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Bangura U, Davis C, Lamin J, Bangura J, Soropogui B, Davison AJ, Nichols J, Vucak M, Dawson M, Ansumana R, Sondufu D, Cadar D, Rieger T, Thomson E, Sahr F, Magassouba N, Ghersi B, Bird BH, Fichet-Calvet E. Spatio-temporal spread of Lassa virus and a new rodent host in the Mano River Union area, West Africa. Emerg Microbes Infect 2024; 13:2290834. [PMID: 38047354 PMCID: PMC10919312 DOI: 10.1080/22221751.2023.2290834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 11/29/2023] [Indexed: 12/05/2023]
Abstract
The spread of Lassa virus (LASV) in Guinea, Liberia and Sierra Leone, which together are named the Mano River Union (MRU) area, was examined phylogeographically. To provide a reliable evolutionary scenario, new rodent-derived, whole LASV sequences were included. These were generated by metatranscriptomic next-generation sequencing from rodents sampled between 2003 and 2020 in 21 localities of Guinea and Sierra Leone. An analysis was performed using BEAST to perform continuous phylogeographic inference and EvoLaps v36 to visualize spatio-temporal spread. LASV was identified as expected in its primary host reservoir, the Natal multimammate mouse (Mastomys natalensis), and also in two Guinean multimammate mice (Mastomys erythroleucus) in northern Sierra Leone and two rusty-bellied brush-furred mice (Lophuromys sikapusi) in southern Sierra Leone. This finding is consistent with the latter two species being secondary host reservoirs. The strains in these three species were very closely related in LASV lineage IV. Phylogenetic analysis indicated that the most recent common ancestor of lineage IV existed 316-374 years ago and revealed distinct, well-supported clades from Sierra Leone (Bo, Kabala and Kenema), Guinea (Faranah, Kissidougou-Guekedou and Macenta) and Liberia (Phebe-Ganta). The phylogeographic scenario suggests southern Guinea as the point of origin of LASV in the MRU area, with subsequent spread to towards Mali, Liberia and Sierra Leone at a mean speed of 1.6 to 1.1 km/year.
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Affiliation(s)
- Umaru Bangura
- Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Centre for Arbovirus and Hemorrhagic Fever Reference and Research, Hamburg, Germany
| | | | - Joyce Lamin
- Mercy Hospital Research Laboratory, Bo, Sierra Leone
| | - James Bangura
- University of Makeni and University of California, Davis One Health Program, Makeni, Sierra Leone
| | - Barré Soropogui
- Laboratoire des Fièvres Hémorragiques en Guinée, Conakry, Guinea
| | | | - Jenna Nichols
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Matej Vucak
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | | | | | | | - Dániel Cadar
- Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Centre for Arbovirus and Hemorrhagic Fever Reference and Research, Hamburg, Germany
| | - Toni Rieger
- Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Centre for Arbovirus and Hemorrhagic Fever Reference and Research, Hamburg, Germany
| | - Emma Thomson
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Foday Sahr
- College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone
| | | | - Bruno Ghersi
- One Health Institute, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | - Brian H. Bird
- One Health Institute, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | - Elisabeth Fichet-Calvet
- Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Centre for Arbovirus and Hemorrhagic Fever Reference and Research, Hamburg, Germany
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2
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Fan Y, Hou Y, Li Q, Dian Z, Wang B, Xia X. RNA virus diversity in rodents. Arch Microbiol 2023; 206:9. [PMID: 38038743 DOI: 10.1007/s00203-023-03732-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 11/01/2023] [Accepted: 11/02/2023] [Indexed: 12/02/2023]
Abstract
Many zoonotic disease emergencies are associated with RNA viruses in rodents that substantially impact public health. With the widespread application of meta-genomics and meta-transcriptomics for virus discovery over the last decade, viral sequences deposited in public databases have expanded rapidly, and the number of novel viruses discovered in rodents has increased. As important reservoirs of zoonotic viruses, rodents have attracted increasing attention for the risk of potential spillover of rodent-borne viruses. However, knowledge of rodent viral diversity and the major factors contributing to the risk of zoonotic epidemic outbreaks remains limited. Therefore, this study analyzes the diversity and composition of rodent RNA viruses using virus records from the Database of Rodent-associated Viruses (DRodVir/ZOVER), which covers the published literatures and records in GenBank database, reviews the main rodent RNA virus-induced human infectious diseases, and discusses potential challenges in this field.
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Affiliation(s)
- Yayu Fan
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, 650500, People's Republic of China
| | - Yutong Hou
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, 650500, People's Republic of China
| | - Qian Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, 650500, People's Republic of China
| | - Ziqin Dian
- Department of Clinical Laboratory, The First People's Hospital of Yunnan Province, Kunming, Yunnan, 650032, People's Republic of China
| | - Binghui Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, 650500, People's Republic of China.
| | - Xueshan Xia
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, 650500, People's Republic of China.
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3
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Erdin M, Stanoeva KR, Mögling R, Korva M, Knap N, Resman Rus K, Domingo C, Reimerink JH, de Vries A, Alburkat H, Utriainen M, Gossner CM, Sironen T, Avšič-Županc T, Reusken CB, Vapalahti O. External quality assessment of orthohantavirus and lymphocytic choriomeningitis virus molecular detection and serology in Europe, 2021. Euro Surveill 2023; 28:2300054. [PMID: 37796441 PMCID: PMC10557384 DOI: 10.2807/1560-7917.es.2023.28.40.2300054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 05/25/2023] [Indexed: 10/06/2023] Open
Abstract
BackgroundRodent-borne viruses such as orthohantaviruses and arenaviruses cause considerable disease burden with regional and temporal differences in incidence and clinical awareness. Therefore, it is important to regularly evaluate laboratory diagnostic capabilities, e.g. by external quality assessments (EQA).AimWe wished to evaluate the performance and diagnostic capability of European expert laboratories to detect orthohantaviruses and lymphocytic choriomeningitis virus (LCMV) and human antibody response towards orthohantaviruses.MethodsWe conducted an EQA in 2021; molecular panels consisted of 12 samples, including different orthohantaviruses (Seoul, Dobrava-Belgrade (DOBV), Puumala (PUUV) and Hantaan orthohantavirus), LCMV and negative controls. Serological panels consisted of six human serum samples reactive to PUUV, DOBV or negative to orthohantaviruses. The EQA was sent to 25 laboratories in 20 countries.ResultsThe accuracy of molecular detection of orthohantaviruses varied (50‒67%, average 62%) among 16 participating laboratories, while LCMV samples were successfully detected in all 11 participating laboratories (91-100%, average 96%). The accuracy of serological diagnosis of acute and past orthohantavirus infections was on average 95% among 20 participating laboratories and 82% in 19 laboratories, respectively. A variety of methods was used, with predominance of in-house assays for molecular tests, and commercial assays for serological ones.ConclusionSerology, the most common tool to diagnose acute orthohantavirus infections, had a high accuracy in this EQA. The molecular detection of orthohantaviruses needs improvement while LCMV detection (performed in fewer laboratories) had 95% accuracy. Further EQAs are recommended to be performed periodically to monitor improvements and challenges in the diagnostics of rodent-borne diseases.
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Affiliation(s)
- Mert Erdin
- These authors contributed equally to the work and share the first authorship
- Department of Virology, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Kamelia R Stanoeva
- These authors contributed equally to the work and share the first authorship
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Ramona Mögling
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Miša Korva
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Nataša Knap
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Katarina Resman Rus
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Cristina Domingo
- Centre for Biological Threats and Special Pathogens, Robert Koch Institute (RKI), Berlin, Germany. Current affiliation: Centre for International Health Protection, RKI, Berlin, Germany
| | - Johan Hj Reimerink
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Ankje de Vries
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Hussein Alburkat
- Department of Virology, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Mira Utriainen
- Department of Virology, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Céline M Gossner
- Diseases Programme Unit, European Centre for Disease Prevention and Control (ECDC), Solna, Sweden
| | - Tarja Sironen
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
- Department of Virology, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Tatjana Avšič-Županc
- These authors contributed equally to the work and share the last authorship
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Chantal Bem Reusken
- These authors contributed equally to the work and share the last authorship
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Olli Vapalahti
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
- These authors contributed equally to the work and share the last authorship
- Department of Virology, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Helsinki University Hospital Diagnostic Center, HUSLAB, Helsinki, Finland
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4
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Smither AR, Koninga J, Kanneh FB, Foday M, Boisen ML, Bond NG, Momoh M, Sandi JD, Kanneh L, Alhasan F, Kanneh IM, Yillah MS, Grant DS, Bush DJ, Nelson DKS, Cruz KM, Klitting R, Pauthner M, Andersen KG, Shaffer JG, Cross RW, Schieffelin JS, Garry RF. Novel Tools for Lassa Virus Surveillance in Peri-domestic Rodents. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.17.23287380. [PMID: 36993465 PMCID: PMC10055574 DOI: 10.1101/2023.03.17.23287380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Background Lassa fever (LF) is a rodent-borne disease endemic to West Africa. In the absence of licensed therapeutics or vaccines, rodent exclusion from living spaces remains the primary method of preventing LF. Zoonotic surveillance of Lassa virus (LASV), the etiologic agent of LF, can assess the burden of LASV in a region and guide public health measures against LF. Methods In this study, we adapted commercially available LASV human diagnostics to assess the prevalence of LASV in peri-domestic rodents in Eastern Sierra Leone. Small mammal trapping was conducted in Kenema district, Sierra Leone between November 2018-July 2019. LASV antigen was detected using a commercially available LASV NP antigen rapid diagnostic test. LASV IgG antibodies against LASV nucleoprotein (NP) and glycoprotein (GP) were tested by adapting a commercially available semi-quantitative enzyme linked immunosorbent assay (ELISA) for detection of mouse-related and rat-related species IgG. Findings Of the 373 tested specimens, 74 (20%) tested positive for LASV antigen. 40 (11%) specimens tested positive for LASV NP IgG, while an additional 12 (3%) specimens only tested positive for LASV GP IgG. Simultaneous antigen presence and IgG antibody presence was linked in Mastomys sp. specimens (p < 0.01), but not Rattus sp. specimens (p = 1). Despite the link between antigen presence and IgG antibody presence in Mastomys sp., the strength of antigen response did not correlate with the strength of IgG response to either GP IgG or NP IgG. Interpretation The tools developed in this study can aid in the generation of valuable public health data for rapid field assessment of LASV burden during outbreak investigations and general LASV surveillance. Funding Funding for this work was supported by the National Institute of Allergy and Infectious Diseases National Institute of Health, Department of Health and Human Services under the following grants: International Collaboration in Infectious Disease Research on Lassa fever and Ebola - ICIDR - U19 AI115589, Consortium for Viral Systems Biology - CViSB - 5U19AI135995, West African Emerging Infectious Disease Research Center - WARN-ID - U01AI151812, West African Center for Emerging Infectious Diseases: U01AI151801.
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Affiliation(s)
- Allison R. Smither
- Tulane University School of Medicine, Department of Microbiology and Immunology, New Orleans, LA, USA
- University of Texas Medical Branch, Galveston National Laboratory, Galveston, TX, USA
| | - James Koninga
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Franklyn B. Kanneh
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Momoh Foday
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | | | - Nell G. Bond
- Tulane University School of Medicine, Department of Microbiology and Immunology, New Orleans, LA, USA
| | - Mambu Momoh
- Tulane University School of Medicine, Department of Microbiology and Immunology, New Orleans, LA, USA
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - John Demby Sandi
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Lansana Kanneh
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Foday Alhasan
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Ibrahim Mustapha Kanneh
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Mohamed S. Yillah
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Donald S. Grant
- Viral Hemorrhagic Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
- College of Medicine and Allied Health Sciences, University of Sierra Leone
| | | | | | - Kaitlin M. Cruz
- Tulane University School of Medicine, Department of Pediatrics, Section of Infectious Disease, New Orleans, LA, USA
| | - Raphaëlle Klitting
- The Scripps Research Institute, Department of Microbiology and Immunology, La Jolla, CA, USA
| | - Matthias Pauthner
- The Scripps Research Institute, Department of Microbiology and Immunology, La Jolla, CA, USA
| | - Kristian G. Andersen
- The Scripps Research Institute, Department of Microbiology and Immunology, La Jolla, CA, USA
| | - Jeffrey G. Shaffer
- Tulane University School of Public Health and Tropical Medicine, Department of Biostatistics, New Orleans, LA, USA
| | - Robert W. Cross
- University of Texas Medical Branch, Galveston National Laboratory, Galveston, TX, USA
| | - John S. Schieffelin
- Tulane University School of Medicine, Department of Pediatrics, Section of Infectious Disease, New Orleans, LA, USA
| | - Robert F. Garry
- Tulane University School of Medicine, Department of Microbiology and Immunology, New Orleans, LA, USA
- Zalgen Labs, LLC, Frederick, MD, USA
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5
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Longet S, Leggio C, Bore JA, Key S, Tipton T, Hall Y, Koundouno FR, Bower H, Bhattacharyya T, Magassouba N, Günther S, Henao-Restrapo AM, Rossman JS, Konde MK, Fornace K, Carroll MW. Influence of Landscape Patterns on Exposure to Lassa Fever Virus, Guinea. Emerg Infect Dis 2023; 29:304-313. [PMID: 36692336 PMCID: PMC9881776 DOI: 10.3201/eid2902.212525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Lassa fever virus (LASV) is the causative agent of Lassa fever, a disease endemic in West Africa. Exploring the relationships between environmental factors and LASV transmission across ecologically diverse regions can provide crucial information for the design of appropriate interventions and disease monitoring. We investigated LASV exposure in 2 ecologically diverse regions of Guinea. Our results showed that exposure to LASV was heterogenous between and within sites. LASV IgG seropositivity was 11.9% (95% CI 9.7%-14.5%) in a coastal study site in Basse-Guinée, but it was 59.6% (95% CI 55.5%-63.5%) in a forested study site located in Guinée Forestière. Seropositivity increased with age in the coastal site. We also found significant associations between exposure risk for LASV and landscape fragmentation in coastal and forested regions. Our study highlights the potential link between environmental change and LASV emergence and the urgent need for research on land management practices that reduce disease risks.
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Abstract
Individuals living in endemic hotspots of Lassa fever have recurrent exposure to Lassa virus (LASV) via spillover from the primary host reservoir Mastomys natalensis. Despite M. natalensis being broadly distributed across sub-Saharan Africa, Lassa fever is only found in West Africa. In recent years, new LASV reservoirs have been identified. Erudition of rodent habitats, reproduction and fecundity, movement patterns, and spatial preferences are essential to institute preventative measures against Lassa fever. Evolutionary insights have also added to our knowledge of closely related mammarenavirus distribution amongst rodents throughout the continent.
