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Li YQ, Ghafari M, Holbrook AJ, Boonen I, Amor N, Catalano S, Webster JP, Li YY, Li HT, Vergote V, Maes P, Chong YL, Laudisoit A, Baelo P, Ngoy S, Mbalitini SG, Gembu GC, Musaba AP, Goüy de Bellocq J, Leirs H, Verheyen E, Pybus OG, Katzourakis A, Alagaili AN, Gryseels S, Li YC, Suchard MA, Bletsa M, Lemey P. The evolutionary history of hepaciviruses. bioRxiv 2023:2023.06.30.547218. [PMID: 37425679 PMCID: PMC10327235 DOI: 10.1101/2023.06.30.547218] [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] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
In the search for natural reservoirs of hepatitis C virus (HCV), a broad diversity of non-human viruses within the Hepacivirus genus has been uncovered. However, the evolutionary dynamics that shaped the diversity and timescale of hepaciviruses evolution remain elusive. To gain further insights into the origins and evolution of this genus, we screened a large dataset of wild mammal samples (n = 1,672) from Africa and Asia, and generated 34 full-length hepacivirus genomes. Phylogenetic analysis of these data together with publicly available genomes emphasizes the importance of rodents as hepacivirus hosts and we identify 13 rodent species and 3 rodent genera (in Cricetidae and Muridae families) as novel hosts of hepaciviruses. Through co-phylogenetic analyses, we demonstrate that hepacivirus diversity has been affected by cross-species transmission events against the backdrop of detectable signal of virus-host co-divergence in the deep evolutionary history. Using a Bayesian phylogenetic multidimensional scaling approach, we explore the extent to which host relatedness and geographic distances have structured present-day hepacivirus diversity. Our results provide evidence for a substantial structuring of mammalian hepacivirus diversity by host as well as geography, with a somewhat more irregular diffusion process in geographic space. Finally, using a mechanistic model that accounts for substitution saturation, we provide the first formal estimates of the timescale of hepacivirus evolution and estimate the origin of the genus to be about 22 million years ago. Our results offer a comprehensive overview of the micro- and macroevolutionary processes that have shaped hepacivirus diversity and enhance our understanding of the long-term evolution of the Hepacivirus genus.
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Affiliation(s)
- YQ Li
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, KU Leuven, Leuven, 3000, Belgium
| | - M Ghafari
- Department of Biology, University of Oxford, Oxford, OX1, UK
| | - AJ Holbrook
- Department of Biostatistics, University of California, Los Angeles, CA 90095, USA
| | - I Boonen
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, KU Leuven, Leuven, 3000, Belgium
| | - N Amor
- Laboratory of Biodiversity, Parasitology, and Ecology of Aquatic Ecosystems, Department of Biology - Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis, 2092, Tunisia
| | - S Catalano
- School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G61 1QH, UK
- Department of Pathobiology and Population Sciences, the Royal Veterinary College, University of London, Herts, AL9 7TA, UK
| | - JP Webster
- Department of Pathobiology and Population Sciences, the Royal Veterinary College, University of London, Herts, AL9 7TA, UK
| | - YY Li
- College of Life Sciences, Linyi University, Linyi, 276000, China
- Marine College, Shandong University (Weihai), Weihai, 264209, China
| | - HT Li
- College of Life Sciences, Liaocheng University, Liaocheng, 252000, China
- Marine College, Shandong University (Weihai), Weihai, 264209, China
| | - V Vergote
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, KU Leuven, Leuven, 3000, Belgium
| | - P Maes
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, KU Leuven, Leuven, 3000, Belgium
| | - YL Chong
- Animal Resource Science and Management Group, Faculty of Resource Science and Technology, Universiti Malaysia Sarawak (UNIMAS), 94300, Malaysia
- Department of Science and Environmental Studies, The Education University of Hong Kong, Hong Kong, 999077, China
| | - A Laudisoit
- EcoHealth Alliance, New York, NY 10018, USA
- Evolutionary Ecology group (EVECO), Department of Biology, University of Antwerp, Antwerp, 2020, Belgium
| | - P Baelo
- Faculty of Sciences, University of Kisangani, Kisangani, Democratic Republic of the Congo
| | - S Ngoy
- Faculty of Sciences, University of Kisangani, Kisangani, Democratic Republic of the Congo
| | - SG Mbalitini
- Faculty of Sciences, University of Kisangani, Kisangani, Democratic Republic of the Congo
| | - GC Gembu
- Faculty of Sciences, University of Kisangani, Kisangani, Democratic Republic of the Congo
| | - Akawa P Musaba
- Faculty of Sciences, University of Kisangani, Kisangani, Democratic Republic of the Congo
| | - J Goüy de Bellocq
- Institute of Vertebrate Biology, The Czech Academy of Sciences, Květná 8, 603 65 Brno, Czech Republic
| | - H Leirs
- Evolutionary Ecology group (EVECO), Department of Biology, University of Antwerp, Antwerp, 2020, Belgium
| | - E Verheyen
- Evolutionary Ecology group (EVECO), Department of Biology, University of Antwerp, Antwerp, 2020, Belgium
| | - OG Pybus
- Department of Biology, University of Oxford, Oxford, OX1, UK
- Department of Pathobiology and Population Sciences, the Royal Veterinary College, University of London, Herts, AL9 7TA, UK
| | - A Katzourakis
- Department of Biology, University of Oxford, Oxford, OX1, UK
| | - AN Alagaili
- Laboratory of Biodiversity, Parasitology, and Ecology of Aquatic Ecosystems, Department of Biology - Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis, 2092, Tunisia
| | - S Gryseels
- Evolutionary Ecology group (EVECO), Department of Biology, University of Antwerp, Antwerp, 2020, Belgium
| | - YC Li
- Marine College, Shandong University (Weihai), Weihai, 264209, China
| | - MA Suchard
- Department of Biostatistics, University of California, Los Angeles, CA 90095, USA
| | - M Bletsa
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, KU Leuven, Leuven, 3000, Belgium
- Department of Hygiene Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, 11527, Greece
| | - P Lemey
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, KU Leuven, Leuven, 3000, Belgium
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2
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Lund MC, Larsen BB, Rowsey DM, Otto HW, Gryseels S, Kraberger S, Custer JM, Steger L, Yule KM, Harris RE, Worobey M, Van Doorslaer K, Upham NS, Varsani A. Using archived and biocollection samples towards deciphering the DNA virus diversity associated with rodent species in the families cricetidae and heteromyidae. Virology 2023; 585:42-60. [PMID: 37276766 DOI: 10.1016/j.virol.2023.05.006] [Citation(s) in RCA: 4] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/15/2023] [Accepted: 05/19/2023] [Indexed: 06/07/2023]
Abstract
Rodentia is the most speciose order of mammals, and they are known to harbor a wide range of viruses. Although there has been significant research on zoonotic viruses in rodents, research on the diversity of other viruses has been limited, especially for rodents in the families Cricetidae and Heteromyidae. In fecal and liver samples of nine species of rodents, we identify 346 distinct circular DNA viral genomes. Of these, a large portion are circular, single-stranded DNA viruses in the families Anelloviridae (n = 3), Circoviridae (n = 5), Genomoviridae (n = 7), Microviridae (n = 297), Naryaviridae (n = 4), Vilyaviridae (n = 15) and in the phylum Cressdnaviricota (n = 13) that cannot be assigned established families. We also identified two large bacteriophages of 36 and 50 kb that are part of the class Caudoviricetes. Some of these viruses are clearly those that infect rodents, however, most of these likely infect various organisms associated with rodents, their environment or their diet.
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Affiliation(s)
- Michael C Lund
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287-5001, USA; The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA
| | - Brendan B Larsen
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA; Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98102, USA
| | - Dakota M Rowsey
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287-5001, USA; Biodiversity Knowledge Integration Center, Arizona State University, Tempe, AZ, 85287, USA
| | - Hans W Otto
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Sophie Gryseels
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA; Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000, Leuven, Belgium; Department of Biology, University of Antwerp, 2000, Antwerp, Belgium; OD Taxonomy and Phylogeny, Royal Belgian Museum of Natural Sciences, 1000, Brussels, Belgium
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA
| | - Joy M Custer
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA
| | - Laura Steger
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287-5001, USA; Biodiversity Knowledge Integration Center, Arizona State University, Tempe, AZ, 85287, USA
| | - Kelsey M Yule
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287-5001, USA; Biodiversity Knowledge Integration Center, Arizona State University, Tempe, AZ, 85287, USA
| | - Robin E Harris
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287-5001, USA
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Koenraad Van Doorslaer
- School of Animal and Comparative Biomedical Sciences, The BIO5 Institute, Department of Immunobiology, Cancer Biology Graduate Interdisciplinary Program, UA Cancer Center, University of Arizona Tucson, AZ, 85724, USA
| | - Nathan S Upham
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287-5001, USA; Biodiversity Knowledge Integration Center, Arizona State University, Tempe, AZ, 85287, USA
| | - Arvind Varsani
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287-5001, USA; The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA; Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Observatory, Cape Town, 7701, South Africa.
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3
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Joffrin L, Cooreman T, Verheyen E, Vercammen F, Mariën J, Leirs H, Gryseels S. SARS-CoV-2 Surveillance between 2020 and 2021 of All Mammalian Species in Two Flemish Zoos (Antwerp Zoo and Planckendael Zoo). Vet Sci 2023; 10:382. [PMID: 37368768 DOI: 10.3390/vetsci10060382] [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: 04/14/2023] [Revised: 05/18/2023] [Accepted: 05/25/2023] [Indexed: 06/29/2023] Open
Abstract
The COVID-19 pandemic has led to millions of human infections and deaths worldwide. Several other mammal species are also susceptible to SARS-CoV-2, and multiple instances of transmission from humans to pets, farmed mink, wildlife and zoo animals have been recorded. We conducted a systematic surveillance of SARS-CoV-2 in all mammal species in two zoos in Belgium between September and December 2020 and July 2021, in four sessions, and a targeted surveillance of selected mammal enclosures following SARS-CoV-2 infection in hippopotamuses in December 2021. A total of 1523 faecal samples from 103 mammal species were tested for SARS-CoV-2 via real-time PCR. None of the samples tested positive for SARS-CoV-2. Additional surrogate virus neutralisation tests conducted on 50 routinely collected serum samples from 26 mammal species were all negative. This study is the first to our knowledge to conduct active SARS-CoV-2 surveillance for several months in all mammal species of a zoo. We conclude that at the time of our investigation, none of the screened animals were excreting SARS-CoV-2.
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Affiliation(s)
- Léa Joffrin
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, 2610 Antwerp, Belgium
| | - Tine Cooreman
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, 2610 Antwerp, Belgium
| | - Erik Verheyen
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, 2610 Antwerp, Belgium
- OD Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, 1000 Brussels, Belgium
| | - Francis Vercammen
- Centre for Research and Conservation, Antwerp Zoo Society, 2018 Antwerp, Belgium
| | - Joachim Mariën
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, 2610 Antwerp, Belgium
| | - Herwig Leirs
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, 2610 Antwerp, Belgium
| | - Sophie Gryseels
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, 2610 Antwerp, Belgium
- OD Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, 1000 Brussels, Belgium
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4
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Cuypers LN, Gryseels S, Van Houtte N, Baird SJE, Sabuni CA, Katakweba AS, van den Burg SRM, Bryja J, Leirs H, Goüy de Bellocq J. Subspecific rodent taxa as the relevant host taxonomic level for mammarenavirus host specificity. Virology 2023; 581:116-127. [PMID: 36958216 DOI: 10.1016/j.virol.2023.02.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/19/2023] [Accepted: 02/23/2023] [Indexed: 03/10/2023]
Abstract
Mastomys natalensis-borne mammarenaviruses appear specific to subspecific M. natalensis taxa rather than to the whole species. Yet mammarenaviruses carried by M. natalensis are known to spill over and jump hosts in northern sub-Saharan Africa. Phylogeographic studies increasingly show that, like M. natalensis, small mammals in sub-Saharan Africa are often genetically structured into several subspecific taxa. Other mammarenaviruses may thus also form virus-subspecific host taxon associations. To investigate this, and if mammarenaviruses carried by M. natalensis in southern Africa are less prone to spill-over, we screened 1225 non-M. natalensis samples from Tanzania where many small mammal taxa meet. We found mammarenavirus RNA in 6 samples. Genetic/genomic characterisation confirmed they were not spill-over from M. natalensis. We detected host jumps among rodent tribe members and an association between mammarenaviruses and subspecific taxa of Mus minutoides and Grammomys surdaster, indicating host genetic structure may be crucial to understand virus distribution and host specificity.
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Affiliation(s)
- Laura N Cuypers
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium.
| | - Sophie Gryseels
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium; OD Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Vautierstraat 29, 1000, Brussels, Belgium
| | - Natalie Van Houtte
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium
| | - Stuart J E Baird
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Květná 8, 603 65, Brno, Czech Republic
| | - Christopher A Sabuni
- Institute of Pest Management, Sokoine University of Agriculture, P.O. Box 3110 Chuo Kikuu, Morogoro, Tanzania
| | - Abdul S Katakweba
- Institute of Pest Management, Sokoine University of Agriculture, P.O. Box 3110 Chuo Kikuu, Morogoro, Tanzania
| | - Sebastiaan R M van den Burg
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium
| | - Josef Bryja
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Květná 8, 603 65, Brno, Czech Republic; Department of Botany and Zoology, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
| | - Herwig Leirs
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium
| | - Joëlle Goüy de Bellocq
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Květná 8, 603 65, Brno, Czech Republic
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5
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Klitting R, Kafetzopoulou LE, Thiery W, Dudas G, Gryseels S, Kotamarthi A, Vrancken B, Gangavarapu K, Momoh M, Sandi JD, Goba A, Alhasan F, Grant DS, Okogbenin S, Ogbaini-Emovo E, Garry RF, Smither AR, Zeller M, Pauthner MG, McGraw M, Hughes LD, Duraffour S, Günther S, Suchard MA, Lemey P, Andersen KG, Dellicour S. Predicting the evolution of the Lassa virus endemic area and population at risk over the next decades. Nat Commun 2022; 13:5596. [PMID: 36167835 PMCID: PMC9515147 DOI: 10.1038/s41467-022-33112-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [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: 09/30/2021] [Accepted: 09/02/2022] [Indexed: 01/27/2023] Open
Abstract
Lassa fever is a severe viral hemorrhagic fever caused by a zoonotic virus that repeatedly spills over to humans from its rodent reservoirs. It is currently not known how climate and land use changes could affect the endemic area of this virus, currently limited to parts of West Africa. By exploring the environmental data associated with virus occurrence using ecological niche modelling, we show how temperature, precipitation and the presence of pastures determine ecological suitability for virus circulation. Based on projections of climate, land use, and population changes, we find that regions in Central and East Africa will likely become suitable for Lassa virus over the next decades and estimate that the total population living in ecological conditions that are suitable for Lassa virus circulation may drastically increase by 2070. By analysing geotagged viral genomes using spatially-explicit phylogeography and simulating virus dispersal, we find that in the event of Lassa virus being introduced into a new suitable region, its spread might remain spatially limited over the first decades.
