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Poghosyan A, Hakobyan S, Avagyan H, Avetisyan A, Bayramyan N, Hakobyan L, Abroyan L, Davtyan A, Poghosyan D, Baghdasaryan B, Arakelova E, Karalova E, Karalyan Z. The role of gastropods in African swine fever virus ecology. Virol J 2024; 21:180. [PMID: 39113041 PMCID: PMC11308590 DOI: 10.1186/s12985-024-02444-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Accepted: 07/23/2024] [Indexed: 08/10/2024] Open
Abstract
The spread of the African swine fever virus (ASF virus) genotype ii in the Eurasian region has been very successful and often inexplicable. The virus spreads rapidly and persists in areas with wild boar populations, but areas without feral pig populations are also affected. The virus has shown the ability to survive for a long time in the environment without a population of susceptible hosts, both pigs and Ornithodoros soft ticks. Published data indicated that ASF viruses persist significantly longer in an environment with some freshwater snails (especially Pomacea bridgesii, Tarebia granifera, Asolene spixii, Melanoides tuberculate, and Physa fontinalis), compared to freshwater without snails. Data obtained in this study suggest that gastropods theoretically can be the hosts of the ASF virus. Also, we have proven the possibility of long-term existence of an infectious virus when infected in vitro.
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Affiliation(s)
- Arpine Poghosyan
- Laboratory of Cell Biology and Virology, Institute of Molecular Biology of NAS RA, Yerevan, Armenia
| | - Sona Hakobyan
- Laboratory of Cell Biology and Virology, Institute of Molecular Biology of NAS RA, Yerevan, Armenia
| | - Hranush Avagyan
- Laboratory of Cell Biology and Virology, Institute of Molecular Biology of NAS RA, Yerevan, Armenia
- Experimental Laboratory of Yerevan State Medical University after M. Heratsi, Yerevan, Armenia
| | - Aida Avetisyan
- Laboratory of Cell Biology and Virology, Institute of Molecular Biology of NAS RA, Yerevan, Armenia
- Experimental Laboratory of Yerevan State Medical University after M. Heratsi, Yerevan, Armenia
| | - Nane Bayramyan
- Laboratory of Cell Biology and Virology, Institute of Molecular Biology of NAS RA, Yerevan, Armenia
| | - Lina Hakobyan
- Laboratory of Cell Biology and Virology, Institute of Molecular Biology of NAS RA, Yerevan, Armenia
| | - Liana Abroyan
- Laboratory of Cell Biology and Virology, Institute of Molecular Biology of NAS RA, Yerevan, Armenia
| | - Aram Davtyan
- A.B. Nalbandyan Institute of Chemical Physics, NAS RA, Yerevan, Armenia
| | - Davit Poghosyan
- Laboratory of Molecular and Cellular Immunology, Institute of Molecular Biology NAS RA, Yerevan, Armenia
| | - Bagrat Baghdasaryan
- Laboratory of Cell Biology and Virology, Institute of Molecular Biology of NAS RA, Yerevan, Armenia
| | - Elina Arakelova
- Laboratory of Cell Biology and Virology, Institute of Molecular Biology of NAS RA, Yerevan, Armenia
| | - Elena Karalova
- Laboratory of Cell Biology and Virology, Institute of Molecular Biology of NAS RA, Yerevan, Armenia
- Experimental Laboratory of Yerevan State Medical University after M. Heratsi, Yerevan, Armenia
| | - Zaven Karalyan
- Laboratory of Cell Biology and Virology, Institute of Molecular Biology of NAS RA, Yerevan, Armenia.
- Yerevan State Medical University after M. Heratsi, Yerevan, Armenia.
