotypic changes of ASFV.
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Affiliation(s)
- Jan H. Forth
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald, Germany
| | - Sten Calvelage
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald, Germany
| | - Melina Fischer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald, Germany
| | - Jan Hellert
- Centre for Structural System Biology (CSSB), Leibnitz-Institut für Virologie, Hamburg, Germany
| | - Julia Sehl-Ewert
- Department of Experimental Animal Facilities and Biorisk Management, Friedrich-Loeffler-Institut, Greifswald, Germany
| | - Hanna Roszyk
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald, Germany
| | - Paul Deutschmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald, Germany
| | - Adam Reichold
- Department of Ecological Modelling, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Martin Lange
- Department of Ecological Modelling, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Hans-Hermann Thulke
- Department of Ecological Modelling, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | | | - Dirk Höper
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald, Germany
| | - Svitlana Mandyhra
- State Scientific and Research Institute of Laboratory Diagnostics and Veterinary and Sanitary Expertise (SSRILDVSE), Kiev, Ukraine
| | - Maryna Sapachova
- State Scientific and Research Institute of Laboratory Diagnostics and Veterinary and Sanitary Expertise (SSRILDVSE), Kiev, Ukraine
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald, Germany
| | - Sandra Blome
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald, Germany, Sandra Blome Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Suedufer 10, 17493, Greifswald – Insel Riems, Germany
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Meene A, Gierse L, Schwaiger T, Karte C, Schröder C, Höper D, Wang H, Groß V, Wünsche C, Mücke P, Kreikemeyer B, Beer M, Becher D, Mettenleiter TC, Riedel K, Urich T. Archaeome structure and function of the intestinal tract in healthy and H1N1 infected swine. Front Microbiol 2023; 14:1250140. [PMID: 37779690 PMCID: PMC10534045 DOI: 10.3389/fmicb.2023.1250140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 08/21/2023] [Indexed: 10/03/2023] Open
Abstract
Background Methanogenic archaea represent a less investigated and likely underestimated part of the intestinal tract microbiome in swine. Aims/Methods This study aims to elucidate the archaeome structure and function in the porcine intestinal tract of healthy and H1N1 infected swine. We performed multi-omics analysis consisting of 16S rRNA gene profiling, metatranscriptomics and metaproteomics. Results and discussion We observed a significant increase from 0.48 to 4.50% of archaea in the intestinal tract microbiome along the ileum and colon, dominated by genera Methanobrevibacter and Methanosphaera. Furthermore, in feces of naïve and H1N1 infected swine, we observed significant but minor differences in the occurrence of archaeal phylotypes over the course of an infection experiment. Metatranscriptomic analysis of archaeal mRNAs revealed the major methanogenesis pathways of Methanobrevibacter and Methanosphaera to be hydrogenotrophic and methyl-reducing, respectively. Metaproteomics of archaeal peptides indicated some effects of the H1N1 infection on central metabolism of the gut archaea. Conclusions/Take home message Finally, this study provides the first multi-omics analysis and high-resolution insights into the structure and function of the porcine intestinal tract archaeome during a non-lethal Influenza A virus infection of the respiratory tract, demonstrating significant alterations in archaeal community composition and central metabolic functions.
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Affiliation(s)
- Alexander Meene
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Laurin Gierse
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | | | | | | | - Dirk Höper
- Friedrich-Loeffler-Institut, Greifswald, Germany
| | - Haitao Wang
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Verena Groß
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Christine Wünsche
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Pierre Mücke
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Bernd Kreikemeyer
- Institute for Medical Microbiology, Virology and Hygiene, Rostock University Medical Centre, Rostock, Germany
| | - Martin Beer
- Friedrich-Loeffler-Institut, Greifswald, Germany
| | - Dörte Becher
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | | | - Katharina Riedel
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Tim Urich
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
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Pannhorst K, Carlson J, Hölper JE, Grey F, Baillie JK, Höper D, Wöhnke E, Franzke K, Karger A, Fuchs W, Mettenleiter TC. The non-classical major histocompatibility complex II protein SLA-DM is crucial for African swine fever virus replication. Sci Rep 2023; 13:10342. [PMID: 37604847 PMCID: PMC10442341 DOI: 10.1038/s41598-023-36788-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 06/09/2023] [Indexed: 08/23/2023] Open
Abstract
African swine fever virus (ASFV) is a lethal animal pathogen that enters its host cells through endocytosis. So far, host factors specifically required for ASFV replication have been barely identified. In this study a genome-wide CRISPR/Cas9 knockout screen in porcine cells indicated that the genes RFXANK, RFXAP, SLA-DMA, SLA-DMB, and CIITA are important for productive ASFV infection. The proteins encoded by these genes belong to the major histocompatibility complex II (MHC II), or swine leucocyte antigen complex II (SLA II). RFXAP and CIITA are MHC II-specific transcription factors, whereas SLA-DMA/B are subunits of the non-classical MHC II molecule SLA-DM. Targeted knockout of either of these genes led to severe replication defects of different ASFV isolates, reflected by substantially reduced plating efficiency, cell-to-cell spread, progeny virus titers and viral DNA replication. Transgene-based reconstitution of SLA-DMA/B fully restored the replication capacity demonstrating that SLA-DM, which resides in late endosomes, plays a crucial role during early steps of ASFV infection.
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Affiliation(s)
- Katrin Pannhorst
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald-Insel Riems, Germany.
| | - Jolene Carlson
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald-Insel Riems, Germany
- Ceva Animal Health, Greifswald-Insel Riems, Germany
| | - Julia E Hölper
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald-Insel Riems, Germany
| | - Finn Grey
- The Roslin Institute, University of Edinburgh, Midlothian, UK
| | | | - Dirk Höper
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Elisabeth Wöhnke
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald-Insel Riems, Germany
| | - Kati Franzke
- Institute of Infectology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Axel Karger
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald-Insel Riems, Germany
| | - Walter Fuchs
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald-Insel Riems, Germany
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Pfaff F, Kramer K, King J, Franzke K, Rosenberger T, Höper D, König P, Hoffmann D, Beer M. Detection of Novel Poxvirus from Gray Seal (Halichoerus grypus), Germany. Emerg Infect Dis 2023; 29:1202-1205. [PMID: 37209672 DOI: 10.3201/eid2906.221817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023] Open
Abstract
We detected a novel poxvirus from a gray seal (Halichoerus grypus) from the North Sea, Germany. The juvenile animal showed pox-like lesions and deteriorating overall health condition and was finally euthanized. Histology, electron microscopy, sequencing, and PCR confirmed a previously undescribed poxvirus of the Chordopoxvirinae subfamily, tentatively named Wadden Sea poxvirus.
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Tsangaras K, Mayer J, Mirza O, Dayaram A, Higgins DP, Bryant B, Campbell-Ward M, Sangster C, Casteriano A, Höper D, Beer M, Greenwood AD. Evolutionarily Young African Rhinoceros Gammaretroviruses. J Virol 2023; 97:e0193222. [PMID: 37022231 PMCID: PMC10134878 DOI: 10.1128/jvi.01932-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 03/17/2023] [Indexed: 04/07/2023] Open
Abstract
High-throughput sequences were generated from DNA and cDNA from four Southern white rhinoceros (Ceratotherium simum simum) located in the Taronga Western Plain Zoo in Australia. Virome analysis identified reads that were similar to Mus caroli endogenous gammaretrovirus (McERV). Previous analysis of perissodactyl genomes did not recover gammaretroviruses. Our analysis, including the screening of the updated white rhinoceros (Ceratotherium simum) and black rhinoceros (Diceros bicornis) draft genomes identified high-copy orthologous gammaretroviral ERVs. Screening of Asian rhinoceros, extinct rhinoceros, domestic horse, and tapir genomes did not identify related gammaretroviral sequences in these species. The newly identified proviral sequences were designated SimumERV and DicerosERV for the white and black rhinoceros retroviruses, respectively. Two long terminal repeat (LTR) variants (LTR-A and LTR-B) were identified in the black rhinoceros, with different copy numbers associated with each (n = 101 and 373, respectively). Only the LTR-A lineage (n = 467) was found in the white rhinoceros. The African and Asian rhinoceros lineages diverged approximately 16 million years ago. Divergence age estimation of the identified proviruses suggests that the exogenous retroviral ancestor of the African rhinoceros ERVs colonized their genomes within the last 8 million years, a result consistent with the absence of these gammaretroviruses from Asian rhinoceros and other perissodactyls. The black rhinoceros germ line was colonized by two lineages of closely related retroviruses and white rhinoceros by one. Phylogenetic analysis indicates a close evolutionary relationship with ERVs of rodents including sympatric African rats, suggesting a possible African origin of the identified rhinoceros gammaretroviruses. IMPORTANCE Rhinoceros genomes were thought to be devoid of gammaretroviruses, as has been determined for other perissodactyls (horses, tapirs, and rhinoceros). While this may be true of most rhinoceros, the African white and black rhinoceros genomes have been colonized by evolutionarily young gammaretroviruses (SimumERV and DicerosERV for the white and black rhinoceros, respectively). These high-copy endogenous retroviruses (ERVs) may have expanded in multiple waves. The closest relative of SimumERV and DicerosERV is found in rodents, including African endemic species. Restriction of the ERVs to African rhinoceros suggests an African origin for the rhinoceros gammaretroviruses.
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Affiliation(s)
- Kyriakos Tsangaras
- Department of Life and Health Sciences, University of Nicosia, Nicosia, Cyprus
| | - Jens Mayer
- Institute of Human Genetics, Medical Faculty, University of Saarland, Homburg, Germany
| | - Omar Mirza
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
| | - Anisha Dayaram
- Institute of Neurophysiology, Charité—Universitätsmedizin Berlin, Berlin, Germany
| | - Damien P. Higgins
- Sydney School of Veterinary Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Benn Bryant
- Taronga Western Plains Zoo, Dubbo, New South Wales, Australia
| | | | - Cheryl Sangster
- Taronga Conservation Society Australia, Mosman, New South Wales, Australia
| | - Andrea Casteriano
- Sydney School of Veterinary Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Dirk Höper
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald, Germany
| | - Alex D. Greenwood
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
- School of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
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Mehl C, Wylezich C, Geiger C, Schauerte N, Mätz-Rensing K, Nesseler A, Höper D, Linnenbrink M, Beer M, Heckel G, Ulrich RG. Reemergence of Lymphocytic Choriomeningitis Mammarenavirus, Germany. Emerg Infect Dis 2023; 29:631-634. [PMID: 36823667 PMCID: PMC9973704 DOI: 10.3201/eid2903.221822] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
Lymphocytic choriomeningitis mammarenavirus (LCMV) is a globally distributed zoonotic pathogen transmitted by house mice (Mus musculus). We report the reemergence of LCMV (lineages I and II) in wild house mice (Mus musculus domesticus) and LCMV lineage I in a diseased golden lion tamarin (Leontopithecus rosalia) from a zoo in Germany.
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Ahrens AK, Selinka HC, Wylezich C, Wonnemann H, Sindt O, Hellmer HH, Pfaff F, Höper D, Mettenleiter TC, Beer M, Harder TC. Investigating Environmental Matrices for Use in Avian Influenza Virus Surveillance-Surface Water, Sediments, and Avian Fecal Samples. Microbiol Spectr 2023; 11:e0266422. [PMID: 36700688 PMCID: PMC10100768 DOI: 10.1128/spectrum.02664-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 12/19/2022] [Indexed: 01/27/2023] Open
Abstract
Surveillance of avian influenza viruses (AIV) in wild water bird populations is important for early warning to protect poultry from incursions of high-pathogenicity (HP) AIV. Access to individual water birds is difficult and restricted and limits sampling depth. Here, we focused on environmental samples such as surface water, sediments, and environmentally deposited fresh avian feces as matrices for AIV detection. Enrichment of viral particles by ultrafiltration of 10-L surface water samples using Rexeed-25-A devices was validated using a bacteriophage ϕ6 internal control system, and AIV detection was attempted using real-time RT-PCR and virus isolation. While validation runs suggested an average enrichment of about 60-fold, lower values of 10 to 15 were observed for field water samples. In total 25/36 (60%) of water samples and 18/36 (50%) of corresponding sediment samples tested AIV positive. Samples were obtained from shallow water bodies in habitats with large numbers of waterfowl during an HPAIV epizootic. Although AIV RNA was detected in a substantial percentage of samples virus isolation failed. Virus loads in samples often were too low to allow further sub- and pathotyping. Similar results were obtained with environmentally deposited avian feces. Moreover, the spectrum of viruses detected by these active surveillance methods did not fully mirror an ongoing HPAIV epizootic among waterfowl as detected by passive surveillance, which, in terms of sensitivity, remains unsurpassed. IMPORTANCE Avian influenza viruses (AIV) have a wide host range in the avian metapopulation and, occasionally, transmission to humans also occurs. Surface water plays a particularly important role in the epidemiology of AIV, as the natural virus reservoir is found in aquatic wild birds. Environmental matrices comprising surface water, sediments, and avian fecal matter deposited in the environment were examined for their usefulness in AIV surveillance. Despite virus enrichment efforts, environmental samples regularly revealed very low virus loads, which hampered further sub- and pathotyping. Passive surveillance based on oral and cloacal swabs of diseased and dead wild birds remained unsurpassed with respect to sensitivity.
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Affiliation(s)
- Ann Kathrin Ahrens
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Isle of Riems, Germany
| | | | - Claudia Wylezich
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Isle of Riems, Germany
| | | | - Ole Sindt
- State Laboratory of Schleswig-Holstein, Neumuenster, Germany
| | - Hartmut H. Hellmer
- Climate Sciences, Physical Oceanography of the Polar Seas, Alfred Wegener Institute, Bremerhaven, Germany
| | - Florian Pfaff
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Isle of Riems, Germany
| | - Dirk Höper
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Isle of Riems, Germany
| | | | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Isle of Riems, Germany
| | - Timm C. Harder
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Isle of Riems, Germany
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10
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Santos PD, Günther A, Keller M, Homeier-Bachmann T, Groschup MH, Beer M, Höper D, Ziegler U. An advanced sequence clustering and designation workflow reveals the enzootic maintenance of a dominant West Nile virus subclade in Germany. Virus Evol 2023; 9:vead013. [PMID: 37197362 PMCID: PMC10184446 DOI: 10.1093/ve/vead013] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 01/13/2023] [Accepted: 03/16/2023] [Indexed: 05/19/2023] Open
Abstract
West Nile virus (WNV) is the most widespread arthropod-borne (arbo) virus and the primary cause of arboviral encephalitis globally. Members of WNV species genetically diverged and are classified into different hierarchical groups below species rank. However, the demarcation criteria for allocating WNV sequences into these groups remain individual and inconsistent, and the use of names for different levels of the hierarchical levels is unstructured. In order to have an objective and comprehensible grouping of WNV sequences, we developed an advanced grouping workflow using the 'affinity propagation clustering' algorithm and newly included the 'agglomerative hierarchical clustering' algorithm for the allocation of WNV sequences into different groups below species rank. In addition, we propose to use a fixed set of terms for the hierarchical naming of WNV below species level and a clear decimal numbering system to label the determined groups. For validation, we applied the refined workflow to WNV sequences that have been previously grouped into various lineages, clades, and clusters in other studies. Although our workflow regrouped some WNV sequences, overall, it generally corresponds with previous groupings. We employed our novel approach to the sequences from the WNV circulation in Germany 2020, primarily from WNV-infected birds and horses. Besides two newly defined minor (sub)clusters comprising only three sequences each, Subcluster 2.5.3.4.3c was the predominant WNV sequence group detected in Germany from 2018 to 2020. This predominant subcluster was also associated with at least five human WNV infections in 2019-20. In summary, our analyses imply that the genetic diversity of the WNV population in Germany is shaped by enzootic maintenance of the dominant WNV subcluster accompanied by sporadic incursions of other rare clusters and subclusters. Moreover, we show that our refined approach for sequence grouping yields meaningful results. Although we primarily aimed at a more detailed WNV classification, the presented workflow can also be applied to the objective genotyping of other virus species.
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Affiliation(s)
| | | | - Markus Keller
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Novel and Emerging Infectious Diseases, 17493, Greifswald-Insel Riems, Germany
| | | | - Martin H Groschup
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Novel and Emerging Infectious Diseases, 17493, Greifswald-Insel Riems, Germany
- German Centre for Infection Research, Partner site Hamburg-Lübeck-Borstel-Riems, 17493, Greifswald-Insel Riems, Germany
| | - Martin Beer
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Diagnostic Virology, 17493, Greifswald-Insel Riems, Germany
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11
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Mehl C, Wylezich C, Geiger C, Schauerte N, Mätz-Rensing K, Nesseler A, Höper D, Linnenbrink M, Beer M, Heckel G, Ulrich RG. Use of Zoo Mice in Study of Lymphocytic Choriomeningitis Mammarenavirus, Germany (Response). Emerg Infect Dis 2023; 30:205-206. [PMID: 38146988 PMCID: PMC10756383 DOI: 10.3201/eid3001.231521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023] Open
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12
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Barut GT, Halwe NJ, Taddeo A, Kelly JN, Schön J, Ebert N, Ulrich L, Devisme C, Steiner S, Trüeb BS, Hoffmann B, Veiga IB, Leborgne NGF, Moreira EA, Breithaupt A, Wylezich C, Höper D, Wernike K, Godel A, Thomann L, Flück V, Stalder H, Brügger M, Esteves BIO, Zumkehr B, Beilleau G, Kratzel A, Schmied K, Ochsenbein S, Lang RM, Wider M, Machahua C, Dorn P, Marti TM, Funke-Chambour M, Rauch A, Widera M, Ciesek S, Dijkman R, Hoffmann D, Alves MP, Benarafa C, Beer M, Thiel V. The spike gene is a major determinant for the SARS-CoV-2 Omicron-BA.1 phenotype. Nat Commun 2022; 13:5929. [PMID: 36207334 PMCID: PMC9543931 DOI: 10.1038/s41467-022-33632-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 09/26/2022] [Indexed: 11/09/2022] Open
Abstract
Variant of concern (VOC) Omicron-BA.1 has achieved global predominance in early 2022. Therefore, surveillance and comprehensive characterization of Omicron-BA.1 in advanced primary cell culture systems and animal models are urgently needed. Here, we characterize Omicron-BA.1 and recombinant Omicron-BA.1 spike gene mutants in comparison with VOC Delta in well-differentiated primary human nasal and bronchial epithelial cells in vitro, followed by in vivo fitness characterization in hamsters, ferrets and hACE2-expressing mice, and immunized hACE2-mice. We demonstrate a spike-mediated enhancement of early replication of Omicron-BA.1 in nasal epithelial cultures, but limited replication in bronchial epithelial cultures. In hamsters, Delta shows dominance over Omicron-BA.1, and in ferrets Omicron-BA.1 infection is abortive. In hACE2-knock-in mice, Delta and a Delta spike clone also show dominance over Omicron-BA.1 and an Omicron-BA.1 spike clone, respectively. Interestingly, in naïve K18-hACE2 mice, we observe Delta spike-mediated increased replication and pathogenicity and Omicron-BA.1 spike-mediated reduced replication and pathogenicity, suggesting that the spike gene is a major determinant of replication and pathogenicity. Finally, the Omicron-BA.1 spike clone is less well-controlled by mRNA-vaccination in K18-hACE2-mice and becomes more competitive compared to the progenitor and Delta spike clones, suggesting that spike gene-mediated immune evasion is another important factor that led to Omicron-BA.1 dominance.
