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Harazim M, Perrot J, Varet H, Bourhy H, Lannoy J, Pikula J, Seidlová V, Dacheux L, Martínková N. Transcriptomic responses of bat cells to European bat lyssavirus 1 infection under conditions simulating euthermia and hibernation. BMC Immunol 2023; 24:7. [PMID: 37085747 PMCID: PMC10120247 DOI: 10.1186/s12865-023-00542-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 03/31/2023] [Indexed: 04/23/2023] Open
Abstract
BACKGROUND Coevolution between pathogens and their hosts decreases host morbidity and mortality. Bats host and can tolerate viruses which can be lethal to other vertebrate orders, including humans. Bat adaptations to infection include localized immune response, early pathogen sensing, high interferon expression without pathogen stimulation, and regulated inflammatory response. The immune reaction is costly, and bats suppress high-cost metabolism during torpor. In the temperate zone, bats hibernate in winter, utilizing a specific behavioural adaptation to survive detrimental environmental conditions and lack of energy resources. Hibernation torpor involves major physiological changes that pose an additional challenge to bat-pathogen coexistence. Here, we compared bat cellular reaction to viral challenge under conditions simulating hibernation, evaluating the changes between torpor and euthermia. RESULTS We infected the olfactory nerve-derived cell culture of Myotis myotis with an endemic bat pathogen, European bat lyssavirus 1 (EBLV-1). After infection, the bat cells were cultivated at two different temperatures, 37 °C and 5 °C, to examine the cell response during conditions simulating euthermia and torpor, respectively. The mRNA isolated from the cells was sequenced and analysed for differential gene expression attributable to the temperature and/or infection treatment. In conditions simulating euthermia, infected bat cells produce an excess signalling by multitude of pathways involved in apoptosis and immune regulation influencing proliferation of regulatory cell types which can, in synergy with other produced cytokines, contribute to viral tolerance. We found no up- or down-regulated genes expressed in infected cells cultivated at conditions simulating torpor compared to non-infected cells cultivated under the same conditions. When studying the reaction of uninfected cells to the temperature treatment, bat cells show an increased production of heat shock proteins (HSPs) with chaperone activity, improving the bat's ability to repair molecular structures damaged due to the stress related to the temperature change. CONCLUSIONS The lack of bat cell reaction to infection in conditions simulating hibernation may contribute to the virus tolerance or persistence in bats. Together with the cell damage repair mechanisms induced in response to hibernation, the immune regulation may promote bats' ability to act as reservoirs of zoonotic viruses such as lyssaviruses.
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Affiliation(s)
- Markéta Harazim
- Institute of Vertebrate Biology, Czech Academy of Sciences, Květná 8, 60300, Brno, Czechia.
- Department of Botany and Zoology, Masaryk University, Kotlářská 2, 61137, Brno, Czechia.
| | - Juliette Perrot
- Institut Pasteur, Université Paris Cité Lyssavirus, Epidemiology and Neuropathology Unit, 28 rue du Docteur Roux, 75724, Paris Cedex 15, France
| | - Hugo Varet
- Institut Pasteur, Université Paris Cité Bioinformatics and Biostatistics Hub, 28 rue du Docteur Roux, 75724, Paris Cedex 15, France
| | - Hervé Bourhy
- Institut Pasteur, Université Paris Cité Lyssavirus, Epidemiology and Neuropathology Unit, 28 rue du Docteur Roux, 75724, Paris Cedex 15, France
| | - Julien Lannoy
- Institut Pasteur, Université Paris Cité Lyssavirus, Epidemiology and Neuropathology Unit, 28 rue du Docteur Roux, 75724, Paris Cedex 15, France
| | - Jiri Pikula
- Department of Ecology and Diseases of Zoo Animals, Game, Fish and Bees, University of Veterinary Sciences Brno, Palackého třída 1946/1, 61242, Brno, Czechia
| | - Veronika Seidlová
- Department of Ecology and Diseases of Zoo Animals, Game, Fish and Bees, University of Veterinary Sciences Brno, Palackého třída 1946/1, 61242, Brno, Czechia
| | - Laurent Dacheux
- Institut Pasteur, Université Paris Cité Lyssavirus, Epidemiology and Neuropathology Unit, 28 rue du Docteur Roux, 75724, Paris Cedex 15, France
| | - Natália Martínková
- Institute of Vertebrate Biology, Czech Academy of Sciences, Květná 8, 60300, Brno, Czechia
- RECETOX, Masaryk University, Kotlářská 2, 61137, Brno, Czechia
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Oral Rabies Vaccine Strain SPBN GASGAS: Genetic Stability after Serial In Vitro and In Vivo Passaging. Viruses 2022; 14:v14102136. [PMID: 36298691 PMCID: PMC9609770 DOI: 10.3390/v14102136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/23/2022] [Accepted: 09/26/2022] [Indexed: 11/17/2022] Open
Abstract