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Affiliation(s)
- Raphaëlle Klitting
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
| | - Liana E. Kafetzopoulou
- grid.5596.f0000 0001 0668 7884Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven - University of Leuven, Leuven, Belgium ,grid.424065.10000 0001 0701 3136Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Wim Thiery
- grid.8767.e0000 0001 2290 8069Department of Hydrology and Hydraulic Engineering, Vrije Universiteit Brussel, Brussels, Belgium
| | - Gytis Dudas
- grid.6441.70000 0001 2243 2806Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Sophie Gryseels
- grid.5284.b0000 0001 0790 3681Evolutionary Ecology group, Department of Biology, University of Antwerp, 2610 Antwerp, Belgium ,grid.20478.390000 0001 2171 9581Vertebrate group, Directorate Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, 1000 Brussels, Belgium
| | - Anjali Kotamarthi
- grid.214007.00000000122199231Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Bram Vrancken
- grid.5596.f0000 0001 0668 7884Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven - University of Leuven, Leuven, Belgium
| | - Karthik Gangavarapu
- grid.214007.00000000122199231Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Mambu Momoh
- grid.442296.f0000 0001 2290 9707Eastern Technical University of Sierra Leone, Kenema, Sierra Leone ,grid.463455.50000 0004 1799 2069Viral Hemorrhagic Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - John Demby Sandi
- grid.463455.50000 0004 1799 2069Viral Hemorrhagic Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Augustine Goba
- grid.463455.50000 0004 1799 2069Viral Hemorrhagic Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Foday Alhasan
- grid.463455.50000 0004 1799 2069Viral Hemorrhagic Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Donald S. Grant
- grid.463455.50000 0004 1799 2069Viral Hemorrhagic Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone ,grid.442296.f0000 0001 2290 9707College of Medicine and Allied Health Sciences, University of Sierra Leone, Kenema, Sierra Leone
| | - Sylvanus Okogbenin
- grid.508091.5Irrua Specialist Teaching Hospital, Irrua, Nigeria ,grid.411357.50000 0000 9018 355XFaculty of Clinical Sciences, College of Medicine, Ambrose Alli University, Ekpoma, Nigeria
| | | | - Robert F. Garry
- grid.265219.b0000 0001 2217 8588Department of Microbiology and Immunology, Tulane University, School of Medicine, New Orleans, LA 70112 USA ,grid.505518.c0000 0004 5901 1919Zalgen Labs, LCC, Frederick, MD 21703 USA ,grid.475149.aGlobal Virus Network (GVN), Baltimore, MD 21201 USA
| | - Allison R. Smither
- grid.265219.b0000 0001 2217 8588Department of Microbiology and Immunology, Tulane University, School of Medicine, New Orleans, LA 70112 USA
| | - Mark Zeller
- grid.214007.00000000122199231Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Matthias G. Pauthner
- grid.214007.00000000122199231Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Michelle McGraw
- grid.214007.00000000122199231Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Laura D. Hughes
- grid.214007.00000000122199231Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Sophie Duraffour
- grid.424065.10000 0001 0701 3136Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany ,grid.452463.2German Center for Infection Research (DZIF), Partner site Hamburg–Lübeck–Borstel–Riems, Hamburg, Germany
| | - Stephan Günther
- grid.424065.10000 0001 0701 3136Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany ,grid.452463.2German Center for Infection Research (DZIF), Partner site Hamburg–Lübeck–Borstel–Riems, Hamburg, Germany
| | - Marc A. Suchard
- grid.19006.3e0000 0000 9632 6718Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, CA USA ,grid.19006.3e0000 0000 9632 6718Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, CA USA ,grid.19006.3e0000 0000 9632 6718Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA USA
| | - Philippe Lemey
- grid.5596.f0000 0001 0668 7884Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven - University of Leuven, Leuven, Belgium
| | - Kristian G. Andersen
- grid.214007.00000000122199231Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037 USA ,grid.214007.00000000122199231Scripps Research Translational Institute, La Jolla, CA 92037 USA
| | - Simon Dellicour
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven - University of Leuven, Leuven, Belgium. .,Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, CP160/12 50, av. FD Roosevelt, 1050, Bruxelles, Belgium.
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6
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Li Y, Bletsa M, Zisi Z, Boonen I, Gryseels S, Kafetzopoulou L, Webster JP, Catalano S, Pybus OG, Van de Perre F, Li H, Li Y, Li Y, Abramov A, Lymberakis P, Lemey P, Lequime S. Endogenous Viral Elements in Shrew Genomes Provide Insights into Pestivirus Ancient History. Mol Biol Evol 2022; 39:6692409. [PMID: 36063436 PMCID: PMC9550988 DOI: 10.1093/molbev/msac190] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
As viral genomic imprints in host genomes, endogenous viral elements (EVEs) shed light on the deep evolutionary history of viruses, ancestral host ranges, and ancient viral-host interactions. In addition, they may provide crucial information for calibrating viral evolutionary timescales. In this study, we conducted a comprehensive in silico screening of a large data set of available mammalian genomes for EVEs deriving from members of the viral family Flaviviridae, an important group of viruses including well-known human pathogens, such as Zika, dengue, or hepatitis C viruses. We identified two novel pestivirus-like EVEs in the reference genome of the Indochinese shrew (Crocidura indochinensis). Homologs of these novel EVEs were subsequently detected in vivo by molecular detection and sequencing in 27 shrew species, including 26 species representing a wide distribution within the Crocidurinae subfamily and one in the Soricinae subfamily on different continents. Based on this wide distribution, we estimate that the integration event occurred before the last common ancestor of the subfamily, about 10.8 million years ago, attesting to an ancient origin of pestiviruses and Flaviviridae in general. Moreover, we provide the first description of Flaviviridae-derived EVEs in mammals even though the family encompasses numerous mammal-infecting members. This also suggests that shrews were past and perhaps also current natural reservoirs of pestiviruses. Taken together, our results expand the current known Pestivirus host range and provide novel insight into the ancient evolutionary history of pestiviruses and the Flaviviridae family in general.
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Affiliation(s)
- Yiqiao Li
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Magda Bletsa
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Zafeiro Zisi
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Ine Boonen
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Sophie Gryseels
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium,Belgium Evolutionary Ecology Group, University of Antwerp, 2610 Wilrijk, Belgium
| | - Liana Kafetzopoulou
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium,Virology Department, Belgium Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany
| | - Joanne P Webster
- Department of Pathobiology and Population Science, Royal Veterinary College, University of London, Herts, AL9 7TA, UK
| | - Stefano Catalano
- Department of Pathobiology and Population Science, Royal Veterinary College, University of London, Herts, AL9 7TA, UK
| | - Oliver G Pybus
- Department of Pathobiology and Population Science, Royal Veterinary College, University of London, Herts, AL9 7TA, UK
| | | | - Haotian Li
- Marine College, Shandong University (Weihai), 264209 Weihai, China
| | - Yaoyao Li
- Marine College, Shandong University (Weihai), 264209 Weihai, China
| | - Yuchun Li
- Marine College, Shandong University (Weihai), 264209 Weihai, China
| | - Alexei Abramov
- Laboratory of Theriology, Zoological Institute of the Russian Academy of Sciences, 190121 Saint Petersburg, Russia
| | | | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
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7
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Colombo VC, Sluydts V, Mariën J, Vanden Broecke B, Van Houtte N, Leirs W, Jacobs L, Iserbyt A, Hubert M, Heyndrickx L, Goris H, Delputte P, De Roeck N, Elst J, Ariën KK, Leirs H, Gryseels S. SARS-CoV-2 surveillance in Norway rats (Rattus norvegicus) from Antwerp sewer system, Belgium. Transbound Emerg Dis 2022; 69:3016-3021. [PMID: 34224205 PMCID: PMC8447303 DOI: 10.1111/tbed.14219] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 06/09/2021] [Revised: 06/30/2021] [Accepted: 07/02/2021] [Indexed: 12/27/2022]
Abstract
SARS-CoV-2 human-to-animal transmission can lead to the establishment of novel reservoirs and the evolution of new variants with the potential to start new outbreaks in humans. We tested Norway rats inhabiting the sewer system of Antwerp, Belgium, for the presence of SARS-CoV-2 following a local COVID-19 epidemic peak. In addition, we discuss the use and interpretation of SARS-CoV-2 serological tests on non-human samples. Between November and December 2020, Norway rat oral swabs, faeces and tissues from the sewer system of Antwerp were collected to be tested by RT-qPCR for the presence of SARS-CoV-2. Serum samples were screened for the presence of anti-SARS-CoV-2 IgG antibodies using a Luminex microsphere immunoassay (MIA). Samples considered positive were then checked for neutralizing antibodies using a conventional viral neutralization test (cVNT). The serum of 35 rats was tested by MIA showing three potentially positive sera that were later negative by cVNT. All tissue samples of 39 rats analysed tested negative for SARS-CoV-2 RNA. This is the first study that evaluates SARS-CoV-2 infection in urban rats. We can conclude that the sample of rats analysed had never been infected with SARS-CoV-2. However, monitoring activities should continue due to the emergence of new variants prone to infect Muridae rodents.
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Affiliation(s)
- Valeria Carolina Colombo
- Evolutionary Ecology GroupDepartment of BiologyUniversity of AntwerpAntwerpBelgium
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)Buenos AiresArgentina
| | - Vincent Sluydts
- Evolutionary Ecology GroupDepartment of BiologyUniversity of AntwerpAntwerpBelgium
| | - Joachim Mariën
- Evolutionary Ecology GroupDepartment of BiologyUniversity of AntwerpAntwerpBelgium
- Virology UnitDepartment of Biomedical SciencesInstitute of Tropical MedicineAntwerpBelgium
| | - Bram Vanden Broecke
- Evolutionary Ecology GroupDepartment of BiologyUniversity of AntwerpAntwerpBelgium
| | - Natalie Van Houtte
- Evolutionary Ecology GroupDepartment of BiologyUniversity of AntwerpAntwerpBelgium
| | - Wannes Leirs
- Evolutionary Ecology GroupDepartment of BiologyUniversity of AntwerpAntwerpBelgium
| | - Lotte Jacobs
- Laboratory for MicrobiologyParasitology and Hygiene (LMPH)University of AntwerpAntwerpBelgium
| | - Arne Iserbyt
- Evolutionary Ecology GroupDepartment of BiologyUniversity of AntwerpAntwerpBelgium
| | - Marine Hubert
- Evolutionary Ecology GroupDepartment of BiologyUniversity of AntwerpAntwerpBelgium
| | - Leo Heyndrickx
- Virology UnitDepartment of Biomedical SciencesInstitute of Tropical MedicineAntwerpBelgium
| | - Hanne Goris
- Evolutionary Ecology GroupDepartment of BiologyUniversity of AntwerpAntwerpBelgium
| | - Peter Delputte
- Laboratory for MicrobiologyParasitology and Hygiene (LMPH)University of AntwerpAntwerpBelgium
| | - Naomi De Roeck
- Laboratory for MicrobiologyParasitology and Hygiene (LMPH)University of AntwerpAntwerpBelgium
| | - Joris Elst
- Evolutionary Ecology GroupDepartment of BiologyUniversity of AntwerpAntwerpBelgium
| | - Kevin K. Ariën
- Virology UnitDepartment of Biomedical SciencesInstitute of Tropical MedicineAntwerpBelgium
| | - Herwig Leirs
- Evolutionary Ecology GroupDepartment of BiologyUniversity of AntwerpAntwerpBelgium
| | - Sophie Gryseels
- Evolutionary Ecology GroupDepartment of BiologyUniversity of AntwerpAntwerpBelgium
- OD Taxonomy and PhylogenyRoyal Belgian Institute of Natural SciencesBrusselsBelgium
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8
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Sluydts V, Sarathchandra SR, Piscitelli AP, Van Houtte N, Gryseels S, Mayer-Scholl A, Bier NS, Htwe NM, Jacob J. Ecology and distribution of Leptospira spp., reservoir hosts and environmental interaction in Sri Lanka, with identification of a new strain. PLoS Negl Trop Dis 2022; 16:e0010757. [PMID: 36112668 PMCID: PMC9518908 DOI: 10.1371/journal.pntd.0010757] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 12/17/2021] [Revised: 09/28/2022] [Accepted: 08/22/2022] [Indexed: 11/19/2022] Open
Abstract
Leptospirosis is a neglected zoonotic disease and one of the leading causes of zoonotic morbidity and mortality, particularly in resource-poor settings. Sri Lanka has one of the highest disease burdens worldwide, with occasional endemic leptospirosis outbreaks (2008, 2011). Rodents are considered the main wildlife reservoir, but due to a scarcity of studies it is unclear which particular species contributes to bacterial transmission and reservoir maintenance in this multi-host multi-parasite system. Several rodent species act as agricultural pests both in rice fields and in food storage facilities. To unravel the interactions among the small mammal communities, pathogenic Leptospira spp. and human transmission pathways, we collected animals from smallholder food storage facilities, where contact between humans and small mammals is most likely, and screened kidney tissue samples for Leptospira spp. using PCR. Samples were collected in three climatic zones along a rainfall gradient. Pathogenic Leptospira spp. were detected in small mammal communities in 37 (74%) out of 50 sampled farms and 61 (12%) out of 500 collected individuals were infected. The small mammal community was comprised of Rattus rattus (87.6%), Suncus shrews (8.8%), Bandicota spp. (2.8%) and Mus booduga (0.8%). Three pathogenic Leptospira spp. were identified, L. borgpetersenii (n = 34), L. interrogans (n = 15), and L. kirschneri (n = 1). Suncus shrews were commonly infected (32%), followed by B. indica (23%) and R. rattus (10%). L. borgpetersenii strains similar to strains previously extracted from human clinal samples in Sri Lanka were detected in R. rattus and Suncus shrews. L. interrogans was observed in R. rattus only. A single L. kirschneri infection was found in M. booduga. The presence of human pathogenic Leptospira species in an agricultural pest rodent (R. rattus) and in commensal shrews (Suncus) calls for management of these species in commensal settings. Further investigation of the interplay between pathogen and reservoir population dynamics, overlap in geographic range and the extent of spill-over to humans in and around rural settlements is required to identify optimal management approaches.
