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Kron NS, Fieber LA, Baker L, Campbell C, Schmale MC. Host response to Aplysia Abyssovirus 1 in nervous system and gill. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2024; 159:105211. [PMID: 38885747 PMCID: PMC11378725 DOI: 10.1016/j.dci.2024.105211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 06/03/2024] [Accepted: 06/06/2024] [Indexed: 06/20/2024]
Abstract
The California sea hare (Aplysia californica) is a model for age associated cognitive decline. Recent researched identified a novel nidovirus, Aplysia Abyssovirus 1, with broad tropism enriched in the Aplysia nervous system. This virus is ubiquitous in wild and maricultured, young and old animals without obvious pathology. Here we re-evaluated gene expression data from several previous studies to investigate differential expression in the nervous system and gill in response to virus and aging as well as the mutational spectrum observed in the viral sequences obtained from these datasets. Viral load and age were highly correlated, indicating persistent infection. Upregulated genes in response to virus were enriched for immune genes and signatures of ER and proteostatic stress, while downregulated genes were enriched for mitochondrial metabolism. Differential expression with respect to age suggested increased iron accumulation and decreased glycolysis, fatty acid metabolism, and proteasome function. Interaction of gene expression trends associated with viral infection and aging suggest that viral infection likely plays a role in aging in the Aplysia nervous system. Mutation analysis of viral RNA identified signatures suggesting ADAR and AID/APOBEC like deaminase act as part of Aplysia anti-viral defense.
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Affiliation(s)
- Nicholas S Kron
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, 4600 Rickenbacker Cswy, Miami, FL, 33149, USA.
| | - Lynne A Fieber
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, 4600 Rickenbacker Cswy, Miami, FL, 33149, USA
| | - Lydia Baker
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, 4600 Rickenbacker Cswy, Miami, FL, 33149, USA
| | | | - Michael C Schmale
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, 4600 Rickenbacker Cswy, Miami, FL, 33149, USA
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Tóth F, Gáspár G, Pankovics P, Urbán P, Herczeg R, Albert M, Reuter G, Boros Á. Co-infecting viruses of species Bovine rhinitis B virus (Picornaviridae) and Bovine nidovirus 1 (Tobaniviridae) identified for the first time from a post-mortem respiratory sample of a sheep (Ovis aries) in Hungary. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 120:105585. [PMID: 38508364 DOI: 10.1016/j.meegid.2024.105585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/26/2024] [Accepted: 03/15/2024] [Indexed: 03/22/2024]
Abstract
In this study, a picornavirus and a nidovirus were identified from a single available nasopharyngeal swab (NPS) sample of a freshly deceased sheep, as the only vertebrate viruses found with viral metagenomics and next-generation sequencing methods. The sample was originated from a mixed feedlot farm in Hungary where sheep and cattle were held together but in separate stalls. Most of the sheep had respiratory signs (coughing and increased respiratory effort) at the time of sampling. Other NPS were not, but additional enteric samples were collected from sheep (n = 27) and cattle (n = 11) of the same farm at that time. The complete/nearly complete genomes of the identified viruses were determined using RT-PCR and Nanopore (MinION-Flonge) / Dye-terminator sequencing techniques. The results of detailed genomic and phylogenetic analyses indicate that the identified picornavirus most likely belongs to a type 4 genotype of species Bovine rhinitis B virus (BRBV-4, OR885914) of genus Aphthovirus, family Picornaviridae while the ovine nidovirus (OvNV, OR885915) - as a novel variant - could belong to the recently created Bovine nidovirus 1 (BoNV) species of genus Bostovirus, family Tobaniviridae. None of the identified viruses were detectable in the enteric samples using RT-PCR and generic screening primer pairs. Both viruses are well-known respiratory pathogens of cattle, but their presence was not demonstrated before in other animals, like sheep. Furthermore, neither BRBV-4 nor BoNVs were investigated in European cattle and/or sheep flocks, therefore it cannot be determined whether the presence of these viruses in sheep was a result of a single host species switch/spillover event or these viruses are circulating in not just cattle but sheep populations as well. Further studies required to investigate the spread of these viruses in Hungarian and European sheep and cattle populations and to identify their pathogenic potential in sheep.
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Affiliation(s)
- Fruzsina Tóth
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary
| | - Gábor Gáspár
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary
| | - Péter Pankovics
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary
| | - Péter Urbán
- János Szentágothai Research Centre of the University of Pécs, Bioinformatics Research Group, Genomics and Bioinformatics Core Facility, Pécs, Hungary
| | - Róbert Herczeg
- János Szentágothai Research Centre of the University of Pécs, Bioinformatics Research Group, Genomics and Bioinformatics Core Facility, Pécs, Hungary
| | | | - Gábor Reuter
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary
| | - Ákos Boros
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary.
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Kron NS, Neuman BW, Kumar S, Blackwelder PL, Vidal D, Walker-Phelan DZ, Gibbs PDI, Fieber LA, Schmale MC. Expression dynamics of the aplysia abyssovirus. Virology 2024; 589:109890. [PMID: 37951086 PMCID: PMC10842508 DOI: 10.1016/j.virol.2023.109890] [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: 07/11/2023] [Revised: 09/12/2023] [Accepted: 09/25/2023] [Indexed: 11/13/2023]
Abstract
Two recent studies documented the genome of a novel, extremely large (35.9 kb), nidovirus in RNA sequence databases from the marine neural model Aplysia californica. The goal of the present study was to document the distribution and transcriptional dynamics of this virus, Aplysia abyssovirus 1 (AAbV), in maricultured and wild animals. We confirmed previous findings that AAbV RNA is widespread and reaches extraordinary levels in apparently healthy animals. Transmission electron microscopy identified viral replication factories in ciliated gill epithelial cells but not in neurons where viral RNA is most highly expressed. Viral transcripts do not exhibit evidence of discontinuous RNA synthesis as in coronaviruses but are consistent with production of a single leaderless subgenomic RNA, as in the Gill-associated virus of Penaeus monodon. Splicing patterns in chronically infected adults suggested high levels of defective genomes, possibly explaining the lack of obvious disease signs in high viral load animals.