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Affiliation(s)
- Allison R Smither
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA, USA.
| | - Antoinette R Bell-Kareem
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA, USA
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7
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Nicolas V, Mikula O, Lavrenchenko LA, Šumbera R, Bartáková V, Bryjová A, Meheretu Y, Verheyen E, Missoup AD, Lemmon AR, Moriarty Lemmon E, Bryja J. Phylogenomics of African radiation of Praomyini (Muridae: Murinae) rodents: First fully resolved phylogeny, evolutionary history and delimitation of extant genera. Mol Phylogenet Evol 2021; 163:107263. [PMID: 34273505 DOI: 10.1016/j.ympev.2021.107263] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/06/2021] [Accepted: 07/12/2021] [Indexed: 11/25/2022]
Abstract
The tribe Praomyini is a diversified group including 64 species and eight extant rodent genera. They live in a broad spectrum of habitats across whole sub-Saharan Africa. Members of this tribe are often very abundant, they have a key ecological role in ecosystems, they are hosts of many potentially pathogenic microorganisms and comprise numerous agricultural pests. Although this tribe is well supported by both molecular and morphological data, its intergeneric relationships and the species contents of several genera are not yet fully resolved. Recent molecular data suggest that at least three genera in current sense are paraphyletic. However, in these studies the species sampling was sparse and the resolution of relationships among genera was poor, probably due to a fast radiation of the tribe dated to the Miocene and insufficient amount of genetic data. Here we used genomic scale data (395 nuclear loci = 610,965 bp long alignment and mitogenomes = 14,745 bp) and produced the first fully resolved species tree containing most major lineages of the Praomyini tribe (i.e. all but one currently delimited genera and major intrageneric clades). Results of a fossil-based divergence dating analysis suggest that the radiation started during the Messinian stage (ca. 7 Ma) and was likely linked to a fragmentation of the pan-African Miocene forest. Some lineages remained in the rain forests, while many others adapted to a broad spectrum of new open lowland and montane habitats that appeared at the beginning of Pliocene. Our analyses clearly confirmed the presence of three polyphyletic genera (Praomys, Myomyscus and Mastomys). We review current knowledge of these three genera and suggest corresponding taxonomic changes. To keep genera monophyletic, we propose taxonomic re-arrangements and delimit four new genera. Furthermore, we discovered a new highly divergent genetic lineage of Praomyini in southwestern Ethiopia, which is described as a new species and genus.
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Affiliation(s)
- Violaine Nicolas
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP51, 75005 Paris, France
| | - Ondřej Mikula
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic
| | - Leonid A Lavrenchenko
- A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences, Leninskii pr. 33, Moscow 119071, Russia
| | - Radim Šumbera
- Department of Zoology, Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic
| | - Veronika Bartáková
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic
| | - Anna Bryjová
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic
| | - Yonas Meheretu
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic; Department of Biology and Institute of Mountain Research and Development, Mekelle University, Mekelle, Tigray, Ethiopia
| | - Erik Verheyen
- Royal Belgian Institute for Natural Sciences, Operational Direction Taxonomy and Phylogeny, 1000 Brussels, Belgium; Evolutionary Ecology Group, Biology Department, University of Antwerp, 2020 Antwerp, Belgium
| | - Alain Didier Missoup
- Zoology Unit, Laboratory of Biology and Physiology of Animal Organisms, Faculty of Science, University of Douala, Douala, Cameroon
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL 32306-4295, United States
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, 319 Stadium Drive, PO Box 3064295, Tallahassee, FL 32306-4295, United States
| | - Josef Bryja
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic; Department of Botany and Zoology, Faculty of Science, Masaryk University, 611 37, Brno, Czech Republic.
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8
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Těšíková J, Krásová J, Goüy de Bellocq J. Multiple Mammarenaviruses Circulating in Angolan Rodents. Viruses 2021; 13:982. [PMID: 34070551 PMCID: PMC8227972 DOI: 10.3390/v13060982] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/17/2021] [Accepted: 05/20/2021] [Indexed: 12/14/2022] Open
Abstract
Rodents are a speciose group of mammals with strong zoonotic potential. Some parts of Africa are still underexplored for the occurrence of rodent-borne pathogens, despite this high potential. Angola is at the convergence of three major biogeographical regions of sub-Saharan Africa, each harbouring a specific rodent community. This rodent-rich area is, therefore, strategic for studying the diversity and evolution of rodent-borne viruses. In this study we examined 290 small mammals, almost all rodents, for the presence of mammarenavirus and hantavirus RNA. While no hantavirus was detected, we found three rodent species positive for distinct mammarenaviruses with a particularly high prevalence in Namaqua rock rats (Micaelamys namaquensis). We characterised four complete virus genomes, which showed typical mammarenavirus organisation. Phylogenetic and genetic distance analyses revealed: (i) the presence of a significantly divergent strain of Luna virus in Angolan representatives of the ubiquitous Natal multimammate mouse (Mastomys natalensis), (ii) a novel Okahandja-related virus associated with the Angolan lineage of Micaelamys namaquensis for which we propose the name Bitu virus (BITV) and (iii) the occurrence of a novel Mobala-like mammarenavirus in the grey-bellied pygmy mouse (Mus triton) for which we propose the name Kwanza virus (KWAV). This high virus diversity in a limited host sample size and in a relatively small geographical area supports the idea that Angola is a hotspot for mammarenavirus diversity.
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Affiliation(s)
- Jana Těšíková
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 603 65 Brno, Czech Republic; (J.K.); (J.G.B.)
- Department of Botany and Zoology, Faculty of Science, Masaryk University, 611 37 Brno, Czech Republic
| | - Jarmila Krásová
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 603 65 Brno, Czech Republic; (J.K.); (J.G.B.)
- Department of Zoology, Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic
| | - Joëlle Goüy de Bellocq
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 603 65 Brno, Czech Republic; (J.K.); (J.G.B.)
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 165 00 Prague, Czech Republic
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9
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Popova OD, Zubkova OV, Ozharovskaia TA, Zrelkin DI, Voronina DV, Dolzhikova IV, Shcheblyakov DV, Naroditsky BS, Logunov DY, Gintsburg AL. [Review of candidate vaccines for the prevention of Lassa fever]. Vopr Virusol 2021; 66:91-102. [PMID: 33993679 DOI: 10.36233/0507-4088-33] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 05/15/2021] [Indexed: 11/05/2022]
Abstract
The Lassa virus one of the main etiological agent of hemorrhagic fevers in the world: according to WHO estimates, it affects 100,000 to 300,000 people annually, which results in up to 10,000 deaths [1]. Although expansion of Lassa fever caused by this pathogen is mostly limited to the West African countries: Sierra Leone, Liberia, Guinea and Nigeria, imported cases have been historically documented in Europe, the United States of America (USA), Canada, Japan, and Israel [2]. In 2017, WHO included the Lassa virus in the list of priority pathogens in need of accelerated research, development of vaccines, therapeutic agents and diagnostic tools regarding infections they cause [3]. This review describes main technological platforms used for the development of vaccines for the prevention of Lassa fever.
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Affiliation(s)
- O D Popova
- FSBI «National Research Centre for Epidemiology and Microbiology named after Honorary Academician N.F. Gamaleya» of the Ministry of Health of Russia
| | - O V Zubkova
- FSBI «National Research Centre for Epidemiology and Microbiology named after Honorary Academician N.F. Gamaleya» of the Ministry of Health of Russia
| | - T A Ozharovskaia
- FSBI «National Research Centre for Epidemiology and Microbiology named after Honorary Academician N.F. Gamaleya» of the Ministry of Health of Russia
| | - D I Zrelkin
- FSBI «National Research Centre for Epidemiology and Microbiology named after Honorary Academician N.F. Gamaleya» of the Ministry of Health of Russia
| | - D V Voronina
- FSBI «National Research Centre for Epidemiology and Microbiology named after Honorary Academician N.F. Gamaleya» of the Ministry of Health of Russia
| | - I V Dolzhikova
- FSBI «National Research Centre for Epidemiology and Microbiology named after Honorary Academician N.F. Gamaleya» of the Ministry of Health of Russia
| | - D V Shcheblyakov
- FSBI «National Research Centre for Epidemiology and Microbiology named after Honorary Academician N.F. Gamaleya» of the Ministry of Health of Russia
| | - B S Naroditsky
- FSBI «National Research Centre for Epidemiology and Microbiology named after Honorary Academician N.F. Gamaleya» of the Ministry of Health of Russia
| | - D Yu Logunov
- FSBI «National Research Centre for Epidemiology and Microbiology named after Honorary Academician N.F. Gamaleya» of the Ministry of Health of Russia
| | - A L Gintsburg
- FSBI «National Research Centre for Epidemiology and Microbiology named after Honorary Academician N.F. Gamaleya» of the Ministry of Health of Russia
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Simo Tchetgna H, Descorps-Declère S, Selekon B, Kwasiborski A, Vandenbogaert M, Manuguerra JC, Gessain A, Caro V, Nakouné E, Berthet N. Molecular characterization of a new highly divergent Mobala related arenavirus isolated from Praomys sp. rodents. Sci Rep 2021; 11:10188. [PMID: 33986310 PMCID: PMC8119949 DOI: 10.1038/s41598-021-88046-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 04/06/2021] [Indexed: 12/02/2022] Open
Abstract
Arenaviruses represent a family of viruses that are naturally present in rodents belonging to subfamily Murinae, Neotominae or Sigmodontinae. Except for Lassa virus, little information is available on other Old-World arenaviruses. Here, we describe strain AnRB3214, a virus isolated from a presumed Praomys sp. rodent in the Central African Republic in 1981 and assigned to Ippy virus based on antigenic similarity. The strain was simultaneously sequenced on Illumina NovaSeq 6000 and MinION Mk1B devices and analysed with various bioinformatics tools. We show that the best genome coverage and depth were obtained with the Kaiju and Minimap2 classification and identification tools, on either the MinION or the Illumina reads. The genetic analysis of AnRB3214 fragments showed 68% to 79% similarity with the Mobala and Gairo mammarenaviruses at the nucleic acid level. Strain AnRB3214 had a truncated nucleoprotein smaller than that of other Old World arenaviruses. Molecular clock analysis suggests that this strain diverged from Mobala virus at least 400 years ago. Finally, this study illustrates the importance of genomics in the identification of archived viruses and expands on the diversity of African arenaviruses, because strain AnRB3214 is either a variant or a close relative of Mobala virus, and not Ippy virus.
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Affiliation(s)
- Huguette Simo Tchetgna
- Centre for Research in Infectious Diseases, Yaoundé, Cameroon.,The Center for Microbes, Development and Health, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai - Chinese Academy of Sciences, Discovery and Molecular Characterization of Pathogens, Shanghai, 200031, China
| | - Stephane Descorps-Declère
- Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), Institut Pasteur, Paris, France
| | | | - Aurelia Kwasiborski
- Cellule d'Intervention Biologique d'Urgence, Institut Pasteur, Unité Environnement et Risques Infectieux, Paris, France
| | - Mathias Vandenbogaert
- Cellule d'Intervention Biologique d'Urgence, Institut Pasteur, Unité Environnement et Risques Infectieux, Paris, France
| | - Jean-Claude Manuguerra
- Cellule d'Intervention Biologique d'Urgence, Institut Pasteur, Unité Environnement et Risques Infectieux, Paris, France
| | - Antoine Gessain
- Unité d'Epidémiologie et Physiopathologie des Virus Oncogènes, Département de Virologie, Institut Pasteur, Paris, France.,Centre National de Recherche Scientifique (CNRS) UMR3569, Paris, France
| | - Valérie Caro
- Cellule d'Intervention Biologique d'Urgence, Institut Pasteur, Unité Environnement et Risques Infectieux, Paris, France
| | | | - Nicolas Berthet
- The Center for Microbes, Development and Health, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai - Chinese Academy of Sciences, Discovery and Molecular Characterization of Pathogens, Shanghai, 200031, China. .,Cellule d'Intervention Biologique d'Urgence, Institut Pasteur, Unité Environnement et Risques Infectieux, Paris, France.
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11
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Basinski AJ, Fichet-Calvet E, Sjodin AR, Varrelman TJ, Remien CH, Layman NC, Bird BH, Wolking DJ, Monagin C, Ghersi BM, Barry PA, Jarvis MA, Gessler PE, Nuismer SL. Bridging the gap: Using reservoir ecology and human serosurveys to estimate Lassa virus spillover in West Africa. PLoS Comput Biol 2021; 17:e1008811. [PMID: 33657095 PMCID: PMC7959400 DOI: 10.1371/journal.pcbi.1008811] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 03/15/2021] [Accepted: 02/17/2021] [Indexed: 01/07/2023] Open
Abstract
Forecasting the risk of pathogen spillover from reservoir populations of wild or domestic animals is essential for the effective deployment of interventions such as wildlife vaccination or culling. Due to the sporadic nature of spillover events and limited availability of data, developing and validating robust, spatially explicit, predictions is challenging. Recent efforts have begun to make progress in this direction by capitalizing on machine learning methodologies. An important weakness of existing approaches, however, is that they generally rely on combining human and reservoir infection data during the training process and thus conflate risk attributable to the prevalence of the pathogen in the reservoir population with the risk attributed to the realized rate of spillover into the human population. Because effective planning of interventions requires that these components of risk be disentangled, we developed a multi-layer machine learning framework that separates these processes. Our approach begins by training models to predict the geographic range of the primary reservoir and the subset of this range in which the pathogen occurs. The spillover risk predicted by the product of these reservoir specific models is then fit to data on realized patterns of historical spillover into the human population. The result is a geographically specific spillover risk forecast that can be easily decomposed and used to guide effective intervention. Applying our method to Lassa virus, a zoonotic pathogen that regularly spills over into the human population across West Africa, results in a model that explains a modest but statistically significant portion of geographic variation in historical patterns of spillover. When combined with a mechanistic mathematical model of infection dynamics, our spillover risk model predicts that 897,700 humans are infected by Lassa virus each year across West Africa, with Nigeria accounting for more than half of these human infections. The 2019 emergence of SARS-CoV-2 is a grim reminder of the threat animal-borne pathogens pose to human health. Even prior to SARS-CoV-2, the spillover of pathogens from animal reservoirs was a persistent problem, with pathogens such as Ebola, Nipah, and Lassa regularly but unpredictably causing outbreaks. Machine-learning models that anticipate when and where pathogen transmission from animals to humans is likely to occur would help guide surveillance efforts and preemptive countermeasures like information campaigns or vaccination programs. We develop a novel machine learning framework that uses datasets describing the distribution of a virus within its host and the range of its animal host, along with data on spatial patterns of human immunity, to infer rates of animal-to-human transmission across a region. By training the model on data from the animal host alone, our framework allows rigorous validation of spillover predictions using human data. We apply our framework to Lassa fever, a viral disease of West Africa that is spread to humans by rodents, and use the predictions to update estimates of Lassa virus infections in humans. Our results suggest that Nigeria is most at risk for the emergence of Lassa virus, and should be prioritized for outbreak-surveillance.
