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Ullah Khan N, Sadiq A, Khan J, Basharat N, Hassan ZU, Ali I, Shah TA, Bourhia M, Bin Jardan YA, Wondmie GF. Molecular characterization of plasma virome of hepatocellular carcinoma (HCC) patients. AMB Express 2024; 14:46. [PMID: 38664337 PMCID: PMC11045709 DOI: 10.1186/s13568-024-01696-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
Hepatocellular carcinoma (HCC) stands as the most common cancer type, arising from various causes, and responsible for a substantial number of cancer-related fatalities. Recent advancements in viral metagenomics have empowered scientists to delve into the intricate diversity of the virosphere, viral evolution, interactions between viruses and their hosts, and the identification of viral causes behind disease outbreaks, the development of specific symptoms, and their potential role in altering the host's physiology. The present study had the objective of "Molecular Characterization of HBV, HCV, anelloviruses, CMV, SENV-D, SENV-H, HEV, and HPV viruses among individuals suffering from HCC." A total of 381 HCC patients contributed 10 cc of blood each for this study. The research encompassed the assessment of tumor markers, followed by molecular characterization of HBV, HCV, Anelloviruses (TTV, TTMV, and TTMDV), SENV-H and SENV-D viruses, HEV, CMV, and HPV, as well as histopathological examinations. The outcomes of this study revealed that majority of the HCC patients 72.4% (276/381) were male as compared to females. HCV infection, at 76.4% (291 out of 381), exhibited a significant association (p < 0.05) with HCC. Most patients displayed singular lesions in the liver, with Child Pugh Score Type B being the predominant finding in 45.2% of cases. Plasma virome analysis indicated the prevalence of TTMDV (75%), followed by TTMV (70%) and TTV (42.1%) among anelloviruses in HCC patients. Similarly, SENV-H (52%) was followed by SENV-D (20%), with co-infections at 15%. The presence of CMV and HEV among the HCC patients was recorded 5% each however 3.5% of the patients showed the presence of HPV. In conclusion, this study underscores that HCC patients serve as reservoirs for various pathogenic and non-pathogenic viruses, potentially contributing to the development, progression, and severity of the disease.
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Affiliation(s)
- Niamat Ullah Khan
- Molecular Virology Laboratory, Department of Biosciences, COMSATS University, Islamabad, Pakistan
| | - Asma Sadiq
- Department of Microbiology, University of Jhang, Punjab, Pakistan
| | - Jadoon Khan
- Molecular Virology Laboratory, Department of Biosciences, COMSATS University, Islamabad, Pakistan.
- Department of Allied Health Sciences, Iqra University, Chak Shahzad Campus, Islamabad, Pakistan.
| | - Nosheen Basharat
- Department of Microbiology, University of Jhang, Punjab, Pakistan
| | - Zulfiqar Ul Hassan
- Department of Allied Health Sciences, Iqra University, Chak Shahzad Campus, Islamabad, Pakistan
| | - Ijaz Ali
- Molecular Virology Laboratory, Department of Biosciences, COMSATS University, Islamabad, Pakistan
- Center for Applied Mathematics and Bioinformatics (CAMB), Gulf University for Science and Technology, West Mishref, Kuwait
| | - Tawaf Ali Shah
- College of Agriculture Engineering and Food Science, Shandong University of Technology, Zibo, 255000, China
| | - Mohammed Bourhia
- Laboratory of Biotechnology and Natural Resources Valorization, Faculty of Sciences, Ibn Zohr University, Agadir, 80060, Morocco.
| | - Yousef A Bin Jardan
- Department of Pharmaceutics, College of Pharmacy, King Saud University, P.O. Box 11451, Riyadh, Saudi Arabia
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Streicher T, Brinker P, Tragust S, Paxton RJ. Host Barriers Limit Viral Spread in a Spillover Host: A Study of Deformed Wing Virus in the Bumblebee Bombus terrestris. Viruses 2024; 16:607. [PMID: 38675948 PMCID: PMC11053533 DOI: 10.3390/v16040607] [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: 03/30/2024] [Revised: 04/13/2024] [Accepted: 04/13/2024] [Indexed: 04/28/2024] Open
Abstract
The transmission of pathogens from reservoir to recipient host species, termed pathogen spillover, can profoundly impact plant, animal, and public health. However, why some pathogens lead to disease emergence in a novel species while others fail to establish or do not elicit disease is often poorly understood. There is strong evidence that deformed wing virus (DWV), an (+)ssRNA virus, spills over from its reservoir host, the honeybee Apis mellifera, into the bumblebee Bombus terrestris. However, the low impact of DWV on B. terrestris in laboratory experiments suggests host barriers to virus spread in this recipient host. To investigate potential host barriers, we followed the spread of DWV genotype B (DWV-B) through a host's body using RT-PCR after experimental transmission to bumblebees in comparison to honeybees. Inoculation was per os, mimicking food-borne transmission, or by injection into the bee's haemocoel, mimicking vector-based transmission. In honeybees, DWV-B was present in both honeybee faeces and haemolymph within 3 days of inoculation per os or by injection. In contrast, DWV-B was not detected in B. terrestris haemolymph after inoculation per os, suggesting a gut barrier that hinders DWV-B's spread through the body of a B. terrestris. DWV-B was, however, detected in B. terrestris faeces after injection and feeding, albeit at a lower abundance than that observed for A. mellifera, suggesting that B. terrestris sheds less DWV-B than A. mellifera in faeces when infected. Barriers to viral spread in B. terrestris following oral infection may limit DWV's impact on this spillover host and reduce its contribution to the community epidemiology of DWV.
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Affiliation(s)
- Tabea Streicher
- General Zoology, Institute for Biology, Martin Luther University Halle-Wittenberg, Hoher Weg 8, 06120 Halle (Saale), Germany
| | - Pina Brinker
- General Zoology, Institute for Biology, Martin Luther University Halle-Wittenberg, Hoher Weg 8, 06120 Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
| | - Simon Tragust
- General Zoology, Institute for Biology, Martin Luther University Halle-Wittenberg, Hoher Weg 8, 06120 Halle (Saale), Germany
| | - Robert J. Paxton
- General Zoology, Institute for Biology, Martin Luther University Halle-Wittenberg, Hoher Weg 8, 06120 Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
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Medina JE, Castañeda S, Páez-Triana L, Camargo M, Garcia-Corredor DJ, Gómez M, Luna N, Ramírez AL, Pulido-Medellín M, Muñoz M, Ramírez JD. High prevalence of Enterovirus E, Bovine Kobuvirus, and Astrovirus revealed by viral metagenomics in fecal samples from cattle in Central Colombia. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 117:105543. [PMID: 38135265 DOI: 10.1016/j.meegid.2023.105543] [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: 11/13/2023] [Revised: 12/13/2023] [Accepted: 12/16/2023] [Indexed: 12/24/2023]
Abstract
Livestock plays a crucial role in ensuring food security and driving the global economy. However, viral infections can have far-reaching consequences beyond economic productivity, affecting the health of cattle, as well as posing risks to human health and other animals. Identifying viruses present in fecal samples, a primary route of pathogen transmission, is essential for developing effective prevention, control, and surveillance strategies. Viral metagenomic approaches offer a broader perspective and hold great potential for detecting previously unknown viruses or uncovering previously undescribed agents. Ubaté Province is Colombia's dairy capital and a key center for livestock production in the country. Therefore, the purpose of this study was to characterize viral communities in fecal samples from cattle in this region. A total of 42 samples were collected from three municipalities in Ubaté Province, located in central Colombia, using a convenient non-probabilistic sampling method. We utilized metagenomic sequencing with Oxford Nanopore Technologies (ONT), combined with diversity and phylogenetic analysis. The findings revealed a consistent and stable viral composition across the municipalities, primarily comprising members of the Picornaviridae family. At the species level, the most frequent viruses were Enterovirus E (EVE) and Bovine Astrovirus (BoAstV). Significantly, this study reported, for the first time in Colombia, the presence of viruses with veterinary importance occurring at notable frequencies: EVE (59%), Bovine Kobuvirus (BKV) (52%), and BoAstV (19%). Additionally, the study confirmed the existence of Circular replicase-encoding single-stranded (CRESS) Virus in animal feces. These sequences were phylogenetically grouped with samples obtained from Asia and Latin America, underscoring the importance of having adequate representation across the continent. The virome of bovine feces in Ubaté Province is characterized by the predominance of potentially pathogenic viruses such as BoAstV and EVE that have been reported with substantial frequency and quantities. Several of these viruses were identified in Colombia for the first time. This study showcases the utility of using metagenomic sequencing techniques in epidemiological surveillance. It also paves the way for further research on the influence of these agents on bovine health and their frecuency across the country.
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Affiliation(s)
- Julián Esteban Medina
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Sergio Castañeda
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Luisa Páez-Triana
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Milena Camargo
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia; Centro de Tecnología en Salud (CETESA), Innovaseq SAS, Funza, Cundinamarca, Colombia
| | - Diego J Garcia-Corredor
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia; Grupo de Investigación en Medicina Veterinaria y Zootecnia, Facultad de Ciencias Agropecuarias, Universidad Pedagógica y Tecnológica de Colombia, Tunja, Colombia
| | - Marcela Gómez
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia; Grupo de Investigación en Ciencias Básicas (NÚCLEO) Facultad de Ciencias e Ingeniería, Universidad de Boyacá, Tunja, Colombia
| | - Nicolas Luna
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Angie L Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Martín Pulido-Medellín
- Grupo de Investigación en Medicina Veterinaria y Zootecnia, Facultad de Ciencias Agropecuarias, Universidad Pedagógica y Tecnológica de Colombia, Tunja, Colombia
| | - Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia.
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François S, Nazki S, Vickers SH, Fournié G, Perrins CM, Broadbent AJ, Pybus OG, Hill SC. Genetic diversity, recombination and cross-species transmission of a waterbird gammacoronavirus in the wild. J Gen Virol 2023; 104. [PMID: 37589541 DOI: 10.1099/jgv.0.001883] [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] [Indexed: 08/18/2023] Open
Abstract
Viruses emerging from wildlife can cause outbreaks in humans and domesticated animals. Predicting the emergence of future pathogens and mitigating their impacts requires an understanding of what shapes virus diversity and dynamics in wildlife reservoirs. In order to better understand coronavirus ecology in wild species, we sampled birds within a coastal freshwater lagoon habitat across 5 years, focussing on a large population of mute swans (Cygnus olor) and the diverse species that they interact with. We discovered and characterised the full genome of a divergent gammacoronavirus belonging to the Goose coronavirus CB17 species. We investigated the genetic diversity and dynamics of this gammacoronavirus using untargeted metagenomic sequencing of 223 faecal samples from swans of known age and sex, and RT-PCR screening of 1632 additional bird samples. The virus circulated persistently within the bird community; virus prevalence in mute swans exhibited seasonal variations, but did not change with swan age-class or epidemiological year. One whole genome was fully characterised, and revealed that the virus originated from a recombination event involving an undescribed gammacoronavirus species. Multiple lineages of this gammacoronavirus co-circulated within our study population. Viruses from this species have recently been detected in aquatic birds from both the Anatidae and Rallidae families, implying that host species habitat sharing may be important in shaping virus host range. As the host range of the Goose coronavirus CB17 species is not limited to geese, we propose that this species name should be updated to 'Waterbird gammacoronavirus 1'. Non-invasive sampling of bird coronaviruses may provide a tractable model system for understanding the evolutionary and cross-species dynamics of coronaviruses.
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Affiliation(s)
- Sarah François
- Department of Biology, University of Oxford, South Park Road, Oxford, OX1 3SY, UK
| | - Salik Nazki
- Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Headington, Oxford, OX3 7FZ, UK
- The Pirbright Institute, Ash Rd, Pirbright, Woking GU24 0NF, UK
| | - Stephen H Vickers
- Department of Pathobiology and Population Science, Royal Veterinary College, Hawkshead Lane, Hatfield, AL9 7TA, UK
| | - Guillaume Fournié
- Department of Pathobiology and Population Science, Royal Veterinary College, Hawkshead Lane, Hatfield, AL9 7TA, UK
- Université de Lyon, INRAE, VetAgro Sup, UMR EPIA, Marcy l'Etoile, France
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, Saint-Gènes-Champanelle, France
| | | | - Andrew J Broadbent
- The Pirbright Institute, Ash Rd, Pirbright, Woking GU24 0NF, UK
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD20742, USA
| | - Oliver G Pybus
- Department of Biology, University of Oxford, South Park Road, Oxford, OX1 3SY, UK
- Department of Pathobiology and Population Science, Royal Veterinary College, Hawkshead Lane, Hatfield, AL9 7TA, UK
| | - Sarah C Hill
- Department of Pathobiology and Population Science, Royal Veterinary College, Hawkshead Lane, Hatfield, AL9 7TA, UK
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Kosoltanapiwat N, van der Hoek L, Kinsella CM, Tongshoob J, Prasittichai L, Klein M, Jebbink MF, Deijs M, Reamtong O, Boonnak K, Khongsiri W, Phadungsombat J, Tongthainan D, Tulayakul P, Yindee M. A Novel Simian Adenovirus Associating with Human Adeno-virus Species G Isolated from Long-Tailed Macaque Feces. Viruses 2023; 15:1371. [PMID: 37376670 PMCID: PMC10303043 DOI: 10.3390/v15061371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/05/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
Metagenomics has demonstrated its capability in outbreak investigations and pathogen surveillance and discovery. With high-throughput and effective bioinformatics, many disease-causing agents, as well as novel viruses of humans and animals, have been identified using metagenomic analysis. In this study, a VIDISCA metagenomics workflow was used to identify potential unknown viruses in 33 fecal samples from asymptomatic long-tailed macaques (Macaca fascicularis) in Ratchaburi Province, Thailand. Putatively novel astroviruses, enteroviruses, and adenoviruses were detected and confirmed by PCR analysis of long-tailed macaque fecal samples collected from areas in four provinces, Ratchaburi, Kanchanaburi, Lopburi, and Prachuap Khiri Khan, where humans and monkeys live in proximity (total n = 187). Astroviruses, enteroviruses, and adenoviruses were present in 3.2%, 7.5%, and 4.8% of macaque fecal samples, respectively. One adenovirus, named AdV-RBR-6-3, was successfully isolated in human cell culture. Whole-genome analysis suggested that it is a new member of the species Human adenovirus G, closely related to Rhesus adenovirus 53, with evidence of genetic recombination and variation in the hexon, fiber, and CR1 genes. Sero-surveillance showed neutralizing antibodies against AdV-RBR-6-3 in 2.9% and 11.2% of monkeys and humans, respectively, suggesting cross-species infection of monkeys and humans. Overall, we reported the use of metagenomics to screen for possible new viruses, as well as the isolation and molecular and serological characterization of the new adenovirus with cross-species transmission potential. The findings emphasize that zoonotic surveillance is important and should be continued, especially in areas where humans and animals interact, to predict and prevent the threat of emerging zoonotic pathogens.