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Akter R, El-Hage CM, Sansom FM, Carrick J, Devlin JM, Legione AR. Metagenomic investigation of potential abortigenic pathogens in foetal tissues from Australian horses. BMC Genomics 2021; 22:713. [PMID: 34600470 PMCID: PMC8487468 DOI: 10.1186/s12864-021-08010-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 09/14/2021] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Abortion in horses leads to economic and welfare losses to the equine industry. Most cases of equine abortions are sporadic, and the cause is often unknown. This study aimed to detect potential abortigenic pathogens in equine abortion cases in Australia using metagenomic deep sequencing methods. RESULTS After sequencing and analysis, a total of 68 and 86 phyla were detected in the material originating from 49 equine abortion samples and 8 samples from normal deliveries, respectively. Most phyla were present in both groups, with the exception of Chlamydiae that were only present in abortion samples. Around 2886 genera were present in the abortion samples and samples from normal deliveries at a cut off value of 0.001% of relative abundance. Significant differences in species diversity between aborted and normal tissues was observed. Several potential abortigenic pathogens were identified at a high level of relative abundance in a number of the abortion cases, including Escherichia coli, Klebsiella pneumoniae, Klebsiella oxytoca, Streptococcus equi subspecies zooepidemicus, Pantoea agglomerans, Acinetobacter lwoffii, Acinetobacter calcoaceticus and Chlamydia psittaci. CONCLUSIONS This work revealed the presence of several potentially abortigenic pathogens in aborted specimens. No novel potential abortigenic agents were detected. The ability to screen samples for multiple pathogens that may not have been specifically targeted broadens the frontiers of diagnostic potential. The future use of metagenomic approaches for diagnostic purposes is likely to be facilitated by further improvements in deep sequencing technologies.
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Affiliation(s)
- Rumana Akter
- Asia Pacific Centre for Animal Health, The Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, 3010, Australia
- Department of Medicine (Royal Melbourne Hospital), The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Charles M El-Hage
- Asia Pacific Centre for Animal Health, The Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Fiona M Sansom
- Asia Pacific Centre for Animal Health, The Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Joan Carrick
- Equine Specialist Consulting, Scone, New South Wales, 2337, Australia
| | - Joanne M Devlin
- Asia Pacific Centre for Animal Health, The Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Alistair R Legione
- Asia Pacific Centre for Animal Health, The Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, 3010, Australia.
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Leo S, Cherkaoui A, Renzi G, Schrenzel J. Mini Review: Clinical Routine Microbiology in the Era of Automation and Digital Health. Front Cell Infect Microbiol 2020; 10:582028. [PMID: 33330127 PMCID: PMC7734209 DOI: 10.3389/fcimb.2020.582028] [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: 07/10/2020] [Accepted: 10/20/2020] [Indexed: 12/13/2022] Open
Abstract
Clinical microbiology laboratories are the first line to combat and handle infectious diseases and antibiotic resistance, including newly emerging ones. Although most clinical laboratories still rely on conventional methods, a cascade of technological changes, driven by digital imaging and high-throughput sequencing, will revolutionize the management of clinical diagnostics for direct detection of bacteria and swift antimicrobial susceptibility testing. Importantly, such technological advancements occur in the golden age of machine learning where computers are no longer acting passively in data mining, but once trained, can also help physicians in making decisions for diagnostics and optimal treatment administration. The further potential of physically integrating new technologies in an automation chain, combined to machine-learning-based software for data analyses, is seducing and would indeed lead to a faster management in infectious diseases. However, if, from one side, technological advancement would achieve a better performance than conventional methods, on the other side, this evolution challenges clinicians in terms of data interpretation and impacts the entire hospital personnel organization and management. In this mini review, we discuss such technological achievements offering practical examples of their operability but also their limitations and potential issues that their implementation could rise in clinical microbiology laboratories.