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Affiliation(s)
- Andrew J. Basinski
- Department of Mathematics, University of Idaho, Moscow, Idaho, United States of America
- * E-mail:
| | | | - Anna R. Sjodin
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Tanner J. Varrelman
- Bioinformatics and Computational Biology, University of Idaho, Moscow, Idaho, United States of America
| | - Christopher H. Remien
- Department of Mathematics, University of Idaho, Moscow, Idaho, United States of America
| | - Nathan C. Layman
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Brian H. Bird
- One Health Institute, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - David J. Wolking
- One Health Institute, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - Corina Monagin
- One Health Institute, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - Bruno M. Ghersi
- One Health Institute, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - Peter A. Barry
- Center for Comparative Medicine, California National Primate Research Center, Department of Pathology and Laboratory Medicine, University of California, Davis, California, United States of America
| | - Michael A. Jarvis
- School of Biomedical and Healthcare Sciences, University of Plymouth, Plymouth, United Kingdom
| | - Paul E. Gessler
- College of Natural Resources, University of Idaho, Moscow, Idaho, United States of America
| | - Scott L. Nuismer
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
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12
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Lassa Virus Circulation in Small Mammal Populations in Bo District, Sierra Leone. BIOLOGY 2021; 10:biology10010028. [PMID: 33466234 PMCID: PMC7824740 DOI: 10.3390/biology10010028] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 12/21/2020] [Accepted: 12/28/2020] [Indexed: 11/26/2022]
Abstract
Simple Summary Lassa fever is a viral hemorrhagic fever caused by the Lassa virus (LASV). It is a deadly rodent-borne zoonosis with outbreaks occurring mostly in Sierra Leone, Guinea, Liberia, and Nigeria, in West Africa. In Sierra Leone, surveillance activities of LASV focus mainly on the Kenema area in the eastern region, known to be the epicentre. Little is known about the presence of the virus in the Bo area, where Mastomys natalensis and Rattus rattus share habitats with humans. Our study investigated the circulation and phylogeny of new LASV strains and virus seroprevalence in rodent populations of villages in Bo district. Information provided here will be of great importance in prioritizing areas for Lassa fever surveillance and preventive measures to mitigate future outbreaks. Our rodent longitudinal survey carried out over two years (2014–2016) identified Mastomys natalensis as the most prevalent species. While seropositive small mammals were found in every village, the four Mastomys natalensis rodents that tested PCR-positive for Lassa virus were found in only two villages. Phylogenetic analysis showed that these sequences belong to the Sierra Leonean clade, within lineage IV. In conclusion, LASV is present, with low circulation, in small mammals in rural settings around Bo. Abstract Lassa fever is a viral hemorrhagic fever caused by the Lassa virus LASV, which was first isolated in the rodent Mastomys natalensis in 1974 in Kenema, Sierra Leone. As little is known about the abundance and the presence of LASV in rodents living in the Bo area, we carried out a small mammal longitudinal population survey. A standardized trapping session was performed in various habitats and seasons in six villages over two years (2014–2016) and samples collected were tested for arenavirus IgG and LASV. A Bayesian phylogenetic analysis was performed on sequences identified by PCR. A total of 1490 small mammals were collected, and 16 rodent species were identified, with M. natalensis (355, 24%) found to be the most prevalent species. Forty-one (2.8%) samples were IgG positive, and 31 of these were trapped in homes and 10 in surrounding vegetation. Twenty-nine of 41 seropositive rodents were M. natalensis. We detected four LASV by PCR in two villages, all found in M. natalensis. Phylogenetic analysis showed that the sequences were distributed within the Sierra Leonean clade within lineage IV, distinguishing a Bo sub-clade older than a Kenema sub-clade. Compared to other settings, we found a low abundance of M. natalensis and a low circulation of LASV in rodents in villages around Bo district.
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Kenmoe S, Tchatchouang S, Ebogo-Belobo JT, Ka'e AC, Mahamat G, Guiamdjo Simo RE, Bowo-Ngandji A, Demeni Emoh CP, Che E, Tchami Ngongang D, Amougou-Atsama M, Nzukui ND, Mbongue Mikangue CA, Mbaga DS, Kenfack S, Kingue Bebey SR, Amvongo Adjia N, Efietngab AN, Tazokong HR, Modiyinji AF, Kengne-Nde C, Sadeuh-Mba SA, Njouom R. Systematic review and meta-analysis of the epidemiology of Lassa virus in humans, rodents and other mammals in sub-Saharan Africa. PLoS Negl Trop Dis 2020; 14:e0008589. [PMID: 32845889 PMCID: PMC7478710 DOI: 10.1371/journal.pntd.0008589] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 09/08/2020] [Accepted: 07/13/2020] [Indexed: 12/27/2022] Open
Abstract
Accurate data on the Lassa virus (LASV) human case fatality rate (CFR) and the prevalence of LASV in humans, rodents and other mammals are needed for better planning of actions that will ultimately reduce the burden of LASV infection in sub-Saharan Africa. In this systematic review with meta-analysis, we searched PubMed, Scopus, Africa Journal Online, and African Index Medicus from 1969 to 2020 to obtain studies that reported enough data to calculate LASV infection CFR or prevalence. Study selection, data extraction, and risk of bias assessment were conducted independently. We extracted all measures of current, recent, and past infections with LASV. Prevalence and CFR estimates were pooled using a random-effect meta-analysis. Factors associated with CFR, prevalence, and sources of between-study heterogeneity were determined using subgroup and metaregression analyses. This review was registered with PROSPERO, CRD42020166465. We initially identified 1,399 records and finally retained 109 reports that contributed to 291 prevalence records from 25 countries. The overall CFR was 29.7% (22.3-37.5) in humans. Pooled prevalence of LASV infection was 8.7% (95% confidence interval: 6.8-10.8) in humans, 3.2% (1.9-4.6) in rodents, and 0.7% (0.0-2.3) in other mammals. Subgroup and metaregression analyses revealed a substantial statistical heterogeneity explained by higher prevalence in tissue organs, in case-control, in hospital outbreak, and surveys, in retrospective studies, in urban and hospital setting, in hospitalized patients, and in West African countries. This study suggests that LASV infections is an important cause of death in humans and that LASV are common in humans, rodents and other mammals in sub-Saharan Africa. These estimates highlight disparities between sub-regions, and population risk profiles. Western Africa, and specific key populations were identified as having higher LASV CFR and prevalence, hence, deserving more attention for cost-effective preventive interventions.
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Affiliation(s)
- Sebastien Kenmoe
- Department of Virology, Centre Pasteur of Cameroon, Yaoundé, Cameroon
| | | | - Jean Thierry Ebogo-Belobo
- Medical Research Centre, Institut of Medical Research and Medicinal Plants Studies, Yaoundé, Cameroon
| | - Aude Christelle Ka'e
- Virology Department, Chantal Biya International Reference Centre, Yaoundé, Cameroon
| | - Gadji Mahamat
- Department of Microbiology, Faculty of Science, The University of Yaounde I, Yaoundé, Cameroon
| | | | - Arnol Bowo-Ngandji
- Department of Microbiology, Faculty of Science, The University of Yaounde I, Yaoundé, Cameroon
| | | | - Emmanuel Che
- Vaccinology and Biobank, Chantal Biya International Reference Centre, Yaounde, Cameroon
| | - Dimitri Tchami Ngongang
- Department of Microbiology, Faculty of Science, The University of Yaounde I, Yaoundé, Cameroon
| | - Marie Amougou-Atsama
- Department of Virology, Centre Pasteur of Cameroon, Yaoundé, Cameroon
- Medical Research Centre, Institut of Medical Research and Medicinal Plants Studies, Yaoundé, Cameroon
| | - Nathalie Diane Nzukui
- School of Health Sciences-Catholic University of Central Africa, Department of Medical Microbiology, Yaoundé, Cameroon
| | | | - Donatien Serge Mbaga
- Department of Microbiology, Faculty of Science, The University of Yaounde I, Yaoundé, Cameroon
| | - Sorel Kenfack
- Department of Microbiology, Faculty of Science, The University of Yaounde I, Yaoundé, Cameroon
| | | | - Nathalie Amvongo Adjia
- Medical Research Centre, Institut of Medical Research and Medicinal Plants Studies, Yaoundé, Cameroon
| | - Atembeh Noura Efietngab
- Medical Research Centre, Institut of Medical Research and Medicinal Plants Studies, Yaoundé, Cameroon
| | - Hervé Raoul Tazokong
- Department of Microbiology, Faculty of Science, The University of Yaounde I, Yaoundé, Cameroon
| | - Abdou Fatawou Modiyinji
- Department of Virology, Centre Pasteur of Cameroon, Yaoundé, Cameroon
- Department of Animals Biology and Physiology, Faculty of Science, The University of Yaoundé I, Yaoundé, Cameroon
| | - Cyprien Kengne-Nde
- Epidemiological Surveillance, Evaluation and Research Unit, National AIDS Control Committee, Yaoundé, Cameroon
| | | | - Richard Njouom
- Department of Virology, Centre Pasteur of Cameroon, Yaoundé, Cameroon
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14
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Asogun DA, Günther S, Akpede GO, Ihekweazu C, Zumla A. Lassa Fever: Epidemiology, Clinical Features, Diagnosis, Management and Prevention. Infect Dis Clin North Am 2020; 33:933-951. [PMID: 31668199 DOI: 10.1016/j.idc.2019.08.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Lassa fever outbreaks West Africa have caused up to 10,000 deaths annually. Primary infection occurs from contact with Lassa virus-infected rodents and exposure to their excreta, blood, or meat. Incubation takes 2 to 21 days. Symptoms are difficult to distinguish from malaria, typhoid, dengue, yellow fever, and other viral hemorrhagic fevers. Clinical manifestations range from asymptomatic, to mild, to severe fulminant disease. Ribavirin can improve outcomes. Overall mortality is between 1% and 15%. Lassa fever should be considered in the differential diagnosis with travel to West Africa. There is an urgent need for rapid field-friendly diagnostics and preventive vaccine.
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Affiliation(s)
- Danny A Asogun
- Department of Public Health, College of Medicine, Ambrose Alli University, Ekpoma, Nigeria; Department of Public Health, Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, P.M.B 008, Kilometre 87, Benin City-Auchi Road, Irrua, Nigeria.
| | - Stephan Günther
- Bernhard-Nocht Institute for Tropical Medicine, Strab 74, Hamburg 20359, Germany; German Centre for Infection Research (DZIF), Partner Site Hamburg, Hamburg, Germany
| | - George O Akpede
- Department of Paediatrics, Faculty of Clinical Sciences, College of Medicine, Ambrose Alli University, Ekpoma, Nigeria
| | - Chikwe Ihekweazu
- Nigeria Centre for Disease Control, Plot 801, Ebitu Ukiwe Street, Jabi, Abuja, Nigeria
| | - Alimuddin Zumla
- Center for Clinical Microbiology, University College London, Royal Free Campus 2nd Floor, Rowland Hill Street, London NW3 2PF, United Kingdom
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15
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Olayemi A, Fichet-Calvet E. Systematics, Ecology, and Host Switching: Attributes Affecting Emergence of the Lassa Virus in Rodents across Western Africa. Viruses 2020; 12:E312. [PMID: 32183319 PMCID: PMC7150792 DOI: 10.3390/v12030312] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/10/2020] [Accepted: 03/11/2020] [Indexed: 12/18/2022] Open
Abstract
Ever since it was established that rodents serve as reservoirs of the zoonotic Lassa virus (LASV), scientists have sought to answer the questions: which populations of rodents carry the virus? How do fluctuations in LASV prevalence and rodent abundance influence Lassa fever outbreaks in humans? What does it take for the virus to adopt additional rodent hosts, proliferating what already are devastating cycles of rodent-to-human transmission? In this review, we examine key aspects of research involving the biology of rodents that affect their role as LASV reservoirs, including phylogeography, demography, virus evolution, and host switching. We discuss how this knowledge can help control Lassa fever and suggest further areas for investigation.
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Affiliation(s)
- Ayodeji Olayemi
- Natural History Museum, Obafemi Awolowo University, Ile Ife HO220005, Nigeria;
| | - Elisabeth Fichet-Calvet
- Department of Virology, Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany
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16
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Mateo M, Picard C, Sylla Y, Kamo E, Odegue D, Journeaux A, Kan SK, Money M, Coulibaly DN, Koffi E, Meite S, Akran V, Kadjo H, Adjogoua E, Kakou SN, Baize S, Dosso M. Fatal Case of Lassa Fever, Bangolo District, Côte d'Ivoire, 2015. Emerg Infect Dis 2020; 25:1753-1756. [PMID: 31441759 PMCID: PMC6711234 DOI: 10.3201/eid2509.190239] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Lassa fever has not been reported in Côte d’Ivoire. We performed a retrospective analysis of human serum samples collected in Côte d’Ivoire in the dry seasons (January–April) during 2015–2018. We identified a fatal human case of Lassa fever in the Bangolo District of western Côte d’Ivoire during 2015.
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17
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Nicolas V, Fabre PH, Bryja J, Denys C, Verheyen E, Missoup AD, Olayemi A, Katuala P, Dudu A, Colyn M, Kerbis Peterhans J, Demos T. The phylogeny of the African wood mice (Muridae, Hylomyscus) based on complete mitochondrial genomes and five nuclear genes reveals their evolutionary history and undescribed diversity. Mol Phylogenet Evol 2019; 144:106703. [PMID: 31816395 DOI: 10.1016/j.ympev.2019.106703] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 11/22/2019] [Accepted: 12/05/2019] [Indexed: 11/26/2022]
Abstract
Wood mice of the genus Hylomyscus, are small-sized rodents widely distributed in lowland and montane rainforests in tropical Africa, where they can be locally abundant. Recent morphological and molecular studies have increased the number of recognized species from 8 to 18 during the last 15 years. We used complete mitochondrial genomes and five nuclear genes to infer the number of candidate species within this genus and depict its evolutionary history. In terms of gene sampling and geographical and taxonomic coverage, this is the most comprehensive review of the genus Hylomyscus to date. The six species groups (aeta, alleni, anselli, baeri, denniae and parvus) defined on morphological grounds are monophyletic. Species delimitation analyses highlight undescribed diversity within this genus: perhaps up to 10 taxa need description or elevation from synonymy, pending review of type specimens. Our divergence dating and biogeographical analyses show that diversification of the genus occurred after the end of the Miocene and is closely linked to the history of the African forest. The formation of the Rift Valley combined with the declining global temperatures during the Late Miocene caused the fragmentation of the forests and explains the first split between the denniae group and remaining lineages. Subsequently, periods of increased climatic instability during Plio-Pleistocene probably resulted in elevated diversification in both lowland and montane forest taxa.