Oral vaccination of wildlife has shown to be a very effective management tool in rabies control. Evaluation of the genetic stability of vaccine viruses before distributing vaccine baits in the environment is essential because all available oral rabies vaccines, including the genetically engineered rabies virus vaccine strain SPBN GASGAS (Rabitec), are based on replication-competent viruses. To evaluate the genetic stability of this vaccine strain, five serial passages of the Master Seed Virus (MSV) in the production cell line BHK21 Cl13 were performed. Furthermore, to test possible reversion to virulence, a back-passage study in suckling mouse brain (SMB) was performed. Subsequently, the pooled 5th SMB passage was inoculated intracerebrally (i.c.) in adult and suckling mice. The full genome sequences of the isolated 5th passage, in vivo and in vitro, were compared at both the consensus and the quasispecies level with the MSV. Additionally, the full genome sequence of the 6th SMB passage from the individual animals was determined and compared. Full-length integration of the double glycoprotein and modified base substitutions at amino acid position 194 and 333 of the glycoprotein could be verified in all 5th and 6th passage samples. Overall, 11 single nucleotide polymorphisms (SNPs) were detected in the 5th pooled SMB passage, 4 with frequency between 10 and 20%, and 7 with between 2.5 and 10%. SNPs that resulted in amino acid exchange were found in genes: N (one SNP), G (four SNPs), and L (three SNPs). However, none of these SNPs were associated with reversion to virulence since all adult mice inoculated i.c. with this material survived. In the individual samples of the 6th SMB passage 24 additional SNPs (>2.5%) were found, of which only 1 SNP (L-gene, position 6969) had a prevalence of >50% in 3 of 17 samples. The obtained results confirmed the stable expression of genetic modifications and the genetic stability of the consensus strain after serial in vivo and in vitro passaging.
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Klein A, Eggerbauer E, Potratz M, Zaeck LM, Calvelage S, Finke S, Müller T, Freuling CM. Comparative pathogenesis of different phylogroup I bat lyssaviruses in a standardized mouse model. PLoS Negl Trop Dis 2022; 16:e0009845. [PMID: 35041652 PMCID: PMC8797209 DOI: 10.1371/journal.pntd.0009845] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 01/28/2022] [Accepted: 12/14/2021] [Indexed: 12/24/2022] Open
Abstract
A plethora of bat-associated lyssaviruses potentially capable of causing the fatal disease rabies are known today. Transmitted via infectious saliva, occasionally-reported spillover infections from bats to other mammals demonstrate the permeability of the species-barrier and highlight the zoonotic potential of bat-related lyssaviruses. However, it is still unknown whether and, if so, to what extent, viruses from different lyssavirus species vary in their pathogenic potential. In order to characterize and systematically compare a broader group of lyssavirus isolates for their viral replication kinetics, pathogenicity, and virus release through saliva-associated virus shedding, we used a mouse infection model comprising a low (102 TCID50) and a high (105 TCID50) inoculation dose as well as three different inoculation routes (intramuscular, intranasal, intracranial). Clinical signs, incubation periods, and survival were investigated. Based on the latter two parameters, a novel pathogenicity matrix was introduced to classify lyssavirus isolates. Using a total of 13 isolates from ten different virus species, this pathogenicity index varied within and between virus species. Interestingly, Irkut virus (IRKV) and Bokeloh bat lyssavirus (BBLV) obtained higher pathogenicity scores (1.14 for IRKV and 1.06 for BBLV) compared to rabies virus (RABV) isolates ranging between 0.19 and 0.85. Also, clinical signs differed significantly between RABV and other bat lyssaviruses. Altogether, our findings suggest a high diversity among lyssavirus isolates concerning survival, incubation period, and clinical signs. Virus shedding significantly differed between RABVs and other lyssaviruses. Our results demonstrated that active shedding of infectious virus was exclusively associated with two RABV isolates (92% for RABV-DogA and 67% for RABV-Insectbat), thus providing a potential explanation as to why sustained spillovers are solely attributed to RABVs. Interestingly, 3D imaging of a selected panel of brain samples from bat-associated lyssaviruses demonstrated a significantly increased percentage of infected astrocytes in mice inoculated with IRKV (10.03%; SD±7.39) compared to RABV-Vampbat (2.23%; SD±2.4), and BBLV (0.78%; SD±1.51), while only individual infected cells were identified in mice infected with Duvenhage virus (DUVV). These results corroborate previous studies on RABV that suggest a role of astrocyte infection in the pathogenicity of lyssaviruses. Globally, there are at present 17 different officially recognized lyssavirus species posing a potential threat for human and animal health. Bats have been identified as carriers for the vast majority of those zoonotic viruses, which cause the fatal disease rabies and are transmitted through infectious saliva. The occurrence of sporadic spillover events where lyssaviruses are spread from bats to other mammalian species highlights the importance of studying pathogenicity and virus shedding in regard to a potentially sustained onward cross-species transmission. Therefore, as part of this study, we compared 13 different isolates from ten lyssavirus species in a standardized mouse infection model, focusing on clinical signs, incubation periods, and survival. Based on the latter two, a novel pathogenicity index to classify different lyssavirus species was established. This pathogenicity index varied within and between different lyssavirus species and revealed a higher ranking of other bat-related lyssaviruses in comparison to the tested Rabies virus (RABV) isolates. Altogether, our results demonstrate a high diversity among the investigated isolates concerning pathogenicity and clinical picture. Furthermore, we comparatively analyzed virus shedding via saliva and while there was no indication towards a reduced pathogenicity of bat-associated lyssaviruses as opposed to RABV, shedding was increased in RABV isolates. Additionally, we investigated neuronal cell tropism and revealed that bat lyssaviruses are not only capable of infecting neurons but also astrocytes.