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Affiliation(s)
- Stefano Leo
- Genomic Research Laboratory, Division of Infectious Diseases, Department of Medicine, Geneva University Hospitals and University of Geneva, Geneva, Switzerland
| | - Abdessalam Cherkaoui
- Bacteriology Laboratory, Division of Laboratory Medicine, Department of Diagnostics, Geneva University Hospitals, Geneva, Switzerland
| | - Gesuele Renzi
- Bacteriology Laboratory, Division of Laboratory Medicine, Department of Diagnostics, Geneva University Hospitals, Geneva, Switzerland
| | - Jacques Schrenzel
- Genomic Research Laboratory, Division of Infectious Diseases, Department of Medicine, Geneva University Hospitals and University of Geneva, Geneva, Switzerland
- Bacteriology Laboratory, Division of Laboratory Medicine, Department of Diagnostics, Geneva University Hospitals, Geneva, Switzerland
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4
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Malogolovkin A, Kolbasov D. Genetic and antigenic diversity of African swine fever virus. Virus Res 2019; 271:197673. [DOI: 10.1016/j.virusres.2019.197673] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 07/18/2019] [Accepted: 07/18/2019] [Indexed: 11/28/2022]
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Takhampunya R, Korkusol A, Pongpichit C, Yodin K, Rungrojn A, Chanarat N, Promsathaporn S, Monkanna T, Thaloengsok S, Tippayachai B, Kumfao N, Richards AL, Davidson SA. Metagenomic Approach to Characterizing Disease Epidemiology in a Disease-Endemic Environment in Northern Thailand. Front Microbiol 2019; 10:319. [PMID: 30863381 PMCID: PMC6399164 DOI: 10.3389/fmicb.2019.00319] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 02/06/2019] [Indexed: 02/01/2023] Open
Abstract
In this study, we used a metagenomic approach to analyze bacterial communities from diverse populations (humans, animals, and vectors) to investigate the role of these microorganisms as causative agents of disease in human and animal populations. Wild rodents and ectoparasites were collected from 2014 to 2018 in Nan province, Thailand where scrub typhus is highly endemic. Samples from undifferentiated febrile illness (UFI) patients were obtained from a local hospital. A total of 200 UFI patient samples were obtained and 309 rodents and 420 pools of ectoparasites were collected from rodents (n = 285) and domestic animals (n = 135). The bacterial 16S rRNA gene was amplified and sequenced with the Illumina. Real-time PCR and Sanger sequencing were used to confirm the next-generation sequencing (NGS) results and to characterize pathogen species. Several pathogens were detected by NGS in all populations studied and the most common pathogens identified included Bartonella spp., Rickettsia spp., Leptospira spp., and Orientia tsutsugamushi. Interestingly, Anaplasma spp. was detected in patient, rodent and tick populations, although they were not previously known to cause human disease from this region. Candidatus Neoehrlichia, Neorickettsia spp., Borrelia spp., and Ehrlichia spp. were detected in rodents and their associated ectoparasites. The same O. tsutsugamushi genotypes were shared among UFI patients, rodents, and chiggers in a single district indicating that the chiggers found on rodents were also likely responsible for transmitting to people. Serological testing using immunofluorescence assays in UFI samples showed high prevalence (IgM/IgG) of Rickettsia and Orientia pathogens, most notably among samples collected during September–November. Additionally, a higher number of seropositive samples belonged to patients in the working age population (20–60 years old). The results presented in this study demonstrate that the increased risk of human infection or exposure to chiggers and their associated pathogen (O. tsutsugamushi) resulted in part from two important factors; working age group and seasons for rice cultivation and harvesting. Evidence of pathogen exposure was shown to occur as there was seropositivity (IgG) in UFI patients for bartonellosis as well as for anaplasmosis. Using a metagenomic approach, this study demonstrated the circulation and transmission of several pathogens in the environment, some of which are known causative agents of illness in human populations.
