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Thiaucourt F, Exbrayat A, Loire E, Boissière A, Nwankpa N, Manso-Silván L. Deep sequencing and variant frequency analysis for the quality control of a live bacterial vaccine against contagious bovine pleuropneumonia, strain T1. Vaccine 2024; 42:1868-1872. [PMID: 38365481 DOI: 10.1016/j.vaccine.2024.02.031] [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: 12/08/2023] [Revised: 02/02/2024] [Accepted: 02/08/2024] [Indexed: 02/18/2024]
Abstract
Vaccination is the most cost-effective tool to control contagious bovine pleuropneumonia. The vaccines currently used in Africa are derived from a live strain called T1, which was attenuated by passage in embryonated eggs and broth culture. The number of passages is directly correlated to the degree of attenuation of the vaccinal strains and inversely correlated to their immunogenicity in cattle. Current quality control protocols applied to vaccine batches allow the assessment of identity, purity, and titers, but cannot assess the level of genetic drift form the parental vaccine strains. Deep sequencing was used to assess the genetic drift generated over controlled in vitro passages of the parental strain, as well as on commercial vaccine batches. Signatures of cloning procedures were detected in some batches, which imply a deviation from the standard production protocol. Deep sequencing is proposed as a new tool for the identity and stability control of T1 vaccines.
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Affiliation(s)
- François Thiaucourt
- CIRAD, UMR ASTRE, F-34398 Montpellier, France; ASTRE, Univ Montpellier, CIRAD, INRAE, F-34398 Montpellier, France
| | - Antoni Exbrayat
- CIRAD, UMR ASTRE, F-34398 Montpellier, France; ASTRE, Univ Montpellier, CIRAD, INRAE, F-34398 Montpellier, France.
| | - Etienne Loire
- CIRAD, UMR ASTRE, F-34398 Montpellier, France; ASTRE, Univ Montpellier, CIRAD, INRAE, F-34398 Montpellier, France.
| | - Anne Boissière
- CIRAD, UMR ASTRE, F-34398 Montpellier, France; ASTRE, Univ Montpellier, CIRAD, INRAE, F-34398 Montpellier, France.
| | - Nick Nwankpa
- Pan-African Veterinary Vaccine Centre of the African Union (AU -PANVAC), PO Box 1746, Bishoftu, Ethiopia
| | - Lucía Manso-Silván
- CIRAD, UMR ASTRE, F-34398 Montpellier, France; ASTRE, Univ Montpellier, CIRAD, INRAE, F-34398 Montpellier, France.
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2
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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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3
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Vázquez R, Díez-Martínez R, Domingo-Calap P, García P, Gutiérrez D, Muniesa M, Ruiz-Ruigómez M, Sanjuán R, Tomás M, Tormo-Mas MÁ, García P. Essential Topics for the Regulatory Consideration of Phages as Clinically Valuable Therapeutic Agents: A Perspective from Spain. Microorganisms 2022; 10:microorganisms10040717. [PMID: 35456768 PMCID: PMC9025261 DOI: 10.3390/microorganisms10040717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/22/2022] [Accepted: 03/24/2022] [Indexed: 01/08/2023] Open
Abstract
Antibiotic resistance is one of the major challenges that humankind shall face in the short term. (Bacterio)phage therapy is a valuable therapeutic alternative to antibiotics and, although the concept is almost as old as the discovery of phages, its wide application was hindered in the West by the discovery and development of antibiotics in the mid-twentieth century. However, research on phage therapy is currently experiencing a renaissance due to the antimicrobial resistance problem. Some countries are already adopting new ad hoc regulations to favor the short-term implantation of phage therapy in clinical practice. In this regard, the Phage Therapy Work Group from FAGOMA (Spanish Network of Bacteriophages and Transducing Elements) recently contacted the Spanish Drugs and Medical Devices Agency (AEMPS) to promote the regulation of phage therapy in Spain. As a result, FAGOMA was asked to provide a general view on key issues regarding phage therapy legislation. This review comes as the culmination of the FAGOMA initiative and aims at appropriately informing the regulatory debate on phage therapy.
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Affiliation(s)
- Roberto Vázquez
- Department of Biotechnology, Ghent University, 9000 Ghent, Belgium;
| | | | - Pilar Domingo-Calap
- Institute for Integrative Systems Biology, University of Valencia-CSIC, 46980 Paterna, Spain; (P.D.-C.); (R.S.)
| | - Pedro García
- Center for Biological Research Margarita Salas (CIB-CSIC) and Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), 28040 Madrid, Spain;
| | - Diana Gutiérrez
- Telum Therapeutics SL, 31110 Noáin, Spain; (R.D.-M.); (D.G.)
| | - Maite Muniesa
- Department of Genetics, Microbiology and Statistics, University of Barcelona, 08028 Barcelona, Spain;
| | - María Ruiz-Ruigómez
- Internal Medicine, Infectious Diseases Unit, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain;
| | - Rafael Sanjuán
- Institute for Integrative Systems Biology, University of Valencia-CSIC, 46980 Paterna, Spain; (P.D.-C.); (R.S.)