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Affiliation(s)
- Violaine Nicolas
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP51, 75005 Paris, France.
| | - Pierre-Henri Fabre
- Institut des Sciences de l'Evolution (ISEM, UMR 5554 CNRS-IRD-UM), Université de Montpellier, Place E. Bataillon CC 064 - 34095, Montpellier Cedex 5, France
| | - Josef Bryja
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Květná 8, 603 65 Brno, Czech Republic; Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Christiane Denys
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP51, 75005 Paris, France
| | - Erik Verheyen
- Royal Belgian Institute for Natural Sciences, Operational Direction Taxonomy and Phylogeny, 1000 Brussels, Belgium
| | - Alain Didier Missoup
- Zoology Unit, Laboratory of Biology and Physiology of Animal Organisms, Faculty of Science, University of Douala, Douala, Cameroon
| | - Ayodeji Olayemi
- Natural History Museum, Obafemi Awolowo University, HO 220005 Ile Ife, Nigeria
| | - Pionus Katuala
- Animal Ecology and Resource Management, Laboratory (LEGERA), University of Kisangani, B.P. 2012, Kisangani, Congo
| | - Akaibe Dudu
- Animal Ecology and Resource Management, Laboratory (LEGERA), University of Kisangani, B.P. 2012, Kisangani, Congo
| | - Marc Colyn
- Université de Rennes 1, CNRS, UMR 6553 Ecobio, Station Biologique, 35380 Paimpont, France
| | - Julian Kerbis Peterhans
- Science & Education, Field Museum of Natural History, 60605 Chicago, IL, USA; College of Arts & Sciences, Roosevelt University, 430 S Michigan, Chicago, IL 60605, USA
| | - Terrence Demos
- College of Arts & Sciences, Roosevelt University, 430 S Michigan, Chicago, IL 60605, USA
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18
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Wiley MR, Fakoli L, Letizia AG, Welch SR, Ladner JT, Prieto K, Reyes D, Espy N, Chitty JA, Pratt CB, Di Paola N, Taweh F, Williams D, Saindon J, Davis WG, Patel K, Holland M, Negrón D, Ströher U, Nichol ST, Sozhamannan S, Rollin PE, Dogba J, Nyenswah T, Bolay F, Albariño CG, Fallah M, Palacios G. Lassa virus circulating in Liberia: a retrospective genomic characterisation. THE LANCET. INFECTIOUS DISEASES 2019; 19:1371-1378. [PMID: 31588039 DOI: 10.1016/s1473-3099(19)30486-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 06/28/2019] [Accepted: 07/18/2019] [Indexed: 01/10/2023]
Abstract
BACKGROUND An alarming rise in reported Lassa fever cases continues in west Africa. Liberia has the largest reported per capita incidence of Lassa fever cases in the region, but genomic information on the circulating strains is scarce. The aim of this study was to substantially increase the available pool of data to help foster the generation of targeted diagnostics and therapeutics. METHODS Clinical serum samples collected from 17 positive Lassa fever cases originating from Liberia (16 cases) and Guinea (one case) within the past decade were processed at the Liberian Institute for Biomedical Research using a targeted-enrichment sequencing approach, producing 17 near-complete genomes. An additional 17 Lassa virus sequences (two from Guinea, seven from Liberia, four from Nigeria, and four from Sierra Leone) were generated from viral stocks at the US Centers for Disease Control and Prevention (Atlanta, GA) from samples originating from the Mano River Union (Guinea, Liberia, and Sierra Leone) region and Nigeria. Sequences were compared with existing Lassa virus genomes and published Lassa virus assays. FINDINGS The 23 new Liberian Lassa virus genomes grouped within two clades (IV.A and IV.B) and were genetically divergent from those circulating elsewhere in west Africa. A time-calibrated phylogeographic analysis incorporating the new genomes suggests Liberia was the entry point of Lassa virus into the Mano River Union region and estimates the introduction to have occurred between 300-350 years ago. A high level of diversity exists between the Liberian Lassa virus genomes. Nucleotide percent difference between Liberian Lassa virus genomes ranged up to 27% in the L segment and 18% in the S segment. The commonly used Lassa Josiah-MGB assay was up to 25% divergent across the target sites when aligned to the Liberian Lassa virus genomes. INTERPRETATION The large amount of novel genomic diversity of Lassa virus observed in the Liberian cases emphasises the need to match deployed diagnostic capabilities with locally circulating strains and underscores the importance of evaluating cross-lineage protection in the development of vaccines and therapeutics. FUNDING Defense Biological Product Assurance Office of the US Department of Defense and the Armed Forces Health Surveillance Branch and its Global Emerging Infections Surveillance and Response Section.
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Affiliation(s)
- Michael R Wiley
- Department of Environmental, Agricultural and Occupational Health, College of Public Health, University of Nebraska Medical Center, Omaha, NE, USA; Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Lawrence Fakoli
- National Public Health Institute of Liberia, Monrovia, Liberia
| | - Andrew G Letizia
- Naval Medical Research Unit Three Ghana Detachment, Accra, Ghana
| | - Stephen R Welch
- US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jason T Ladner
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA; Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Karla Prieto
- Department of Environmental, Agricultural and Occupational Health, College of Public Health, University of Nebraska Medical Center, Omaha, NE, USA; Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Daniel Reyes
- Department of Environmental, Agricultural and Occupational Health, College of Public Health, University of Nebraska Medical Center, Omaha, NE, USA; Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Nicole Espy
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Joseph A Chitty
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Catherine B Pratt
- Department of Environmental, Agricultural and Occupational Health, College of Public Health, University of Nebraska Medical Center, Omaha, NE, USA; Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Nicholas Di Paola
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Fahn Taweh
- National Public Health Institute of Liberia, Monrovia, Liberia
| | - Desmond Williams
- US Centers for Disease Control and Prevention, Atlanta, GA, USA; US Centers for Disease Control and Prevention, Monrovia, Liberia
| | - Jon Saindon
- US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - William G Davis
- US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Ketan Patel
- US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | | | - Ute Ströher
- US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Stuart T Nichol
- US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Shanmuga Sozhamannan
- Defense Biological Product Assurance Office, Joint Program Executive Office for Chemical, Biological, Radiological and Nuclear Defense (CBRND)-Joint Project Lead, CBRND Enabling Biotechnologies, Frederick, MD, USA; Logistics Management Institute, Tysons, VA, USA
| | - Pierre E Rollin
- US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - John Dogba
- National Public Health Institute of Liberia, Monrovia, Liberia
| | | | - Fatorma Bolay
- National Public Health Institute of Liberia, Monrovia, Liberia
| | | | - Mosoka Fallah
- National Public Health Institute of Liberia, Monrovia, Liberia
| | - Gustavo Palacios
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA.
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19
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Nieto‐Rabiela F, Wiratsudakul A, Suzán G, Rico‐Chávez O. Viral networks and detection of potential zoonotic viruses in bats and rodents: A worldwide analysis. Zoonoses Public Health 2019; 66:655-666. [PMID: 31219223 PMCID: PMC7165641 DOI: 10.1111/zph.12618] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 04/11/2019] [Accepted: 05/28/2019] [Indexed: 12/13/2022]
Abstract
Bats and rodents are recognized to host a great diversity of viruses and several important viral zoonoses, but how this viral diversity is structured and how viruses are connected, shared and distributed among host networks is not well understood. To address this gap in knowledge, we compared the associative capacity of the host-virus networks in rodents and bats with the identification of those viruses with zoonotic potential. A virus database, detected by molecular methods, was constructed in the two taxonomic groups. We compiled 5,484 records: 825 in rodents and 4,659 in bats. We identified a total of 173 and 166 viruses, of which 53 and 40 are zoonotic viruses, in rodents and bats, respectively. Based on a network theory, a non-directed bipartite host-virus network was built for each group. Subsequently, the networks were collapsed to represent the connections among hosts and viruses. We identified both discrete and connected communities. We observed a greater degree of connectivity in bat viruses and more discrete communities in rodents. The Coronaviridae recorded in bats have the highest values of degree, betweenness and closeness centralities. In rodents, higher degree positions were distributed homogeneously between viruses and hosts. At least in our database, a higher proportion of rodent viruses were zoonotic. Rodents should thus not be underestimated as important reservoirs of zoonotic disease. We found that viruses were more frequently shared among bats than in rodents. Network theory can reveal some macroecological patterns and identify risks that were previously unrecognized. For example, we found that parvovirus in megabats and Gbagroube virus in rodents may represent a zoonotic risk due to the proximity to humans and other zoonotic viruses. We propose that epidemiological surveillance programmes should consider the connectivity of network actors as a measure of the risks of dispersion and transmission.
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Affiliation(s)
- Fabiola Nieto‐Rabiela
- Laboratorio de Ecología de Enfermedades y Una Salud, Facultad de Medicina Veterinaria y ZootecniaUniversidad Nacional Autónoma de MéxicoMéxico CityMéxico
| | - Anuwat Wiratsudakul
- Department of Clinical Sciences and Public Health, Faculty of Veterinary ScienceMahidol UniversityNakhon PathomThailand
| | - Gerardo Suzán
- Laboratorio de Ecología de Enfermedades y Una Salud, Facultad de Medicina Veterinaria y ZootecniaUniversidad Nacional Autónoma de MéxicoMéxico CityMéxico
| | - Oscar Rico‐Chávez
- Laboratorio de Ecología de Enfermedades y Una Salud, Facultad de Medicina Veterinaria y ZootecniaUniversidad Nacional Autónoma de MéxicoMéxico CityMéxico
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20
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Proteomics Computational Analyses Suggest that the Antennavirus Glycoprotein Complex Includes a Class I Viral Fusion Protein (α-Penetrene) with an Internal Zinc-Binding Domain and a Stable Signal Peptide. Viruses 2019; 11:v11080750. [PMID: 31416162 PMCID: PMC6722660 DOI: 10.3390/v11080750] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 08/06/2019] [Accepted: 08/13/2019] [Indexed: 12/22/2022] Open
Abstract
A metatranscriptomic study of RNA viruses in cold-blooded vertebrates identified two related viruses from frogfish (Antennarius striatus) that represent a new genus Antennavirus in the family Arenaviridae (Order: Bunyavirales). Computational analyses were used to identify features common to class I viral fusion proteins (VFPs) in antennavirus glycoproteins, including an N-terminal fusion peptide, two extended alpha-helices, an intrahelical loop, and a carboxyl terminal transmembrane domain. Like mammarenavirus and hartmanivirus glycoproteins, the antennavirus glycoproteins have an intracellular zinc-binding domain and a long virion-associated stable signal peptide (SSP). The glycoproteins of reptarenaviruses are also class I VFPs, but do not contain zinc-binding domains nor do they encode SSPs. Divergent evolution from a common progenitor potentially explains similarities of antennavirus, mammarenavirus, and hartmanivirus glycoproteins, with an ancient recombination event resulting in a divergent reptarenavirus glycoprotein.
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21
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Mazzola LT, Kelly-Cirino C. Diagnostics for Lassa fever virus: a genetically diverse pathogen found in low-resource settings. BMJ Glob Health 2019; 4:e001116. [PMID: 30899575 PMCID: PMC6407561 DOI: 10.1136/bmjgh-2018-001116] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 10/31/2018] [Accepted: 11/06/2018] [Indexed: 11/18/2022] Open
Abstract
Lassa fever virus (LASV) causes acute viral haemorrhagic fever with symptoms similar to those seen with Ebola virus infections. LASV is endemic to West Africa and is transmitted through contact with excretions of infected Mastomys natalensis rodents and other rodent species. Due to a high fatality rate, lack of treatment options and difficulties with prevention and control, LASV is one of the high-priority pathogens included in the WHO R&D Blueprint. The WHO LASV vaccine strategy relies on availability of effective diagnostic tests. Current diagnostics for LASV include in-house and commercial (primarily research-only) laboratory-based serological and nucleic acid amplification tests. There are two commercially available (for research use only) rapid diagnostic tests (RDTs), and a number of multiplex panels for differential detection of LASV infection from other endemic diseases with similar symptoms have been evaluated. However, a number of diagnostic gaps remain. Lineage detection is a challenge due to the genomic diversity of LASV, as pan-lineage sensitivity for both molecular and immunological detection is necessary for surveillance and outbreak response. While pan-lineage ELISA and RDTs are commercially available (for research use only), validation and external quality assessment (EQA) is needed to confirm detection sensitivity for all known or relevant strains. Variable sensitivity of LASV PCR tests also highlights the need for improved validation and EQA. Given that LASV outbreaks typically occur in low-resource settings, more options for point-of-care testing would be valuable. These requirements should be taken into account in target product profiles for improved LASV diagnostics.
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22
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Virome profiling of rodents in Xinjiang Uygur Autonomous Region, China: Isolation and characterization of a new strain of Wenzhou virus. Virology 2019; 529:122-134. [PMID: 30685659 DOI: 10.1016/j.virol.2019.01.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 01/09/2019] [Accepted: 01/09/2019] [Indexed: 11/21/2022]
Abstract
Rodents, as the most diverse and widest distributed mammals, are a natural reservoir of many zoonotic viruses. However, little is known about the viral diversity harbored by rodents in China. Here we performed viral metagenomic analyses of 314 wild rodents covering 7 species, sampled in North-western China. We also conducted a systematic virological characterization of a new Wenzhou virus (WENV) isolate, QARn1, from a brown rat (Rattus norvegicus). Full genomic and phylogenetic analyses showed that QARn1 is a previously unidentified strain of Wenzhou mammarenavirus and forms a new branch within the Asian clade. Experimental infection of Sprague-Dawley rats with QARn1 did not present overt pathology, but specific humoral immune responses developed and mild hemorrhage and immunocyte infiltration of the lungs and thymus were observed. These observations have expanded the geographic distribution of WENV to Central Asia, and further confirm that brown rats are natural hosts of Wenzhou virus.
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23
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Madu IG, Files M, Gharaibeh DN, Moore AL, Jung KH, Gowen BB, Dai D, Jones KF, Tyavanagimatt SR, Burgeson JR, Korth MJ, Bedard KM, Iadonato SP, Amberg SM. A potent Lassa virus antiviral targets an arenavirus virulence determinant. PLoS Pathog 2018; 14:e1007439. [PMID: 30576397 PMCID: PMC6322784 DOI: 10.1371/journal.ppat.1007439] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 01/07/2019] [Accepted: 10/25/2018] [Indexed: 11/25/2022] Open
Abstract
Arenaviruses are a significant cause of hemorrhagic fever, an often-fatal disease for which there is no approved antiviral therapy. Lassa fever in particular generates high morbidity and mortality in West Africa, where the disease is endemic, and a recent outbreak in Nigeria was larger and more geographically diverse than usual. We are developing LHF-535, a small-molecule viral entry inhibitor that targets the arenavirus envelope glycoprotein, as a therapeutic candidate for Lassa fever and other hemorrhagic fevers of arenavirus origin. Using a lentiviral pseudotype infectivity assay, we determined that LHF-535 had sub-nanomolar potency against the viral envelope glycoproteins from all Lassa virus lineages, with the exception of the glycoprotein from the LP strain from lineage I, which was 100-fold less sensitive than that of other strains. This reduced sensitivity was mediated by a unique amino acid substitution, V434I, in the transmembrane domain of the envelope glycoprotein GP2 subunit. This position corresponds to the attenuation determinant of Candid#1, a live-attenuated Junín virus vaccine strain used to prevent Argentine hemorrhagic fever. Using a virus-yield reduction assay, we determined that LHF-535 potently inhibited Junín virus, but not Candid#1, and the Candid#1 attenuation determinant, F427I, regulated this difference in sensitivity. We also demonstrated that a daily oral dose of LHF-535 at 10 mg/kg protected mice from a lethal dose of Tacaribe virus. Serial passage of Tacaribe virus in LHF-535-treated Vero cells yielded viruses that were resistant to LHF-535, and the majority of drug-resistant viruses exhibited attenuated pathogenesis. These findings provide a framework for the clinical development of LHF-535 as a broad-spectrum inhibitor of arenavirus entry and provide an important context for monitoring the emergence of drug-resistant viruses. Lassa fever is a viral hemorrhagic fever disease that is transmitted to humans primarily through contact with the urine or feces of infected rodents. The disease is endemic in West Africa, and an unusually large outbreak occurred in Nigeria in early 2018. The case fatality rate was 25% among confirmed cases, underscoring the need for an effective antiviral therapy. Here, we evaluated the small-molecule drug LHF-535, which targets the arenavirus envelope glycoprotein, for broad-spectrum activity against Lassa viruses of different lineages and related arenaviruses that cause hemorrhagic fever diseases in South America. We also selected for LHF-535-resistant viruses and characterized their genotype and phenotype. Using a combination of surrogate systems and wild-type viruses, we determined that all tested Lassa virus strains and New World hemorrhagic fever arenaviruses were sensitive to LHF-535. Sensitivity to the drug was modulated by specific amino acid changes in the viral envelope glycoprotein, and the majority of emerging drug-resistant viruses were attenuated for virulence. Similarly, the live-attenuated vaccine strain for Argentine hemorrhagic fever was also resistant to LHF-535. These findings indicate that LHF-535 targets a viral virulence determinant, the mutation of which may result in the emergence of drug-resistant viruses, but with reduced capacity for virulence.