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Affiliation(s)
- Nathamon Kosoltanapiwat
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (J.T.); (W.K.)
| | - Lia van der Hoek
- Amsterdam UMC, Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (L.v.d.H.); (C.M.K.); (M.K.); (M.F.J.); (M.D.)
| | - Cormac M. Kinsella
- Amsterdam UMC, Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (L.v.d.H.); (C.M.K.); (M.K.); (M.F.J.); (M.D.)
| | - Jarinee Tongshoob
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (J.T.); (W.K.)
| | - Luxsana Prasittichai
- Wildlife Conservation Division, Protected Areas Regional Office 3 (Ban Pong), Department of National Parks, Wildlife and Plant Conservation, Ministry of Natural Resources and Environment, Ratchaburi 70110, Thailand;
| | - Michelle Klein
- Amsterdam UMC, Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (L.v.d.H.); (C.M.K.); (M.K.); (M.F.J.); (M.D.)
| | - Maarten F. Jebbink
- Amsterdam UMC, Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (L.v.d.H.); (C.M.K.); (M.K.); (M.F.J.); (M.D.)
| | - Martin Deijs
- Amsterdam UMC, Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (L.v.d.H.); (C.M.K.); (M.K.); (M.F.J.); (M.D.)
| | - Onrapak Reamtong
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand;
| | - Kobporn Boonnak
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand;
| | - Wathusiri Khongsiri
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (J.T.); (W.K.)
| | - Juthamas Phadungsombat
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan;
| | - Daraka Tongthainan
- Faculty of Veterinary Medicine, Rajamangala University of Technology Tawan-ok, Chonburi 20110, Thailand;
| | - Phitsanu Tulayakul
- Department of Veterinary Public Health, Faculty of Veterinary Medicine, Kasetsart University, Nakhon Pathom 73140, Thailand;
| | - Marnoch Yindee
- Akkhraratchakumari Veterinary College, Walailak University, Nakhonsithammarat 80161, Thailand;
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Wallau GL, Barbier E, Tomazatos A, Schmidt-Chanasit J, Bernard E. The Virome of Bats Inhabiting Brazilian Biomes: Knowledge Gaps and Biases towards Zoonotic Viruses. Microbiol Spectr 2023; 11:e0407722. [PMID: 36625641 PMCID: PMC9927472 DOI: 10.1128/spectrum.04077-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 12/09/2022] [Indexed: 01/11/2023] Open
Abstract
Bats host a large variety of viruses, including some that may infect other vertebrates and humans. Research on bat-borne viruses attracted significant attention in recent years mainly due to epizootics caused by viruses having bats as hosts. The characterization of the viral communities of bats was then prioritized, but despite increasing efforts, there are large disparities in the geographical ranges covered and the methodologies employed around the world. As a result, large gaps remain in our current understanding of bat viromes and their role in disease emergence. This is particularly true for megadiverse regions in Latin America. This review aims to summarize the current understanding about bat viruses that inhabit Brazilian biomes, one of the most bat species-rich and diverse regions of the globe. Taking into account all known bat-associated viral families studied in Brazilian biomes, we found that almost half of all bat species (86/181 species) were not investigated for viruses at all. Moreover, only a small fraction of viral lineages or families have been studied more in depth, usually employing targeted methods with limited power to characterize a broad virus diversity. Additionally, these studies relied on limited spatiotemporal sampling and small sample sizes. Therefore, our current understanding of bat viral communities in the Brazilian biomes is limited and biased at different levels, limiting zoonotic risk assessments of bat-borne viruses. Considering these limitations, we propose strategies to bridge the existing gaps in the near future. IMPORTANCE Bat-borne viruses have attracted much attention due to zoonotic outbreaks with large consequences to humans. Because of that, virus characterization in bats has been prioritized in tropical regions of the globe. However, bat-virus research in Latin America and particularly in Brazil, which are among the most bat species-rich regions of the world, are highly biased toward zoonotic viruses and known bat reservoir species. These results have direct implication for virus studies in general but also for new zoonotic virus and spillover events characterization. The limited knowledge we currently have about the virome of Brazilian bats drastically limits any broad assessment of zoonotic viruses they carry and calls for coordinated and large-scale studies to fill this crucial knowledge gap.
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Affiliation(s)
- Gabriel Luz Wallau
- Departamento de Entomologia and Núcleo de Bioinformática, Instituto Aggeu Magalhães (IAM) - Fundação Oswaldo Cruz (Fiocruz), Cidade Universitária, Recife, Brazil
- Department of Arbovirology, Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Center for Arbovirus and Hemorrhagic Fever Reference and Research, National Reference Center for Tropical Infectious Diseases, Hamburg, Germany
| | - Eder Barbier
- Laboratório de Ciência Aplicada à Conservação da Biodiversidade, Departamento de Zoologia, Centro de Biociências, Universidade Federal de Pernambuco, Cidade Universitária, Recife, Brazil
| | - Alexandru Tomazatos
- Department of Arbovirology, Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Center for Arbovirus and Hemorrhagic Fever Reference and Research, National Reference Center for Tropical Infectious Diseases, Hamburg, Germany
| | - Jonas Schmidt-Chanasit
- Department of Arbovirology, Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Center for Arbovirus and Hemorrhagic Fever Reference and Research, National Reference Center for Tropical Infectious Diseases, Hamburg, Germany
- Faculty of Mathematics, Informatics and Natural Sciences, University of Hamburg, Hamburg, Germany
| | - Enrico Bernard
- Laboratório de Ciência Aplicada à Conservação da Biodiversidade, Departamento de Zoologia, Centro de Biociências, Universidade Federal de Pernambuco, Cidade Universitária, Recife, Brazil
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Plasma Virome Reveals Blooms and Transmission of Anellovirus in Intravenous Drug Users with HIV-1, HCV, and/or HBV Infections. Microbiol Spectr 2022; 10:e0144722. [PMID: 35758682 PMCID: PMC9431549 DOI: 10.1128/spectrum.01447-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Intravenous drug users (IDUs) are a high-risk group for HIV-1, hepatitis C virus (HCV), and hepatitis B virus (HBV) infections, which are the leading causes of death in IDUs. However, the plasma virome of IDUs and how it is influenced by above viral infections remain unclear. Using viral metagenomics, we determined the plasma virome of IDUs and its association with HIV-1, HCV, and/or HBV infections. Compared with healthy individuals, IDUs especially those with major viral infections had higher viral abundance and diversity. Anelloviridae dominated plasma virome. Coinfections of multiple anelloviruses were common, and anelloviruses from the same genus tended to coexist together. In this study, 4,487 anellovirus ORF1 sequences were identified, including 1,620 (36.1%) with less than 69% identity to any known sequences, which tripled the current number. Compared with healthy controls (HC), more anellovirus sequences were observed in neg-IDUs, and HIV-1, HCV, and/or HBV infections further expanded the sequence number in IDUs, which was characterized by the emergence of novel divergent taxons and blooms of resident anelloviruses. Pegivirus was mainly identified in infected IDUs. Five main pegivirus transmission clusters (TCs) were identified by phylogenetic analysis, suggesting a transmission link. Similar anellovirus profiles were observed in IDUs within the same TC, suggesting transmission of anellome among IDUs. Our data suggested that IDUs suffered higher plasma viral burden especially anelloviruses, which was associated with HIV-1, HCV, and/or HBV infections. Blooms in abundance and unprecedented diversity of anellovirus highlighted active evolution and replication of this virus in blood circulation, and an uncharacterized role it may engage with the host. IMPORTANCE Virome is associated with immune status and determines or influences disease progression through both pathogenic and resident viruses. Increased viral burden in IDUs especially those with major viral infections indicated the suboptimal immune status and high infection risks of these population. Blooms in abundance and unprecedented diversity of anellovirus highlighted its active evolution and replication in the blood circulation, and sensitive response to other viral infections. In addition, transmission cluster analysis revealed the transmission link of pegivirus among IDUs, and the individuals with transmission links shared similar anellome profiles. In-depth monitoring of the plasma virome in high-risk populations is not only needed for surveillance for emerging viruses and transmission networks of major and neglected bloodborne viruses, but also important for a better understanding of commensal viruses and their role it may engage with immune system.
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Abstract
The coronavirus disease 2019 (COVID-19) pandemic has had a profound impact on human health, economic well-being, and societal function. It is essential that we use this generational experience to better understand the processes that underpin the emergence of COVID-19 and other zoonotic diseases. Herein, I review the mechanisms that determine why and how viruses emerge in new hosts, as well as the barriers to this process. I show that traditional studies of virus emergence have an inherent anthropocentric bias, with disease in humans considered the inevitable outcome of virus emergence, when in reality viruses are integral components of a global ecosystem characterized by continual host jumping with humans also transmitting their viruses to other animals. I illustrate these points using coronaviruses, including severe acute respiratory syndrome coronavirus 2, as a case study. I also outline the potential steps that can be followed to help mitigate and prevent future pandemics, with combating climate change a central component. Expected final online publication date for the Annual Review of Virology, Volume 9 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia;
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9
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Dynamics of the Enteric Virome in a Swine Herd Affected by Non-PCV2/PRRSV Postweaning Wasting Syndrome. Viruses 2021; 13:v13122538. [PMID: 34960807 PMCID: PMC8705478 DOI: 10.3390/v13122538] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 12/13/2021] [Indexed: 12/24/2022] Open
Abstract
A commercial pig farm with no history of porcine circovirus 2 (PCV2) or porcine reproductive and respiratory syndrome virus (PRRSV) repeatedly reported a significant reduction in body weight gain and wasting symptoms in approximately 20–30% of the pigs in the period between three and six weeks after weaning. As standard clinical interventions failed to tackle symptomatology, viral metagenomics were used to describe and monitor the enteric virome at birth, 3 weeks, 4 weeks, 6 weeks, and 9 weeks of age. The latter four sampling points were 7 days, 3 weeks, and 6 weeks post weaning, respectively. Fourteen distinct enteric viruses were identified within the herd, which all have previously been linked to enteric diseases. Here we show that wasting is associated with alterations in the enteric virome of the pigs, characterized by: (1) the presence of enterovirus G at 3 weeks of age, followed by a higher prevalence of the virus in wasting pigs at 6 weeks after weaning; (2) rotaviruses at 3 weeks of age; and (3) porcine sapovirus one week after weaning. However, the data do not provide a causal link between specific viral infections and the postweaning clinical problems on the farm. Together, our results offer evidence that disturbances in the enteric virome at the preweaning stage and early after weaning have a determining role in the development of intestinal barrier dysfunctions and nutrient uptake in the postweaning growth phase. Moreover, we show that the enteric viral load sharply increases in the week after weaning in both healthy and wasting pigs. This study is also the first to report the dynamics and co-infection of porcine rotavirus species and porcine astrovirus genetic lineages during the first 9 weeks of the life of domestic pigs.
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10
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Cordey S, Laubscher F, Hartley MA, Junier T, Keitel K, Docquier M, Guex N, Iseli C, Vieille G, Le Mercier P, Gleizes A, Samaka J, Mlaganile T, Kagoro F, Masimba J, Said Z, Temba H, Elbanna GH, Tapparel C, Zanella MC, Xenarios I, Fellay J, D’Acremont V, Kaiser L. Blood virosphere in febrile Tanzanian children. Emerg Microbes Infect 2021; 10:982-993. [PMID: 33929935 PMCID: PMC8171259 DOI: 10.1080/22221751.2021.1925161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/13/2021] [Accepted: 04/28/2021] [Indexed: 12/16/2022]
Abstract
Viral infections are the leading cause of childhood acute febrile illnesses motivating consultation in sub-Saharan Africa. The majority of causal viruses are never identified in low-resource clinical settings as such testing is either not part of routine screening or available diagnostic tools have limited ability to detect new/unexpected viral variants. An in-depth exploration of the blood virome is therefore necessary to clarify the potential viral origin of fever in children. Metagenomic next-generation sequencing is a powerful tool for such broad investigations, allowing the detection of RNA and DNA viral genomes. Here, we describe the blood virome of 816 febrile children (<5 years) presenting at outpatient departments in Dar es Salaam over one-year. We show that half of the patients (394/816) had at least one detected virus recognized as causes of human infection/disease (13.8% enteroviruses (enterovirus A, B, C, and rhinovirus A and C), 12% rotaviruses, 11% human herpesvirus type 6). Additionally, we report the detection of a large number of viruses (related to arthropod, vertebrate or mammalian viral species) not yet known to cause human infection/disease, highlighting those who should be on the radar, deserve specific attention in the febrile paediatric population and, more broadly, for surveillance of emerging pathogens.Trial registration: ClinicalTrials.gov identifier: NCT02225769.