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Affiliation(s)
- G Tuba Barut
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Nico Joel Halwe
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Greifswald, Germany
| | - Adriano Taddeo
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Jenna N Kelly
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland.,European Virus Bioinformatics Center, Jena, Germany
| | - Jacob Schön
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Greifswald, Germany
| | - Nadine Ebert
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Lorenz Ulrich
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Greifswald, Germany
| | - Christelle Devisme
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Silvio Steiner
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Bettina Salome Trüeb
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Bernd Hoffmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Greifswald, Germany
| | - Inês Berenguer Veiga
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Nathan Georges François Leborgne
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Etori Aguiar Moreira
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Angele Breithaupt
- Department of Experimental Animal Facilities and Biorisk Management, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Greifswald, Germany
| | - Claudia Wylezich
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Greifswald, Germany
| | - Dirk Höper
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Greifswald, Germany
| | - Kerstin Wernike
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Greifswald, Germany
| | - Aurélie Godel
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Lisa Thomann
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Vera Flück
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Hanspeter Stalder
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Melanie Brügger
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Blandina I Oliveira Esteves
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Beatrice Zumkehr
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Guillaume Beilleau
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Annika Kratzel
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Kimberly Schmied
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Sarah Ochsenbein
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Reto M Lang
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Manon Wider
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Carlos Machahua
- Department of Pulmonary Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.,Department for Pulmonary Medicine, BioMedical Research, University of Bern, Bern, Switzerland
| | - Patrick Dorn
- Division of General Thoracic Surgery, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.,Department for BioMedical Research, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Thomas M Marti
- Division of General Thoracic Surgery, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.,Department for BioMedical Research, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Manuela Funke-Chambour
- Department of Pulmonary Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.,Department for Pulmonary Medicine, BioMedical Research, University of Bern, Bern, Switzerland
| | - Andri Rauch
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland.,Department of Infectious Diseases, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Marek Widera
- Institute of Medical Virology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| | - Sandra Ciesek
- Institute of Medical Virology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| | - Ronald Dijkman
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland.,European Virus Bioinformatics Center, Jena, Germany.,Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Donata Hoffmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Greifswald, Germany
| | - Marco P Alves
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland. .,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland. .,Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland.
| | - Charaf Benarafa
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland. .,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland. .,Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland.
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Greifswald, Germany. .,European Virus Bioinformatics Center, Jena, Germany.
| | - Volker Thiel
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland. .,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland. .,Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland. .,European Virus Bioinformatics Center, Jena, Germany.
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13
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Blaurock C, Breithaupt A, Weber S, Wylezich C, Keller M, Mohl BP, Görlich D, Groschup MH, Sadeghi B, Höper D, Mettenleiter TC, Balkema-Buschmann A. Compellingly high SARS-CoV-2 susceptibility of Golden Syrian hamsters suggests multiple zoonotic infections of pet hamsters during the COVID-19 pandemic. Sci Rep 2022; 12:15069. [PMID: 36064749 PMCID: PMC9442591 DOI: 10.1038/s41598-022-19222-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 08/25/2022] [Indexed: 12/01/2022] Open
Abstract
Golden Syrian hamsters (Mesocricetus auratus) are used as a research model for severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2). Millions of Golden Syrian hamsters are also kept as pets in close contact to humans. To determine the minimum infective dose (MID) for assessing the zoonotic transmission risk, and to define the optimal infection dose for experimental studies, we orotracheally inoculated hamsters with SARS-CoV-2 doses from 1 * 105 to 1 * 10−4 tissue culture infectious dose 50 (TCID50). Body weight and virus shedding were monitored daily. 1 * 10−3 TCID50 was defined as the MID, and this was still sufficient to induce virus shedding at levels up to 102.75 TCID50/ml, equaling the estimated MID for humans. Virological and histological data revealed 1 * 102 TCID50 as the optimal dose for experimental infections. This compelling high susceptibility leading to productive infections in Golden Syrian hamsters must be considered as a potential source of SARS-CoV-2 infection for humans that come into close contact with pet hamsters.
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Affiliation(s)
- Claudia Blaurock
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Angele Breithaupt
- Department of Experimental Animal Facilities and Biorisk Management, Friedrich-Loeffler- Institut, Greifswald-Insel Riems, Germany
| | - Saskia Weber
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Claudia Wylezich
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Markus Keller
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Björn-Patrick Mohl
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Dirk Görlich
- Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Martin H Groschup
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Balal Sadeghi
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Dirk Höper
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Thomas C Mettenleiter
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Anne Balkema-Buschmann
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany.
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14
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Rau J, Werner D, Beer M, Höper D, Kampen H. The microbial RNA metagenome of Aedes albopictus (Diptera: Culicidae) from Germany. Parasitol Res 2022; 121:2587-2599. [PMID: 35857094 PMCID: PMC9378336 DOI: 10.1007/s00436-022-07576-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 06/10/2022] [Indexed: 12/04/2022]
Abstract
Aedes albopictus is a highly invasive mosquito species that has become widespread across the globe. In addition, it is an efficient vector of numerous pathogens of medical and veterinary importance, including dengue, chikungunya and Zika viruses. Among others, the vector potential of mosquitoes is influenced by their microbiome. However, this influence is very dynamic and can vary between individuals and life stages. To obtain a rough overview on the microbiome of Ae. albopictus populations in Germany, pooled female and pooled male individuals from seven German locations were investigated by total RNA sequencing. The mosquito specimens had been collected as larvae in the field and processed immediately after adult emergence, i.e. without females having fed on blood. RNA fragments with high degrees of identity to a large number of viruses and microorganisms were identified, including, for example, Wolbachia pipientis and Acinetobacter baumannii, with differences between male and female mosquitoes. Knowledge about the natural occurrence of microorganisms in mosquitoes may be translated into new approaches to vector control, for example W. pipientis can be exploited to manipulate mosquito reproduction and vector competence. The study results show how diverse the microbiome of Ae. albopictus can be, and the more so needs to be adequately analysed and interpreted.
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Affiliation(s)
- Janine Rau
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Germany.
| | - Doreen Werner
- Leibniz Centre for Agricultural Landscape Research, Muencheberg, Germany
| | - Martin Beer
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Germany
| | - Dirk Höper
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Germany
| | - Helge Kampen
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Germany
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15
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Schlottau K, Feldmann F, Hanley PW, Lovaglio J, Tang-Huau TL, Meade-White K, Callison J, Williamson BN, Rosenke R, Long D, Wylezich C, Höper D, Herden C, Scott D, Hoffmann D, Saturday G, Beer M, Feldmann H. Development of a nonhuman primate model for mammalian bornavirus infection. PNAS Nexus 2022; 1:pgac073. [PMID: 35860599 PMCID: PMC9291224 DOI: 10.1093/pnasnexus/pgac073] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/30/2022] [Indexed: 02/05/2023]
Abstract
Until recently, it was assumed that members of the family Bornaviridae could not induce severe disease in humans. Today, however, Borna disease virus 1 (BoDV-1), as well as the more recently emerged variegated squirrel bornavirus 1 (VSBV-1), are known as causative agents of lethal encephalitis in humans. In order to establish animal models reflecting the pathogenesis in humans and for countermeasure efficacy testing, we infected twelve rhesus macaques (Macaca mulatta) either with VSBV-1 or with BoDV-1. For each virus, three monkeys each were inoculated with 2 × 104 focus forming units by the intracerebral route or by multiple peripheral routes (intranasal, conjunctival, intramuscular, and subcutaneous; same dose in total). All BoDV-1 and VSBV-1 intracerebrally infected monkeys developed severe neurological signs around 5 to 6 or 8 to 12 weeks postinfection, respectively. Focal myoclonus and tremors were the most prominent observations in BoDV-1 and VSBV-1-infected animals. VSBV-1-infected animals also showed behavioral changes. Only one BoDV-1 peripherally infected animal developed similar disease manifestations. All animals with severe clinical disease showed high viral loads in brain tissues and displayed perivascular mononuclear cuffs with a predominance of lymphocytes and similar meningeal inflammatory infiltrates. In summary, rhesus macaques intracerebrally infected with mammalian bornaviruses develop a human-like disease and may serve as surrogate models for human bornavirus infection.
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Affiliation(s)
| | - Friederike Feldmann
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Patrick W Hanley
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Jamie Lovaglio
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Tsing-Lee Tang-Huau
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Kimberly Meade-White
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Julie Callison
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Brandi N Williamson
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Rebecca Rosenke
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Dan Long
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Claudia Wylezich
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Dirk Höper
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Christiane Herden
- Justus-Liebig-Universität, Institute of Veterinary Pathology, 35390 Gießen, Germany
| | - Dana Scott
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Donata Hoffmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Greg Saturday
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Heinz Feldmann
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
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16
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Stadler J, Junker S, Gründl J, Fröhlich S, Beisl M, Zöls S, Ritzmann M, Eddicks M, Palzer A, Sehl J, Höper D, Unterweger C, Ladinig A, Mayer C. [Hind limb paralysis in fattening pigs due to a new strain of porcine Teschovirus A11]. Tierarztl Prax Ausg G Grosstiere Nutztiere 2022; 50:59-67. [PMID: 35235983 DOI: 10.1055/a-1729-3677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
In a fattening farm in southern Germany, paralysis of the hind limbs was observed in 2 age groups (50 kg as well as 60 kg) during a 4 week period. Despite a low morbidity of 3.3 % the majority of the affected animals needed to be euthanized in consequence to the progression of their hind limb paralysis. During pathomorphological examinations of 2 affected fattening pigs severe lymphohistiocytic meningoencephalomyelitis and vasculitis were detected. Immunhistochemistry revealed the presence of Porcine Teschovirus antigen in all parts of the central nervous system as well as in several cell types (neurons, glia cells, endothelial cells, mononuclear cells). Porcine Teschovirus was detected by PCR in spinal cord samples. The subsequently performed phylogenetic analysis PCR revealed a close relation (88 % full genome sequence) to porcine Teschovirus A11 strain "Dresden". Other swine relevant pathogens were excluded by PCR, bacteriologic examination and sequencing. Following a period of 4 weeks no additional cases of hind limb paralysis were observed in the fattening farm.
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Affiliation(s)
- Julia Stadler
- Klinik für Schweine am Zentrum für Klinische Tiermedizin, Ludwig-Maximilians-Universität München
| | - Sigena Junker
- Klinik für Schweine am Zentrum für Klinische Tiermedizin, Ludwig-Maximilians-Universität München
| | - Julia Gründl
- Klinik für Schweine am Zentrum für Klinische Tiermedizin, Ludwig-Maximilians-Universität München
| | - Sebastian Fröhlich
- Klinik für Schweine am Zentrum für Klinische Tiermedizin, Ludwig-Maximilians-Universität München
| | - Marina Beisl
- Klinik für Schweine am Zentrum für Klinische Tiermedizin, Ludwig-Maximilians-Universität München
| | - Susanne Zöls
- Klinik für Schweine am Zentrum für Klinische Tiermedizin, Ludwig-Maximilians-Universität München
| | - Mathias Ritzmann
- Klinik für Schweine am Zentrum für Klinische Tiermedizin, Ludwig-Maximilians-Universität München
| | - Matthias Eddicks
- Klinik für Schweine am Zentrum für Klinische Tiermedizin, Ludwig-Maximilians-Universität München
| | - Andreas Palzer
- Klinik für Schweine am Zentrum für Klinische Tiermedizin, Ludwig-Maximilians-Universität München
| | - Julia Sehl
- Friedrich-Loeffler-Institut, Bundesforschungsinstitut für Tiergesundheit
| | - Dirk Höper
- Friedrich-Loeffler-Institut, Bundesforschungsinstitut für Tiergesundheit
| | - Christine Unterweger
- Universitätsklinik für Schweine, Department für Nutztiere und öffentliches Gesundheitswesen in der Veterinärmedizin, Veterinärmedizinische Universität Wien
| | - Andrea Ladinig
- Universitätsklinik für Schweine, Department für Nutztiere und öffentliches Gesundheitswesen in der Veterinärmedizin, Veterinärmedizinische Universität Wien
| | - Christian Mayer
- Institut für Tierpathologie am Zentrum für klinische Tiermedizin, Ludwig-Maximilians-Universität München
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17
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Schäfer M, Pfaff F, Höper D, Silaghi C. Early Transcriptional Changes in the Midgut of Ornithodoros moubata after Feeding and Infection with Borrelia duttonii. Microorganisms 2022; 10:microorganisms10030525. [PMID: 35336101 PMCID: PMC8948914 DOI: 10.3390/microorganisms10030525] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 02/22/2022] [Indexed: 12/16/2022] Open
Abstract
Studies on tick-pathogen-host interactions are helping to identify candidates for vaccines against ticks and tick-borne diseases and to discover potent bioactive tick molecules. The tick midgut is the main tissue involved in blood feeding and, moreover, the first organ to have contact with pathogens ingested through the blood meal. As little is known about the molecular biology of feeding and tick defence mechanisms against microorganisms, but important for understanding vector-pathogen interactions, we explored the early transcriptional changes in the midgut of Ornithodoros moubata after feeding and in response to challenge with the relapsing-fever spirochete Borrelia duttonii using the Ion S5XL platform. Besides transcripts with metabolic function and immune-related transcripts we discovered numerous putative and uncharacterized protein sequences. Overall, our analyses support previous studies and provides a valuable reference database for further functional proteomic analysis of midgut proteins of O. moubata.
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Affiliation(s)
- Mandy Schäfer
- Institute of Infectology, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany;
- Correspondence:
| | - Florian Pfaff
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany; (F.P.); (D.H.)
| | - Dirk Höper
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany; (F.P.); (D.H.)
| | - Cornelia Silaghi
- Institute of Infectology, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany;
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18
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Cichon N, Barry Y, Stoek F, Diambar A, Ba A, Ziegler U, Rissmann M, Schulz J, Haki ML, Höper D, Doumbia BA, Bah MY, Groschup MH, Eiden M. Co-circulation of Orthobunyaviruses and Rift Valley Fever Virus in Mauritania, 2015. Front Microbiol 2022; 12:766977. [PMID: 35003005 PMCID: PMC8739971 DOI: 10.3389/fmicb.2021.766977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 10/26/2021] [Indexed: 12/02/2022] Open
Abstract
Ngari virus (NRIV) has been mostly detected during concurrent outbreaks of Rift Valley fever virus (RVFV). NRIV is grouped in the genus Orthobunyavirus within the Bunyaviridae family and RVFV in the genus Phlebovirus in the family Phenuiviridae. Both are zoonotic arboviruses and can induce hemorrhagic fever displaying the same clinical picture in humans and small ruminants. To investigate if NRIV and its parental viruses, Bunyamwera virus (BUNV) and Batai virus (BATV), played a role during the Mauritanian RVF outbreak in 2015/16, we analyzed serum samples of sheep and goats from central and southern regions in Mauritania by quantitative real-time RT-PCR, serum neutralization test (SNT) and ELISA. 41 of 458 samples exhibited neutralizing reactivity against NRIV, nine against BATV and three against BUNV. Moreover, complete virus genomes from BUNV could be recovered from two sheep as well as two NRIV isolates from a goat and a sheep. No RVFV-derived viral RNA was detected, but 81 seropositive animals including 22 IgM-positive individuals were found. Of these specimens, 61 samples revealed antibodies against RVFV and at least against one of the three orthobunyaviruses. An indirect ELISA based on NRIV/BATV and BUNV derived Gc protein was established as complement to SNT, which showed high performance regarding NRIV, but decreased sensitivity and specificity regarding BATV and BUNV. Moreover, we observed high cross-reactivity among NRIV and BATV serological assays. Taken together, the data indicate the co-circulation of at least BUNV and NRIV in the Mauritanian sheep and goat populations.
