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Alves RS, do Canto Olegário J, Weber MN, da Silva MS, Canova R, Sauthier JT, Baumbach LF, Witt AA, Varela APM, Mayer FQ, da Fontoura Budaszewski R, Canal CW. Detection of coronavirus in vampire bats (Desmodus rotundus) in southern Brazil. Transbound Emerg Dis 2022; 69. [PMID: 33977671 PMCID: PMC8242716 DOI: 10.1111/tbed.14150+10.1111/tbed.14150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
Abstract
The vampire bat (Desmodus rotundus) is a haematophagous animal that feeds exclusively on the blood of domestic mammals. Vampire bat feeding habits enable their contact with mammalian hosts and may enhance zoonotic spillover. Moreover, they may carry several pathogenic organisms, including coronaviruses (CoVs), for which they are important hosts. The human pathogens that cause severe acute respiratory syndrome (SARS-CoV), Middle East respiratory syndrome (MERS-CoV) and possibly coronavirus disease 2019 (SARS-CoV-2) all originated in bats but required bridge hosts to spread into human populations. To monitor the presence of potential zoonotic viruses in bats, the present work evaluated the presence of CoVs in vampire bats from southern Brazil. A total of 101 vampire bats were captured and euthanized between 2017 and 2019 in Rio Grande do Sul state, southern Brazil. The brain, heart, liver, lungs, kidneys and intestines were collected and macerated individually. The samples were pooled and submitted to high-throughput sequencing (HTS) using the Illumina MiSeq platform and subsequently individually screened using a pancoronavirus RT-PCR protocol. We detected CoV-related sequences in HTS, but only two (2/101; 1.98%) animals had CoV detected in the intestines by RT-PCR. Partial sequences of RdRp and spike genes were obtained in the same sample and the RdRp region in the other sample. The sequences were classified as belonging to Alphacoronavirus. The sequences were closely related to alphacoronaviruses detected in vampire bats from Peru. The continuous monitoring of bat CoVs may help to map and predict putative future zoonotic agents with great impacts on human health.
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Affiliation(s)
- Raquel Silva Alves
- Laboratório de VirologiaFaculdade de VeterináriaUniversidade Federal do Rio Grande do Sul (UFRGS)Porto AlegreBrazil
| | - Juliana do Canto Olegário
- Laboratório de VirologiaFaculdade de VeterináriaUniversidade Federal do Rio Grande do Sul (UFRGS)Porto AlegreBrazil
| | - Matheus Nunes Weber
- Laboratório de Microbiologia MolecularInstituto de Ciências da SaúdeUniversidade FeevaleNovo HamburgoBrazil
| | - Mariana Soares da Silva
- Laboratório de VirologiaFaculdade de VeterináriaUniversidade Federal do Rio Grande do Sul (UFRGS)Porto AlegreBrazil
| | - Raissa Canova
- Laboratório de VirologiaFaculdade de VeterináriaUniversidade Federal do Rio Grande do Sul (UFRGS)Porto AlegreBrazil
| | - Jéssica Tatiane Sauthier
- Laboratório de VirologiaFaculdade de VeterináriaUniversidade Federal do Rio Grande do Sul (UFRGS)Porto AlegreBrazil
| | - Letícia Ferreira Baumbach
- Laboratório de VirologiaFaculdade de VeterináriaUniversidade Federal do Rio Grande do Sul (UFRGS)Porto AlegreBrazil
| | - André Alberto Witt
- Laboratório de VirologiaFaculdade de VeterináriaUniversidade Federal do Rio Grande do Sul (UFRGS)Porto AlegreBrazil
- Secretaria Estadual de AgriculturaPecuária e Desenvolvimento Rural (SEAPDR)Rio Grande do Sul Rio Grande do SulBrazil
| | - Ana Paula Muterle Varela
- Centro de Pesquisa em Saúde AnimalInstituto de Pesquisas Veterinárias Desidério Finamor (IPVDF)Departamento de Diagnóstico e Pesquisa Agropecuária (DDPA)Secretaria da AgriculturaPecuária e Desenvolvimento Rural (SEAPDR)Rio Grande do SulBrazil
