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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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Rau J, Köchling K, Schäfer M, Tews BA, Wylezich C, Schaub GA, Werner D, Kampen H. Viral RNA in Mosquitoes (Diptera: Culicidae) Collected between 2019 and 2021 in Germany. Viruses 2023; 15:2298. [PMID: 38140539 PMCID: PMC10746995 DOI: 10.3390/v15122298] [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: 10/13/2023] [Revised: 11/18/2023] [Accepted: 11/20/2023] [Indexed: 12/24/2023] Open
Abstract
Due to globalisation and climate change, mosquito-borne pathogens are emerging in new areas on all continents, including Europe, which has recently faced outbreaks of dengue, chikungunya and West Nile fever. The present study complements previous investigations to evaluate the circulation of mosquito-borne viruses in Germany, with the aim of identifying potential vector species and risk areas. Mosquitoes collected from 2019 to 2021 and identified to species or species group level were screened for viruses of the families Flaviviridae, Peribunyaviridae and the genus Alphavirus of the family Togaviridae. In total, 22,528 mosquitoes were examined, thus providing the most comprehensive study on West Nile virus (WNV) circulation so far in the German mosquito population. Usutu virus (USUV) RNA was detected in six samples, Sindbis virus (SINV) RNA in 21 samples and WNV RNA in 11 samples. Samples containing RNA of USUV and WNV consisted of mosquitoes collected in the East German federal states of Brandenburg, Saxony and Saxony-Anhalt, while samples with RNA of SINV originated from more widespread locations. Although minimum infection rates have remained relatively low, the intensity of virus circulation appears to be increasing compared to previous studies. Continuous mosquito screening contributes to the early detection of the introduction and spread of mosquito-borne pathogens.
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Affiliation(s)
- Janine Rau
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald, Germany; (M.S.); (B.A.T.); (C.W.); (H.K.)
| | - Katharina Köchling
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald, Germany; (M.S.); (B.A.T.); (C.W.); (H.K.)
| | - Mandy Schäfer
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald, Germany; (M.S.); (B.A.T.); (C.W.); (H.K.)
| | - Birke A. Tews
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald, Germany; (M.S.); (B.A.T.); (C.W.); (H.K.)
| | - Claudia Wylezich
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald, Germany; (M.S.); (B.A.T.); (C.W.); (H.K.)
| | - Günter A. Schaub
- Zoology/Parasitology Department, Ruhr-University, Universitätsstr. 150, 44801 Bochum, Germany;
| | - Doreen Werner
- Leibniz Centre for Agricultural Landscape Research, Eberswalder Str. 84, 15374 Müncheberg, Germany;
| | - Helge Kampen
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald, Germany; (M.S.); (B.A.T.); (C.W.); (H.K.)
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3
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Nippert S, Rubbenstroth D, Geers JA, Ebinger A, Hoffmann D, Breithaupt A, Wylezich C, Wang X, Haring VC, Starcky P, Fruci P, Langner C, Trapp C, Schulz H, Stubbe W, Imholt C, Heckel G, Beer M, Pfaff F, Ulrich RG. Continuous presence of genetically diverse rustrela virus lineages in yellow-necked field mouse reservoir populations in northeastern Germany. Virus Evol 2023; 9:vead048. [PMID: 37744713 PMCID: PMC10516363 DOI: 10.1093/ve/vead048] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 06/14/2023] [Accepted: 07/26/2023] [Indexed: 09/26/2023] Open
Abstract
Rustrela virus (RusV; species Rubivirus strelense, family Matonaviridae) was discovered in different zoo animal species affected by fatal encephalitis. Simultaneous RusV RNA detection in multiple yellow-necked field mice (Apodemus flavicollis) suggested this rodent as a reservoir of RusV. Here, we investigated 1,264 yellow-necked field mice and sympatric other small mammals from different regions in Germany for RusV RNA using an optimized reverse transcription-quantitative polymerase chain reaction (RT-qPCR) protocol and high-throughput sequencing. The investigation resulted in the detection of RusV RNA exclusively in 50 of 396 (12.6 per cent) yellow-necked field mice but absence in other sympatric species. RT-qPCR-determined tissue distribution of RusV RNA revealed the highest viral loads in the central nervous system, with other tissues being only very rarely affected. The histopathological evaluation did not reveal any hints of encephalitis in the brains of infected animals despite the detection of viral RNA in neurons by in situ hybridization (ISH). The positive association between the body mass of yellow-necked field mice and RusV RNA detection suggests a persistent infection. Phylogenetic analysis of partial E1 and full-genome sequences showed a high diversification with at least four RusV lineages (1A-1D) in northeastern Germany. Moreover, phylogenetic and isolation-by-distance analyses indicated evolutionary processes of RusV mostly in local reservoir populations. A comparison of complete genome sequences from all detected RusV lineages demonstrated a high level of amino acid and nucleotide sequence variability within a part of the p150 peptide of the non-structural polyprotein and its coding sequence, respectively. The location of this region within the RusV genome and its genetic properties were comparable to the hypervariable region of the rubella virus. The broad range of detected RusV spillover hosts in combination with its geographical distribution in northeastern Germany requires the assessment of its zoonotic potential and further analysis of encephalitis cases in mammals. Future studies have to prove a putative co-evolution scenario for RusV in the yellow-necked field mouse reservoir.
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Affiliation(s)
- Sina Nippert
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, Greifswald-Insel Riems 17493, Germany
| | - Dennis Rubbenstroth
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, Greifswald-Insel Riems 17493, Germany
| | - Jessica Anna Geers
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, Greifswald-Insel Riems 17493, Germany
| | - Arnt Ebinger
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, Greifswald-Insel Riems 17493, Germany
| | - Donata Hoffmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, Greifswald-Insel Riems 17493, Germany
| | - Angele Breithaupt
- Department of Experimental Animal Facilities and Biorisk Management, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, Greifswald-Insel Riems 17493, Germany
| | - Claudia Wylezich
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, Greifswald-Insel Riems 17493, Germany
- Department of Experimental Animal Facilities and Biorisk Management, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, Greifswald-Insel Riems 17493, Germany
| | - Xuejing Wang
- Institute of Ecology and Evolution, University of Bern, Baltzerstraße 6, Bern CH-3012, Switzerland
| | - Viola C Haring
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, Greifswald-Insel Riems 17493, Germany
| | - Philip Starcky
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, Greifswald-Insel Riems 17493, Germany
| | - Paola Fruci
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, Greifswald-Insel Riems 17493, Germany
- Laboratory of Infectious Diseases, Faculty of Veterinary Medicine, University of Teramo, Via Renato Balzarini 1, Teramo 64100, Italy
| | - Christoph Langner
- Stralsund Zoological Garden, Grünhufer Bogen 2, Stralsund 18437, Germany
| | - Christin Trapp
- Tierpark Grimmen, Friedrichstraße 20, Grimmen 18507, Germany
| | - Heiko Schulz
- Betriebsteil Forstplanung/Versuchswesen/Informationssysteme, Landesforst Mecklenburg-Vorpommern—Anstalt des öffentlichen Rechts, Zeppelinstraße 3, Schwerin 19061, Germany
| | - Wilko Stubbe
- Institut für Allgemeine und Systematische Zoologie, Universität Greifswald, Loitzer Straße 26, Greifswald 17489, Germany
| | - Christian Imholt
- Rodent Research, Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institute (JKI), Federal Research Centre for Cultivated Plants, Toppheideweg 88, Münster 48161, Germany
| | - Gerald Heckel
- Institute of Ecology and Evolution, University of Bern, Baltzerstraße 6, Bern CH-3012, Switzerland
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, Greifswald-Insel Riems 17493, Germany
| | - Florian Pfaff
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, Greifswald-Insel Riems 17493, Germany
| | - Rainer G Ulrich
- Partner Site Hamburg-Lübeck-Borstel-Riems, German Center for Infection Research (DZIF), Germany
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Schotte U, Binder A, Goller KV, Faulde M, Ruhl S, Sauer S, Schlegel M, Teifke JP, Ulrich RG, Wylezich C. Field survey and molecular characterization of apicomplexan parasites in small mammals from military camps in Afghanistan. Parasitol Res 2023; 122:1199-1211. [PMID: 36944808 PMCID: PMC10097762 DOI: 10.1007/s00436-023-07820-8] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 03/05/2023] [Indexed: 03/23/2023]
Abstract
Small mammals are an important reservoir for causative agents of numerous infectious diseases, including zoonotic and vector-borne diseases. The occurrence of these pathogens represents a regional but permanent threat for humans and animals in general and might especially weaken military personnel and companion animals in abroad missions. In our study, small mammals collected in military camps in Afghanistan (Feyzabad, Mazar-e Sharif, and Kunduz) were investigated for the presence of apicomplexans using histopathology and molecular methods. For this purpose, well-established and newly developed real-time PCR assays were applied. A high prevalence was detected not only in house mice (Mus musculus), but also in shrews (Crocidura cf. suaveolens) and grey dwarf hamsters (Cricetulus migratorius). The molecular characterization based on the 18S rRNA gene revealed a close relationship to a cluster of Hepatozoon sp. detected in voles of the genus Microtus. Hepatozoon canis DNA was detected in one house mouse as well as in two Rhipicephalus ticks from a dog puppy. In addition, around 5% of the house mice were found to be infected with far related adeleorinids showing the highest sequence identity of 91.5% to Klossiella equi, the only published Klossiella sequence at present. For their better phylogenetic characterization, we conducted metagenomics by sequencing of two selected samples. The resulting 18S rRNA gene sequences have a length of about 2400 base pairs including an insertion of about 500 base pairs and are 100% identical to each other. Histopathology together with organ tropism and detection rates verified this sequence as of Klossiella muris. In conclusion, we documented naturally occurring protozoan stages and the additional taxonomic characterization of a well-known commensal in mice by applying a combination of different approaches. The study is of medical, social, and biological importance for ensuring human and animal health in military camps and also stresses the required awareness for the potential risk of zoonoses.