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Affiliation(s)
- Ikenna G. Madu
- Kineta, Inc., Seattle, Washington, United States of America
| | - Megan Files
- Kineta, Inc., Seattle, Washington, United States of America
| | - Dima N. Gharaibeh
- SIGA Technologies, Inc., Corvallis, Oregon, United States of America
| | - Amy L. Moore
- SIGA Technologies, Inc., Corvallis, Oregon, United States of America
| | - Kie-Hoon Jung
- Institute for Antiviral Research, Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, Utah, United States of America
| | - Brian B. Gowen
- Institute for Antiviral Research, Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, Utah, United States of America
| | - Dongcheng Dai
- SIGA Technologies, Inc., Corvallis, Oregon, United States of America
| | - Kevin F. Jones
- SIGA Technologies, Inc., Corvallis, Oregon, United States of America
| | | | - James R. Burgeson
- SIGA Technologies, Inc., Corvallis, Oregon, United States of America
| | | | | | | | - Sean M. Amberg
- Kineta, Inc., Seattle, Washington, United States of America
- * E-mail:
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24
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Forni D, Pontremoli C, Pozzoli U, Clerici M, Cagliani R, Sironi M. Ancient Evolution of Mammarenaviruses: Adaptation via Changes in the L Protein and No Evidence for Host-Virus Codivergence. Genome Biol Evol 2018; 10:863-874. [PMID: 29608723 PMCID: PMC5863214 DOI: 10.1093/gbe/evy050] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/02/2018] [Indexed: 01/03/2023] Open
Abstract
The Mammarenavirus genus includes several pathogenic species of rodent-borne viruses. Old World (OW) mammarenaviruses infect rodents in the Murinae subfamily and are mainly transmitted in Africa and Asia; New World (NW) mammarenaviruses are found in rodents of the Cricetidae subfamily in the Americas. We applied a selection-informed method to estimate that OW and NW mammarenaviruses diverged less than ∼45,000 years ago (ya). By incorporating phylogeographic inference, we show that NW mammarenaviruses emerged in the Latin America-Caribbean region ∼41,400–3,300 ya, whereas OW mammarenaviruses originated ∼23,100–1,880 ya, most likely in Southern Africa. Cophylogenetic analysis indicated that cospeciation did not contribute significantly to mammarenavirus–host associations. Finally, we show that extremely strong selective pressure on the viral polymerase accompanied the speciation of NW viruses. These data suggest that the evolutionary history of mammarenaviruses was not driven by codivergence with their hosts. The viral polymerase should be regarded as a major determinant of mammarenavirus adaptation.
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Affiliation(s)
- Diego Forni
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, Bosisio Parini, Italy
| | - Chiara Pontremoli
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, Bosisio Parini, Italy
| | - Uberto Pozzoli
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, Bosisio Parini, Italy
| | - Mario Clerici
- Department of Physiopathology and Transplantation, University of Milan, Italy.,Don C. Gnocchi Foundation ONLUS, IRCCS, Milan, Italy
| | - Rachele Cagliani
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, Bosisio Parini, Italy
| | - Manuela Sironi
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, Bosisio Parini, Italy
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25
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Widespread arenavirus occurrence and seroprevalence in small mammals, Nigeria. Parasit Vectors 2018; 11:416. [PMID: 30005641 PMCID: PMC6045851 DOI: 10.1186/s13071-018-2991-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Accepted: 07/03/2018] [Indexed: 11/10/2022] Open
Abstract
Background Lassa fever, killing thousands of people annually, is the most reported viral zoonotic disease in Nigeria. Recently, different rodent species carrying diverse lineages of the Lassa virus (LASV) in addition to a novel Mobala-like genetic sequence were detected within the country. Here, screening 906 small mammal specimens from 11 localities for IgG antibodies and incorporating previous PCR detection data involving the same populations, we further describe arenavirus prevalence across Nigeria in relation to host species and geographical location. Methods Small mammals were trapped during the period 2011–2015 according to geographical location (endemic and non-endemic zones for Lassa fever), season (rainy and dry seasons between 2011 and 2012 for certain localities) and habitat (indoors, peridomestic settings and sylvatic vegetation). Identification of animal specimens from genera such as Mastomys and Mus (Nannomys) was assisted by DNA sequencing. Small mammals were tested for LASV IgG antibody using an indirect immunofluorescence assay (IFA). Results Small mammals were infected in both the endemic and non-endemic zones for Lassa fever, with a wider range of species IgG-positive (n = 8) than those which had been previously detected to be PCR-positive (n = 3). IgG-positive species, according to number of infected individuals, were Mastomys natalensis (n = 40), Mastomys erythroleucus (n = 15), Praomys daltoni (n = 6), Mus baoulei (n = 5), Rattus rattus (n = 2), Crocidura spp. (n = 2), Mus minutoides (n = 1) and Praomys misonnei (n = 1). Multimammate mice (Mastomys natalensis and M. erythroleucus) were the most ubiquitously infected, with animals testing positive by either PCR or IgG in 7 out of the 11 localities sampled. IgG prevalence in M. natalensis ranged from 1% in Abagboro, 17–36 % in Eguare Egoro, Ekpoma and Ngel Nyaki, up to 52 % in Mayo Ranewo. Prevalence according to locality, season and age was not, however, statistically significant for M. natalensis in Eguare Egoro and Ekpoma, localities that were sampled longitudinally. Conclusions Overall, our study demonstrates that arenavirus occurrence is probably more widely distributed geographically and in extent of host taxa than is currently realized. This expanded scope should be taken into consideration in Lassa fever control efforts. Further sampling should also be carried out to isolate and characterize potential arenaviruses present in small mammal populations we found to be seropositive.
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26
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Complete Genome Sequence of a Mammarenavirus Harbored by Rodents on Hainan Island, China. GENOME ANNOUNCEMENTS 2018. [PMID: 29519835 PMCID: PMC5843740 DOI: 10.1128/genomea.00129-18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Wenzhou virus (WENV) is a rodent-borne mammarenavirus that was recently found to infect humans. In this study, we sequenced and analyzed the complete genome of a genetic variant of WENV, HMU (Hainan Medical University) virus. The virus was harbored by a Rattus norvegicus individual in the residential areas of Hainan Province in southern China.
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27
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Pontremoli C, Forni D, Cagliani R, Pozzoli U, Riva S, Bravo IG, Clerici M, Sironi M. Evolutionary analysis of Old World arenaviruses reveals a major adaptive contribution of the viral polymerase. Mol Ecol 2017; 26:5173-5188. [PMID: 28779541 DOI: 10.1111/mec.14282] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 07/25/2017] [Accepted: 07/31/2017] [Indexed: 12/17/2022]
Abstract
The Old World (OW) arenavirus complex includes several species of rodent-borne viruses, some of which (i.e., Lassa virus, LASV and Lymphocytic choriomeningitis virus, LCMV) cause human diseases. Most LCMV and LASV infections are caused by rodent-to-human transmissions. Thus, viral evolution is largely determined by events that occur in the wildlife reservoirs. We used a set of human- and rodent-derived viral sequences to investigate the evolutionary history underlying OW arenavirus speciation, as well as the more recent selective events that accompanied LASV spread in West Africa. We show that the viral RNA polymerase (L protein) was a major positive selection target in OW arenaviruses and during LASV out-of-Nigeria migration. No evidence of selection was observed for the glycoprotein, whereas positive selection acted on the nucleoprotein (NP) during LCMV speciation. Positively selected sites in L and NP are surrounded by highly conserved residues, and the bulk of the viral genome evolves under purifying selection. Several positively selected sites are likely to modulate viral replication/transcription. In both L and NP, structural features (solvent exposed surface area) are important determinants of site-wise evolutionary rate variation. By incorporating several rodent-derived sequences, we also performed an analysis of OW arenavirus codon adaptation to the human host. Results do not support a previously hypothesized role of codon adaptation in disease severity for non-Nigerian strains. In conclusion, L and NP represent the major selection targets and possible determinants of disease presentation; these results suggest that field surveys and experimental studies should primarily focus on these proteins.
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Affiliation(s)
- Chiara Pontremoli
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, Bosisio Parini, Italy
| | - Diego Forni
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, Bosisio Parini, Italy
| | - Rachele Cagliani
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, Bosisio Parini, Italy
| | - Uberto Pozzoli
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, Bosisio Parini, Italy
| | - Stefania Riva
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, Bosisio Parini, Italy
| | - Ignacio G Bravo
- Laboratory MIVEGEC, UMR CNRS 5290, IRD 224, UM, Centre National de la Recherche Scientifique, Montpellier, France
| | - Mario Clerici
- Department of Physiopathology and Transplantation, University of Milan, Milan, Italy.,Don C. Gnocchi Foundation ONLUS, IRCCS, Milan, Italy
| | - Manuela Sironi
- Bioinformatics, Scientific Institute IRCCS E. MEDEA, Bosisio Parini, Italy
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28
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Gibb R, Moses LM, Redding DW, Jones KE. Understanding the cryptic nature of Lassa fever in West Africa. Pathog Glob Health 2017; 111:276-288. [PMID: 28875769 PMCID: PMC5694855 DOI: 10.1080/20477724.2017.1369643] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Lassa fever (LF) is increasingly recognized by global health institutions as an important rodent-borne disease with severe impacts on some of West Africa's poorest communities. However, our knowledge of LF ecology, epidemiology and distribution is limited, which presents barriers to both short-term disease forecasting and prediction of long-term impacts of environmental change on Lassa virus (LASV) zoonotic transmission dynamics. Here, we synthesize current knowledge to show that extrapolations from past research have produced an incomplete picture of the incidence and distribution of LF, with negative consequences for policy planning, medical treatment and management interventions. Although the recent increase in LF case reports is likely due to improved surveillance, recent studies suggest that future socio-ecological changes in West Africa may drive increases in LF burden. Future research should focus on the geographical distribution and disease burden of LF, in order to improve its integration into public policy and disease control strategies.
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Affiliation(s)
- Rory Gibb
- Centre for Biodiversity and Environment Research, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Lina M. Moses
- Department of Global Community Health and Behavioral Sciences, Tulane University, New Orleans, LA, USA
| | - David W. Redding
- Centre for Biodiversity and Environment Research, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Kate E. Jones
- Centre for Biodiversity and Environment Research, Department of Genetics, Evolution and Environment, University College London, London, UK
- Institute of Zoology, Zoological Society of London, London, UK
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29
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Anthony SJ, Johnson CK, Greig DJ, Kramer S, Che X, Wells H, Hicks AL, Joly DO, Wolfe ND, Daszak P, Karesh W, Lipkin WI, Morse SS, Mazet JAK, Goldstein T. Global patterns in coronavirus diversity. Virus Evol 2017. [PMID: 28630747 PMCID: PMC5467638 DOI: 10.1093/ve/vex012] [Citation(s) in RCA: 239] [Impact Index Per Article: 34.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Since the emergence of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and Middle East Respiratory Syndrom Coronavirus (MERS-CoV) it has become increasingly clear that bats are important reservoirs of CoVs. Despite this, only 6% of all CoV sequences in GenBank are from bats. The remaining 94% largely consist of known pathogens of public health or agricultural significance, indicating that current research effort is heavily biased towards describing known diseases rather than the ‘pre-emergent’ diversity in bats. Our study addresses this critical gap, and focuses on resource poor countries where the risk of zoonotic emergence is believed to be highest. We surveyed the diversity of CoVs in multiple host taxa from twenty countries to explore the factors driving viral diversity at a global scale. We identified sequences representing 100 discrete phylogenetic clusters, ninety-one of which were found in bats, and used ecological and epidemiologic analyses to show that patterns of CoV diversity correlate with those of bat diversity. This cements bats as the major evolutionary reservoirs and ecological drivers of CoV diversity. Co-phylogenetic reconciliation analysis was also used to show that host switching has contributed to CoV evolution, and a preliminary analysis suggests that regional variation exists in the dynamics of this process. Overall our study represents a model for exploring global viral diversity and advances our fundamental understanding of CoV biodiversity and the potential risk factors associated with zoonotic emergence.
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Affiliation(s)
- Simon J Anthony
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 West 168 Street, New York, NY 10032, USA.,Department of Epidemiology, Mailman School of Public Health, Columbia University, 722 West 168 Street, New York, NY 10032, USA.,EcoHealth Alliance, 460 West 34 Street, New York, NY 10001, USA
| | - Christine K Johnson
- One Health Institute & Karen C Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA
| | - Denise J Greig
- One Health Institute & Karen C Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA
| | - Sarah Kramer
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 West 168 Street, New York, NY 10032, USA.,Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, 722 West 168 Street, New York, NY 10032, USA
| | - Xiaoyu Che
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 West 168 Street, New York, NY 10032, USA
| | - Heather Wells
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 West 168 Street, New York, NY 10032, USA
| | - Allison L Hicks
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 West 168 Street, New York, NY 10032, USA
| | - Damien O Joly
- Metabiota, Inc. One Sutter, Suite 600, San Francisco, CA 94104, USA.,Wildlife Conservation Society, New York, NY 10460, USA
| | - Nathan D Wolfe
- Metabiota, Inc. One Sutter, Suite 600, San Francisco, CA 94104, USA
| | - Peter Daszak
- EcoHealth Alliance, 460 West 34 Street, New York, NY 10001, USA
| | - William Karesh
- EcoHealth Alliance, 460 West 34 Street, New York, NY 10001, USA
| | - W I Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 West 168 Street, New York, NY 10032, USA.,Department of Epidemiology, Mailman School of Public Health, Columbia University, 722 West 168 Street, New York, NY 10032, USA
| | - Stephen S Morse
- Department of Epidemiology, Mailman School of Public Health, Columbia University, 722 West 168 Street, New York, NY 10032, USA
| | | | - Jonna A K Mazet
- One Health Institute & Karen C Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA
| | - Tracey Goldstein
- One Health Institute & Karen C Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA
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30
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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: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [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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31
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Anthony SJ, Johnson CK, Greig DJ, Kramer S, Che X, Wells H, Hicks AL, Joly DO, Wolfe ND, Daszak P, Karesh W, Lipkin WI, Morse SS, Mazet JAK, Goldstein T. Global patterns in coronavirus diversity. Virus Evol 2017; 3:vex012. [PMID: 28630747 DOI: 10.1093/ve] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023] Open
Abstract
Since the emergence of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and Middle East Respiratory Syndrom Coronavirus (MERS-CoV) it has become increasingly clear that bats are important reservoirs of CoVs. Despite this, only 6% of all CoV sequences in GenBank are from bats. The remaining 94% largely consist of known pathogens of public health or agricultural significance, indicating that current research effort is heavily biased towards describing known diseases rather than the 'pre-emergent' diversity in bats. Our study addresses this critical gap, and focuses on resource poor countries where the risk of zoonotic emergence is believed to be highest. We surveyed the diversity of CoVs in multiple host taxa from twenty countries to explore the factors driving viral diversity at a global scale. We identified sequences representing 100 discrete phylogenetic clusters, ninety-one of which were found in bats, and used ecological and epidemiologic analyses to show that patterns of CoV diversity correlate with those of bat diversity. This cements bats as the major evolutionary reservoirs and ecological drivers of CoV diversity. Co-phylogenetic reconciliation analysis was also used to show that host switching has contributed to CoV evolution, and a preliminary analysis suggests that regional variation exists in the dynamics of this process. Overall our study represents a model for exploring global viral diversity and advances our fundamental understanding of CoV biodiversity and the potential risk factors associated with zoonotic emergence.