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Affiliation(s)
- Nicole Cichon
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Yahya Barry
- Office National de Recherche et de Développement de l'Elevage (ONARDEL), Nouakchott, Mauritania
| | - Franziska Stoek
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Abdellah Diambar
- Office National de Recherche et de Développement de l'Elevage (ONARDEL), Nouakchott, Mauritania
| | - Aliou Ba
- Office National de Recherche et de Développement de l'Elevage (ONARDEL), Nouakchott, Mauritania
| | - Ute Ziegler
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Melanie Rissmann
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany.,Department of Viroscience, Erasmus Medical Center, Rotterdam, Netherlands
| | - Jana Schulz
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany.,Institute of Epidemiology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Mohamed L Haki
- Office National de Recherche et de Développement de l'Elevage (ONARDEL), Nouakchott, Mauritania
| | - Dirk Höper
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Baba A Doumbia
- Ministère du Développement Rural, Nouakchott, Mauritania
| | - Mohamed Y Bah
- Ministère du Développement Rural, Nouakchott, Mauritania
| | - Martin H Groschup
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Martin Eiden
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
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19
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Müller T, Hassel R, Jago M, Khaiseb S, van der Westhuizen J, Vos A, Calvelage S, Fischer S, Marston DA, Fooks AR, Höper D, Freuling CM. Rabies in kudu: Revisited. Adv Virus Res 2022; 112:115-173. [DOI: 10.1016/bs.aivir.2022.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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20
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Weissenböck H, Ebinger A, Gager AM, Thaller D, Höper D, Lichtmannsperger K, Weissenbacher-Lang C, Matt J, Beer M. A novel enterovirus in lambs with poliomyelitis and brain stem encephalitis. Transbound Emerg Dis 2021; 69:227-234. [PMID: 34874614 PMCID: PMC9305294 DOI: 10.1111/tbed.14412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 11/23/2021] [Accepted: 11/24/2021] [Indexed: 11/26/2022]
Abstract
An Austrian organic dairy sheep farm experienced cases of recumbency and sudden deaths in 3- to 4-week-old lambs. Two animals were subjected to thorough clinical and pathological investigations. Pathohistological analysis identified severe nonsuppurative myelitis and mild nonsuppurative encephalitis. A reverse-transcription quantitative PCR (RT-qPCR) assay for the recently discovered ovine picornavirus causing comparable lesions scored negative. By next-generation sequencing-based metagenomics, a nearly complete genome of a novel enterovirus could be detected and assembled. In situ hybridization using a specifically designed probe revealed robust signals in affected motoneurons of the spinal cord suggesting a causative role of the novel virus.
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Affiliation(s)
| | - Arnt Ebinger
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Diagnostic Virology, Greifswald, Germany
| | - Anna Maria Gager
- Institute of Pathology, Department of Pathobiology, Vienna, Austria
| | - Denise Thaller
- Institute of Pathology, Department of Pathobiology, Vienna, Austria
| | - Dirk Höper
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Diagnostic Virology, Greifswald, Germany
| | | | | | - Julia Matt
- Institute of Pathology, Department of Pathobiology, Vienna, Austria
| | - Martin Beer
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Diagnostic Virology, Greifswald, Germany
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21
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Santos PD, Ziegler U, Szillat KP, Szentiks CA, Strobel B, Skuballa J, Merbach S, Grothmann P, Tews BA, Beer M, Höper D. In action-an early warning system for the detection of unexpected or novel pathogens. Virus Evol 2021; 7:veab085. [PMID: 34703624 PMCID: PMC8542707 DOI: 10.1093/ve/veab085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 09/06/2021] [Accepted: 09/23/2021] [Indexed: 12/27/2022] Open
Abstract
Proactive approaches in preventing future epidemics include pathogen discovery prior to their emergence in human and/or animal populations. Playing an important role in pathogen discovery, high-throughput sequencing (HTS) enables the characterization of microbial and viral genetic diversity within a given sample. In particular, metagenomic HTS allows the unbiased taxonomic profiling of sequences; hence, it can identify novel and highly divergent pathogens such as viruses. Newly discovered viral sequences must be further investigated using genomic characterization, molecular and serological screening, and/or invitro and invivo characterization. Several outbreak and surveillance studies apply unbiased generic HTS to characterize the whole genome sequences of suspected pathogens. In contrast, this study aimed to screen for novel and unexpected pathogens in previously generated HTS datasets and use this information as a starting point for the establishment of an early warning system (EWS). As a proof of concept, the EWS was applied to HTS datasets and archived samples from the 2018–9 West Nile virus (WNV) epidemic in Germany. A metagenomics read classifier detected sequences related to genome sequences of various members of Riboviria. We focused the further EWS investigation on viruses belonging to the families Peribunyaviridae and Reoviridae, under suspicion of causing co-infections in WNV-infected birds. Phylogenetic analyses revealed that the reovirus genome sequences clustered with sequences assigned to the species Umatilla virus (UMAV), whereas a new peribunyavirid, tentatively named ‘Hedwig virus’ (HEDV), belonged to a putative novel genus of the family Peribunyaviridae. In follow-up studies, newly developed molecular diagnostic assays detected fourteen UMAV-positive wild birds from different German cities and eight HEDV-positive captive birds from two zoological gardens. UMAV was successfully cultivated in mosquito C6/36 cells inoculated with a blackbird liver. In conclusion, this study demonstrates the power of the applied EWS for the discovery and characterization of unexpected viruses in repurposed sequence datasets, followed by virus screening and cultivation using archived sample material. The EWS enhances the strategies for pathogen recognition before causing sporadic cases and massive outbreaks and proves to be a reliable tool for modern outbreak preparedness.
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Affiliation(s)
- Pauline Dianne Santos
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Diagnostic Virology, Südufer 10, Greifswald, Insel Riems 17493, Germany
| | - Ute Ziegler
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Novel and Emerging Infectious Diseases, Südufer 10, Greifswald, Insel Riems 17493, Germany
| | - Kevin P Szillat
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Diagnostic Virology, Südufer 10, Greifswald, Insel Riems 17493, Germany
| | - Claudia A Szentiks
- 4Department of Wildlife Diseases, Leibniz-Institute for Zoo- and Wildlife Research (IZW), Alfred-Kowalke-Straße 17, Berlin 10315, Germany
| | - Birte Strobel
- Chemical and Veterinary Investigations Office Karlsruhe (CVUA Karlsruhe), Weissenburgerstrasse 3, Karlsruhe 76187, Germany
| | - Jasmin Skuballa
- Chemical and Veterinary Investigations Office Karlsruhe (CVUA Karlsruhe), Weissenburgerstrasse 3, Karlsruhe 76187, Germany
| | - Sabine Merbach
- State Institute for Chemical and Veterinary Analysis (CVUA) Westfalen, Zur Taubeneiche 10-12, Arnsberg 59821, Germany
| | - Pierre Grothmann
- Practice for Zoo, Game and Wild Animals, Lintiger Str. 74, Geestland 27624, Germany
| | - Birke Andrea Tews
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Infectology, Südufer 10, Greifswald, Insel Riems 17493, Germany
| | - Martin Beer
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Diagnostic Virology, Südufer 10, Greifswald, Insel Riems 17493, Germany
| | - Dirk Höper
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Diagnostic Virology, Südufer 10, Greifswald, Insel Riems 17493, Germany
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22
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Nitschel S, Zaeck LM, Potratz M, Nolden T, te Kamp V, Franzke K, Höper D, Pfaff F, Finke S. Point Mutations in the Glycoprotein Ectodomain of Field Rabies Viruses Mediate Cell Culture Adaptation through Improved Virus Release in a Host Cell Dependent and Independent Manner. Viruses 2021; 13:v13101989. [PMID: 34696419 PMCID: PMC8538267 DOI: 10.3390/v13101989] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/21/2021] [Accepted: 09/29/2021] [Indexed: 11/29/2022] Open
Abstract
Molecular details of field rabies virus (RABV) adaptation to cell culture replication are insufficiently understood. A better understanding of adaptation may not only reveal requirements for efficient RABV replication in cell lines, but may also provide novel insights into RABV biology and adaptation-related loss of virulence and pathogenicity. Using two recombinant field rabies virus clones (rRABV Dog and rRABV Fox), we performed virus passages in three different cell lines to identify cell culture adaptive mutations. Ten passages were sufficient for the acquisition of adaptive mutations in the glycoprotein G and in the C-terminus of phosphoprotein P. Apart from the insertion of a glycosylation sequon via the mutation D247N in either virus, both acquired additional and cell line-specific mutations after passages on BHK (K425N) and MDCK-II (R346S or R350G) cells. As determined by virus replication kinetics, complementation, and immunofluorescence analysis, the major bottleneck in cell culture replication was the intracellular accumulation of field virus G protein, which was overcome after the acquisition of the adaptive mutations. Our data indicate that limited release of extracellular infectious virus at the plasma membrane is a defined characteristic of highly virulent field rabies viruses and we hypothesize that the observed suboptimal release of infectious virions is due to the inverse correlation of virus release and virulence in vivo.
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Affiliation(s)
- Sabine Nitschel
- Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, Institute of Molecular Virology and Cell Biology (IMVZ), 17493 Greifswald-Insel Riems, Germany; (S.N.); (L.M.Z.); (M.P.); (T.N.); (V.t.K.)
| | - Luca M. Zaeck
- Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, Institute of Molecular Virology and Cell Biology (IMVZ), 17493 Greifswald-Insel Riems, Germany; (S.N.); (L.M.Z.); (M.P.); (T.N.); (V.t.K.)
| | - Madlin Potratz
- Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, Institute of Molecular Virology and Cell Biology (IMVZ), 17493 Greifswald-Insel Riems, Germany; (S.N.); (L.M.Z.); (M.P.); (T.N.); (V.t.K.)
| | - Tobias Nolden
- Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, Institute of Molecular Virology and Cell Biology (IMVZ), 17493 Greifswald-Insel Riems, Germany; (S.N.); (L.M.Z.); (M.P.); (T.N.); (V.t.K.)
| | - Verena te Kamp
- Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, Institute of Molecular Virology and Cell Biology (IMVZ), 17493 Greifswald-Insel Riems, Germany; (S.N.); (L.M.Z.); (M.P.); (T.N.); (V.t.K.)
| | - Kati Franzke
- Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, Institute of Infectiology (IMED), 17493 Greifswald-Insel Riems, Germany;
| | - Dirk Höper
- Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, Institute of Diagnostic Virology (IVD), 17493 Greifswald-Insel Riems, Germany; (D.H.); (F.P.)
| | - Florian Pfaff
- Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, Institute of Diagnostic Virology (IVD), 17493 Greifswald-Insel Riems, Germany; (D.H.); (F.P.)
| | - Stefan Finke
- Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, Institute of Molecular Virology and Cell Biology (IMVZ), 17493 Greifswald-Insel Riems, Germany; (S.N.); (L.M.Z.); (M.P.); (T.N.); (V.t.K.)
- Correspondence: ; Tel.: +49-38351-71283
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23
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Wylezich C, Schaller T, Claus R, Hirschbühl K, Märkl B, Kling E, Spring O, Höper D, Schlegel J, Beer M, Dintner S. Whole-genome analysis of SARS-CoV-2 samples indicate no tissue specific genetic adaptation of the virus in COVID-19 patients' upper and lower respiratory tract. Diagn Microbiol Infect Dis 2021; 101:115520. [PMID: 34536911 PMCID: PMC8376524 DOI: 10.1016/j.diagmicrobio.2021.115520] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 06/28/2021] [Accepted: 08/15/2021] [Indexed: 12/30/2022]
Abstract
Sample panels of SARS-CoV-2 cases were retrospectively whole-genome sequenced. In three individuals, samples of upper and lower respiratory tract resulted in identical sequences suggesting virus stability including the spike protein cleavage site. In a fourth case, low-level intra-host genomic evolution and a unique 5-nucleotide deletion was observed.
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Affiliation(s)
- Claudia Wylezich
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany.
| | - Tina Schaller
- Department of General Pathology and Molecular Diagnostics, University of Augsburg, Augsburg, Germany
| | - Rainer Claus
- Department of Hematology and Oncology, University of Augsburg, Augsburg, Germany
| | - Klaus Hirschbühl
- Department of Hematology and Oncology, University of Augsburg, Augsburg, Germany
| | - Bruno Märkl
- Department of General Pathology and Molecular Diagnostics, University of Augsburg, Augsburg, Germany
| | - Elisabeth Kling
- Department of Microbiology, University of Augsburg, Augsburg, Germany
| | - Oliver Spring
- Anesthesiology and Operative Intensive Care Medicine,University of Augsburg, Augsburg, Germany
| | - Dirk Höper
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Jürgen Schlegel
- Department of Neuropathology, School of Medicine, Institute of Pathology, Technical University Munich, Munich, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Sebastian Dintner
- Department of General Pathology and Molecular Diagnostics, University of Augsburg, Augsburg, Germany
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24
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Keller M, Hagag IT, Balzer J, Beyer K, Kersebohm JC, Sadeghi B, Wernike K, Höper D, Wylezich C, Beer M, Groschup MH. Detection of SARS-CoV-2 variant B.1.1.7 in a cat in Germany. Res Vet Sci 2021; 140:229-232. [PMID: 34534904 DOI: 10.1016/j.rvsc.2021.09.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/27/2021] [Accepted: 09/06/2021] [Indexed: 01/04/2023]
Abstract
Several non-variant of concern SARS-CoV-2 infections in pets have been reported as documented in the OIE and GISAID databases and there is only one fully documented case of an alpha variant of concern (VOC)(B.1.1.7) in the United States so far. Here, we describe the first case in a cat infected with the alpha SARS-CoV-2 variant in Germany. A cat suffering from pneumonia was presented to a veterinary practice. The pneumonia was treated symptomatically, but 16 days later the cat was presented again. Since the owner had been tested positive for a SARS-CoV-2 infection in the meantime, swab samples were taken from the cat and analyzed for SARS-CoV-2 specific nucleic acids. The various RT-qPCR analyses and whole-genome sequencing revealed the presence of the SARS-CoV-2 B.1.1.7 variant in this cat. This study shows that pets living in close contact with SARS-CoV-2 B.1.1.7 infected owners can contract this virus and also suffer from a respiratory disease. It is not clear yet whether onward transmissions to other cats and humans can occur. To minimize transmission risks, pet owners and veterinarians should comply to the hygienic rules published by OIE and others. It must be stated, that infections of cats with SARS-CoV-2 is still a rare event. Cats with clinical signs of a respiratory disease should be presented to a veterinarian, who will decide on further steps.
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Affiliation(s)
- Markus Keller
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Ibrahim T Hagag
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Jörg Balzer
- Vet Med Labor GmbH, Division of IDEXX Laboratories, Kornwestheim, Germany
| | | | | | - Balal Sadeghi
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Kerstin Wernike
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Dirk Höper
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Claudia Wylezich
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Martin H Groschup
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany.
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25
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Wylezich C, Höper D. Meta-Ribosomalomics: RNA Sequencing Is an Unbiased Method for Parasite Detection of Different Sample Types. Front Microbiol 2021; 12:614553. [PMID: 34234748 PMCID: PMC8256892 DOI: 10.3389/fmicb.2021.614553] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 05/26/2021] [Indexed: 01/23/2023] Open
Abstract
In this perspective article, we review the past use of ribosomal sequences to address scientific and diagnostic questions. We highlight a variety of sequencing approaches including metagenomics and DNA barcoding and their different demands and requirements. Meta-ribosomalomics is introduced as an unbiased approach to exploit high-throughput sequencing datasets for eukaryotic and prokaryotic ribosomal sequences. Prerequisites, benefits, drawbacks, and future perspectives are elaborated and compared to other sequencing approaches.
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Affiliation(s)
- Claudia Wylezich
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
| | - Dirk Höper
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
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26
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Naguib MM, Höper D, Elkady MF, Afifi MA, Erfan A, Abozeid HH, Hasan WM, Arafa AS, Shahein M, Beer M, Harder TC, Grund C. Comparison of genomic and antigenic properties of Newcastle Disease virus genotypes II, XXI and VII from Egypt do not point to antigenic drift as selection marker. Transbound Emerg Dis 2021; 69:849-863. [PMID: 33955204 DOI: 10.1111/tbed.14121] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 04/12/2021] [Accepted: 04/20/2021] [Indexed: 01/27/2023]
Abstract
Newcastle disease (ND), caused by avian orthoavulavirus type-1 (NDV), is endemic in poultry in many regions of the world and causes continuing outbreaks in poultry populations. In the Middle East, genotype XXI, used to be present in poultry in Egypt but has been replaced by genotype VII. We investigated whether virus evolution contributed to superseding and focussed on the antigenic sites within the hemagglutinin-neuraminidase (HN) spike protein. Full-length sequences of an NDV genotype VII isolate currently circulating in Egypt was compared to a genotype XXI isolate that was present as co-infection with vaccine-type viruses (II) in a historical virus isolated in 2011. Amino acid differences in the HN glycoprotein for both XXI and VII viruses amounted to 11.7% and 11.9%, respectively, compared to the La Sota vaccine type. However, mutations within the globular head (aa 126-570), bearing relevant antigenic sites, were underrepresented (a divergence of 8.8% and 8.1% compared to 22.4% and 25.6% within the protein domains encompassing cytoplasmic tail, transmembrane part and stalk regions (aa 1-125) for genotypes XXI and VII, respectively). Nevertheless, reaction patterns of HN-specific monoclonal antibodies inhibiting receptor binding revealed differences between vaccine-type viruses and genotype XXI and VII viruses for epitopes located in the head domain. Accordingly, compared to Egyptian vaccine-type isolates and the La Sota vaccine reference strain, single aa substitutions in 6 of 10 described neutralizing epitopes of HN were found. However, the same alterations in neutralization sensitive epitopes were present in old genotype XXI as well as in newly emerged genotype VII isolates. In addition, isolates were indistinguishable by polyclonal chicken sera raised against different genotypes including vaccine viruses. These findings suggest that factors other than antigenic differences within the HN protein account for facilitating the spread of genotype VII versus genotype XXI viruses in Egypt.