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Affiliation(s)
- Ulrich Schotte
- Department of Veterinary Medicine, Central Institute of the Bundeswehr Medical Service Kiel, Kopperpahler Allee 120, 24119, Kronshagen, Germany.
| | - Alfred Binder
- Department of Veterinary Medicine, Central Institute of the Bundeswehr Medical Service Kiel, Kopperpahler Allee 120, 24119, Kronshagen, Germany
| | - Katja V Goller
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald Insel Riems, Germany
- Institute for Hygiene and Environmental Medicine and Central Unit for Infection Prevention and Control, University Medicine Greifswald, Fleischmannstraße 8, 17475, Greifswald, Germany
| | - Michael Faulde
- Department of Medicine, Central Institute of the Bundeswehr Medical Service Koblenz, Andernacher Str. 100, 56070, Koblenz, Germany
- Bundeswehr Research Institute (WIWeB), Institutsweg 1, 85435, Erding, Germany
| | - Silke Ruhl
- Department of Veterinary Medicine, Central Institute of the Bundeswehr Medical Service Kiel, Kopperpahler Allee 120, 24119, Kronshagen, Germany
- Bundeswehr Medical Academy, Deployment Health Surveillance Center, Neuherbergstr. 11, 80937, Munich, Germany
| | - Sabine Sauer
- Division E, Bundeswehr Medical Academy, Military Medical Research and Development, Neuherbergstr. 11, 80937, Munich, Germany
| | - Mathias Schlegel
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald Insel Riems, Germany
- Seramun Diagnostica GmbH, Spreenhagener Str. 1, 15754, Heidesee, Germany
| | - Jens P Teifke
- Department of Experimental Animal Facilities and Biorisk Management (ATB), Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald Insel Riems, Germany
| | - Rainer G Ulrich
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald Insel Riems, Germany
| | - Claudia Wylezich
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald Insel Riems, Germany.
- Department of Experimental Animal Facilities and Biorisk Management (ATB), Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald Insel Riems, Germany.
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5
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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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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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8
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Voss A, Schlieben P, Gerst S, Wylezich C, Pfaff F, Langner C, Niesler M, Schad P, Beer M, Rubbenstroth D, Breithaupt A, Mundhenk L. Rustrela virus infection - An emerging neuropathogen of red-necked wallabies (Macropus rufogriseus). Transbound Emerg Dis 2022; 69:4016-4021. [PMID: 36135593 DOI: 10.1111/tbed.14708] [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: 06/01/2022] [Revised: 09/06/2022] [Accepted: 09/15/2022] [Indexed: 02/07/2023]
Abstract
The rustrela virus (RusV) was recently described as a novel pathogen in a circumscribed area of northern Germany close to the Baltic Sea. Up to now, the virus has been detected in cases of fatal non-suppurative meningoencephalitis in zoo animals of different species and a single wild carnivore as well as in apparently healthy yellow-necked field mice (Apodemus flavicollis). Data regarding the background of this previously undiscovered pathogen, including clinical presentation of the disease, host range and distribution of the virus, are still limited. Here, three euthanized red-necked wallabies (Macropus rufogriseus) from zoos of different areas in northeastern Germany were submitted for necropsy after presenting with apathy and therapeutically unresponsive neurological signs. A moderate to severe, non-suppurative meningoencephalitis was diagnosed in all three cases. RusV was consistently detected via RT-qPCR and RNA in situ hybridization in the brains of all wallabies. Other commonly known neuropathogens could not be detected.
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Affiliation(s)
- Anne Voss
- Institute, of Veterinary Pathology, Freie Universität Berlin, Berlin, Germany
| | - Patricia Schlieben
- Berlin-Brandenburg State Laboratory, Frankfurt (Oder), Frankfurt, Germany
| | - Sascha Gerst
- Department for Diagnostic Investigation of Epizootics, State Office for Agriculture, Food Safety and Fishery Mecklenburg-Vorpommern, Rostock, Germany
| | - Claudia Wylezich
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald - Isle of Riems, Greifswald, Germany
| | - Florian Pfaff
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald - Isle of Riems, Greifswald, Germany
| | | | | | - Petra Schad
- Veterinary Practice Pausin, Schönwalde im Glien, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald - Isle of Riems, Greifswald, Germany
| | - Dennis Rubbenstroth
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald - Isle of Riems, Greifswald, Germany
| | - Angele Breithaupt
- Department of Experimental Animal Facilities and Biorisk Management, Friedrich-Loeffler-Institut, Greifswald - Isle of Riems, Greifswald, Germany
| | - Lars Mundhenk
- Institute, of Veterinary Pathology, Freie Universität Berlin, Berlin, Germany
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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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10
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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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11
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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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12
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Stoek F, Barry Y, Ba A, Schulz A, Rissmann M, Wylezich C, Sadeghi B, Beyit AD, Eisenbarth A, N’diaye FB, Haki ML, Doumbia BA, Gueya MB, Bah MY, Eiden M, Groschup MH. Mosquito survey in Mauritania: Detection of Rift Valley fever virus and dengue virus and the determination of feeding patterns. PLoS Negl Trop Dis 2022; 16:e0010203. [PMID: 35427361 PMCID: PMC9113561 DOI: 10.1371/journal.pntd.0010203] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 05/17/2022] [Accepted: 01/26/2022] [Indexed: 11/28/2022] Open
Abstract
In Mauritania, several mosquito-borne viruses have been reported that can cause devastating diseases in animals and humans. However, monitoring data on their occurrence and local distribution are limited. Rift Valley fever virus (RVFV) is an arthropod-borne virus that causes major outbreaks throughout the African continent and the Arabian Peninsula. The first Rift Valley fever (RVF) epidemic in Mauritania occurred in 1987 and since then the country has been affected by recurrent outbreaks of the disease. To gain information on the occurrence of RVFV as well as other mosquito-borne viruses and their vectors in Mauritania, we collected and examined 4,950 mosquitoes, belonging to four genera and 14 species. The mosquitoes were captured during 2018 in the capital Nouakchott and in southern parts of Mauritania. Evidence of RVFV was found in a mosquito pool of female Anopheles pharoensis mosquitoes collected in December on a farm near the Senegal River. At that time, 37.5% of 16 tested Montbéliarde cattle on the farm showed RVFV-specific IgM antibodies. Additionally, we detected IgM antibodies in 10.7% of 28 indigenous cattle that had been sampled on the same farm one month earlier. To obtain information on potential RVFV reservoir hosts, blood meals of captured engorged mosquitoes were analyzed. The mosquitoes mainly fed on humans (urban areas) and cattle (rural areas), but also on small ruminants, donkeys, cats, dogs and straw-colored fruit bats. Results of this study demonstrate the circulation of RVFV in Mauritania and thus the need for further research to investigate the distribution of the virus and its vectors. Furthermore, factors that may contribute to its maintenance should be analyzed more closely. In addition, two mosquito pools containing Aedes aegypti and Culex quinquefasciatus mosquitoes showed evidence of dengue virus (DENV) 2 circulation in the city of Rosso. Further studies are therefore needed to also examine DENV circulation in Mauritania. In Mauritania, various mosquito-borne viruses responsible for devastating diseases in livestock and/or humans occur, threatening both human and animal health. One of these viruses is the Rift Valley fever phlebovirus (RVFV), which is widespread throughout the African continent and the Arabian Peninsula. The first outbreak in Mauritania occurred in 1987, and epidemics have recurred since then. However, little is known about the maintenance of RVFV during inter-epidemic periods, in the absence of reported outbreaks, and although there is evidence of an active circulation of the virus during these times, only limited data are available on the abundance of RVFV and its vectors in Mauritania. Therefore, this study aimed to collect and examine mosquitoes in different areas where outbreaks have already occurred. Additionally, blood of collected blood-fed mosquitoes was analyzed to identify feeding patterns and thus wildlife potentially acting as RVFV reservoir hosts. Furthermore, the collected mosquitoes were analyzed for the presence of other neglected viruses in order to participate in an elucidation of the circulation of different viruses within the mosquito population in Mauritania and to be able to better prevent disease outbreaks.