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Affiliation(s)
- Simon J Anthony
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 West 168 Street, New York, NY 10032, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, 722 West 168 Street, New York, NY 10032, USA
- EcoHealth Alliance, 460 West 34 Street, New York, NY 10001, USA
| | - Christine K Johnson
- One Health Institute & Karen C Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA
| | - Denise J Greig
- One Health Institute & Karen C Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA
| | - Sarah Kramer
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 West 168 Street, New York, NY 10032, USA
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, 722 West 168 Street, New York, NY 10032, USA
| | - Xiaoyu Che
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 West 168 Street, New York, NY 10032, USA
| | - Heather Wells
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 West 168 Street, New York, NY 10032, USA
| | - Allison L Hicks
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 West 168 Street, New York, NY 10032, USA
| | - Damien O Joly
- Metabiota, Inc. One Sutter, Suite 600, San Francisco, CA 94104, USA
- Wildlife Conservation Society, New York, NY 10460, USA
| | - Nathan D Wolfe
- Metabiota, Inc. One Sutter, Suite 600, San Francisco, CA 94104, USA
| | - Peter Daszak
- EcoHealth Alliance, 460 West 34 Street, New York, NY 10001, USA
| | - William Karesh
- EcoHealth Alliance, 460 West 34 Street, New York, NY 10001, USA
| | - W I Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 West 168 Street, New York, NY 10032, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, 722 West 168 Street, New York, NY 10032, USA
| | - Stephen S Morse
- Department of Epidemiology, Mailman School of Public Health, Columbia University, 722 West 168 Street, New York, NY 10032, USA
| | - Jonna A K Mazet
- One Health Institute & Karen C Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA
| | - Tracey Goldstein
- One Health Institute & Karen C Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA
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32
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Redding DW, Moses LM, Cunningham AA, Wood J, Jones KE. Environmental-mechanistic modelling of the impact of global change on human zoonotic disease emergence: a case study of Lassa fever. Methods Ecol Evol 2016. [DOI: 10.1111/2041-210x.12549] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- David W. Redding
- Centre for Biodiversity and Environment Research; Department of Genetics, Evolution and Environment; University College London; Gower Street London WC1E 6BT UK
| | - Lina M. Moses
- Department of Microbiology and Immunology; Tulane University; New Orleans Louisiana USA
| | - Andrew A. Cunningham
- Institute of Zoology; Zoological Society of London; Regent's Park London NW1 4RY UK
| | - James Wood
- Department of Veterinary Medicine; Disease Dynamics Unit; University of Cambridge; Cambridge UK
| | - Kate E. Jones
- Centre for Biodiversity and Environment Research; Department of Genetics, Evolution and Environment; University College London; Gower Street London WC1E 6BT UK
- Institute of Zoology; Zoological Society of London; Regent's Park London NW1 4RY UK
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33
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Blasdell KR, Duong V, Eloit M, Chretien F, Ly S, Hul V, Deubel V, Morand S, Buchy P. Evidence of human infection by a new mammarenavirus endemic to Southeastern Asia. eLife 2016; 5. [PMID: 27278118 PMCID: PMC4900801 DOI: 10.7554/elife.13135] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 05/10/2016] [Indexed: 11/16/2022] Open
Abstract
Southeastern Asia is a recognised hotspot for emerging infectious diseases, many of which have an animal origin. Mammarenavirus infections contribute significantly to the human disease burden in both Africa and the Americas, but little data exists for Asia. To date only two mammarenaviruses, the widely spread lymphocytic choriomeningitis virus and the recently described Wēnzhōu virus have been identified in this region, but the zoonotic impact in Asia remains unknown. Here we report the presence of a novel mammarenavirus and of a genetic variant of the Wēnzhōu virus and provide evidence of mammarenavirus-associated human infection in Asia. The association of these viruses with widely distributed mammals of diverse species, commonly found in human dwellings and in peridomestic habitats, illustrates the potential for widespread zoonotic transmission and adds to the known aetiologies of infectious diseases for this region. DOI:http://dx.doi.org/10.7554/eLife.13135.001 Rodents have long been notorious for spreading disease among humans. Often the animals can carry viruses and transmit them to humans without becoming ill. Certain species thrive in cities and agricultural areas where they come in close contact with humans; this creates many opportunities to spread infection. As humans urbanize and farm larger swaths of previously wild lands, the risk of rodent-transmitted infections increases. As a result, some scientists are working to identify viruses carried by rodents in human settlements and hopefully prevent them from spreading to humans. The mammarenavirsuses are a group of rodent-transmitted viruses that commonly cause illness in people in Africa and Latin America. Each year, one such virus – the Lassa virus –sickens as many as 300,000 people in Africa and kills 5,000. So far, only two mammarenaviruses have been found in Asia: one called the Wēnzhōu virus and another called LCMV. However only LCMV is known to cause human illness and many cases of illness caused by mammarenaviruses in Asia may go undetected because they often cause mild symptoms similar to the common cold. Blasdell et al. have now tested lung samples from 20 species of rodents collected at 7 sites in Cambodia, Thailand, and Laos to look for molecules produced by mammarenaviruses. The tests revealed a strain of Wēnzhōu virus circulating in Cambodian rats that often live in urban areas. A new mammarenavirus was also detected in rodents that live in Thai rice fields. However, infecting wild and domestic rodents with the viruses in the laboratory did not cause many noticeable signs of illness. Blasdell et al. then tested samples from Cambodian patients who either had influenza-like symptoms or more serious symptoms that are associated with a condition called Dengue fever (which is common in the area). Some patients with respiratory symptoms tested positive for the Wēnzhōu virus. Because the symptoms are mild and similar to those of other common diseases it is likely that the Wēnzhōu virus may be spreading more widely among humans in Asia. The next challenges are to provide a better estimate of the frequency of this disease in the human population in Asia and to describe the full spectrum of disease that might be associated with this newly discovered infectious disease. DOI:http://dx.doi.org/10.7554/eLife.13135.002
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Affiliation(s)
- Kim R Blasdell
- Institut Pasteur in Cambodia, Phnom Penh, Cambodia.,Commonwealth Scientific and Industrial Research Organisation, Australian Animal Health Laboratory, Geelong, Australia
| | - Veasna Duong
- Institut Pasteur in Cambodia, Phnom Penh, Cambodia
| | | | | | - Sowath Ly
- Institut Pasteur in Cambodia, Phnom Penh, Cambodia
| | - Vibol Hul
- Institut Pasteur in Cambodia, Phnom Penh, Cambodia
| | | | - Serge Morand
- Institut des Sciences de l'Evolution, CNRS, IRD, Université Montpellier, Montpellier, France
| | - Philippe Buchy
- Institut Pasteur in Cambodia, Phnom Penh, Cambodia.,GlaxoSmithKline Vaccines R&D, Singapore, Singapore
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34
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Olayemi A, Cadar D, Magassouba N, Obadare A, Kourouma F, Oyeyiola A, Fasogbon S, Igbokwe J, Rieger T, Bockholt S, Jérôme H, Schmidt-Chanasit J, Garigliany M, Lorenzen S, Igbahenah F, Fichet JN, Ortsega D, Omilabu S, Günther S, Fichet-Calvet E. New Hosts of The Lassa Virus. Sci Rep 2016; 6:25280. [PMID: 27140942 PMCID: PMC4853722 DOI: 10.1038/srep25280] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Accepted: 04/14/2016] [Indexed: 11/27/2022] Open
Abstract
Lassa virus (LASV) causes a deadly haemorrhagic fever in humans, killing several thousand people in West Africa annually. For 40 years, the Natal multimammate rat, Mastomys natalensis, has been assumed to be the sole host of LASV. We found evidence that LASV is also hosted by other rodent species: the African wood mouse Hylomyscus pamfi in Nigeria, and the Guinea multimammate mouse Mastomys erythroleucus in both Nigeria and Guinea. Virus strains from these animals were isolated in the BSL-4 laboratory and fully sequenced. Phylogenetic analyses of viral genes coding for glycoprotein, nucleoprotein, polymerase and matrix protein show that Lassa strains detected in M. erythroleucus belong to lineages III and IV. The strain from H. pamfi clusters close to lineage I (for S gene) and between II & III (for L gene). Discovery of new rodent hosts has implications for LASV evolution and its spread into new areas within West Africa.
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Affiliation(s)
- Ayodeji Olayemi
- Natural History Museum, Obafemi Awolowo University, HO 220005 Ile-Ife, Nigeria
| | - Daniel Cadar
- Department of Virology, Bernhard Nocht Institute for Tropical Medicine, D-20324, Hamburg, Germany
| | - N'Faly Magassouba
- Service des Maladies Infectieuses et Tropicales, Hospital Donka, Conakry, Guinea
| | - Adeoba Obadare
- Natural History Museum, Obafemi Awolowo University, HO 220005 Ile-Ife, Nigeria
| | - Fode Kourouma
- Service des Maladies Infectieuses et Tropicales, Hospital Donka, Conakry, Guinea
| | - Akinlabi Oyeyiola
- Natural History Museum, Obafemi Awolowo University, HO 220005 Ile-Ife, Nigeria
| | | | - Joseph Igbokwe
- Natural History Museum, Obafemi Awolowo University, HO 220005 Ile-Ife, Nigeria
| | - Toni Rieger
- Department of Virology, Bernhard Nocht Institute for Tropical Medicine, D-20324, Hamburg, Germany
| | - Sabrina Bockholt
- Department of Virology, Bernhard Nocht Institute for Tropical Medicine, D-20324, Hamburg, Germany
| | - Hanna Jérôme
- Department of Virology, Bernhard Nocht Institute for Tropical Medicine, D-20324, Hamburg, Germany
| | - Jonas Schmidt-Chanasit
- Department of Virology, Bernhard Nocht Institute for Tropical Medicine, D-20324, Hamburg, Germany
| | - Mutien Garigliany
- Department of Veterinary Pathology, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Stephan Lorenzen
- Department of Molecular Medicine, Bernhard Nocht Institute for Tropical Medicine, D-20324, Hamburg, Germany
| | - Felix Igbahenah
- Department of Geography, Benue State University, Makurdi, Nigeria
| | | | - Daniel Ortsega
- Department of Geography, Benue State University, Makurdi, Nigeria
| | - Sunday Omilabu
- Department of Medical Microbiology and Parasitology, College of Medicine, University of Lagos, Nigeria
| | - Stephan Günther
- Department of Virology, Bernhard Nocht Institute for Tropical Medicine, D-20324, Hamburg, Germany
| | - Elisabeth Fichet-Calvet
- Department of Virology, Bernhard Nocht Institute for Tropical Medicine, D-20324, Hamburg, Germany
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35
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Mélade J, Wieseke N, Ramasindrazana B, Flores O, Lagadec E, Gomard Y, Goodman SM, Dellagi K, Pascalis H. An eco-epidemiological study of Morbilli-related paramyxovirus infection in Madagascar bats reveals host-switching as the dominant macro-evolutionary mechanism. Sci Rep 2016; 6:23752. [PMID: 27068130 PMCID: PMC4828640 DOI: 10.1038/srep23752] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 03/08/2016] [Indexed: 11/09/2022] Open
Abstract
An eco-epidemiological investigation was carried out on Madagascar bat communities to better understand the evolutionary mechanisms and environmental factors that affect virus transmission among bat species in closely related members of the genus Morbillivirus, currently referred to as Unclassified Morbilli-related paramyxoviruses (UMRVs). A total of 947 bats were investigated originating from 52 capture sites (22 caves, 18 buildings, and 12 outdoor sites) distributed over different bioclimatic zones of the island. Using RT-PCR targeting the L-polymerase gene of the Paramyxoviridae family, we found that 10.5% of sampled bats were infected, representing six out of seven families and 15 out of 31 species analyzed. Univariate analysis indicates that both abiotic and biotic factors may promote viral infection. Using generalized linear modeling of UMRV infection overlaid on biotic and abiotic variables, we demonstrate that sympatric occurrence of bats is a major factor for virus transmission. Phylogenetic analyses revealed that all paramyxoviruses infecting Malagasy bats are UMRVs and showed little host specificity. Analyses using the maximum parsimony reconciliation tool CoRe-PA, indicate that host-switching, rather than co-speciation, is the dominant macro-evolutionary mechanism of UMRVs among Malagasy bats.
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Affiliation(s)
- Julien Mélade
- Centre de Recherche et de Veille sur les Maladies Emergentes dans l’Océan Indien (CRVOI), Plateforme de Recherche CYROI, 2 rue Maxime Rivière, 97490 Sainte Clotilde, La Réunion, France
- Université de La Réunion, UMR PIMIT “Processus Infectieux en Milieu Insulaire Tropical”, INSERM U1187, CNRS 9192, IRD 249, Plateforme de Recherche CYROI, Saint Denis, La Réunion, France
- Institut de Recherche pour le Développement (IRD), IRD – BP 50172, 97492 Sainte-Clotilde, La Réunion, France
| | - Nicolas Wieseke
- University of Leipzig, Department of Computer Science, Augustusplatz 10, D-04109 Leipzig, Germany
| | - Beza Ramasindrazana
- Centre de Recherche et de Veille sur les Maladies Emergentes dans l’Océan Indien (CRVOI), Plateforme de Recherche CYROI, 2 rue Maxime Rivière, 97490 Sainte Clotilde, La Réunion, France
- Université de La Réunion, UMR PIMIT “Processus Infectieux en Milieu Insulaire Tropical”, INSERM U1187, CNRS 9192, IRD 249, Plateforme de Recherche CYROI, Saint Denis, La Réunion, France
- Institut de Recherche pour le Développement (IRD), IRD – BP 50172, 97492 Sainte-Clotilde, La Réunion, France
- Association Vahatra, BP 3972, Antananarivo 101, Madagascar
- Institut Pasteur de Madagascar, BP 1274 Ambohitrakely, Antananarivo 101, Madagascar
| | - Olivier Flores
- UMR C53 CIRAD, Peuplements Végétaux et Bioagresseurs en Milieu Tropical, 7 chemin de l’IRAT, 97410 St Pierre, France
- Université de La Réunion, 15 Avenue René Cassin, 97400 Saint-Denis, France
| | - Erwan Lagadec
- Centre de Recherche et de Veille sur les Maladies Emergentes dans l’Océan Indien (CRVOI), Plateforme de Recherche CYROI, 2 rue Maxime Rivière, 97490 Sainte Clotilde, La Réunion, France
- Université de La Réunion, UMR PIMIT “Processus Infectieux en Milieu Insulaire Tropical”, INSERM U1187, CNRS 9192, IRD 249, Plateforme de Recherche CYROI, Saint Denis, La Réunion, France
- Institut de Recherche pour le Développement (IRD), IRD – BP 50172, 97492 Sainte-Clotilde, La Réunion, France
| | - Yann Gomard
- Centre de Recherche et de Veille sur les Maladies Emergentes dans l’Océan Indien (CRVOI), Plateforme de Recherche CYROI, 2 rue Maxime Rivière, 97490 Sainte Clotilde, La Réunion, France
- Université de La Réunion, UMR PIMIT “Processus Infectieux en Milieu Insulaire Tropical”, INSERM U1187, CNRS 9192, IRD 249, Plateforme de Recherche CYROI, Saint Denis, La Réunion, France
- Institut de Recherche pour le Développement (IRD), IRD – BP 50172, 97492 Sainte-Clotilde, La Réunion, France
| | - Steven M. Goodman
- Association Vahatra, BP 3972, Antananarivo 101, Madagascar
- Field Museum of Natural History, 1400 S. Lake Shore Dr, Chicago, IL 60605-2496, USA
| | - Koussay Dellagi
- Centre de Recherche et de Veille sur les Maladies Emergentes dans l’Océan Indien (CRVOI), Plateforme de Recherche CYROI, 2 rue Maxime Rivière, 97490 Sainte Clotilde, La Réunion, France
- Université de La Réunion, UMR PIMIT “Processus Infectieux en Milieu Insulaire Tropical”, INSERM U1187, CNRS 9192, IRD 249, Plateforme de Recherche CYROI, Saint Denis, La Réunion, France
- Institut de Recherche pour le Développement (IRD), IRD – BP 50172, 97492 Sainte-Clotilde, La Réunion, France
| | - Hervé Pascalis
- Centre de Recherche et de Veille sur les Maladies Emergentes dans l’Océan Indien (CRVOI), Plateforme de Recherche CYROI, 2 rue Maxime Rivière, 97490 Sainte Clotilde, La Réunion, France
- Université de La Réunion, UMR PIMIT “Processus Infectieux en Milieu Insulaire Tropical”, INSERM U1187, CNRS 9192, IRD 249, Plateforme de Recherche CYROI, Saint Denis, La Réunion, France
- Institut de Recherche pour le Développement (IRD), IRD – BP 50172, 97492 Sainte-Clotilde, La Réunion, France
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36
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Witkowski PT, Kallies R, Hoveka J, Auste B, Ithete NL, Šoltys K, Szemes T, Drosten C, Preiser W, Klempa B, Mfune JKE, Kruger DH. Novel Arenavirus Isolates from Namaqua Rock Mice, Namibia, Southern Africa. Emerg Infect Dis 2016; 21:1213-6. [PMID: 26079174 PMCID: PMC4480381 DOI: 10.3201/eid2107.141341] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Arenaviruses are feared as agents that cause viral hemorrhagic fevers. We report the identification, isolation, and genetic characterization of 2 novel arenaviruses from Namaqua rock mice in Namibia. These findings extend knowledge of the distribution and diversity of arenaviruses in Africa.