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Affiliation(s)
- Antonia Klein
- Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Elisa Eggerbauer
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Madlin Potratz
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Luca M. Zaeck
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Sten Calvelage
- Institute of Diagnostic Virology, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institut (FLI), Greifswald-Insel Riems, Germany
| | - Stefan Finke
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Thomas Müller
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Conrad M. Freuling
- Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
- * E-mail:
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Regnault B, Evrard B, Plu I, Dacheux L, Troadec E, Cozette P, Chrétien D, Duchesne M, Jean-Michel V, Jamet A, Leruez M, Pérot P, Bourhy H, Eloit M, Seilhean D. First case of lethal encephalitis in Western Europe due to European bat lyssavirus type 1. Clin Infect Dis 2021; 74:461-466. [PMID: 33991184 DOI: 10.1093/cid/ciab443] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Inaccurate diagnosis of encephalitis is a major issue as immunosuppressive treatments can be deleterious in case of viral infection. The European bat lyssavirus type 1, a virus related to rabies virus, is endemic in European bats. No human case has yet been reported in Western Europe. A 59 year-old patient without specific past medical history died from encephalitis. A colony of bats lived in an outbuilding of his house. No diagnosis was made using standard procedures. METHODS We used a Next Generation Sequencing (NGS) based transcriptomic protocol to search for pathogens in autopsy samples (meninges and brain frontal lobe). Results were confirmed by PCR and by antibody testing in serum. Immunochemistry was used to characterize inflammatory cells and viral antigens in brain lesions. Cells and mice were inoculated with brain extracts for virus isolation. RESULTS The patient's brain lesions were severe and diffuse in white and gray matter. Perivascular inflammatory infiltrates were abundant and rich in plasma cells. NGS identified European bat lyssavirus type 1a in brain, which was confirmed by PCR. A high titer of neutralizing antibodies was found in serum. No viral antigen was detected and the virus could not be isolated by cell culture or by mouse inoculation. CONCLUSIONS The patient died from European bat lyssavirus type 1a infection. NGS was key to identifying this unexpected viral etiology in an epidemiological context that did not suggest rabies. People exposed to bats should be strongly advised to be vaccinated with rabies vaccines, which are effective against EBLV-1.