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Affiliation(s)
- Franziska Stoek
- 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
| | - Aliou Ba
- Office National de Recherche et de Développement de l’Elevage (ONARDEL), Nouakchott, Mauritania
| | - Ansgar Schulz
- 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
| | - Claudia Wylezich
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Balal Sadeghi
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Abdellahi Diambar Beyit
- Office National de Recherche et de Développement de l’Elevage (ONARDEL), Nouakchott, Mauritania
| | - Albert Eisenbarth
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | | | - Mohamed Lemine Haki
- Office National de Recherche et de Développement de l’Elevage (ONARDEL), Nouakchott, Mauritania
| | | | | | | | - Martin Eiden
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Martin H. Groschup
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
- * E-mail:
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13
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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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14
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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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15
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Hirschbühl K, Dintner S, Beer M, Wylezich C, Schlegel J, Delbridge C, Borcherding L, Lippert J, Schiele S, Müller G, Moiraki D, Spring O, Wittmann M, Kling E, Braun G, Kröncke T, Claus R, Märkl B, Schaller T. Viral mapping in COVID-19 deceased in the Augsburg autopsy series of the first wave: A multiorgan and multimethodological approach. PLoS One 2021; 16:e0254872. [PMID: 34280238 PMCID: PMC8289110 DOI: 10.1371/journal.pone.0254872] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 07/05/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND COVID-19 is only partly understood, and the level of evidence available in terms of pathophysiology, epidemiology, therapy, and long-term outcome remains limited. During the early phase of the pandemic, it was necessary to effectively investigate all aspects of this new disease. Autopsy can be a valuable procedure to investigate the internal organs with special techniques to obtain information on the disease, especially the distribution and type of organ involvement. METHODS During the first wave of COVID-19 in Germany, autopsies of 19 deceased patients were performed. Besides gross examination, the organs were analyzed with standard histology and polymerase-chain-reaction for SARS-CoV-2. Polymerase chain reaction positive localizations were further analyzed with immunohistochemistry and RNA-in situ hybridization for SARS-CoV-2. RESULTS Eighteen of 19 patients were found to have died due to COVID-19. Clinically relevant histological changes were only observed in the lungs. Diffuse alveolar damage in considerably different degrees was noted in 18 cases. Other organs, including the central nervous system, did not show specific micromorphological alterations. In terms of SARS-CoV-2 detection, the focus remains on the upper airways and lungs. This is true for both the number of positive samples and the viral load. A highly significant inverse correlation between the stage of diffuse alveolar damage and viral load was found on a case and a sample basis. Mediastinal lymph nodes and fat were also affected by the virus at high frequencies. By contrast, other organs rarely exhibited a viral infection. Moderate to strong correlations between the methods for detecting SARS-CoV-2 were observed for the lungs and for other organs. CONCLUSIONS The lung is the most affected organ in gross examination, histology and polymerase chain reaction. SARS-CoV-2 detection in other organs did not reveal relevant or specific histological changes. Moreover, we did not find CNS involvement.
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Affiliation(s)
- Klaus Hirschbühl
- Hematology and Oncology, Medical Faculty, University of Augsburg, Augsburg, Germany
| | - Sebastian Dintner
- General Pathology and Molecular Diagnostics, Medical Faculty, University of Augsburg, Augsburg, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institute, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Claudia Wylezich
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institute, 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
| | - Claire Delbridge
- Department of Neuropathology, School of Medicine, Institute of Pathology, Technical University Munich, Munich, Germany
| | - Lukas Borcherding
- General Pathology and Molecular Diagnostics, Medical Faculty, University of Augsburg, Augsburg, Germany
| | - Jirina Lippert
- General Pathology and Molecular Diagnostics, Medical Faculty, University of Augsburg, Augsburg, Germany
| | - Stefan Schiele
- Computational Statistics and Data Analysis, Institute of Mathematics, University of Augsburg, Augsburg, Germany
| | - Gernot Müller
- Computational Statistics and Data Analysis, Institute of Mathematics, University of Augsburg, Augsburg, Germany
| | - Dimitra Moiraki
- General Pathology and Molecular Diagnostics, Medical Faculty, University of Augsburg, Augsburg, Germany
| | - Oliver Spring
- Anesthesiology and Operative Intensive Care Medicine, Medical Faculty, University of Augsburg, Augsburg, Germany
| | - Michael Wittmann
- Hematology and Oncology, Medical Faculty, University of Augsburg, Augsburg, Germany
| | - Elisabeth Kling
- Microbiology, Medical Faculty, University of Augsburg, Augsburg, Germany
| | - Georg Braun
- Department of Gastroenterology, University Hospital Augsburg, Augsburg, Germany
| | - Thomas Kröncke
- Diagnostic and Interventional Radiology, Medical Faculty, University of Augsburg, Augsburg, Germany
| | - Rainer Claus
- Hematology and Oncology, Medical Faculty, University of Augsburg, Augsburg, Germany
| | - Bruno Märkl
- General Pathology and Molecular Diagnostics, Medical Faculty, University of Augsburg, Augsburg, Germany
| | - Tina Schaller
- General Pathology and Molecular Diagnostics, Medical Faculty, University of Augsburg, Augsburg, Germany
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16
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Schulz C, Wylezich C, Wernike K, Gründl M, Dangel A, Baechlein C, Hoffmann D, Röhrs S, Hepner S, Ackermann N, Sing A, Pink I, Länger B, Volk HA, Becher P, Sutter G, Neubauer-Juric A, von Köckritz-Blickwede M, Beer M, Volz A. Prolonged SARS-CoV-2 RNA Shedding from Therapy Cat after Cluster Outbreak in Retirement Home. Emerg Infect Dis 2021; 27:1974-1976. [PMID: 34152973 PMCID: PMC8237873 DOI: 10.3201/eid2707.204670] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
We report a therapy cat in a nursing home in Germany infected with severe acute respiratory syndrome coronavirus 2 during a cluster outbreak in the home residents. Although we confirmed prolonged presence of virus RNA in the asymptomatic cat, genome sequencing showed no further role of the cat in human infections on site.