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Affiliation(s)
- Vincent Sluydts
- Julius Kühn-Institute, Federal Research Institute for Cultivated Plants, Institute for Plant Protection in Horticulture and Forests, Vertebrate Research, Münster, Germany
- University of Antwerp, Department of Biology, Evolutionary Ecology Group, University of Antwerp, Wilrijk, Belgium
| | | | - Anna Pia Piscitelli
- University of Antwerp, Department of Biology, Evolutionary Ecology Group, University of Antwerp, Wilrijk, Belgium
| | - Natalie Van Houtte
- University of Antwerp, Department of Biology, Evolutionary Ecology Group, University of Antwerp, Wilrijk, Belgium
| | - Sophie Gryseels
- University of Antwerp, Department of Biology, Evolutionary Ecology Group, University of Antwerp, Wilrijk, Belgium
| | - Anne Mayer-Scholl
- Federal Institute for Risk Assessment, Department of Biological Safety, Berlin, Germany
| | - Nadja Seyhan Bier
- Federal Institute for Risk Assessment, Department of Biological Safety, Berlin, Germany
| | - Nyo Me Htwe
- University of Antwerp, Department of Biology, Evolutionary Ecology Group, University of Antwerp, Wilrijk, Belgium
| | - Jens Jacob
- Julius Kühn-Institute, Federal Research Institute for Cultivated Plants, Institute for Plant Protection in Horticulture and Forests, Vertebrate Research, Münster, Germany
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9
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Harding C, Larsen BB, Gryseels S, Otto HW, Suazo C, Kraberger S, Upham NS, Worobey M, Van Doorslaer K, Varsani A. Discovery of three cycloviruses in fecal samples from silver-haired bats (Lasionycteris noctivagans) in Arizona (USA). Arch Virol 2022; 167:2771-2775. [PMID: 36045303 PMCID: PMC9432798 DOI: 10.1007/s00705-022-05574-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 08/03/2022] [Indexed: 12/14/2022]
Abstract
Bats harbour a diverse array of viruses, some of which are zoonotic, and are one of the most speciose groups of mammals on earth. As part of an ongoing bat-associated viral diversity research project, we identified three cycloviruses (family Circoviridae) in fecal samples of silver-haired bats (Lasionycteris noctivagans) caught in Cave Creek Canyon of Arizona (USA). Two of the three identified genomes represent two new species in the genus Cyclovirus. Cycloviruses have been found in a wide range of environments and hosts; however, little is known about their biology. These new genomes of cycloviruses are the first from silver-haired bats, adding to the broader knowledge of cyclovirus diversity. With continuing studies, it is likely that additional viruses of the family Circoviridae will be identified in Arizona bat populations.
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Affiliation(s)
- Ciara Harding
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, 85287-5001, Tempe, AZ, USA
- School of Life Sciences, Arizona State University, 85287-5001, Tempe, AZ, USA
| | - Brendan B Larsen
- Department of Ecology and Evolutionary Biology, University of Arizona, 85721, Tucson, Arizona, USA
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 98102, Seattle, WA, USA
| | - Sophie Gryseels
- Department of Ecology and Evolutionary Biology, University of Arizona, 85721, Tucson, Arizona, USA
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000, Leuven, Belgium
- Department of Biology, University of Antwerp, 2000, Antwerp, Belgium
| | - Hans W Otto
- Department of Ecology and Evolutionary Biology, University of Arizona, 85721, Tucson, Arizona, USA
| | - Crystal Suazo
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, 85287-5001, Tempe, AZ, USA
- School of Life Sciences, Arizona State University, 85287-5001, Tempe, AZ, USA
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, 85287-5001, Tempe, AZ, USA
| | - Nathan S Upham
- School of Life Sciences, Arizona State University, 85287-5001, Tempe, AZ, USA
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, 85721, Tucson, Arizona, USA
| | - Koenraad Van Doorslaer
- School of Animal and Comparative Biomedical Sciences, The BIO5 Institute, Department of Immunobiology, Cancer Biology Graduate Interdisciplinary Program, UA Cancer Center, University of Arizona, 85724, Tucson, AZ, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, 85287-5001, Tempe, AZ, USA.
- School of Life Sciences, Arizona State University, 85287-5001, Tempe, AZ, USA.
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, 7701, Observatory, Cape Town, South Africa.
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10
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Vanmechelen B, Zisi Z, Gryseels S, Goüy de Bellocq J, Vrancken B, Lemey P, Maes P, Bletsa M. Phylogenomic Characterization of Lopma Virus and Praja Virus, Two Novel Rodent-Borne Arteriviruses. Viruses 2021; 13:1842. [PMID: 34578423 PMCID: PMC8473226 DOI: 10.3390/v13091842] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/05/2021] [Accepted: 09/08/2021] [Indexed: 11/16/2022] Open
Abstract
Recent years have witnessed the discovery of several new viruses belonging to the family Arteriviridae, expanding the known diversity and host range of this group of complex RNA viruses. Although the pathological relevance of these new viruses is not always clear, several well-studied members of the family Arteriviridae are known to be important animal pathogens. Here, we report the complete genome sequences of four new arterivirus variants, belonging to two putative novel species. These new arteriviruses were discovered in African rodents and were given the names Lopma virus and Praja virus. Their genomes follow the characteristic genome organization of all known arteriviruses, even though they are only distantly related to currently known rodent-borne arteriviruses. Phylogenetic analysis shows that Lopma virus clusters in the subfamily Variarterivirinae, while Praja virus clusters near members of the subfamily Heroarterivirinae: the yet undescribed forest pouched giant rat arterivirus and hedgehog arterivirus 1. A co-divergence analysis of rodent-borne arteriviruses confirms that they share similar phylogenetic patterns with their hosts, with only very few cases of host shifting events throughout their evolutionary history. Overall, the genomes described here and their unique clustering with other arteriviruses further illustrate the existence of multiple rodent-borne arterivirus lineages, expanding our knowledge of the evolutionary origin of these viruses.
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Affiliation(s)
- Bert Vanmechelen
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Herestraat 49/Box 1040, 3000 Leuven, Belgium; (B.V.); (Z.Z.); (B.V.); (P.L.); (P.M.)
| | - Zafeiro Zisi
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Herestraat 49/Box 1040, 3000 Leuven, Belgium; (B.V.); (Z.Z.); (B.V.); (P.L.); (P.M.)
| | - Sophie Gryseels
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium;
- OD Taxonomy and Phylogeny, Royal Institute of Natural Sciences, Vautierstreet 29, 1000 Brussels, Belgium
| | - Joëlle Goüy de Bellocq
- Institute of Vertebrate Biology, The Czech Academy of Sciences, Květná 8, 603 65 Brno, Czech Republic;
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, 165 21 Prague, Czech Republic
| | - Bram Vrancken
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Herestraat 49/Box 1040, 3000 Leuven, Belgium; (B.V.); (Z.Z.); (B.V.); (P.L.); (P.M.)
| | - Philippe Lemey
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Herestraat 49/Box 1040, 3000 Leuven, Belgium; (B.V.); (Z.Z.); (B.V.); (P.L.); (P.M.)
| | - Piet Maes
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Herestraat 49/Box 1040, 3000 Leuven, Belgium; (B.V.); (Z.Z.); (B.V.); (P.L.); (P.M.)
| | - Magda Bletsa
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Herestraat 49/Box 1040, 3000 Leuven, Belgium; (B.V.); (Z.Z.); (B.V.); (P.L.); (P.M.)
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11
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Gryseels S, Mbala-Kingebeni P, Akonda I, Angoyo R, Ayouba A, Baelo P, Mukadi DB, Bugentho E, Bushmaker T, Butel C, Calvignac-Spencer S, Delaporte E, De Smet B, Düx A, Edidi-Atani F, Fischer R, Kahandi C, Kapetshi J, Sumba SK, Kouadio L, Bendeke AM, Mande C, Sepolo GM, Moudindo J, Ngole EM, Musaba P, Mutombo P, Bass IN, Nebesse C, Ngoy S, Kumogo SPN, Seifert SN, Tanzito J, Akaibe D, Amundala N, Ariën KK, Gembu GC, Leendertz FH, Leirs H, Mukinzi JC, Munster V, Muyembe-Tamfum JJ, Peeters M, Verheyen E, Ahuka-Mundeke S. Role of Wildlife in Emergence of Ebola Virus in Kaigbono (Likati), Democratic Republic of the Congo, 2017. Emerg Infect Dis 2021; 26:2205-2209. [PMID: 32818404 PMCID: PMC7454093 DOI: 10.3201/eid2609.191552] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [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: 11/23/2022] Open
Abstract
After the 2017 Ebola virus (EBOV) outbreak in Likati, a district in northern Democratic Republic of the Congo, we sampled small mammals from the location where the primary case-patient presumably acquired the infection. None tested positive for EBOV RNA or antibodies against EBOV, highlighting the ongoing challenge in detecting animal reservoirs for EBOV.
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12
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Gryseels S, De Bruyn L, Gyselings R, Calvignac‐Spencer S, Leendertz FH, Leirs H. Risk of human-to-wildlife transmission of SARS-CoV-2. Mamm Rev 2021; 51:272-292. [PMID: 33230363 PMCID: PMC7675675 DOI: 10.1111/mam.12225] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 08/04/2020] [Indexed: 01/08/2023]
Abstract
It has been a long time since the world has experienced a pandemic with such a rapid devastating impact as the current COVID-19 pandemic. The causative agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is unusual in that it appears capable of infecting many different mammal species. As a significant proportion of people worldwide are infected with SARS-CoV-2 and may spread the infection unknowingly before symptoms occur or without any symptoms ever occurring, there is a non-negligible risk of humans spreading SARS-CoV-2 to wildlife, in particular to wild non-human mammals. Because of SARS-CoV-2's apparent evolutionary origins in bats and reports of humans transmitting the virus to pets and zoo animals, regulations for the prevention of human-to-animal transmission have so far focused mostly on these animal groups. We summarise recent studies and reports that show that a wide range of distantly related mammals are likely to be susceptible to SARS-CoV-2, and that susceptibility or resistance to the virus is, in general, not predictable, or only predictable to some extent, from phylogenetic proximity to known susceptible or resistant hosts. In the absence of solid evidence on the susceptibility and resistance to SARS-CoV-2 for each of the >6500 mammal species, we argue that sanitary precautions should be taken by humans interacting with any other mammal species in the wild. Preventing human-to-wildlife SARS-CoV-2 transmission is important to protect these animals (some of which are classed as threatened) from disease, but also to avoid establishment of novel SARS-CoV-2 reservoirs in wild mammals. The risk of repeated re-infection of humans from such a wildlife reservoir could severely hamper SARS-CoV-2 control efforts. Activities during which direct or indirect interaction with wild mammals may occur include wildlife research, conservation activities, forestry work, pest control, management of feral populations, ecological consultancy work, management of protected areas and natural environments, wildlife tourism and wildlife rehabilitation in animal shelters. During such activities, we recommend sanitary precautions, such as physical distancing, wearing face masks and gloves, and frequent decontamination, which are very similar to regulations currently imposed to prevent transmission among humans. We further recommend active surveillance of domestic and feral animals that could act as SARS-CoV-2 intermediate hosts between humans and wild mammals.
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Affiliation(s)
- Sophie Gryseels
- Department of Microbiology, Immunology and TransplantationRega Institute, KU LeuvenHerestraat 49Leuven3000Belgium
- Department of Ecology and Evolutionary BiologyUniversity of Arizona1041 E. Lowell St.TucsonAZ85721USA
- Department of BiologyUniversity of AntwerpUniversiteitsplein 1Antwerp2610Belgium
| | - Luc De Bruyn
- Department of BiologyUniversity of AntwerpUniversiteitsplein 1Antwerp2610Belgium
- Research Institute for Nature and Forest (INBO)Havenlaan 88Brussels1000Belgium
| | - Ralf Gyselings
- Research Institute for Nature and Forest (INBO)Havenlaan 88Brussels1000Belgium
| | | | | | - Herwig Leirs
- Department of BiologyUniversity of AntwerpUniversiteitsplein 1Antwerp2610Belgium
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13
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Bletsa M, Vrancken B, Gryseels S, Boonen I, Fikatas A, Li Y, Laudisoit A, Lequime S, Bryja J, Makundi R, Meheretu Y, Akaibe BD, Mbalitini SG, Van de Perre F, Van Houtte N, Těšíková J, Wollants E, Van Ranst M, Pybus OG, Drexler JF, Verheyen E, Leirs H, Gouy de Bellocq J, Lemey P. Molecular detection and genomic characterization of diverse hepaciviruses in African rodents. Virus Evol 2021; 7:veab036. [PMID: 34221451 PMCID: PMC8242229 DOI: 10.1093/ve/veab036] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Hepatitis C virus (HCV; genus Hepacivirus) represents a major public health problem, infecting about three per cent of the human population. Because no animal reservoir carrying closely related hepaciviruses has been identified, the zoonotic origins of HCV still remain unresolved. Motivated by recent findings of divergent hepaciviruses in rodents and a plausible African origin of HCV genotypes, we have screened a large collection of small mammals samples from seven sub-Saharan African countries. Out of 4,303 samples screened, eighty were found positive for the presence of hepaciviruses in twenty-nine different host species. We, here, report fifty-six novel genomes that considerably increase the diversity of three divergent rodent hepacivirus lineages. Furthermore, we provide strong evidence for hepacivirus co-infections in rodents, which were exclusively found in four sampled species of brush-furred mice. We also detect evidence of recombination within specific host lineages. Our study expands the available hepacivirus genomic data and contributes insights into the relatively deep evolutionary history of these pathogens in rodents. Overall, our results emphasize the importance of rodents as a potential hepacivirus reservoir and as models for investigating HCV infection dynamics.