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Affiliation(s)
- Béatrice Regnault
- Pathogen Discovery Laboratory, Institut Pasteur, Paris, France.,The OIE Collaborating Center for the detection and identification in humans of emerging animal pathogens, Institut Pasteur, Paris, France)
| | - Bruno Evrard
- Medical-Surgical Intensive Care Unit, Dupuytren University Hospital, Limoges, France.,Inserm CIC 1435 and UMR 1092, Dupuytren Teaching Hospital, Limoges, France
| | - Isabelle Plu
- Sorbonne Université, Brain Institute (ICM; INSERM, UMRS 1127; CNRS, UMR 7225), Paris, France.,Département de Neuropathologie Raymond Escourolle, AP-HP-Sorbonne, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | - Laurent Dacheux
- Lyssavirus Epidemiology and Neuropathology Unit, National Reference Centre for Rabies, WHO Collaborative Centre for Reference and Research on Rabies, Institut Pasteur, Paris, France
| | - Eric Troadec
- Pathogen Discovery Laboratory, Institut Pasteur, Paris, France.,The OIE Collaborating Center for the detection and identification in humans of emerging animal pathogens, Institut Pasteur, Paris, France)
| | - Pascal Cozette
- Lyssavirus Epidemiology and Neuropathology Unit, National Reference Centre for Rabies, WHO Collaborative Centre for Reference and Research on Rabies, Institut Pasteur, Paris, France
| | - Delphine Chrétien
- Pathogen Discovery Laboratory, Institut Pasteur, Paris, France.,The OIE Collaborating Center for the detection and identification in humans of emerging animal pathogens, Institut Pasteur, Paris, France)
| | - Mathilde Duchesne
- Pathology Department, Dupuytren University Hospital, Limoges, France
| | | | - Anne Jamet
- Department of Clinical Microbiology, Necker Enfants-Malades Hospital, AP-HP, Centre Université de Paris, Paris, France
| | - Marianne Leruez
- Department of Clinical Microbiology, Necker Enfants-Malades Hospital, AP-HP, Centre Université de Paris, Paris, France
| | - Philippe Pérot
- Pathogen Discovery Laboratory, Institut Pasteur, Paris, France.,The OIE Collaborating Center for the detection and identification in humans of emerging animal pathogens, Institut Pasteur, Paris, France)
| | - Hervé Bourhy
- Lyssavirus Epidemiology and Neuropathology Unit, National Reference Centre for Rabies, WHO Collaborative Centre for Reference and Research on Rabies, Institut Pasteur, Paris, France
| | - Marc Eloit
- Pathogen Discovery Laboratory, Institut Pasteur, Paris, France.,The OIE Collaborating Center for the detection and identification in humans of emerging animal pathogens, Institut Pasteur, Paris, France).,Ecole Nationale Vétérinaire d'Alfort, Maisons-Alfort, France
| | - Danielle Seilhean
- Sorbonne Université, Brain Institute (ICM; INSERM, UMRS 1127; CNRS, UMR 7225), Paris, France.,Lyssavirus Epidemiology and Neuropathology Unit, National Reference Centre for Rabies, WHO Collaborative Centre for Reference and Research on Rabies, Institut Pasteur, Paris, France
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5
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Full-Genome Sequences and Phylogenetic Analysis of Archived Danish European Bat Lyssavirus 1 (EBLV-1) Emphasize a Higher Genetic Resolution and Spatial Segregation for Sublineage 1a. Viruses 2021; 13:v13040634. [PMID: 33917139 PMCID: PMC8067844 DOI: 10.3390/v13040634] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/25/2021] [Accepted: 04/01/2021] [Indexed: 11/16/2022] Open
Abstract
European bat lyssavirus type 1 (EBLV-1) is the causative agent for almost all reported rabies cases found in European bats. In recent years, increasing numbers of available EBLV-1 full genomes and their phylogenetic analyses helped to further elucidate the distribution and genetic characteristics of EBLV-1 and its two subtypes, namely EBLV-1a and EBLV-1b. Nonetheless, the absence of full-genome sequences from regions with known detections of EBLV-1 still limit the understanding of the phylogeographic relations between viruses from different European regions. In this study, a set of 21 archived Danish EBLV-1 samples from the years 1985 to 2009 was processed for the acquisition of full-genome sequences using a high-throughput sequencing approach. Subsequent phylogenetic analysis encompassing all available EBLV-1 full genomes from databases revealed the Danish sequences belong to the EBLV-1a subtype and further highlighted the distinct, close phylogenetic relationship of Danish, Dutch and German isolates in this region. In addition, the formation of five putative groups nearly exclusively formed by Danish isolates and the overall increased resolution of the EBLV-1a branch indicate a higher genetic diversity and spatial segregation for this sublineage than was previously known. These results emphasize the importance of phylogenetic analyses of full-genome sequences of lyssaviruses for genetic geography.
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AL-Eitan LN, Tarkhan AH, Alghamdi MA, Marston DA, Wu G, McElhinney LM, Brown IH, Fooks AR. Bat-Borne Coronaviruses in Jordan and Saudi Arabia: A Threat to Public Health? Viruses 2020; 12:E1413. [PMID: 33316899 PMCID: PMC7764733 DOI: 10.3390/v12121413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/30/2020] [Accepted: 12/03/2020] [Indexed: 11/22/2022] Open
Abstract
Emerging infectious diseases are of great concern to public health, as highlighted by the ongoing coronavirus disease 2019 (COVID-19) pandemic. Such diseases are of particular danger during mass gathering and mass influx events, as large crowds of people in close proximity to each other creates optimal opportunities for disease transmission. The Hashemite Kingdom of Jordan and the Kingdom of Saudi Arabia are two countries that have witnessed mass gatherings due to the arrival of Syrian refugees and the annual Hajj season. The mass migration of people not only brings exotic diseases to these regions but also brings new diseases back to their own countries, e.g., the outbreak of MERS in South Korea. Many emerging pathogens originate in bats, and more than 30 bat species have been identified in these two countries. Some of those bat species are known to carry viruses that cause deadly diseases in other parts of the world, such as the rabies virus and coronaviruses. However, little is known about bats and the pathogens they carry in Jordan and Saudi Arabia. Here, the importance of enhanced surveillance of bat-borne infections in Jordan and Saudi Arabia is emphasized, promoting the awareness of bat-borne diseases among the general public and building up infrastructure and capability to fill the gaps in public health preparedness to prevent future pandemics.