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17
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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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18
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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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19
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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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20
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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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21
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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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22
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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; 13:69. [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] [Track Full Text] [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
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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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24
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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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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: 357] [Impact Index Per Article: 89.3] [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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26
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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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27
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De Cesare A, Oliveri C, Lucchi A, Pasquali F, Pamp SJ, Mordhorst H, Wylezich C, Poulsen C, Manfreda G. ERRATUM TO: Application of shotgun metagenomics to smoked salmon experimentally spiked: Comparison between sequencing and microbiological data using different bioinformatic approaches. Ital J Food Saf 2020; 9:8991. [PMID: 32300574 PMCID: PMC7154600 DOI: 10.4081/ijfs.2020.8991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 03/30/2020] [Indexed: 12/05/2022] Open
Affiliation(s)
| | - Chiara Oliveri
- Department of Agricultural and Food Sciences, Alma Mater Studiorum University of Bologna, Italy
| | - Alex Lucchi
- Department of Agricultural and Food Sciences, Alma Mater Studiorum University of Bologna, Italy
| | - Frederique Pasquali
- Department of Agricultural and Food Sciences, Alma Mater Studiorum University of Bologna, Italy
| | | | | | - Claudia Wylezich
- Friedrich-Loeffler- Institut, Federal Research Institute for Animal Health, Greifswald Insel Riems, Germany
| | | | - Gerardo Manfreda
- Department of Agricultural and Food Sciences, Alma Mater Studiorum University of Bologna, Italy
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28
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Rubbenstroth D, Ulrich R, Wylezich C, Rautenschlein S, Beer M, Mohr L. First experimental proof of Rotavirus A (RVA) genotype G18P[17] inducing the clinical presentation of 'young pigeon disease syndrome' (YPDS) in domestic pigeons (Columba livia). Transbound Emerg Dis 2020; 67:1507-1516. [PMID: 31967734 DOI: 10.1111/tbed.13485] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 12/03/2019] [Accepted: 01/15/2020] [Indexed: 11/27/2022]
Abstract
Young pigeon disease syndrome (YPDS) is characterized as a seasonally occurring, acute and primarily enteric medical condition of mainly juvenile domestic pigeons (Columba livia) with highly variable mortality reaching more than 50%. Although the syndrome has been known in Europe for almost three decades, its aetiology remains largely obscure. Recently, a previously unknown pigeon-associated clade of Rotavirus A (RVA) genotype G18P[17] was detected in Europe and Australia in association with fatal diseases resembling YPDS. Here we show for the first time, that peroral inoculation of healthy juvenile homing pigeons with two genetically different cell culture isolates of RVA G18P[17] (106.3 foci-forming units per bird) induces an acute and self-limiting YPDS-like disease in all infected birds. Clinical signs included regurgitation, diarrhoea, congested crops, anorexia and weight loss, as described for naturally RVA-infected pigeons. In agreement with the original outbreaks, RVA isolate DR-7 induced more pronounced clinical signs as compared to isolate DR-5, indicating strain-dependent virulence factors to contribute to variable disease outcomes observed in the field. All inoculated birds developed rotavirus-reactive antibodies starting at seven days after inoculation. High levels of viral RNA and infectious virus were detectable in cloacal swabs and faecal samples already three days after inoculation. While shedding of infectious virus subsided within few days, moderate viral RNA levels were still detectable in cloacal swabs, faeces, and tissue samples at the end of the experiment three weeks after inoculation. Histopathological analysis at this time point revealed inflammatory lesions in spleens and livers of pigeons from both infected groups. In summary, we fulfilled Henle-Koch's postulates and confirmed RVA G18P[17] as a primary cause of YPDS-like diseases in domestic pigeons. By establishing an infection model, we provide a crucial tool for future research, such as identification of transmission routes and establishing vaccination regimes.
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Affiliation(s)
- Dennis Rubbenstroth
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald - Insel Riems, Germany
| | - Reiner Ulrich
- Institute of Veterinary-Pathology, Leipzig University, Leipzig, Germany.,Department of Experimental Animal Facilities and Biorisk Management, Friedrich-Loeffler-Institut, Greifswald - Insel Riems, Germany
| | - Claudia Wylezich
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald - Insel Riems, Germany
| | - Silke Rautenschlein
- Clinic for Poultry, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald - Insel Riems, Germany
| | - Lydia Mohr
- Clinic for Poultry, University of Veterinary Medicine Hannover, Hannover, Germany
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29
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Schoenle A, Hohlfeld M, Rosse M, Filz P, Wylezich C, Nitsche F, Arndt H. Global comparison of bicosoecid Cafeteria-like flagellates from the deep ocean and surface waters, with reorganization of the family Cafeteriaceae. Eur J Protistol 2020; 73:125665. [PMID: 31978633 DOI: 10.1016/j.ejop.2019.125665] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [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: 05/22/2019] [Revised: 12/11/2019] [Accepted: 12/16/2019] [Indexed: 02/04/2023]
Abstract
Cafeteria is one of the most common and ecologically significant genera of heterotrophic nanoflagellates in marine plankton. We could isolate and cultivate 29 strains morphologically similar to Cafeteria obtained from surface waters and the deep sea all over the world's ocean. Morphological characterization obtained by high resolution microscopy revealed only small differences between the strains. Sequencing the type material of the type species C. roenbergensis (CCAP 1900/1) and molecular analyses (18S rDNA, 28S rDNA) of newly isolated strains resulted in a revision and separation of the Cafeteriaceae into two known species (C. roenbergensis, C. mylnikovii) and six new species (C. maldiviensis, C. biegae, C. loberiensis, C. chilensis, C. graefeae, C. burkhardae). Many deposited Cafeteria sequences at GenBank and most of our own sequences clustered within one clade (C. burkhardae) with a p-distance of 5% to strain CCAP 1900/1. Only C. maldiviensis clustered together with the type species C. roenbergensis. While C. burkhardae seems to have a cosmopolitan distribution, the distribution of the other species seems to be more restricted. A strain from the Angola Basin had a p-distance of 10% to Cafeteria species and clustered separately within the Anoecales requiring the erection of a new genus, Bilabrum gen. nov., with B. latius sp. nov. as type species.
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Affiliation(s)
- Alexandra Schoenle
- University of Cologne, Biocenter, Institute of Zoology, General Ecology, 50674 Cologne, Germany
| | - Manon Hohlfeld
- University of Cologne, Biocenter, Institute of Zoology, General Ecology, 50674 Cologne, Germany
| | - Mona Rosse
- University of Cologne, Biocenter, Institute of Zoology, General Ecology, 50674 Cologne, Germany
| | - Paulina Filz
- University of Cologne, Biocenter, Institute of Zoology, General Ecology, 50674 Cologne, Germany
| | - Claudia Wylezich
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Diagnostic Virology, Südufer 10, D-17493 Greifswald, Insel Riems, Germany
| | - Frank Nitsche
- University of Cologne, Biocenter, Institute of Zoology, General Ecology, 50674 Cologne, Germany
| | - Hartmut Arndt
- University of Cologne, Biocenter, Institute of Zoology, General Ecology, 50674 Cologne, Germany.
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30
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Mylnikov AP, Tikhonenkov DV, Karpov SA, Wylezich C. Microscopical Studies on Ministeria vibrans Tong, 1997 (Filasterea) Highlight the Cytoskeletal Structure of the Common Ancestor of Filasterea, Metazoa and Choanoflagellata. Protist 2019; 170:385-396. [DOI: 10.1016/j.protis.2019.07.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 06/22/2019] [Accepted: 07/23/2019] [Indexed: 01/06/2023]
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31
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Brinkmann A, Andrusch A, Belka A, Wylezich C, Höper D, Pohlmann A, Nordahl Petersen T, Lucas P, Blanchard Y, Papa A, Melidou A, Oude Munnink BB, Matthijnssens J, Deboutte W, Ellis RJ, Hansmann F, Baumgärtner W, van der Vries E, Osterhaus A, Camma C, Mangone I, Lorusso A, Marcacci M, Nunes A, Pinto M, Borges V, Kroneman A, Schmitz D, Corman VM, Drosten C, Jones TC, Hendriksen RS, Aarestrup FM, Koopmans M, Beer M, Nitsche A. Proficiency Testing of Virus Diagnostics Based on Bioinformatics Analysis of Simulated In Silico High-Throughput Sequencing Data Sets. J Clin Microbiol 2019; 57:e00466-19. [PMID: 31167846 PMCID: PMC6663916 DOI: 10.1128/jcm.00466-19] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [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: 03/22/2019] [Accepted: 05/28/2019] [Indexed: 12/22/2022] Open
Abstract
Quality management and independent assessment of high-throughput sequencing-based virus diagnostics have not yet been established as a mandatory approach for ensuring comparable results. The sensitivity and specificity of viral high-throughput sequence data analysis are highly affected by bioinformatics processing using publicly available and custom tools and databases and thus differ widely between individuals and institutions. Here we present the results of the COMPARE [Collaborative Management Platform for Detection and Analyses of (Re-)emerging and Foodborne Outbreaks in Europe] in silico virus proficiency test. An artificial, simulated in silico data set of Illumina HiSeq sequences was provided to 13 different European institutes for bioinformatics analysis to identify viral pathogens in high-throughput sequence data. Comparison of the participants' analyses shows that the use of different tools, programs, and databases for bioinformatics analyses can impact the correct identification of viral sequences from a simple data set. The identification of slightly mutated and highly divergent virus genomes has been shown to be most challenging. Furthermore, the interpretation of the results, together with a fictitious case report, by the participants showed that in addition to the bioinformatics analysis, the virological evaluation of the results can be important in clinical settings. External quality assessment and proficiency testing should become an important part of validating high-throughput sequencing-based virus diagnostics and could improve the harmonization, comparability, and reproducibility of results. There is a need for the establishment of international proficiency testing, like that established for conventional laboratory tests such as PCR, for bioinformatics pipelines and the interpretation of such results.