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Affiliation(s)
- Nicholas S Kron
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, 4600 Rickenbacker Cswy, Miami, FL, USA, 33149.
| | - Benjamin W Neuman
- Department of Biology, Department of Molecular Pathogenesis and Immunology and Division of Research, Texas A&M University, 400 Bizzell St., College Station, TX, USA, 77843
| | - Sathish Kumar
- Department of Biology, Department of Molecular Pathogenesis and Immunology and Division of Research, Texas A&M University, 400 Bizzell St., College Station, TX, USA, 77843
| | - Patricia L Blackwelder
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, 4600 Rickenbacker Cswy, Miami, FL, USA, 33149; University of Miami Center for Advanced Microscopy, University of Miami, 142B Physics, Coral Gables, FL, USA, 33146
| | - Dayana Vidal
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, 4600 Rickenbacker Cswy, Miami, FL, USA, 33149
| | - Delphina Z Walker-Phelan
- Department of Immunology, University of Washington, South Lake Union E-411 750 Republican St. UW Box 358059, Seattle, WA, 98109, USA
| | - Patrick D I Gibbs
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, 4600 Rickenbacker Cswy, Miami, FL, USA, 33149
| | - Lynne A Fieber
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, 4600 Rickenbacker Cswy, Miami, FL, USA, 33149
| | - Michael C Schmale
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, 4600 Rickenbacker Cswy, Miami, FL, USA, 33149
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Brito BP, Frost MJ, Anantanawat K, Jaya F, Batterham T, Djordjevic SP, Chang WS, Holmes EC, Darling AE, Kirkland PD. Expanding the range of the respiratory infectome in Australian feedlot cattle with and without respiratory disease using metatranscriptomics. MICROBIOME 2023; 11:158. [PMID: 37491320 PMCID: PMC10367309 DOI: 10.1186/s40168-023-01591-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 06/03/2023] [Indexed: 07/27/2023]
Abstract
BACKGROUND Bovine respiratory disease (BRD) is one of the most common diseases in intensively managed cattle, often resulting in high morbidity and mortality. Although several pathogens have been isolated and extensively studied, the complete infectome of the respiratory complex consists of a more extensive range unrecognised species. Here, we used total RNA sequencing (i.e., metatranscriptomics) of nasal and nasopharyngeal swabs collected from animals with and without BRD from two cattle feedlots in Australia. RESULTS A high abundance of bovine nidovirus, influenza D, bovine rhinitis A and bovine coronavirus was found in the samples. Additionally, we obtained the complete or near-complete genome of bovine rhinitis B, enterovirus E1, bovine viral diarrhea virus (sub-genotypes 1a and 1c) and bovine respiratory syncytial virus, and partial sequences of other viruses. A new species of paramyxovirus was also identified. Overall, the most abundant RNA virus, was the bovine nidovirus. Characterisation of bacterial species from the transcriptome revealed a high abundance and diversity of Mollicutes in BRD cases and unaffected control animals. Of the non-Mollicutes species, Histophilus somni was detected, whereas there was a low abundance of Mannheimia haemolytica. CONCLUSION This study highlights the use of untargeted sequencing approaches to study the unrecognised range of microorganisms present in healthy or diseased animals and the need to study previously uncultured viral species that may have an important role in cattle respiratory disease. Video Abstract.
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Affiliation(s)
- Barbara P Brito
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, New South Wales, Australia.
- New South Wales Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, New South Wales, Australia.
- Present Address: Biosecurity and Food Safety, NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute (EMAI), Menangle, New South Wales, Australia.
| | - Melinda J Frost
- New South Wales Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, New South Wales, Australia
| | - Kay Anantanawat
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, New South Wales, Australia
- Illumina Australia, Ultimo, New South Wales, Australia
| | - Frederick Jaya
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, New South Wales, Australia
| | | | - Steven P Djordjevic
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, New South Wales, Australia
| | - Wei-Shan Chang
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Aaron E Darling
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, New South Wales, Australia
- Illumina Australia, Ultimo, New South Wales, Australia
| | - Peter D Kirkland
- New South Wales Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, New South Wales, Australia
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Characterisation of the Upper Respiratory Tract Virome of Feedlot Cattle and Its Association with Bovine Respiratory Disease. Viruses 2023; 15:v15020455. [PMID: 36851669 PMCID: PMC9961997 DOI: 10.3390/v15020455] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/11/2023] [Accepted: 01/13/2023] [Indexed: 02/10/2023] Open
Abstract
Bovine respiratory disease (BRD) is a major health problem within the global cattle industry. This disease has a complex aetiology, with viruses playing an integral role. In this study, metagenomics was used to sequence viral nucleic acids in the nasal swabs of BRD-affected cattle. The viruses detected included those that are well known for their association with BRD in Australia (bovine viral diarrhoea virus 1), as well as viruses known to be present but not fully characterised (bovine coronavirus) and viruses that have not been reported in BRD-affected cattle in Australia (bovine rhinitis, bovine influenza D, and bovine nidovirus). The nasal swabs from a case-control study were subsequently tested for 10 viruses, and the presence of at least one virus was found to be significantly associated with BRD. Some of the more recently detected viruses had inconsistent associations with BRD. Full genome sequences for bovine coronavirus, a virus increasingly associated with BRD, and bovine nidovirus were completed. Both viruses belong to the Coronaviridae family, which are frequently associated with disease in mammals. This study has provided greater insights into the viral pathogens associated with BRD and highlighted the need for further studies to more precisely elucidate the roles viruses play in BRD.