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37
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Kouadio L, Nowak K, Akoua-Koffi C, Weiss S, Allali BK, Witkowski PT, Krüger DH, Couacy-Hymann E, Calvignac-Spencer S, Leendertz FH. Lassa Virus in Multimammate Rats, Côte d'Ivoire, 2013. Emerg Infect Dis 2016. [PMID: 26196447 PMCID: PMC4517737 DOI: 10.3201/eid2108.150312] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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38
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Fichet-Calvet E, Ölschläger S, Strecker T, Koivogui L, Becker-Ziaja B, Camara AB, Soropogui B, Magassouba N, Günther S. Spatial and temporal evolution of Lassa virus in the natural host population in Upper Guinea. Sci Rep 2016; 6:21977. [PMID: 26911443 PMCID: PMC4766397 DOI: 10.1038/srep21977] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 02/03/2016] [Indexed: 11/09/2022] Open
Abstract
This study aimed at reconstructing the spatial and temporal evolution of Lassa virus (LASV) in the natural host population. To this end, we generated 132 partial nucleoprotein sequences of LASV from M. natalensis trapped in 12 villages around Faranah, Upper Guinea, over a period of 12 years. This study reveals two main features of LASV evolution in M. natalensis. First, the virus evolves in the reservoir with a molecular clock rate of 9 (7-11) × 10(-4) position(-1) year(-1) implying that contemporary LASV lineages circulate in the Faranah area since less than 100 years. Second, viruses circulating in a specific village are diverse and polyphyletic. We observed, however, there are monophyletic clusters at village and sub-village level at specific points in time. In conclusion, our data indicate that the temporal and spatial pattern of LASV evolution in the natural reservoir is characterized by a combination of stationary circulation within a village and virus movement between villages. The latter feature is relevant for rodent control strategies, as it implies that recurrence of the virus from neighbouring villages may occur in villages where the virus has previously been eradicated.
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Affiliation(s)
| | | | - Thomas Strecker
- Institute of Virology, Philipps University Marburg, Marburg, Germany
| | - Lamine Koivogui
- Projet des Fièvres Hémorragiques en Guinée, Hopital Donka, Conakry, Guinea
| | | | - Amara Bongo Camara
- Projet des Fièvres Hémorragiques en Guinée, Hopital Donka, Conakry, Guinea
| | - Barré Soropogui
- Projet des Fièvres Hémorragiques en Guinée, Hopital Donka, Conakry, Guinea
| | - N'Faly Magassouba
- Projet des Fièvres Hémorragiques en Guinée, Hopital Donka, Conakry, Guinea
| | - Stephan Günther
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
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39
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Abstract
The family Arenaviridae currently comprises over 20 viral species, each of them associated with a main rodent species as the natural reservoir and in one case possibly phyllostomid bats. Moreover, recent findings have documented a divergent group of arenaviruses in captive alethinophidian snakes. Human infections occur through mucosal exposure to aerosols or by direct contact of abraded skin with infectious materials. Arenaviruses merit interest both as highly tractable experimental model systems to study acute and persistent infections and as clinically important human pathogens including Lassa (LASV) and Junin (JUNV) viruses, the causative agents of Lassa and Argentine hemorrhagic fevers (AHFs), respectively, for which there are no FDA-licensed vaccines, and current therapy is limited to an off-label use of ribavirin (Rib) that has significant limitations. Arenaviruses are enveloped viruses with a bi-segmented negative strand (NS) RNA genome. Each genome segment, L (ca 7.3 kb) and S (ca 3.5 kb), uses an ambisense coding strategy to direct the synthesis of two polypeptides in opposite orientation, separated by a noncoding intergenic region (IGR). The S genomic RNA encodes the virus nucleoprotein (NP) and the precursor (GPC) of the virus surface glycoprotein that mediates virus receptor recognition and cell entry via endocytosis. The L genome RNA encodes the viral RNA-dependent RNA polymerase (RdRp, or L polymerase) and the small (ca 11 kDa) RING finger protein Z that has functions of a bona fide matrix protein including directing virus budding. Arenaviruses were thought to be relatively stable genetically with intra- and interspecies amino acid sequence identities of 90-95 % and 44-63 %, respectively. However, recent evidence has documented extensive arenavirus genetic variability in the field. Moreover, dramatic phenotypic differences have been documented among closely related LCMV isolates. These data provide strong evidence of viral quasispecies involvement in arenavirus adaptability and pathogenesis. Here, we will review several aspects of the molecular biology of arenaviruses, phylogeny and evolution, and quasispecies dynamics of arenavirus populations for a better understanding of arenavirus pathogenesis, as well as for the development of novel antiviral strategies to combat arenavirus infections.
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Affiliation(s)
- Esteban Domingo
- Campus de Cantoblanco, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Madrid, Spain
| | - Peter Schuster
- The Santa Fe Institute, Santa Fe, NM, USA and Institut f. Theoretische Chemie, Universität Wien, Vienna, Austria
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Abstract
Until recently, members of the monogeneric family Arenaviridae (arenaviruses) have been known to infect only muroid rodents and, in one case, possibly phyllostomid bats. The paradigm of arenaviruses exclusively infecting small mammals shifted dramatically when several groups independently published the detection and isolation of a divergent group of arenaviruses in captive alethinophidian snakes. Preliminary phylogenetic analyses suggest that these reptilian arenaviruses constitute a sister clade to mammalian arenaviruses. Here, the members of the International Committee on Taxonomy of Viruses (ICTV) Arenaviridae Study Group, together with other experts, outline the taxonomic reorganization of the family Arenaviridae to accommodate reptilian arenaviruses and other recently discovered mammalian arenaviruses and to improve compliance with the Rules of the International Code of Virus Classification and Nomenclature (ICVCN). PAirwise Sequence Comparison (PASC) of arenavirus genomes and NP amino acid pairwise distances support the modification of the present classification. As a result, the current genus Arenavirus is replaced by two genera, Mammarenavirus and Reptarenavirus, which are established to accommodate mammalian and reptilian arenaviruses, respectively, in the same family. The current species landscape among mammalian arenaviruses is upheld, with two new species added for Lunk and Merino Walk viruses and minor corrections to the spelling of some names. The published snake arenaviruses are distributed among three new separate reptarenavirus species. Finally, a non-Latinized binomial species name scheme is adopted for all arenavirus species. In addition, the current virus abbreviations have been evaluated, and some changes are introduced to unequivocally identify each virus in electronic databases, manuscripts, and oral proceedings.
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Fichet-Calvet E, Becker-Ziaja B, Koivogui L, Günther S. Lassa serology in natural populations of rodents and horizontal transmission. Vector Borne Zoonotic Dis 2015; 14:665-74. [PMID: 25229705 DOI: 10.1089/vbz.2013.1484] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Lassa virus causes hemorrhagic fever in West Africa. Previously, we demonstrated by PCR screening that only the multimammate mouse, Mastomys natalensis, hosts Lassa virus in Guinea. In the present study, we used the same specimen collection from 17 villages in Coastal, Upper, and Forest Guinea to investigate the Lassa virus serology in the rodent population. The aim was to determine the dynamics of antibody development in M. natalensis and to detect potential spillover infections in other rodent species. Immunoglobulin G (IgG) antibody screening was performed using the indirect immunofluorescence assay with the Guinean Lassa virus strain Bantou 289 as antigen. The overall seroprevalence was 8% (129/1551) with the following rodents testing positive: 109 M. natalensis, seven Mastomys erythroleucus, four Lemniscomys striatus, four Praomys daltoni, three Mus minutoides, and two Praomys rostratus. Nearly all of them (122/129) originated from Bantou, Tanganya, and Gbetaya, where Lassa virus is highly endemic in M. natalensis. The antibody seroprevalence in M. natalensis from this high-endemic area (27%; 108/396) depended on the village, habitat, host age, and host abundance. A main positive factor was age; the maximum seroprevalence reached 50% in older animals. Our data fit with a model implicating that most M. natalensis rodents become horizontally infected, clear the virus within a period significantly shorter than their life span, and develop antibodies. In addition, the detection of antibodies in other species trapped in the habitats of M. natalensis suggests spillover infections.
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Nikisins S, Rieger T, Patel P, Müller R, Günther S, Niedrig M. International external quality assessment study for molecular detection of Lassa virus. PLoS Negl Trop Dis 2015; 9:e0003793. [PMID: 25996783 PMCID: PMC4440764 DOI: 10.1371/journal.pntd.0003793] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 04/28/2015] [Indexed: 12/02/2022] Open
Abstract
Lassa virus (LASV) is a causative agent of hemorrhagic fever in West Africa. In recent years, it has been imported several times to Europe and North America. The method of choice for early detection of LASV in blood is RT-PCR. Therefore, the European Network for Diagnostics of 'Imported' Viral Diseases (ENIVD) performed an external quality assessment (EQA) study for molecular detection of LASV. A proficiency panel of 13 samples containing various concentrations of inactivated LASV strains Josiah, Lib-1580/121, CSF, or AV was prepared. Samples containing the LASV-related lymphocytic choriomeningitis virus (LCMV) and negative sera were included as specificity controls. Twenty-four laboratories from 17 countries (13 European, one African, one Asian, two American countries) participated in the study. Thirteen laboratories (54%) reported correct results, 4 (17%) laboratories reported 1 to 2 false-negative results, and 7 (29%) laboratories reported 3 to 5 false-negative results. This EQA study indicates that most participating laboratories have a good or acceptable performance in molecular detection of LASV. However, several laboratories need to review and improve their diagnostic procedures.
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Affiliation(s)
- Sergejs Nikisins
- Highly Pathogenic Viruses (ZBS 1), Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
- European Public Health Microbiology Training Programme (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Toni Rieger
- Bernhard-Nocht-Institute for Tropical Medicine, WHO Collaborating Centre for Arboviruses and Hemorrhagic Fever Reference and Research, Hamburg, Germany
| | - Pranav Patel
- Highly Pathogenic Viruses (ZBS 1), Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
| | - Rolf Müller
- Biomatrica, San Diego, California, United States of America
| | - Stephan Günther
- Bernhard-Nocht-Institute for Tropical Medicine, WHO Collaborating Centre for Arboviruses and Hemorrhagic Fever Reference and Research, Hamburg, Germany
| | - Matthias Niedrig
- Highly Pathogenic Viruses (ZBS 1), Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
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Bryja J, Mikula O, Šumbera R, Meheretu Y, Aghová T, Lavrenchenko LA, Mazoch V, Oguge N, Mbau JS, Welegerima K, Amundala N, Colyn M, Leirs H, Verheyen E. Pan-African phylogeny of Mus (subgenus Nannomys) reveals one of the most successful mammal radiations in Africa. BMC Evol Biol 2014; 14:256. [PMID: 25496476 PMCID: PMC4280006 DOI: 10.1186/s12862-014-0256-2] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 11/27/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Rodents of the genus Mus represent one of the most valuable biological models for biomedical and evolutionary research. Out of the four currently recognized subgenera, Nannomys (African pygmy mice, including the smallest rodents in the world) comprises the only original African lineage. Species of this subgenus became important models for the study of sex determination in mammals and they are also hosts of potentially dangerous pathogens. Nannomys ancestors colonized Africa from Asia at the end of Miocene and Eastern Africa should be considered as the place of their first radiation. In sharp contrast with this fact and despite the biological importance of Nannomys, the specimens from Eastern Africa were obviously under-represented in previous studies and the phylogenetic and distributional patterns were thus incomplete. RESULTS We performed comprehensive genetic analysis of 657 individuals of Nannomys collected at approximately 300 localities across the whole sub-Saharan Africa. Phylogenetic reconstructions based on mitochondrial (CYTB) and nuclear (IRBP) genes identified five species groups and three monotypic ancestral lineages. We provide evidence for important cryptic diversity and we defined and mapped the distribution of 27 molecular operational taxonomic units (MOTUs) that may correspond to presumable species. Biogeographical reconstructions based on data spanning all of Africa modified the previous evolutionary scenarios. First divergences occurred in Eastern African mountains soon after the colonization of the continent and the remnants of these old divergences still occur there, represented by long basal branches of M. (previously Muriculus) imberbis and two undescribed species from Ethiopia and Malawi. The radiation in drier lowland habitats associated with the decrease of body size is much younger, occurred mainly in a single lineage (called the minutoides group, and especially within the species M. minutoides), and was probably linked to aridification and climatic fluctuations in middle Pliocene/Pleistocene. CONCLUSIONS We discovered very high cryptic diversity in African pygmy mice making the genus Mus one of the richest genera of African mammals. Our taxon sampling allowed reliable phylogenetic and biogeographic reconstructions that (together with detailed distributional data of individual MOTUs) provide a solid basis for further evolutionary, ecological and epidemiological studies of this important group of rodents.
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Affiliation(s)
- Josef Bryja
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic.
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic.
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Research Facility Studenec, Studenec 122, 675 02, Koněšín, Czech Republic.
| | - Ondřej Mikula
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic.
- Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, Brno, Czech Republic.
| | - Radim Šumbera
- Department of Zoology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic.
| | - Yonas Meheretu
- Department of Biology, College of Natural and Computational Sciences, Mekelle University, Tigray, Ethiopia.
| | - Tatiana Aghová
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic.