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Affiliation(s)
- Samuel Cordey
- Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
- Laboratory of Virology, Division of Infectious Diseases and Division of Laboratory Medicine, University Hospitals of Geneva & Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Florian Laubscher
- Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
- Laboratory of Virology, Division of Infectious Diseases and Division of Laboratory Medicine, University Hospitals of Geneva & Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Mary-Anne Hartley
- Centre for Primary Care and Public Health (Unisanté), University of Lausanne, Lausanne, Switzerland
- Intelligent Global Health, Machine Learning and Optimization Laboratory, EPFL, Lausanne, Switzerland
| | - Thomas Junier
- Global Health Institute, School of Life Sciences, EPFL, Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Kristina Keitel
- Swiss Tropical and Public Health Institute, University of Basel, Basel, Switzerland
- Department of Paediatric Emergency Medicine, Department of Pediatrics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Mylène Docquier
- iGE3 Genomics Platform, University of Geneva, Geneva, Switzerland
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Nicolas Guex
- Bioinformatics Competence Center, University of Lausanne and EPFL, Lausanne, Switzerland
| | - Christian Iseli
- Bioinformatics Competence Center, University of Lausanne and EPFL, Lausanne, Switzerland
| | - Gael Vieille
- Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
- Laboratory of Virology, Division of Infectious Diseases and Division of Laboratory Medicine, University Hospitals of Geneva & Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | | | - Anne Gleizes
- SwissProt group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
| | | | | | - Frank Kagoro
- Ifakara Health Institute, Dar es Salaam, Tanzania
| | - John Masimba
- Ifakara Health Institute, Dar es Salaam, Tanzania
| | - Zamzam Said
- Ifakara Health Institute, Dar es Salaam, Tanzania
| | | | - Gasser H. Elbanna
- Intelligent Global Health, Machine Learning and Optimization Laboratory, EPFL, Lausanne, Switzerland
| | - Caroline Tapparel
- Department of Microbiology and Molecular Medicine, University of Geneva Medical School, Geneva, Switzerland
| | - Marie-Celine Zanella
- Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
- Laboratory of Virology, Division of Infectious Diseases and Division of Laboratory Medicine, University Hospitals of Geneva & Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Ioannis Xenarios
- Health2030 Genome Center, Geneva, Switzerland
- Agora Center, University of Lausanne, Lausanne, Switzerland
| | - Jacques Fellay
- Global Health Institute, School of Life Sciences, EPFL, Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Valérie D’Acremont
- Centre for Primary Care and Public Health (Unisanté), University of Lausanne, Lausanne, Switzerland
- Swiss Tropical and Public Health Institute, University of Basel, Basel, Switzerland
| | - Laurent Kaiser
- Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
- Laboratory of Virology, Division of Infectious Diseases and Division of Laboratory Medicine, University Hospitals of Geneva & Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals, Geneva, Switzerland
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11
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Deep viral blood metagenomics reveals extensive anellovirus diversity in healthy humans. Sci Rep 2021; 11:6921. [PMID: 33767340 PMCID: PMC7994813 DOI: 10.1038/s41598-021-86427-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/15/2021] [Indexed: 02/08/2023] Open
Abstract
Human blood metagenomics has revealed the presence of different types of viruses in apparently healthy subjects. By far, anelloviruses constitute the viral family that is more frequently found in human blood, although amplification biases and contaminations pose a major challenge in this field. To investigate this further, we subjected pooled plasma samples from 120 healthy donors in Spain to high-speed centrifugation, RNA and DNA extraction, random amplification, and massive parallel sequencing. Our results confirm the extensive presence of anelloviruses in such samples, which represented nearly 97% of the total viral sequence reads obtained. We assembled 114 different viral genomes belonging to this family, revealing remarkable diversity. Phylogenetic analysis of ORF1 suggested 28 potentially novel anellovirus species, 24 of which were validated by Sanger sequencing to discard artifacts. These findings underscore the importance of implementing more efficient purification procedures that enrich the viral fraction as an essential step in virome studies and question the suggested pathological role of anelloviruses.
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12
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Abstract
Host-associated microbiomes contribute in many ways to the homeostasis of the metaorganism. The microbiome's contributions range from helping to provide nutrition and aiding growth, development, and behavior to protecting against pathogens and toxic compounds. Here we summarize the current knowledge of the diversity and importance of the microbiome to animals, using representative examples of wild and domesticated species. We demonstrate how the beneficial ecological roles of animal-associated microbiomes can be generally grouped into well-defined main categories and how microbe-based alternative treatments can be applied to mitigate problems for both economic and conservation purposes and to provide crucial knowledge about host-microbiota symbiotic interactions. We suggest a Customized Combination of Microbial-Based Therapies to promote animal health and contribute to the practice of sustainable husbandry. We also discuss the ecological connections and threats associated with animal biodiversity loss, microorganism extinction, and emerging diseases, such as the COVID-19 pandemic.
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Affiliation(s)
- Raquel S Peixoto
- Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil; .,Current affiliation: Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900 Saudia Arabia;
| | - Derek M Harkins
- J. Craig Venter Institute, Rockville, Maryland 20850, USA; ,
| | - Karen E Nelson
- J. Craig Venter Institute, Rockville, Maryland 20850, USA; ,
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13
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Comparative Metagenomics of Palearctic and Neotropical Avian Cloacal Viromes Reveal Geographic Bias in Virus Discovery. Microorganisms 2020; 8:microorganisms8121869. [PMID: 33256173 PMCID: PMC7761369 DOI: 10.3390/microorganisms8121869] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/20/2020] [Accepted: 11/24/2020] [Indexed: 01/11/2023] Open
Abstract
Our understanding about viruses carried by wild animals is still scarce. The viral diversity of wildlife may be best described with discovery-driven approaches to the study of viral diversity that broaden research efforts towards non-canonical hosts and remote geographic regions. Birds have been key organisms in the transmission of viruses causing important diseases, and wild birds are threatened by viral spillovers associated with human activities. However, our knowledge of the avian virome may be biased towards poultry and highly pathogenic diseases. We describe and compare the fecal virome of two passerine-dominated bird assemblages sampled in a remote Neotropical rainforest in French Guiana (Nouragues Natural Reserve) and a Mediterranean forest in central Spain (La Herrería). We used metagenomic data to quantify the degree of functional and genetic novelty of viruses recovered by examining if the similarity of the contigs we obtained to reference sequences differed between both locations. In general, contigs from Nouragues were significantly less similar to viruses in databases than contigs from La Herrería using Blastn but not for Blastx, suggesting that pristine regions harbor a yet unknown viral diversity with genetically more singular viruses than more studied areas. Additionally, we describe putative novel viruses of the families Picornaviridae, Reoviridae and Hepeviridae. These results highlight the importance of wild animals and remote regions as sources of novel viruses that substantially broaden the current knowledge of the global diversity of viruses.
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14
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François S, Pybus OG. Towards an understanding of the avian virome. J Gen Virol 2020; 101:785-790. [PMID: 32519942 PMCID: PMC7641393 DOI: 10.1099/jgv.0.001447] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 05/21/2020] [Indexed: 02/06/2023] Open
Abstract
The last two decades have seen the rise of viromics, the study of viral communities through the detection and characterization of virus genome sequences. Here we systematically review and summarize the scope and limitations of our current understanding of avian viromes, in both domesticated and wild-bird populations. We compare this viromic work to the broader literature on avian prokaryotic microbiomes, and highlight the growing importance of structured sampling and experimental design for testing explanatory hypotheses. We provide a number of recommendations for sample collection and preliminary data analysis to guide the development of avian viromics. Avian viromes have the potential to inform disease surveillance in poultry and improve our understanding of the risk of zoonotic viruses to human health.
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Affiliation(s)
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, UK
- Department of Pathobiology and Population Sciences, Royal Veterinary College London, UK
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15
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Yin D, Gao Q, Zhu H, Li J. Public perception of urban companion animals during the COVID-19 outbreak in China. Health Place 2020; 65:102399. [PMID: 32736203 PMCID: PMC7386851 DOI: 10.1016/j.healthplace.2020.102399] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 07/12/2020] [Accepted: 07/13/2020] [Indexed: 11/30/2022]
Abstract
This paper responds to the increasing concern regarding the role of non-human life in shaping urban space by exploring the public perception of urban companion animals during the coronavirus disease 2019 (COVID-19) outbreak in China. We argue that the public's perception of urban companion animals during emerging infectious disease outbreaks is related to medical and life science issues and reflects the political, economic, and emotional struggles involved in human-animal multispecies cohabitation. We find that the public has mainly followed and reconstructed medical discourses about the risk of companion animal-to-human transmission and discussed sustainable ethical animal practices in urban public health emergency management during the COVID-19 outbreak. Concerns regarding the risk of companion animal-related infection reflect the increasing prominence of more-than-human families, the pet industry, and multispecies leisure conflicts in public space in Chinese cities. The public's attention to animal ethics has prompted Chinese policy makers to adopt a more morally acceptable model for urban public health emergency management that can be sustained and supported by responsible non-governmental organizations and ethical urban residents. Public's perception reflects the struggles involved in human-animal multispecies cohabitation. The public is concerned and fear the risk of companion animal-to-human transmission. Such concern and fear caused companion animals to experience tragic and caring experiences during the epidemic. The morally acceptable model of urban public health emergency management is prompted by the public's attention.
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Affiliation(s)
- Duo Yin
- School of Geographical Sciences, Guangzhou University, Higher Education Mega Center, Guangzhou, 510006, China.
| | - Quan Gao
- Department of Geography, Newcastle University, Newcastle, NE1 7RU, United Kingdom.
| | - Hong Zhu
- School of Geographical Sciences, Guangzhou University, Higher Education Mega Center, Guangzhou, 510006, China.
| | - Jie Li
- School of Geographical Sciences, Guangzhou University, Higher Education Mega Center, Guangzhou, 510006, China.
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16
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Sosa-Gómez DR, Morgado FS, Corrêa RFT, Silva LA, Ardisson-Araújo DMP, Rodrigues BMP, Oliveira EE, Aguiar RWS, Ribeiro BM. Entomopathogenic Viruses in the Neotropics: Current Status and Recently Discovered Species. NEOTROPICAL ENTOMOLOGY 2020; 49:315-331. [PMID: 32358711 DOI: 10.1007/s13744-020-00770-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 03/03/2020] [Indexed: 06/11/2023]
Abstract
The market for biological control of insect pests in the world and in Brazil has grown in recent years due to the unwanted ecological and human health impacts of chemical insecticides. Therefore, research on biological control agents for pest management has also increased. For instance, insect viruses have been used to protect crops and forests around the world for decades. Among insect viruses, the baculoviruses are the most studied and used viral biocontrol agent. More than 700 species of insects have been found to be naturally infected by baculoviruses, with 90% isolated from lepidopteran insects. In this review, some basic aspects of baculovirus infection in vivo and in vitro infection, gene content, viral replication will be discussed. Furthermore, we provide examples of the use of insect viruses for biological pest control and recently characterized baculoviruses in Brazil.
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Affiliation(s)
- D R Sosa-Gómez
- Empresa Brasileira de Pesquisa Agropecuária, Embrapa Soja, Londrina, PR, Brasil
| | - F S Morgado
- Depto de Biologia Celular, Univ of Brasília, Brasília, DF, Brasil
| | - R F T Corrêa
- Depto de Biotecnologia, Univ Federal de Tocantins, Gurupi, TO, Brasil
| | - L A Silva
- Depto de Biologia Celular, Univ of Brasília, Brasília, DF, Brasil
| | - D M P Ardisson-Araújo
- Depto de Bioquímica e Biologia Molecular, Univ Federal de Santa Maria, Santa Maria, RS, Brasil
| | - B M P Rodrigues
- Depto de Biologia Celular, Univ of Brasília, Brasília, DF, Brasil
| | - E E Oliveira
- Depto de Entomologia, Univ Federal de Viçosa, Viçosa, MG, Brasil
| | - R W S Aguiar
- Depto de Biotecnologia, Univ Federal de Tocantins, Gurupi, TO, Brasil
| | - B M Ribeiro
- Depto de Biologia Celular, Univ of Brasília, Brasília, DF, Brasil.