| | - Fabiana Quoos Mayer
- Centro de Pesquisa em Saúde AnimalInstituto de Pesquisas Veterinárias Desidério Finamor (IPVDF)Departamento de Diagnóstico e Pesquisa Agropecuária (DDPA)Secretaria da AgriculturaPecuária e Desenvolvimento Rural (SEAPDR)Rio Grande do SulBrazil
| | | | - Cláudio Wageck Canal
- Laboratório de VirologiaFaculdade de VeterináriaUniversidade Federal do Rio Grande do Sul (UFRGS)Porto AlegreBrazil
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Zhu F, Duong V, Lim XF, Hul V, Chawla T, Keatts L, Goldstein T, Hassanin A, Tu VT, Buchy P, Sessions OM, Wang LF, Dussart P, Anderson DE. Presence of Recombinant Bat Coronavirus GCCDC1 in Cambodian Bats. Viruses 2022; 14:v14020176. [PMID: 35215769 PMCID: PMC8877364 DOI: 10.3390/v14020176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/12/2022] [Accepted: 01/15/2022] [Indexed: 12/04/2022] Open
Abstract
Bats have been recognized as an exceptional viral reservoir, especially for coronaviruses. At least three bat zoonotic coronaviruses (SARS-CoV, MERS-CoV and SARS-CoV-2) have been shown to cause severe diseases in humans and it is expected more will emerge. One of the major features of CoVs is that they are all highly prone to recombination. An extreme example is the insertion of the P10 gene from reoviruses in the bat CoV GCCDC1, first discovered in Rousettus leschenaultii bats in China. Here, we report the detection of GCCDC1 in four different bat species (Eonycteris spelaea, Cynopterus sphinx, Rhinolophus shameli and Rousettus sp.) in Cambodia. This finding demonstrates a much broader geographic and bat species range for this virus and indicates common cross-species transmission. Interestingly, one of the bat samples showed a co-infection with an Alpha CoV most closely related to RsYN14, a virus recently discovered in the same genus (Rhinolophus) of bat in Yunnan, China, 2020. Taken together, our latest findings highlight the need to conduct active surveillance in bats to assess the risk of emerging CoVs, especially in Southeast Asia.
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Affiliation(s)
- Feng Zhu
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; (F.Z.); (X.F.L.); (T.C.); (O.M.S.)
| | - Veasna Duong
- Virology Unit, Institut Pasteur du Cambodge, Pasteur Network, Phnom Penh 120210, Cambodia; (V.D.); (V.H.); (P.B.)
| | - Xiao Fang Lim
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; (F.Z.); (X.F.L.); (T.C.); (O.M.S.)
| | - Vibol Hul
- Virology Unit, Institut Pasteur du Cambodge, Pasteur Network, Phnom Penh 120210, Cambodia; (V.D.); (V.H.); (P.B.)
- Unité des Virus Émergents, (UVÉ: Aix-Marseille Univ-IRD 190-INSERM 1207), 13005 Marseille, France
| | - Tanu Chawla
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; (F.Z.); (X.F.L.); (T.C.); (O.M.S.)
| | - Lucy Keatts
- Wildlife Conservation Society, Health Program, Bronx, NY 10460, USA;
- One Health Institute, School of Veterinary Medicine, University of California, Davis, CA 95616, USA;
| | - Tracey Goldstein
- One Health Institute, School of Veterinary Medicine, University of California, Davis, CA 95616, USA;
| | - Alexandre Hassanin
- Institut de Systématique, Évolution, Biodiversité, Sorbonne Université, MNHN, CNRS, EPHE, UA, 75005 Paris, France;
| | - Vuong Tan Tu
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, No. 18, Hoang Quoc Viet Road, Cau Giay District, Hanoi 10072, Vietnam;
| | - Philippe Buchy
- Virology Unit, Institut Pasteur du Cambodge, Pasteur Network, Phnom Penh 120210, Cambodia; (V.D.); (V.H.); (P.B.)
| | - October M. Sessions
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; (F.Z.); (X.F.L.); (T.C.); (O.M.S.)