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Affiliation(s)
- Magda Bletsa
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Bram Vrancken
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Sophie Gryseels
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
- Department of Biology, Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium
| | - Ine Boonen
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Antonios Fikatas
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Yiqiao Li
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | | | - Sebastian Lequime
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Josef Bryja
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic
| | - Rhodes Makundi
- Pest Management Center -Sokoine University of Agriculture, Morogoro, Tanzania
| | - Yonas Meheretu
- Department of Biology and Institute of Mountain Research & Development, Mekelle University, Mekelle, Ethiopia
| | - Benjamin Dudu Akaibe
- Department of Ecology and Animal Resource Management, Faculty of Science, Biodiversity Monitoring Center, University of Kisangani, Kisangani, Democratic Republic of the Congo
| | - Sylvestre Gambalemoke Mbalitini
- Department of Ecology and Animal Resource Management, Faculty of Science, Biodiversity Monitoring Center, University of Kisangani, Kisangani, Democratic Republic of the Congo
| | - Frederik Van de Perre
- Department of Biology, Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium
| | - Natalie Van Houtte
- Department of Biology, Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium
| | - Jana Těšíková
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Elke Wollants
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Marc Van Ranst
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, UK
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, London, UK
| | - Jan Felix Drexler
- Charite-Universitatsmedizin Berlin, Berlin, Germany
- German Center for Infection Research (DZIF), Berlin, Germany
| | - Erik Verheyen
- Department of Biology, Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium
- OD Taxonomy and Phylogeny-Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Herwig Leirs
- Department of Biology, Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium
| | | | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
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14
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Cuypers LN, Baird SJE, Hánová A, Locus T, Katakweba AS, Gryseels S, Bryja J, Leirs H, Goüy de Bellocq J. Three arenaviruses in three subspecific natal multimammate mouse taxa in Tanzania: same host specificity, but different spatial genetic structure? Virus Evol 2020; 6:veaa039. [PMID: 33033629 PMCID: PMC7532547 DOI: 10.1093/ve/veaa039] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Mastomys natalensis is widespread in sub-Saharan Africa and hosts several arenavirus species, including the pathogenic zoonotic Lassa virus in West Africa. Mitochondrial lineages sub-divide the range of M. natalensis and have been associated with cryptic structure within the species. To test specificity of arenaviruses to hosts carrying these lineages, we screened 1772 M. natalensis in a large area of Tanzania where three mitochondrial lineages meet. We detected fifty-two individuals that were positive for one of three arenaviruses: Gairo, Morogoro, and Luna virus. This is the first record of Luna virus in Tanzania. We confirmed the specificity of each arenavirus to a distinct host mitochondrial lineage except for three cases in one locality at the centre of a host hybrid zone. No arenaviruses were detected in a large part of the study area. Morogoro and Gairo virus showed differences in prevalence (Morogoro virus lower than Gairo virus) and in genetic structure (Morogoro virus more structured than Gairo virus). However, both viruses have genetic neighbourhood size estimates of the same order of magnitude as Lassa virus. While differences in arenavirus and/or host evolutionary and ecological dynamics may exist, Tanzanian arenaviruses could be suited to model Lassa virus dynamics in M. natalensis.
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Affiliation(s)
- Laura N Cuypers
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Stuart J E Baird
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic
| | - Alexandra Hánová
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic.,Department of Botany and Zoology, Masaryk University, Brno, Czech Republic
| | - Tatjana Locus
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Abdul S Katakweba
- Pest Management Centre, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Sophie Gryseels
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium.,Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA.,Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Josef Bryja
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic.,Department of Botany and Zoology, Masaryk University, Brno, Czech Republic
| | - Herwig Leirs
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium
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15
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Mariën J, Borremans B, Verhaeren C, Kirkpatrick L, Gryseels S, Goüy de Bellocq J, Günther S, Sabuni CA, Massawe AW, Reijniers J, Leirs H. Density dependence and persistence of Morogoro arenavirus transmission in a fluctuating population of its reservoir host. J Anim Ecol 2019; 89:506-518. [PMID: 31545505 DOI: 10.1111/1365-2656.13107] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 06/21/2019] [Accepted: 07/21/2019] [Indexed: 11/28/2022]
Abstract
A key aim in wildlife disease ecology is to understand how host and parasite characteristics influence parasite transmission and persistence. Variation in host population density can have strong impacts on transmission and outbreaks, and theory predicts particular transmission-density patterns depending on how parasites are transmitted between individuals. Here, we present the results of a study on the dynamics of Morogoro arenavirus in a population of multimammate mice (Mastomys natalensis). This widespread African rodent, which is also the reservoir host of Lassa arenavirus in West Africa, is known for its strong seasonal density fluctuations driven by food availability. We investigated to what degree virus transmission changes with host population density and how the virus might be able to persist during periods of low host density. A seven-year capture-mark-recapture study was conducted in Tanzania where rodents were trapped monthly and screened for the presence of antibodies against Morogoro virus. Observed seasonal seroprevalence patterns were compared with those generated by mathematical transmission models to test different hypotheses regarding the degree of density dependence and the role of chronically infected individuals. We observed that Morogoro virus seroprevalence correlates positively with host density with a lag of 1-4 months. Model results suggest that the observed seasonal seroprevalence dynamics can be best explained by a combination of vertical and horizontal transmission and that a small number of animals need to be infected chronically to ensure viral persistence. Transmission dynamics and viral persistence were best explained by the existence of both acutely and chronically infected individuals and by seasonally changing transmission rates. Due to the presence of chronically infected rodents, rodent control is unlikely to be a feasible approach for eliminating arenaviruses such as Lassa virus from Mastomys populations.
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Affiliation(s)
- Joachim Mariën
- Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium
| | - Benny Borremans
- Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium.,Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, LA, USA.,Interuniversity Institute for Biostatistics and Statistical Bioinformatics (I-BIOSTAT), Hasselt University, Hasselt, Belgium
| | | | | | - Sophie Gryseels
- Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium.,Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA.,Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Joëlle Goüy de Bellocq
- Institute of Vertebrate Biology, Research Facility Studenec, The Czech Academy of Sciences, Brno, Czech Republic
| | - Stephan Günther
- Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany
| | | | - Apia W Massawe
- PestManagement Centre, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Jonas Reijniers
- Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium.,Department of Engineering Management, University of Antwerp, Antwerp, Belgium
| | - Herwig Leirs
- Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium
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16
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Bletsa M, Suchard MA, Ji X, Gryseels S, Vrancken B, Baele G, Worobey M, Lemey P. Divergence dating using mixed effects clock modelling: An application to HIV-1. Virus Evol 2019; 5:vez036. [PMID: 31720009 PMCID: PMC6830409 DOI: 10.1093/ve/vez036] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The need to estimate divergence times in evolutionary histories in the presence of various sources of substitution rate variation has stimulated a rich development of relaxed molecular clock models. Viral evolutionary studies frequently adopt an uncorrelated clock model as a generic relaxed molecular clock process, but this may impose considerable estimation bias if discrete rate variation exists among clades or lineages. For HIV-1 group M, rate variation among subtypes has been shown to result in inconsistencies in time to the most recent common ancestor estimation. Although this calls into question the adequacy of available molecular dating methods, no solution to this problem has been offered so far. Here, we investigate the use of mixed effects molecular clock models, which combine both fixed and random effects in the evolutionary rate, to estimate divergence times. Using simulation, we demonstrate that this model outperforms existing molecular clock models in a Bayesian framework for estimating time-measured phylogenies in the presence of mixed sources of rate variation, while also maintaining good performance in simpler scenarios. By analysing a comprehensive HIV-1 group M complete genome data set we confirm considerable rate variation among subtypes that is not adequately modelled by uncorrelated relaxed clock models. The mixed effects clock model can accommodate this rate variation and results in a time to the most recent common ancestor of HIV-1 group M of 1920 (1915-25), which is only slightly earlier than the uncorrelated relaxed clock estimate for the same data set. The use of complete genome data appears to have a more profound impact than the molecular clock model because it reduces the credible intervals by 50 per cent relative to similar estimates based on short envelope gene sequences.
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Affiliation(s)
- Magda Bletsa
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven – University of Leuven, Leuven, Belgium
| | - Marc A Suchard
- Department of Biomathematics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA, USA
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, CA, USA
| | - Xiang Ji
- Department of Biomathematics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA, USA
| | - Sophie Gryseels
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven – University of Leuven, Leuven, Belgium
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Bram Vrancken
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven – University of Leuven, Leuven, Belgium
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven – University of Leuven, Leuven, Belgium
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven – University of Leuven, Leuven, Belgium
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17
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Vanmechelen B, Bletsa M, Laenen L, Lopes AR, Vergote V, Beller L, Deboutte W, Korva M, Avšič Županc T, Goüy de Bellocq J, Gryseels S, Leirs H, Lemey P, Vrancken B, Maes P. Discovery and genome characterization of three new Jeilongviruses, a lineage of paramyxoviruses characterized by their unique membrane proteins. BMC Genomics 2018; 19:617. [PMID: 30115009 PMCID: PMC6097224 DOI: 10.1186/s12864-018-4995-0] [Citation(s) in RCA: 27] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 08/03/2018] [Indexed: 11/20/2022] Open
Abstract
Background In the past decade, many new paramyxoviruses that do not belong to any of the seven established genera in the family Paramyxoviridae have been discovered. Amongst them are J-virus (JPV), Beilong virus (BeiPV) and Tailam virus (TlmPV), three paramyxovirus species found in rodents. Based on their similarities, it has been suggested that these viruses should compose a new genus, tentatively called ‘Jeilongvirus’. Results Here we present the complete genomes of three newly discovered paramyxoviruses, one found in a bank vole (Myodes glareolus) from Slovenia and two in a single, co-infected Rungwe brush-furred rat (Lophuromys machangui) from Mozambique, that represent three new, separate species within the putative genus ‘Jeilongvirus’. The genome organization of these viruses is similar to other paramyxoviruses, but like JPV, BeiPV and TlmPV, they possess an additional open reading frame, encoding a transmembrane protein, that is located between the F and G genes. As is the case for all Jeilongviruses, the G genes of the viruses described here are unusually large, and their encoded proteins are characterized by a remarkable amino acid composition pattern that is not seen in other paramyxoviruses, but resembles certain motifs found in Orthopneumovirus G proteins. Conclusions The phylogenetic clustering of JPV, BeiPV and TlmPV with the viruses described here, as well as their shared features that set them apart from other paramyxoviruses, provide additional support for the recognition of the genus ‘Jeilongvirus’. Electronic supplementary material The online version of this article (10.1186/s12864-018-4995-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bert Vanmechelen
- Department of Microbiology and Immunology, Laboratory of Clinical Virology, Rega Institute for Medical Research, KU Leuven - University of Leuven, Herestraat 49, Box 1040, BE3000, Leuven, Belgium
| | - Magda Bletsa
- Department of Microbiology and Immunology, Laboratory of Evolutionary and Computational Virology, Rega Institute for Medical Research, KU Leuven - University of Leuven, Herestraat 49, Box 1040, BE3000, Leuven, Belgium
| | - Lies Laenen
- Department of Microbiology and Immunology, Laboratory of Clinical Virology, Rega Institute for Medical Research, KU Leuven - University of Leuven, Herestraat 49, Box 1040, BE3000, Leuven, Belgium
| | - Ana Rita Lopes
- Department of Microbiology and Immunology, Laboratory of Clinical Virology, Rega Institute for Medical Research, KU Leuven - University of Leuven, Herestraat 49, Box 1040, BE3000, Leuven, Belgium
| | - Valentijn Vergote
- Department of Microbiology and Immunology, Laboratory of Clinical Virology, Rega Institute for Medical Research, KU Leuven - University of Leuven, Herestraat 49, Box 1040, BE3000, Leuven, Belgium
| | - Leen Beller
- Department of Microbiology and Immunology, Laboratory of Viral Metagenomics, Rega Institute for Medical Research, KU Leuven - University of Leuven, Herestraat 49, Box 1040, BE3000, Leuven, Belgium
| | - Ward Deboutte
- Department of Microbiology and Immunology, Laboratory of Viral Metagenomics, Rega Institute for Medical Research, KU Leuven - University of Leuven, Herestraat 49, Box 1040, BE3000, Leuven, Belgium
| | - Miša Korva
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška 4, SI-1000, Ljubljana, Slovenia
| | - Tatjana Avšič Županc
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška 4, SI-1000, Ljubljana, Slovenia
| | - Joëlle Goüy de Bellocq
- The Czech Academy of Sciences, Institute of Vertebrate Biology, Květná 8, 603 65, Brno, Czech Republic
| | - Sophie Gryseels
- Department of Microbiology and Immunology, Laboratory of Evolutionary and Computational Virology, Rega Institute for Medical Research, KU Leuven - University of Leuven, Herestraat 49, Box 1040, BE3000, Leuven, Belgium.,Department of Biology, Evolutionary Ecology Group, University of Antwerp, Universiteitsplein 1, 2610, Antwerpen, Belgium.,Ecology and Evolutionary Biology Department, University of Arizona, 1041 E. Lowell St, Tucson, AZ, 85719, USA
| | - Herwig Leirs
- Department of Biology, Evolutionary Ecology Group, University of Antwerp, Universiteitsplein 1, 2610, Antwerpen, Belgium
| | - Philippe Lemey
- Department of Microbiology and Immunology, Laboratory of Evolutionary and Computational Virology, Rega Institute for Medical Research, KU Leuven - University of Leuven, Herestraat 49, Box 1040, BE3000, Leuven, Belgium
| | - Bram Vrancken
- Department of Microbiology and Immunology, Laboratory of Evolutionary and Computational Virology, Rega Institute for Medical Research, KU Leuven - University of Leuven, Herestraat 49, Box 1040, BE3000, Leuven, Belgium
| | - Piet Maes
- Department of Microbiology and Immunology, Laboratory of Clinical Virology, Rega Institute for Medical Research, KU Leuven - University of Leuven, Herestraat 49, Box 1040, BE3000, Leuven, Belgium.
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18
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Mariën J, Sluydts V, Borremans B, Gryseels S, Vanden Broecke B, Sabuni CA, Katakweba AAS, Mulungu LS, Günther S, de Bellocq JG, Massawe AW, Leirs H. Arenavirus infection correlates with lower survival of its natural rodent host in a long-term capture-mark-recapture study. Parasit Vectors 2018; 11:90. [PMID: 29422075 PMCID: PMC5806307 DOI: 10.1186/s13071-018-2674-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 01/24/2018] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Parasite evolution is hypothesized to select for levels of parasite virulence that maximise transmission success. When host population densities fluctuate, low levels of virulence with limited impact on the host are expected, as this should increase the likelihood of surviving periods of low host density. We examined the effects of Morogoro arenavirus on the survival and recapture probability of multimammate mice (Mastomys natalensis) using a seven-year capture-mark-recapture time series. Mastomys natalensis is the natural host of Morogoro virus and is known for its strong seasonal density fluctuations. RESULTS Antibody presence was negatively correlated with survival probability (effect size: 5-8% per month depending on season) but positively with recapture probability (effect size: 8%). CONCLUSIONS The small negative correlation between host survival probability and antibody presence suggests that either the virus has a negative effect on host condition, or that hosts with lower survival probability are more likely to obtain Morogoro virus infection, for example due to particular behavioural or immunological traits. The latter hypothesis is supported by the positive correlation between antibody status and recapture probability which suggests that risky behaviour might increase the probability of becoming infected.