| | - María Tomás
- Department of Microbiology, Hospital Universitario de A Coruña (INIBIC-CHUAC, SERGAS), 15006 A Coruña, Spain;
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) on behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), 28003 Madrid, Spain
- Spanish Network for Research in Infectious Diseases (REIPI), 41071 Sevilla, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - María Ángeles Tormo-Mas
- Severe Infection Group, Hospital Universitari i Politècnic La Fe, Health Research Institute Hospital La Fe, IISLaFe, 46026 Valencia, Spain;
| | - Pilar García
- Dairy Research Institute of Asturias, IPLA-CSIC, 33300 Villaviciosa, Spain
- DairySafe Group, Health Research Institute of Asturias (ISPA), 33011 Oviedo, Spain
- Correspondence:
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Suminda GGD, Bhandari S, Won Y, Goutam U, Kanth Pulicherla K, Son YO, Ghosh M. High-throughput sequencing technologies in the detection of livestock pathogens, diagnosis, and zoonotic surveillance. Comput Struct Biotechnol J 2022; 20:5378-5392. [PMID: 36212529 PMCID: PMC9526013 DOI: 10.1016/j.csbj.2022.09.028] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 12/03/2022] Open
Abstract
Increasing globalization, agricultural intensification, urbanization, and climatic changes have resulted in a significant recent increase in emerging infectious zoonotic diseases. Zoonotic diseases are becoming more common, so innovative, effective, and integrative research is required to better understand their transmission, ecological implications, and dynamics at wildlife-human interfaces. High-throughput sequencing (HTS) methodologies have enormous potential for unraveling these contingencies and improving our understanding, but they are only now beginning to be realized in livestock research. This study investigates the current state of use of sequencing technologies in the detection of livestock pathogens such as bovine, dogs (Canis lupus familiaris), sheep (Ovis aries), pigs (Sus scrofa), horses (Equus caballus), chicken (Gallus gallus domesticus), and ducks (Anatidae) as well as how it can improve the monitoring and detection of zoonotic infections. We also described several high-throughput sequencing approaches for improved detection of known, unknown, and emerging infectious agents, resulting in better infectious disease diagnosis, as well as surveillance of zoonotic infectious diseases. In the coming years, the continued advancement of sequencing technologies will improve livestock research and hasten the development of various new genomic and technological studies on farm animals.
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Vos A, Nokireki T, Isomursu M, Gadd T, Kovacs F. Oral vaccination of foxes and raccoon dogs against rabies with the 3rd generation oral rabies virus vaccine, SPBN GASGAS, in Finland. Acta Vet Scand 2021; 63:40. [PMID: 34645487 PMCID: PMC8513320 DOI: 10.1186/s13028-021-00605-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/28/2021] [Indexed: 12/04/2022] Open
Abstract
Background To prevent re-emergence of wildlife-mediated rabies in Finland, oral rabies vaccine baits are distributed every year during autumn in southern Finland in a vaccination zone bordering Russia. Recently, Finland introduced a 3rd generation oral rabies virus vaccine bait. By analysing bait uptake and seroconversion in red foxes and raccoon dogs, the field efficacy of this new vaccine strain, SPBN GASGAS, was compared with the originally used highly efficacious 1st generation vaccine SAD B19. Results Overall, 74.6% and 53.9% of the animals submitted from the vaccination area after the campaigns (2017–2019) tested positive for the presence of the bait marker and anti-rabiesvirus antibodies, respectively. No significant difference was observed between years, species and vaccine. Conclusions The field performance of the highly attenuated 3rd generation oral rabies vaccine, SPBN GASGAS, in terms of bait uptake and seroconversion was similar to the 1st generation vaccine, SAD B19, and therefore offers a suitable alternative.
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BMT: Bioinformatics mini toolbox for comprehensive DNA and protein analysis. Genomics 2020; 112:4561-4566. [PMID: 32791200 DOI: 10.1016/j.ygeno.2020.08.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/01/2020] [Accepted: 08/07/2020] [Indexed: 01/05/2023]
Abstract
Background Bioinformatics tools are of great significance and are used in different spheres of life sciences. There are wide variety of tools available to perform primary analysis of DNA and protein but most of them are available on different platforms and many remain undetected. Accessing these tools separately to perform individual task is uneconomical and inefficient. Objective Our aim is to bring different bioinformatics models on a single platform to ameliorate scientific research. Hence, our objective is to make a tool for comprehensive DNA and protein analysis. Methods To develop a reliable, straight-forward and standalone desktop application we used state of the art python packages and libraries. Bioinformatics Mini Toolbox (BMT) is combination of seven tools including FastqTrimmer, Gene Prediction, DNA Analysis, Translation, Protein analysis and Pairwise and Multiple alignment. Results FastqTrimmer assists in quality assurance of NGS data. Gene prediction predicts the genes by homology from novel genome on the basis of reference sequence. Protein analysis and DNA analysis calculates physiochemical properties of nucleotide and protein sequences, respectively. Translation translates the DNA sequence into six open reading frames. Pairwise alignment performs pairwise global and local alignment of DNA and protein sequences on the basis or multiple matrices. Multiple alignment aligns multiple sequences and generates a phylogenetic tree. Conclusion We developed a tool for comprehensive DNA and protein analysis. The link to download BMT is https://github.com/nasiriqbal012/BMT_SETUP.git.
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Stromberg ZR, Fischer W, Bradfute SB, Kubicek-Sutherland JZ, Hraber P. Vaccine Advances against Venezuelan, Eastern, and Western Equine Encephalitis Viruses. Vaccines (Basel) 2020; 8:vaccines8020273. [PMID: 32503232 PMCID: PMC7350001 DOI: 10.3390/vaccines8020273] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 05/29/2020] [Accepted: 05/31/2020] [Indexed: 01/21/2023] Open
Abstract
Vaccinations are a crucial intervention in combating infectious diseases. The three neurotropic Alphaviruses, Eastern (EEEV), Venezuelan (VEEV), and Western (WEEV) equine encephalitis viruses, are pathogens of interest for animal health, public health, and biological defense. In both equines and humans, these viruses can cause febrile illness that may progress to encephalitis. Currently, there are no licensed treatments or vaccines available for these viruses in humans. Experimental vaccines have shown variable efficacy and may cause severe adverse effects. Here, we outline recent strategies used to generate vaccines against EEEV, VEEV, and WEEV with an emphasis on virus-vectored and plasmid DNA delivery. Despite candidate vaccines protecting against one of the three viruses, few studies have demonstrated an effective trivalent vaccine. We evaluated the potential of published vaccines to generate cross-reactive protective responses by comparing DNA vaccine sequences to a set of EEEV, VEEV, and WEEV genomes and determining the vaccine coverages of potential epitopes. Finally, we discuss future directions in the development of vaccines to combat EEEV, VEEV, and WEEV.