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Affiliation(s)
- Ratree Takhampunya
- Department of Entomology, US Army Medical Directorate of the Armed Forces Research Institute of Medical Sciences (USAMD-AFRIMS), Bangkok, Thailand
| | - Achareeya Korkusol
- Department of Entomology, US Army Medical Directorate of the Armed Forces Research Institute of Medical Sciences (USAMD-AFRIMS), Bangkok, Thailand
| | | | | | - Artharee Rungrojn
- Department of Entomology, US Army Medical Directorate of the Armed Forces Research Institute of Medical Sciences (USAMD-AFRIMS), Bangkok, Thailand
| | - Nitima Chanarat
- Department of Entomology, US Army Medical Directorate of the Armed Forces Research Institute of Medical Sciences (USAMD-AFRIMS), Bangkok, Thailand
| | - Sommai Promsathaporn
- Department of Entomology, US Army Medical Directorate of the Armed Forces Research Institute of Medical Sciences (USAMD-AFRIMS), Bangkok, Thailand
| | - Taweesak Monkanna
- Department of Entomology, US Army Medical Directorate of the Armed Forces Research Institute of Medical Sciences (USAMD-AFRIMS), Bangkok, Thailand
| | - Sasikanya Thaloengsok
- Department of Entomology, US Army Medical Directorate of the Armed Forces Research Institute of Medical Sciences (USAMD-AFRIMS), Bangkok, Thailand
| | - Bousaraporn Tippayachai
- Department of Entomology, US Army Medical Directorate of the Armed Forces Research Institute of Medical Sciences (USAMD-AFRIMS), Bangkok, Thailand
| | | | - Allen L Richards
- Viral and Rickettsial Diseases Department, Naval Medical Research Center, Silver Spring, MD, United States
| | - Silas A Davidson
- Department of Entomology, US Army Medical Directorate of the Armed Forces Research Institute of Medical Sciences (USAMD-AFRIMS), Bangkok, Thailand
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Methods in Metagenomics and Environmental Biotechnology. NANOSCIENCE AND BIOTECHNOLOGY FOR ENVIRONMENTAL APPLICATIONS 2019. [DOI: 10.1007/978-3-319-97922-9_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Patel JG, Patel BJ, Patel SS, Raval SH, Parmar RS, Joshi DV, Chauhan HC, Chandel BS, Patel BK. Metagenomic of clinically diseased and healthy broiler affected with respiratory disease complex. Data Brief 2018; 19:82-85. [PMID: 29892620 PMCID: PMC5993000 DOI: 10.1016/j.dib.2018.05.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 05/03/2018] [Indexed: 10/25/2022] Open
Abstract
In recent past, the respiratory infection has emerged as a great challenge to the poultry farmers. Various pathogens including Avian pneumovirus (APV), Avian influenza virus (AIV), Infectious bronchitis virus (IBV) and Newcastle disease virus (NDV), Avibacterium paragallinarum, Ornithobacterium rhinotracheale (ORT), Mycoplasma synoviae (MS), Mycoplasma gallisepticum (MG) and Avian pathogenic Escherichia coli (APEC) are involved in the respiratory disease complex in birds [1], [2] (Bradbury, 1984; Roussan et al., 2008). Hence, respiratory disease complex is the most serious disease affecting to poultry and causes heavy economic losses in the poultry industry worldwide [3] (Murthy et al., 2008). In recent years, metagenomics is powerful analyzing tool for detection of pathogens directly from clinical samples without any prior knowledge of the organism in a given sample [4], [5] (Schuster, 2008; Pereira et al., 2010). High throughput Next-Generation-Sequencing technology was used for sequencing the isolated genomic DNA. These data provides an insight about taxonomic and functional status of microorganisms responsible for causing respiratory infection in broiler. The data of these metagenome are available in the BioSample Submission Portal as Bioproject PRJNA339659 and SRA accession number SRR5997823, SRR5992854, SRR6037376, SRR6024702, SRR6012248 and SRR6008913.