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Affiliation(s)
- Mahmoud M Naguib
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.,Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agriculture Research Center, Giza, Egypt
| | - Dirk Höper
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Diagnostic Virology, Greifswald Insel-Riems, Germany
| | - Magdy F Elkady
- Department of poultry Diseases, Faculty of Veterinary Medicine, Beni-Suef University, Beni-Suef, Egypt
| | - Manal A Afifi
- Department of Poultry Diseases, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - Ahmed Erfan
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agriculture Research Center, Giza, Egypt
| | - Hassanein H Abozeid
- Department of Poultry Diseases, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - Wafaa M Hasan
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agriculture Research Center, Giza, Egypt
| | - Abdel-Satar Arafa
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agriculture Research Center, Giza, Egypt
| | - Momtaz Shahein
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agriculture Research Center, Giza, Egypt
| | - Martin Beer
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Diagnostic Virology, Greifswald Insel-Riems, Germany
| | - Timm C Harder
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Diagnostic Virology, Greifswald Insel-Riems, Germany
| | - Christian Grund
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Diagnostic Virology, Greifswald Insel-Riems, Germany
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Schön J, Breithaupt A, Höper D, King J, Pohlmann A, Parvin R, Behr KP, Schwarz BA, Beer M, Stech J, Harder T, Grund C. Neuraminidase-associated plasminogen recruitment enables systemic spread of natural avian Influenza viruses H3N1. PLoS Pathog 2021; 17:e1009490. [PMID: 33891662 PMCID: PMC8118554 DOI: 10.1371/journal.ppat.1009490] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 05/13/2021] [Accepted: 03/19/2021] [Indexed: 12/21/2022] Open
Abstract
Repeated outbreaks due to H3N1 low pathogenicity avian influenza viruses (LPAIV) in Belgium were associated with unusually high mortality in chicken in 2019. Those events caused considerable economic losses and prompted restriction measures normally implemented for eradicating high pathogenicity avian influenza viruses (HPAIV). Initial pathology investigations and infection studies suggested this virus to be able to replicate systemically, being very atypical for H3 LPAIV. Here, we investigate the pathogenesis of this H3N1 virus and propose a mechanism explaining its unusual systemic replication capability. By intravenous and intracerebral inoculation in chicken, we demonstrate systemic spread of this virus, extending to the central nervous system. Endoproteolytic viral hemagglutinin (HA) protein activation by either tissue-restricted serine peptidases or ubiquitous subtilisin-like proteases is the functional hallmark distinguishing (H5 or H7) LPAIV from HPAIV. However, luciferase reporter assays show that HA cleavage in case of the H3N1 strain in contrast to the HPAIV is not processed by intracellular proteases. Yet the H3N1 virus replicates efficiently in cell culture without trypsin, unlike LPAIVs. Moreover, this trypsin-independent virus replication is inhibited by 6-aminohexanoic acid, a plasmin inhibitor. Correspondingly, in silico analysis indicates that plasminogen is recruitable by the viral neuraminidase for proteolytic activation due to the loss of a strongly conserved N-glycosylation site at position 130. This mutation was shown responsible for plasminogen recruitment and neurovirulence of the mouse brain-passaged laboratory strain A/WSN/33 (H1N1). In conclusion, our findings provide good evidence in natural chicken strains for N1 neuraminidase-operated recruitment of plasminogen, enabling systemic replication leading to an unusual high pathogenicity phenotype. Such a gain of function in naturally occurring AIVs representing an established human influenza HA-subtype raises concerns over potential zoonotic threats. Avian influenza viruses (AIV) of subtype H3N1 caused outbreaks among gallinaceous poultry associated with an unusual high mortality in Belgium in 2019. Although those strains shared properties of a high pathogenicity (HP)-like phenotype in chicken experiments, still the viral hemagglutinin endoproteolytic cleavage site (HACS) matches that of canonical low pathogenicity (LP) AIV. Above all, the HACS motif is the molecular marker to distinguish low from high pathogenicity phenotypes in H5 and H7 AIV. Monobasic HACS motifs restrict the LPAIV to use tissue-specific host proteases and therefore confine their organ tropism to the respiratory and digestive tracts. By contrast, the polybasic HACS of HPAIV provides access to the ubiquitously expressed prohormone convertase furin, resulting in a grossly broadened organ tropism. Here, we show that the systemic spread of the Belgian H3N1 chicken viruses is independent from tissue-specific proteases and that their proteolytic HA activation is processed by plasminogen and associated to the loss of a conserved N-glycosylation site at position 130 of the neuraminidase. To date, this mechanism was only described for the mouse-adapted laboratory H1N1 strain WSN/33. Our data, however, provide evidence that this mechanism can also evolve in natural circulating AIV, as well as in human strains, suggesting a certain zoonotic potential.
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Affiliation(s)
- Jacob Schön
- Institute of Diagnostic Virology, Greifswald–Insel Riems, Germany
| | - Angele Breithaupt
- Department of Experimental Animal Facilities and Biorisk Management, Greifswald–Insel Riems, Germany
| | - Dirk Höper
- Institute of Diagnostic Virology, Greifswald–Insel Riems, Germany
| | - Jacqueline King
- Institute of Diagnostic Virology, Greifswald–Insel Riems, Germany
| | - Anne Pohlmann
- Institute of Diagnostic Virology, Greifswald–Insel Riems, Germany
| | - Rokshana Parvin
- Department of Pathology, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | | | | | - Martin Beer
- Institute of Diagnostic Virology, Greifswald–Insel Riems, Germany
| | - Jürgen Stech
- Institute of Molecular Virology and Cell Biology, Greifswald–Insel Riems, Germany
| | - Timm Harder
- Institute of Diagnostic Virology, Greifswald–Insel Riems, Germany
| | - Christian Grund
- Institute of Diagnostic Virology, Greifswald–Insel Riems, Germany
- * E-mail:
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28
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de Vries JJC, Brown JR, Couto N, Beer M, Le Mercier P, Sidorov I, Papa A, Fischer N, Oude Munnink BB, Rodriquez C, Zaheri M, Sayiner A, Hönemann M, Cataluna AP, Carbo EC, Bachofen C, Kubacki J, Schmitz D, Tsioka K, Matamoros S, Höper D, Hernandez M, Puchhammer-Stöckl E, Lebrand A, Huber M, Simmonds P, Claas ECJ, López-Labrador FX. Recommendations for the introduction of metagenomic next-generation sequencing in clinical virology, part II: bioinformatic analysis and reporting. J Clin Virol 2021; 138:104812. [PMID: 33819811 DOI: 10.1016/j.jcv.2021.104812] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 03/20/2021] [Indexed: 12/11/2022]
Abstract
Metagenomic next-generation sequencing (mNGS) is an untargeted technique for determination of microbial DNA/RNA sequences in a variety of sample types from patients with infectious syndromes. mNGS is still in its early stages of broader translation into clinical applications. To further support the development, implementation, optimization and standardization of mNGS procedures for virus diagnostics, the European Society for Clinical Virology (ESCV) Network on Next-Generation Sequencing (ENNGS) has been established. The aim of ENNGS is to bring together professionals involved in mNGS for viral diagnostics to share methodologies and experiences, and to develop application guidelines. Following the ENNGS publication Recommendations for the introduction of mNGS in clinical virology, part I: wet lab procedure in this journal, the current manuscript aims to provide practical recommendations for the bioinformatic analysis of mNGS data and reporting of results to clinicians.
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Affiliation(s)
- Jutte J C de Vries
- Clinical Microbiological Laboratory, department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands.
| | - Julianne R Brown
- Microbiology, Virology and Infection Prevention & Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom.
| | - Natacha Couto
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom.
| | - Martin Beer
- Friedrich-Loeffler-Institute, Institute of Diagnostic Virology, Greifswald, Germany.
| | | | - Igor Sidorov
- Clinical Microbiological Laboratory, department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands.
| | - Anna Papa
- Department of Microbiology, Medical School, Aristotle University of Thessaloniki, Greece.
| | - Nicole Fischer
- University Medical Center Hamburg-Eppendorf, UKE Institute for Medical Microbiology, Virology and Hygiene, Germany.
| | | | - Christophe Rodriquez
- Department of Virology, University hospital Henri Mondor, Assistance Public des Hopitaux de Paris, Créteil, France.
| | - Maryam Zaheri
- Institute of Medical Virology, University of Zurich, Switzerland.
| | - Arzu Sayiner
- Dokuz Eylul University, Medical Faculty, Department of Medical Microbiology, Izmir, Turkey.
| | - Mario Hönemann
- Institute of Virology, Leipzig University, Leipzig, Germany.
| | - Alba Perez Cataluna
- Department of Preservation and Food Safety Technologies, IATA-CSIC, Paterna, Valencia, Spain.
| | - Ellen C Carbo
- Clinical Microbiological Laboratory, department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands.
| | | | - Jakub Kubacki
- Institute of Virology, University of Zurich, Switzerland.
| | - Dennis Schmitz
- RIVM National Institute for Public Health and Environment, Bilthoven, the Netherlands.
| | - Katerina Tsioka
- Department of Microbiology, Medical School, Aristotle University of Thessaloniki, Greece.
| | - Sébastien Matamoros
- Medical Microbiology and Infection Control, Amsterdam UMC, Amsterdam, the Netherlands.
| | - Dirk Höper
- Friedrich-Loeffler-Institute, Institute of Diagnostic Virology, Greifswald, Germany.
| | - Marta Hernandez
- Laboratory of Molecular Biology and Microbiology, Instituto Tecnologico Agrario de Castilla y Leon, Valladolid, Spain.
| | | | | | - Michael Huber
- Institute of Medical Virology, University of Zurich, Switzerland.
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - Eric C J Claas
- Clinical Microbiological Laboratory, department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands.
| | - F Xavier López-Labrador
- Virology Laboratory, Genomics and Health Area, Centre for Public Health Research (FISABIO-Public Health), Valencia, Spain; Department of Microbiology, Medical School, University of Valencia, Spain; CIBERESP, Instituto de Salud Carlos III, Madrid, Spain.
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Billenkamp F, Schnabel K, Hüther L, Frahm J, von Soosten D, Meyer U, Höper D, Beer M, Seyboldt C, Neubauer H, Dänicke S. No hints at glyphosate-induced ruminal dysbiosis in cows. NPJ Biofilms Microbiomes 2021; 7:30. [PMID: 33767196 PMCID: PMC7994389 DOI: 10.1038/s41522-021-00198-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 02/12/2021] [Indexed: 01/31/2023] Open
Abstract
Glyphosate-based herbicides are among the most used non-selective herbicides worldwide and inhibit synthesis of aromatic amino acids in plants, bacteria, and fungi. Given the broad usage, controversies concerning potential effects of glyphosate on health and especially on gut microbiomes arose. For cattle, it has been proposed based on in vitro data that glyphosate has detrimental effects on the ruminal microbiome, which manifest as a specific inhibition of bacteria involved in fiber degradation and as an enrichment of specific pathogens. In the present study, glyphosate effects on the ruminal microbiome were analyzed in vivo using glyphosate contaminated feedstuffs with strong differences in dietary fiber and dietary energy content in order to reproduce the proposed detrimental glyphosate effects on the rumen microbiome. While significant impact of dietary factors on the ruminal microbiome and its products are pointed out, no adverse glyphosate effects on ruminal microbiome composition, diversity, and microbial metabolites are observed.
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Affiliation(s)
- Fabian Billenkamp
- Institute of Animal Nutrition, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institute, Brunswick, Germany.
| | - Karina Schnabel
- Institute of Animal Nutrition, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institute, Brunswick, Germany
| | - Liane Hüther
- Institute of Animal Nutrition, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institute, Brunswick, Germany
| | - Jana Frahm
- Institute of Animal Nutrition, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institute, Brunswick, Germany
| | - Dirk von Soosten
- Institute of Animal Nutrition, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institute, Brunswick, Germany
| | - Ulrich Meyer
- Institute of Animal Nutrition, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institute, Brunswick, Germany
| | - Dirk Höper
- Institute of Diagnostic Virology, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institute, Greifswald-Riems, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institute, Greifswald-Riems, Germany
| | - Christian Seyboldt
- Institute of Bacterial Infections and Zoonoses, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institute, Jena, Germany
| | - Heinrich Neubauer
- Institute of Bacterial Infections and Zoonoses, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institute, Jena, Germany
| | - Sven Dänicke
- Institute of Animal Nutrition, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institute, Brunswick, Germany
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Alleweldt F, Kara Ş, Best K, Aarestrup FM, Beer M, Bestebroer TM, Campos J, Casadei G, Chinen I, Van Domselaar G, Dominguez C, Everett HE, Fouchier RA, Grant K, Green J, Höper D, Johnston J, Koopmans MP, Oude Munnink BB, Myers R, Nadon C, Patel A, Pohlmann A, Pongolini S, Reimer A, Thiessen S, Wylezich C. Economic evaluation of whole genome sequencing for pathogen identification and surveillance - results of case studies in Europe and the Americas 2016 to 2019. ACTA ACUST UNITED AC 2021; 26. [PMID: 33663647 PMCID: PMC7934224 DOI: 10.2807/1560-7917.es.2021.26.9.1900606] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Background Whole genome sequencing (WGS) is increasingly used for pathogen identification and surveillance. Aim We evaluated costs and benefits of routine WGS through case studies at eight reference laboratories in Europe and the Americas which conduct pathogen surveillance for avian influenza (two laboratories), human influenza (one laboratory) and food-borne pathogens (five laboratories). Methods The evaluation focused on the institutional perspective, i.e. the ‘investment case’ for implementing WGS compared with conventional methods, based on costs and benefits during a defined reference period, mostly covering at least part of 2017. A break-even analysis estimated the number of cases of illness (for the example of Salmonella surveillance) that would need to be avoided through WGS in order to ‘break even’ on costs. Results On a per-sample basis, WGS was between 1.2 and 4.3 times more expensive than routine conventional methods. However, WGS brought major benefits for pathogen identification and surveillance, substantially changing laboratory workflows, analytical processes and outbreaks detection and control. Between 0.2% and 1.1% (on average 0.7%) of reported salmonellosis cases would need to be prevented to break even with respect to the additional costs of WGS. Conclusions Even at cost levels documented here, WGS provides a level of additional information that more than balances the additional costs if used effectively. The substantial cost differences for WGS between reference laboratories were due to economies of scale, degree of automation, sequencing technology used and institutional discounts for equipment and consumables, as well as the extent to which sequencers are used at full capacity.
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Affiliation(s)
| | | | | | - Frank M Aarestrup
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Martin Beer
- Friedrich-Loeffler-Institut, Greifswald, Germany
| | | | | | - Gabriele Casadei
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Parma, Italy
| | - Isabel Chinen
- INEI-ANLIS Dr Carlos G Malbrán, Buenos Aires, Argentina
| | | | | | | | - Ron Am Fouchier
- Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Kathie Grant
- Retired.,Public Health England, London, United Kingdom
| | | | - Dirk Höper
- Friedrich-Loeffler-Institut, Greifswald, Germany
| | | | | | | | - Robert Myers
- Maryland Department of Health, Baltimore, United States
| | - Celine Nadon
- Public Health Agency of Canada, Winnipeg, Canada
| | - Ami Patel
- Maryland Department of Health, Baltimore, United States
| | | | - Stefano Pongolini
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Parma, Italy
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Santos PD, Michel F, Wylezich C, Höper D, Keller M, Holicki CM, Szentiks CA, Eiden M, Muluneh A, Neubauer-Juric A, Thalheim S, Globig A, Beer M, Groschup MH, Ziegler U. Co-infections: Simultaneous detections of West Nile virus and Usutu virus in birds from Germany. Transbound Emerg Dis 2021; 69:776-792. [PMID: 33655706 DOI: 10.1111/tbed.14050] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/18/2021] [Accepted: 02/25/2021] [Indexed: 12/22/2022]
Abstract
The emergence of West Nile virus (WNV) and Usutu virus (USUV) in Europe resulted in significant outbreaks leading to avifauna mortality and human infections. Both viruses have overlapping geographical, host and vector ranges, and are often co-circulating in Europe. In Germany, a nationwide bird surveillance network was established to monitor these zoonotic arthropod-borne viruses in migratory and resident birds. In this framework, co-infections with WNV and USUV were detected in six dead birds collected in 2018 and 2019. Genomic sequencing and phylogenetic analyses classified the detected WNV strains as lineage 2 and the USUV strains as lineages Africa 2 (n = 2), Africa 3 (n = 3) and Europe 2 (n = 1). Preliminary attempts to co-propagate both viruses in vitro failed. However, we successfully cultivated WNV from two animals. Further evidence for WNV-USUV co-infection was obtained by sampling live birds in four zoological gardens with confirmed WNV cases. Three snowy owls had high neutralizing antibody titres against both WNV and USUV, of which two were also positive for USUV-RNA. In conclusion, further reports of co-infections in animals as well as in humans are expected in the future, particularly in areas where both viruses are present in the vector population.