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Affiliation(s)
- Zachary R. Stromberg
- Physical Chemistry and Applied Spectroscopy, Chemistry Division, Los Alamos National Laboratory, Los Alamos, NM 505, USA; (Z.R.S.); (J.Z.K.-S.)
| | - Will Fischer
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 505, USA;
| | - Steven B. Bradfute
- Center for Global Health, Division of Infectious Diseases, Department of Internal Medicine, University of New Mexico, Albuquerque, NM 505, USA;
| | - Jessica Z. Kubicek-Sutherland
- Physical Chemistry and Applied Spectroscopy, Chemistry Division, Los Alamos National Laboratory, Los Alamos, NM 505, USA; (Z.R.S.); (J.Z.K.-S.)
| | - Peter Hraber
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 505, USA;
- Correspondence:
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8
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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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9
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Calvelage S, Smreczak M, Orłowska A, Freuling CM, Müller T, Fehlner-Gardiner C, Nadin-Davis S, Höper D, Trębas P. Population- and Variant-Based Genome Analyses of Viruses from Vaccine-Derived Rabies Cases Demonstrate Product Specific Clusters and Unique Patterns. Viruses 2020; 12:v12010115. [PMID: 31963517 PMCID: PMC7020022 DOI: 10.3390/v12010115] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/10/2020] [Accepted: 01/13/2020] [Indexed: 12/24/2022] Open
Abstract
Rabies in wildlife has been successfully controlled in parts of Europe and North America using oral rabies vaccination, i.e., the distribution of baits containing live-attenuated virus strains. Occasionally, these vaccines caused vaccine virus-induced rabies cases. To elucidate the mechanisms of genetic selection and the effect of viral populations on these rabies cases, a next generation sequencing approach as well as comprehensive data analyses of the genetic diversity of Street Alabama Dufferin (SAD) and ERA vaccine virus strains and vaccine-induced rabies cases from Canada and several European countries were conducted. As a result, twelve newly generated sets of sequencing data from Canada and Poland were added to a pool of previously investigated samples. While the population-based analysis showed a segregation of viruses of ERA vaccine-induced rabies cases from those of SAD Bern original (SAD Bernorig)-derived rabies cases, the in-depth variant analysis revealed three distinct combinations of selected variants for the ERA vaccine-induced cases, suggesting the presence of multiple replication-competent haplotypes in the investigated ERA-BHK21 vaccine. Our findings demonstrate the potential of a deep sequencing approach in combination with comprehensive analyses on the consensus, population, and variant level.
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Affiliation(s)
- Sten Calvelage
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany; (S.C.); (D.H.)
| | - Marcin Smreczak
- Department of Virology, National Veterinary Research Institute, 24-100 Puławy, Poland; (M.S.); (A.O.); (P.T.)
| | - Anna Orłowska
- Department of Virology, National Veterinary Research Institute, 24-100 Puławy, Poland; (M.S.); (A.O.); (P.T.)
| | - Conrad Martin Freuling
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, WHO Collaborating Centre for Rabies Surveillance and Research, OIE Reference Laboratory for Rabies, 17493 Greifswald-Insel Riems, Germany;
- Correspondence:
| | - Thomas Müller
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, WHO Collaborating Centre for Rabies Surveillance and Research, OIE Reference Laboratory for Rabies, 17493 Greifswald-Insel Riems, Germany;
| | - Christine Fehlner-Gardiner
- National Reference Centre for Rabies, Ottawa Laboratory–Fallowfield, Canadian Food Inspection Agency, Ottawa, ON K2H 8P91, Canada; (C.F.-G.); (S.N.-D.)
| | - Susan Nadin-Davis
- National Reference Centre for Rabies, Ottawa Laboratory–Fallowfield, Canadian Food Inspection Agency, Ottawa, ON K2H 8P91, Canada; (C.F.-G.); (S.N.-D.)
| | - Dirk Höper
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany; (S.C.); (D.H.)
| | - Paweł Trębas
- Department of Virology, National Veterinary Research Institute, 24-100 Puławy, Poland; (M.S.); (A.O.); (P.T.)
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Mutti M, Corsini L. Robust Approaches for the Production of Active Ingredient and Drug Product for Human Phage Therapy. Front Microbiol 2019; 10:2289. [PMID: 31649636 PMCID: PMC6791927 DOI: 10.3389/fmicb.2019.02289] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 09/19/2019] [Indexed: 01/17/2023] Open
Abstract
To be successful, academic and commercial efforts to reintroduce phage therapy must ensure that only safe and efficacious products are used to treat patients. This raises a number of manufacturing, formulation, and delivery challenges. Since phages are biologics, robust manufacturing processes will be crucial to avoid unwanted variability in each step of the process. The quality standards themselves need to be developed, as patients are currently being treated with phages produced under quality standards ranging from cGMP for clinical trials in EMA and FDA regulated environments to no standards at all in some last resort treatments. In this short review, we will systematically review the literature covering technical issues and approaches to increase robustness at every step of the production process: the identity of the phage and bacterial production strains, the fermentation process and purification, the formulation of the drug product, the quality controls and the documentation standards themselves. We conclude that it is possible to control cost at the same time, which is critical to re-introduce phage therapy to western medicine.
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Forth JH, Forth LF, King J, Groza O, Hübner A, Olesen AS, Höper D, Dixon LK, Netherton CL, Rasmussen TB, Blome S, Pohlmann A, Beer M. A Deep-Sequencing Workflow for the Fast and Efficient Generation of High-Quality African Swine Fever Virus Whole-Genome Sequences. Viruses 2019; 11:v11090846. [PMID: 31514438 PMCID: PMC6783980 DOI: 10.3390/v11090846] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 09/05/2019] [Accepted: 09/09/2019] [Indexed: 12/14/2022] Open
Abstract
African swine fever (ASF) is a severe disease of suids caused by African swine fever virus (ASFV). Its dsDNA genome (170-194 kbp) is scattered with homopolymers and repeats as well as inverted-terminal-repeats (ITR), which hamper whole-genome sequencing. To date, only a few genome sequences have been published and only for some are data on sequence quality available enabling in-depth investigations. Especially in Europe and Asia, where ASFV has continuously spread since its introduction into Georgia in 2007, a very low genetic variability of the circulating ASFV-strains was reported. Therefore, only whole-genome sequences can serve as a basis for detailed virus comparisons. Here, we report an effective workflow, combining target enrichment, Illumina and Nanopore sequencing for ASFV whole-genome sequencing. Following this approach, we generated an improved high-quality ASFV Georgia 2007/1 whole-genome sequence leading to the correction of 71 sequencing errors and the addition of 956 and 231 bp at the respective ITRs. This genome, derived from the primary outbreak in 2007, can now serve as a reference for future whole-genome analyses of related ASFV strains and molecular approaches. Using both workflow and the reference genome, we generated the first ASFV-whole-genome sequence from Moldova, expanding the sequence knowledge from Eastern Europe.