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; (F.Z.); (X.F.L.); (T.C.); (O.M.S.)
- Correspondence: (L.-F.W.); (P.D.); (D.E.A.)
| | - Philippe Dussart
- Virology Unit, Institut Pasteur du Cambodge, Pasteur Network, Phnom Penh 120210, Cambodia; (V.D.); (V.H.); (P.B.)
- Correspondence: (L.-F.W.); (P.D.); (D.E.A.)
| | - Danielle E. Anderson
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; (F.Z.); (X.F.L.); (T.C.); (O.M.S.)
- Peter Doherty Institute for Infection and Immunity, Department of Microbiology and Immunology, University of Melbourne, Melbourne 3000, Australia
- Correspondence: (L.-F.W.); (P.D.); (D.E.A.)
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Ghai RR, Carpenter A, Liew AY, Martin KB, Herring MK, Gerber SI, Hall AJ, Sleeman JM, VonDobschuetz S, Behravesh CB. Animal Reservoirs and Hosts for Emerging Alphacoronaviruses and Betacoronaviruses. Emerg Infect Dis 2021; 27:1015-1022. [PMID: 33770472 PMCID: PMC8007319 DOI: 10.3201/eid2704.203945] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The ongoing global pandemic caused by coronavirus disease has once again demonstrated the role of the family Coronaviridae in causing human disease outbreaks. Because severe acute respiratory syndrome coronavirus 2 was first detected in December 2019, information on its tropism, host range, and clinical manifestations in animals is limited. Given the limited information, data from other coronaviruses might be useful for informing scientific inquiry, risk assessment, and decision-making. We reviewed endemic and emerging infections of alphacoronaviruses and betacoronaviruses in wildlife, livestock, and companion animals and provide information on the receptor use, known hosts, and clinical signs associated with each host for 15 coronaviruses detected in humans and animals. This information can be used to guide implementation of a One Health approach that involves human health, animal health, environmental, and other relevant partners in developing strategies for preparedness, response, and control to current and future coronavirus disease threats.
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Acera Mateos P, Balboa RF, Easteal S, Eyras E, Patel HR. PACIFIC: a lightweight deep-learning classifier of SARS-CoV-2 and co-infecting RNA viruses. Sci Rep 2021; 11:3209. [PMID: 33547380 PMCID: PMC7864945 DOI: 10.1038/s41598-021-82043-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 01/12/2021] [Indexed: 01/30/2023] Open
Abstract
Viral co-infections occur in COVID-19 patients, potentially impacting disease progression and severity. However, there is currently no dedicated method to identify viral co-infections in patient RNA-seq data. We developed PACIFIC, a deep-learning algorithm that accurately detects SARS-CoV-2 and other common RNA respiratory viruses from RNA-seq data. Using in silico data, PACIFIC recovers the presence and relative concentrations of viruses with > 99% precision and recall. PACIFIC accurately detects SARS-CoV-2 and other viral infections in 63 independent in vitro cell culture and patient datasets. PACIFIC is an end-to-end tool that enables the systematic monitoring of viral infections in the current global pandemic.