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17
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French RK, Holmes EC. An Ecosystems Perspective on Virus Evolution and Emergence. Trends Microbiol 2019; 28:165-175. [PMID: 31744665 DOI: 10.1016/j.tim.2019.10.010] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 10/19/2019] [Accepted: 10/21/2019] [Indexed: 12/18/2022]
Abstract
Understanding the emergence of pathogenic viruses has dominated studies of virus evolution. However, new metagenomic studies imply that relatively few of an immense number of viruses may lead to overt disease. This suggests a change in emphasis, from viruses as habitual pathogens to integral components of ecosystems. Here we show how viruses alter interactions between host individuals, populations, and ecosystems, impacting ecosystem health, resilience, and function, and how host ecology in turn impacts viral abundance and diversity. Moving to an ecosystems perspective will put virus evolution and disease emergence in its true context, and enhance our understanding of ecological processes.
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Affiliation(s)
- Rebecca K French
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia.
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18
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Sawaswong V, Fahsbender E, Altan E, Kemthong T, Deng X, Malaivijitnond S, Payungporn S, Delwart E. High Diversity and Novel Enteric Viruses in Fecal Viromes of Healthy Wild and Captive Thai Cynomolgus Macaques ( Macaca fascicularis). Viruses 2019; 11:E971. [PMID: 31652508 PMCID: PMC6832579 DOI: 10.3390/v11100971] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 10/06/2019] [Accepted: 10/07/2019] [Indexed: 02/06/2023] Open
Abstract
Cynomolgus macaques are common across South East Asian countries including Thailand. The National Primate Research Center of Thailand, Chulalongkorn University (NPRCT-CU) captures wild-borne cynomolgus macaque for research use. Limited information is available on the enteric viruses and possible zoonotic infections into or from cynomolgus macaques. We characterized and compare the fecal virome of two populations; healthy wild-originated captive cynomolgus macaques (n = 43) reared in NPRCT-CU and healthy wild cynomolgus macaques (n = 35). Over 90% of recognized viral sequence reads amplified from feces were from bacterial viruses. Viruses from seven families of mammalian viruses were also detected (Parvoviridae, Anelloviridae, Picornaviridae, Adenoviridae, Papillomaviridae, Herpesviridae, and Caliciviridae). The genomes of a member of a new picornavirus genus we named Mafapivirus, a primate chapparvovirus, and a circular Rep-encoding single-strand (CRESS) DNA virus were also characterized. Higher abundance of CRESS DNA viruses of unknown tropism and invertebrate-tropic ambidensovirus were detected in wild versus captive macaques likely reflecting dietary differences. Short term rearing in captivity did not have a pronounced effect on the diversity of mammalian viruses of wild cynomolgus macaques. This study is the first report of the fecal virome of cynomolgus macaques, non-human primates frequently used in biomedical research and vaccination studies.
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Affiliation(s)
- Vorthon Sawaswong
- Vitalant Research Institute, San Francisco, CA 94118, USA.
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand.
| | - Elizabeth Fahsbender
- Vitalant Research Institute, San Francisco, CA 94118, USA.
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 9413, USA.
| | - Eda Altan
- Vitalant Research Institute, San Francisco, CA 94118, USA.
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 9413, USA.
| | - Taratorn Kemthong
- National Primate Research Center-Chulalongkorn University, Saraburi 18110, Thailand.
| | - Xutao Deng
- Vitalant Research Institute, San Francisco, CA 94118, USA.
| | | | - Sunchai Payungporn
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand.
- Center of Excellence in Systems Biology, Chulalongkorn University (CUSB), Bangkok 10330, Thailand.
| | - Eric Delwart
- Vitalant Research Institute, San Francisco, CA 94118, USA.
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 9413, USA.
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19
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Abstract
Although viruses comprise the most abundant genetic material in the biosphere, to date only several thousand virus species have been formally defined. Such a limited perspective on virus diversity has in part arisen because viruses were traditionally considered only as etiologic agents of overt disease in humans or economically important species and were often difficult to identify using cell culture. This view has dramatically changed with the rise of metagenomics, which is transforming virus discovery and revealing a remarkable diversity of viruses sampled from diverse cellular organisms. These newly discovered viruses help fill major gaps in the evolutionary history of viruses, revealing a near continuum of diversity among genera, families, and even orders of RNA viruses. Herein, we review some of the recent advances in our understanding of the RNA virosphere that have stemmed from metagenomics, note future directions, and highlight some of the remaining challenges to this rapidly developing field.
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Affiliation(s)
- Yong-Zhen Zhang
- Shanghai Public Health Clinical Center and School of Public Health, Fudan University, Shanghai 200433, China; .,Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, China
| | - Yan-Mei Chen
- Shanghai Public Health Clinical Center and School of Public Health, Fudan University, Shanghai 200433, China; .,Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, China
| | - Wen Wang
- Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, China
| | - Xin-Chen Qin
- Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, China
| | - Edward C Holmes
- Shanghai Public Health Clinical Center and School of Public Health, Fudan University, Shanghai 200433, China; .,Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, China.,Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales 2006, Australia
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20
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Goh SG, Saeidi N, Gu X, Vergara GGR, Liang L, Fang H, Kitajima M, Kushmaro A, Gin KYH. Occurrence of microbial indicators, pathogenic bacteria and viruses in tropical surface waters subject to contrasting land use. WATER RESEARCH 2019; 150:200-215. [PMID: 30528917 PMCID: PMC7112093 DOI: 10.1016/j.watres.2018.11.058] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 11/18/2018] [Accepted: 11/19/2018] [Indexed: 05/21/2023]
Abstract
Fecal indicator bacteria, such as Escherichia coli (E.coli) and Enterococcus, have been widely used to indicate the presence of pathogens. However, the suitability of fecal indicator bacteria to represent health risks is still being challenged, particularly in tropical aquatic environments. The objective of this study is to understand the occurrence and prevalence of indicators and pathogens in areas with contrasting land use, as well as to identify the major correlations between indicators, pathogens and environmental parameters. The spatial and temporal variation of indicators and pathogens was studied to examine the distribution patterns for areas with different land use, and the impact of seasonal changes on microbial populations. A total of 234 water samples were sampled for two years from reservoirs and their tributaries, and tested for fecal indicator bacteria, coliphages, human specific markers, pathogenic bacteria and viruses. The prevalence of indicators and pathogens in reservoirs were generally low, while relatively high concentrations were observed in tributaries to varying degrees. Of the enteric viruses, norovirus GII was among the most prevalent and had the highest concentration. Although strong correlations were found between indicators, only relatively weak correlations were found between indicators and pathogens. The results in this study showed that none of the bacteria/phage indicators were universal predictors for pathogens. Inclusion of the alternative indicators, Methanobrevibacter smithii, Bacteroides and human polyomaviruses (HPyVs) to monitoring programs could help to determine whether the fecal source was human. The microbial distribution patterns allow the classification of sampling sites to different clusters and thus, help to identify sites which have poor water quality. This approach will be useful for water quality management to pinpoint factors that influence water quality and help to prioritize sites for restoration of water quality.
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Affiliation(s)
- Shin Giek Goh
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore
| | - Nazanin Saeidi
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore
| | - Xiaoqiong Gu
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore
| | | | - Liang Liang
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore
| | - Haoming Fang
- NUS Environmental Research Institute, National University of Singapore, Singapore
| | - Masaaki Kitajima
- Division of Environmental Engineering, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Ariel Kushmaro
- School of Material Science and Engineering, Nanyang Technological University, Singapore
| | - Karina Yew-Hoong Gin
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore; NUS Environmental Research Institute, National University of Singapore, Singapore.
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21
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Bento MC, Canha R, Eira C, Vingada J, Nicolau L, Ferreira M, Domingo M, Tavares L, Duarte A. Herpesvirus infection in marine mammals: A retrospective molecular survey of stranded cetaceans in the Portuguese coastline. INFECTION GENETICS AND EVOLUTION 2018; 67:222-233. [PMID: 30445114 DOI: 10.1016/j.meegid.2018.11.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 11/12/2018] [Accepted: 11/12/2018] [Indexed: 10/27/2022]
Abstract
Herpesvirus (HVs) infection has already been reported in cetaceans, but available information on its epidemiology is scarce. In this study we surveyed a total of 179 cetaceans belonging to 6 different species. Samples were obtained from cetaceans stranded along the Portuguese coastline, belonging to populations that roam the north-east region of the Atlantic Ocean. Detection of HVs was performed by conventional nested PCR. Amplicons were sequenced by Sanger's method and sequences used to construct phylogenetic trees by Maximum Likelihood method. Our results show that prevalence of positive samples, among fresh carcasses, reached 14.3% (10/70) and both alpha and gammaherpesvirus were detected. Histopathology showed that herpesvirus infection varied from absence of signs compatible with disease, localized genital lesions and systemic disease. Phylogenetic analysis revealed three clusters within the alphaherpesvirus family; within the gammaherpesvirus no subdivision was detected. All clusters included animals from different species and geographic origins. In seven of the positive HVs samples, co-infections with other agents such as morbillivirus and toxoplasma gondii were detected. The viral nucleotide sequences were not assigned to a specific animal species, nor presented a given geographic distribution, which may imply a wider distribution of herpesvirus in these animal populations. Our results are also the first report of herpesvirus infection in common dolphins (Delphinus delphis), with both alpha and gammaherpesvirus detected.
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Affiliation(s)
- M C Bento
- CIISA Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisbon, Portugal.
| | - R Canha
- CIISA Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisbon, Portugal
| | - C Eira
- Department of Biology and CESAM, University of Aveiro, 3810-193 Aveiro, Portugal; Portuguese Wildlife Society, Department of Biology, Minho University, 4710-057 Braga, Portugal
| | - J Vingada
- Portuguese Wildlife Society, Department of Biology, Minho University, 4710-057 Braga, Portugal; Department of Biology and CESAM, Minho University, 4710-057 Braga, Portugal
| | - L Nicolau
- Department of Biology and CESAM, University of Aveiro, 3810-193 Aveiro, Portugal; Portuguese Wildlife Society, Department of Biology, Minho University, 4710-057 Braga, Portugal
| | - M Ferreira
- Portuguese Wildlife Society, Department of Biology, Minho University, 4710-057 Braga, Portugal; Department of Biology and CBMA, Minho University, 4710-057 Braga, Portugal
| | - M Domingo
- Departament de Sanitat i Anatomia Animals, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - L Tavares
- CIISA Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisbon, Portugal
| | - A Duarte
- CIISA Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisbon, Portugal
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22
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Blomström AL, Ye X, Fossum C, Wallgren P, Berg M. Characterisation of the Virome of Tonsils from Conventional Pigs and from Specific Pathogen-Free Pigs. Viruses 2018; 10:v10070382. [PMID: 30036964 PMCID: PMC6071052 DOI: 10.3390/v10070382] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 07/17/2018] [Accepted: 07/19/2018] [Indexed: 12/31/2022] Open
Abstract
Porcine respiratory disease is a multifactorial disease that can be influenced by a number of different microorganisms, as well as by non-infectious factors such as the management and environment of the animals. It is generally believed that the interaction between different infectious agents plays an important role in regard to respiratory diseases. Therefore, we used high-throughput sequencing combined with viral metagenomics to characterise the viral community of tonsil samples from pigs coming from a conventional herd with lesions in the respiratory tract at slaughter. In parallel, samples from specific pathogen-free pigs were also analysed. This study showed a variable co-infection rate in the different pigs. The differences were not seen at the group level but in individual pigs. Some viruses such as adenoviruses and certain picornaviruses could be found in most pigs, while others such as different parvoviruses and anelloviruses were only identified in a few pigs. In addition, the complete coding region of porcine parvovirus 7 was obtained, as were the complete genomes of two teschoviruses. The results from this study will aid in elucidating which viruses are circulating in both healthy pigs and in pigs associated with respiratory illness. This knowledge is needed for future investigations into the role of viral-viral interactions in relation to disease development.
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Affiliation(s)
- Anne-Lie Blomström
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Box 7028, 750 07 Uppsala, Sweden.
| | - Xingyu Ye
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Box 7028, 750 07 Uppsala, Sweden.
- Guangyuan Center for Animal Disease Control and Prevention, Guangyuan 628017, China.
| | - Caroline Fossum
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Box 7028, 750 07 Uppsala, Sweden.
| | - Per Wallgren
- National veterinary institute (SVA), 751 89 Uppsala Sweden.
| | - Mikael Berg
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Box 7028, 750 07 Uppsala, Sweden.
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Metagenomic analysis of Sichuan takin fecal sample viromes reveals novel enterovirus and astrovirus. Virology 2018; 521:77-91. [PMID: 29886344 DOI: 10.1016/j.virol.2018.05.027] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 05/30/2018] [Indexed: 12/27/2022]
Abstract
The Sichuan takin inhabits the bamboo forests in the Eastern Himalayas and is considered as a national treasure of China with the highest legal protection and conservation status considered as vulnerable according to The IUCN Red List of Threatened Species. In this study, fecal samples of 71 Sichuan takins were pooled and deep sequenced. Among the 103,553 viral sequences, 21,961 were assigned to mammalian viruses. De novo assembly revealed genomes of an enterovirus and an astrovirus and contigs of circoviruses and genogroup I picobirnaviruses. Complete genome sequencing and phylogenetic analysis showed that Sichuan takin enterovirus is a novel serotype/genotype of the species Enterovirus G, with evidence of recombination. Sichuan takin astrovirus is a new subtype of bovine astrovirus, probably belonging to a new genogroup in the genus Mamastrovirus. Further studies will reveal whether these viruses can also be found in Mishmi takin and Shaanxi takin and their pathogenic potentials.