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Affiliation(s)
- Joachim Mariën
- Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium
| | - Vincent Sluydts
- Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium
| | - Benny Borremans
- Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, USA
- Interuniversity Institute for Biostatistics and statistical Bioinformatics (I-BIOSTAT), Hasselt University, Hasselt, Belgium
| | - Sophie Gryseels
- Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, USA
| | | | | | | | - Loth S. Mulungu
- Pest Management Center, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Stephan Günther
- Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany
| | - Joëlle Goüy de Bellocq
- Institute of Vertebrate Biology, Research Facility Studenec, The Czech Academy of Sciences, Brno, Czech Republic
| | - Apia W. Massawe
- Pest Management Center, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Herwig Leirs
- Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium
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19
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Mariën J, Borremans B, Gryseels S, Broecke BV, Becker-Ziaja B, Makundi R, Massawe A, Reijniers J, Leirs H. Arenavirus Dynamics in Experimentally and Naturally Infected Rodents. Ecohealth 2017; 14:463-473. [PMID: 28616660 DOI: 10.1007/s10393-017-1256-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 04/23/2017] [Accepted: 06/01/2017] [Indexed: 05/04/2023]
Abstract
Infectious diseases of wildlife are typically studied using data on antibody and pathogen levels. In order to interpret these data, it is necessary to know the course of antibodies and pathogen levels after infection. Such data are typically collected using experimental infection studies in which host individuals are inoculated in the laboratory and sampled over an extended period, but because laboratory conditions are controlled and much less variable than natural conditions, the immune response and pathogen dynamics may differ. Here, we compared Morogoro arenavirus infection patterns between naturally and experimentally infected multimammate mice (Mastomys natalensis). Longitudinal samples were collected during three months of bi-weekly trapping in Morogoro, Tanzania, and antibody titer and viral RNA presence were determined. The time of infection was estimated from these data using a recently developed Bayesian approach, which allowed us to assess whether the natural temporal patterns match the previously observed patterns in the laboratory. A good match was found for 52% of naturally infected individuals, while most of the mismatches can be explained by the presence of chronically infected individuals (35%), maternal antibodies (10%), and an antibody detection limit (25%). These results suggest that while laboratory data are useful for interpreting field samples, there can still be differences due to conditions that were not tested in the laboratory.
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Affiliation(s)
- Joachim Mariën
- Evolutionary Ecology Group, University of Antwerp, Campus Drie Eiken, Universiteitsplein 1, 2610, Wilrijk, Antwerp, Belgium.
| | - Benny Borremans
- Evolutionary Ecology Group, University of Antwerp, Campus Drie Eiken, Universiteitsplein 1, 2610, Wilrijk, Antwerp, Belgium
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Sophie Gryseels
- Evolutionary Ecology Group, University of Antwerp, Campus Drie Eiken, Universiteitsplein 1, 2610, Wilrijk, Antwerp, Belgium
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Bram Vanden Broecke
- Evolutionary Ecology Group, University of Antwerp, Campus Drie Eiken, Universiteitsplein 1, 2610, Wilrijk, Antwerp, Belgium
| | | | - Rhodes Makundi
- Pest Management Center, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Apia Massawe
- Pest Management Center, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Jonas Reijniers
- Evolutionary Ecology Group, University of Antwerp, Campus Drie Eiken, Universiteitsplein 1, 2610, Wilrijk, Antwerp, Belgium
- Department of Engineering Management, University of Antwerp, Antwerp, Belgium
| | - Herwig Leirs
- Evolutionary Ecology Group, University of Antwerp, Campus Drie Eiken, Universiteitsplein 1, 2610, Wilrijk, Antwerp, Belgium
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20
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Cuypers LN, Cuypers WL, Gildemyn-Blomme A, Abraham L, Aertbeliën S, Massawe AW, Borremans B, Gryseels S, Leirs H. No evidence for avoidance of black rat scent by the presumably less competitive Natal multimammate mouse in a choice experiment. African Zoology 2017. [DOI: 10.1080/15627020.2017.1307139] [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] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Laura N Cuypers
- Evolutionary Ecology Group, University of Antwerp, Campus Drie Eiken, Wilrijk, Belgium
| | - Wim L Cuypers
- Evolutionary Ecology Group, University of Antwerp, Campus Drie Eiken, Wilrijk, Belgium
| | | | - Laura Abraham
- Evolutionary Ecology Group, University of Antwerp, Campus Drie Eiken, Wilrijk, Belgium
| | - Senne Aertbeliën
- Evolutionary Ecology Group, University of Antwerp, Campus Drie Eiken, Wilrijk, Belgium
| | - Apia W Massawe
- Pest Management Centre, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Benny Borremans
- Evolutionary Ecology Group, University of Antwerp, Campus Drie Eiken, Wilrijk, Belgium
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, USA
| | - Sophie Gryseels
- Evolutionary Ecology Group, University of Antwerp, Campus Drie Eiken, Wilrijk, Belgium
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, USA
| | - Herwig Leirs
- Evolutionary Ecology Group, University of Antwerp, Campus Drie Eiken, Wilrijk, Belgium
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21
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Mariën J, Borremans B, Gryseels S, Soropogui B, De Bruyn L, Bongo GN, Becker-Ziaja B, de Bellocq JG, Günther S, Magassouba N, Leirs H, Fichet-Calvet E. No measurable adverse effects of Lassa, Morogoro and Gairo arenaviruses on their rodent reservoir host in natural conditions. Parasit Vectors 2017; 10:210. [PMID: 28449693 PMCID: PMC5408478 DOI: 10.1186/s13071-017-2146-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [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: 01/19/2017] [Accepted: 04/19/2017] [Indexed: 01/11/2023] Open
Abstract
Background In order to optimize net transmission success, parasites are hypothesized to evolve towards causing minimal damage to their reservoir host while obtaining high shedding rates. For many parasite species however this paradigm has not been tested, and conflicting results have been found regarding the effect of arenaviruses on their rodent host species. The rodent Mastomys natalensis is the natural reservoir host of several arenaviruses, including Lassa virus that is known to cause Lassa haemorrhagic fever in humans. Here, we examined the effect of three arenaviruses (Gairo, Morogoro and Lassa virus) on four parameters of wild-caught Mastomys natalensis: body mass, head-body length, sexual maturity and fertility. After correcting for the effect of age, we compared these parameters between arenavirus-positive (arenavirus RNA or antibody) and negative animals using data from different field studies in Guinea (Lassa virus) and Tanzania (Morogoro and Gairo viruses). Results Although the sample sizes of our studies (1297, 749 and 259 animals respectively) were large enough to statistically detect small differences in body conditions, we did not observe any adverse effects of these viruses on Mastomys natalensis. We did find that sexual maturity was significantly positively related with Lassa virus antibody presence until a certain age, and with Gairo virus antibody presence in general. Gairo virus antibody-positive animals were also significantly heavier and larger than antibody-free animals. Conclusion Together, these results suggest that the pathogenicity of arenaviruses is not severe in M. natalensis, which is likely to be an adaptation of these viruses to optimize transmission success. They also suggest that sexual behaviour might increase the probability of M. natalensis to become infected with arenaviruses. Electronic supplementary material The online version of this article (doi:10.1186/s13071-017-2146-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joachim Mariën
- Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium.
| | - Benny Borremans
- Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium.,Department of Ecology and Evolutionary Biology, University of California, Los Angeles, USA
| | - Sophie Gryseels
- Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium.,Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, USA
| | - Barré Soropogui
- Projet des Fièvre Hémorragiques en Guinée, Hôpital Donka, Conakry, Guinea
| | - Luc De Bruyn
- Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium
| | - Gédéon Ngiala Bongo
- Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany.,Department of Biology, University of Kinshasa, P.O. Box. 190, Kinshasa XI, Democratic Republic of the Congo
| | | | - Joëlle Goüy de Bellocq
- Institute of Vertebrate Biology, Research Facility Studenec, The Czech Academy of Sciences, Brno, Czech Republic
| | - Stephan Günther
- Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany
| | - N'Faly Magassouba
- Projet des Fièvre Hémorragiques en Guinée, Hôpital Donka, Conakry, Guinea
| | - Herwig Leirs
- Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium
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22
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Gryseels S, Baird SJE, Borremans B, Makundi R, Leirs H, Goüy de Bellocq J. When Viruses Don't Go Viral: The Importance of Host Phylogeographic Structure in the Spatial Spread of Arenaviruses. PLoS Pathog 2017; 13:e1006073. [PMID: 28076397 PMCID: PMC5226678 DOI: 10.1371/journal.ppat.1006073] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [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: 07/14/2016] [Accepted: 11/17/2016] [Indexed: 01/07/2023] Open
Abstract
Many emerging infections are RNA virus spillovers from animal reservoirs. Reservoir identification is necessary for predicting the geographic extent of infection risk, but rarely are taxonomic levels below the animal species considered as reservoir, and only key circumstances in nature and methodology allow intrinsic virus-host associations to be distinguished from simple geographic (co-)isolation. We sampled and genetically characterized in detail a contact zone of two subtaxa of the rodent Mastomys natalensis in Tanzania. We find two distinct arenaviruses, Gairo and Morogoro virus, each spatially confined to a single M. natalensis subtaxon, only co-occurring at the contact zone’s centre. Inter-subtaxon hybridization at this centre and a continuum of quality habitat for M. natalensis show that both viruses have the ecological opportunity to spread into the other substaxon’s range, but do not, strongly suggesting host-intrinsic barriers. Such barriers could explain why human cases of another M. natalensis-borne arenavirus, Lassa virus, are limited to West Africa. Reservoirs of zoonotic viruses are usually equated with a particular wildlife species. It is rarely assessed whether genetic groups below the species level may instead represent the actual reservoir, though this would have major implications on estimations of the zoonosis’ spatial distribution. Here we investigate whether geographically and genetically distinct subtaxa of the widespread African rodent Mastomys natalensis carry distinct arenaviruses, by sampling in detail across a contact zone of two of these subtaxa. Ongoing hybridization shows that individuals of the subtaxa are in direct physical contact, in principle allowing viral exchange, yet neither of the two arenaviruses -Gairo and Morogoro virus- were found to have crossed the zone. Such intraspecific genetic barriers to arenavirus spatial spread have important implications for our understanding of the related Lassa arenavirus, a pathogen potentially lethal to humans of which Mastomys natalensis is also the main reservoir. Although Lassa virus appears to infect several secondary hosts, its distribution is restricted to West Africa and matches that of another M. natalensis subtaxon. Our data thus indicates that it is because of M. natalensis intraspecific distinctions that the human Lassa fever endemic area has not expanded to the rest of sub-Saharan Africa.
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Affiliation(s)
- Sophie Gryseels
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium
- * E-mail:
| | - Stuart J. E. Baird
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Research Facility Studenec, Brno, Czech Republic
| | - Benny Borremans
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Rhodes Makundi
- Pest Management Centre, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Herwig Leirs
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Joëlle Goüy de Bellocq
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Research Facility Studenec, Brno, Czech Republic
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23
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Borremans B, Reijniers J, Hughes NK, Godfrey SS, Gryseels S, Makundi RH, Leirs H. Nonlinear scaling of foraging contacts with rodent population density. OIKOS 2016. [DOI: 10.1111/oik.03623] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Benny Borremans
- Evolutionary Ecology Group, Univ. of Antwerp; Antwerp Belgium
| | - Jonas Reijniers
- Evolutionary Ecology Group, Univ. of Antwerp; Antwerp Belgium
- Dept of Engineering Management; Univ. of Antwerp; Antwerp Belgium
| | - Nelika K. Hughes
- Evolutionary Ecology Group, Univ. of Antwerp; Antwerp Belgium
- School of BioSciences, Univ. of Melbourne; Melbourne Australia
| | - Stephanie S. Godfrey
- School of Veterinary and Life Sciences, Murdoch Univ.; Western Australia Australia
| | - Sophie Gryseels
- Evolutionary Ecology Group, Univ. of Antwerp; Antwerp Belgium
| | - Rhodes H. Makundi
- Pest Management Center, Sokoine Univ. of Agriculture; Morogoro Tanzania
| | - Herwig Leirs
- Evolutionary Ecology Group, Univ. of Antwerp; Antwerp Belgium
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24
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Sabuni CA, Van Houtte N, Gryseels S, Maganga SLS, Makundi RH, Leirs H, Goüy de Bellocq J. Genetic structure and diversity of the black and rufous sengi in Tanzanian coastal forests. J Zool (1987) 2016. [DOI: 10.1111/jzo.12384] [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: 11/27/2022]
Affiliation(s)
- C. A. Sabuni
- Pest Management Centre Sokoine University of Agriculture Morogoro Tanzania
| | - N. Van Houtte
- Evolutionary Ecology Group University of Antwerp Antwerpen Belgium
| | - S. Gryseels
- Evolutionary Ecology Group University of Antwerp Antwerpen Belgium
| | - S. L. S. Maganga
- Department of Wildlife Management Sokoine University of Agriculture Morogoro Tanzania
| | - R. H. Makundi
- Pest Management Centre Sokoine University of Agriculture Morogoro Tanzania
| | - H. Leirs
- Evolutionary Ecology Group University of Antwerp Antwerpen Belgium
| | - J. Goüy de Bellocq
- Evolutionary Ecology Group University of Antwerp Antwerpen Belgium
- Institute of Vertebrate Biology The Czech Academy of Sciences Brno Czech Republic
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25
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Kerber R, Krumkamp R, Diallo B, Jaeger A, Rudolf M, Lanini S, Bore JA, Koundouno FR, Becker-Ziaja B, Fleischmann E, Stoecker K, Meschi S, Mély S, Newman ENC, Carletti F, Portmann J, Korva M, Wolff S, Molkenthin P, Kis Z, Kelterbaum A, Bocquin A, Strecker T, Fizet A, Castilletti C, Schudt G, Ottowell L, Kurth A, Atkinson B, Badusche M, Cannas A, Pallasch E, Bosworth A, Yue C, Pályi B, Ellerbrok H, Kohl C, Oestereich L, Logue CH, Lüdtke A, Richter M, Ngabo D, Borremans B, Becker D, Gryseels S, Abdellati S, Vermoesen T, Kuisma E, Kraus A, Liedigk B, Maes P, Thom R, Duraffour S, Diederich S, Hinzmann J, Afrough B, Repits J, Mertens M, Vitoriano I, Bah A, Sachse A, Boettcher JP, Wurr S, Bockholt S, Nitsche A, Županc TA, Strasser M, Ippolito G, Becker S, Raoul H, Carroll MW, De Clerck H, Van Herp M, Sprecher A, Koivogui L, Magassouba N, Keïta S, Drury P, Gurry C, Formenty P, May J, Gabriel M, Wölfel R, Günther S, Di Caro A. Analysis of Diagnostic Findings From the European Mobile Laboratory in Guéckédou, Guinea, March 2014 Through March 2015. J Infect Dis 2016; 214:S250-S257. [PMID: 27638946 PMCID: PMC5050480 DOI: 10.1093/infdis/jiw269] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Background. A unit of the European Mobile Laboratory (EMLab) consortium was deployed to the Ebola virus disease (EVD) treatment unit in Guéckédou, Guinea, from March 2014 through March 2015. Methods. The unit diagnosed EVD and malaria, using the RealStar Filovirus Screen reverse transcription–polymerase chain reaction (RT-PCR) kit and a malaria rapid diagnostic test, respectively. Results. The cleaned EMLab database comprised 4719 samples from 2741 cases of suspected EVD from Guinea. EVD was diagnosed in 1231 of 2178 hospitalized patients (57%) and in 281 of 563 who died in the community (50%). Children aged <15 years had the highest proportion of Ebola virus–malaria parasite coinfections. The case-fatality ratio was high in patients aged <5 years (80%) and those aged >74 years (90%) and low in patients aged 10–19 years (40%). On admission, RT-PCR analysis of blood specimens from patients who died in the hospital yielded a lower median cycle threshold (Ct) than analysis of blood specimens from survivors (18.1 vs 23.2). Individuals who died in the community had a median Ct of 21.5 for throat swabs. Multivariate logistic regression on 1047 data sets revealed that low Ct values, ages of <5 and ≥45 years, and, among children aged 5–14 years, malaria parasite coinfection were independent determinants of a poor EVD outcome. Conclusions. Virus load, age, and malaria parasite coinfection play a role in the outcome of EVD.