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Affiliation(s)
- J G Patel
- Department of Veterinary Pathology, College of Veterinary Science and Anima Husbandry, Sardarkrushinagar Dantiwada Agricultural University, Sardarkrushinagar, Gujarat, India
| | - B J Patel
- Department of Veterinary Pathology, College of Veterinary Science and Anima Husbandry, Sardarkrushinagar Dantiwada Agricultural University, Sardarkrushinagar, Gujarat, India
| | - S S Patel
- Department of Veterinary Microbiology, College of Veterinary Science and Animal, Husbandry, Sardarkrushinagar Dantiwada Agricultural University, Sardarkrushinagar, Gujarat, India
| | - S H Raval
- Department of Veterinary Pathology, College of Veterinary Science and Anima Husbandry, Sardarkrushinagar Dantiwada Agricultural University, Sardarkrushinagar, Gujarat, India
| | - R S Parmar
- Department of Veterinary Pathology, College of Veterinary Science and Anima Husbandry, Sardarkrushinagar Dantiwada Agricultural University, Sardarkrushinagar, Gujarat, India
| | - D V Joshi
- Department of Veterinary Pathology, College of Veterinary Science and Anima Husbandry, Sardarkrushinagar Dantiwada Agricultural University, Sardarkrushinagar, Gujarat, India
| | - H C Chauhan
- Department of Veterinary Microbiology, College of Veterinary Science and Animal, Husbandry, Sardarkrushinagar Dantiwada Agricultural University, Sardarkrushinagar, Gujarat, India
| | - B S Chandel
- Department of Animal Biotechnology, College of Veterinary Science and Animal, Husbandry, Sardarkrushinagar Dantiwada Agricultural University, Sardarkrushinagar, Gujarat, India
| | - B K Patel
- Department of Animal Biotechnology, College of Veterinary Science and Animal, Husbandry, Sardarkrushinagar Dantiwada Agricultural University, Sardarkrushinagar, Gujarat, India
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Benamar S, Reteno DGI, Bandaly V, Labas N, Raoult D, La Scola B. Faustoviruses: Comparative Genomics of New Megavirales Family Members. Front Microbiol 2016; 7:3. [PMID: 26903952 PMCID: PMC4742530 DOI: 10.3389/fmicb.2016.00003] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 01/05/2016] [Indexed: 01/04/2023] Open
Abstract
An emerging interest for the giant virus discovery process, genome sequencing and analysis has allowed an expansion of the number of known Megavirales members. Using the protist Vermamoeba sp. as cell support, a new giant virus named Faustovirus has been isolated. In this study, we describe the genome sequences of nine Faustoviruses and build a genomic comparison in order to have a comprehensive overview of genomic composition and diversity among this new virus family. The average sequence length of these viruses is 467,592.44 bp (ranging from 455,803 to 491,024 bp), making them the fourth largest Megavirales genome after Mimiviruses, Pandoraviruses, and Pithovirus sibericum. Faustovirus genomes displayed an average G+C content of 37.14 % (ranging from 36.22 to 39.59%) which is close to the G+C content range of the Asfarviridae genomes (38%). The proportion of best matches and the phylogenetic analysis suggest a shared origin with Asfarviridae without belonging to the same family. The core-gene-based phylogeny of Faustoviruses study has identified four lineages. These results were confirmed by the analysis of amino acids and COGs category distribution. The diversity of the gene composition of these lineages is mainly explained by gene deletion or acquisition and some exceptions for gene duplications. The high proportion of best matches from Bacteria and Phycodnaviridae on the pan-genome and unique genes may be explained by an interaction occurring after the separation of the lineages. The Faustovirus core-genome appears to consolidate the surrounding of 207 genes whereas the pan-genome is described as an open pan-genome, its enrichment via the discovery of new Faustoviruses is required to better seize all the genomic diversity of this family.