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Affiliation(s)
- Jan H Forth
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald - Insel Riems, Germany.
| | - Leonie F Forth
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald - Insel Riems, Germany.
| | - Jacqueline King
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald - Insel Riems, Germany.
| | - Oxana Groza
- Animal Health Diagnostic Laboratory, Republican Center for Veterinary Diagnostic, str. Murelor, 3, MD-2051, mun. Chișinău, Moldova.
| | - Alexandra Hübner
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald - Insel Riems, Germany.
| | - Ann Sofie Olesen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, DK-1870 Frederiksberg C, Denmark.
| | - Dirk Höper
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald - Insel Riems, Germany.
| | - Linda K Dixon
- The Pirbright Institute, Ash Road, Pirbright, Woking, GU24 0NF, UK.
| | | | - Thomas Bruun Rasmussen
- DTU National Veterinary Institute, Technical University of Denmark, Lindholm, DK-4771 Kalvehave, Denmark.
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, DK-2300 Copenhagen S, Denmark.
| | - Sandra Blome
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald - Insel Riems, Germany.
| | - Anne Pohlmann
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald - Insel Riems, Germany.
| | - Martin Beer
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald - Insel Riems, Germany.
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12
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Freuling CM, Kamp VT, Klein A, Günther M, Zaeck L, Potratz M, Eggerbauer E, Bobe K, Kaiser C, Kretzschmar A, Ortmann S, Schuster P, Vos A, Finke S, Müller T. Long-Term Immunogenicity and Efficacy of the Oral Rabies Virus Vaccine Strain SPBN GASGAS in Foxes. Viruses 2019; 11:v11090790. [PMID: 31461981 PMCID: PMC6784248 DOI: 10.3390/v11090790] [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: 08/12/2019] [Revised: 08/23/2019] [Accepted: 08/26/2019] [Indexed: 12/24/2022] Open
Abstract
To evaluate the long-term immunogenicity of the live-attenuated, oral rabies vaccine SPBN GASGAS in a full good clinical practice (GCP) compliant study, forty-six (46) healthy, seronegative red foxes (Vulpes vulpes) were allocated to two treatment groups: group 1 (n = 31) received a vaccine bait containing 1.7 ml of the vaccine of minimum potency (106.6 FFU/mL) and group 2 (n = 15) received a placebo-bait. In total, 29 animals of group 1 and 14 animals of group 2 were challenged at 12 months post-vaccination with a fox rabies virus isolate (103.0 MICLD50/mL). While 90% of the animals offered a vaccine bait resisted the challenge, only one animal (7%) of the controls survived. All animals that had seroconverted following vaccination survived the challenge infection at 12 months post-vaccination. Rabies specific antibodies could be detected as early as 14 days post-vaccination. Based on the kinetics of the antibody response to SPBN GASGAS as measured in ELISA and RFFIT, the animals maintained stable antibody titres during the 12-month pre-challenge observation period at a high level. The results indicate that successful vaccination using the oral route with this new rabies virus vaccine strain confers long-term duration of immunity beyond one year, meeting the same requirements as for licensure as laid down by the European Pharmacopoeia.
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Affiliation(s)
- Conrad M Freuling
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut (FLI), WHO Collaborating Centre for Rabies Surveillance and Research, OIE Reference Laboratory for Rabies, 17493 Greifswald-Insel Riems, Germany.
| | - Verena Te Kamp
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut (FLI), WHO Collaborating Centre for Rabies Surveillance and Research, OIE Reference Laboratory for Rabies, 17493 Greifswald-Insel Riems, Germany
| | - Antonia Klein
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut (FLI), WHO Collaborating Centre for Rabies Surveillance and Research, OIE Reference Laboratory for Rabies, 17493 Greifswald-Insel Riems, Germany
| | - Maria Günther
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut (FLI), WHO Collaborating Centre for Rabies Surveillance and Research, OIE Reference Laboratory for Rabies, 17493 Greifswald-Insel Riems, Germany
| | - Luca Zaeck
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut (FLI), WHO Collaborating Centre for Rabies Surveillance and Research, OIE Reference Laboratory for Rabies, 17493 Greifswald-Insel Riems, Germany
| | - Madlin Potratz
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut (FLI), WHO Collaborating Centre for Rabies Surveillance and Research, OIE Reference Laboratory for Rabies, 17493 Greifswald-Insel Riems, Germany
| | - Elisa Eggerbauer
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut (FLI), WHO Collaborating Centre for Rabies Surveillance and Research, OIE Reference Laboratory for Rabies, 17493 Greifswald-Insel Riems, Germany
| | | | | | | | | | | | - Adriaan Vos
- IDT Biologika GmbH, 06861 Dessau-Rosslau, Germany
| | - Stefan Finke
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut (FLI), WHO Collaborating Centre for Rabies Surveillance and Research, OIE Reference Laboratory for Rabies, 17493 Greifswald-Insel Riems, Germany
| | - Thomas Müller
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut (FLI), WHO Collaborating Centre for Rabies Surveillance and Research, OIE Reference Laboratory for Rabies, 17493 Greifswald-Insel Riems, Germany
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13
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Eloiflin RJ, Boyer M, Kwiatek O, Guendouz S, Loire E, Servan de Almeida R, Libeau G, Bataille A. Evolution of Attenuation and Risk of Reversal in Peste des Petits Ruminants Vaccine Strain Nigeria 75/1. Viruses 2019; 11:E724. [PMID: 31394790 PMCID: PMC6724400 DOI: 10.3390/v11080724] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 08/03/2019] [Accepted: 08/03/2019] [Indexed: 12/11/2022] Open
Abstract
Peste des Petits Ruminants (PPR) is a highly infectious disease caused by a virus of the Morbillivirus genus. The current PPR eradication effort relies mainly on the implementation of massive vaccination campaigns. One of the most widely used PPR vaccines is the Nigeria 75/1 strain obtained after attenuation by 75 serial passages of the wild type isolate in cell cultures. Here we use high throughput deep sequencing of the historical passages that led to the Nigeria 75/1 attenuated strain to understand the evolution of PPRV attenuation and to assess the risk of reversal in different cell types. Comparison of the consensus sequences of the wild type and vaccine strains showed that only 18 fixed mutations separate the two strains. At the earliest attenuation passage at our disposal (passage 47), 12 out of the 18 mutations were already present at a frequency of 100%. Low-frequency variants were identified along the genome in all passages. Sequencing of passages after the vaccine strain showed evidence of genetic drift during cell passages, especially in cells expressing the SLAM receptor targeted by PPRV. However, 15 out of the 18 mutations related to attenuation remained fixed in the population. In vitro experiments suggest that one mutation in the leader region of the PPRV genome affects virus replication. Our results suggest that only a few mutations can have a serious impact on the pathogenicity of PPRV. Risk of reversion to virulence of the attenuated PPRV strain Nigeria 75/1 during serial passages in cell cultures seems low but limiting the number of passages during vaccine production is recommended.