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Zhou Z, Qiu Y, Ge X. The taxonomy, host range and pathogenicity of coronaviruses and other viruses in the Nidovirales order. ANIMAL DISEASES 2021; 1:5. [PMID: 34778878 PMCID: PMC8062217 DOI: 10.1186/s44149-021-00005-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/04/2021] [Indexed: 12/17/2022] Open
Abstract
The frequent emergence of coronavirus (CoV) epidemics has seriously threatened public health and stock farming. The major hosts for CoVs are birds and mammals. Although most CoVs inhabit their specific natural hosts, some may occasionally cross the host barrier to infect livestock and even people, causing a variety of diseases. Since the beginning of the new century, increasing attention has been given to research on CoVs due to the emergence of highly pathogenic and genetically diverse CoVs that have caused several epidemics, including the recent COVID-19 pandemic. CoVs belong to the Coronaviridae family of the Nidovirales order. Recently, advanced techniques for viral detection and viral genome analyses have enabled characterization of many new nidoviruses than ever and have greatly expanded the Nidovirales order with new classification and nomenclature. Here, we first provide an overview of the latest research progress in the classification of the Nidovirales order and then introduce the host range, genetic variation, genomic pattern and pathogenic features of epidemic CoVs and other epidemic viruses. This information will promote understanding of the phylogenetic relationship and infectious transmission of various pathogenic nidoviruses, including epidemic CoVs, which will benefit virological research and viral disease control.
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Affiliation(s)
- Zhijian Zhou
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, 27 Tianma Rd., Changsha, Hunan China
| | - Ye Qiu
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, 27 Tianma Rd., Changsha, Hunan China
| | - Xingyi Ge
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, 27 Tianma Rd., Changsha, Hunan China
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Parrish K, Kirkland PD, Skerratt LF, Ariel E. Nidoviruses in Reptiles: A Review. Front Vet Sci 2021; 8:733404. [PMID: 34621811 PMCID: PMC8490724 DOI: 10.3389/fvets.2021.733404] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/19/2021] [Indexed: 12/17/2022] Open
Abstract
Since their discovery in 2014, reptile nidoviruses (also known as serpentoviruses) have emerged as significant pathogens worldwide. They are known for causing severe and often fatal respiratory disease in various captive snake species, especially pythons. Related viruses have been detected in other reptiles with and without respiratory disease, including captive and wild populations of lizards, and wild populations of freshwater turtles. There are many opportunities to better understand the viral diversity, species susceptibility, and clinical presentation in different species in this relatively new field of research. In captive snake collections, reptile nidoviruses can spread quickly and be associated with high morbidity and mortality, yet the potential disease risk to wild reptile populations remains largely unknown, despite reptile species declining on a global scale. Experimental studies or investigations of disease outbreaks in wild reptile populations are scarce, leaving the available literature limited mostly to exploring findings of naturally infected animals in captivity. Further studies into the pathogenesis of different reptile nidoviruses in a variety of reptile species is required to explore the complexity of disease and routes of transmission. This review focuses on the biology of these viruses, hosts and geographic distribution, clinical signs and pathology, laboratory diagnosis and management of reptile nidovirus infections to better understand nidovirus infections in reptiles.
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Affiliation(s)
- Kate Parrish
- Virology Laboratory, Elizabeth Macarthur Agricultural Institute, New South Wales (NSW) Department of Primary Industries, Menangle, NSW, Australia.,College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, Australia
| | - Peter D Kirkland
- Virology Laboratory, Elizabeth Macarthur Agricultural Institute, New South Wales (NSW) Department of Primary Industries, Menangle, NSW, Australia.,College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, Australia
| | - Lee F Skerratt
- Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, University of Melbourne, Melbourne, VIC, Australia
| | - Ellen Ariel
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, Australia
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Hafez HM, Attia YA, Bovera F, Abd El-Hack ME, Khafaga AF, de Oliveira MC. Influence of COVID-19 on the poultry production and environment. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:44833-44844. [PMID: 34244934 PMCID: PMC8269985 DOI: 10.1007/s11356-021-15052-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 05/20/2021] [Indexed: 05/17/2023]
Abstract
Although chickens are not susceptible to SARS-CoV-2, several coronavirus disease outbreaks have been described concerning poultry processing facilities in different countries. The COVID-19 pandemic and the developed strain caused 2nd, 3rd, and recent Indian strain waves of epidemics that have led to unexpected consequences, such as forced reductions in demands for some industries, transportation systems, employment, and businesses due to public confinement. Besides, poultry processing plants' conditions exacerbate the risks due to the proximity on the line, cold, and humidity. Most workers do not have access to paid sick time or adequate health care, and because of the low wages, they have limited reserves to enable them to leave steady employment. In addition, workers in meat and poultry slaughterhouses may be infected through respiratory droplets in the air and/or from touching dirty surfaces or objects such as workstations, break room tables, or tools. Egg prices have increased dramatically during the lockdown as consumers have started to change their behaviors and habits. The COVID pandemic might also substantially impact the international poultry trade over the next several months. This review will focus on the effect of COVID-19 on poultry production, environmental sustainability, and earth systems from different process points of view.
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Affiliation(s)
- Hafez M Hafez
- Institute of Poultry Diseases, Faculty of Veterinary Medicine, Free University Berlin, Berlin, Germany.
| | - Youssef A Attia
- Department of Agriculture, Faculty of Environmental Sciences, King Abdulaziz University, P.O. Box 80208, Jeddah, 21589, Saudi Arabia.
- The Strategic Center to Kingdom Vision Realization, King Abdulaziz University, P.O. Box 80200, Jeddah, 21589, Saudi Arabia.