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Affiliation(s)
- Annika Brinkmann
- Robert Koch Institute, Centre for Biological Threats and Special Pathogens 1, Berlin, Germany
| | - Andreas Andrusch
- Robert Koch Institute, Centre for Biological Threats and Special Pathogens 1, Berlin, Germany
| | - Ariane Belka
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
| | - 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
| | - Anne Pohlmann
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
| | - Thomas Nordahl Petersen
- Technical University of Denmark, National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Foodborne Pathogens and Genomics and European Union Reference Laboratory for Antimicrobial Resistance, Kongens Lyngby, Denmark
| | - Pierrick Lucas
- French Agency for Food, Environmental and Occupational Health and Safety, Laboratory of Ploufragan, Unit of Viral Genetics and Biosafety, Ploufragan, France
| | - Yannick Blanchard
- French Agency for Food, Environmental and Occupational Health and Safety, Laboratory of Ploufragan, Unit of Viral Genetics and Biosafety, Ploufragan, France
| | - Anna Papa
- Microbiology Department, Aristotle University of Thessaloniki, School of Medicine, Thessaloniki, Greece
| | - Angeliki Melidou
- Microbiology Department, Aristotle University of Thessaloniki, School of Medicine, Thessaloniki, Greece
| | - Bas B Oude Munnink
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, The Netherlands
| | | | | | | | - Florian Hansmann
- Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Wolfgang Baumgärtner
- Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Erhard van der Vries
- Department of Infectious Diseases and Immunology, University of Utrecht, Utrecht, The Netherlands
| | | | - Cesare Camma
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise G. Caporale, National Reference Center for Whole Genome Sequencing of Microbial Pathogens: Database and Bioinformatic Analysis, Teramo, Italy
| | - Iolanda Mangone
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise G. Caporale, National Reference Center for Whole Genome Sequencing of Microbial Pathogens: Database and Bioinformatic Analysis, Teramo, Italy
| | - Alessio Lorusso
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise G. Caporale, National Reference Center for Whole Genome Sequencing of Microbial Pathogens: Database and Bioinformatic Analysis, Teramo, Italy
| | - Maurilia Marcacci
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise G. Caporale, National Reference Center for Whole Genome Sequencing of Microbial Pathogens: Database and Bioinformatic Analysis, Teramo, Italy
| | - Alexandra Nunes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), Lisbon, Portugal
| | - Miguel Pinto
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), Lisbon, Portugal
| | - Vítor Borges
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), Lisbon, Portugal
| | - Annelies Kroneman
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Dennis Schmitz
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, The Netherlands
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Victor Max Corman
- Institute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Christian Drosten
- Institute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Terry C Jones
- Institute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Rene S Hendriksen
- Technical University of Denmark, National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Foodborne Pathogens and Genomics and European Union Reference Laboratory for Antimicrobial Resistance, Kongens Lyngby, Denmark
| | - Frank M Aarestrup
- Technical University of Denmark, National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Foodborne Pathogens and Genomics and European Union Reference Laboratory for Antimicrobial Resistance, Kongens Lyngby, Denmark
| | - Marion Koopmans
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Martin Beer
- Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
| | - Andreas Nitsche
- Robert Koch Institute, Centre for Biological Threats and Special Pathogens 1, Berlin, Germany
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Wylezich C, Belka A, Hanke D, Beer M, Blome S, Höper D. Metagenomics for broad and improved parasite detection: a proof-of-concept study using swine faecal samples. Int J Parasitol 2019; 49:769-777. [PMID: 31361998 DOI: 10.1016/j.ijpara.2019.04.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [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: 02/26/2019] [Revised: 04/18/2019] [Accepted: 04/24/2019] [Indexed: 01/10/2023]
Abstract
Efficient and reliable identification of emerging pathogens is crucial for the design and implementation of timely and proportionate control strategies. This is difficult if the pathogen is so far unknown or only distantly related with known pathogens. Diagnostic metagenomics - an undirected, broad and sensitive method for the efficient identification of pathogens - was frequently used for virus and bacteria detection, but seldom applied to parasite identification. Here, metagenomics datasets prepared from swine faeces using an unbiased sample processing approach with RNA serving as starting material were re-analysed with respect to parasite detection. The taxonomic identification tool RIEMS, used for initial detection, provided basic hints on potential pathogens contained in the datasets. The suspected parasites/intestinal protists (Blastocystis, Entamoeba, Iodamoeba, Neobalantidium, Tetratrichomonas) were verified using subsequently applied reference mapping analyses on the base of rRNA sequences. Nearly full-length gene sequences could be extracted from the RNA-derived datasets. In the case of Blastocystis, subtyping was possible with subtype (ST)15 discovered for the first known time in swine faeces. Using RIEMS, some of the suspected candidates turned out to be false-positives caused by the poor status of sequences in publicly available databases. Altogether, 11 different species/STs of parasites/intestinal protists were detected in 34 out of 41 datasets extracted from metagenomics data. The approach operates without any primer bias that typically hampers the analysis of amplicon-based approaches, and allows the detection and taxonomic classification including subtyping of protist and metazoan endobionts (parasites, commensals or mutualists) based on an abundant biomarker, the 18S rRNA. The generic nature of the approach also allows evaluation of interdependencies that induce mutualistic or pathogenic effects that are often not clear for many intestinal protists and perhaps other parasites. Thus, metagenomics has the potential for generic pathogen identification beyond the characterisation of viruses and bacteria when starting from RNA instead of DNA.
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Affiliation(s)
- Claudia Wylezich
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut (FLI), Südufer 10, 17493 Greifswald-Insel Riems, Germany.
| | - Ariane Belka
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut (FLI), Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Dennis Hanke
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut (FLI), Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut (FLI), Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Sandra Blome
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut (FLI), Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Dirk Höper
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut (FLI), Südufer 10, 17493 Greifswald-Insel Riems, Germany.