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Affiliation(s)
- Roger-Junior Eloiflin
- CIRAD, UMR ASTRE, F-34398 Montpellier, France
- ASTRE, Univ Montpellier, CIRAD, INRA, Montpellier, France
| | - Marie Boyer
- ASTRE, Univ Montpellier, CIRAD, INRA, Montpellier, France
| | - Olivier Kwiatek
- CIRAD, UMR ASTRE, F-34398 Montpellier, France
- ASTRE, Univ Montpellier, CIRAD, INRA, Montpellier, France
| | - Samia Guendouz
- CIRAD, UMR ASTRE, F-34398 Montpellier, France
- ASTRE, Univ Montpellier, CIRAD, INRA, Montpellier, France
| | - Etienne Loire
- CIRAD, UMR ASTRE, F-34398 Montpellier, France
- ASTRE, Univ Montpellier, CIRAD, INRA, Montpellier, France
| | - Renata Servan de Almeida
- CIRAD, UMR ASTRE, F-34398 Montpellier, France
- ASTRE, Univ Montpellier, CIRAD, INRA, Montpellier, France
| | - Geneviève Libeau
- CIRAD, UMR ASTRE, F-34398 Montpellier, France
- ASTRE, Univ Montpellier, CIRAD, INRA, Montpellier, France
| | - Arnaud Bataille
- CIRAD, UMR ASTRE, F-34398 Montpellier, France.
- ASTRE, Univ Montpellier, CIRAD, INRA, Montpellier, France.
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14
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Comparison of intra- and inter-host genetic diversity in rabies virus during experimental cross-species transmission. PLoS Pathog 2019; 15:e1007799. [PMID: 31220188 PMCID: PMC6615636 DOI: 10.1371/journal.ppat.1007799] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 07/09/2019] [Accepted: 04/29/2019] [Indexed: 12/25/2022] Open
Abstract
The development of high-throughput genome sequencing enables accurate measurements of levels of sub-consensus intra-host virus genetic diversity and analysis of the role played by natural selection during cross-species transmission. We analysed the natural and experimental evolution of rabies virus (RABV), an important example of a virus that is able to make multiple host jumps. In particular, we (i) analyzed RABV evolution during experimental host switching with the goal of identifying possible genetic markers of host adaptation, (ii) compared the mutational changes observed during passage with those observed in natura, and (iii) determined whether the colonization of new hosts or tissues requires adaptive evolution in the virus. To address these aims, animal infection models (dog and fox) and primary cell culture models (embryo brain cells of dog and fox) were developed and viral variation was studied in detail through deep genome sequencing. Our analysis revealed a strong unidirectional host evolutionary effect, as dog-adapted rabies virus was able to replicate in fox and fox cells relatively easily, while dogs or neuronal dog cells were not easily susceptible to fox adapted-RABV. This suggests that dog RABV may be able to adapt to some hosts more easily than other host variants, or that when RABV switched from dogs to red foxes it lost its ability to adapt easily to other species. Although no difference in patterns of mutation variation between different host organs was observed, mutations were common following both in vitro and in vivo passage. However, only a small number of these mutations also appeared in natura, suggesting that adaptation during successful cross-species virus transmission is a complex, multifactorial evolutionary process. Understanding the mechanisms that underpin the cross-species transmission and host adaptation of rabies virus (RABV) remains an important part of the ongoing goal to reduce and eliminate rabies. We utilized next-generation sequencing to perform a deep comparative analysis of the genomic evolution of RABV subpopulations during host adaptation in culture and in animals, with the aim of determining the molecular mechanisms involved in the host-species or tissue adaptation of rabies virus. In particular, we aimed to determine whether experimental evolution can recapitulate evolution in nature. Our results suggest that a limited number of mutations that appeared following both in vitro and in vivo passage were observed in natura. This study also suggests that dog RABV may be able to adapt to some hosts more easily than other host variants.
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15
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Forró B, Marton S, Kecskeméti S, Hornyák Á, Bányai K. Vaccine-associated rabies in red fox, Hungary. Vaccine 2019; 37:3535-3538. [PMID: 31109719 DOI: 10.1016/j.vaccine.2019.05.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 05/02/2019] [Accepted: 05/03/2019] [Indexed: 10/26/2022]
Abstract
Rabies vaccine strain was isolated from a red fox (Vulpes vulpes) with signs of neurological disorder during an oral vaccination campaign in 2015, Hungary. The whole genome sequence of the isolated strain shared >99.9% nucleotide sequence identity to the whole genomes of vaccines strains recently used in Hungarian oral vaccination campaigns. The neuroinvasive potential of rabies vaccines that leads to development of clinical manifestations is rarely seen among wild animals; however, the observed residual pathogenicity needs awareness of field experts and requires close monitoring of rabies cases in areas where elimination programs are implemented.
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Affiliation(s)
- Barbara Forró
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Szilvia Marton
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Sándor Kecskeméti
- Veterinary Diagnostic Directorate, National Food Chain Safety Office, Debrecen, Hungary
| | - Ákos Hornyák
- Veterinary Diagnostic Directorate, National Food Chain Safety Office, Budapest, Hungary
| | - Krisztián Bányai
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary.