- Animal and Poultry Production Department, Faculty of Agriculture, Damanhour University, Damanhour, 22516, Egypt.
| | - Fulvia Bovera
- Department of Veterinary Medicine and Animal Production, University of Napoli Federico II, via F. Delpino 1, 80137, Naples, Italy
| | - Mohamed E Abd El-Hack
- Poultry Department, Faculty of Agriculture, Zagazig University, Zagazig, 44511, Egypt
| | - Asmaa F Khafaga
- Department of Pathology, Faculty of Veterinary Medicine, Alexandria University, Edfina, 22758, Egypt
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Li WT, Lee MS, Tseng YC, Yang NY. A case report of reptile-associated nidovirus (serpentovirus) in a ball python (Python regius) in Taiwan. J Vet Med Sci 2020; 82:788-792. [PMID: 32378646 PMCID: PMC7324828 DOI: 10.1292/jvms.20-0166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Reptile-associated nidoviruses (serpentoviruses) have been reported to cause
proliferative interstitial pneumonia in pythons and other reptile species. A captive,
younger than 2 years old, intact female ball python (Python regius)
showed increased oral mucus, wheezing, and audible breathing with weight loss. Gross and
microscopic examination revealed large amounts of mucus in the esophagus and proliferative
interstitial pneumonia. Serpentovirus genes were detected from the lung tissues by
polymerase chain reaction. The current serpentoviruses was phylogenetically grouped with
the serpentovirus previously identified in the US. No case of serpentovirus infection has
been reported in Asia. The present report provides information of complete genome sequence
and global distribution of serpentovirus.
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Affiliation(s)
- Wen-Ta Li
- Department of Pathology, Fishhead Labs, LLC, 5658 SE Pine Ave, Stuart, FL 34997, USA
| | - Ming-Shiuh Lee
- Animal Health Research Institute, Council of Agriculture, Executive Yuan, No. 376, Zhongzheng Rd., Tamsui Dist., New Taipei 251032, Taiwan
| | - Yi-Chia Tseng
- Jong-Shing Animal Hospital, No. 118-1, Dafeng 2nd Rd., Sanmin Dist., Kaohsiung City 807508, Taiwan
| | - Ning-Ya Yang
- Jong-Shing Animal Hospital, No. 118-1, Dafeng 2nd Rd., Sanmin Dist., Kaohsiung City 807508, Taiwan
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Blahak S, Jenckel M, Höper D, Beer M, Hoffmann B, Schlottau K. Investigations into the presence of nidoviruses in pythons. Virol J 2020; 17:6. [PMID: 31952524 PMCID: PMC6969405 DOI: 10.1186/s12985-020-1279-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 01/09/2020] [Indexed: 01/17/2023] Open
Abstract
Background Pneumonia and stomatitis represent severe and often fatal diseases in different captive snakes. Apart from bacterial infections, paramyxo-, adeno-, reo- and arenaviruses cause these diseases. In 2014, new viruses emerged as the cause of pneumonia in pythons. In a few publications, nidoviruses have been reported in association with pneumonia in ball pythons and a tiger python. The viruses were found using new sequencing methods from the organ tissue of dead animals. Methods Severe pneumonia and stomatitis resulted in a high mortality rate in a captive breeding collection of green tree pythons. Unbiased deep sequencing lead to the detection of nidoviral sequences. A developed RT-qPCR was used to confirm the metagenome results and to determine the importance of this virus. A total of 1554 different boid snakes, including animals suffering from respiratory diseases as well as healthy controls, were screened for nidoviruses. Furthermore, in addition to two full-length sequences, partial sequences were generated from different snake species. Results The assembled full-length snake nidovirus genomes share only an overall genome sequence identity of less than 66.9% to other published snake nidoviruses and new partial sequences vary between 99.89 and 79.4%. Highest viral loads were detected in lung samples. The snake nidovirus was not only present in diseased animals, but also in snakes showing no typical clinical signs. Conclusions Our findings further highlight the possible importance of snake nidoviruses in respiratory diseases and proof multiple circulating strains with varying disease potential. Nidovirus detection in clinical healthy individuals might represent testing during the incubation period or reconvalescence. Our investigations show new aspects of nidovirus infections in pythons. Nidoviruses should be included in routine diagnostic workup of diseased reptiles.
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Affiliation(s)
- Silvia Blahak
- Chemical and Veterinary Investigation Office, Westerfeldstraße 1, D-32758, Detmold, Germany
| | - Maria Jenckel
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, D-17493, Greifswald-Insel Riems, Germany.,Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT, 2601, Australia
| | - Dirk Höper
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, D-17493, Greifswald-Insel Riems, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, D-17493, Greifswald-Insel Riems, Germany
| | - Bernd Hoffmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, D-17493, Greifswald-Insel Riems, Germany
| | - Kore Schlottau
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, D-17493, Greifswald-Insel Riems, Germany.
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Virus Metagenomics in Farm Animals: A Systematic Review. Viruses 2020; 12:v12010107. [PMID: 31963174 PMCID: PMC7019290 DOI: 10.3390/v12010107] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 01/12/2020] [Accepted: 01/14/2020] [Indexed: 02/07/2023] Open
Abstract
A majority of emerging infectious diseases are of zoonotic origin. Metagenomic Next-Generation Sequencing (mNGS) has been employed to identify uncommon and novel infectious etiologies and characterize virus diversity in human, animal, and environmental samples. Here, we systematically reviewed studies that performed viral mNGS in common livestock (cattle, small ruminants, poultry, and pigs). We identified 2481 records and 120 records were ultimately included after a first and second screening. Pigs were the most frequently studied livestock and the virus diversity found in samples from poultry was the highest. Known animal viruses, zoonotic viruses, and novel viruses were reported in available literature, demonstrating the capacity of mNGS to identify both known and novel viruses. However, the coverage of metagenomic studies was patchy, with few data on the virome of small ruminants and respiratory virome of studied livestock. Essential metadata such as age of livestock and farm types were rarely mentioned in available literature, and only 10.8% of the datasets were publicly available. Developing a deeper understanding of livestock virome is crucial for detection of potential zoonotic and animal pathogens and One Health preparedness. Metagenomic studies can provide this background but only when combined with essential metadata and following the “FAIR” (Findable, Accessible, Interoperable, and Reusable) data principles.