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33
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Rubbenstroth D, Peus E, Schramm E, Kottmann D, Bartels H, McCowan C, Schulze C, Akimkin V, Fischer N, Wylezich C, Hlinak A, Spadinger A, Großmann E, Petersen H, Grundhoff A, Rautenschlein S, Teske L. Cover Image. Transbound Emerg Dis 2019. [DOI: 10.1111/tbed.13074] [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: 11/28/2022]
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Rubbenstroth D, Peus E, Schramm E, Kottmann D, Bartels H, McCowan C, Schulze C, Akimkin V, Fischer N, Wylezich C, Hlinak A, Spadinger A, Großmann E, Petersen H, Grundhoff A, Rautenschlein S, Teske L. Identification of a novel clade of group A rotaviruses in fatally diseased domestic pigeons in Europe. Transbound Emerg Dis 2018; 66:552-561. [DOI: 10.1111/tbed.13065] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Revised: 10/31/2018] [Accepted: 11/01/2018] [Indexed: 11/29/2022]
Affiliation(s)
- Dennis Rubbenstroth
- Institute of Virology Medical Center – University of Freiburg Faculty of Medicine University of Freiburg Freiburg Germany
- Institute of Diagnostic Virology Friedrich‐Loeffler‐Institut Greifswald – Insel Riems Germany
| | - Elisabeth Peus
- Clinic for Pigeons of the German Pigeon‐Breeders Association Essen Germany
| | - Eva Schramm
- Institute of Virology Medical Center – University of Freiburg Faculty of Medicine University of Freiburg Freiburg Germany
| | - Daniel Kottmann
- Institute of Virology Medical Center – University of Freiburg Faculty of Medicine University of Freiburg Freiburg Germany
| | - Hilke Bartels
- Clinic for Poultry University of Veterinary Medicine Hannover Hannover Germany
| | - Christina McCowan
- Agriculture Victoria, Veterinary Diagnostics Bundoora Victoria Australia
| | | | - Valerij Akimkin
- Chemical and Veterinary Investigations Office Stuttgart Fellbach Germany
| | - Nicole Fischer
- Institute for Medical Microbiology, Virology and Hygiene University Medical Center Hamburg‐Eppendorf Hamburg Germany
- German Center for Research on Infection (DZIF) Partner Site Hamburg‐Borstel‐Lübeck‐Riems Hamburg Germany
| | - Claudia Wylezich
- Institute of Diagnostic Virology Friedrich‐Loeffler‐Institut Greifswald – Insel Riems Germany
| | - Andreas Hlinak
- Berlin‐Brandenburg State Laboratory Frankfurt (Oder) Germany
| | - Anja Spadinger
- Aulendorf state veterinary diagnostic centre Aulendorf Germany
| | - Ernst Großmann
- Aulendorf state veterinary diagnostic centre Aulendorf Germany
| | - Henning Petersen
- Clinic for Poultry University of Veterinary Medicine Hannover Hannover Germany
- Chemical and Veterinary Investigations Office Ostwestfalen‐Lippe DetmoldGermany
| | - Adam Grundhoff
- German Center for Research on Infection (DZIF) Partner Site Hamburg‐Borstel‐Lübeck‐Riems Hamburg Germany
- Heinrich‐Pette Institute Leibniz Institute for Experimental Virology Hamburg Germany
| | - Silke Rautenschlein
- Clinic for Poultry University of Veterinary Medicine Hannover Hannover Germany
| | - Lydia Teske
- Clinic for Poultry University of Veterinary Medicine Hannover Hannover Germany
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Wernike K, Wylezich C, Höper D, Schneider J, Lurz PWW, Meredith A, Milne E, Beer M, Ulrich RG. Widespread occurrence of squirrel adenovirus 1 in red and grey squirrels in Scotland detected by a novel real-time PCR assay. Virus Res 2018; 257:113-118. [PMID: 30237072 DOI: 10.1016/j.virusres.2018.09.007] [Citation(s) in RCA: 4] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 08/13/2018] [Accepted: 09/17/2018] [Indexed: 01/12/2023]
Abstract
The Eurasian Red Squirrel (Sciurus vulgaris) is distributed throughout large parts of Europe and Asia. However, its distribution in certain regions of Europe is endangered by the invasive, non-native Grey Squirrel (Sciurus carolinensis). Adenoviruses were already described in squirrels in Great Britain almost two decades ago. In 2013, a squirrel adenovirus (SqAdV-1) was additionally found in a red squirrel from Germany, which suffered from acute diffuse catarrhal enteritis, and the complete genome sequence was determined. Here, samples from dead red (n = 25) and grey (n = 12) squirrels collected in Scotland, UK, were analysed for the presence of this squirrel-associated virus. By using a newly developed real-time PCR targeting the adenoviral polymerase gene, viral DNA was detected in at least one of four tissue samples tested per animal in 64.0% of the red squirrels and 41.7% of the grey squirrels. Exceptionally high viral genome loads were detected in the intestine and liver, but SqAdV-1 DNA was also present in lung and kidney samples of affected animals. Almost complete genome sequence determination of a red squirrel-derived SqAdV-1 strain from Scotland indicated a very high degree of identity to the first German strain. Sequence analysis of the hexon gene, which encodes one of the major antigens of the virion, revealed an identity of 100% between viruses found in red and grey squirrels from Scotland. In conclusion, SqAdV-1 appears to be widespread in the Scottish red and grey squirrel population, which highlights the necessity for continuous wildlife surveillance. The novel real-time PCR assay offers a highly sensitive and robust method for SqAdV-1 surveillance.
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Affiliation(s)
- Kerstin Wernike
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald-Insel Riems, Germany.
| | - 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.
| | - Julia Schneider
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald-Insel Riems, Germany; NMI TT Pharmaservices, c/o CoLaborator, Müllerstraße 178, 13353, Berlin, Germany.
| | - Peter W W Lurz
- Royal (Dick) School of Veterinary Studies, The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Roslin, Midlothian, EH25 9RG, UK.
| | - Anna Meredith
- Royal (Dick) School of Veterinary Studies, The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Roslin, Midlothian, EH25 9RG, UK; Melbourne Veterinary School, The University of Melbourne, Royal Parade Parkville 3010, Melbourne, Australia.
| | - Elspeth Milne
- Royal (Dick) School of Veterinary Studies, The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Roslin, Midlothian, EH25 9RG, UK.
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald-Insel Riems, Germany.
| | - Rainer G Ulrich
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald-Insel Riems, Germany.
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Abstract
Metagenomics is currently the only generic method for pathogen detection. Starting from RNA allows the assessment of the whole sample community including RNA viruses. Here we present our modular concerted protocol for sample processing for diagnostic metagenomics analysis of human, animal, and food samples. The workflow does not rely on dedicated amplification steps at any stage in the process and, in contrast to published methods, libraries prepared accordingly will yield only minute amounts of unclassifiable reads. We confirmed the performance of the approach using a spectrum of pathogen/matrix-combinations showing it has the potential to become a commonly usable analytical framework.
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Affiliation(s)
- Claudia Wylezich
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut (FLI), 17493, Greifswald-Insel Riems, Germany.
| | - Anna Papa
- Department of Microbiology, Medical School, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut (FLI), 17493, Greifswald-Insel Riems, Germany
| | - Dirk Höper
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut (FLI), 17493, Greifswald-Insel Riems, Germany.
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37
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Corsaro D, Köhsler M, Wylezich C, Venditti D, Walochnik J, Michel R. New insights from molecular phylogenetics of amoebophagous fungi (Zoopagomycota, Zoopagales). Parasitol Res 2017; 117:157-167. [PMID: 29170872 DOI: 10.1007/s00436-017-5685-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [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: 04/20/2017] [Accepted: 11/15/2017] [Indexed: 12/21/2022]
Abstract
Amoebophagous fungi are represented in all fungal groups: Basidiomycota, Ascomycota, Zygomycota, and Chytridiomycota. The amoebophagous fungi, within the zygomycota (Zoopagales, Zoopagomycota), mainly affect naked amoebae as ectoparasites or endoparasites. It is rather difficult to isolate members of the Zoopagales, because of their parasitic lifestyle, and to bring them into culture. Consequently, gene sequences of this group are undersampled, and its species composition and phylogeny are relatively unknown. In the present study, we were able to isolate amoebophagous fungi together with their amoeba hosts from various habitats (moss, pond, bark, and soil). Altogether, four fungal strains belonging to the genera Acaulopage and Stylopage plus one unidentified isolate were detected. Sequences of the 18S rDNA and the complete ITS region and partial 28S (LSU) rDNA were generated. Subsequent phylogenetic analyses showed that all new isolates diverge at one branch together with two environmental clonal sequences within the Zoopagomycota. Here, we provide the first molecular characterization of the genus Stylopage. Stylopage is closely related to the genus Acaulopage. In addition, taxonomy and phylogeny of amoebophagous fungi and their ecological importance are reviewed based on new sequence data, which includes environmental clonal sequences.
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Affiliation(s)
- Daniele Corsaro
- Chlamydia Research Association (CHLAREAS), 12 rue du Maconnais, F-54500, Vandoeuvre-lès-Nancy, France.
| | - Martina Köhsler
- Molecular Parasitology, Institute for Specific Prophylaxis and Tropical Medicine, Medical University of Vienna, Kinderspitalgasse 15, 1090, Vienna, Austria
| | - Claudia Wylezich
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald-Insel Riems, Germany
| | - Danielle Venditti
- Chlamydia Research Association (CHLAREAS), 12 rue du Maconnais, F-54500, Vandoeuvre-lès-Nancy, France.,TREDI Research Department, Faculty of Medicine, Technopôle de Nancy-Brabois, 9, Avenue de la Forêt de Haye, B.P. 184, 54505, Vandœuvre-lès-Nancy, France
| | - Julia Walochnik
- Molecular Parasitology, Institute for Specific Prophylaxis and Tropical Medicine, Medical University of Vienna, Kinderspitalgasse 15, 1090, Vienna, Austria
| | - Rolf Michel
- Central Institute of the Federal Armed Forces Medical Services, P.O. Box 7340, D 56070, Koblenz, Germany
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38
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Abstract
A new world of possibilities for “virus discovery” was opened up with high-throughput sequencing becoming available in the last decade. While scientifically metagenomic analysis was established before the start of the era of high-throughput sequencing, the availability of the first second-generation sequencers was the kick-off for diagnosticians to use sequencing for the detection of novel pathogens. Today, diagnostic metagenomics is becoming the standard procedure for the detection and genetic characterization of new viruses or novel virus variants. Here, we provide an overview about technical considerations of high-throughput sequencing-based diagnostic metagenomics together with selected examples of “virus discovery” for animal diseases or zoonoses and metagenomics for food safety or basic veterinary research.