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Affiliation(s)
- Pablo Acera Mateos
- John Curtin School of Medical Research, Australian National University, Canberra, ACT 2600 Australia
- EMBL Australia Partner Laboratory Network at the Australian National University, Canberra, ACT 2600 Australia
| | - Renzo F. Balboa
- John Curtin School of Medical Research, Australian National University, Canberra, ACT 2600 Australia
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT 2600 Australia
| | - Simon Easteal
- John Curtin School of Medical Research, Australian National University, Canberra, ACT 2600 Australia
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT 2600 Australia
| | - Eduardo Eyras
- John Curtin School of Medical Research, Australian National University, Canberra, ACT 2600 Australia
- EMBL Australia Partner Laboratory Network at the Australian National University, Canberra, ACT 2600 Australia
- IMIM - Hospital del Mar Medical Research Institute, 08003 Barcelona, Spain
- Catalan Institution for Research and Advanced Studies, 08010 Barcelona, Spain
| | - Hardip R. Patel
- John Curtin School of Medical Research, Australian National University, Canberra, ACT 2600 Australia
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT 2600 Australia
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Pan Z, Lu J, Wang N, He WT, Zhang L, Zhao W, Su S. Development of a TaqMan-probe-based multiplex real-time PCR for the simultaneous detection of emerging and reemerging swine coronaviruses. Virulence 2020; 11:707-718. [PMID: 32490723 PMCID: PMC7549975 DOI: 10.1080/21505594.2020.1771980] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 04/23/2020] [Accepted: 05/03/2020] [Indexed: 01/03/2023] Open
Abstract
With the outbreak of the recent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 2019, coronaviruses have become a global research hotspot in the field of virology. Coronaviruses mainly cause respiratory and digestive tract diseases, several coronaviruses are responsible for porcine diarrhea, such as porcine epidemic diarrhea virus (PEDV), porcine deltacoronavirus (PDCoV), and emerging swine acute diarrhea syndrome coronavirus (SADS-CoV). Those viruses have caused huge economic losses and are considered as potential public health threats. Porcine torovirus (PToV) and coronaviruses, sharing similar genomic structure and replication strategy, belong to the same order Nidovirales. Here, we developed a multiplex TaqMan-probe-based real-time PCR for the simultaneous detection of PEDV, PDCoV, PToV, and SADS-CoV for the first time. Specific primers and TaqMan fluorescent probes were designed targeting the ORF1a region of PDEV, PToV, and SADS-CoV and the ORF1b region of PDCoV. The method showed high sensitivity and specificity, with a detection limit of 1 × 102 copies/μL for each pathogen. A total of 101 clinical swine samples with signs of diarrhea were analyzed using this method, and the result showed good consistency with conventional reverse transcription PCR (RT-PCR). This method improves the efficiency for surveillance of these emerging and reemerging swine enteric viruses and can help reduce economic losses to the pig industry, which also benefits animal and public health.
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Affiliation(s)
- Zhongzhou Pan
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Jiaxuan Lu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Ningning Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Wan-Ting He
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Letian Zhang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Wen Zhao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Shuo Su
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
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Jia S, Feng B, Wang Z, Ma Y, Gao X, Jiang Y, Cui W, Qiao X, Tang L, Li Y, Wang L, Xu Y. Dual priming oligonucleotide (DPO)-based real-time RT-PCR assay for accurate differentiation of four major viruses causing porcine viral diarrhea. Mol Cell Probes 2019; 47:101435. [PMID: 31415867 PMCID: PMC7127266 DOI: 10.1016/j.mcp.2019.101435] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 07/28/2019] [Accepted: 08/12/2019] [Indexed: 01/25/2023]
Abstract