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Hoon-Hanks LL, Ossiboff RJ, Bartolini P, Fogelson SB, Perry SM, Stöhr AC, Cross ST, Wellehan JFX, Jacobson ER, Dubovi EJ, Stenglein MD. Longitudinal and Cross-Sectional Sampling of Serpentovirus (Nidovirus) Infection in Captive Snakes Reveals High Prevalence, Persistent Infection, and Increased Mortality in Pythons and Divergent Serpentovirus Infection in Boas and Colubrids. Front Vet Sci 2019; 6:338. [PMID: 31632990 PMCID: PMC6786048 DOI: 10.3389/fvets.2019.00338] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 09/19/2019] [Indexed: 12/24/2022] Open
Abstract
The aim of this study of serpentovirus infection in captive snakes was to assess the susceptibility of different types of snakes to infection and disease, to survey viral genetic diversity, and to evaluate management practices that may limit infection and disease. Antemortem oral swabs were collected from 639 snakes from 12 US collections, including 62 species, 28 genera, and 6 families: Pythonidae (N = 414 snakes; pythons were overrepresented in the sample population), Boidae (79), Colubridae (116), Lamprophiidae (4), Elapidae (12), and Viperidae (14). Infection was more common in pythons (38%; 95% CI: 33.1-42.4%), and in boas (10%; 95% CI: 5.2-18.7%) than in colubrids (0.9%, 95% CI: <0.01-4.7%); infection was not detected in other snake families (lamprophiids 0/4, 95% CI: 0-49%; elapids 0/12, 95% CI: 0-24.2%; and vipers 0/14, 95% CI: 0-21.5%), but more of these snakes need to be tested to confirm these findings. Clinical signs of respiratory disease were common in infected pythons (85 of 144). Respiratory signs were only observed in 1 of 8 infected boas and were absent in the single infected colubrid. Divergent serpentoviruses were detected in pythons, boas, and colubrids, suggesting that different serpentoviruses might vary in their ability to infect snakes of different families. Older snakes were more likely to be infected than younger snakes (p-value < 0.001) but males and females were equally likely to be infected (female prevalence: 23.4%, 95% CI 18.7-28.9%; male prevalence: 23.5%, 95% CI 18-30.1%; p-value = 0.144). Neither age (p-value = 0.32) nor sex (p-value = 0.06) was statistically associated with disease severity. Longitudinal sampling of pythons in a single collection over 28 months revealed serpentovirus infection is persistent, and viral clearance was not observed. In this collection, infection was associated with significantly increased rates of mortality (p-value = 0.001) with death of 75% of infected pythons and no uninfected pythons over this period. Offspring of infected parents were followed: vertical transmission either does not occur or occurs with a much lower efficiency than horizontal transmission. Overall, these findings confirm that serpentoviruses pose a significant threat to the health of captive python populations and can cause infection in boa and colubrid species.
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Affiliation(s)
- Laura L. Hoon-Hanks
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, United States
| | - Robert J. Ossiboff
- Department of Comparative Diagnostic and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States
| | - Pia Bartolini
- Terrestrial & Arboreal, LLC, Melrose, FL, United States
| | | | - Sean M. Perry
- Department of Veterinary Clinical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, United States
| | - Anke C. Stöhr
- Department of Veterinary Clinical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, United States
| | - Shaun T. Cross
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, United States
| | - James F. X. Wellehan
- Department of Comparative Diagnostic and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States
| | - Elliott R. Jacobson
- Department of Comparative Diagnostic and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States
| | - Edward J. Dubovi
- Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States
| | - Mark D. Stenglein
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, United States
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13
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Rampacci E, Masi M, Origgi FC, Stefanetti V, Bottinelli M, Selleri P, Coletti M, Passamonti F. First molecular detection of ball python nidovirus in Italy - Short communication. Acta Vet Hung 2019; 67:127-134. [PMID: 30922084 DOI: 10.1556/004.2019.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A retrospective study was conducted to investigate the presence of ferlavirus, ball python nidovirus and bacteria in 32 tracheobronchial lavages from ball pythons raised in captivity and affected by respiratory disease. A touchdown reverse transcription polymerase reaction (RT-PCR) was performed to detect ball python nidovirus RNA targeting a 260-bp portion of the ORF1a gene, while a nested RT-PCR was applied to identify RNA targeting the 518-bp ferlavirus partial L gene. RT-PCR positive products were submitted for Sanger's sequencing and phylogeny reconstruction. Bacteriological examinations were performed to diagnose a possible bacterial involvement. BLAST analysis revealed that the nucleotide sequences of the six (18.8%) RT-PCR positive amplicons were 90-97% identical to the partial sequence of the ORF1a gene of the recently described ball python nidovirus. All tested snakes were negative for ferlavirus. Thirteen out of 32 samples (40.6%) were bacteriologically positive. Respiratory tract diseases can be a substantial problem for snake breeders, considering the rapid transmission of respiratory pathogens. The results and published studies show that ball python nidovirus is circulating in python collections and could be linked to suboptimal management practices. Surveillance programs are desirable as part of the routine snake health assessment. Tracheobronchial lavage is a fast, practical, cost-effective procedure for sample collection.