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24
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Bodewes R. Novel viruses in birds: Flying through the roof or is a cage needed? Vet J 2018; 233:55-62. [PMID: 29486880 DOI: 10.1016/j.tvjl.2017.12.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Revised: 09/28/2017] [Accepted: 12/28/2017] [Indexed: 01/17/2023]
Abstract
Emerging viral diseases continue to have a major global impact on human beings and animals. To be able to take adequate measures in case of an outbreak of an emerging disease, rapid detection of the causative agent is a crucial first step. In this review, various aspects of virus discovery are discussed, with a special focus on recently discovered viruses in birds. Novel viruses with a potential major impact have been discovered in domestic and wild bird species in recent years using various virus discovery methods. Only a few studies report the detection of novel viruses in endangered bird species, although increased knowledge about viruses circulating in these species is important. Additional studies focusing on the exact role of a novel virus in disease and on the impact of a novel virus on bird populations are often lacking. Intensive collaboration between different disciplines is needed to obtain useful information about the role of these novel viruses.
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Affiliation(s)
- R Bodewes
- Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.
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25
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Abstract
Omics technologies have been developed in recent decades and applied to different subjects, although the greatest advancements have been achieved in human biology and disease. Genome sequencing and the exploration of its coding and noncoding regions are rapidly yielding meaningful answers to diverse questions, relating genome information to protein activity to environmental changes. In the past, marine mammal genetic and transcriptional studies have been restricted due to the lack of reference genomes. But the advance of high-throughput sequencing is revolutionizing the life sciences technologies. As long-lived organisms, at the top of the food chain, marine mammals play an important role in marine ecosystems and while their protected status is in favor of conservation of the species, it also complicates the researcher's approach to traditional measurements of health. Omics data generated by high-throughput technologies will represent an important key for improving the scientific basis for understanding both marine mammal and environment health.
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A Multicenter Study To Evaluate the Performance of High-Throughput Sequencing for Virus Detection. mSphere 2017; 2:mSphere00307-17. [PMID: 28932815 PMCID: PMC5597969 DOI: 10.1128/msphere.00307-17] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 08/23/2017] [Indexed: 11/20/2022] Open
Abstract
Recent high-throughput sequencing (HTS) investigations have resulted in unexpected discoveries of known and novel viruses in a variety of sample types, including research materials, clinical materials, and biological products. Therefore, HTS can be a powerful tool for supplementing current methods for demonstrating the absence of adventitious or unwanted viruses in biological products, particularly when using a new cell line. However, HTS is a complex technology with different platforms, which needs standardization for evaluation of biologics. This collaborative study was undertaken to investigate detection of different virus types using two different HTS platforms. The results of the independently performed studies demonstrated a similar sensitivity of virus detection, regardless of the different sample preparation and processing procedures and bioinformatic analyses done in the three laboratories. Comparable HTS detection of different virus types supports future development of reference virus materials for standardization and validation of different HTS platforms. The capability of high-throughput sequencing (HTS) for detection of known and unknown viruses makes it a powerful tool for broad microbial investigations, such as evaluation of novel cell substrates that may be used for the development of new biological products. However, like any new assay, regulatory applications of HTS need method standardization. Therefore, our three laboratories initiated a study to evaluate performance of HTS for potential detection of viral adventitious agents by spiking model viruses in different cellular matrices to mimic putative materials for manufacturing of biologics. Four model viruses were selected based upon different physical and biochemical properties and commercial availability: human respiratory syncytial virus (RSV), Epstein-Barr virus (EBV), feline leukemia virus (FeLV), and human reovirus (REO). Additionally, porcine circovirus (PCV) was tested by one laboratory. Independent samples were prepared for HTS by spiking intact viruses or extracted viral nucleic acids, singly or mixed, into different HeLa cell matrices (resuspended whole cells, cell lysate, or total cellular RNA). Data were obtained using different sequencing platforms (Roche 454, Illumina HiSeq1500 or HiSeq2500). Bioinformatic analyses were performed independently by each laboratory using available tools, pipelines, and databases. The results showed that comparable virus detection was obtained in the three laboratories regardless of sample processing, library preparation, sequencing platform, and bioinformatic analysis: between 0.1 and 3 viral genome copies per cell were detected for all of the model viruses used. This study highlights the potential for using HTS for sensitive detection of adventitious viruses in complex biological samples containing cellular background. IMPORTANCE Recent high-throughput sequencing (HTS) investigations have resulted in unexpected discoveries of known and novel viruses in a variety of sample types, including research materials, clinical materials, and biological products. Therefore, HTS can be a powerful tool for supplementing current methods for demonstrating the absence of adventitious or unwanted viruses in biological products, particularly when using a new cell line. However, HTS is a complex technology with different platforms, which needs standardization for evaluation of biologics. This collaborative study was undertaken to investigate detection of different virus types using two different HTS platforms. The results of the independently performed studies demonstrated a similar sensitivity of virus detection, regardless of the different sample preparation and processing procedures and bioinformatic analyses done in the three laboratories. Comparable HTS detection of different virus types supports future development of reference virus materials for standardization and validation of different HTS platforms.
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27
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Zhang W, Yang S, Shan T, Hou R, Liu Z, Li W, Guo L, Wang Y, Chen P, Wang X, Feng F, Wang H, Chen C, Shen Q, Zhou C, Hua X, Cui L, Deng X, Zhang Z, Qi D, Delwart E. Virome comparisons in wild-diseased and healthy captive giant pandas. MICROBIOME 2017; 5:90. [PMID: 28780905 PMCID: PMC5545856 DOI: 10.1186/s40168-017-0308-0] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 07/13/2017] [Indexed: 05/12/2023]
Abstract
BACKGROUND The giant panda (Ailuropoda melanoleuca) is a vulnerable mammal herbivore living wild in central China. Viral infections have become a potential threat to the health of these endangered animals, but limited information related to these infections is available. METHODS Using a viral metagenomic approach, we surveyed viruses in the feces, nasopharyngeal secretions, blood, and different tissues from a wild giant panda that died from an unknown disease, a healthy wild giant panda, and 46 healthy captive animals. RESULTS The previously uncharacterized complete or near complete genomes of four viruses from three genera in Papillomaviridae family, six viruses in a proposed new Picornaviridae genus (Aimelvirus), two unclassified viruses related to posaviruses in Picornavirales order, 19 anelloviruses in four different clades of Anelloviridae family, four putative circoviruses, and 15 viruses belonging to the recently described Genomoviridae family were sequenced. Reflecting the diet of giant pandas, numerous insect virus sequences related to the families Iflaviridae, Dicistroviridae, Iridoviridae, Baculoviridae, Polydnaviridae, and subfamily Densovirinae and plant viruses sequences related to the families Tombusviridae, Partitiviridae, Secoviridae, Geminiviridae, Luteoviridae, Virgaviridae, and Rhabdoviridae; genus Umbravirus, Alphaflexiviridae, and Phycodnaviridae were also detected in fecal samples. A small number of insect virus sequences were also detected in the nasopharyngeal secretions of healthy giant pandas and lung tissues from the dead wild giant panda. Although the viral families present in the sick giant panda were also detected in the healthy ones, a higher proportion of papillomaviruses, picornaviruses, and anelloviruses reads were detected in the diseased panda. CONCLUSION This viral survey increases our understanding of eukaryotic viruses in giant pandas and provides a baseline for comparison to viruses detected in future infectious disease outbreaks. The similar viral families detected in sick and healthy giant pandas indicate that these viruses result in commensal infections in most immuno-competent animals.
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Affiliation(s)
- Wen Zhang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013 China
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081 China
| | - Shixing Yang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013 China
| | - Tongling Shan
- Department of Swine Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241 China
| | - Rong Hou
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081 China
| | - Zhijian Liu
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013 China
| | - Wang Li
- Department of Laboratory Medicine, Jiangsu Taizhou People’s Hospital, Taizhou, Jiangsu 225300 China
| | - Lianghua Guo
- School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, 200240 China
| | - Yan Wang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013 China
| | - Peng Chen
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081 China
| | - Xiaochun Wang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013 China
| | - Feifei Feng
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081 China
| | - Hua Wang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013 China
| | - Chao Chen
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081 China
| | - Quan Shen
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013 China
| | - Chenglin Zhou
- Department of Laboratory Medicine, Jiangsu Taizhou People’s Hospital, Taizhou, Jiangsu 225300 China
| | - Xiuguo Hua
- School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, 200240 China
| | - Li Cui
- School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, 200240 China
| | - Xutao Deng
- Blood Systems Research Institute, Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94118 USA
| | - Zhihe Zhang
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081 China
| | - Dunwu Qi
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081 China
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610000 China
| | - Eric Delwart
- Blood Systems Research Institute, Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94118 USA
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28
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Knutson TP, Velayudhan BT, Marthaler DG. A porcine enterovirus G associated with enteric disease contains a novel papain-like cysteine protease. J Gen Virol 2017; 98:1305-1310. [PMID: 28590234 PMCID: PMC5656790 DOI: 10.1099/jgv.0.000799] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Identification of unknown pathogens in pigs displaying enteric illness is difficult due to the large diversity of bacterial and viral species found within faecal samples. Current methods often require bacterial or viral isolation, or testing only a limited number of known species using quantitative PCR analysis. Herein, faeces from two 25-day-old piglets with diarrhoea from Texas, USA, were analysed by metagenomic next-generation sequencing to rapidly identify possible pathogens. Our analysis included a bioinformatics pipeline of rapid short-read classification and de novo genome assembly which resulted in the identification of a porcine enterovirus G (EV-G), a complete genome with substantial nucleotide differences (>30 %) among current sequences, and a novel non-structural protein similar in sequence to the Torovirus papain-like cysteine protease (PLpro). This discovery led to the identification and circulation of an EV-G with a novel PLpro in the USA that has not been previously reported.
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Affiliation(s)
- Todd P Knutson
- Veterinary Diagnostic Laboratory, Department of Veterinary Population Medicine, University of Minnesota, St Paul, MN 55108, USA
| | - Binu T Velayudhan
- Texas A&M Veterinary Medical Diagnostic Laboratory, Amarillo, TX 79106, USA
| | - Douglas G Marthaler
- Veterinary Diagnostic Laboratory, Department of Veterinary Population Medicine, University of Minnesota, St Paul, MN 55108, USA
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29
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Lempp C, Jungwirth N, Grilo ML, Reckendorf A, Ulrich A, van Neer A, Bodewes R, Pfankuche VM, Bauer C, Osterhaus ADME, Baumgärtner W, Siebert U. Pathological findings in the red fox (Vulpes vulpes), stone marten (Martes foina) and raccoon dog (Nyctereutes procyonoides), with special emphasis on infectious and zoonotic agents in Northern Germany. PLoS One 2017; 12:e0175469. [PMID: 28399176 PMCID: PMC5388480 DOI: 10.1371/journal.pone.0175469] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 03/27/2017] [Indexed: 11/18/2022] Open
Abstract
Anthropogenic landscape changes contributed to the reduction of availability of habitats to wild animals. Hence, the presence of wild terrestrial carnivores in urban and peri-urban sites has increased considerably over the years implying an increased risk of interspecies spillover of infectious diseases and the transmission of zoonoses. The present study provides a detailed characterisation of the health status of the red fox (Vulpes vulpes), stone marten (Martes foina) and raccoon dog (Nyctereutes procyonoides) in their natural rural and peri-urban habitats in Schleswig-Holstein, Germany between November 2013 and January 2016 with focus on zoonoses and infectious diseases that are potentially threatening to other wildlife or domestic animal species. 79 red foxes, 17 stone martens and 10 raccoon dogs were collected from traps or hunts. In order to detect morphological changes and potential infectious diseases, necropsy and pathohistological work-up was performed. Additionally, in selected animals immunohistochemistry (influenza A virus, parvovirus, feline leukemia virus, Borna disease virus, tick-borne encephalitis, canine adenovirus, Neospora caninum, Toxoplasma gondii and Listeria monocytogenes), next-generation sequencing, polymerase chain reaction (fox circovirus) and serum-neutralisation analysis (canine distemper virus) were performed. Furthermore, all animals were screened for fox rabies virus (immunofluorescence), canine distemper virus (immunohistochemistry) and Aujeszky's disease (virus cultivation). The most important findings included encephalitis (n = 16) and pneumonia (n = 20). None of the investigations revealed a specific cause for the observed morphological alterations except for one animal with an elevated serum titer of 1:160 for canine distemper. Animals displayed macroscopically and/or histopathologically detectable infections with parasites, including Taenia sp., Toxocara sp. and Alaria alata. In summary, wildlife predators carry zoonotic parasitic disease and suffer from inflammatory diseases of yet unknown etiology, possibly bearing infectious potential for other animal species and humans. This study highlights the value of monitoring terrestrial wildlife following the "One Health" notion, to estimate the incidence and the possible spread of zoonotic pathogens and to avoid animal to animal spillover as well as transmission to humans.