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Affiliation(s)
- Laith N. AL-Eitan
- Department of Biotechnology and Genetic Engineering, Jordan University of Science and Technology, Irbid 22110, Jordan;
| | - Amneh H. Tarkhan
- Department of Biotechnology and Genetic Engineering, Jordan University of Science and Technology, Irbid 22110, Jordan;
| | - Mansour A. Alghamdi
- Department of Anatomy, College of Medicine, King Khalid University, Abha 61421, Saudi Arabia;
- Genomics and Personalized Medicine Unit, College of Medicine, King Khalid University, Abha 61421, Saudi Arabia
| | - Denise A. Marston
- Department of Virology, Animal and Plant Health Agency (APHA, Weybridge), Surrey KT15 3NB, UK; (D.A.M.); (G.W.); (L.M.M.); (I.H.B.); (A.R.F.)
| | - Guanghui Wu
- Department of Virology, Animal and Plant Health Agency (APHA, Weybridge), Surrey KT15 3NB, UK; (D.A.M.); (G.W.); (L.M.M.); (I.H.B.); (A.R.F.)
| | - Lorraine M. McElhinney
- Department of Virology, Animal and Plant Health Agency (APHA, Weybridge), Surrey KT15 3NB, UK; (D.A.M.); (G.W.); (L.M.M.); (I.H.B.); (A.R.F.)
| | - Ian H. Brown
- Department of Virology, Animal and Plant Health Agency (APHA, Weybridge), Surrey KT15 3NB, UK; (D.A.M.); (G.W.); (L.M.M.); (I.H.B.); (A.R.F.)
| | - Anthony R. Fooks
- Department of Virology, Animal and Plant Health Agency (APHA, Weybridge), Surrey KT15 3NB, UK; (D.A.M.); (G.W.); (L.M.M.); (I.H.B.); (A.R.F.)
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Astrocyte Infection during Rabies Encephalitis Depends on the Virus Strain and Infection Route as Demonstrated by Novel Quantitative 3D Analysis of Cell Tropism. Cells 2020; 9:cells9020412. [PMID: 32053954 PMCID: PMC7072253 DOI: 10.3390/cells9020412] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/01/2020] [Accepted: 02/05/2020] [Indexed: 12/25/2022] Open
Abstract
Although conventional immunohistochemistry for neurotropic rabies virus (RABV) usually shows high preference for neurons, non-neuronal cells are also potential targets, and abortive astrocyte infection is considered a main trigger of innate immunity in the CNS. While in vitro studies indicated differences between field and less virulent lab-adapted RABVs, a systematic, quantitative comparison of astrocyte tropism in vivo is lacking. Here, solvent-based tissue clearing was used to measure RABV cell tropism in infected brains. Immunofluorescence analysis of 1 mm-thick tissue slices enabled 3D-segmentation and quantification of astrocyte and neuron infection frequencies. Comparison of three highly virulent field virus clones from fox, dog, and raccoon with three lab-adapted strains revealed remarkable differences in the ability to infect astrocytes in vivo. While all viruses and infection routes led to neuron infection frequencies between 7–19%, striking differences appeared for astrocytes. Whereas astrocyte infection by field viruses was detected independent of the inoculation route (8–27%), only one lab-adapted strain infected astrocytes route-dependently [0% after intramuscular (i.m.) and 13% after intracerebral (i.c.) inoculation]. Two lab-adapted vaccine viruses lacked astrocyte infection altogether (0%, i.c. and i.m.). This suggests a model in which the ability to establish productive astrocyte infection in vivo functionally distinguishes field and attenuated lab RABV strains.