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Affiliation(s)
- Pauline Dianne Santos
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Friederike Michel
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Claudia Wylezich
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Dirk Höper
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Markus Keller
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Cora M Holicki
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | | | - Martin Eiden
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Aemero Muluneh
- Saxon State Laboratory of Health and Veterinary Affairs, Dresden, Germany
| | | | - Sabine Thalheim
- Berlin-Brandenburg State Laboratory, Frankfurt (Oder), Germany
| | - Anja Globig
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Martin H Groschup
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany.,German Centre for Infection Research, partner site Hamburg-Luebeck-Borstel-Riems, Hamburg, Germany
| | - Ute Ziegler
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany.,German Centre for Infection Research, partner site Hamburg-Luebeck-Borstel-Riems, Hamburg, Germany
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Wylezich C, Calvelage S, Schlottau K, Ziegler U, Pohlmann A, Höper D, Beer M. Next-generation diagnostics: virus capture facilitates a sensitive viral diagnosis for epizootic and zoonotic pathogens including SARS-CoV-2. Microbiome 2021; 9:51. [PMID: 33610182 DOI: 10.1186/s40168-020-00973-z/figures/4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 12/07/2020] [Indexed: 05/18/2023]
Abstract
BACKGROUND The detection of pathogens in clinical and environmental samples using high-throughput sequencing (HTS) is often hampered by large amounts of background information, which is especially true for viruses with small genomes. Enormous sequencing depth can be necessary to compile sufficient information for identification of a certain pathogen. Generic HTS combining with in-solution capture enrichment can markedly increase the sensitivity for virus detection in complex diagnostic samples. METHODS A virus panel based on the principle of biotinylated RNA baits was developed for specific capture enrichment of epizootic and zoonotic viruses (VirBaits). The VirBaits set was supplemented by a SARS-CoV-2 predesigned bait set for testing recent SARS-CoV-2-positive samples. Libraries generated from complex samples were sequenced via generic HTS (without enrichment) and afterwards enriched with the VirBaits set. For validation, an internal proficiency test for emerging epizootic and zoonotic viruses (African swine fever virus, Ebolavirus, Marburgvirus, Nipah henipavirus, Rift Valley fever virus) was conducted. RESULTS The VirBaits set consists of 177,471 RNA baits (80-mer) based on about 18,800 complete viral genomes targeting 35 epizootic and zoonotic viruses. In all tested samples, viruses with both DNA and RNA genomes were clearly enriched ranging from about 10-fold to 10,000-fold for viruses including distantly related viruses with at least 72% overall identity to viruses represented in the bait set. Viruses showing a lower overall identity (38% and 46%) to them were not enriched but could nonetheless be detected based on capturing conserved genome regions. The internal proficiency test supports the improved virus detection using the combination of HTS plus targeted enrichment but also points to the risk of cross-contamination between samples. CONCLUSIONS The VirBaits approach showed a high diagnostic performance, also for distantly related viruses. The bait set is modular and expandable according to the favored diagnostics, health sector, or research question. The risk of cross-contamination needs to be taken into consideration. The application of the RNA-baits principle turned out to be user friendly, and even non-experts can easily use the VirBaits workflow. The rapid extension of the established VirBaits set adapted to actual outbreak events is possible as shown for SARS-CoV-2. Video abstract.
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Affiliation(s)
- Claudia Wylezich
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald-Insel Riems, Germany.
| | - Sten Calvelage
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald-Insel Riems, Germany
| | - Kore Schlottau
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald-Insel Riems, Germany
| | - Ute Ziegler
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald-Insel Riems, Germany
| | - Anne Pohlmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald-Insel Riems, Germany
| | - Dirk Höper
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald-Insel Riems, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald-Insel Riems, Germany
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Wylezich C, Calvelage S, Schlottau K, Ziegler U, Pohlmann A, Höper D, Beer M. Next-generation diagnostics: virus capture facilitates a sensitive viral diagnosis for epizootic and zoonotic pathogens including SARS-CoV-2. Microbiome 2021; 9:51. [PMID: 33610182 PMCID: PMC7896545 DOI: 10.1186/s40168-020-00973-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 12/07/2020] [Indexed: 05/15/2023]
Abstract
BACKGROUND The detection of pathogens in clinical and environmental samples using high-throughput sequencing (HTS) is often hampered by large amounts of background information, which is especially true for viruses with small genomes. Enormous sequencing depth can be necessary to compile sufficient information for identification of a certain pathogen. Generic HTS combining with in-solution capture enrichment can markedly increase the sensitivity for virus detection in complex diagnostic samples. METHODS A virus panel based on the principle of biotinylated RNA baits was developed for specific capture enrichment of epizootic and zoonotic viruses (VirBaits). The VirBaits set was supplemented by a SARS-CoV-2 predesigned bait set for testing recent SARS-CoV-2-positive samples. Libraries generated from complex samples were sequenced via generic HTS (without enrichment) and afterwards enriched with the VirBaits set. For validation, an internal proficiency test for emerging epizootic and zoonotic viruses (African swine fever virus, Ebolavirus, Marburgvirus, Nipah henipavirus, Rift Valley fever virus) was conducted. RESULTS The VirBaits set consists of 177,471 RNA baits (80-mer) based on about 18,800 complete viral genomes targeting 35 epizootic and zoonotic viruses. In all tested samples, viruses with both DNA and RNA genomes were clearly enriched ranging from about 10-fold to 10,000-fold for viruses including distantly related viruses with at least 72% overall identity to viruses represented in the bait set. Viruses showing a lower overall identity (38% and 46%) to them were not enriched but could nonetheless be detected based on capturing conserved genome regions. The internal proficiency test supports the improved virus detection using the combination of HTS plus targeted enrichment but also points to the risk of cross-contamination between samples. CONCLUSIONS The VirBaits approach showed a high diagnostic performance, also for distantly related viruses. The bait set is modular and expandable according to the favored diagnostics, health sector, or research question. The risk of cross-contamination needs to be taken into consideration. The application of the RNA-baits principle turned out to be user friendly, and even non-experts can easily use the VirBaits workflow. The rapid extension of the established VirBaits set adapted to actual outbreak events is possible as shown for SARS-CoV-2. Video abstract.
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Affiliation(s)
- Claudia Wylezich
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald-Insel Riems, Germany.
| | - Sten Calvelage
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald-Insel Riems, Germany
| | - Kore Schlottau
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald-Insel Riems, Germany
| | - Ute Ziegler
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald-Insel Riems, Germany
| | - Anne Pohlmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald-Insel Riems, Germany
| | - Dirk Höper
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald-Insel Riems, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald-Insel Riems, Germany
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Calvelage S, Tammiranta N, Nokireki T, Gadd T, Eggerbauer E, Zaeck LM, Potratz M, Wylezich C, Höper D, Müller T, Finke S, Freuling CM. Genetic and Antigenetic Characterization of the Novel Kotalahti Bat Lyssavirus (KBLV). Viruses 2021; 13:v13010069. [PMID: 33419096 PMCID: PMC7825429 DOI: 10.3390/v13010069] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/14/2020] [Accepted: 12/17/2020] [Indexed: 02/07/2023] Open
Abstract
There is a growing diversity of bat-associated lyssaviruses in the Old World. In August 2017, a dead Brandt’s bat (Myotis brandtii) tested positive for rabies and based on partial sequence analysis, the novel Kotalahti bat lyssavirus (KBLV) was identified. Because the bat was in an autolyzed state, isolation of KBLV was neither successful after three consecutive cell passages on cells nor in mice. Next generation sequencing (NGS) was applied using Ion Torrent ™ S5 technology coupled with target enrichment via hybridization-based capture (myBaits®) was used to sequence 99% of the genome, comprising of 11,878 nucleotides (nt). KBLV is most closely related to EBLV-2 (78.7% identity), followed by KHUV (79.0%) and BBLV (77.6%), supporting the assignment as phylogroup I lyssavirus. Interestingly, all of these lyssaviruses were also isolated from bat species of the genus Myotis, thus supporting that M. brandtii is likely the reservoir host. All information on antigenic and genetic divergence fulfil the species demarcation criteria by ICTV, so that we recommend KBLV as a novel species within the Lyssavirus genus. Next to sequence analyses, assignment to phylogroup I was functionally corroborated by cross-neutralization of G-deleted RABV, pseudotyped with KBLV-G by sera from RABV vaccinated humans. This suggests that conventional RABV vaccines also confer protection against the novel KBLV.
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Affiliation(s)
- Sten Calvelage
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut (FLI), 17493 Greifswald-Insel Riems, Germany; (S.C.); (C.W.); (D.H.)
| | - Niina Tammiranta
- Finnish Food Authority, Research Department, Virology Unit, Mustialankatu 3, FI-00790 Helsinki, Finland; (N.T.); (T.N.); (T.G.)
| | - Tiina Nokireki
- Finnish Food Authority, Research Department, Virology Unit, Mustialankatu 3, FI-00790 Helsinki, Finland; (N.T.); (T.N.); (T.G.)
| | - Tuija Gadd
- Finnish Food Authority, Research Department, Virology Unit, Mustialankatu 3, FI-00790 Helsinki, Finland; (N.T.); (T.N.); (T.G.)
| | - Elisa Eggerbauer
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut (FLI), WHO Collaborating Centre for Rabies Surveillance and Research, OIE Reference Laboratory for Rabies, 17493 Greifswald-Insel Riems, Germany; (E.E.); (L.M.Z.); (M.P.); (T.M.); (S.F.)
| | - Luca M. Zaeck
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut (FLI), WHO Collaborating Centre for Rabies Surveillance and Research, OIE Reference Laboratory for Rabies, 17493 Greifswald-Insel Riems, Germany; (E.E.); (L.M.Z.); (M.P.); (T.M.); (S.F.)
| | - Madlin Potratz
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut (FLI), WHO Collaborating Centre for Rabies Surveillance and Research, OIE Reference Laboratory for Rabies, 17493 Greifswald-Insel Riems, Germany; (E.E.); (L.M.Z.); (M.P.); (T.M.); (S.F.)
| | - Claudia Wylezich
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut (FLI), 17493 Greifswald-Insel Riems, Germany; (S.C.); (C.W.); (D.H.)
| | - Dirk Höper
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut (FLI), 17493 Greifswald-Insel Riems, Germany; (S.C.); (C.W.); (D.H.)
| | - Thomas Müller
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut (FLI), WHO Collaborating Centre for Rabies Surveillance and Research, OIE Reference Laboratory for Rabies, 17493 Greifswald-Insel Riems, Germany; (E.E.); (L.M.Z.); (M.P.); (T.M.); (S.F.)
| | - Stefan Finke
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut (FLI), WHO Collaborating Centre for Rabies Surveillance and Research, OIE Reference Laboratory for Rabies, 17493 Greifswald-Insel Riems, Germany; (E.E.); (L.M.Z.); (M.P.); (T.M.); (S.F.)
| | - Conrad M. Freuling
- Central Duties, Friedrich-Loeffler-Institut (FLI), 17493 Greifswald-Insel Riems, Germany
- Correspondence:
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Ebinger A, Fischer S, Höper D. A theoretical and generalized approach for the assessment of the sample-specific limit of detection for clinical metagenomics. Comput Struct Biotechnol J 2020; 19:732-742. [PMID: 33552445 PMCID: PMC7822954 DOI: 10.1016/j.csbj.2020.12.040] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 12/16/2020] [Accepted: 12/24/2020] [Indexed: 12/18/2022] Open
Abstract
Metagenomics is a powerful tool to identify novel or unexpected pathogens, since it is generic and relatively unbiased. The limit of detection (LOD) is a critical parameter for the routine application of methods in the clinical diagnostic context. Although attempts for the determination of LODs for metagenomics next-generation sequencing (mNGS) have been made previously, these were only applicable for specific target species in defined samples matrices. Therefore, we developed and validated a generalized probability-based model to assess the sample-specific LOD of mNGS experiments (LODmNGS). Initial rarefaction analyses with datasets of Borna disease virus 1 human encephalitis cases revealed a stochastic behavior of virus read detection. Based on this, we transformed the Bernoulli formula to predict the minimal necessary dataset size to detect one virus read with a probability of 99%. We validated the formula with 30 datasets from diseased individuals, resulting in an accuracy of 99.1% and an average of 4.5 ± 0.4 viral reads found in the calculated minimal dataset size. We demonstrated by modeling the virus genome size, virus-, and total RNA-concentration that the main determinant of mNGS sensitivity is the virus-sample background ratio. The predicted LODmNGS for the respective pathogenic virus in the datasets were congruent with the virus-concentration determined by RT-qPCR. Theoretical assumptions were further confirmed by correlation analysis of mNGS and RT-qPCR data from the samples of the analyzed datasets. This approach should guide standardization of mNGS application, due to the generalized concept of LODmNGS.
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Affiliation(s)
- Arnt Ebinger
- Institute for Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald-Insel Riems, Mecklenburg-Western Pomerania, Germany
| | - Susanne Fischer
- Institute of Infectology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald-Insel Riems, Mecklenburg-Western Pomerania, Germany
| | - Dirk Höper
- Institute for Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald-Insel Riems, Mecklenburg-Western Pomerania, Germany
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Kuhn JH, Adkins S, Alioto D, Alkhovsky SV, Amarasinghe GK, Anthony SJ, Avšič-Županc T, Ayllón MA, Bahl J, Balkema-Buschmann A, Ballinger MJ, Bartonička T, Basler C, Bavari S, Beer M, Bente DA, Bergeron É, Bird BH, Blair C, Blasdell KR, Bradfute SB, Breyta R, Briese T, Brown PA, Buchholz UJ, Buchmeier MJ, Bukreyev A, Burt F, Buzkan N, Calisher CH, Cao M, Casas I, Chamberlain J, Chandran K, Charrel RN, Chen B, Chiumenti M, Choi IR, Clegg JCS, Crozier I, da Graça JV, Dal Bó E, Dávila AMR, de la Torre JC, de Lamballerie X, de Swart RL, Di Bello PL, Di Paola N, Di Serio F, Dietzgen RG, Digiaro M, Dolja VV, Dolnik O, Drebot MA, Drexler JF, Dürrwald R, Dufkova L, Dundon WG, Duprex WP, Dye JM, Easton AJ, Ebihara H, Elbeaino T, Ergünay K, Fernandes J, Fooks AR, Formenty PBH, Forth LF, Fouchier RAM, Freitas-Astúa J, Gago-Zachert S, Gāo GF, García ML, García-Sastre A, Garrison AR, Gbakima A, Goldstein T, Gonzalez JPJ, Griffiths A, Groschup MH, Günther S, Guterres A, Hall RA, Hammond J, Hassan M, Hepojoki J, Hepojoki S, Hetzel U, Hewson R, Hoffmann B, Hongo S, Höper D, Horie M, Hughes HR, Hyndman TH, Jambai A, Jardim R, Jiāng D, Jin Q, Jonson GB, Junglen S, Karadağ S, Keller KE, Klempa B, Klingström J, Kobinger G, Kondō H, Koonin EV, Krupovic M, Kurath G, Kuzmin IV, Laenen L, Lamb RA, Lambert AJ, Langevin SL, Lee B, Lemos ERS, Leroy EM, Li D, Lǐ J, Liang M, Liú W, Liú Y, Lukashevich IS, Maes P, Marciel de Souza W, Marklewitz M, Marshall SH, Martelli GP, Martin RR, Marzano SYL, Massart S, McCauley JW, Mielke-Ehret N, Minafra A, Minutolo M, Mirazimi A, Mühlbach HP, Mühlberger E, Naidu R, Natsuaki T, Navarro B, Navarro JA, Netesov SV, Neumann G, Nowotny N, Nunes MRT, Nylund A, Økland AL, Oliveira RC, Palacios G, Pallas V, Pályi B, Papa A, Parrish CR, Pauvolid-Corrêa A, Pawęska JT, Payne S, Pérez DR, Pfaff F, Radoshitzky SR, Rahman AU, Ramos-González PL, Resende RO, Reyes CA, Rima BK, Romanowski V, Robles Luna G, Rota P, Rubbenstroth D, Runstadler JA, Ruzek D, Sabanadzovic S, Salát J, Sall AA, Salvato MS, Sarpkaya K, Sasaya T, Schwemmle M, Shabbir MZ, Shí X, Shí Z, Shirako Y, Simmonds P, Širmarová J, Sironi M, Smither S, Smura T, Song JW, Spann KM, Spengler JR, Stenglein MD, Stone DM, Straková P, Takada A, Tesh RB, Thornburg NJ, Tomonaga K, Tordo N, Towner JS, Turina M, Tzanetakis I, Ulrich RG, Vaira AM, van den Hoogen B, Varsani A, Vasilakis N, Verbeek M, Wahl V, Walker PJ, Wang H, Wang J, Wang X, Wang LF, Wèi T, Wells H, Whitfield AE, Williams JV, Wolf YI, Wú Z, Yang X, Yáng X, Yu X, Yutin N, Zerbini FM, Zhang T, Zhang YZ, Zhou G, Zhou X. 2020 taxonomic update for phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales. Arch Virol 2020; 165:3023-3072. [PMID: 32888050 PMCID: PMC7606449 DOI: 10.1007/s00705-020-04731-2] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 07/04/2020] [Indexed: 12/13/2022]
Abstract
In March 2020, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. At the genus rank, 20 new genera were added, two were deleted, one was moved, and three were renamed. At the species rank, 160 species were added, four were deleted, ten were moved and renamed, and 30 species were renamed. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.