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16
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Schröder L, Klafack S, Bergmann SM, Lee PYA, Franzke K, Höper D, Mettenleiter TC, Fuchs W. Characterization of gene deletion mutants of Cyprinid herpesvirus 3 (koi herpesvirus) lacking the immunogenic envelope glycoproteins pORF25, pORF65, pORF148 and pORF149. Virus Res 2018; 261:21-30. [PMID: 30543872 DOI: 10.1016/j.virusres.2018.12.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 12/07/2018] [Accepted: 12/08/2018] [Indexed: 12/20/2022]
Abstract
Cyprinid herpesvirus 3 (CyHV-3) or koi herpesvirus is a global pathogen causing mass mortality in koi and common carp, against which improved vaccines are urgently needed. In this study we investigated the role of four nonessential, but immunogenic envelope glycoproteins encoded by members of the ORF25 gene family (ORF25, ORF65, ORF148 and ORF149) during CyHV-3 replication. Single deletion of ORF65 did not affect in vitro replication, and deletion of ORF148 even slightly enhanced virus growth on common carp brain (CCB) cells. Deletions of ORF25 or ORF149 led to reduced plaque sizes and virus titers, which was due to delayed entry into host cells. An ORF148/ORF149 double deletion mutant exhibited wild-type like growth indicating opposing functions of the two proteins. Electron microscopy of CCB cells infected with either mutant did not indicate any effects on virion formation and maturation in nucleus or cytoplasm, nor on release of enveloped particles. The ORF148, ORF149 and double deletion mutants were also tested in animal experiments using juvenile carp, and proved to be insufficiently attenuated for use as live virus vaccines. However, surviving fish were protected against challenge with wild-type CyHV-3, demonstrating that these antibody inducing proteins are dispensable for an efficient immune response in vivo.
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Affiliation(s)
- Lars Schröder
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Sandro Klafack
- Institute of Infectology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Sven M Bergmann
- Institute of Infectology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | | | - Kati Franzke
- Institute of Infectology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Dirk Höper
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Thomas C Mettenleiter
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Walter Fuchs
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany.
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17
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Schröder L, Klafack S, Bergmann SM, Fichtner D, Jin Y, Lee PY, Höper D, Mettenleiter TC, Fuchs W. Generation of a potential koi herpesvirus live vaccine by simultaneous deletion of the viral thymidine kinase and dUTPase genes. J Gen Virol 2018; 100:642-655. [PMID: 30230443 DOI: 10.1099/jgv.0.001148] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Koi herpesvirus (KHV, Cyprinidherpesvirus 3) causes a fatal disease of koi and common carp. To obtain safe and efficacious live vaccines, we generated deletion mutants of KHV lacking the nonessential genes encoding two enzymes of nucleotide metabolism, thymidine kinase (TK, ORF55) and deoxyuridine-triphosphatase (DUT, ORF123). Since single-deletion mutants based on a KHV isolate from Israel (KHV-I) only exhibited partial attenuation (Fuchs W, Fichtner D, Bergmann SM, Mettenleiter TC. Arch Virol 2011;156 : 1059-1063), a corresponding double mutant was generated and tested in vivo, and shown to be almost avirulent but still protective. To overcome the low in vitro virus titres of KHV-I (≤105 p.f.u. ml-1), single and double TK and DUT deletions were also introduced into a cell culture-adapted KHV strain from Taiwan (KHV-T). The deletions did not affect in vitro virus replication, and all KHV-T mutants exhibited wild-type-like plaque sizes and titres exceeding 107 p.f.u. ml-1, as a prerequisite for economic vaccine production. Compared to wild-type and revertant viruses, the single-deletion mutants of KHV-T were significantly attenuated in vivo, and immersion of juvenile carp in water containing high doses of the double mutant caused almost no fatalities. Nevertheless, the deletion mutants induced similar levels of KHV-specific serum antibodies to the parental wild-type virus, and conferred solid protection against disease after challenge with wild-type KHV. For the convenient differentiation of DNA samples prepared from gill swabs of carp infected with wild-type and TK-deleted KHV we developed a triplex real-time PCR. Thus, KHV-TΔDUT/TK might be suitable as a genetic DIVA vaccine in the field.
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Affiliation(s)
- Lars Schröder
- 1Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Sandro Klafack
- 2Institute of Infectology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Sven M Bergmann
- 2Institute of Infectology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Dieter Fichtner
- 2Institute of Infectology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Yeonhwa Jin
- 2Institute of Infectology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Pei-Yu Lee
- 3GeneReach Biotechnology Corporation, Taichung, Taiwan, ROC
| | - Dirk Höper
- 4Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Thomas C Mettenleiter
- 1Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Walter Fuchs
- 1Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
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18
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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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19
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Efficacy of the oral rabies virus vaccine strain SPBN GASGAS in foxes and raccoon dogs. Vaccine 2017; 37:4750-4757. [PMID: 29042202 DOI: 10.1016/j.vaccine.2017.09.093] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 09/19/2017] [Accepted: 09/20/2017] [Indexed: 11/21/2022]
Abstract
To test the immunogenicity and efficacy of a new oral rabies virus vaccine strain SPBN GASGAS in wildlife target species, one group of foxes and two groups of raccoon dogs were offered a bait containing 1.7 ml of the vaccine (106.6 FFU/ml; 106.8 FFU/dose) and subsequently challenged approximately 180 days later with a fox rabies virus isolate. One group of raccoon dogs (n=30) received the same challenge dose (100.7 MICLD50/ml) as the red foxes (n=29). The other group with raccoon dogs (n=28) together with 8 animals that received the vaccine dose by direct instillation into the oral cavity (DIOC) were infected with a 40-fold higher dose of the challenge virus (102.3 MICLD50/ml). All but one of the 29 vaccinated foxes survived the challenge infection; meanwhile all 12 control foxes succumbed to rabies. Twenty-eight of 30 vaccinated raccoon dogs challenged with the same dose survived the infection, however only six of 12 control animals succumbed. When the higher challenge dose was administered, all 12 control animals died from rabies and all 36 vaccinated animals (28 baited plus 8 DIOC) survived. Blood samples were collected at different time points post vaccination and examined by both RFFIT and ELISA. The kinetics of the measured immune response was similar for both species, although in RFFIT slightly higher values were observed in foxes than in raccoon dogs. However, the immune response as measured in ELISA was identical for both species. The oral rabies virus vaccine SPBN GASGAS meets the efficacy requirements for live rabies virus vaccines as laid down by the European Pharmacopoeia.