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Affiliation(s)
- Elisa Rampacci
- 1 Department of Veterinary Medicine, University of Perugia, San Costanzo 4, 06126, Perugia, Italy
| | - Marco Masi
- 2 Centro Veterinario Specialistico, Rome, Italy
| | - Francesco Carlo Origgi
- 3 Department of Infectious Diseases and Pathobiology, Centre for Fish and Wildlife Health, University of Bern, Bern, Switzerland
| | - Valentina Stefanetti
- 1 Department of Veterinary Medicine, University of Perugia, San Costanzo 4, 06126, Perugia, Italy
| | - Marco Bottinelli
- 1 Department of Veterinary Medicine, University of Perugia, San Costanzo 4, 06126, Perugia, Italy
| | | | - Mauro Coletti
- 1 Department of Veterinary Medicine, University of Perugia, San Costanzo 4, 06126, Perugia, Italy
| | - Fabrizio Passamonti
- 1 Department of Veterinary Medicine, University of Perugia, San Costanzo 4, 06126, Perugia, Italy
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14
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Saberi A, Gulyaeva AA, Brubacher JL, Newmark PA, Gorbalenya AE. A planarian nidovirus expands the limits of RNA genome size. PLoS Pathog 2018; 14:e1007314. [PMID: 30383829 PMCID: PMC6211748 DOI: 10.1371/journal.ppat.1007314] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 09/02/2018] [Indexed: 12/28/2022] Open
Abstract
RNA viruses are the only known RNA-protein (RNP) entities capable of autonomous replication (albeit within a permissive host environment). A 33.5 kilobase (kb) nidovirus has been considered close to the upper size limit for such entities; conversely, the minimal cellular DNA genome is in the 100–300 kb range. This large difference presents a daunting gap for the transition from primordial RNP to contemporary DNA-RNP-based life. Whether or not RNA viruses represent transitional steps towards DNA-based life, studies of larger RNA viruses advance our understanding of the size constraints on RNP entities and the role of genome size in virus adaptation. For example, emergence of the largest previously known RNA genomes (20–34 kb in positive-stranded nidoviruses, including coronaviruses) is associated with the acquisition of a proofreading exoribonuclease (ExoN) encoded in the open reading frame 1b (ORF1b) in a monophyletic subset of nidoviruses. However, apparent constraints on the size of ORF1b, which encodes this and other key replicative enzymes, have been hypothesized to limit further expansion of these viral RNA genomes. Here, we characterize a novel nidovirus (planarian secretory cell nidovirus; PSCNV) whose disproportionately large ORF1b-like region including unannotated domains, and overall 41.1-kb genome, substantially extend the presumed limits on RNA genome size. This genome encodes a predicted 13,556-aa polyprotein in an unconventional single ORF, yet retains canonical nidoviral genome organization and expression, as well as key replicative domains. These domains may include functionally relevant substitutions rarely or never before observed in highly conserved sites of RdRp, NiRAN, ExoN and 3CLpro. Our evolutionary analysis suggests that PSCNV diverged early from multi-ORF nidoviruses, and acquired additional genes, including those typical of large DNA viruses or hosts, e.g. Ankyrin and Fibronectin type II, which might modulate virus-host interactions. PSCNV's greatly expanded genome, proteomic complexity, and unique features–impressive in themselves–attest to the likelihood of still-larger RNA genomes awaiting discovery. RNA viruses are the only known RNA-protein (RNP) entities capable of autonomous replication. The upper genome size for such entities was assumed to be <35 kb; conversely, the minimal cellular DNA genome is in the 100–300 kilobase (kb) range. This large difference presents a daunting gap for the proposed evolution of contemporary DNA-RNP-based life from primordial RNP entities. Here, we describe a nidovirus from planarians, named planarian secretory cell nidovirus (PSCNV), whose 41.1 kb genome is 23% larger than any riboviral genome yet discovered. This increase is nearly equivalent in size to the entire poliovirus genome, and it equips PSCNV with an unprecedented extra coding capacity to adapt. PSCNV has broken apparent constraints on the size of the genomic subregion that encodes core replication machinery in other nidoviruses, including coronaviruses, and has acquired genes not previously observed in RNA viruses. This virus challenges and advances our understanding of the limits to RNA genome size.
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Affiliation(s)
- Amir Saberi
- Howard Hughes Medical Institute, Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America
| | - Anastasia A. Gulyaeva
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - John L. Brubacher
- Department of Biology, Canadian Mennonite University, Winnipeg, Canada
| | - Phillip A. Newmark
- Howard Hughes Medical Institute, Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America
- * E-mail: (PAN); (AEG)
| | - Alexander E. Gorbalenya
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
- * E-mail: (PAN); (AEG)
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15
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Bukhari K, Mulley G, Gulyaeva AA, Zhao L, Shu G, Jiang J, Neuman BW. Description and initial characterization of metatranscriptomic nidovirus-like genomes from the proposed new family Abyssoviridae, and from a sister group to the Coronavirinae, the proposed genus Alphaletovirus. Virology 2018; 524:160-171. [PMID: 30199753 PMCID: PMC7112036 DOI: 10.1016/j.virol.2018.08.010] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 08/11/2018] [Accepted: 08/11/2018] [Indexed: 01/12/2023]
Abstract
Transcriptomics has the potential to discover new RNA virus genomes by sequencing total intracellular RNA pools. In this study, we have searched publicly available transcriptomes for sequences similar to viruses of the Nidovirales order. We report two potential nidovirus genomes, a highly divergent 35.9 kb likely complete genome from the California sea hare Aplysia californica, which we assign to a nidovirus named Aplysia abyssovirus 1 (AAbV), and a coronavirus-like 22.3 kb partial genome from the ornamented pygmy frog Microhyla fissipes, which we assign to a nidovirus named Microhyla alphaletovirus 1 (MLeV). AAbV was shown to encode a functional main proteinase, and a translational readthrough signal. Phylogenetic analysis suggested that AAbV represents a new family, proposed here as Abyssoviridae. MLeV represents a sister group to the other known coronaviruses. The importance of MLeV and AAbV for understanding nidovirus evolution, and the origin of terrestrial nidoviruses are discussed.