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Pfaff F, Müller T, Freuling CM, Fehlner-Gardiner C, Nadin-Davis S, Robardet E, Cliquet F, Vuta V, Hostnik P, Mettenleiter TC, Beer M, Höper D. In-depth genome analyses of viruses from vaccine-derived rabies cases and corresponding live-attenuated oral rabies vaccines. Vaccine 2018; 37:4758-4765. [PMID: 29439868 DOI: 10.1016/j.vaccine.2018.01.083] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 01/19/2018] [Accepted: 01/28/2018] [Indexed: 01/23/2023]
Abstract
Live-attenuated rabies virus strains such as those derived from the field isolate Street Alabama Dufferin (SAD) have been used extensively and very effectively as oral rabies vaccines for the control of fox rabies in both Europe and Canada. Although these vaccines are safe, some cases of vaccine-derived rabies have been detected during rabies surveillance accompanying these campaigns. In recent analysis it was shown that some commercial SAD vaccines consist of diverse viral populations, rather than clonal genotypes. For cases of vaccine-derived rabies, only consensus sequence data have been available to date and information concerning their population diversity was thus lacking. In our study, we used high-throughput sequencing to analyze 11 cases of vaccine-derived rabies, and compared their viral population diversity to the related oral rabies vaccines using pairwise Manhattan distances. This extensive deep sequencing analysis of vaccine-derived rabies cases observed during oral vaccination programs provided deeper insights into the effect of accidental in vivo replication of genetically diverse vaccine strains in the central nervous system of target and non-target species under field conditions. The viral population in vaccine-derived cases appeared to be clonal in contrast to their parental vaccines. The change from a state of high population diversity present in the vaccine batches to a clonal genotype in the affected animal may indicate the presence of a strong bottleneck during infection. In conclusion, it is very likely that these few cases are the consequence of host factors and not the result of the selection of a more virulent genotype. Furthermore, this type of vaccine-derived rabies leads to the selection of clonal genotypes and the selected variants were genetically very similar to potent SAD vaccines that have undergone a history of in vitro selection.
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Affiliation(s)
- Florian Pfaff
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Germany.
| | - Thomas Müller
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Germany.
| | - Conrad M Freuling
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Germany.
| | - Christine Fehlner-Gardiner
- Centre of Expertise for Rabies, Ottawa Laboratory-Fallowfield, Canadian Food Inspection Agency, Ottawa, Canada.
| | - Susan Nadin-Davis
- Centre of Expertise for Rabies, Ottawa Laboratory-Fallowfield, Canadian Food Inspection Agency, Ottawa, Canada.
| | - Emmanuelle Robardet
- Nancy Laboratory for Rabies and Wildlife, French Agency for Food, Environmental and Occupational Health & Safety, Malzéville, France.
| | - Florence Cliquet
- Nancy Laboratory for Rabies and Wildlife, French Agency for Food, Environmental and Occupational Health & Safety, Malzéville, France.
| | - Vlad Vuta
- Institute for Diagnosis and Animal Health, University of Agronomic Study and Veterinary Medicine, Faculty of Veterinary Medicine, Bucharest, Romania.
| | - Peter Hostnik
- Virology Unit, Veterinary Faculty, Institute of Microbiology and Parasitology, University of Ljubljana, Ljubljana, Slovenia.
| | - Thomas C Mettenleiter
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Germany.
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Germany.
| | - Dirk Höper
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Germany.
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9
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Fischer S, Freuling CM, Müller T, Pfaff F, Bodenhofer U, Höper D, Fischer M, Marston DA, Fooks AR, Mettenleiter TC, Conraths FJ, Homeier-Bachmann T. Defining objective clusters for rabies virus sequences using affinity propagation clustering. PLoS Negl Trop Dis 2018; 12:e0006182. [PMID: 29357361 PMCID: PMC5794188 DOI: 10.1371/journal.pntd.0006182] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 02/01/2018] [Accepted: 12/19/2017] [Indexed: 11/18/2022] Open
Abstract
Rabies is caused by lyssaviruses, and is one of the oldest known zoonoses. In recent years, more than 21,000 nucleotide sequences of rabies viruses (RABV), from the prototype species rabies lyssavirus, have been deposited in public databases. Subsequent phylogenetic analyses in combination with metadata suggest geographic distributions of RABV. However, these analyses somewhat experience technical difficulties in defining verifiable criteria for cluster allocations in phylogenetic trees inviting for a more rational approach. Therefore, we applied a relatively new mathematical clustering algorythm named ‘affinity propagation clustering’ (AP) to propose a standardized sub-species classification utilizing full-genome RABV sequences. Because AP has the advantage that it is computationally fast and works for any meaningful measure of similarity between data samples, it has previously been applied successfully in bioinformatics, for analysis of microarray and gene expression data, however, cluster analysis of sequences is still in its infancy. Existing (516) and original (46) full genome RABV sequences were used to demonstrate the application of AP for RABV clustering. On a global scale, AP proposed four clusters, i.e. New World cluster, Arctic/Arctic-like, Cosmopolitan, and Asian as previously assigned by phylogenetic studies. By combining AP with established phylogenetic analyses, it is possible to resolve phylogenetic relationships between verifiably determined clusters and sequences. This workflow will be useful in confirming cluster distributions in a uniform transparent manner, not only for RABV, but also for other comparative sequence analyses. Rabies is one of the oldest known zoonoses, caused by lyssaviruses. In recent years, more than 21,000 nucleotide sequences for rabies viruses (RABV) have been deposited in public databases. In this study, a novel mathematical approach called affinity propagation (AP) clustering, a highly powerful tool, to verifiably divide full genome RABV sequences into genetic clusters, was used. A panel of existing and novel RABV full genome sequences was used to demonstrate the application of AP for RABV clustering. Using a combination of AP with established phylogenetic analyses is useful in resolving phylogenetic relationships between more objectively determined clusters and sequences. This workflow will help to substantiate a transparent cluster distribution, not only for RABV, but also for other comparative sequence analyses.