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Affiliation(s)
- Charlotte Lempp
- Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Lower Saxony, Germany
| | - Nicole Jungwirth
- Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Lower Saxony, Germany
- Center for Systems Neuroscience, Hannover, Germany
| | - Miguel L. Grilo
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Büsum, Schleswig-Holstein, Germany
| | - Anja Reckendorf
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Büsum, Schleswig-Holstein, Germany
| | - Arlena Ulrich
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Büsum, Schleswig-Holstein, Germany
| | - Abbo van Neer
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Büsum, Schleswig-Holstein, Germany
| | - Rogier Bodewes
- Department of Viroscience, The Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Vanessa M. Pfankuche
- Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Lower Saxony, Germany
- Center for Systems Neuroscience, Hannover, Germany
| | - Christian Bauer
- Institute of Parasitology, Justus Liebig University Giessen, Giessen, Germany
| | - Albert D. M. E. Osterhaus
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Hannover, Lower Saxony, Germany
| | - Wolfgang Baumgärtner
- Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Lower Saxony, Germany
- Center for Systems Neuroscience, Hannover, Germany
| | - Ursula Siebert
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Büsum, Schleswig-Holstein, Germany
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30
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Blomström AL, Fossum C, Wallgren P, Berg M. Viral Metagenomic Analysis Displays the Co-Infection Situation in Healthy and PMWS Affected Pigs. PLoS One 2016; 11:e0166863. [PMID: 27907010 PMCID: PMC5131951 DOI: 10.1371/journal.pone.0166863] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 11/05/2016] [Indexed: 11/18/2022] Open
Abstract
The development of high-throughput sequencing technologies have allowed the possibility to investigate and characterise the entire microbiome of individuals, providing better insight to the complex interaction between different microorganisms. This will help to understand how the microbiome influence the susceptibility of secondary agents and development of disease. We have applied viral metagenomics to investigate the virome of lymph nodes from Swedish pigs suffering from the multifactorial disease postweaning multisystemic wasting syndrome (PMWS) as well as from healthy pigs. The aim is to increase knowledge of potential viruses, apart from porcine circovirus type 2 (PCV2), involved in PMWS development as well as to increase knowledge on the virome of healthy individuals. In healthy individuals, a diverse viral flora was seen with several different viruses present simultaneously. The majority of the identified viruses were small linear and circular DNA viruses, such as different circoviruses, anelloviruses and bocaviruses. In the pigs suffering from PMWS, PCV2 sequences were, as expected, detected to a high extent but other viruses were also identified in the background of PCV2. Apart from DNA viruses also RNA viruses were identified, among them were a porcine pestivirus showing high similarity to a recently (in 2015) discovered atypical porcine pestivirus in the US. Majority of the viruses identified in the background of PCV2 in PMWS pigs could also be identified in the healthy pigs. PCV2 sequences were also identified in the healthy pigs but to a much lower extent than in PMWS affected pigs. Although the method used here is not quantitative the very clear difference in amount of PCV2 sequences in PMWS affected pigs and healthy pigs most likely reflect the very strong replication of PCV2 known to be a hallmark of PMWS. Taken together, these findings illustrate that pigs appear to have a considerable viral flora consisting to a large extent of small single-stranded and circular DNA viruses. Future research on these types of viruses will help to better understand the role that these ubiquitous viruses may have on health and disease of pigs. We also demonstrate for the first time, in Europe, the presence of a novel porcine pestivirus.
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Affiliation(s)
- Anne-Lie Blomström
- Department of Biomedical Sciences and Veterinary Public Health, Section of Virology, Swedish University of Agricultural Sciences, Uppsala, Sweden
- * E-mail:
| | - Caroline Fossum
- Department of Biomedical Sciences and Veterinary Public Health, Section of Immunology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Per Wallgren
- National Veterinary Institute (SVA), Uppsala, Sweden
| | - Mikael Berg
- Department of Biomedical Sciences and Veterinary Public Health, Section of Virology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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31
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Abstract
Understanding pathogen exchange among human, wildlife, and livestock populations, and the varying ecological and cultural contexts in which this exchange takes place, is a major challenge. The present review contextualizes the risk factors that result from human interactions with livestock, companion animals, animal exhibits, wildlife through nature-based tourism, and wildlife through consumption. Given their phylogenetic relatedness to humans, primates are emphasized in this discussion; primates serve as reservoirs for several human pathogens, and some human pathogens can decimate wild primate populations. Anthropologists must play a central role in understanding cultural variation in attitudes toward other species as well as perceived risks when interacting with animals. I argue that the remediation of emerging infectious diseases will be accomplished primarily through human behavioral changes rather than through efforts in pathogen discovery. Given the history of human interactions with wildlife, candid discussions on zoonotic diseases will be increasingly important for our combined survival.
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32
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Jacobsen KH, Aguirre AA, Bailey CL, Baranova AV, Crooks AT, Croitoru A, Delamater PL, Gupta J, Kehn-Hall K, Narayanan A, Pierobon M, Rowan KE, Schwebach JR, Seshaiyer P, Sklarew DM, Stefanidis A, Agouris P. Lessons from the Ebola Outbreak: Action Items for Emerging Infectious Disease Preparedness and Response. ECOHEALTH 2016; 13:200-212. [PMID: 26915507 PMCID: PMC7087787 DOI: 10.1007/s10393-016-1100-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 09/30/2015] [Accepted: 01/06/2016] [Indexed: 05/29/2023]
Abstract
As the Ebola outbreak in West Africa wanes, it is time for the international scientific community to reflect on how to improve the detection of and coordinated response to future epidemics. Our interdisciplinary team identified key lessons learned from the Ebola outbreak that can be clustered into three areas: environmental conditions related to early warning systems, host characteristics related to public health, and agent issues that can be addressed through the laboratory sciences. In particular, we need to increase zoonotic surveillance activities, implement more effective ecological health interventions, expand prediction modeling, support medical and public health systems in order to improve local and international responses to epidemics, improve risk communication, better understand the role of social media in outbreak awareness and response, produce better diagnostic tools, create better therapeutic medications, and design better vaccines. This list highlights research priorities and policy actions the global community can take now to be better prepared for future emerging infectious disease outbreaks that threaten global public health and security.
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Affiliation(s)
- Kathryn H Jacobsen
- Department of Global and Community Health, College of Health and Human Services, George Mason University, 4400 University Drive 5B7, Fairfax, VA, 22030, USA.
| | - A Alonso Aguirre
- Department of Environmental Science and Policy, College of Science, George Mason University, Fairfax, VA, USA
| | - Charles L Bailey
- National Center for Biodefense and Infectious Diseases, School of Systems Biology, College of Science, George Mason University, Manassas, VA, USA
| | - Ancha V Baranova
- Department of Environmental Science and Policy, College of Science, George Mason University, Fairfax, VA, USA
- Center for the Study of Chronic Metabolic Diseases, School of Systems Biology, College of Science, George Mason University, Manassas, VA, USA
| | - Andrew T Crooks
- Department of Computational and Data Sciences, College of Science, George Mason University, Fairfax, VA, USA
| | - Arie Croitoru
- Department of Geography and Geoinformation Science, College of Science, George Mason University, Fairfax, VA, USA
| | - Paul L Delamater
- Department of Geography and Geoinformation Science, College of Science, George Mason University, Fairfax, VA, USA
| | - Jhumka Gupta
- Department of Global and Community Health, College of Health and Human Services, George Mason University, 4400 University Drive 5B7, Fairfax, VA, 22030, USA
| | - Kylene Kehn-Hall
- National Center for Biodefense and Infectious Diseases, School of Systems Biology, College of Science, George Mason University, Manassas, VA, USA
| | - Aarthi Narayanan
- National Center for Biodefense and Infectious Diseases, School of Systems Biology, College of Science, George Mason University, Manassas, VA, USA
| | - Mariaelena Pierobon
- Center for Applied Proteomics and Molecular Medicine, School of Systems Biology, College of Science, George Mason University, Manassas, VA, USA
| | - Katherine E Rowan
- Department of Communication, College of Humanities and Social Sciences, George Mason University, Fairfax, VA, USA
| | - J Reid Schwebach
- Department of Biology, College of Science, George Mason University, Fairfax, VA, USA
| | - Padmanabhan Seshaiyer
- Department of Mathematical Sciences, College of Science, George Mason University, Fairfax, VA, USA
| | - Dann M Sklarew
- Department of Environmental Science and Policy, College of Science, George Mason University, Fairfax, VA, USA
| | - Anthony Stefanidis
- Department of Geography and Geoinformation Science, College of Science, George Mason University, Fairfax, VA, USA
| | - Peggy Agouris
- Department of Geography and Geoinformation Science, College of Science, George Mason University, Fairfax, VA, USA
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Rosales SM, Vega Thurber R. Brain Meta-Transcriptomics from Harbor Seals to Infer the Role of the Microbiome and Virome in a Stranding Event. PLoS One 2015; 10:e0143944. [PMID: 26630132 PMCID: PMC4668051 DOI: 10.1371/journal.pone.0143944] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 11/11/2015] [Indexed: 11/18/2022] Open
Abstract
Marine diseases are becoming more frequent, and tools for identifying pathogens and disease reservoirs are needed to help prevent and mitigate epizootics. Meta-transcriptomics provides insights into disease etiology by cataloguing and comparing sequences from suspected pathogens. This method is a powerful approach to simultaneously evaluate both the viral and bacterial communities, but few studies have applied this technique in marine systems. In 2009 seven harbor seals, Phoca vitulina, stranded along the California coast from a similar brain disease of unknown cause of death (UCD). We evaluated the differences between the virome and microbiome of UCDs and harbor seals with known causes of death. Here we determined that UCD stranded animals had no viruses in their brain tissue. However, in the bacterial community, we identified Burkholderia and Coxiella burnetii as important pathogens associated with this stranding event. Burkholderia were 100% prevalent and ~2.8 log2 fold more abundant in the UCD animals. Further, while C. burnetii was found in only 35.7% of all samples, it was highly abundant (~94% of the total microbial community) in a single individual. In this harbor seal, C. burnetii showed high transcription rates of invading and translation genes, implicating it in the pathogenesis of this animal. Based on these data we propose that Burkholderia taxa and C. burnetii are potentially important opportunistic neurotropic pathogens in UCD stranded harbor seals.
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Affiliation(s)
- Stephanie M. Rosales
- Oregon State University, Dept. of Microbiology, 226 Nash Hall, Corvallis, OR, 97331, United States of America
- * E-mail:
| | - Rebecca Vega Thurber
- Oregon State University, Dept. of Microbiology, 226 Nash Hall, Corvallis, OR, 97331, United States of America
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Capps B, Bailey MM, Bickford D, Coker R, Lederman Z, Lover A, Lysaght T, Tambyah P. Introducing One Health to the Ethical Debate About Zoonotic Diseases in Southeast Asia. BIOETHICS 2015; 29:588-96. [PMID: 25675899 PMCID: PMC7161875 DOI: 10.1111/bioe.12145] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Pandemic plans recommend phases of response to an emergent infectious disease (EID) outbreak, and are primarily aimed at preventing and mitigating human-to-human transmission. These plans carry presumptive weight and are increasingly being operationalized at the national, regional and international level with the support of the World Health Organization (WHO). The conventional focus of pandemic preparedness for EIDs of zoonotic origin has been on public health and human welfare. However, this focus on human populations has resulted in strategically important disciplinary silos. As the risks of zoonotic diseases have implications that reach across many domains outside traditional public health, including anthropological, environmental, and veterinary fora, a more inclusive ecological perspective is paramount for an effective response to future outbreaks.
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Bellehumeur C, Boyle B, Charette SJ, Harel J, L'Homme Y, Masson L, Gagnon CA. Propidium monoazide (PMA) and ethidium bromide monoazide (EMA) improve DNA array and high-throughput sequencing of porcine reproductive and respiratory syndrome virus identification. J Virol Methods 2015; 222:182-91. [PMID: 26129867 PMCID: PMC7119533 DOI: 10.1016/j.jviromet.2015.06.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 06/11/2015] [Accepted: 06/25/2015] [Indexed: 11/29/2022]
Abstract
Pan-viral DNA array (PVDA) and high-throughput sequencing (HTS) are useful tools to identify novel viruses of emerging diseases. However, both techniques have difficulties to identify viruses in clinical samples because of the host genomic nucleic acid content (hg/cont). Both propidium monoazide (PMA) and ethidium bromide monoazide (EMA) have the capacity to bind free DNA/RNA, but are cell membrane-impermeable. Thus, both are unable to bind protected nucleic acid such as viral genomes within intact virions. However, EMA/PMA modified genetic material cannot be amplified by enzymes. In order to assess the potential of EMA/PMA to lower the presence of amplifiable hg/cont in samples and improve virus detection, serum and lung tissue homogenates were spiked with porcine reproductive and respiratory virus (PRRSV) and were processed with EMA/PMA. In addition, PRRSV RT-qPCR positive clinical samples were also tested. EMA/PMA treatments significantly decreased amplifiable hg/cont and significantly increased the number of PVDA positive probes and their signal intensity compared to untreated spiked lung samples. EMA/PMA treatments also increased the sensitivity of HTS by increasing the number of specific PRRSV reads and the PRRSV percentage of coverage. Interestingly, EMA/PMA treatments significantly increased the sensitivity of PVDA and HTS in two out of three clinical tissue samples. Thus, EMA/PMA treatments offer a new approach to lower the amplifiable hg/cont in clinical samples and increase the success of PVDA and HTS to identify viruses.