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Affiliation(s)
- Romy Kerber
- Bernhard Nocht Institute for Tropical Medicine European Mobile Laboratory Consortium German Center for Infection Research, Hamburg-Munich-Marburg-Riems
| | - Ralf Krumkamp
- Bernhard Nocht Institute for Tropical Medicine German Center for Infection Research, Hamburg-Munich-Marburg-Riems
| | | | - Anna Jaeger
- Bernhard Nocht Institute for Tropical Medicine German Center for Infection Research, Hamburg-Munich-Marburg-Riems
| | - Martin Rudolf
- Bernhard Nocht Institute for Tropical Medicine European Mobile Laboratory Consortium German Center for Infection Research, Hamburg-Munich-Marburg-Riems
| | - Simone Lanini
- European Mobile Laboratory Consortium National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy
| | | | | | - Beate Becker-Ziaja
- Bernhard Nocht Institute for Tropical Medicine European Mobile Laboratory Consortium German Center for Infection Research, Hamburg-Munich-Marburg-Riems
| | - Erna Fleischmann
- European Mobile Laboratory Consortium German Center for Infection Research, Hamburg-Munich-Marburg-Riems Bundeswehr Institute of Microbiology, Munich
| | - Kilian Stoecker
- European Mobile Laboratory Consortium German Center for Infection Research, Hamburg-Munich-Marburg-Riems Bundeswehr Institute of Microbiology, Munich
| | - Silvia Meschi
- European Mobile Laboratory Consortium National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Stéphane Mély
- European Mobile Laboratory Consortium National Reference Center for Viral Hemorrhagic Fevers Laboratoire P4 Inserm-Jean Mérieux
| | - Edmund N C Newman
- European Mobile Laboratory Consortium Public Health England, Porton Down
| | - Fabrizio Carletti
- European Mobile Laboratory Consortium National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Jasmine Portmann
- European Mobile Laboratory Consortium Spiez Laboratory, Federal Office for Civil Protection
| | - Misa Korva
- European Mobile Laboratory Consortium Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Slovenia
| | - Svenja Wolff
- European Mobile Laboratory Consortium German Center for Infection Research, Hamburg-Munich-Marburg-Riems Institute of Virology, Philipps University Marburg
| | - Peter Molkenthin
- European Mobile Laboratory Consortium German Center for Infection Research, Hamburg-Munich-Marburg-Riems Bundeswehr Institute of Microbiology, Munich
| | - Zoltan Kis
- European Mobile Laboratory Consortium National Biosafety Laboratory, National Center for Epidemiology, Budapest, Hungary
| | - Anne Kelterbaum
- European Mobile Laboratory Consortium German Center for Infection Research, Hamburg-Munich-Marburg-Riems Institute of Virology, Philipps University Marburg
| | - Anne Bocquin
- European Mobile Laboratory Consortium National Reference Center for Viral Hemorrhagic Fevers Laboratoire P4 Inserm-Jean Mérieux
| | - Thomas Strecker
- European Mobile Laboratory Consortium German Center for Infection Research, Hamburg-Munich-Marburg-Riems Institute of Virology, Philipps University Marburg
| | - Alexandra Fizet
- European Mobile Laboratory Consortium National Reference Center for Viral Hemorrhagic Fevers Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, Lyon, France
| | - Concetta Castilletti
- European Mobile Laboratory Consortium National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Gordian Schudt
- European Mobile Laboratory Consortium German Center for Infection Research, Hamburg-Munich-Marburg-Riems Institute of Virology, Philipps University Marburg
| | - Lisa Ottowell
- European Mobile Laboratory Consortium Public Health England, Porton Down
| | - Andreas Kurth
- European Mobile Laboratory Consortium Robert Koch Institute, Berlin
| | - Barry Atkinson
- European Mobile Laboratory Consortium Public Health England, Porton Down
| | - Marlis Badusche
- Bernhard Nocht Institute for Tropical Medicine European Mobile Laboratory Consortium German Center for Infection Research, Hamburg-Munich-Marburg-Riems
| | - Angela Cannas
- European Mobile Laboratory Consortium National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Elisa Pallasch
- Bernhard Nocht Institute for Tropical Medicine European Mobile Laboratory Consortium German Center for Infection Research, Hamburg-Munich-Marburg-Riems
| | - Andrew Bosworth
- European Mobile Laboratory Consortium Public Health England, Porton Down
| | - Constanze Yue
- European Mobile Laboratory Consortium Robert Koch Institute, Berlin
| | - Bernadett Pályi
- European Mobile Laboratory Consortium National Biosafety Laboratory, National Center for Epidemiology, Budapest, Hungary
| | - Heinz Ellerbrok
- European Mobile Laboratory Consortium Robert Koch Institute, Berlin
| | - Claudia Kohl
- European Mobile Laboratory Consortium Robert Koch Institute, Berlin
| | - Lisa Oestereich
- Bernhard Nocht Institute for Tropical Medicine European Mobile Laboratory Consortium German Center for Infection Research, Hamburg-Munich-Marburg-Riems
| | | | - Anja Lüdtke
- European Mobile Laboratory Consortium Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Hamburg German Center for Infection Research, Hamburg-Munich-Marburg-Riems
| | - Martin Richter
- European Mobile Laboratory Consortium Robert Koch Institute, Berlin
| | - Didier Ngabo
- European Mobile Laboratory Consortium Public Health England, Porton Down
| | - Benny Borremans
- European Mobile Laboratory Consortium Evolutionary Ecology Group, Department of Biology, University of Antwerp
| | - Dirk Becker
- European Mobile Laboratory Consortium German Center for Infection Research, Hamburg-Munich-Marburg-Riems Institute of Virology, Philipps University Marburg
| | - Sophie Gryseels
- European Mobile Laboratory Consortium Evolutionary Ecology Group, Department of Biology, University of Antwerp
| | - Saïd Abdellati
- European Mobile Laboratory Consortium Institute of Tropical Medicine, Antwerp
| | - Tine Vermoesen
- European Mobile Laboratory Consortium Institute of Tropical Medicine, Antwerp
| | - Eeva Kuisma
- European Mobile Laboratory Consortium Public Health England, Porton Down
| | - Annette Kraus
- European Mobile Laboratory Consortium Public Health Agency of Sweden, Solna
| | - Britta Liedigk
- Bernhard Nocht Institute for Tropical Medicine European Mobile Laboratory Consortium German Center for Infection Research, Hamburg-Munich-Marburg-Riems
| | - Piet Maes
- European Mobile Laboratory Consortium Department of Microbiology and Immunology, Rega Institute, KU Leuven
| | - Ruth Thom
- European Mobile Laboratory Consortium Public Health England, Porton Down
| | - Sophie Duraffour
- European Mobile Laboratory Consortium Department of Microbiology and Immunology, Rega Institute, KU Leuven
| | - Sandra Diederich
- European Mobile Laboratory Consortium German Center for Infection Research, Hamburg-Munich-Marburg-Riems Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Insel Riems, Germany
| | - Julia Hinzmann
- European Mobile Laboratory Consortium Robert Koch Institute, Berlin
| | - Babak Afrough
- European Mobile Laboratory Consortium Public Health England, Porton Down
| | - Johanna Repits
- European Mobile Laboratory Consortium Janssen-Cilag, Stockholm, Sweden
| | - Marc Mertens
- European Mobile Laboratory Consortium German Center for Infection Research, Hamburg-Munich-Marburg-Riems Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Insel Riems, Germany
| | - Inês Vitoriano
- European Mobile Laboratory Consortium Public Health England, Porton Down
| | - Amadou Bah
- European Mobile Laboratory Consortium Swiss Tropical and Public Health Institute, Basel
| | - Andreas Sachse
- European Mobile Laboratory Consortium Robert Koch Institute, Berlin
| | | | - Stephanie Wurr
- Bernhard Nocht Institute for Tropical Medicine European Mobile Laboratory Consortium German Center for Infection Research, Hamburg-Munich-Marburg-Riems
| | - Sabrina Bockholt
- Bernhard Nocht Institute for Tropical Medicine European Mobile Laboratory Consortium German Center for Infection Research, Hamburg-Munich-Marburg-Riems
| | - Andreas Nitsche
- European Mobile Laboratory Consortium Robert Koch Institute, Berlin
| | - Tatjana Avšič Županc
- European Mobile Laboratory Consortium Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Slovenia
| | - Marc Strasser
- European Mobile Laboratory Consortium Spiez Laboratory, Federal Office for Civil Protection
| | - Giuseppe Ippolito
- European Mobile Laboratory Consortium National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Stephan Becker
- European Mobile Laboratory Consortium German Center for Infection Research, Hamburg-Munich-Marburg-Riems Institute of Virology, Philipps University Marburg
| | - Herve Raoul
- European Mobile Laboratory Consortium Laboratoire P4 Inserm-Jean Mérieux
| | - Miles W Carroll
- European Mobile Laboratory Consortium Public Health England, Porton Down South General Hospital, University of Southampton, United Kingdom
| | | | | | | | | | - N'Faly Magassouba
- Université Gamal Abdel Nasser de Conakry, Laboratoire des Fièvres Hémorragiques en Guinée, Guinea
| | | | | | | | | | - Jürgen May
- Bernhard Nocht Institute for Tropical Medicine German Center for Infection Research, Hamburg-Munich-Marburg-Riems
| | - Martin Gabriel
- Bernhard Nocht Institute for Tropical Medicine European Mobile Laboratory Consortium German Center for Infection Research, Hamburg-Munich-Marburg-Riems
| | - Roman Wölfel
- European Mobile Laboratory Consortium German Center for Infection Research, Hamburg-Munich-Marburg-Riems Bundeswehr Institute of Microbiology, Munich
| | - Stephan Günther
- Bernhard Nocht Institute for Tropical Medicine European Mobile Laboratory Consortium German Center for Infection Research, Hamburg-Munich-Marburg-Riems
| | - Antonino Di Caro
- European Mobile Laboratory Consortium National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, Rome, Italy
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26
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Gryseels S, Goüy de Bellocq J, Makundi R, Vanmechelen K, Broeckhove J, Mazoch V, Šumbera R, Zima J, Leirs H, Baird SJE. Genetic distinction between contiguous urban and rural multimammate mice in Tanzania despite gene flow. J Evol Biol 2016; 29:1952-1967. [PMID: 27306876 DOI: 10.1111/jeb.12919] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [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: 05/27/2016] [Accepted: 06/14/2016] [Indexed: 01/03/2023]
Abstract
Special conditions are required for genetic differentiation to arise at a local geographical scale in the face of gene flow. The Natal multimammate mouse, Mastomys natalensis, is the most widely distributed and abundant rodent in sub-Saharan Africa. A notorious agricultural pest and a natural host for many zoonotic diseases, it can live in close proximity to humans and appears to compete with other rodents for the synanthropic niche. We surveyed its population genetic structure across a 180-km transect in central Tanzania along which the landscape varied between agricultural land in a rural setting and natural woody vegetation, rivers, roads and a city (Morogoro). We sampled M. natalensis across 10 localities and genotyped 15 microsatellite loci from 515 individuals. Hierarchical STRUCTURE analyses show a K-invariant pattern distinguishing Morogoro suburbs (located in the centre of the transect) from nine surrounding rural localities. Landscape connectivity analyses in Circuitscape and comparison of rainfall patterns suggest that neither geographical isolation nor natural breeding asynchrony could explain the genetic differentiation of the urban population. Using the isolation-with-migration model implemented in IMa2, we inferred that a split between suburban and rural populations would have occurred recently (<150 years ago) with higher urban effective population density consistent with an urban source to rural sink of effective migration. The observed genetic differentiation of urban multimammate mice is striking given the uninterrupted distribution of the animal throughout the landscape and the high estimates of effective migration (2Ne M = 3.0 and 29.7), suggesting a strong selection gradient across the urban boundary.