Currently in China, porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), porcine rotavirus (PoRV), and porcine deltacoronavirus (PDCoV) are the major causes of porcine viral diarrhea, and mixed infections in clinics are common, resulting in significant economic losses in pig industry. Here, a dual priming oligonucleotide (DPO)-based multiplex real-time SYBR Green RT-PCR assay were developed for accurately differentiating PEDV, TGEV, PoRV, and PDCoV in clinical specimens targeting the N gene of TGEV, PEDV, and PDCoV, and the VP7 gene of PoRV. Results showed that the DPO primer allowed a wider annealing temperature range (40–65 °C) and had a higher priming specificity compared to conventional primer, in which more than 3 nucleotides in the 3′- or 5′-segment of DPO primer mismatched with DNA template, PCR amplification efficiency would decrease substantially or extension would not proceed. DPO-based multiplex real-time RT-PCR method had analytical detection limit of 8.63 × 102 copies/μL, 1.92 × 102 copies/μL, 1.74 × 102 copies/μL, and 1.76 × 102 copies/μL for PEDV, TGEV, PoRV, and PDCoV in clinical specimens, respectively. A total of 672 clinical specimens of piglets with diarrheal symptoms were collected in Northeastern China from 2017 to 2018 followed by analysis using the assay, and epidemiological investigation results showed that PEDV, TGEV, PoRV, and PDCoV prevalence was 19.05%, 5.21%, 4.32%, and 3.87%, respectively. The assay developed in this study showed higher detection accuracy than conventional RT-PCR method, suggesting a useful tool for the accurate differentiation of the four major viruses causing porcine viral diarrhea in practice. DPO-based real-time RT-PCR assay for differentiating PEDV, TGEV, PoRV, and PDCoV was developed. The assay has strong specificity and high sensitivity. The test of clinical specimens showed that accuracy of the assay was higher than traditional RT-PCR. The assay is useful tool for epidemiological investigation of the four viruses.
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Affiliation(s)
- Shuo Jia
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, College of Veterinary Medicine, Northeast Agricultural University, Harbin, PR China
| | - Baohua Feng
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, College of Veterinary Medicine, Northeast Agricultural University, Harbin, PR China
| | - Zhuo Wang
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, College of Veterinary Medicine, Northeast Agricultural University, Harbin, PR China
| | - Yingying Ma
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, College of Veterinary Medicine, Northeast Agricultural University, Harbin, PR China
| | - Xuwen Gao
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, College of Veterinary Medicine, Northeast Agricultural University, Harbin, PR China
| | - Yanping Jiang
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, College of Veterinary Medicine, Northeast Agricultural University, Harbin, PR China
| | - Wen Cui
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, College of Veterinary Medicine, Northeast Agricultural University, Harbin, PR China
| | - Xinyuan Qiao
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, College of Veterinary Medicine, Northeast Agricultural University, Harbin, PR China
| | - Lijie Tang
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, College of Veterinary Medicine, Northeast Agricultural University, Harbin, PR China; Northeastern Science Inspection Station, China Ministry of Agriculture Key Laboratory of Animal Pathogen Biology, Harbin, PR China
| | - Yijing Li
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, College of Veterinary Medicine, Northeast Agricultural University, Harbin, PR China; Northeastern Science Inspection Station, China Ministry of Agriculture Key Laboratory of Animal Pathogen Biology, Harbin, PR China
| | - Li Wang
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, College of Veterinary Medicine, Northeast Agricultural University, Harbin, PR China; Northeastern Science Inspection Station, China Ministry of Agriculture Key Laboratory of Animal Pathogen Biology, Harbin, PR China.
| | - Yigang Xu
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, College of Veterinary Medicine, Northeast Agricultural University, Harbin, PR China; Northeastern Science Inspection Station, China Ministry of Agriculture Key Laboratory of Animal Pathogen Biology, Harbin, PR China.