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Affiliation(s)
| | | | - Anastasia A Gulyaeva
- Dept. Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Lanying Zhao
- Chengdu Institute of Biology, Chinese Academy of Science, Chengdu, China
| | - Guocheng Shu
- Chengdu Institute of Biology, Chinese Academy of Science, Chengdu, China
| | - Jianping Jiang
- Chengdu Institute of Biology, Chinese Academy of Science, Chengdu, China
| | - Benjamin W Neuman
- Texas A&M University-Texarkana, 7101 University Ave, Texarkana, TX 75503, United States.
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16
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Respiratory disease in ball pythons (Python regius) experimentally infected with ball python nidovirus. Virology 2018; 517:77-87. [DOI: 10.1016/j.virol.2017.12.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 12/01/2017] [Accepted: 12/11/2017] [Indexed: 01/22/2023]
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17
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Dervas E, Hepojoki J, Laimbacher A, Romero-Palomo F, Jelinek C, Keller S, Smura T, Hepojoki S, Kipar A, Hetzel U. Nidovirus-Associated Proliferative Pneumonia in the Green Tree Python (Morelia viridis). J Virol 2017; 91:e00718-17. [PMID: 28794044 PMCID: PMC5640870 DOI: 10.1128/jvi.00718-17] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Accepted: 07/24/2017] [Indexed: 12/20/2022] Open
Abstract
In 2014 we observed a noticeable increase in the number of sudden deaths among green tree pythons (Morelia viridis). Pathological examination revealed the accumulation of mucoid material within the airways and lungs in association with enlargement of the entire lung. We performed a full necropsy and histological examination on 12 affected green tree pythons from 7 different breeders to characterize the pathogenesis of this mucinous pneumonia. By histology we could show a marked hyperplasia of the airway epithelium and of faveolar type II pneumocytes. Since routine microbiological tests failed to identify a causative agent, we studied lung tissue samples from a few diseased snakes by next-generation sequencing (NGS). From the NGS data we could assemble a piece of RNA genome whose sequence was <85% identical to that of nidoviruses previously identified in ball pythons and Indian pythons. We then employed reverse transcription-PCR to demonstrate the presence of the novel nidovirus in all diseased snakes. To attempt virus isolation, we established primary cultures of Morelia viridis liver and brain cells, which we inoculated with homogenates of lung tissue from infected individuals. Ultrastructural examination of concentrated cell culture supernatants showed the presence of nidovirus particles, and subsequent NGS analysis yielded the full genome of the novel virus Morelia viridis nidovirus (MVNV). We then generated an antibody against MVNV nucleoprotein, which we used alongside RNA in situ hybridization to demonstrate viral antigen and RNA in the affected lungs. This suggests that in natural infection MVNV damages the respiratory tract epithelium, which then results in epithelial hyperplasia, most likely as an exaggerated regenerative attempt in association with increased epithelial turnover.IMPORTANCE Novel nidoviruses associated with severe respiratory disease were fairly recently identified in ball pythons and Indian pythons. Herein we report on the isolation and identification of a further nidovirus from green tree pythons (Morelia viridis) with fatal pneumonia. We thoroughly characterized the pathological changes in the infected individuals and show that nidovirus infection is associated with marked epithelial proliferation in the respiratory tract. We speculate that this and the associated excess mucus production can lead to the animals' death by inhibiting normal gas exchange in the lungs. The virus was predominantly detected in the respiratory tract, which renders transmission via the respiratory route likely. Nidoviruses cause sudden outbreaks with high rates of mortality in breeding collections, and most affected snakes die without prior clinical signs. These findings, together with those of other groups, indicate that nidoviruses are a likely cause of severe pneumonia in pythons.
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Affiliation(s)
- Eva Dervas
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Jussi Hepojoki
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
- University of Helsinki, Medicum, Department of Virology, Helsinki, Finland
| | - Andrea Laimbacher
- Institute of Virology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Fernando Romero-Palomo
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Christine Jelinek
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Saskia Keller
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Teemu Smura
- University of Helsinki, Medicum, Department of Virology, Helsinki, Finland
| | - Satu Hepojoki
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Anja Kipar
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Udo Hetzel
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
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18
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Toohey-Kurth K, Sibley SD, Goldberg TL. Metagenomic assessment of adventitious viruses in commercial bovine sera. Biologicals 2017; 47:64-68. [PMID: 28366627 DOI: 10.1016/j.biologicals.2016.10.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 10/19/2016] [Accepted: 10/20/2016] [Indexed: 11/29/2022] Open
Abstract
Animal serum is an essential supplement for cell culture media. Contamination of animal serum with adventitious viruses has led to major regulatory action and product recalls. We used metagenomic methods to detect and characterize viral contaminants in 26 bovine serum samples from 12 manufacturers. Across samples, we detected sequences with homology to 20 viruses at depths of up to 50,000 viral reads per million. The viruses detected represented nine viral families plus four taxonomically unassigned viruses and had both RNA genomes and DNA genomes. Sequences ranged from 28% to 96% similar at the amino acid level to viruses in the GenBank database. The number of viruses varied from zero to 11 among samples and from one to 11 among suppliers, with only one product from one supplier being entirely "clean." For one common adventitious virus, bovine viral diarrhea virus (BVDV), abundance estimates calculated from metagenomic data (viral reads per million) closely corresponded to Ct values from quantitative real-time reverse transcription polymerase chain reaction (rtq-PCR), with metagenomics being approximately as sensitive as rtq-PCR. Metagenomics is useful for detecting taxonomically and genetically diverse adventitious viruses in commercial serum products, and it provides sensitive and quantitative information.