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Affiliation(s)
- S Gryseels
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium.
| | - J Goüy de Bellocq
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium.,Institute of Vertebrate Biology, Research Facility Studenec, Academy of Sciences of the Czech Republic, Brno, Czech Republic
| | - R Makundi
- Pest Management Centre, Sokoine University of Agriculture, Morogoro, Tanzania
| | - K Vanmechelen
- Computational Modelling and Programming, Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium
| | - J Broeckhove
- Computational Modelling and Programming, Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium
| | - V Mazoch
- Department of Zoology, University of South Bohemia, České Budějovice, Czech Republic
| | - R Šumbera
- Department of Zoology, University of South Bohemia, České Budějovice, Czech Republic
| | - J Zima
- Institute of Vertebrate Biology, Research Facility Studenec, Academy of Sciences of the Czech Republic, Brno, Czech Republic.,Department of Zoology, University of South Bohemia, České Budějovice, Czech Republic
| | - H Leirs
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium
| | - S J E Baird
- Institute of Vertebrate Biology, Research Facility Studenec, Academy of Sciences of the Czech Republic, Brno, Czech Republic
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27
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Carroll MW, Matthews DA, Hiscox JA, Elmore MJ, Pollakis G, Rambaut A, Hewson R, García-Dorival I, Bore JA, Koundouno R, Abdellati S, Afrough B, Aiyepada J, Akhilomen P, Asogun D, Atkinson B, Badusche M, Bah A, Bate S, Baumann J, Becker D, Becker-Ziaja B, Bocquin A, Borremans B, Bosworth A, Boettcher JP, Cannas A, Carletti F, Castilletti C, Clark S, Colavita F, Diederich S, Donatus A, Duraffour S, Ehichioya D, Ellerbrok H, Fernandez-Garcia MD, Fizet A, Fleischmann E, Gryseels S, Hermelink A, Hinzmann J, Hopf-Guevara U, Ighodalo Y, Jameson L, Kelterbaum A, Kis Z, Kloth S, Kohl C, Korva M, Kraus A, Kuisma E, Kurth A, Liedigk B, Logue CH, Lüdtke A, Maes P, McCowen J, Mély S, Mertens M, Meschi S, Meyer B, Michel J, Molkenthin P, Muñoz-Fontela C, Muth D, Newman ENC, Ngabo D, Oestereich L, Okosun J, Olokor T, Omiunu R, Omomoh E, Pallasch E, Pályi B, Portmann J, Pottage T, Pratt C, Priesnitz S, Quartu S, Rappe J, Repits J, Richter M, Rudolf M, Sachse A, Schmidt KM, Schudt G, Strecker T, Thom R, Thomas S, Tobin E, Tolley H, Trautner J, Vermoesen T, Vitoriano I, Wagner M, Wolff S, Yue C, Capobianchi MR, Kretschmer B, Hall Y, Kenny JG, Rickett NY, Dudas G, Coltart CEM, Kerber R, Steer D, Wright C, Senyah F, Keita S, Drury P, Diallo B, de Clerck H, Van Herp M, Sprecher A, Traore A, Diakite M, Konde MK, Koivogui L, Magassouba N, Avšič-Županc T, Nitsche A, Strasser M, Ippolito G, Becker S, Stoecker K, Gabriel M, Raoul H, Di Caro A, Wölfel R, Formenty P, Günther S. Temporal and spatial analysis of the 2014-2015 Ebola virus outbreak in West Africa. Nature 2015; 524:97-101. [PMID: 26083749 PMCID: PMC10601607 DOI: 10.1038/nature14594] [Citation(s) in RCA: 216] [Impact Index Per Article: 24.0] [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: 04/09/2015] [Accepted: 06/01/2015] [Indexed: 01/17/2023]
Abstract
West Africa is currently witnessing the most extensive Ebola virus (EBOV) outbreak so far recorded. Until now, there have been 27,013 reported cases and 11,134 deaths. The origin of the virus is thought to have been a zoonotic transmission from a bat to a two-year-old boy in December 2013 (ref. 2). From this index case the virus was spread by human-to-human contact throughout Guinea, Sierra Leone and Liberia. However, the origin of the particular virus in each country and time of transmission is not known and currently relies on epidemiological analysis, which may be unreliable owing to the difficulties of obtaining patient information. Here we trace the genetic evolution of EBOV in the current outbreak that has resulted in multiple lineages. Deep sequencing of 179 patient samples processed by the European Mobile Laboratory, the first diagnostics unit to be deployed to the epicentre of the outbreak in Guinea, reveals an epidemiological and evolutionary history of the epidemic from March 2014 to January 2015. Analysis of EBOV genome evolution has also benefited from a similar sequencing effort of patient samples from Sierra Leone. Our results confirm that the EBOV from Guinea moved into Sierra Leone, most likely in April or early May. The viruses of the Guinea/Sierra Leone lineage mixed around June/July 2014. Viral sequences covering August, September and October 2014 indicate that this lineage evolved independently within Guinea. These data can be used in conjunction with epidemiological information to test retrospectively the effectiveness of control measures, and provides an unprecedented window into the evolution of an ongoing viral haemorrhagic fever outbreak.
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Affiliation(s)
- Miles W. Carroll
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- University of Southampton, South General Hospital, Southampton, SO16 6YD UK
| | - David A. Matthews
- Department of Cellular and Molecular Medicine, School of Medical Sciences, University of Bristol, Bristol, BS8 1TD UK
| | - Julian A. Hiscox
- Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 2BE UK
| | | | - Georgios Pollakis
- Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 2BE UK
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 2FL UK
- Fogarty International Center, National Institutes of Health, Bethesda, 20892 Maryland USA
- Centre for Immunology, Infection and Evolution, University of Edinburgh, Edinburgh, EH9 2FL UK
| | - Roger Hewson
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - Isabel García-Dorival
- Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 2BE UK
| | - Joseph Akoi Bore
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Université Gamal Abdel Nasser de Conakry, Laboratoire des Fièvres Hémorragiques en Guinée, Conakry, Guinea
- Institut National de Santé Publique, Conakry, Guinea
| | - Raymond Koundouno
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Université Gamal Abdel Nasser de Conakry, Laboratoire des Fièvres Hémorragiques en Guinée, Conakry, Guinea
- Institut National de Santé Publique, Conakry, Guinea
| | - Saïd Abdellati
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Institute of Tropical Medicine, Antwerp, B-2000 Belgium
| | - Babak Afrough
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
| | - John Aiyepada
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State Nigeria
| | - Patience Akhilomen
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State Nigeria
| | - Danny Asogun
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State Nigeria
| | - Barry Atkinson
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
| | - Marlis Badusche
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
| | - Amadou Bah
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Swiss Tropical and Public Health Institute, University of Basel, Basel, CH-4002 Switzerland
| | - Simon Bate
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
| | - Jan Baumann
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, D-20359 Germany
| | - Dirk Becker
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
- Institute of Virology, Philipps University Marburg, Marburg, 35043 Germany
| | - Beate Becker-Ziaja
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
| | - Anne Bocquin
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- National Reference Center for Viral Hemorrhagic Fevers, Lyon, 69365 France
- Laboratoire P4 Inserm-Jean Mérieux, US003 Inserm, Lyon, 69365 France
| | - Benny Borremans
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Department of Biology, University of Antwerp, Antwerp, B-2020 Belgium
| | - Andrew Bosworth
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 2BE UK
| | - Jan Peter Boettcher
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Robert Koch Institute, Berlin, 13353 Germany
| | - Angela Cannas
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- National Institute for Infectious Diseases (INMI) Lazzaro Spallanzani, Rome, 00149 Italy
| | - Fabrizio Carletti
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- National Institute for Infectious Diseases (INMI) Lazzaro Spallanzani, Rome, 00149 Italy
| | - Concetta Castilletti
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- National Institute for Infectious Diseases (INMI) Lazzaro Spallanzani, Rome, 00149 Italy
| | - Simon Clark
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
| | - Francesca Colavita
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- National Institute for Infectious Diseases (INMI) Lazzaro Spallanzani, Rome, 00149 Italy
| | - Sandra Diederich
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
- Friedrich Loeffler Institute, Federal Research Institute for Animal Health, Greifswald, 17493 Insel Riems Germany
| | - Adomeh Donatus
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State Nigeria
| | - Sophie Duraffour
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, D-20359 Germany
- KU Leuven Rega institute, Leuven, B-3000 Belgium
| | - Deborah Ehichioya
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Redeemer’s University, Osun State Nigeria
| | - Heinz Ellerbrok
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Robert Koch Institute, Berlin, 13353 Germany
| | - Maria Dolores Fernandez-Garcia
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Centro Nacional de Microbiologia, Instituto de Salud Carlos III, Madrid, 28029 Spain
| | - Alexandra Fizet
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- National Reference Center for Viral Hemorrhagic Fevers, Lyon, 69365 France
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, Lyon, 69365 France
| | - Erna Fleischmann
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
- Bundeswehr Institute of Microbiology, Munich, 80937 Germany
| | - Sophie Gryseels
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Department of Biology, University of Antwerp, Antwerp, B-2020 Belgium
| | - Antje Hermelink
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Robert Koch Institute, Berlin, 13353 Germany
| | - Julia Hinzmann
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Robert Koch Institute, Berlin, 13353 Germany
| | - Ute Hopf-Guevara
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Robert Koch Institute, Berlin, 13353 Germany
| | - Yemisi Ighodalo
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State Nigeria
| | - Lisa Jameson
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
| | - Anne Kelterbaum
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
- Institute of Virology, Philipps University Marburg, Marburg, 35043 Germany
| | - Zoltan Kis
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- National Center for Epidemiology, National Biosafety Laboratory, Budapest, H-1097 Hungary
| | - Stefan Kloth
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Robert Koch Institute, Berlin, 13353 Germany
| | - Claudia Kohl
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Robert Koch Institute, Berlin, 13353 Germany
| | - Miša Korva
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, SI-1000 Slovenia
| | - Annette Kraus
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Public Health Agency of Sweden, Solna, 171 82 Sweden
| | - Eeva Kuisma
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
| | - Andreas Kurth
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Robert Koch Institute, Berlin, 13353 Germany
| | - Britta Liedigk
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
| | - Christopher H. Logue
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
| | - Anja Lüdtke
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
- Heinrich Pette Institute – Leibniz Institute for Experimental Virology, Hamburg, 20251 Germany
| | - Piet Maes
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- KU Leuven Rega institute, Leuven, B-3000 Belgium
| | - James McCowen
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
| | - Stéphane Mély
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- National Reference Center for Viral Hemorrhagic Fevers, Lyon, 69365 France
- Laboratoire P4 Inserm-Jean Mérieux, US003 Inserm, Lyon, 69365 France
| | - Marc Mertens
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
- Friedrich Loeffler Institute, Federal Research Institute for Animal Health, Greifswald, 17493 Insel Riems Germany
| | - Silvia Meschi
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- National Institute for Infectious Diseases (INMI) Lazzaro Spallanzani, Rome, 00149 Italy
| | - Benjamin Meyer
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
- Institute of Virology, University of Bonn, Bonn, 53127 Germany
| | - Janine Michel
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Robert Koch Institute, Berlin, 13353 Germany
| | - Peter Molkenthin
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
- Bundeswehr Institute of Microbiology, Munich, 80937 Germany
| | - César Muñoz-Fontela
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
- Heinrich Pette Institute – Leibniz Institute for Experimental Virology, Hamburg, 20251 Germany
| | - Doreen Muth
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
- Institute of Virology, University of Bonn, Bonn, 53127 Germany
| | - Edmund N. C. Newman
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
| | - Didier Ngabo
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
| | - Lisa Oestereich
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
| | - Jennifer Okosun
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State Nigeria
| | - Thomas Olokor
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State Nigeria
| | - Racheal Omiunu
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State Nigeria
| | - Emmanuel Omomoh
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State Nigeria
| | - Elisa Pallasch
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
| | - Bernadett Pályi
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- National Center for Epidemiology, National Biosafety Laboratory, Budapest, H-1097 Hungary
| | - Jasmine Portmann
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Federal Office for Civil Protection, Spiez Laboratory, Spiez, CH-3700 Switzerland
| | - Thomas Pottage
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
| | - Catherine Pratt
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
| | - Simone Priesnitz
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Bundeswehr Hospital, Hamburg, 22049 Germany
| | - Serena Quartu
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- National Institute for Infectious Diseases (INMI) Lazzaro Spallanzani, Rome, 00149 Italy
| | - Julie Rappe
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Institute of Virology and Immunology, Mittelhäusern, CH-3147 Switzerland
| | - Johanna Repits
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Janssen-Cilag, Sollentuna, SE-192 07 Sweden
| | - Martin Richter
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Robert Koch Institute, Berlin, 13353 Germany
| | - Martin Rudolf
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
| | - Andreas Sachse
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Robert Koch Institute, Berlin, 13353 Germany
| | - Kristina Maria Schmidt
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Robert Koch Institute, Berlin, 13353 Germany
| | - Gordian Schudt
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
- Institute of Virology, Philipps University Marburg, Marburg, 35043 Germany
| | - Thomas Strecker
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
- Institute of Virology, Philipps University Marburg, Marburg, 35043 Germany
| | - Ruth Thom
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
| | - Stephen Thomas
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
| | - Ekaete Tobin
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State Nigeria
| | - Howard Tolley
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
| | - Jochen Trautner
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Thünen Institute, Hamburg, D-22767 Germany
| | - Tine Vermoesen
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Institute of Tropical Medicine, Antwerp, B-2000 Belgium
| | - Inês Vitoriano
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
| | - Matthias Wagner
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
- Bundeswehr Institute of Microbiology, Munich, 80937 Germany
| | - Svenja Wolff
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
- Institute of Virology, Philipps University Marburg, Marburg, 35043 Germany
| | - Constanze Yue
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Robert Koch Institute, Berlin, 13353 Germany
| | - Maria Rosaria Capobianchi
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- National Institute for Infectious Diseases (INMI) Lazzaro Spallanzani, Rome, 00149 Italy
| | - Birte Kretschmer
- Eurice - European Research and Project Office GmbH, Berlin, 10115 Germany
| | - Yper Hall
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
| | - John G. Kenny
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB UK
| | - Natasha Y. Rickett
- Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 2BE UK
| | - Gytis Dudas
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 2FL UK
| | - Cordelia E. M. Coltart
- Department of Infection and Population Health, University College London, London, WC1E 6JB UK
| | - Romy Kerber
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
| | - Damien Steer
- Research IT, University of Bristol, Bristol, BS8 1HH UK
| | - Callum Wright
- Advanced Computing Research Centre, University of Bristol, Bristol, BS8 1HH UK
| | - Francis Senyah
- Public Health England, Porton Down, SP4 0JG Wiltshire UK
| | | | - Patrick Drury
- World Health Organization, Geneva 27, 1211 Switzerland
| | | | | | | | | | - Alexis Traore
- Section Prévention et Lutte contre la Maladie à la Direction Préfectorale de la Santé de Guéckédou, Guéckédou, Guinea
| | - Mandiou Diakite
- Université Gamal Abdel Nasser de Conakry, CHU Donka, Conakry, Guinea
| | | | | | - N’Faly Magassouba
- Université Gamal Abdel Nasser de Conakry, Laboratoire des Fièvres Hémorragiques en Guinée, Conakry, Guinea
| | - Tatjana Avšič-Županc
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, SI-1000 Slovenia
| | - Andreas Nitsche
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Robert Koch Institute, Berlin, 13353 Germany
| | - Marc Strasser
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Federal Office for Civil Protection, Spiez Laboratory, Spiez, CH-3700 Switzerland
| | - Giuseppe Ippolito
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- National Institute for Infectious Diseases (INMI) Lazzaro Spallanzani, Rome, 00149 Italy
| | - Stephan Becker
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
- Institute of Virology, Philipps University Marburg, Marburg, 35043 Germany
| | - Kilian Stoecker
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
- Bundeswehr Institute of Microbiology, Munich, 80937 Germany
| | - Martin Gabriel
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
| | - Hervé Raoul
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Laboratoire P4 Inserm-Jean Mérieux, US003 Inserm, Lyon, 69365 France
| | - Antonino Di Caro
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- National Institute for Infectious Diseases (INMI) Lazzaro Spallanzani, Rome, 00149 Italy
| | - Roman Wölfel
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
- Bundeswehr Institute of Microbiology, Munich, 80937 Germany
| | | | - Stephan Günther
- The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, D-20359 Germany
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, D-20359 Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124 Germany
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Abstract
Resistance of rodents to anticoagulant rodenticides has emerged in several areas across the world. Single nucleotide mutations in the vkorc1 gene have been shown to elicit various levels of anticoagulant resistance, and these mutations are prevalent in several Rattus and Mus musculus populations. In sub-Saharan Africa, the Natal multimammate mouse, Mastomys natalensis, is one of the most damaging pests to crops, and anticoagulant poisons such as bromadiolone are frequently used to control these rodents in agricultural fields. Here, we investigate if vkorc1 shows any polymorphism in natural populations of M. natalensis. We sequenced the third exon of vkorc1 of 162 M. natalensis captured from 14 different agricultural sites in Morogoro Region, Tanzania. In addition to 6 SNPs in the noncoding flanking region, we detected 3 nonsynonymous SNPs in this exon: 10 animals (6.2%) carried a Leu108Val variant, 2 animals (1.2%) an Ala140Thr variant, and 1 animal (0.6 %) an Arg100His variant, all 3 in heterozygous form. Ala140Thr is just one residue from a mutation known to be involved in anticoagulant resistance in Rattus and Mus. While in vitro or in vivo experiments are needed to link vkorc1 genetic polymorphisms to level of VKOR activity and anticoagulant susceptibility, our results suggest that M. natalensis individuals may vary in their response to anticoagulant rodenticides. This is the first vkorc1 sequence data from a species outside the Rattus or Mus genera, and for the first time from a rodent species endemic to Africa.