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Affiliation(s)
- Samia Benamar
- UM63 CNRS 7278 IRD 198 INSERM U1095, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Facultés de Médecine et de Pharmacie, Aix-Marseille University Marseille, France
| | - Dorine G I Reteno
- UM63 CNRS 7278 IRD 198 INSERM U1095, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Facultés de Médecine et de Pharmacie, Aix-Marseille University Marseille, France
| | - Victor Bandaly
- Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Institut Hospitalo-Universitaire Méditerranée Infection, Centre Hospitalo-Universitaire Timone, Assistance Publique - Hôpitaux de Marseille Marseille, France
| | - Noémie Labas
- UM63 CNRS 7278 IRD 198 INSERM U1095, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Facultés de Médecine et de Pharmacie, Aix-Marseille University Marseille, France
| | - Didier Raoult
- UM63 CNRS 7278 IRD 198 INSERM U1095, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Facultés de Médecine et de Pharmacie, Aix-Marseille UniversityMarseille, France; Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Institut Hospitalo-Universitaire Méditerranée Infection, Centre Hospitalo-Universitaire Timone, Assistance Publique - Hôpitaux de MarseilleMarseille, France
| | - Bernard La Scola
- UM63 CNRS 7278 IRD 198 INSERM U1095, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Facultés de Médecine et de Pharmacie, Aix-Marseille UniversityMarseille, France; Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Institut Hospitalo-Universitaire Méditerranée Infection, Centre Hospitalo-Universitaire Timone, Assistance Publique - Hôpitaux de MarseilleMarseille, France
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Rodríguez JM, Moreno LT, Alejo A, Lacasta A, Rodríguez F, Salas ML. Genome Sequence of African Swine Fever Virus BA71, the Virulent Parental Strain of the Nonpathogenic and Tissue-Culture Adapted BA71V. PLoS One 2015; 10:e0142889. [PMID: 26618713 PMCID: PMC4664411 DOI: 10.1371/journal.pone.0142889] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 10/27/2015] [Indexed: 02/02/2023] Open
Abstract
The strain BA71V has played a key role in African swine fever virus (ASFV) research. It was the first genome sequenced, and remains the only genome completely determined. A large part of the studies on the function of ASFV genes, viral transcription, replication, DNA repair and morphogenesis, has been performed using this model. This avirulent strain was obtained by adaptation to grow in Vero cells of the highly virulent BA71 strain. We report here the analysis of the genome sequence of BA71 in comparison with that of BA71V. They possess the smallest genomes for a virulent or an attenuated ASFV, and are essentially identical except for a relatively small number of changes. We discuss the possible contribution of these changes to virulence. Analysis of the BA71 sequence allowed us to identify new similarities among ASFV proteins, and with database proteins including two ASFV proteins that could function as a two-component signaling network.
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Affiliation(s)
- Javier M. Rodríguez
- Centro Nacional de Microbiología, Instituto Nacional de Salud Carlos III, Majadahonda, Madrid, Spain
- * E-mail: (JMR); (MLS)
| | | | - Alí Alejo
- Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid), Universidad Autónoma de Madrid, Madrid, Spain
| | - Anna Lacasta
- Centre de Recerca en Sanitat Animal (CReSA)—Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Bellaterra, Barcelona, Spain
| | - Fernando Rodríguez
- Centre de Recerca en Sanitat Animal (CReSA)—Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Bellaterra, Barcelona, Spain
| | - María L. Salas
- Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid), Universidad Autónoma de Madrid, Madrid, Spain
- * E-mail: (JMR); (MLS)
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10
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Metagenomic Human Repiratory Air in a Hospital Environment. PLoS One 2015; 10:e0139044. [PMID: 26431488 PMCID: PMC4592066 DOI: 10.1371/journal.pone.0139044] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 09/07/2015] [Indexed: 01/22/2023] Open
Abstract
Hospital-acquired infection (HAI) or nosocomial infection is an issue that frequent hospital environment. We believe conventional regulated Petri dish method is insufficient to evaluate HAI. To address this problem, metagenomic sequencing was applied to screen airborne microbes in four rooms of Beijing Hospital. With air-in amount of sampler being setup to one person’s respiration quantity, metagenomic sequencing identified huge numbers of species in the rooms which had already qualified widely accepted petridish exposing standard, imposing urgency for new technology. Meanwhile,the comparative culture only got small portion of recovered species and remain blind for even cultivable pathogens reminded us the limitations of old technologies. To the best of our knowledge, the method demonstrated in this study could be broadly applied in hospital indoor environment for various monitoring activities as well as HAI study. It is also potential as a transmissible pathogen real-time modelling system worldwide.