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic.
| | | | - Vladimír Mazoch
- Department of Zoology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic.
| | | | - Judith S Mbau
- College of Agriculture and Veterinary Sciences, University of Nairobi, Nairobi, Kenya.
| | - Kiros Welegerima
- Department of Biology, College of Natural and Computational Sciences, Mekelle University, Tigray, Ethiopia.
| | - Nicaise Amundala
- University of Kisangani, Eastern Province, Kisangani, DR, Congo.
| | - Marc Colyn
- CNRS UMR 6552/53, Université de Rennes 1, Station Biologique, Paimpont, France.
| | - Herwig Leirs
- Evolutionary Ecology Group, Biology Department, University of Antwerp, Antwerpen, Belgium.
| | - Erik Verheyen
- Evolutionary Ecology Group, Biology Department, University of Antwerp, Antwerpen, Belgium.
- Royal Belgian Institute for Natural Sciences, Operational Direction Taxonomy and Phylogeny, Brussels, Belgium.
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Li K, Lin XD, Wang W, Shi M, Guo WP, Zhang XH, Xing JG, He JR, Wang K, Li MH, Cao JH, Jiang ML, Holmes EC, Zhang YZ. Isolation and characterization of a novel arenavirus harbored by Rodents and Shrews in Zhejiang province, China. Virology 2014; 476:37-42. [PMID: 25506671 DOI: 10.1016/j.virol.2014.11.026] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 07/08/2014] [Accepted: 11/25/2014] [Indexed: 11/17/2022]
Abstract
To determine the biodiversity of arenaviruses in China, we captured and screened rodents and shrews in Wenzhou city, Zhejiang province, a locality where hemorrhagic fever diseases are endemic in humans. Accordingly, arenaviruses were detected in 42 of 351 rodents from eight species, and in 12 of 272 Asian house shrews (Suncus murinus), by RT-PCR targeting the L segment. From these, a single arenavirus was successfully isolated in cell culture. The virion particles exhibited a typical arenavirus morphology under transmission electron microscopy. Comparison of the S and L segment sequences revealed high levels of nucleotide (>32.2% and >39.6%) and amino acid (>28.8% and >43.8%) sequence differences from known arenaviruses, suggesting that it represents a novel arenavirus, which we designated Wenzhou virus (WENV). Phylogenetic analysis revealed that all WENV strains harbored by both rodents and Asian house shrews formed a distinct lineage most closely related to Old World arenaviruses.
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Affiliation(s)
- Kun Li
- State Key Laboratory for Infectious Disease Prevention and Control, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Xian-Dan Lin
- Wenzhou Center for Disease Control and Prevention, Wenzhou, Zhejiang Province, China
| | - Wen Wang
- State Key Laboratory for Infectious Disease Prevention and Control, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Mang Shi
- State Key Laboratory for Infectious Disease Prevention and Control, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China; Wencheng Center for Disease Control and Prevention, Wenzhou, Zhejiang Province, China
| | - Wen-Ping Guo
- State Key Laboratory for Infectious Disease Prevention and Control, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Xiao-He Zhang
- Wenzhou Center for Disease Control and Prevention, Wenzhou, Zhejiang Province, China
| | - Jian-Guang Xing
- Wencheng Center for Disease Control and Prevention, Wenzhou, Zhejiang Province, China
| | - Jin-Rong He
- State Key Laboratory for Infectious Disease Prevention and Control, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Ke Wang
- Lucheng Center for Disease Control and Prevention, Wenzhou, Zhejiang Province, China
| | - Ming-Hui Li
- State Key Laboratory for Infectious Disease Prevention and Control, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Jian-Hai Cao
- Longwan Center for Disease Control and Prevention, Wenzhou, Zhejiang Province, China
| | - Mu-Liu Jiang
- Ruian Center for Disease Control and Prevention, Ruian, Zhejiang Province, China
| | - Edward C Holmes
- State Key Laboratory for Infectious Disease Prevention and Control, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China; Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Yong-Zhen Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China.
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Drinkwater B, Charleston MA. Introducing TreeCollapse: a novel greedy algorithm to solve the cophylogeny reconstruction problem. BMC Bioinformatics 2014; 15 Suppl 16:S14. [PMID: 25521705 PMCID: PMC4290644 DOI: 10.1186/1471-2105-15-s16-s14] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cophylogeny mapping is used to uncover deep coevolutionary associations between two or more phylogenetic histories at a macro coevolutionary scale. As cophylogeny mapping is NP-Hard, this technique relies heavily on heuristics to solve all but the most trivial cases. One notable approach utilises a metaheuristic to search only a subset of the exponential number of fixed node orderings possible for the phylogenetic histories in question. This is of particular interest as it is the only known heuristic that guarantees biologically feasible solutions. This has enabled research to focus on larger coevolutionary systems, such as coevolutionary associations between figs and their pollinator wasps, including over 200 taxa. Although able to converge on solutions for problem instances of this size, a reduction from the current cubic running time is required to handle larger systems, such as Wolbachia and their insect hosts. RESULTS Rather than solving this underlying problem optimally this work presents a greedy algorithm called TreeCollapse, which uses common topological patterns to recover an approximation of the coevolutionary history where the internal node ordering is fixed. This approach offers a significant speed-up compared to previous methods, running in linear time. This algorithm has been applied to over 100 well-known coevolutionary systems converging on Pareto optimal solutions in over 68% of test cases, even where in some cases the Pareto optimal solution has not previously been recoverable. Further, while TreeCollapse applies a local search technique, it can guarantee solutions are biologically feasible, making this the fastest method that can provide such a guarantee. CONCLUSION As a result, we argue that the newly proposed algorithm is a valuable addition to the field of coevolutionary research. Not only does it offer a significantly faster method to estimate the cost of cophylogeny mappings but by using this approach, in conjunction with existing heuristics, it can assist in recovering a larger subset of the Pareto front than has previously been possible.
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Affiliation(s)
- Benjamin Drinkwater
- School of Information Technologies, 1 Cleveland St, 2006 University of Sydney, Australia Full list of author information is available at the end of the article
| | - Michael A Charleston
- School of Information Technologies, 1 Cleveland St, 2006 University of Sydney, Australia Full list of author information is available at the end of the article
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Schmidt S, Essbauer SS, Mayer-Scholl A, Poppert S, Schmidt-Chanasit J, Klempa B, Henning K, Schares G, Groschup MH, Spitzenberger F, Richter D, Heckel G, Ulrich RG. Multiple infections of rodents with zoonotic pathogens in Austria. Vector Borne Zoonotic Dis 2014; 14:467-75. [PMID: 24915446 PMCID: PMC4098071 DOI: 10.1089/vbz.2013.1504] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Rodents are important reservoirs for a large number of zoonotic pathogens. We examined the occurrence of 11 viral, bacterial, and parasitic agents in rodent populations in Austria, including three different hantaviruses, lymphocytic choriomeningitis virus, orthopox virus, Leptospira spp., Borrelia spp., Rickettsia spp., Bartonella spp., Coxiella burnetii, and Toxoplasma gondii. In 2008, 110 rodents of four species (40 Clethrionomys glareolus, 29 Apodemus flavicollis, 26 Apodemus sylvaticus, and 15 Microtus arvalis) were trapped at two rural sites in Lower Austria. Chest cavity fluid and samples of lung, spleen, kidney, liver, brain, and ear pinna skin were collected. We screened selected tissue samples for hantaviruses, lymphocytic choriomeningitis virus, orthopox viruses, Leptospira, Borrelia, Rickettsia, Bartonella spp., C. burnetii, and T. gondii by RT-PCR/PCR and detected nucleic acids of Tula hantavirus, Leptospira spp., Borrelia afzelii, Rickettsia spp., and different Bartonella species. Serological investigations were performed for hantaviruses, lymphocytic choriomeningitis virus, orthopox viruses, and Rickettsia spp. Here, Dobrava-Belgrade hantavirus-, Tula hantavirus-, lymphocytic choriomeningitis virus-, orthopox virus-, and rickettsia-specific antibodies were demonstrated. Puumala hantavirus, C. burnetii, and T. gondii were neither detected by RT-PCR/PCR nor by serological methods. In addition, multiple infections with up to three pathogens were shown in nine animals of three rodent species from different trapping sites. In conclusion, these results show that rodents in Austria may host multiple zoonotic pathogens. Our observation raises important questions regarding the interactions of different pathogens in the host, the countermeasures of the host's immune system, the impact of the host-pathogen interaction on the fitness of the host, and the spread of infectious agents among wild rodents and from those to other animals or humans.
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Affiliation(s)
- Sabrina Schmidt
- Friedrich-Loeffler-Institut, Institute for Novel and Emerging Infectious Diseases, Greifswald–Insel Riems, Germany
| | - Sandra S. Essbauer
- Bundeswehr Institute of Microbiology, Department of Virology & Rickettsiology, Munich, Germany
| | | | - Sven Poppert
- Institute of Medical Microbiology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Jonas Schmidt-Chanasit
- Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Centre for Arbovirus and Hemorrhagic Fever Reference and Research, Hamburg, Germany and German Centre for Infection Research (DZIF), partner site Hamburg-Luebeck-Borstel, Hamburg, Germany
| | - Boris Klempa
- Institute of Virology, Slovak Academy of Science, Bratislava, Slovakia, and Institute of Virology, Charité Medical School, Berlin, Germany
| | - Klaus Henning
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, Jena, Germany
| | - Gereon Schares
- Friedrich-Loeffler-Institut, Institute of Epidemiology, Greifswald-Insel Riems, Germany
| | - Martin H. Groschup
- Friedrich-Loeffler-Institut, Institute for Novel and Emerging Infectious Diseases, Greifswald–Insel Riems, Germany
| | | | - Dania Richter
- Environmental Systems Analysis, Institute of Geoecology, Technical University of Braunschweig, Germany
| | - Gerald Heckel
- Computational and Molecular Population Genetics (CMPG), Institute of Ecology and Evolution, University of Bern and Swiss Institute of Bioinformatics, Genopode, Lausanne, Switzerland
| | - Rainer G. Ulrich
- Friedrich-Loeffler-Institut, Institute for Novel and Emerging Infectious Diseases, Greifswald–Insel Riems, Germany
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Kronmann KC, Nimo-Paintsil S, Guirguis F, Kronmann LC, Bonney K, Obiri-Danso K, Ampofo W, Fichet-Calvet E. Two novel arenaviruses detected in pygmy mice, Ghana. Emerg Infect Dis 2014; 19:1832-5. [PMID: 24188212 PMCID: PMC3837667 DOI: 10.3201/eid1911.121491] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Two arenaviruses were detected in pygmy mice (Mus spp.) by screening 764 small mammals in Ghana. The Natal multimammate mouse (Mastomys natalensis), the known Lassa virus reservoir, was the dominant indoor rodent species in 4 of 10 sites, and accounted for 27% of all captured rodents. No rodent captured indoors tested positive for an arenavirus.
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McDonough MM, Sotero-Caio CG, Ferguson AW, Lewis PJ, Tswiio M, Thies ML. Mitochondrial DNA and karyotypic data confirm the presence of Mus indutus and Mus minutoides (Mammalia, Rodentia, Muridae, Nannomys) in Botswana. Zookeys 2013:35-51. [PMID: 24363588 PMCID: PMC3867174 DOI: 10.3897/zookeys.359.6247] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 11/25/2013] [Indexed: 11/16/2022] Open
Abstract
We use a combination of cytochrome b sequence data and karyological evidence to confirm the presence of Mus indutus and Mus minutoides in Botswana. Our data include sampling from five localities from across the country, including one site in northwestern Botswana where both species were captured in syntopy. Additionally, we find evidence for two mitochondrial lineages of M. minutoides in northwestern Botswana that differ by 5% in sequence variation. Also, we report that M. minutoides in Botswana have the 2n=34 karyotype with the presence of a (X.1) sex-autosome translocation.
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Affiliation(s)
- Molly M McDonough
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, 79409-3131, USA
| | - Cibele G Sotero-Caio
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, 79409-3131, USA
| | - Adam W Ferguson
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, 79409-3131, USA
| | - Patrick J Lewis
- Department of Biological Sciences, Sam Houston State University, Huntsville, Texas, 77341, USA
| | | | - Monte L Thies
- Department of Biological Sciences, Sam Houston State University, Huntsville, Texas, 77341, USA
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Infection of type I interferon receptor-deficient mice with various old world arenaviruses: a model for studying virulence and host species barriers. PLoS One 2013; 8:e72290. [PMID: 23991083 PMCID: PMC3750052 DOI: 10.1371/journal.pone.0072290] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 07/13/2013] [Indexed: 11/26/2022] Open
Abstract
Lassa virus causes hemorrhagic Lassa fever in humans, while the related Old World arenaviruses Mopeia, Morogoro, and Mobala are supposedly apathogenic to humans and cause only inapparent infection in non-human primates. Here, we studied whether the virulence of Old World arenaviruses in humans and non-human primates is reflected in type I interferon receptor deficient (IFNAR-/-) mice by testing several strains of Lassa virus vs. the apathogenic viruses Mopeia, Morogoro, and Mobala. All Lassa virus strains tested—Josiah, AV, BA366, and Nig04-10—replicated to high titers in blood, lung, kidney, heart, spleen, brain, and liver and caused disease as evidenced by weight loss and elevation of aspartate and alanine aminotransferase (AST and ALT) levels with a high AST/ALT ratio. Lassa fever-like pathology included acute hepatitis, interstitial pneumonia, and pronounced disturbance of splenic cytoarchitecture. Infiltrations of activated monocytes/macrophages expressing inducible nitric oxide synthase and T cells were found in liver and lung. In contrast, Mopeia, Morogoro, and Mobala virus replicated poorly in the animals and acute inflammatory alterations were not noted. Depletion of CD4+ and CD8+ T cells strongly enhanced susceptibility of IFNAR-/- mice to the apathogenic viruses. In conclusion, the virulence of Old World arenaviruses in IFNAR-/- mice correlates with their virulence in humans and non-human primates. In addition to the type I interferon system, T cells seem to regulate whether or not an arenavirus can productively infect non-host rodent species. The observation that Lassa virus overcomes the species barrier without artificial depletion of T cells suggests it is able to impair T cell functionality in a way that corresponds to depletion.
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50
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Lukashevich IS. The search for animal models for Lassa fever vaccine development. Expert Rev Vaccines 2013; 12:71-86. [PMID: 23256740 DOI: 10.1586/erv.12.139] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Lassa virus (LASV) is the most prevalent arenavirus in West Africa and is responsible for several hundred thousand infections and thousands of deaths annually. The sizeable disease burden, numerous imported cases of Lassa fever (LF) and the possibility that LASV can be used as an agent of biological warfare make a strong case for vaccine development. Currently there is no licensed LF vaccine and research and devlopment is hampered by the high cost of nonhuman primate animal models and by biocontainment requirements (BSL-4). In addition, a successful LF vaccine has to induce a strong cell-mediated cross-protective immunity against different LASV lineages. All of these challenges will be addressed in this review in the context of available and novel animal models recently described for evaluation of LF vaccine candidates.
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Affiliation(s)
- Igor S Lukashevich
- Department of Pharmacology and Toxicology, School of Medicine and the Center for Predictive Medicine for Biodefense and Emerging Infectious Diseases, University of Louisville, Louisville, KY 40202, USA.
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