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Affiliation(s)
- Sophie Gryseels
- From the Department of Biology, Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium (Gryseels, Leirs, and Goüy de Bellocq); Pest Management Centre, Sokoine University of Agriculture, Morogoro, Tanzania (Makundi); Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Studenec, Czech Republic (Goüy de Bellocq).
| | - Herwig Leirs
- From the Department of Biology, Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium (Gryseels, Leirs, and Goüy de Bellocq); Pest Management Centre, Sokoine University of Agriculture, Morogoro, Tanzania (Makundi); Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Studenec, Czech Republic (Goüy de Bellocq)
| | - Rhodes Makundi
- From the Department of Biology, Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium (Gryseels, Leirs, and Goüy de Bellocq); Pest Management Centre, Sokoine University of Agriculture, Morogoro, Tanzania (Makundi); Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Studenec, Czech Republic (Goüy de Bellocq)
| | - Joëlle Goüy de Bellocq
- From the Department of Biology, Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium (Gryseels, Leirs, and Goüy de Bellocq); Pest Management Centre, Sokoine University of Agriculture, Morogoro, Tanzania (Makundi); Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Studenec, Czech Republic (Goüy de Bellocq)
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29
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Borremans B, Vossen R, Becker-Ziaja B, Gryseels S, Hughes N, Van Gestel M, Van Houtte N, Günther S, Leirs H. Shedding dynamics of Morogoro virus, an African arenavirus closely related to Lassa virus, in its natural reservoir host Mastomys natalensis. Sci Rep 2015; 5:10445. [PMID: 26022445 PMCID: PMC4448520 DOI: 10.1038/srep10445] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [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: 01/20/2015] [Accepted: 04/10/2015] [Indexed: 12/15/2022] Open
Abstract
Arenaviruses can cause mild to severe hemorrhagic fevers. Humans mainly get infected through contact with infected rodents or their excretions, yet little is known about transmission dynamics within rodent populations. Morogoro virus (MORV) is an Old World arenavirus closely related to Lassa virus with which it shares the same host species Mastomys natalensis. We injected MORV in its host, and sampled blood and excretions at frequent intervals. Infection in adults was acute; viral RNA disappeared from blood after 18 days post infection (dpi) and from excretions after 39 dpi. Antibodies were present from 7 dpi and never disappeared. Neonatally infected animals acquired a chronic infection with RNA and antibodies in blood for at least 3 months. The quantified excretion and antibody patterns can be used to inform mathematical transmission models, and are essential for understanding and controlling transmission in the natural rodent host populations.
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Affiliation(s)
- Benny Borremans
- Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium
| | - Raphaël Vossen
- Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium
| | | | - Sophie Gryseels
- Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium
| | - Nelika Hughes
- Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium
| | - Mats Van Gestel
- Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium
| | | | - Stephan Günther
- Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany
| | - Herwig Leirs
- Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium
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Gryseels S, Rieger T, Oestereich L, Cuypers B, Borremans B, Makundi R, Leirs H, Günther S, Goüy de Bellocq J. Gairo virus, a novel arenavirus of the widespread Mastomys natalensis : Genetically divergent, but ecologically similar to Lassa and Morogoro viruses. Virology 2015; 476:249-256. [DOI: 10.1016/j.virol.2014.12.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 12/05/2014] [Accepted: 12/06/2014] [Indexed: 10/24/2022]
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Moreau M, Spencer C, Gozalbes JG, Colebunders R, Lefevre A, Gryseels S, Borremans B, Gunther S, Becker D, Bore JA, Koundouno FR, Di Caro A, Wölfel R, Decroo T, Van Herp M, Peetermans L, Camara AM. Lactating mothers infected with Ebola virus: EBOV RT-PCR of blood only may be insufficient. ACTA ACUST UNITED AC 2015; 20. [PMID: 25635320 DOI: 10.2807/1560-7917.es2015.20.3.21017] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [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]
Abstract
Binary file ES_Abstracts_Final_ECDC.txt matches
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Affiliation(s)
- M Moreau
- Department of Emergency Medicine, Centre Hospitalier Chretien, Liege, Belgium
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Amissah NA, Gryseels S, Tobias NJ, Ravadgar B, Suzuki M, Vandelannoote K, Durnez L, Leirs H, Stinear TP, Portaels F, Ablordey A, Eddyani M. Investigating the role of free-living amoebae as a reservoir for Mycobacterium ulcerans. PLoS Negl Trop Dis 2014; 8:e3148. [PMID: 25188535 PMCID: PMC4154674 DOI: 10.1371/journal.pntd.0003148] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 07/25/2014] [Indexed: 11/20/2022] Open
Abstract
Background The reservoir and mode of transmission of Mycobacterium ulcerans, the causative agent of Buruli ulcer, still remain a mystery. It has been suggested that M. ulcerans persists with difficulty as a free-living organism due to its natural fragility and inability to withstand exposure to direct sunlight, and thus probably persists within a protective host environment. Methodology/Principal Findings We investigated the role of free-living amoebae as a reservoir of M. ulcerans by screening the bacterium in free-living amoebae (FLA) cultures isolated from environmental specimens using real-time PCR. We also followed the survival of M. ulcerans expressing green fluorescence protein (GFP) in Acanthameoba castellanii by flow cytometry and observed the infected cells using confocal and transmission electron microscopy for four weeks in vitro. IS2404 was detected by quantitative PCR in 4.64% of FLA cultures isolated from water, biofilms, detritus and aerosols. While we could not isolate M. ulcerans, 23 other species of mycobacteria were cultivated from inside FLA and/or other phagocytic microorganisms. Laboratory experiments with GFP-expressing M. ulcerans in A. castellani trophozoites for 28 days indicated the bacteria did not replicate inside amoebae, but they could remain viable at low levels in cysts. Transmission electron microscopy of infected A. castellani confirmed the presence of bacteria within both trophozoite vacuoles and cysts. There was no correlation of BU notification rate with detection of the IS2404 in FLA (r = 0.07, n = 539, p = 0.127). Conclusion/Significance This study shows that FLA in the environment are positive for the M. ulcerans insertion sequence IS2404. However, the detection frequency and signal strength of IS2404 positive amoabae was low and no link with the occurrence of BU was observed. We conclude that FLA may host M. ulcerans at low levels in the environment without being directly involved in the transmission to humans. Mycobacterium ulcerans, the causative agent of Buruli ulcer (BU) is an environmental pathogen known to reside in aquatic habitat. However, the reservoir and modes of transmission to humans still remain unknown. M. ulcerans can probably not live freely due to its natural fragility and inability to withstand exposure to direct sunlight. This study investigated the hypothesis that free-living amoebae (FLA) can serve as a reservoir of M. ulcerans by testing for its presence in amoebae isolated from water bodies in BU endemic and non-endemic communities and whether the pathogen can remain viable when experimentally infected in amoebae in the laboratory. We detected only one (IS2404) of the three (IS2606 and KRB) targets for the presence of M. ulcerans in amoebae cultures and found no correlation between its presence in the environment and BU notification rate. M. ulcerans remained viable at low levels in amoebae for 28 days in vitro. We therefore conclude that FLA may host M. ulcerans at low levels in the environment without being directly involved in the transmission to humans.
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Affiliation(s)
- Nana Ama Amissah
- Bacteriology Department, Noguchi Memorial Institute for Medical Research, Accra, Ghana
- * E-mail:
| | - Sophie Gryseels
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Nicholas J. Tobias
- Department of Microbiology, University of Melbourne, Melbourne, Victoria, Australia
| | - Bahram Ravadgar
- Department of Microbiology, Monash University, Victoria, Australia
| | - Mitsuko Suzuki
- Parasitology Department, Noguchi Memorial Institute for Medical Research, Accra, Ghana
| | - Koen Vandelannoote
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Lies Durnez
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Herwig Leirs
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Timothy P. Stinear
- Department of Microbiology, University of Melbourne, Melbourne, Victoria, Australia
- Department of Microbiology, Monash University, Victoria, Australia
| | - Françoise Portaels
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Anthony Ablordey
- Bacteriology Department, Noguchi Memorial Institute for Medical Research, Accra, Ghana
| | - Miriam Eddyani
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
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Veyrunes F, Perez J, Borremans B, Gryseels S, Richards LR, Duran A, Chevret P, Robinson TJ, Britton-Davidian J. A new cytotype of the African pygmy mouse Mus minutoides in Eastern Africa. Implications for the evolution of sex-autosome translocations. Chromosome Res 2014; 22:533-43. [PMID: 25159220 DOI: 10.1007/s10577-014-9440-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 07/31/2014] [Accepted: 08/17/2014] [Indexed: 11/27/2022]
Abstract
The African pygmy mice (genus Mus, subgenus Nannomys) are recognized for their highly conserved morphology but extensive chromosomal diversity, particularly involving sex-autosome translocations, one of the rarest chromosomal rearrangements among mammals. It has been shown that in the absence of unambiguous diagnostic morphological traits, sex-autosome translocations offer accurate taxonomic markers. For example, in Mus minutoides, irrespective of the diploid number (which ranges from 2n = 18 to 34), all specimens possess the sex-autosome translocations (X.1) and (Y.1) that are unique to this species. In this study, we describe a new cytotype that challenges this view. Males are characterized by the translocation (Y.1) only, while females carry no sex-autosome translocation, the X chromosome being acrocentric. Hence, although sex-autosome translocations (X.1) and (Y.1) are still diagnostic when one or both are present, their absence does not rule out M. minutoides. This cytotype has a large distribution, with specimens found in Tanzania and in the eastern part of South Africa. The nonpervasive distribution of Rb(X.1) provides an opportunity to investigate different evolutionary scenarios of sex-autosome translocations using a phylogenetic framework and the distribution of telomeric repeats. The results tend to support a scenario involving a reversal event, i.e., fusion then fission of Rb(X.1), and highlighted the existence of a new X1X1X2X2/X1X2Y sex chromosome system, confirming the remarkable diversity of neo-sex chromosomes and sex determination systems in the African pygmy mice.
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Affiliation(s)
- F Veyrunes
- Institut des Sciences de l'Evolution de Montpellier, Université Montpellier 2, UMR CNRS 5554, Montpellier, France,
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Gryseels S, Amissah D, Durnez L, Vandelannoote K, Leirs H, De Jonckheere J, Silva MT, Portaels F, Ablordey A, Eddyani M. Amoebae as potential environmental hosts for Mycobacterium ulcerans and other mycobacteria, but doubtful actors in Buruli ulcer epidemiology. PLoS Negl Trop Dis 2012; 6:e1764. [PMID: 22880141 PMCID: PMC3413716 DOI: 10.1371/journal.pntd.0001764] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Accepted: 06/21/2012] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND The reservoir and mode of transmission of Mycobacterium ulcerans, the causative agent of Buruli ulcer, remain unknown. Ecological, genetic and epidemiological information nonetheless suggests that M. ulcerans may reside in aquatic protozoa. METHODOLOGY/PRINCIPAL FINDINGS We experimentally infected Acanthamoeba polyphaga with M. ulcerans and found that the bacilli were phagocytised, not digested and remained viable for the duration of the experiment. Furthermore, we collected 13 water, 90 biofilm and 45 detritus samples in both Buruli ulcer endemic and non-endemic communities in Ghana, from which we cultivated amoeboid protozoa and mycobacteria. M. ulcerans was not isolated, but other mycobacteria were as frequently isolated from intracellular as from extracellular sources, suggesting that they commonly infect amoebae in nature. We screened the samples as well as the amoeba cultures for the M. ulcerans markers IS2404, IS2606 and KR-B. IS2404 was detected in 2% of the environmental samples and in 4% of the amoeba cultures. The IS2404 positive amoeba cultures included up to 5 different protozoan species, and originated both from Buruli ulcer endemic and non-endemic communities. CONCLUSIONS/SIGNIFICANCE This is the first report of experimental infection of amoebae with M. ulcerans and of the detection of the marker IS2404 in amoeba cultures isolated from the environment. We conclude that amoeba are potential natural hosts for M. ulcerans, yet remain sceptical about their implication in the transmission of M. ulcerans to humans and their importance in the epidemiology of Buruli ulcer.
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Affiliation(s)
- Sophie Gryseels
- Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium.
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De Jonckheere JF, Gryseels S, Eddyani M. Knowledge of morphology is still required when identifying new amoeba isolates by molecular techniques. Eur J Protistol 2012; 48:178-84. [DOI: 10.1016/j.ejop.2012.01.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Revised: 01/04/2012] [Accepted: 01/05/2012] [Indexed: 11/29/2022]
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Borremans B, Leirs H, Gryseels S, Günther S, Makundi R, de Bellocq JG. Presence of Mopeia Virus, an African Arenavirus, Related to Biotope and Individual Rodent Host Characteristics: Implications for Virus Transmission. Vector Borne Zoonotic Dis 2011; 11:1125-31. [DOI: 10.1089/vbz.2010.0010] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Benny Borremans
- Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium
| | - Herwig Leirs
- Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium
- Danish Pest Infestation Laboratory, Department of Integrated Pest Management, University of Aarhus, Kongens Lyngby, Denmark
| | - Sophie Gryseels
- Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium
| | - Stephan Günther
- Department of Virology, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany
| | - Rhodes Makundi
- Pest Management Centre, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Joëlle Goüy de Bellocq
- Evolutionary Ecology Group, University of Antwerp, Antwerp, Belgium
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Vairão, Portugal
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Vandelannoote K, Durnez L, Amissah D, Gryseels S, Dodoo A, Yeboah S, Addo P, Eddyani M, Leirs H, Ablordey A, Portaels F. Application of real-time PCR in Ghana, a Buruli ulcer-endemic country, confirms the presence ofMycobacterium ulceransin the environment. FEMS Microbiol Lett 2010; 304:191-4. [DOI: 10.1111/j.1574-6968.2010.01902.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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