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20
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Marston DA, Horton DL, Nunez J, Ellis RJ, Orton RJ, Johnson N, Banyard AC, McElhinney LM, Freuling CM, Fırat M, Ünal N, Müller T, de Lamballerie X, Fooks AR. Genetic analysis of a rabies virus host shift event reveals within-host viral dynamics in a new host. Virus Evol 2017; 3:vex038. [PMID: 29255631 PMCID: PMC5729694 DOI: 10.1093/ve/vex038] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Host shift events play an important role in epizootics as adaptation to new hosts can profoundly affect the spread of the disease and the measures needed to control it. During the late 1990s, an epizootic in Turkey resulted in a sustained maintenance of rabies virus (RABV) within the fox population. We used Bayesian inferences to investigate whole genome sequences from fox and dog brain tissues from Turkey to demonstrate that the epizootic occurred in 1997 (±1 year). Furthermore, these data indicated that the epizootic was most likely due to a host shift from locally infected domestic dogs, rather than an incursion of a novel fox or dog RABV. No evidence was observed for genetic adaptation to foxes at consensus sequence level and dN/dS analysis suggested purifying selection. Therefore, the deep sequence data were analysed to investigate the sub-viral population during a host shift event. Viral heterogeneity was measured in all RABV samples; viruses from the early period after the host shift exhibited greater sequence variation in comparison to those from the later stage, and to those not involved in the host shift event, possibly indicating a role in establishing transmission within a new host. The transient increase in variation observed in the new host species may represent virus replication within a new environment, perhaps due to increased replication within the CNS, resulting in a larger population of viruses, or due to the lack of host constraints present in the new host reservoir.
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Affiliation(s)
- Denise A Marston
- Wildlife Zoonoses & Vector-Borne Diseases Research Group, Animal and Plant Health Agency, New Haw, Addlestone, Surrey, KT15 3NB, UK
- UMR “Émergence des Pathologies Virales” (EPV: Aix-Marseille Univ—IRD 190—Inserm 1207 – EHESP – IHU Méditerranée Infection), Faculté de Médecine de Marseille, 27, Bd Jean Moulin,13005 Marseille, cedex 05 France
| | - Daniel L Horton
- School of Veterinary Medicine, University of Surrey, Guildford, GU2 7AL UK
| | - Javier Nunez
- Surveillance and Laboratory Services Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey, KT15 3NB UK
| | - Richard J Ellis
- Surveillance and Laboratory Services Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey, KT15 3NB UK
| | - Richard J Orton
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
- Centre for Virus Research, MRC-University of Glasgow, University of Glasgow, Glasgow, G61 1QH UK
| | - Nicholas Johnson
- Wildlife Zoonoses & Vector-Borne Diseases Research Group, Animal and Plant Health Agency, New Haw, Addlestone, Surrey, KT15 3NB, UK
- Faculty of Health and Medical Science, University of Surrey, Guildford, GU2 7XH, UK
| | - Ashley C Banyard
- Wildlife Zoonoses & Vector-Borne Diseases Research Group, Animal and Plant Health Agency, New Haw, Addlestone, Surrey, KT15 3NB, UK
| | - Lorraine M McElhinney
- Wildlife Zoonoses & Vector-Borne Diseases Research Group, Animal and Plant Health Agency, New Haw, Addlestone, Surrey, KT15 3NB, UK
- Institute of Infection and Global Health, University of Liverpool, UK
| | - Conrad M Freuling
- Friedrich-Loeffler-Institute, (FLI), Institute of Molecular Virology and Cell Biology, Greifswald-Insel Riems, D-17493, Germany
| | - Müge Fırat
- Etlik Veterinary Control Central Research Institute A.S.Kolayli Street. No.21-21/A, 06020, Etlik, Ankara, Turkey
| | - Nil Ünal
- Etlik Veterinary Control Central Research Institute A.S.Kolayli Street. No.21-21/A, 06020, Etlik, Ankara, Turkey
| | - Thomas Müller
- Friedrich-Loeffler-Institute, (FLI), Institute of Molecular Virology and Cell Biology, Greifswald-Insel Riems, D-17493, Germany
| | - Xavier de Lamballerie
- UMR “Émergence des Pathologies Virales” (EPV: Aix-Marseille Univ—IRD 190—Inserm 1207 – EHESP – IHU Méditerranée Infection), Faculté de Médecine de Marseille, 27, Bd Jean Moulin,13005 Marseille, cedex 05 France
| | - Anthony R Fooks
- Wildlife Zoonoses & Vector-Borne Diseases Research Group, Animal and Plant Health Agency, New Haw, Addlestone, Surrey, KT15 3NB, UK
- Institute of Infection and Global Health, University of Liverpool, UK
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21
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Pfaff F, Schulze C, König P, Franzke K, Bock S, Hlinak A, Kämmerling J, Ochs A, Schüle A, Mettenleiter TC, Höper D, Beer M. A novel alphaherpesvirus associated with fatal diseases in banded Penguins. J Gen Virol 2017; 98:89-95. [PMID: 28036249 DOI: 10.1099/jgv.0.000698] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel avian alphaherpesvirus, preliminarily designated sphenicid alphaherpesvirus 1 (SpAHV-1), has been independently isolated from juvenile Humboldt and African penguins (Spheniscus humboldti and Spheniscus demersus) kept in German zoos suffering from diphtheroid oropharyngitis/laryngotracheitis and necrotizing enteritis (collectively designated as penguin-diphtheria-like disease). High-throughput sequencing was used to determine the complete genome sequences of the first two SpAHV-1 isolates. SpAHV-1 comprises a class D genome with a length of about 164 kbp, a G+C content of 45.6 mol% and encodes 86 predicted ORFs. Taxonomic association of SpAHV-1 to the genus Mardivirus was supported by gene content clustering and phylogenetic analysis of herpesvirus core genes. The presented results imply that SpAHV-1 could be the primary causative agent of penguin-diphtheria-like fatal diseases in banded penguins. These results may serve as a basis for the development of diagnostic tools in order to investigate similar cases of penguin diphtheria in wild and captive penguins.