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Affiliation(s)
- Susanne Fischer
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Epidemiology, Greifswald-Insel Riems, Germany
| | - Conrad M. Freuling
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Molecular Virology and Cell Biology, OIE Reference Laboratory for Rabies, WHO Collaborating Centre for Rabies Surveillance and Research, Greifswald-Insel Riems, Germany
| | - Thomas Müller
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Molecular Virology and Cell Biology, OIE Reference Laboratory for Rabies, WHO Collaborating Centre for Rabies Surveillance and Research, Greifswald-Insel Riems, Germany
- * E-mail:
| | - Florian Pfaff
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Diagnostic Virology, Greifswald-Insel Riems, Germany
| | - Ulrich Bodenhofer
- Institute of Bioinformatics, Johannes Kepler University Linz, Linz, Austria
| | - Dirk Höper
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Molecular Virology and Cell Biology, OIE Reference Laboratory for Rabies, WHO Collaborating Centre for Rabies Surveillance and Research, Greifswald-Insel Riems, Germany
| | - Mareike Fischer
- Institute of Mathematics and Computer Science, University Greifswald, Greifswald, Germany
| | - Denise A. Marston
- Wildlife Zoonoses and Vector-Borne Diseases Research Group, Animal and Plant Health Agency (APHA), OIE Reference Laboratory for Rabies, WHO Collaborating Centre for Characterization of Lyssaviruses, Weybridge, United Kingdom
| | - Anthony R. Fooks
- Wildlife Zoonoses and Vector-Borne Diseases Research Group, Animal and Plant Health Agency (APHA), OIE Reference Laboratory for Rabies, WHO Collaborating Centre for Characterization of Lyssaviruses, Weybridge, United Kingdom
| | - Thomas C. Mettenleiter
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Molecular Virology and Cell Biology, OIE Reference Laboratory for Rabies, WHO Collaborating Centre for Rabies Surveillance and Research, Greifswald-Insel Riems, Germany
| | - Franz J. Conraths
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Epidemiology, Greifswald-Insel Riems, Germany
| | - Timo Homeier-Bachmann
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Epidemiology, Greifswald-Insel Riems, Germany
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10
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Teeling EC, Vernes SC, Dávalos LM, Ray DA, Gilbert MTP, Myers E. Bat Biology, Genomes, and the Bat1K Project: To Generate Chromosome-Level Genomes for All Living Bat Species. Annu Rev Anim Biosci 2017; 6:23-46. [PMID: 29166127 DOI: 10.1146/annurev-animal-022516-022811] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Bats are unique among mammals, possessing some of the rarest mammalian adaptations, including true self-powered flight, laryngeal echolocation, exceptional longevity, unique immunity, contracted genomes, and vocal learning. They provide key ecosystem services, pollinating tropical plants, dispersing seeds, and controlling insect pest populations, thus driving healthy ecosystems. They account for more than 20% of all living mammalian diversity, and their crown-group evolutionary history dates back to the Eocene. Despite their great numbers and diversity, many species are threatened and endangered. Here we announce Bat1K, an initiative to sequence the genomes of all living bat species (n∼1,300) to chromosome-level assembly. The Bat1K genome consortium unites bat biologists (>148 members as of writing), computational scientists, conservation organizations, genome technologists, and any interested individuals committed to a better understanding of the genetic and evolutionary mechanisms that underlie the unique adaptations of bats. Our aim is to catalog the unique genetic diversity present in all living bats to better understand the molecular basis of their unique adaptations; uncover their evolutionary history; link genotype with phenotype; and ultimately better understand, promote, and conserve bats. Here we review the unique adaptations of bats and highlight how chromosome-level genome assemblies can uncover the molecular basis of these traits. We present a novel sequencing and assembly strategy and review the striking societal and scientific benefits that will result from the Bat1K initiative.