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Affiliation(s)
- 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
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39
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Jeuck A, Nitsche F, Wylezich C, Wirth O, Bergfeld T, Brutscher F, Hennemann M, Monir S, Scherwaß A, Troll N, Arndt H. A Comparison of Methods to Analyze Aquatic Heterotrophic Flagellates of Different Taxonomic Groups. Protist 2017; 168:375-391. [PMID: 28654859 DOI: 10.1016/j.protis.2017.04.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [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: 10/23/2015] [Revised: 04/24/2017] [Accepted: 04/30/2017] [Indexed: 11/19/2022]
Abstract
Heterotrophic flagellates contribute significantly to the matter flux in aquatic and terrestrial ecosystems. Still today their quantification and taxonomic classification bear several problems in field studies, though these methodological problems seem to be increasingly ignored in current ecological studies. Here we describe and test different methods, the live-counting technique, different fixation techniques, cultivation methods like the liquid aliquot method (LAM), and a molecular single cell survey called aliquot PCR (aPCR). All these methods have been tested either using aquatic field samples or cultures of freshwater and marine taxa. Each of the described methods has its advantages and disadvantages, which have to be considered in every single case. With the live-counting technique a detection of living cells up to morphospecies level is possible. Fixation of cells and staining methods are advantageous due to the possible long-term storage and observation of samples. Cultivation methods (LAM) offer the possibility of subsequent molecular analyses, and aPCR tools might complete the deficiency of LAM in terms of the missing detection of non-cultivable flagellates. In summary, we propose a combination of several investigation techniques reducing the gap between the different methodological problems.
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Affiliation(s)
- Alexandra Jeuck
- Department of General Ecology, Institute for Zoology, Biocenter Cologne, University of Cologne, Zülpicher Straße 47b, D-50674 Cologne, Germany
| | - Frank Nitsche
- Department of General Ecology, Institute for Zoology, Biocenter Cologne, University of Cologne, Zülpicher Straße 47b, D-50674 Cologne, Germany
| | - Claudia Wylezich
- Department of General Ecology, Institute for Zoology, Biocenter Cologne, University of Cologne, Zülpicher Straße 47b, D-50674 Cologne, Germany
| | - Olaf Wirth
- Department of General Ecology, Institute for Zoology, Biocenter Cologne, University of Cologne, Zülpicher Straße 47b, D-50674 Cologne, Germany
| | - Tanja Bergfeld
- Department of General Ecology, Institute for Zoology, Biocenter Cologne, University of Cologne, Zülpicher Straße 47b, D-50674 Cologne, Germany
| | - Fabienne Brutscher
- Department of General Ecology, Institute for Zoology, Biocenter Cologne, University of Cologne, Zülpicher Straße 47b, D-50674 Cologne, Germany
| | - Melanie Hennemann
- Department of General Ecology, Institute for Zoology, Biocenter Cologne, University of Cologne, Zülpicher Straße 47b, D-50674 Cologne, Germany
| | - Shahla Monir
- Department of General Ecology, Institute for Zoology, Biocenter Cologne, University of Cologne, Zülpicher Straße 47b, D-50674 Cologne, Germany
| | - Anja Scherwaß
- Department of General Ecology, Institute for Zoology, Biocenter Cologne, University of Cologne, Zülpicher Straße 47b, D-50674 Cologne, Germany
| | - Nicole Troll
- Department of General Ecology, Institute for Zoology, Biocenter Cologne, University of Cologne, Zülpicher Straße 47b, D-50674 Cologne, Germany
| | - Hartmut Arndt
- Department of General Ecology, Institute for Zoology, Biocenter Cologne, University of Cologne, Zülpicher Straße 47b, D-50674 Cologne, Germany.
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40
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Koehsler M, Walochnik J, Michel R, Lugauer J, Wylezich C. Molecular identification and classification ofCochlonema euryblastum, a zoopagalean parasite ofThecamoeba quadrilineata. Mycologia 2017. [DOI: 10.1080/15572536.2007.11832580] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
| | - Julia Walochnik
- Department of Medical Parasitology, Clinical Institute of Hygiene and Medical Microbiology, Medical University of Vienna, Kinderspitalgasse 15, 1095 Vienna, Austria
| | | | - Johannes Lugauer
- Central Institute of the Federal Armed Forces Medical Services, Department of Parasitology, Andernacher Straße 100, 56070 Koblenz, Germany
| | - Claudia Wylezich
- Department of Ecology and Limnology, Institute of Zoology, University of Cologne, Weyertal 119, 50923 Cologne, Germany
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Weber F, Mylnikov AP, Jürgens K, Wylezich C. Culturing Heterotrophic Protists from the Baltic Sea: Mostly the "Usual Suspects" but a Few Novelties as Well. J Eukaryot Microbiol 2016; 64:153-163. [PMID: 27432754 DOI: 10.1111/jeu.12347] [Citation(s) in RCA: 8] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 07/13/2016] [Accepted: 07/13/2016] [Indexed: 11/30/2022]
Abstract
The study of cultured strains has a long tradition in protistological research and has greatly contributed to establishing the morphology, taxonomy, and ecology of many protist species. However, cultivation-independent techniques, based on 18S rRNA gene sequences, have demonstrated that natural protistan assemblages mainly consist of hitherto uncultured protist lineages. This mismatch impedes the linkage of environmental diversity data with the biological features of cultured strains. Thus, novel taxa need to be obtained in culture to close this knowledge gap. In this study, traditional cultivation techniques were applied to samples from coastal surface waters and from deep oxygen-depleted waters of the Baltic Sea. Based on 18S rRNA gene sequencing, 126 monoclonal cultures of heterotrophic protists were identified. The majority of the isolated strains were affiliated with already cultured and described taxa, mainly chrysophytes and bodonids. This was likely due to "culturing bias" but also to the eutrophic nature of the Baltic Sea. Nonetheless, ~ 12% of the isolates in our culture collection showed highly divergent 18S rRNA gene sequences compared to those of known organisms and thus may represent novel taxa, either at the species level or at the genus level. Moreover, we also obtained evidence that some of the isolated taxa are ecologically relevant, under certain conditions, in the Baltic Sea.
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Affiliation(s)
- Felix Weber
- Biological Oceanography, IOW-Leibniz Institute for Baltic Sea Research Warnemünde, Seestr. 15, Rostock, 18119, Germany
| | - Alexander P Mylnikov
- Biological Oceanography, IOW-Leibniz Institute for Baltic Sea Research Warnemünde, Seestr. 15, Rostock, 18119, Germany.,Institute for the Biology of Inland Waters, Russian Academy of Sciences, Borok, Yaroslavskaya Obl., 152742, Russia
| | - Klaus Jürgens
- Biological Oceanography, IOW-Leibniz Institute for Baltic Sea Research Warnemünde, Seestr. 15, Rostock, 18119, Germany
| | - Claudia Wylezich
- Biological Oceanography, IOW-Leibniz Institute for Baltic Sea Research Warnemünde, Seestr. 15, Rostock, 18119, Germany
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42
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Mylnikov AP, Weber F, Jürgens K, Wylezich C. Massisteria marina has a sister: Massisteria voersi sp. nov., a rare species isolated from coastal waters of the Baltic Sea. Eur J Protistol 2015; 51:299-310. [DOI: 10.1016/j.ejop.2015.05.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 05/20/2015] [Accepted: 05/20/2015] [Indexed: 11/27/2022]
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Quintela-Alonso P, Nitsche F, Wylezich C, Arndt H, Foissner W. A new tetrahymena (ciliophora, oligohymenophorea) from groundwater of cape town, South Africa. J Eukaryot Microbiol 2013; 60:235-46. [PMID: 23346896 DOI: 10.1111/jeu.12021] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Revised: 11/12/2012] [Accepted: 11/12/2012] [Indexed: 11/28/2022]
Abstract
The identification of species within the genus Tetrahymena is known to be difficult due to their essentially identical morphology, the occurrence of cryptic and sibling species and the phenotypic plasticity associated with the polymorphic life cycle of some species. We have combined morphology and molecular biology to describe Tetrahymena aquasubterranea n. sp. from groundwater of Cape Town, Republic of South Africa. The phylogenetic analysis compares the cox1 gene sequence of T. aquasubterranea with the cox1 gene sequences of other Tetrahymena species and uses the interior-branch test to improve the resolution of the evolutionary relationships. This showed a considerable genetic divergence of T. aquasubterranea to its next relative, T. farlyi, of 9.2% (the average cox1 divergence among bona fide species of Tetrahymena is ~ 10%). Moreover, the analysis also suggested a sister relationship between T. aquasubterranea and a big clade comprising T. farleyi, T. tropicalis, T. furgasoni and T. mobilis. The morphological data available for these species show that they share with T. aquasubterranea a pyriformis-like life style and at least two of them, T. farleyi and T. mobilis, a similar type II silverline pattern consisting of primary and secondary meridians. Tetrahymena aquasubterranea exhibits a biphasic life cycle with trophonts and theronts, is amicronucleate, and feeds on bacteria.