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Affiliation(s)
- Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA.
| | - Scott Adkins
- United States Department of Agriculture, Agricultural Research Service, US Horticultural Research Laboratory, Fort Pierce, FL, USA
| | - Daniela Alioto
- Dipartimento di Agraria, Università degli Studi di Napoli Federico II, Portici, Italy
| | - Sergey V Alkhovsky
- D.I. Ivanovsky Institute of Virology of N.F. Gamaleya National Center on Epidemiology and Microbiology of Ministry of Health of Russian Federation, Moscow, Russia
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Simon J Anthony
- Mailman School of Public Health, Columbia University, New York, NY, USA
- EcoHealth Alliance, New York, NY, USA
| | | | - María A Ayllón
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Justin Bahl
- Department of Infectious Diseases, Department of Epidemiology and Biostatistics, Institute of Bioinformatics, Center for Ecology of Infectious Diseases, University of Georgia, Athens, GA, USA
| | - Anne Balkema-Buschmann
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Novel and Emerging Infectious Diseases, Greifswald-Insel Riems, Germany
| | - Matthew J Ballinger
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Tomáš Bartonička
- Department of Botany and Zoology, Masaryk University, Brno, Czech Republic
| | - Christopher Basler
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Sina Bavari
- Edge BioInnovation Consulting and Mgt, Frederick, MD, USA
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Dennis A Bente
- Galveston National Laboratory, The University of Texas, Medical Branch at Galveston, Galveston, TX, USA
| | - Éric Bergeron
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Brian H Bird
- School of Veterinary Medicine, One Health Institute, University of California, Davis, CA, USA
| | - Carol Blair
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Kim R Blasdell
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Steven B Bradfute
- University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Rachel Breyta
- US Geological Survey, Western Fisheries Research Center, Seattle, WA, USA
| | - Thomas Briese
- Department of Epidemiology, Mailman School of Public Health, Center for Infection and Immunity, Columbia University, New York, NY, USA
| | - Paul A Brown
- Laboratory of Ploufragan-Plouzané-Niort, French Agency for Food, Environmental and Occupational Heath Safety ANSES, Ploufragan, France
| | - Ursula J Buchholz
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Michael J Buchmeier
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA
| | - Alexander Bukreyev
- Galveston National Laboratory, The University of Texas, Medical Branch at Galveston, Galveston, TX, USA
- Department of Pathology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Felicity Burt
- Division of Virology, National Health Laboratory Service, University of the Free State, Bloemfontein, Republic of South Africa
| | - Nihal Buzkan
- Department of Plant Protection, Faculty of Agriculture, Kahramanmaras Sütçü Imam University, Avsar Campus, 46060, Kahramanmaras, Turkey
| | | | - Mengji Cao
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, 400712, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Inmaculada Casas
- Respiratory Virus and Influenza Unit, National Microbiology Center, Instituto de Salud Carlos III, Madrid, Spain
| | - John Chamberlain
- Virology and Pathogenesis Group, National Infection Service, Public Health England, Porton Down, UK
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Rémi N Charrel
- Unité des Virus Emergents (Aix-Marseille Univ-IRD 190-Inserm 1207-IHU Méditerranée Infection), Marseille, France
| | - Biao Chen
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangdong, China
| | - Michela Chiumenti
- Istituto per la Protezione Sostenibile delle Piante-Consiglio Nazionale delle ricerche (Institute for Sustainable Plant Protection-National Research Council), Bari, Italy
| | - Il-Ryong Choi
- Plant Breeding Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines
| | | | - Ian Crozier
- Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - John V da Graça
- Texas A&M University-Kingsville Citrus Center, Weslaco, TX, USA
| | - Elena Dal Bó
- CIDEFI. Facultad de Ciencias Agrarias y Forestales, Universidad de La Plata, La Plata, Argentina
| | - Alberto M R Dávila
- Laboratório de Biologia Computacional e Sistemas, Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
| | - Juan Carlos de la Torre
- Department of Immunology and Microbiology IMM-6, The Scripps Research Institute, La Jolla, CA, USA
| | - Xavier de Lamballerie
- Unité des Virus Emergents (Aix-Marseille Univ-IRD 190-Inserm 1207-IHU Méditerranée Infection), Marseille, France
| | - Rik L de Swart
- Department Viroscience, Erasmus MC University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Patrick L Di Bello
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Nicholas Di Paola
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Francesco Di Serio
- Istituto per la Protezione Sostenibile delle Piante-Consiglio Nazionale delle ricerche (Institute for Sustainable Plant Protection-National Research Council), Bari, Italy
| | - Ralf G Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | - Michele Digiaro
- CIHEAM, Istituto Agronomico Mediterraneo di Bari, Valenzano, Italy
| | - Valerian V Dolja
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Olga Dolnik
- Institute of Virology, Philipps University Marburg, Marburg, Germany
| | - Michael A Drebot
- Zoonotic Diseases and Special Pathogens, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Jan Felix Drexler
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Berlin, Germany
| | | | | | - William G Dundon
- Animal Production and Health Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Vienna, Austria
| | - W Paul Duprex
- School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - John M Dye
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Andrew J Easton
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Hideki Ebihara
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Koray Ergünay
- Virology Unit, Department of Medical Microbiology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Jorlan Fernandes
- Laboratório de Hantaviroses e Rickettsioses, Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
| | | | | | - Leonie F Forth
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Ron A M Fouchier
- Department Viroscience, Erasmus MC University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | | | - Selma Gago-Zachert
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Halle/Saale, Germany
| | - George Fú Gāo
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - María Laura García
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, CONICET UNLP, La Plata, Argentina
| | | | - Aura R Garrison
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Aiah Gbakima
- Metabiota, Inc. Sierra Leone, Freetown, Sierra Leone
| | - Tracey Goldstein
- One Health Institute, Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Jean-Paul J Gonzalez
- Department of Microbiology and Immunology, Division of Biomedical Graduate Research Organization, School of Medicine, Georgetown University, Washington, DC, 20057, USA
- Centaurus Biotechnologies, CTP, Manassas, VA, USA
| | - Anthony Griffiths
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA, USA
| | - Martin H Groschup
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Novel and Emerging Infectious Diseases, Greifswald-Insel Riems, Germany
| | - Stephan Günther
- Department of Virology, Bernhard-Nocht Institute for Tropical Medicine, WHO Collaborating Centre for Arboviruses and Hemorrhagic Fever Reference and Research, Hamburg, Germany
| | - Alexandro Guterres
- Laboratório de Hantaviroses e Rickettsioses, Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
| | - Roy A Hall
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - John Hammond
- United States Department of Agriculture, Agricultural Research Service, USNA, Floral and Nursery Plants Research Unit, Beltsville, MD, USA
| | - Mohamed Hassan
- Department of Agricultural Botany, Faculty of Agriculture, Fayoum University, Fayoum, Egypt
| | - Jussi Hepojoki
- Department of Virology, University of Helsinki, Medicum, Helsinki, Finland
- Vetsuisse Faculty, Institute of Veterinary Pathology, University of Zurich, Zurich, Switzerland
| | - Satu Hepojoki
- Department of Virology, University of Helsinki, Medicum, Helsinki, Finland
- Mobidiag Ltd, Espoo, Finland
| | - Udo Hetzel
- Institute of Veterinary Pathology, University of Zuerich, Zurich, Switzerland
| | - Roger Hewson
- Public Health England, Porton Down, Salisbury, Wiltshire, UK
| | - Bernd Hoffmann
- Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Seiji Hongo
- Department of Infectious Diseases, Faculty of Medicine, Yamagata University, Yamagata, Japan
| | - Dirk Höper
- Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Masayuki Horie
- Hakubi Center for Advanced Research, Kyoto University, Kyoto, Japan
| | - Holly R Hughes
- Centers for Disease Control and Prevention, Fort Collins, CO, USA
| | - Timothy H Hyndman
- School of Veterinary Medicine, Murdoch University, Murdoch, WA, Australia
| | - Amara Jambai
- Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Rodrigo Jardim
- Laboratório de Biologia Computacional e Sistemas, Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
| | - Dàohóng Jiāng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Qi Jin
- Ministry of Health Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Gilda B Jonson
- Department of Agricultural Biotechnology, Center for Fungal Pathogenesis, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Sandra Junglen
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Berlin, Germany
- German Center for Infection Research (DZIF), Berlin, Germany
| | - Serpil Karadağ
- Republic Of Turkey Ministry Of Agriculture And Forestry, Pistachio Research Institute, Gaziantep, Turkey
| | - Karen E Keller
- United States Department of Agriculture, Agricultural Research Service, Horticulture Crops Research Unit, Corvallis, OR, USA
| | - Boris Klempa
- Institute of Virology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Jonas Klingström
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Gary Kobinger
- Department of Microbiology, Immunology and Infectious Diseases, Université Laval, Quebec City, Canada
| | - Hideki Kondō
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Paris, France
| | - Gael Kurath
- US Geological Survey Western Fisheries Research Center, Seattle, WA, USA
| | - Ivan V Kuzmin
- US Department of Agriculture, Animal and Plant Health Inspection, National Veterinary Services Laboratories, Diagnostic Virology Laboratory, Ames, USA
| | - Lies Laenen
- Zoonotic Infectious Diseases Unit, KU Leuven, Rega Institute, Leuven, Belgium
- Department of Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Robert A Lamb
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
- Howard Hughes Medical Institute, Northwestern University, Evanston, IL, USA
| | - Amy J Lambert
- Centers for Disease Control and Prevention, Fort Collins, CO, USA
| | | | - Benhur Lee
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Elba R S Lemos
- Laboratório de Hantaviroses e Rickettsioses, Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
| | - Eric M Leroy
- MIVEGEC (IRD-CNRS-Montpellier university) Unit, French National Research Institute for Sustainable Development (IRD), Montpellier, France
| | - Dexin Li
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jiànróng Lǐ
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
| | - Mifang Liang
- Key Laboratory for Medical Virology, NHFPC, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Wénwén Liú
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yàn Liú
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Igor S Lukashevich
- Department of Pharmacology and Toxicology, School of Medicine, The Center for Predictive Medicine for Biodefense and Emerging Infectious Diseases, University of Louisville, Louisville, KY, USA
| | - Piet Maes
- Department of Agricultural Biotechnology, Center for Fungal Pathogenesis, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | | | - Marco Marklewitz
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Berlin, Germany
- German Center for Infection Research (DZIF), Berlin, Germany
| | - Sergio H Marshall
- Pontificia Universidad Católica de Valparaíso, Campus Curauma, Valparaíso, Chile
| | - Giovanni P Martelli
- Department of Plant, Soil and Food Sciences, University "Aldo Moro", Bari, Italy
| | - Robert R Martin
- United States Department of Agriculture, Horticultural Crops Research Unit, Corvallis, OR, USA
| | - Shin-Yi L Marzano
- Department of Biology and Microbiology, Department of Plant Sciences, South Dakota State University, Brookings, SD, USA
| | - Sébastien Massart
- Gembloux Agro-Bio Tech, TERRA, Plant Pathology Laboratory, Liège University, Liège, Belgium
| | - John W McCauley
- Worldwide Influenza Centre, Francis Crick Institute, London, UK
| | | | - Angelantonio Minafra
- Istituto per la Protezione Sostenibile delle Piante-Consiglio Nazionale delle ricerche (Institute for Sustainable Plant Protection-National Research Council), Bari, Italy
| | - Maria Minutolo
- Dipartimento di Agraria, Università degli Studi di Napoli Federico II, Portici, Italy
| | | | | | - Elke Mühlberger
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA, USA
| | - Rayapati Naidu
- Department of Plant Pathology, Irrigated Agricultural Research and Extension Center, Washington State University, Prosser, WA, USA
| | - Tomohide Natsuaki
- School of Agriculture, Utsunomiya University, Utsunomiya, Tochigi, Japan
| | - Beatriz Navarro
- Istituto per la Protezione Sostenibile delle Piante-Consiglio Nazionale delle ricerche (Institute for Sustainable Plant Protection-National Research Council), Bari, Italy
| | - José A Navarro
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Sergey V Netesov
- Novosibirsk State University, Novosibirsk, Novosibirsk Oblast, Russia
| | - Gabriele Neumann
- Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison, Madison, USA
| | - Norbert Nowotny
- Institute of Virology, University of Veterinary Medicine Vienna, Vienna, Austria
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | | | - Are Nylund
- Fish Disease Research Group, Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Arnfinn L Økland
- Fish Disease Research Group, Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Renata C Oliveira
- Laboratório de Hantaviroses e Rickettsioses, Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
| | - Gustavo Palacios
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Vicente Pallas
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Cientificas-Universidad Politécnica de Valencia, Valencia, Spain
| | - Bernadett Pályi
- National Biosafety Laboratory, National Public Health Center, Budapest, Hungary
| | - Anna Papa
- National Reference Centre for Arboviruses and Haemorrhagic Fever Viruses, Department of Microbiology, Medical School, Aristotle University of Thessaloniki, Thessaloníki, Greece
| | - Colin R Parrish
- College of Veterinary Medicine, Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA
| | - Alex Pauvolid-Corrêa
- Department of Veterinary Integrated Biosciences and Department of Entomology, Texas A&M University, College Station, USA
| | - Janusz T Pawęska
- Center for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham-Johannesburg, Gauteng, South Africa
| | - Susan Payne
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Daniel R Pérez
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Florian Pfaff
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Sheli R Radoshitzky
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Aziz-Ul Rahman
- Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | | | - Renato O Resende
- Departamento de Biologia Celular, Universidade de Brasília, Brasília, Brazil
| | - Carina A Reyes
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET-UNLP, La Plata, Buenos Aires, Argentina
| | - Bertus K Rima
- Centre for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, The Queen's University of Belfast, Belfast, Northern Ireland, UK
| | - Víctor Romanowski
- Instituto de Biotecnología y Biología Molecular, Centro Cientifico Technológico-La Plata, Consejo Nacional de Investigaciones Científico Tecnológico-Universidad Nacional de La Plata, La Plata, Argentina
| | - Gabriel Robles Luna
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET-UNLP, La Plata, Buenos Aires, Argentina
| | - Paul Rota
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Dennis Rubbenstroth
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Jonathan A Runstadler
- Department of Infectious Disease and Global Health, Tufts University Cummings School of Veterinary Medicine, 200 Westboro Road, North Grafton, MA, 01536, USA
| | - Daniel Ruzek
- Veterinary Research Institute, Brno, Czech Republic
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branisovska 31, 37005, Ceske Budejovice, Czech Republic
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS, USA
| | - Jiří Salát
- Veterinary Research Institute, Brno, Czech Republic
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branisovska 31, 37005, Ceske Budejovice, Czech Republic
| | | | - Maria S Salvato
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Kamil Sarpkaya
- Department of Forestry Engineering, Faculty of Forestry, Karabuk University (UNIKA), Karabük, Turkey
| | - Takahide Sasaya
- Western Region Agricultural Research Center, National Agriculture and Food Research Organization, Fukuyama, Japan
| | - Martin Schwemmle
- Faculty of Medicine, University Medical Center-University Freiburg, Freiburg, Germany
| | - Muhammad Z Shabbir
- Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Xiǎohóng Shí
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, UK
| | - Zhènglì Shí
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, People's Republic of China
| | - Yukio Shirako
- Asian Center for Bioresources and Environmental Sciences, University of Tokyo, Tokyo, Japan
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Manuela Sironi
- Bioinformatics Unit, Scientific Institute IRCCS "E. Medea", Bosisio Parini, Italy
| | - Sophie Smither
- CBR Division, Dstl, Porton Down, Salisbury, Wiltshire, UK
| | - Teemu Smura
- Department of Virology, University of Helsinki, Medicum, Helsinki, Finland
| | - Jin-Won Song
- Department of Microbiology, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Kirsten M Spann
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
| | - Jessica R Spengler
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Mark D Stenglein
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - David M Stone
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, Dorset, UK
| | | | - Ayato Takada
- Division of Global Epidemiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Robert B Tesh
- Department of Pathology, The University of Texas Medical Branch, Galveston, TX, USA
| | | | - Keizō Tomonaga
- Institute for Frontier Life and Medical Sciences (inFront), Kyoto University, Kyoto, Japan
| | - Noël Tordo
- Institut Pasteur, Unité des Stratégies Antivirales, WHO Collaborative Centre for Viral Haemorrhagic Fevers and Arboviruses, OIE Reference Laboratory for RVFV and CCHFV, Paris, France
- Institut Pasteur de Guinée, Conakry, Guinea
| | - Jonathan S Towner
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Massimo Turina
- Institute for Sustainable Plant Protection, National Research Council of Italy (CNR), Strada delle Cacce 73, 10135, Turin, Italy
| | - Ioannis Tzanetakis
- Division of Agriculture, Department of Entomology and Plant Pathology, University of Arkansas System, Fayetteville, AR, 72701, USA
| | - Rainer G Ulrich
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Novel and Emerging Infectious Diseases, Südufer 10, 17493, Greifswald-Insel Riems, Germany
- German Center of Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel-Insel Riems, Greifswald-Insel Riems, Germany
| | - Anna Maria Vaira
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), 73 Strada delle Cacce, 10135, Turin, Italy
| | - Bernadette van den Hoogen
- Department of Viroscience, Erasmus MC University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory, Cape Town, South Africa
| | - Nikos Vasilakis
- Department of Pathology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Martin Verbeek
- Wageningen University and Research, Biointeractions and Plant Health, Wageningen, The Netherlands
| | - Victoria Wahl
- National Biodefense Analysis and Countermeasures Center, Fort Detrick, Frederick, MD, USA
| | - Peter J Walker
- School of Biological Sciences, University of Queensland, St. Lucia, Queensland, Australia
| | - Hui Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jianwei Wang
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, IPB-Fondation Mérieux, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xifeng Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Tàiyún Wèi
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Heather Wells
- Mailman School of Public Health, Center for Infection and Immunity, Columbia University, New York, USA
| | - Anna E Whitfield
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
| | - John V Williams
- School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Zhìqiáng Wú
- MOH Key Laboratory of Systems Biology of Pathogens, IPB, CAMS, Beijing, China
| | - Xin Yang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangdong, China
| | - Xīnglóu Yáng
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, People's Republic of China
| | - Xuejie Yu
- Wuhan University School of Health Sciences, Wuhan, China
| | - Natalya Yutin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - F Murilo Zerbini
- Departamento de Fitopatologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Tong Zhang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangdong, China
| | - Yong-Zhen Zhang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
- Shanghai Public Health Clinical Center, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Guohui Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangdong, China
| | - Xueping Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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Szillat KP, Höper D, Beer M, König P. Full-genome sequencing of German rabbit haemorrhagic disease virus uncovers recombination between RHDV (GI.2) and EBHSV (GII.1). Virus Evol 2020; 6:veaa080. [PMID: 33324492 PMCID: PMC7724246 DOI: 10.1093/ve/veaa080] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Rabbit haemorrhagic disease virus (RHDV; genotypes GI.1 and GI.2) and European brown hare syndrome virus (EBHSV; genotype GII.1) are caliciviruses belonging to the genus Lagovirus. These viruses pose a serious threat to wild and domestic rabbit and hare populations around the world. In recent years, an expanding genetic diversity has been described within the genus, with recombination events occurring between the different genotypes. Here, we generated and analysed 56 full-genome sequences of RHDV and EBHSV from rabbit and hare livers, collected in Germany between the years 2013 and 2020. We could show that genotype Gl.2 (RHDV-2) almost entirely replaced Gl.1 (classical RHDV) in the German rabbit population. However, GI.1 is still present in Germany and has to be included into disease control and vaccination strategies. Three recombinant strains were identified from rabbit samples that contain the structural genes of genotype Gl.2 and the non-structural genes of genotype Gl.1b. Of special interest is the finding that sequences from two hare samples showed recombination events between structural genes of RHDV Gl.2 and non-structural genes of EBHSV GII.1, a recombination between different genogroups that has not been described before. These findings lead to the assumption that also a recombination of the non-structural genes of RHDV Gl.2 with the structural genes of EBHSV Gll.1 might be possible and therefore increase the potential genetic variability of lagoviruses immensely. Our findings underline the importance of whole genome analysis with next-generation sequencing technology as one of new tools now available for in-depth studies that allow in depth molecular epidemiology with continuous monitoring of the genetic variability of viruses that would otherwise likely stay undetected if only routine diagnostic assays are used.