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Affiliation(s)
- Emma C Teeling
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland;
| | - Sonja C Vernes
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, 6500 AH, The Netherlands.,Donders Centre for Cognitive Neuroimaging, Nijmegen, 6525 EN, The Netherlands
| | - Liliana M Dávalos
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794-5245, USA
| | - David A Ray
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas 79409, USA
| | - M Thomas P Gilbert
- Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark.,University Museum, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Eugene Myers
- Max Planck Institute for Molecular Cell Biology and Genetics, 01307 Dresden, Germany
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- *Full list of Bat1K Consortium members in Supplemental Appendix
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11
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Troupin C, Picard-Meyer E, Dellicour S, Casademont I, Kergoat L, Lepelletier A, Dacheux L, Baele G, Monchâtre-Leroy E, Cliquet F, Lemey P, Bourhy H. Host Genetic Variation Does Not Determine Spatio-Temporal Patterns of European Bat 1 Lyssavirus. Genome Biol Evol 2017; 9:3202-3213. [PMID: 29165566 PMCID: PMC5721339 DOI: 10.1093/gbe/evx236] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/17/2017] [Indexed: 12/22/2022] Open
Abstract
The majority of bat rabies cases in Europe are attributed to European bat 1 lyssavirus (EBLV-1), circulating mainly in serotine bats (Eptesicus serotinus). Two subtypes have been defined (EBLV-1a and EBLV-1b), each associated with a different geographical distribution. In this study, we undertake a comprehensive sequence analysis based on 80 newly obtained EBLV-1 nearly complete genome sequences from nine European countries over a 45-year period to infer selection pressures, rates of nucleotide substitution, and evolutionary time scale of these two subtypes in Europe. Our results suggest that the current lineage of EBLV-1 arose in Europe ∼600 years ago and the virus has evolved at an estimated average substitution rate of ∼4.19×10-5 subs/site/year, which is among the lowest recorded for RNA viruses. In parallel, we investigate the genetic structure of French serotine bats at both the nuclear and mitochondrial level and find that they constitute a single genetic cluster. Furthermore, Mantel tests based on interindividual distances reveal the absence of correlation between genetic distances estimated between viruses and between host individuals. Taken together, this indicates that the genetic diversity observed in our E. serotinus samples does not account for EBLV-1a and -1b segregation and dispersal in Europe.
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Affiliation(s)
- Cécile Troupin
- Institut Pasteur, Unit Lyssavirus Dynamics and Host Adaptation, WHO Collaborating Centre for Reference and Research on Rabies, Paris, France
| | - Evelyne Picard-Meyer
- Laboratory for Rabies and Wildlife ANSES, Nancy, OIE Reference Laboratory for Rabies, European Union Reference Laboratory for Rabies, European Union Reference Laboratory for Rabies Serology, WHO Collaborating Centre for Research and Management on Zoonoses, Malzeville, France
| | - Simon Dellicour
- Institut Pasteur, Laboratory for Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute, KU Leuven – University of Leuven, Belgium
| | - Isabelle Casademont
- Unité de la Génétique Fonctionnelle des Maladies Infectieuses, Paris, France
| | - Lauriane Kergoat
- Institut Pasteur, Unit Lyssavirus Dynamics and Host Adaptation, WHO Collaborating Centre for Reference and Research on Rabies, Paris, France
| | - Anthony Lepelletier
- Institut Pasteur, Unit Lyssavirus Dynamics and Host Adaptation, WHO Collaborating Centre for Reference and Research on Rabies, Paris, France
| | - Laurent Dacheux
- Institut Pasteur, Unit Lyssavirus Dynamics and Host Adaptation, WHO Collaborating Centre for Reference and Research on Rabies, Paris, France
| | - Guy Baele
- Institut Pasteur, Laboratory for Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute, KU Leuven – University of Leuven, Belgium
| | - Elodie Monchâtre-Leroy
- Laboratory for Rabies and Wildlife ANSES, Nancy, OIE Reference Laboratory for Rabies, European Union Reference Laboratory for Rabies, European Union Reference Laboratory for Rabies Serology, WHO Collaborating Centre for Research and Management on Zoonoses, Malzeville, France
| | - Florence Cliquet
- Laboratory for Rabies and Wildlife ANSES, Nancy, OIE Reference Laboratory for Rabies, European Union Reference Laboratory for Rabies, European Union Reference Laboratory for Rabies Serology, WHO Collaborating Centre for Research and Management on Zoonoses, Malzeville, France
| | - Philippe Lemey
- Institut Pasteur, Laboratory for Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute, KU Leuven – University of Leuven, Belgium
| | - Hervé Bourhy
- Institut Pasteur, Unit Lyssavirus Dynamics and Host Adaptation, WHO Collaborating Centre for Reference and Research on Rabies, Paris, France
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