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Affiliation(s)
- Pablo Quintela-Alonso
- Department of General Ecology, Cologne Biocenter, Institute for Zoology, University of Cologne, Zülpicher Str. 47b, D-50674, Köln, Germany.
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44
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Anderson R, Wylezich C, Glaubitz S, Labrenz M, Jürgens K. Impact of protist grazing on a key bacterial group for biogeochemical cycling in Baltic Sea pelagic oxic/anoxic interfaces. Environ Microbiol 2013; 15:1580-94. [PMID: 23368413 DOI: 10.1111/1462-2920.12078] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Revised: 12/17/2012] [Accepted: 12/20/2012] [Indexed: 11/27/2022]
Abstract
Barrier zones between oxic and anoxic water masses (redoxclines) host highly active prokaryotic communities with important roles in biogeochemical cycling. In Baltic Sea pelagic redoxclines, Epsilonproteobacteria of the genus Sulfurimonas (subgroup GD17) have been shown to dominate chemoautotrophic denitrification. However, little is known on the loss processes affecting this prokaryotic group. In the present study, the protist grazing impact on the Sulfurimonas subgroup GD17 was determined for suboxic and oxygen/hydrogen sulphide interface depths of Baltic Sea redoxclines, using predator exclusion assays and bacterial amendment with the cultured representative 'Sulfurimonas gotlandica' strain GD1. Additionally, the principal bacterivores were identified by RNA-Stable Isotope Probing (RNA-SIP). The natural Sulfurimonas subgroup GD17 population grew strongly under oxygen/hydrogen sulphide interface conditions (doubling time: 1-1.5 days), but protist grazing could consume the complete new cell production per day. In suboxic samples, little or no growth of Sulfurimonas subgroup GD17 was observed. RNA-SIP identified five active grazers, belonging to typical redoxcline ciliates (Oligohymenophorea, Prostomatea) and globally widespread marine flagellate groups (MAST-4, Chrysophyta, Cercozoa). Overall, we demonstrate for the first time that protist grazing can control the growth, and potentially the vertical distribution, of a chemolithoautotrophic key-player of oxic/anoxic interfaces.
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Affiliation(s)
- Ruth Anderson
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research, Seestrasse 15, 18119, Rostock-Warnemünde, Germany.
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Wylezich C, Karpov SA, Mylnikov AP, Anderson R, Jürgens K. Ecologically relevant choanoflagellates collected from hypoxic water masses of the Baltic Sea have untypical mitochondrial cristae. BMC Microbiol 2012; 12:271. [PMID: 23171165 PMCID: PMC3579758 DOI: 10.1186/1471-2180-12-271] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [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: 08/24/2012] [Accepted: 11/08/2012] [Indexed: 11/17/2022] Open
Abstract
Background Protist communities inhabiting oxygen depleted waters have so far been characterized through both microscopical observations and sequence based techniques. However, the lack of cultures for abundant taxa severely hampers our knowledge on the morphology, ecology and energy metabolism of hypoxic protists. Cultivation of such protists has been unsuccessful in most cases, and has never yet succeeded for choanoflagellates, even though these small bacterivorous flagellates are known to be ecologically relevant components of aquatic protist communities. Results Quantitative data for choanoflagellates and the vertical distribution of Codosiga spp. at Gotland and Landsort Deep (Baltic Sea) indicate its preference for oxygen-depleted zones. Strains isolated and cultivated from these habitats revealed ultrastructural peculiarities such as mitochondria showing tubular cristae never seen before for choanoflagellates, and the first observation of intracellular prokaryotes in choanoflagellates. Analysis of their partial 28S rRNA gene sequence complements the description of two new species, Codosiga minima n. sp. and C. balthica n. sp. These are closely related with but well separated from C. gracilis (C. balthica and C. minima p-distance to C. gracilis 4.8% and 11.6%, respectively). In phylogenetic analyses the 18S rRNA gene sequences branch off together with environmental sequences from hypoxic habitats resulting in a wide cluster of hypoxic Codosiga relatives so far only known from environmental sequencing approaches. Conclusions Here, we establish the morphological and ultrastructural identity of an environmental choanoflagellate lineage. Data from microscopical observations, supplemented by findings from previous culture-independent methods, indicate that C. balthica is likely an ecologically relevant player of Baltic Sea hypoxic waters. The possession of derived mitochondria could be an adaptation to life in hypoxic environments periodically influenced by small-scale mixing events and changing oxygen content allowing the reduction of oxygen consuming components. In view of the intricacy of isolating and cultivating choanoflagellates, the two new cultured species represent an important advance to the understanding of the ecology of this group, and mechanisms of adaptations to hypoxia in protists in general.
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Affiliation(s)
- Claudia Wylezich
- IOW-Leibniz Institute for Baltic Sea Research Warnemünde, Rostock, Germany.
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Weber F, del Campo J, Wylezich C, Massana R, Jürgens K. Unveiling trophic functions of uncultured protist taxa by incubation experiments in the brackish Baltic Sea. PLoS One 2012; 7:e41970. [PMID: 22860041 PMCID: PMC3408427 DOI: 10.1371/journal.pone.0041970] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [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: 04/19/2012] [Accepted: 06/28/2012] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Our knowledge of the phylogeny and diversity of aquatic protists is rapidly increasing due to molecular surveys and next-generation sequencing approaches. This has led to a considerable discrepancy between the taxa known from cultures and those known from environmental 18S rRNA gene sequences. Hence, it is generally difficult to assign ecological functions to new taxa detected by culture-independent molecular approaches. METHODOLOGY/PRINCIPAL FINDINGS A combination of unamended dark incubations and 18S rRNA sequencing was chosen to link molecular diversity data of uncultured protists with heterotrophic, presumably bacterivorous, growth. The incubations, conducted with Baltic Sea brackish water, resulted in a consistent shift from a protistan community dominated by phototrophs to one in which heterotrophs predominated. This was determined on the basis of cell abundance and 18S rRNA sequences derived from fingerprint analysis and clone libraries. The bulk of enriched phylotypes after incubation were related to hitherto uncultured marine taxa within chrysophytes, ochrophytes, choanoflagellates, cercozoans, and picobiliphytes, mostly represented in recently established or here defined environmental clades. Their growth in the dark, together with coinciding results from studies with a similar objective, provides evidence that these uncultured taxa represent heterotrophic or mixotrophic species. CONCLUSIONS/SIGNIFICANCE These findings shed some light into the trophic role of diverse uncultured protists especially within functionally heterogeneous groups (e.g., chrysophytes, ochrophytes) and groups that appear to be puzzling with regard to their nutrition (picobiliphytes). Additionally, our results indicate that the heterotrophic flagellate community in the southwestern Baltic Sea is dominated by species of marine origin. The combination of unamended incubations with molecular diversity analysis is thus confirmed as a promising approach to explore the trophic mode of environmentally relevant protist taxa for which only sequence data are currently available.
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Affiliation(s)
- Felix Weber
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde, Rostock, Germany.
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Kudryavtsev A, Wylezich C, Pawlowski J. Ovalopodium desertum n. sp. and the Phylogenetic Relationships of Cochliopodiidae (Amoebozoa). Protist 2011; 162:571-89. [DOI: 10.1016/j.protis.2011.04.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2010] [Accepted: 04/02/2011] [Indexed: 11/16/2022]
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Scheckenbach F, Hausmann K, Wylezich C, Weitere M, Arndt H. WITHDRAWN: Wide distribution ranges of several microbial eukaryotes of nanofaunal size at abyssal depths of the South-East Atlantic and the Mediterranean. Appl Environ Microbiol 2011:AEM.00068-10. [PMID: 21317248 DOI: 10.1128/aem.00068-10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This article has been withdrawn.
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Affiliation(s)
- Frank Scheckenbach
- University of Cologne, Zoological Institute, Department of General Ecology & Limnology, 50923 Cologne, Germany
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Walochnik J, Wylezich C, Michel R. The genus Sappinia: History, phylogeny and medical relevance. Exp Parasitol 2010; 126:4-13. [DOI: 10.1016/j.exppara.2009.11.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2009] [Revised: 11/08/2009] [Accepted: 11/30/2009] [Indexed: 11/29/2022]
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