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Affiliation(s)
- Kevin P Szillat
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, Greifswald-Insel Riems 17493, Germany
| | - Dirk Höper
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, Greifswald-Insel Riems 17493, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, Greifswald-Insel Riems 17493, Germany
| | - Patricia König
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, Greifswald-Insel Riems 17493, Germany
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38
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Bennett AJ, Paskey AC, Ebinger A, Pfaff F, Priemer G, Höper D, Breithaupt A, Heuser E, Ulrich RG, Kuhn JH, Bishop-Lilly KA, Beer M, Goldberg TL. Author Correction: Relatives of rubella virus in diverse mammals. Nature 2020; 588:E2. [PMID: 33199919 DOI: 10.1038/s41586-020-2897-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Andrew J Bennett
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Adrian C Paskey
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.,Leidos, Reston, VA, USA.,Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Frederick, MD, USA
| | - Arnt Ebinger
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Florian Pfaff
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Grit Priemer
- State Office for Agriculture, Food Safety and Fisheries, Rostock, Germany
| | - Dirk Höper
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Angele Breithaupt
- Department of Experimental Animal Facilities and Biorisk Management, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Elisa Heuser
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany.,German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Insel Riems, Greifswald-Insel Riems, Germany
| | - Rainer G Ulrich
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany.,German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Insel Riems, Greifswald-Insel Riems, Germany
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Kimberly A Bishop-Lilly
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.,Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Frederick, MD, USA
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany.
| | - Tony L Goldberg
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA. .,Global Health Institute, University of Wisconsin-Madison, Madison, WI, USA.
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39
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López-Labrador FX, Brown JR, Fischer N, Harvala H, Van Boheemen S, Cinek O, Sayiner A, Madsen TV, Auvinen E, Kufner V, Huber M, Rodriguez C, Jonges M, Hönemann M, Susi P, Sousa H, Klapper PE, Pérez-Cataluňa A, Hernandez M, Molenkamp R, der Hoek LV, Schuurman R, Couto N, Leuzinger K, Simmonds P, Beer M, Höper D, Kamminga S, Feltkamp MCW, Rodríguez-Díaz J, Keyaerts E, Nielsen XC, Puchhammer-Stöckl E, Kroes ACM, Buesa J, Breuer J, Claas ECJ, de Vries JJC. Recommendations for the introduction of metagenomic high-throughput sequencing in clinical virology, part I: Wet lab procedure. J Clin Virol 2020; 134:104691. [PMID: 33278791 DOI: 10.1016/j.jcv.2020.104691] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 10/16/2020] [Accepted: 11/11/2020] [Indexed: 02/06/2023]
Abstract
Metagenomic high-throughput sequencing (mHTS) is a hypothesis-free, universal pathogen detection technique for determination of the DNA/RNA sequences in a variety of sample types and infectious syndromes. mHTS is still in its early stages of translating into clinical application. To support the development, implementation and standardization of mHTS procedures for virus diagnostics, the European Society for Clinical Virology (ESCV) Network on Next-Generation Sequencing (ENNGS) has been established. The aim of ENNGS is to bring together professionals involved in mHTS for viral diagnostics to share methodologies and experiences, and to develop application recommendations. This manuscript aims to provide practical recommendations for the wet lab procedures necessary for implementation of mHTS for virus diagnostics and to give recommendations for development and validation of laboratory methods, including mHTS quality assurance, control and quality assessment protocols.
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Affiliation(s)
- F Xavier López-Labrador
- Virology Laboratory, Genomics and Health Area, Centre for Public Health Research (FISABIO-Public Health), Valencia, Spain; CIBERESP, Instituto de Salud Carlos III, Madrid, Spain.
| | - Julianne R Brown
- Microbiology, Virology and Infection Prevention and Control, Great Ormond Street Hospital for Children NHS Foundation Trust, United Kingdom.
| | - Nicole Fischer
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
| | - Heli Harvala
- Microbiology Services, NHS Blood and Transplant, London, United Kingdom.
| | - Sander Van Boheemen
- ErasmusMC, Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands.
| | - Ondrej Cinek
- Department of Paediatrics and Medical Microbiology, 2nd Faculty of Medicine, Charles University Prague, Czech Republic.
| | - Arzu Sayiner
- Dokuz Eylul University, Faculty of Medicine, Department of Medical Microbiology, Division of Medical Virology. Izmir, Turkey.
| | - Tina Vasehus Madsen
- Department of Clinical Microbiology, University Hospital of Region Zealand, Slagelse, Denmark.
| | - Eeva Auvinen
- Department of Virology, Helsinki University Hospital Laboratory and University of Helsinki, Helsinki, Finland.
| | - Verena Kufner
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland.
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland.
| | - Christophe Rodriguez
- Microbiology Department and NGS Platform, University Hospital Henri Mondor (APHP), Créteil, France.
| | - Marcel Jonges
- Medical Microbiology and Infection Control, Amsterdam UMC, Amsterdam, the Netherlands; Laboratory of Experimental Virology, Medical Microbiology and Infection Control, Amsterdam UMC, Amsterdam, the Netherlands.
| | - Mario Hönemann
- Institute of Virology, Leipzig University, Leipzig, Germany.
| | - Petri Susi
- Institute of Biomedicine, University of Turku, Finland.
| | - Hugo Sousa
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga, Guimarães, Portugal; Virology Service, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal; Molecular Oncology and Viral Pathology Group, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.
| | - Paul E Klapper
- Faculty of Biology, Medicine, and Health, Division of Infection, Immunity, and Respiratory Medicine, University of Manchester, Manchester, United Kingdom.
| | - Alba Pérez-Cataluňa
- Department of Preservation and Food Safety Technologies, IATA-CSIC, Paterna, Valencia, Spain.
| | - Marta Hernandez
- Laboratory of Molecular Biology and Microbiology, Instituto Tecnologico Agrario de Castilla y Leon, Valladolid, Spain.
| | - Richard Molenkamp
- ErasmusMC, Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands.
| | - Lia van der Hoek
- Medical Microbiology and Infection Control, Amsterdam UMC, Amsterdam, the Netherlands; Laboratory of Experimental Virology, Medical Microbiology and Infection Control, Amsterdam UMC, Amsterdam, the Netherlands.
| | - Rob Schuurman
- Department of Virology, University Medical Center Utrecht, Utrecht, the Netherlands.
| | - Natacha Couto
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, the Netherlands; Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom.
| | - Karoline Leuzinger
- Clinical Virology, Laboratory Medicine, University Hospital Basel, Basel, Switzerland; Transplantation & Clinical Virology, Department Biomedicine, University of Basel, Basel, Switzerland.
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.
| | - Martin Beer
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Insel Riems, Germany.
| | - Dirk Höper
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Insel Riems, Germany.
| | - Sergio Kamminga
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands.
| | - Mariet C W Feltkamp
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands.
| | - Jesús Rodríguez-Díaz
- Department of Microbiology and Ecology, Faculty of Medicine, University of Valencia, Valencia, Spain.
| | - Els Keyaerts
- Laboratorium Klinische en Epidemiologische Virologie (Rega Instituut), Leuven, Belgium.
| | - Xiaohui Chen Nielsen
- Department of Clinical Microbiology, University Hospital of Region Zealand, Slagelse, Denmark.
| | | | - Aloys C M Kroes
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands.
| | - Javier Buesa
- Department of Microbiology and Ecology, Faculty of Medicine, University of Valencia, Valencia, Spain.
| | - Judy Breuer
- Microbiology, Virology and Infection Prevention and Control, Great Ormond Street Hospital for Children NHS Foundation Trust, United Kingdom.
| | - Eric C J Claas
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands.
| | - Jutte J C de Vries
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands.
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Höper D, Grützke J, Brinkmann A, Mossong J, Matamoros S, Ellis RJ, Deneke C, Tausch SH, Cuesta I, Monzón S, Juliá M, Petersen TN, Hendriksen RS, Pamp SJ, Leijon M, Hakhverdyan M, Walsh AM, Cotter PD, Chandrasekaran L, Tay MYF, Schlundt J, Sala C, De Cesare A, Nitsche A, Beer M, Wylezich C. Proficiency Testing of Metagenomics-Based Detection of Food-Borne Pathogens Using a Complex Artificial Sequencing Dataset. Front Microbiol 2020; 11:575377. [PMID: 33250869 PMCID: PMC7672002 DOI: 10.3389/fmicb.2020.575377] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 10/13/2020] [Indexed: 01/16/2023] Open
Abstract
Metagenomics-based high-throughput sequencing (HTS) enables comprehensive detection of all species comprised in a sample with a single assay and is becoming a standard method for outbreak investigation. However, unlike real-time PCR or serological assays, HTS datasets generated for pathogen detection do not easily provide yes/no answers. Rather, results of the taxonomic read assignment need to be assessed by trained personnel to gain information thereof. Proficiency tests are important instruments of validation, harmonization, and standardization. Within the European Union funded project COMPARE [COllaborative Management Platform for detection and Analyses of (Re-) emerging and foodborne outbreaks in Europe], we conducted a proficiency test to scrutinize the ability to assess diagnostic metagenomics data. An artificial dataset resembling shotgun sequencing of RNA from a sample of contaminated trout was provided to 12 participants with the request to provide a table with per-read taxonomic assignments at species level and a report with a summary and assessment of their findings, considering different categories like pathogen, background, or contaminations. Analysis of the read assignment tables showed that the software used reliably classified the reads taxonomically overall. However, usage of incomplete reference databases or inappropriate data pre-processing caused difficulties. From the combination of the participants’ reports with their read assignments, we conclude that, although most species were detected, a number of important taxa were not or not correctly categorized. This implies that knowledge of and awareness for potentially dangerous species and contaminations need to be improved, hence, capacity building for the interpretation of diagnostic metagenomics datasets is necessary.
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Affiliation(s)
- Dirk Höper
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Josephine Grützke
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Annika Brinkmann
- Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
| | - Joël Mossong
- Département de Microbiologie, Laboratoire National de Santé, Dudelange, Luxembourg
| | - Sébastien Matamoros
- Department of Medical Microbiology, Amsterdam UMC University of Amsterdam, Amsterdam, Netherlands
| | | | - Carlus Deneke
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Simon H Tausch
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Isabel Cuesta
- Bioinformatics Unit, Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - Sara Monzón
- Bioinformatics Unit, Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - Miguel Juliá
- Bioinformatics Unit, Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - Thomas Nordahl Petersen
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Rene S Hendriksen
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Sünje J Pamp
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Mikael Leijon
- Department of Microbiology, National Veterinary Institute (SVA), Uppsala, Sweden
| | - Mikhayil Hakhverdyan
- Department of Microbiology, National Veterinary Institute (SVA), Uppsala, Sweden
| | - Aaron M Walsh
- Teagasc Food Research Centre, APC Microbiome Ireland and Vistamilk, Moorepark, Ireland
| | - Paul D Cotter
- Teagasc Food Research Centre, APC Microbiome Ireland and Vistamilk, Moorepark, Ireland
| | - Lakshmi Chandrasekaran
- Nanyang Technological University Food Technology Centre (NAFTEC), Nanyang Technological University (NTU), Singapore, Singapore
| | - Moon Y F Tay
- Nanyang Technological University Food Technology Centre (NAFTEC), Nanyang Technological University (NTU), Singapore, Singapore
| | - Joergen Schlundt
- Nanyang Technological University Food Technology Centre (NAFTEC), Nanyang Technological University (NTU), Singapore, Singapore
| | - Claudia Sala
- Department of Physics and Astronomy, University of Bologna, Bologna, Italy
| | - Alessandra De Cesare
- Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
| | - Andreas Nitsche
- Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Claudia Wylezich
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
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Moharam I, Sultan H, Hassan K, Ibrahim M, Shany S, Shehata AA, Abo-ElKhair M, Pfaff F, Höper D, EL Kady M, Beer M, Harder T, Hafez H, Grund C. Emerging infectious bronchitis virus (IBV) in Egypt: Evidence for an evolutionary advantage of a new S1 variant with a unique gene 3ab constellation. Infect Genet Evol 2020; 85:104433. [PMID: 32622080 PMCID: PMC7327463 DOI: 10.1016/j.meegid.2020.104433] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 06/05/2020] [Accepted: 06/16/2020] [Indexed: 12/21/2022]
Abstract
Infectious bronchitis virus (IBV), a gamma-coronavirus, causes infectious bronchitis (IB), a major respiratory disease of chicken. Its high mutation rate in conjunction with recombination of the RNA genome constantly creates IBV variants that are difficult to control by currently available vaccines. In this study, we addressed the question whether small-scale holdings might harbor IBV variants that serve as a reservoir for newly emerging variants. Egyptian IBV isolate EGY/NR725/2016 (NR725/16) from a small-scale broiler farm was assigned to genotype I, clade 23 (S1:GI-23), based on partial S1 gene sequences and corroborated by full genome sequencing. Analysis of the S1 gene established three subclades for historical IBV strains (S1:GI-23.1, S1:GI-23.2.1 and S1:GI-23.2.2) and confirmed NR725/16 as being part of a separate fourth subclade (S1:GI-23.3). Samples from the years 2018 and 2019 revealed that the new subclade prevails in Egypt, carrying fixed mutations within the hypervariable regions (HVR) 1-3 of the S1 protein that affect two neutralization sensitive epitopes at sites 294F, 297S and 306Y (48.2) and 329R (62.1). In addition, recombination was recognized in isolate NR 725/16, with intra-subtype mixing for the entire genes 3ab and E and inter-subtype mixing for the entire gene 6b with a close match to QX like viruses of genotype GI-19. Further analysis of gene 3ab detected the homologous gene pool to NR725/16 in samples from 2013 (3ab:C) and closely related 3ab genotypes in IBV Egyptian isolates from 2016, 2018 and 2019. These data prove a flourishing exchange between poultry holdings with a common gene pool. The continued circulation of viruses harboring genes S1:GI-23.3 and 3ab:C indicates an evolutionary advantage of this combination possibly by combining antigenic escape with modulated pathogenicity to facilitate IBV spread in the vaccinated poultry population in Egypt.
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Affiliation(s)
- Ibrahim Moharam
- Institute of Diagnostic Virology Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Germany,Department of Birds and Rabbits Medicine, University of Sadat City, Monufia, Egypt
| | - Hesham Sultan
- Department of Birds and Rabbits Medicine, University of Sadat City, Monufia, Egypt
| | - K. Hassan
- Institute of Diagnostic Virology Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Germany,Department of Poultry Diseases, Beni-Suef University, Beni-Suef, Egypt
| | - Mahmoud Ibrahim
- Department of Birds and Rabbits Medicine, University of Sadat City, Monufia, Egypt
| | - Salama Shany
- Department of Poultry Diseases, Beni-Suef University, Beni-Suef, Egypt
| | - Awad A. Shehata
- Department of Birds and Rabbits Medicine, University of Sadat City, Monufia, Egypt
| | | | - Florian Pfaff
- Institute of Diagnostic Virology Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Germany
| | - Dirk Höper
- Institute of Diagnostic Virology Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Germany
| | - Magdy EL Kady
- Department of Poultry Diseases, Beni-Suef University, Beni-Suef, Egypt
| | - Martin Beer
- Institute of Diagnostic Virology Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Germany
| | - Timm Harder
- Institute of Diagnostic Virology Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Germany
| | - Hafez Hafez
- Institute of Poultry Disease, Freie Universität Berlin, Germany
| | - Christian Grund
- Institute of Diagnostic Virology Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Germany.
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42
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Freuling CM, Breithaupt A, Müller T, Sehl J, Balkema-Buschmann A, Rissmann M, Klein A, Wylezich C, Höper D, Wernike K, Aebischer A, Hoffmann D, Friedrichs V, Dorhoi A, Groschup MH, Beer M, Mettenleiter TC. Susceptibility of Raccoon Dogs for Experimental SARS-CoV-2 Infection. Emerg Infect Dis 2020; 26:2982-2985. [PMID: 33089771 PMCID: PMC7706974 DOI: 10.3201/eid2612.203733] [Citation(s) in RCA: 116] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Raccoon dogs might have been intermediate hosts for severe acute respiratory syndrome-associated coronavirus in 2002-2004. We demonstrated susceptibility of raccoon dogs to severe acute respiratory syndrome coronavirus 2 infection and transmission to in-contact animals. Infected animals had no signs of illness. Virus replication and tissue lesions occurred in the nasal conchae.