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Affiliation(s)
- Florian Pfaff
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald - Insel Riems, Germany
| | | | - Patricia König
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald - Insel Riems, Germany
| | - Kati Franzke
- Institute of Infectology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald - Insel Riems, Germany
| | - Sabine Bock
- Berlin-Brandenburg State Laboratory, Frankfurt (Oder), Germany
| | - Andreas Hlinak
- Berlin-Brandenburg State Laboratory, Frankfurt (Oder), Germany
| | | | | | | | - Thomas C Mettenleiter
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald - Insel Riems, Germany
| | - Dirk Höper
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald - Insel Riems, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald - Insel Riems, Germany
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22
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Simonyan V, Chumakov K, Donaldson E, Karagiannis K, Lam PV, Dingerdissen H, Voskanian A. HIVE-heptagon: A sensible variant-calling algorithm with post-alignment quality controls. Genomics 2017; 109:131-140. [PMID: 28188908 DOI: 10.1016/j.ygeno.2017.01.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 12/19/2016] [Accepted: 01/24/2017] [Indexed: 10/20/2022]
Abstract
Advances in high-throughput sequencing (HTS) technologies have greatly increased the availability of genomic data and potential discovery of clinically significant genomic variants. However, numerous issues still exist with the analysis of these data, including data complexity, the absence of formally agreed upon best practices, and inconsistent reproducibility. Toward a more robust and reproducible variant-calling paradigm, we propose a series of selective noise filtrations and post-alignment quality control (QC) techniques that may reduce the rate of false variant calls. We have implemented both novel and refined post-alignment QC mechanisms to augment existing pre-alignment QC measures. These techniques can be used independently or in combination to identify and correct issues caused during data generation or early analysis stages. The adoption of these procedures by the broader scientific community is expected to improve the identification of clinically significant variants both in terms of computational efficiency and in the confidence of the results. AVAILABILITY https://hive.biochemistry.gwu.edu/.
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Affiliation(s)
- Vahan Simonyan
- Center for Biologics Evaluation and Research, US Food and Drug Administration, 10993 New Hampshire Ave., Silver Spring, MD, United States.
| | - Konstantin Chumakov
- Center for Biologics Evaluation and Research, US Food and Drug Administration, 10993 New Hampshire Ave., Silver Spring, MD, United States.
| | - Eric Donaldson
- Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, 10993 New Hampshire Ave., United States.
| | - Konstantinos Karagiannis
- Center for Biologics Evaluation and Research, US Food and Drug Administration, 10993 New Hampshire Ave., Silver Spring, MD, United States; Department of Biochemistry and Molecular Medicine, George Washington University Medical Center, 2300 Eye St. NW, Washington DC, United States.
| | - Phuc VinhNguyen Lam
- Center for Biologics Evaluation and Research, US Food and Drug Administration, 10993 New Hampshire Ave., Silver Spring, MD, United States.
| | - Hayley Dingerdissen
- Center for Biologics Evaluation and Research, US Food and Drug Administration, 10993 New Hampshire Ave., Silver Spring, MD, United States; Department of Biochemistry and Molecular Medicine, George Washington University Medical Center, 2300 Eye St. NW, Washington DC, United States.
| | - Alin Voskanian
- Center for Biologics Evaluation and Research, US Food and Drug Administration, 10993 New Hampshire Ave., Silver Spring, MD, United States.
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23
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Jenckel M, Blome S, Beer M, Höper D. Quasispecies composition and diversity do not reveal any predictors for chronic classical swine fever virus infection. Arch Virol 2016; 162:775-786. [PMID: 27885563 DOI: 10.1007/s00705-016-3161-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 10/20/2016] [Indexed: 10/20/2022]
Abstract
Classical swine fever (CSF) can run acute, chronic, and prenatal courses in both domestic pigs and wild boar. Although chronic infections are rare events, their epidemiological impact is very high due to the long-term shedding of virus. So far, little is known about the factors that influence disease course and outcome from either the host or virus's perspective. To elucidate the viral determinants, we analyzed the role of the viral populations for the development of chronic CSF virus (CSFV) infections. Three different animal trials that had led to both chronic and acute infections were chosen for a detailed analysis by deep sequencing. The three inocula represented sub-genogroups 2.1 and 2.3, and two viruses were wild-type CSFV, one derived from an infectious cDNA clone. These viruses and samples derived from acutely and chronically infected animals were subjected to next-generation sequencing. Subsequently, the derived full-length genomes were compared at both the consensus and the quasispecies level. At consensus level, no differences were observed between the parental viruses and the viruses obtained from chronically infected animals. Despite a considerable level of variability at the quasispecies level, no indications were found for any predictive pattern with regard to the chronicity of the CSFV infections. While there might be no direct marker for chronicity, moderate virulence of some CSFV strains in itself seems to be a crucial prerequisite for the establishment of long-term infections which does not need further genetic adaption. Thus, general host and virus factors need further investigation.
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Affiliation(s)
- Maria Jenckel
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald-Insel Riems, Germany
| | - Sandra Blome
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald-Insel Riems, Germany.
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald-Insel Riems, Germany
| | - Dirk Höper
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald-Insel Riems, Germany
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24
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Rupprecht CE, Nagarajan T, Ertl H. Current Status and Development of Vaccines and Other Biologics for Human Rabies Prevention. Expert Rev Vaccines 2016; 15:731-49. [PMID: 26796599 DOI: 10.1586/14760584.2016.1140040] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Rabies is a neglected viral zoonosis with the highest case fatality of any infectious disease. Pasteur's historical accomplishments during the late 19(th) century began the process of human vaccine development, continuing to evolve into the 21(st) century. Over the past 35 years, great improvements occurred in the production of potent tissue culture vaccines and the gradual removal from the market of unsafe nerve tissue products. Timely and appropriate administration of modern biologics virtually assures survivorship, even after severe exposures. Nevertheless, in the developing world, if not provided for free nationally, the cost of a single course of human prophylaxis exceeds the average monthly wage of the common worker. Beyond traditional approaches, recombinant, sub-unit and other novel methods are underway to improve the availability of safe, effective and more affordable rabies biologics.
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