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Abstract
UNLABELLED Giant viruses are protist-associated viruses belonging to the proposed order Megavirales; almost all have been isolated from Acanthamoeba spp. Their isolation in humans suggests that they are part of the human virome. Using a high-throughput strategy to isolate new giant viruses from their original protozoan hosts, we obtained eight isolates of a new giant viral lineage from Vermamoeba vermiformis, the most common free-living protist found in human environments. This new lineage was proposed to be the faustovirus lineage. The prototype member, faustovirus E12, forms icosahedral virions of ≈ 200 nm that are devoid of fibrils and that encapsidate a 466-kbp genome encoding 451 predicted proteins. Of these, 164 are found in the virion. Phylogenetic analysis of the core viral genes showed that faustovirus is distantly related to the mammalian pathogen African swine fever virus, but it encodes ≈ 3 times more mosaic gene complements. About two-thirds of these genes do not show significant similarity to genes encoding any known proteins. These findings show that expanding the panel of protists to discover new giant viruses is a fruitful strategy. IMPORTANCE By using Vermamoeba, a protist living in humans and their environment, we isolated eight strains of a new giant virus that we named faustovirus. The genomes of these strains were sequenced, and their sequences showed that faustoviruses are related to but different from the vertebrate pathogen African swine fever virus (ASFV), which belongs to the family Asfarviridae. Moreover, the faustovirus gene repertoire is ≈ 3 times larger than that of ASFV and comprises approximately two-thirds ORFans (open reading frames [ORFs] with no detectable homology to other ORFs in a database).
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12
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Miller RR, Montoya V, Gardy JL, Patrick DM, Tang P. Metagenomics for pathogen detection in public health. Genome Med 2013; 5:81. [PMID: 24050114 PMCID: PMC3978900 DOI: 10.1186/gm485] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Traditional pathogen detection methods in public health infectious disease surveillance rely upon the identification of agents that are already known to be associated with a particular clinical syndrome. The emerging field of metagenomics has the potential to revolutionize pathogen detection in public health laboratories by allowing the simultaneous detection of all microorganisms in a clinical sample, without a priori knowledge of their identities, through the use of next-generation DNA sequencing. A single metagenomics analysis has the potential to detect rare and novel pathogens, and to uncover the role of dysbiotic microbiomes in infectious and chronic human disease. Making use of advances in sequencing platforms and bioinformatics tools, recent studies have shown that metagenomics can even determine the whole-genome sequences of pathogens, allowing inferences about antibiotic resistance, virulence, evolution and transmission to be made. We are entering an era in which more novel infectious diseases will be identified through metagenomics-based methods than through traditional laboratory methods. The impetus is now on public health laboratories to integrate metagenomics techniques into their diagnostic arsenals.
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Affiliation(s)
- Ruth R Miller
- UBC School of Population and Public Health, Faculty of Medicine, University of British Columbia, 2206 East Mall, Vancouver, BC V6T 1Z3, Canada
| | - Vincent Montoya
- Department of Pathology and Laboratory Medicine, University of British Columbia, 2211 Wesbrook Mall, Vancouver, BC V6T 2B5, Canada
| | - Jennifer L Gardy
- UBC School of Population and Public Health, Faculty of Medicine, University of British Columbia, 2206 East Mall, Vancouver, BC V6T 1Z3, Canada
| | - David M Patrick
- UBC School of Population and Public Health, Faculty of Medicine, University of British Columbia, 2206 East Mall, Vancouver, BC V6T 1Z3, Canada
| | - Patrick Tang
- Department of Pathology and Laboratory Medicine, University of British Columbia, 2211 Wesbrook Mall, Vancouver, BC V6T 2B5, Canada ; Public Health Microbiology and Reference Laboratory, British Columbia Centre for Disease Control, 655 West 12th Avenue, Vancouver, BC V5Z 2B4, Canada
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