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Affiliation(s)
- Kathy Toohey-Kurth
- University of Wisconsin-Madison, Department of Pathobiological Sciences, 1656 Linden Drive, Madison, WI 53706, USA; Wisconsin Veterinary Diagnostic Laboratory, 445 Easterday Lane, Madison, WI 53706, USA
| | - Samuel D Sibley
- University of Wisconsin-Madison, Department of Pathobiological Sciences, 1656 Linden Drive, Madison, WI 53706, USA
| | - Tony L Goldberg
- University of Wisconsin-Madison, Department of Pathobiological Sciences, 1656 Linden Drive, Madison, WI 53706, USA; University of Wisconsin-Madison Global Health Institute, 1300 University Avenue, Madison, WI 53706, USA.
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19
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O’Dea MA, Jackson B, Jackson C, Xavier P, Warren K. Discovery and Partial Genomic Characterisation of a Novel Nidovirus Associated with Respiratory Disease in Wild Shingleback Lizards (Tiliqua rugosa). PLoS One 2016; 11:e0165209. [PMID: 27828982 PMCID: PMC5102451 DOI: 10.1371/journal.pone.0165209] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 10/07/2016] [Indexed: 12/17/2022] Open
Abstract
A respiratory disease syndrome has been observed in large numbers of wild shingleback lizards (Tiliqua rugosa) admitted to wildlife care facilities in the Perth metropolitan region of Western Australia. Mortality rates are reportedly high without supportive treatment and care. Here we used next generation sequencing techniques to screen affected and unaffected individuals admitted to Kanyana Wildlife Rehabilitation Centre in Perth between April and December 2015, with the resultant discovery of a novel nidovirus significantly associated with cases of respiratory disease according to a case definition based on clinical signs. Interestingly this virus was also found in 12% of apparently healthy individuals, which may reflect testing during the incubation period or a carrier status, or it may be that this agent is not causative in the disease process. This is the first report of a nidovirus in lizards globally. In addition to detection of this virus, characterisation of a 23,832 nt segment of the viral genome revealed the presence of characteristic nidoviral genomic elements providing phylogenetic support for the inclusion of this virus in a novel genus alongside Ball Python nidovirus, within the Torovirinae sub-family of the Coronaviridae. This study highlights the importance of next generation sequencing technologies to detect and describe emerging infectious diseases in wildlife species, as well as the importance of rehabilitation centres to enhance early detection mechanisms through passive and targeted health surveillance. Further development of diagnostic tools from these findings will aid in detection and control of this agent across Australia, and potentially in wild lizard populations globally.
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Affiliation(s)
- Mark A. O’Dea
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, Australia
- * E-mail:
| | - Bethany Jackson
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, Australia
| | - Carol Jackson
- Kanyana Wildlife Rehabilitation Centre, 120 Gilchrist Rd, Lesmurdie, WA, Australia
| | - Pally Xavier
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, Australia
| | - Kristin Warren
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, Australia
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20
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Mitra N, Cernicchiaro N, Torres S, Li F, Hause BM. Metagenomic characterization of the virome associated with bovine respiratory disease in feedlot cattle identified novel viruses and suggests an etiologic role for influenza D virus. J Gen Virol 2016; 97:1771-1784. [PMID: 27154756 DOI: 10.1099/jgv.0.000492] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bovine respiratory disease (BRD) is the most costly disease affecting the cattle industry. The pathogenesis of BRD is complex and includes contributions from microbial pathogens as well as host, environmental and animal management factors. In this study, we utilized viral metagenomic sequencing to explore the virome of nasal swab samples obtained from feedlot cattle with acute BRD and asymptomatic pen-mates at six and four feedlots in Mexico and the USA, respectively, in April-October 2015. Twenty-one viruses were detected, with bovine rhinitis A (52.7 %) and B (23.7 %) virus, and bovine coronavirus (24.7 %) being the most commonly identified. The emerging influenza D virus (IDV) tended to be significantly associated (P=0.134; odds ratio=2.94) with disease, whereas viruses commonly associated with BRD such as bovine viral diarrhea virus, bovine herpesvirus 1, bovine respiratory syncytial virus and bovine parainfluenza 3 virus were detected less frequently. The detection of IDV was further confirmed using a real-time PCR assay. Nasal swabs from symptomatic animals had significantly more IDV RNA than those collected from healthy animals (P=0.04). In addition to known viruses, new genotypes of bovine rhinitis B virus and enterovirus E were identified and a newly proposed species of bocaparvovirus, Ungulate bocaparvovirus 6, was characterized. Ungulate tetraparvovirus 1 was also detected for the first time in North America to our knowledge. These results illustrate the complexity of the virome associated with BRD and highlight the need for further research into the contribution of other viruses to BRD pathogenesis.
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Affiliation(s)
- Namita Mitra
- Veterinary Diagnostic Laboratory, 1800 Denison Avenue, Kansas State University, Manhattan, KS 66506, USA
| | - Natalia Cernicchiaro
- Department of Diagnostic Medicine and Pathobiology, 1800 Denison Avenue, Kansas State University, Manhattan, KS 66506, USA
| | - Siddartha Torres
- Merck Animal Health, 2 Giralda Farms, Madison City, NJ 07940, USA
| | - Feng Li
- Departments of Biology and Microbiology and Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD 57007, USA
| | - Ben M Hause
- Department of Diagnostic Medicine and Pathobiology, 1800 Denison Avenue, Kansas State University, Manhattan, KS 66506, USA.,Veterinary Diagnostic Laboratory, 1800 Denison Avenue, Kansas State University, Manhattan, KS 66506, USA
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