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Affiliation(s)
- Christian Bellehumeur
- Groupe de recherche sur les maladies infectieuses du porc (GREMIP), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, QC, Canada; Swine and Poultry Infectious Diseases Research Center (CRIPA), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, QC, Canada
| | - Brian Boyle
- Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Steve J Charette
- Swine and Poultry Infectious Diseases Research Center (CRIPA), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, QC, Canada; Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Québec, QC, Canada; Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, QC, Canada; Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec, Québec, QC, Canada
| | - Josée Harel
- Groupe de recherche sur les maladies infectieuses du porc (GREMIP), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, QC, Canada; Swine and Poultry Infectious Diseases Research Center (CRIPA), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, QC, Canada
| | - Yvan L'Homme
- Swine and Poultry Infectious Diseases Research Center (CRIPA), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, QC, Canada; Canadian Food Inspection Agency, Saint-Hyacinthe, QC, Canada
| | - Luke Masson
- Swine and Poultry Infectious Diseases Research Center (CRIPA), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, QC, Canada; National Research Council Canada, Montréal, QC, Canada
| | - Carl A Gagnon
- Groupe de recherche sur les maladies infectieuses du porc (GREMIP), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, QC, Canada; Swine and Poultry Infectious Diseases Research Center (CRIPA), Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, QC, Canada.
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Li L, Giannitti F, Low J, Keyes C, Ullmann LS, Deng X, Aleman M, Pesavento PA, Pusterla N, Delwart E. Exploring the virome of diseased horses. J Gen Virol 2015; 96:2721-2733. [PMID: 26044792 DOI: 10.1099/vir.0.000199] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Metagenomics was used to characterize viral genomes in clinical specimens of horses with various organ-specific diseases of unknown aetiology. A novel parvovirus as well as a previously described hepacivirus closely related to human hepatitis C virus and equid herpesvirus 2 were identified in the cerebrospinal fluid of horses with neurological signs. Four co-infecting picobirnaviruses, including an unusual genome with fused RNA segments, and a divergent anellovirus were found in the plasma of two febrile horses. A novel cyclovirus genome was characterized from the nasal secretion of another febrile animal. Lastly, a small circular DNA genome with a Rep gene, from a virus we called kirkovirus, was identified in the liver and spleen of a horse with fatal idiopathic hepatopathy. This study expands the number of viruses found in horses, and characterizes their genomes to assist future epidemiological studies of their transmission and potential association with various equine diseases.
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Affiliation(s)
- Linlin Li
- Blood Systems Research Institute, San Francisco, CA, USA.,Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Federico Giannitti
- California Animal Health and Food Safety Laboratory, School of Veterinary Medicine, University of California, Davis, CA, USA.,Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, USA.,Instituto Nacional de Investigación Agropecuaria, La Estanzuela, Colonia, Uruguay
| | - Jason Low
- Department of Bioengineering, University of California, Los Angeles, CA, USA
| | - Casey Keyes
- Department of Biology, University of San Francisco, San Francisco, CA, USA
| | - Leila S Ullmann
- Department of Microbiology and Immunology, UNESP Sao Paulo State University, Sao Paulo, Brazil
| | - Xutao Deng
- Blood Systems Research Institute, San Francisco, CA, USA.,Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Monica Aleman
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Patricia A Pesavento
- Department of Pathology, Microbiology and Immunology, University of California, Davis, CA, USA
| | - Nicola Pusterla
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, CA, USA.,Department of Laboratory Medicine, University of California, San Francisco, CA, USA
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Jensen RH, Mollerup S, Mourier T, Hansen TA, Fridholm H, Nielsen LP, Willerslev E, Hansen AJ, Vinner L. Target-dependent enrichment of virions determines the reduction of high-throughput sequencing in virus discovery. PLoS One 2015; 10:e0122636. [PMID: 25853649 PMCID: PMC4390369 DOI: 10.1371/journal.pone.0122636] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 02/23/2015] [Indexed: 11/20/2022] Open
Abstract
Viral infections cause many different diseases stemming both from well-characterized viral pathogens but also from emerging viruses, and the search for novel viruses continues to be of great importance. High-throughput sequencing is an important technology for this purpose. However, viral nucleic acids often constitute a minute proportion of the total genetic material in a sample from infected tissue. Techniques to enrich viral targets in high-throughput sequencing have been reported, but the sensitivity of such methods is not well established. This study compares different library preparation techniques targeting both DNA and RNA with and without virion enrichment. By optimizing the selection of intact virus particles, both by physical and enzymatic approaches, we assessed the effectiveness of the specific enrichment of viral sequences as compared to non-enriched sample preparations by selectively looking for and counting read sequences obtained from shotgun sequencing. Using shotgun sequencing of total DNA or RNA, viral targets were detected at concentrations corresponding to the predicted level, providing a foundation for estimating the effectiveness of virion enrichment. Virion enrichment typically produced a 1000-fold increase in the proportion of DNA virus sequences. For RNA virions the gain was less pronounced with a maximum 13-fold increase. This enrichment varied between the different sample concentrations, with no clear trend. Despite that less sequencing was required to identify target sequences, it was not evident from our data that a lower detection level was achieved by virion enrichment compared to shotgun sequencing.
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Affiliation(s)
- Randi Holm Jensen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- * E-mail:
| | - Sarah Mollerup
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Tobias Mourier
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Arn Hansen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Helena Fridholm
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Lars Peter Nielsen
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Anders Johannes Hansen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Lasse Vinner
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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A metagenomics and case-control study to identify viruses associated with bovine respiratory disease. J Virol 2015; 89:5340-9. [PMID: 25740998 DOI: 10.1128/jvi.00064-15] [Citation(s) in RCA: 169] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 02/21/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Bovine respiratory disease (BRD) is a common health problem for both dairy and beef cattle, resulting in significant economic loses. In order to identify viruses associated with BRD, we used a metagenomics approach to enrich and sequence viral nucleic acids in the nasal swabs of 50 young dairy cattle with symptoms of BRD. Following deep sequencing, de novo assembly, and translated protein sequence similarity searches, numerous known and previously uncharacterized viruses were identified. Bovine adenovirus 3, bovine adeno-associated virus, bovine influenza D virus, bovine parvovirus 2, bovine herpesvirus 6, bovine rhinitis A virus, and multiple genotypes of bovine rhinitis B virus were identified. The genomes of a previously uncharacterized astrovirus and picobirnaviruses were also partially or fully sequenced. Using real-time PCR, the rates of detection of the eight viruses that generated the most reads were compared for the nasal secretions of 50 animals with BRD versus 50 location-matched healthy control animals. Viruses were detected in 68% of BRD-affected animals versus 16% of healthy control animals. Thirty-eight percent of sick animals versus 8% of controls were infected with multiple respiratory viruses. Significantly associated with BRD were bovine adenovirus 3 (P < 0.0001), bovine rhinitis A virus (P = 0.005), and the recently described bovine influenza D virus (P = 0.006), which were detected either alone or in combination in 62% of animals with BRD. A metagenomics and real-time PCR detection approach in carefully matched cases and controls can provide a rapid means to identify viruses associated with a complex disease, paving the way for further confirmatory tests and ultimately to effective intervention strategies. IMPORTANCE Bovine respiratory disease is the most economically important disease affecting the cattle industry, whose complex root causes include environmental, genetics, and infectious factors. Using an unbiased metagenomics approach, we characterized the viruses in respiratory secretions from BRD cases and identified known and previously uncharacterized viruses belonging to seven viral families. Using a case-control format with location-matched animals, we compared the rates of viral detection and identified 3 viruses associated with severe BRD signs. Combining a metagenomics and case-control format can provide candidate pathogens associated with complex infectious diseases and inform further studies aimed at reducing their impact.
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Virus characterization and discovery in formalin-fixed paraffin-embedded tissues. J Virol Methods 2015; 214:54-9. [PMID: 25681526 PMCID: PMC7119673 DOI: 10.1016/j.jviromet.2015.02.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 12/04/2014] [Accepted: 02/05/2015] [Indexed: 01/09/2023]
Abstract
Detection and characterization of novel viruses is often hampered by the lack of adequately stored materials. Formalin-fixed paraffin embedded (FFPE) tissues can be used to detect known viral sequences. The application of FFPE tissues for detection of novel viral sequences is currently unclear. Sequence-independent amplification and next-generation was performed on FFPE tissues. Sequences of known viruses and a novel rotavirus were detected, with relatively low sensitivity but standard accuracy.
Detection and characterization of novel viruses is hampered frequently by the lack of properly stored materials. Especially for the retrospective identification of viruses responsible for past disease outbreaks, often only formalin-fixed paraffin-embedded (FFPE) tissue samples are available. Although FFPE tissues can be used to detect known viral sequences, the application of FFPE tissues for detection of novel viruses is currently unclear. In the present study it was shown that sequence-independent amplification in combination with next-generation sequencing can be used to detect sequences of known and unknown viruses, although with relatively low sensitivity. These findings indicate that this technique could be useful for detecting novel viral sequences in FFPE tissues collected from humans and animals with disease of unknown origin, when other samples are not available. In addition, application of this method to FFPE tissues allows to correlate with the presence of histopathological changes in the corresponding tissue sections.
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Li L, Deng X, Mee ET, Collot-Teixeira S, Anderson R, Schepelmann S, Minor PD, Delwart E. Comparing viral metagenomics methods using a highly multiplexed human viral pathogens reagent. J Virol Methods 2014; 213:139-46. [PMID: 25497414 PMCID: PMC4344864 DOI: 10.1016/j.jviromet.2014.12.002] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 11/26/2014] [Accepted: 12/03/2014] [Indexed: 10/29/2022]
Abstract
Unbiased metagenomic sequencing holds significant potential as a diagnostic tool for the simultaneous detection of any previously genetically described viral nucleic acids in clinical samples. Viral genome sequences can also inform on likely phenotypes including drug susceptibility or neutralization serotypes. In this study, different variables of the laboratory methods often used to generate viral metagenomics libraries were compared for their abilities to detect multiple viruses and generate full genome coverage. A biological reagent consisting of 25 different human RNA and DNA viral pathogens was used to estimate the effect of filtration and nuclease digestion, DNA/RNA extraction methods, pre-amplification and the use of different library preparation kits on the detection of viral nucleic acids. Filtration and nuclease treatment led to slight decreases in the percentage of viral sequence reads and number of viruses detected. For nucleic acid extractions silica spin columns improved viral sequence recovery relative to magnetic beads and Trizol extraction. Pre-amplification using random RT-PCR while generating more viral sequence reads resulted in detection of fewer viruses, more overlapping sequences, and lower genome coverage. The ScriptSeq library preparation method retrieved more viruses and a greater fraction of their genomes than the TruSeq and Nextera methods. Viral metagenomics sequencing was able to simultaneously detect up to 22 different viruses in the biological reagent analyzed including all those detected by qPCR. Further optimization will be required for the detection of viruses in biologically more complex samples such as tissues, blood, or feces.
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Affiliation(s)
- Linlin Li
- Blood Systems Research Institute, San Francisco, CA, USA; Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Xutao Deng
- Blood Systems Research Institute, San Francisco, CA, USA; Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Edward T Mee
- Division of Virology, National Institute for Biological Reagents and Control, Medicines and Healthcare Products Regulatory Agency, Hertfordshire, UK
| | - Sophie Collot-Teixeira
- Division of Virology, National Institute for Biological Reagents and Control, Medicines and Healthcare Products Regulatory Agency, Hertfordshire, UK
| | - Rob Anderson
- Division of Virology, National Institute for Biological Reagents and Control, Medicines and Healthcare Products Regulatory Agency, Hertfordshire, UK
| | - Silke Schepelmann
- Division of Virology, National Institute for Biological Reagents and Control, Medicines and Healthcare Products Regulatory Agency, Hertfordshire, UK
| | - Philip D Minor
- Division of Virology, National Institute for Biological Reagents and Control, Medicines and Healthcare Products Regulatory Agency, Hertfordshire, UK
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, CA, USA; Department of Laboratory Medicine, University of California, San Francisco, CA, USA.
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Boros Á, Pankovics P, Reuter G. Avian picornaviruses: molecular evolution, genome diversity and unusual genome features of a rapidly expanding group of viruses in birds. INFECTION GENETICS AND EVOLUTION 2014; 28:151-66. [PMID: 25278047 DOI: 10.1016/j.meegid.2014.09.027] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 09/15/2014] [Accepted: 09/21/2014] [Indexed: 12/29/2022]
Abstract
Picornaviridae is one of the most diverse families of viruses infecting vertebrate species. In contrast to the relative small number of mammal species compared to other vertebrates, the abundance of mammal-infecting picornaviruses was significantly overrepresented among the presently known picornaviruses. Therefore most of the current knowledge about the genome diversity/organization patterns and common genome features were based on the analysis of mammal-infecting picornaviruses. Beside the well known reservoir role of birds in case of several emerging viral pathogens, little is known about the diversity of picornaviruses circulating among birds, although in the last decade the number of known avian picornavirus species with complete genome was increased from one to at least 15. However, little is known about the geographic distribution, host spectrum or pathogenic potential of the recently described picornaviruses of birds. Despite the low number of known avian picornaviruses, the phylogenetic and genome organization diversity of these viruses were remarkable. Beside the common L-4-3-4 and 4-3-4 genome layouts unusual genome patterns (3-4-4; 3-5-4, 3-6-4; 3-8-4) with variable, multicistronic 2A genome regions were found among avian picornaviruses. The phylogenetic and genomic analysis revealed the presence of several conserved structures at the untranslated regions among phylogenetically distant avian and non-avian picornaviruses as well as at least five different avian picornavirus phylogenetic clusters located in every main picornavirus lineage with characteristic genome layouts which suggests the complex evolution history of these viruses. Based on the remarkable genetic diversity of the few known avian picornaviruses, the emergence of further divergent picornaviruses causing challenges in the current taxonomy and also in the understanding of the evolution and genome organization of picornaviruses will be strongly expected. In this review we would like to summarize the current knowledge about the taxonomy, pathogenic potential, phylogenetic/genomic diversity and evolutional relationship of avian picornaviruses.