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43
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Forth JH, Forth LF, Lycett S, Bell-Sakyi L, Keil GM, Blome S, Calvignac-Spencer S, Wissgott A, Krause J, Höper D, Kampen H, Beer M. Identification of African swine fever virus-like elements in the soft tick genome provides insights into the virus' evolution. BMC Biol 2020; 18:136. [PMID: 33032594 PMCID: PMC7542975 DOI: 10.1186/s12915-020-00865-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 09/04/2020] [Indexed: 12/20/2022] Open
Abstract
Background African swine fever virus (ASFV) is a most devastating pathogen affecting swine. In 2007, ASFV was introduced into Eastern Europe where it continuously circulates and recently reached Western Europe and Asia, leading to a socio-economic crisis of global proportion. In Africa, where ASFV was first described in 1921, it is transmitted between warthogs and soft ticks of the genus Ornithodoros in a so-called sylvatic cycle. However, analyses into this virus’ evolution are aggravated by the absence of any closely related viruses. Even ancient endogenous viral elements, viral sequences integrated into a host’s genome many thousand years ago that have proven extremely valuable to analyse virus evolution, remain to be identified. Therefore, the evolution of ASFV, the only known DNA virus transmitted by arthropods, remains a mystery. Results For the identification of ASFV-like sequences, we sequenced DNA from different recent Ornithodoros tick species, e.g. O. moubata and O. porcinus, O. moubata tick cells and also 100-year-old O. moubata and O. porcinus ticks using high-throughput sequencing. We used BLAST analyses for the identification of ASFV-like sequences and further analysed the data through phylogenetic reconstruction and molecular clock analyses. In addition, we performed tick infection experiments as well as additional small RNA sequencing of O. moubata and O. porcinus soft ticks. Conclusion Here, we show that soft ticks of the Ornithodoros moubata group, the natural arthropod vector of ASFV, harbour African swine fever virus-like integrated (ASFLI) elements corresponding to up to 10% (over 20 kb) of the ASFV genome. Through orthologous dating and molecular clock analyses, we provide data suggesting that integration could have occurred over 1.47 million years ago. Furthermore, we provide data showing ASFLI-element specific siRNA and piRNA in ticks and tick cells allowing for speculations on a possible role of ASFLI-elements in RNA interference-based protection against ASFV in ticks. We suggest that these elements, shaped through many years of co-evolution, could be part of an evolutionary virus-vector ‘arms race’, a finding that has not only high impact on our understanding of the co-evolution of viruses with their hosts but also provides a glimpse into the evolution of ASFV.
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Affiliation(s)
- Jan H Forth
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald-Insel Riems, Germany
| | - Leonie F Forth
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald-Insel Riems, Germany
| | - Samantha Lycett
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland, UK
| | - Lesley Bell-Sakyi
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, 146 Brownlow Hill, Liverpool, L3 5RF, UK
| | - Günther M Keil
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald-Insel Riems, Germany
| | - Sandra Blome
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald-Insel Riems, Germany
| | | | - Antje Wissgott
- Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745, Jena, Germany
| | - Johannes Krause
- Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745, Jena, Germany
| | - Dirk Höper
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald-Insel Riems, Germany
| | - Helge Kampen
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald-Insel Riems, Germany
| | - Martin Beer
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald-Insel Riems, Germany.
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Bennett AJ, Paskey AC, Ebinger A, Pfaff F, Priemer G, Höper D, Breithaupt A, Heuser E, Ulrich RG, Kuhn JH, Bishop-Lilly KA, Beer M, Goldberg TL. Relatives of rubella virus in diverse mammals. Nature 2020; 586:424-428. [PMID: 33029010 PMCID: PMC7572621 DOI: 10.1038/s41586-020-2812-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Accepted: 07/17/2020] [Indexed: 12/17/2022]
Abstract
Since 1814, when rubella was first described, the origins of the disease and its causative agent, rubella virus (Matonaviridae: Rubivirus), have remained unclear1. Here we describe ruhugu virus and rustrela virus in Africa and Europe, respectively, which are, to our knowledge, the first known relatives of rubella virus. Ruhugu virus, which is the closest relative of rubella virus, was found in apparently healthy cyclops leaf-nosed bats (Hipposideros cyclops) in Uganda. Rustrela virus, which is an outgroup to the clade that comprises rubella and ruhugu viruses, was found in acutely encephalitic placental and marsupial animals at a zoo in Germany and in wild yellow-necked field mice (Apodemus flavicollis) at and near the zoo. Ruhugu and rustrela viruses share an identical genomic architecture with rubella virus2,3. The amino acid sequences of four putative B cell epitopes in the fusion (E1) protein of the rubella, ruhugu and rustrela viruses and two putative T cell epitopes in the capsid protein of the rubella and ruhugu viruses are moderately to highly conserved4-6. Modelling of E1 homotrimers in the post-fusion state predicts that ruhugu and rubella viruses have a similar capacity for fusion with the host-cell membrane5. Together, these findings show that some members of the family Matonaviridae can cross substantial barriers between host species and that rubella virus probably has a zoonotic origin. Our findings raise concerns about future zoonotic transmission of rubella-like viruses, but will facilitate comparative studies and animal models of rubella and congenital rubella syndrome.
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Affiliation(s)
- Andrew J Bennett
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Adrian C Paskey
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Leidos, Reston, VA, USA
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Frederick, MD, USA
| | - Arnt Ebinger
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Florian Pfaff
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Grit Priemer
- State Office for Agriculture, Food Safety and Fisheries, Rostock, Germany
| | - Dirk Höper
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Angele Breithaupt
- Department of Experimental Animal Facilities and Biorisk Management, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Elisa Heuser
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Insel Riems, Greifswald-Insel Riems, Germany
| | - Rainer G Ulrich
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Insel Riems, Greifswald-Insel Riems, Germany
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Kimberly A Bishop-Lilly
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Frederick, MD, USA
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany.
| | - Tony L Goldberg
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA.
- Global Health Institute, University of Wisconsin-Madison, Madison, WI, USA.
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Karte C, Platje N, Bullermann J, Beer M, Höper D, Blome S. Re-emergence of porcine epidemic diarrhea virus in a piglet-producing farm in northwestern Germany in 2019. BMC Vet Res 2020; 16:329. [PMID: 32912228 PMCID: PMC7481547 DOI: 10.1186/s12917-020-02548-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 08/27/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Porcine epidemic diarrhea (PED) is a viral enteric disease of pigs. It affects all age classes of animals but lethality is mainly seen in suckling piglets. After its first appearance in England in 1971, Porcine epidemic diarrhea virus (PEDV) has spread worldwide. While sporadic outbreaks prevailed in Europe, the disease had high impact in Asia. Following particularly severe outbreaks in 2011, high impact cases were also reported in the United States and neighboring countries in 2013. Subsequently, outbreaks were also reported in several European countries including Germany. These outbreaks were less severe. This case report describes a recent case of PED re-emergence in Germany and the sequence analyses of the causative PEDV. CASE PRESENTATION In spring 2019 5 years after re-introduction of PED into Central Europe, a piglet-producer in northwestern Germany experienced an outbreak that affected sows, their suckling piglets, and weaners. After initial confirmation of PEDV by real-time RT-PCR, fecal material and small intestine samples from affected pigs were subjected to metagenomic analyses employing next-generation sequencing. Phylogenetic analyses showed high identities among the PEDV sequences obtained from samples of different animals and a close relation to recent strains from Hungary and France. Compared to the PEDV strains analyzed in 2014, genetic drift could be confirmed. Changes were mainly observed in the spike protein encoding S gene segment. In addition, metagenomic analyses showed multiple Picobirnavirus reads in all investigated samples. CONCLUSION This case report shows that PEDV is still circulating in Europe. The causative strains are moderately virulent and are still closely related to the so-called INDEL strains reported previously in Europe, including Germany. However, a genetic drift has taken place that can be seen in a novel cluster comprising strains from Germany, Hungary and France in 2019. Relevance and impact of the detected Picobirna sequences need further investigations.
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Affiliation(s)
- Claudia Karte
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Suedufer 10, 17493 Greifswald - Insel Riems, Greifswald, Germany
| | | | | | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Suedufer 10, 17493 Greifswald - Insel Riems, Greifswald, Germany
| | - Dirk Höper
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Suedufer 10, 17493 Greifswald - Insel Riems, Greifswald, Germany
| | - Sandra Blome
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Suedufer 10, 17493 Greifswald - Insel Riems, Greifswald, Germany.
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Schulze V, Große R, Fürstenau J, Forth LF, Ebinger A, Richter MT, Tappe D, Mertsch T, Klose K, Schlottau K, Hoffmann B, Höper D, Mundhenk L, Ulrich RG, Beer M, Müller KE, Rubbenstroth D. Borna disease outbreak with high mortality in an alpaca herd in a previously unreported endemic area in Germany. Transbound Emerg Dis 2020; 67:2093-2107. [PMID: 32223069 DOI: 10.1111/tbed.13556] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 03/09/2020] [Accepted: 03/16/2020] [Indexed: 12/22/2022]
Abstract
Borna disease virus 1 (BoDV-1) is the causative agent of Borna disease, an often fatal neurologic condition of domestic mammals, including New World camelids, in endemic areas in Central Europe. Recently, BoDV-1 gained further attention by the confirmation of fatal zoonotic infections in humans. Although Borna disease and BoDV-1 have been described already over the past decades, comprehensive reports of Borna disease outbreaks in domestic animals employing state-of-the-art diagnostic methods are missing. Here, we report a series of BoDV-1 infections in a herd of 27 alpacas (Vicugna pacos) in the federal state of Brandenburg, Germany, which resulted in eleven fatalities (41%) within ten months. Clinical courses ranged from sudden death without previous clinical signs to acute or chronic neurologic disease with death occurring after up to six months. All animals that underwent necropsy exhibited a non-suppurative encephalitis. In addition, six apparently healthy seropositive individuals were identified within the herd, suggesting subclinical BoDV-1 infections. In infected animals, BoDV-1 RNA and antigen were mainly restricted to the central nervous system and the eye, and sporadically detectable in large peripheral nerves and neuronal structures in other tissues. Pest control measures on the farm resulted in the collection of a BoDV-1-positive bicoloured white-toothed shrew (Crocidura leucodon), while all other trapped small mammals were negative. A phylogeographic analysis of BoDV-1 sequences from the alpacas, the shrew and BoDV-1-positive equine cases from the same region in Brandenburg revealed a previously unreported endemic area of BoDV-1 cluster 4 in North-Western Brandenburg. In conclusion, alpacas appear to be highly susceptible to BoDV-1 infection and display a highly variable clinical picture ranging from peracute death to subclinical forms. In addition to horses and sheep, they can serve as sensitive sentinels used for the identification of endemic areas.
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Affiliation(s)
- Vanessa Schulze
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Reinhard Große
- Clinic for Ruminants and Swine, Freie Universität Berlin, Berlin, Germany
| | - Jenny Fürstenau
- Institute of Veterinary Pathology, Freie Universität Berlin, Berlin, Germany
| | - Leonie F Forth
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Arnt Ebinger
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Madita T Richter
- Institute of Veterinary Pathology, Freie Universität Berlin, Berlin, Germany
| | - Dennis Tappe
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | | | - Kristin Klose
- Institute of Veterinary Pathology, Leipzig University, Leipzig, Germany
| | - Kore Schlottau
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Bernd Hoffmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Dirk Höper
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Lars Mundhenk
- Institute of Veterinary Pathology, Freie Universität Berlin, Berlin, Germany
| | - Rainer G Ulrich
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | | | - Dennis Rubbenstroth
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
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Abstract
The pandemic spread of African swine fever virus (ASFV) genotype II (GTII) has led to a global crisis. Since the circulating strains are almost identical, time and money have been mis-invested in whole-genome sequencing the last years. New methods, harmonised protocols for sample selection, sequencing, and bioinformatics are therefore urgently needed.
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Affiliation(s)
- Jan H. Forth
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald—Insel Riems, Germany
| | - Leonie F. Forth
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald—Insel Riems, Germany
| | - Sandra Blome
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald—Insel Riems, Germany
| | - Dirk Höper
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald—Insel Riems, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald—Insel Riems, Germany
- * E-mail:
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48
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Abd El Rahman S, Hoffmann B, Karam R, El-beskawy M, Hamed MF, Forth LF, Höper D, Eschbaumer M. Sequence Analysis of Egyptian Foot-And-Mouth Disease Virus Field and Vaccine Strains: Intertypic Recombination and Evidence for Accidental Release of Virulent Virus.. [DOI: 10.20944/preprints202008.0285.v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
In addition to the risk of vaccine failure caused by strain mismatch, the production of inactivated FMD vaccines is dangerous if adequate biosafety cannot be maintained. Using a high-throughput sequencing protocol optimized for short nucleic acid fragments, the composition of a local inactivated vaccine was analyzed in depth. The serotype O strain identified in the vaccine was genetically identical to viruses found in recent FMD outbreaks in Egypt.
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49
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Schlottau K, Rissmann M, Graaf A, Schön J, Sehl J, Wylezich C, Höper D, Mettenleiter TC, Balkema-Buschmann A, Harder T, Grund C, Hoffmann D, Breithaupt A, Beer M. SARS-CoV-2 in fruit bats, ferrets, pigs, and chickens: an experimental transmission study. Lancet Microbe 2020; 1:e218-e225. [PMID: 32838346 PMCID: PMC7340389 DOI: 10.1016/s2666-5247(20)30089-6] [Citation(s) in RCA: 356] [Impact Index Per Article: 89.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Background In December, 2019, a novel zoonotic severe acute respiratory syndrome-related coronavirus emerged in China. The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) became pandemic within weeks and the number of human infections and severe cases is increasing. We aimed to investigate the susceptibilty of potential animal hosts and the risk of anthropozoonotic spill-over infections. Methods We intranasally inoculated nine fruit bats (Rousettus aegyptiacus), ferrets (Mustela putorius), pigs (Sus scrofa domesticus), and 17 chickens (Gallus gallus domesticus) with 105 TCID50 of a SARS-CoV-2 isolate per animal. Direct contact animals (n=3) were included 24 h after inoculation to test viral transmission. Animals were monitored for clinical signs and for virus shedding by nucleic acid extraction from nasal washes and rectal swabs (ferrets), oral swabs and pooled faeces samples (fruit bats), nasal and rectal swabs (pigs), or oropharyngeal and cloacal swabs (chickens) on days 2, 4, 8, 12, 16, and 21 after infection by quantitative RT-PCR (RT-qPCR). On days 4, 8, and 12, two inoculated animals (or three in the case of chickens) of each species were euthanised, and all remaining animals, including the contacts, were euthanised at day 21. All animals were subjected to autopsy and various tissues were collected for virus detection by RT-qPCR, histopathology immunohistochemistry, and in situ hybridisation. Presence of SARS-CoV-2 reactive antibodies was tested by indirect immunofluorescence assay and virus neutralisation test in samples collected before inoculation and at autopsy. Findings Pigs and chickens were not susceptible to SARS-CoV-2. All swabs, organ samples, and contact animals were negative for viral RNA, and none of the pigs or chickens seroconverted. Seven (78%) of nine fruit bats had a transient infection, with virus detectable by RT-qPCR, immunohistochemistry, and in situ hybridisation in the nasal cavity, associated with rhinitis. Viral RNA was also identified in the trachea, lung, and lung-associated lymphatic tissue in two animals euthanised at day 4. One of three contact bats became infected. More efficient virus replication but no clinical signs were observed in ferrets, with transmission to all three direct contact animals. Mild rhinitis was associated with viral antigen detection in the respiratory and olfactory epithelium. Prominent viral RNA loads of 0–104 viral genome copies per mL were detected in the upper respiratory tract of fruit bats and ferrets, and both species developed SARS-CoV-2-reactive antibodies reaching neutralising titres of up to 1/1024 after 21 days. Interpretation Pigs and chickens could not be infected intranasally by SARS-CoV-2, whereas fruit bats showed characteristics of a reservoir host. Virus replication in ferrets resembled a subclinical human infection with efficient spread. Ferrets might serve as a useful model for further studies—eg, testing vaccines or antivirals. Funding German Federal Ministry of Food and Agriculture.
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Affiliation(s)
- Kore Schlottau
- Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
| | - Melanie Rissmann
- Institute of Novel and Emerging Infectious Diseases, Greifswald-Insel Riems, Germany
| | - Annika Graaf
- Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
| | - Jacob Schön
- Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
| | - Julia Sehl
- Department of Experimental Animal Facilities and Biorisk Management, Greifswald-Insel Riems, Germany
| | - Claudia Wylezich
- Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
| | - Dirk Höper
- Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
| | | | | | - Timm Harder
- Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
| | - Christian Grund
- Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
| | - Donata Hoffmann
- Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
| | - Angele Breithaupt
- Department of Experimental Animal Facilities and Biorisk Management, Greifswald-Insel Riems, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
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50
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Wylezich C, Caccio SM, Walochnik J, Beer M, Höper D. Untargeted metagenomics shows a reliable performance for synchronous detection of parasites. Parasitol Res 2020; 119:2623-2629. [PMID: 32591865 PMCID: PMC7366571 DOI: 10.1007/s00436-020-06754-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 06/03/2020] [Indexed: 12/17/2022]
Abstract
Shotgun metagenomics with high-throughput sequencing (HTS) techniques is increasingly used for pathogen identification and characterization. While many studies apply targeted amplicon sequencing, here we used untargeted metagenomics to simultaneously identify protists and helminths in pre-diagnosed faecal and tissue samples. The approach starts from RNA and operates without an amplification step, therefore allowing the detection of all eukaryotes, including pathogens, since it circumvents the bias typically observed in amplicon-based HTS approaches. The generated metagenomics datasets were analysed using the RIEMS tool for initial taxonomic read assignment. Mapping analyses against ribosomal reference sequences were subsequently applied to extract 18S rRNA sequences abundantly present in the sequence datasets. The original diagnosis, which was based on microscopy and/or PCR, could be confirmed in nearly all cases using ribosomal RNA metagenomics. In addition to the pre-diagnosed taxa, we detected other intestinal eukaryotic parasites of uncertain pathogenicity (of the genera Dientamoeba, Entamoeba, Endolimax, Hymenolepis) that are often excluded from routine diagnostic protocols. The study clearly demonstrates the applicability of untargeted RNA metagenomics for the parallel detection of parasites.
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Affiliation(s)
- Claudia Wylezich
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald-Insel Riems, Germany.
| | - Simone M Caccio
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Julia Walochnik
- Molecular Parasitology, Institute for Specific Prophylaxis and Tropical Medicine, Medical University of Vienna, Kinderspitalgasse 15, 1090, Vienna, Austria
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald-Insel Riems, Germany
| | - Dirk Höper
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald-Insel Riems, Germany
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