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Affiliation(s)
- Ákos Boros
- Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, Pécs, Hungary
| | - Péter Pankovics
- Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, Pécs, Hungary
| | - Gábor Reuter
- Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, Pécs, Hungary.
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Malham SK, Rajko-Nenow P, Howlett E, Tuson KE, Perkins TL, Pallett DW, Wang H, Jago CF, Jones DL, McDonald JE. The interaction of human microbial pathogens, particulate material and nutrients in estuarine environments and their impacts on recreational and shellfish waters. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2014; 16:2145-2155. [PMID: 25043898 DOI: 10.1039/c4em00031e] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Anthropogenic activities have increased the load of faecal bacteria, pathogenic viruses and nutrients in rivers, estuaries and coastal areas through point and diffuse sources such as sewage discharges and agricultural runoff. These areas are used by humans for both commercial and recreational activities and are therefore protected by a range of European Directives. If water quality declines in these zones, significant economic losses can occur. Identifying the sources of pollution, however, is notoriously difficult due to the ephemeral nature of discharges, their diffuse source, and uncertainties associated with transport and transformation of the pollutants through the freshwater-marine interface. Further, significant interaction between nutrients, microorganisms and particulates can occur in the water column making prediction of the fate and potential infectivity of human pathogenic organisms difficult to ascertain. This interaction is most prevalent in estuarine environments due to the formation of flocs (suspended sediment) at the marine-freshwater interface. A range of physical, chemical and biological processes can induce the co-flocculation of microorganisms, organic matter and mineral particles resulting in pathogenic organisms becoming potentially protected from a range of biotic (e.g. predation) and abiotic stresses (e.g. UV, salinity). These flocs contain and retain macro- and micro- nutrients allowing the potential survival, growth and transfer of pathogenic organisms to commercially sensitive areas (e.g. beaches, shellfish harvesting waters). The flocs can either be transported directly to the coastal environment or can become deposited in the estuary forming cohesive sediments where pathogens can survive for long periods. Especially in response to storms, these sediments can be subsequently remobilised releasing pulses of potential pathogenic organisms back into the water column leading to contamination of marine waters long after the initial contamination event occurred. Further work, however, is still required to understand and predict the potential human infectivity of pathogenic organisms alongside the better design of early warning systems and surveillance measures for risk assessment purposes.
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Affiliation(s)
- Shelagh K Malham
- Centre for Applied Marine Science, Bangor University, Menai Bridge, Anglesey LL59 5AB, UK
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Bodewes R, Ruiz-Gonzalez A, Schapendonk CME, van den Brand JMA, Osterhaus ADME, Smits SL. Viral metagenomic analysis of feces of wild small carnivores. Virol J 2014; 11:89. [PMID: 24886057 PMCID: PMC4030737 DOI: 10.1186/1743-422x-11-89] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 05/08/2014] [Indexed: 11/10/2022] Open
Abstract
Background Recent studies have clearly demonstrated the enormous virus diversity that exists among wild animals. This exemplifies the required expansion of our knowledge of the virus diversity present in wildlife, as well as the potential transmission of these viruses to domestic animals or humans. Methods In the present study we evaluated the viral diversity of fecal samples (n = 42) collected from 10 different species of wild small carnivores inhabiting the northern part of Spain using random PCR in combination with next-generation sequencing. Samples were collected from American mink (Neovison vison), European mink (Mustela lutreola), European polecat (Mustela putorius), European pine marten (Martes martes), stone marten (Martes foina), Eurasian otter (Lutra lutra) and Eurasian badger (Meles meles) of the family of Mustelidae; common genet (Genetta genetta) of the family of Viverridae; red fox (Vulpes vulpes) of the family of Canidae and European wild cat (Felis silvestris) of the family of Felidae. Results A number of sequences of possible novel viruses or virus variants were detected, including a theilovirus, phleboviruses, an amdovirus, a kobuvirus and picobirnaviruses. Conclusions Using random PCR in combination with next generation sequencing, sequences of various novel viruses or virus variants were detected in fecal samples collected from Spanish carnivores. Detected novel viruses highlight the viral diversity that is present in fecal material of wild carnivores.
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Affiliation(s)
- Rogier Bodewes
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands.
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Abstract
Next-generation sequencing is a new research tool in our hands helping us to explore still unknown fields of human and veterinary virology. Metagenomic analysis has enabled the discovery of putative novel pathogens and the identification of the etiologic agents of several diseases, solving long-standing mysteries caused by divergent viruses. This approach has been used in several studies investigating fecal samples of livestock, and companion animal species, providing information on the diversity of animal fecal virome, helping the elucidation of the etiology of diarrheal disease in animals and identifying potential zoonotic and emerging viruses.
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Abstract
The beneficial role that animal shelters play is unquestionable. An estimated 3 to 4 million animals are cared for or placed in homes each year, and most shelters promote public health and support responsible pet ownership. It is, nonetheless, inevitable that shelters are prime examples of anthropogenic biological instability: even well-run shelters often house transient, displaced, and mixed populations of animals. Many of these animals have received minimal to no prior health care, and some have a history of scavenging or predation to survive. Overcrowding and poor shelter conditions further magnify these inherent risks to create individual, intraspecies, and interspecies stress and provide an environment conducive to exposure to numerous potentially collaborative pathogens. All of these factors can contribute to the evolution and emergence of new pathogens or to alterations in virulence of endemic pathogens. While it is not possible to effectively anticipate the timing or the pathogen type in emergence events, their sites of origin are less enigmatic, and pathologists and diagnosticians who work with sheltered animal populations have recognized several such events in the past decade. This article first considers the contribution of the shelter environment to canine and feline disease. This is followed by summaries of recent research on the pathogenesis of common shelter pathogens, as well as research that has led to the discovery of novel or emerging diseases and the methods that are used for their diagnosis and discovery. For the infectious agents that commonly affect sheltered dogs and cats, including canine distemper virus, canine influenza virus, Streptococcus spp, parvoviruses, feline herpesvirus, feline caliciviruses, and feline infectious peritonitis virus, we present familiar as well as newly recognized lesions associated with infection. Preliminary studies on recently discovered viruses like canine circovirus, canine bocavirus, and feline norovirus indicate that these pathogens can cause or contribute to canine and feline disease.
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Affiliation(s)
- P A Pesavento
- School of Veterinary Medicine, UC Davis, Vet Med: PMI, 4206 VM3A, 1 Shields Ave, Davis, CA 95616, USA.
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Li L, McGraw S, Zhu K, Leutenegger CM, Marks SL, Kubiski S, Gaffney P, Dela Cruz FN, Wang C, Delwart E, Pesavento PA. Circovirus in tissues of dogs with vasculitis and hemorrhage. Emerg Infect Dis 2013; 19:534-41. [PMID: 23628223 PMCID: PMC3647419 DOI: 10.3201/eid1904.121390] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
We characterized the complete genome of a novel dog circovirus (DogCV) from the liver of a dog with severe hemorrhagic gastroenteritis, vasculitis, and granulomatous lymphadenitis. DogCV was detected by PCR in fecal samples from 19/168 (11.3%) dogs with diarrhea and 14/204 (6.9%) healthy dogs and in blood from 19/409 (3.3%) of dogs with thrombocytopenia and neutropenia, fever of unknown origin, or past tick bite. Co-infection with other canine pathogens was detected for 13/19 (68%) DogCV-positive dogs with diarrhea. DogCV capsid proteins from different dogs varied by up to 8%. In situ hybridization and transmission electron microscopy detected DogCV in the lymph nodes and spleens of 4 dogs with vascular compromise and histiocytic inflammation. The detection of a circovirus in tissues of dogs expands the known tropism of these viruses to a second mammalian host. Our results indicate that circovirus, alone or in co-infection with other pathogens, might contribute to illness and death in dogs.
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Affiliation(s)
- Linlin Li
- Blood Systems Research Institute, and Department of Laboratory Medicine, University of California, San Francisco, California, USA
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Bernardo P, Golden M, Akram M, Naimuddin, Nadarajan N, Fernandez E, Granier M, Rebelo AG, Peterschmitt M, Martin DP, Roumagnac P. Identification and characterisation of a highly divergent geminivirus: evolutionary and taxonomic implications. Virus Res 2013; 177:35-45. [PMID: 23886668 DOI: 10.1016/j.virusres.2013.07.006] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 07/08/2013] [Accepted: 07/09/2013] [Indexed: 01/08/2023]
Abstract
During a large scale "non a priori" survey in 2010 of South African plant-infecting single stranded DNA viruses, a highly divergent geminivirus genome was isolated from a wild spurge, Euphorbia caput-medusae. In addition to being infectious in E. caput-medusae, the cloned viral genome was also infectious in tomato and Nicotiana benthamiana. The virus, named Euphorbia caput-medusae latent virus (EcmLV) due to the absence of infection symptoms displayed by its natural host, caused severe symptoms in both tomato and N. benthamiana. The genome organisation of EcmLV is unique amongst geminiviruses and it likely expresses at least two proteins without any detectable homologues within public sequence databases. Although clearly a geminivirus, EcmLV is so divergent that we propose its placement within a new genus that we have tentatively named Capulavirus. Using a set of highly divergent geminiviruses genomes, it is apparent that recombination has likely been a primary process in the genus-level diversification of geminiviruses. It is also demonstrated how this insight, taken together with phylogenetic analyses of predicted coat protein and replication associated protein (Rep) amino acid sequences indicate that the most recent common ancestor of the geminiviruses was likely a dicot-infecting virus that, like modern day mastreviruses and becurtoviruses, expressed its Rep from a spliced complementary strand transcript.
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Affiliation(s)
- Pauline Bernardo
- CIRAD/UMR BGPI, TA A54/K, Campus International de Baillarguet, 34398 Montpellier Cedex 5, France; INRA/UMR, BGPI, TA A54/K, Campus International de Baillarguet, 34398 Montpellier Cedex 5, France
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Xie G, Yu J, Duan Z. New strategy for virus discovery: viruses identified in human feces in the last decade. SCIENCE CHINA-LIFE SCIENCES 2013; 56:688-96. [PMID: 23917840 PMCID: PMC7089042 DOI: 10.1007/s11427-013-4516-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Accepted: 06/16/2013] [Indexed: 02/08/2023]
Abstract
Emerging and re-emerging viruses continue to surface all over the world. Some of these viruses have the potential for rapid and global spread with high morbidity and mortality, such as the SARS coronavirus outbreak. It is extremely urgent and important to identify a novel virus near-instantaneously to develop an active preventive and/or control strategy. As a culture-independent approach, viral metagenomics has been widely used to investigate highly divergent and completely new viruses in humans, animals, and even environmental samples in the past decade. A new model of Koch’s postulates, named the metagenomic Koch’s postulates, has provided guidance for the study of the pathogenicity of novel viruses. This review explains the viral metagenomics strategy for virus discovery and describes viruses discovered in human feces in the past 10 years using this approach. This review also addresses issues related to the metagenomic Koch’s postulates and the challenges for virus discovery in the future.
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Affiliation(s)
- GuangCheng Xie
- National Institute of Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
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Junglen S, Drosten C. Virus discovery and recent insights into virus diversity in arthropods. Curr Opin Microbiol 2013; 16:507-13. [PMID: 23850098 PMCID: PMC7108301 DOI: 10.1016/j.mib.2013.06.005] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 06/18/2013] [Accepted: 06/19/2013] [Indexed: 11/29/2022]
Abstract
Overview on arthropod-associated virus discovery. Description of newly characterized virus species. Projections for further research.
Recent studies on virus discovery have focused mainly on mammalian and avian viruses. Arbovirology with its long tradition of ecologically oriented investigation is now catching up, with important novel insights into the diversity of arthropod-associated viruses. Recent discoveries include taxonomically outlying viruses within the families Flaviviridae, Togaviridae, and Bunyaviridae, and even novel virus families within the order Nidovirales. However, the current focusing of studies on blood-feeding arthropods has restricted the range of arthropod hosts analyzed for viruses so far. Future investigations should include species from other arthropod taxa than Ixodita, Culicidae and Phlebotominae in order to shed light on the true diversity of arthropod viruses.
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Affiliation(s)
- Sandra Junglen
- Institute of Virology, University of Bonn Medical Center, Bonn, Germany.
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50
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Bodewes R, van der Giessen J, Haagmans BL, Osterhaus ADME, Smits SL. Identification of multiple novel viruses, including a parvovirus and a hepevirus, in feces of red foxes. J Virol 2013; 87:7758-64. [PMID: 23616657 PMCID: PMC3700315 DOI: 10.1128/jvi.00568-13] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 04/12/2013] [Indexed: 02/07/2023] Open
Abstract
Red foxes (Vulpes vulpes) are the most widespread members of the order of Carnivora. Since they often live in (peri)urban areas, they are a potential reservoir of viruses that transmit from wildlife to humans or domestic animals. Here we evaluated the fecal viral microbiome of 13 red foxes by random PCR in combination with next-generation sequencing. Various novel viruses, including a parvovirus, bocavirus, adeno-associated virus, hepevirus, astroviruses, and picobirnaviruses, were identified.
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Affiliation(s)
- Rogier Bodewes
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, The Netherlands.
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