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Bukhari K, Mulley G, Gulyaeva AA, Zhao L, Shu G, Jiang J, Neuman BW. Description and initial characterization of metatranscriptomic nidovirus-like genomes from the proposed new family Abyssoviridae, and from a sister group to the Coronavirinae, the proposed genus Alphaletovirus. Virology 2018; 524:160-171. [PMID: 30199753 PMCID: PMC7112036 DOI: 10.1016/j.virol.2018.08.010] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 08/11/2018] [Accepted: 08/11/2018] [Indexed: 01/12/2023]
Abstract
Transcriptomics has the potential to discover new RNA virus genomes by sequencing total intracellular RNA pools. In this study, we have searched publicly available transcriptomes for sequences similar to viruses of the Nidovirales order. We report two potential nidovirus genomes, a highly divergent 35.9 kb likely complete genome from the California sea hare Aplysia californica, which we assign to a nidovirus named Aplysia abyssovirus 1 (AAbV), and a coronavirus-like 22.3 kb partial genome from the ornamented pygmy frog Microhyla fissipes, which we assign to a nidovirus named Microhyla alphaletovirus 1 (MLeV). AAbV was shown to encode a functional main proteinase, and a translational readthrough signal. Phylogenetic analysis suggested that AAbV represents a new family, proposed here as Abyssoviridae. MLeV represents a sister group to the other known coronaviruses. The importance of MLeV and AAbV for understanding nidovirus evolution, and the origin of terrestrial nidoviruses are discussed.
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Affiliation(s)
| | | | - Anastasia A Gulyaeva
- Dept. Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Lanying Zhao
- Chengdu Institute of Biology, Chinese Academy of Science, Chengdu, China
| | - Guocheng Shu
- Chengdu Institute of Biology, Chinese Academy of Science, Chengdu, China
| | - Jianping Jiang
- Chengdu Institute of Biology, Chinese Academy of Science, Chengdu, China
| | - Benjamin W Neuman
- Texas A&M University-Texarkana, 7101 University Ave, Texarkana, TX 75503, United States.
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Chen Q, Wang L, Zheng Y, Zhang J, Guo B, Yoon KJ, Gauger PC, Harmon KM, Main RG, Li G. Metagenomic analysis of the RNA fraction of the fecal virome indicates high diversity in pigs infected by porcine endemic diarrhea virus in the United States. Virol J 2018; 15:95. [PMID: 29801460 PMCID: PMC5970503 DOI: 10.1186/s12985-018-1001-z] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 05/13/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Emergence and re-emergence of porcine epidemic diarrhea virus (PEDV) in North America, Asia and Europe has caused severe economic loss to the global swine industry. However, the virome of PEDV infected pigs and its effect on disease severity remains unknown. The advancements of sequencing technology have made it possible to characterize the entire microbiome of different body sites for any host. METHODS The objective of this study was to characterize the RNA virome in PEDV-positive pigs using the hypothesis-free metagenomics approach based on next-generation sequencing. Specifically, 217 PEDV-positive swine fecal swab samples collected from diarrheic piglets over 17 US states during 2015-2016 were analyzed. RESULTS A Kraken algorithm-based bioinformatics analysis revealed the presence of up to 9 different RNA genera besides PEDV (Alphacoronavirus genus), including Mamastrovirus (52%, 113/217), Enterovirus (39%, 85/217), Sapelovirus (31%, 67/217), Posavirus (30%, 66/217), Kobuvirus (23%, 49/217), Sapovirus (13%, 28/217), Teschovirus (10%, 22/217), Pasivirus (9%, 20/217), and Deltacoronavirus (3%, 6/217). There were 58 out of 217 piglets (27%) have PEDV infection alone whereas the remaining 159 (73%) shed 2 up to 9 different viruses. CONCLUSION These findings demonstrated that PEDV infected diarrheic pigs had an extensive RNA viral flora consisting of four different families: Astroviridae, Picornaviridae, Caliciviridae, and Coronaviridae.
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Affiliation(s)
- Qi Chen
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, 1907 ISU C-Drive, VMRI#1, Ames, IA, 50011, USA
| | - Leyi Wang
- Department of Veterinary Clinical Medicine and the Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, IL, 61802, USA
| | - Ying Zheng
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, 1907 ISU C-Drive, VMRI#1, Ames, IA, 50011, USA
| | - Jianqiang Zhang
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, 1907 ISU C-Drive, VMRI#1, Ames, IA, 50011, USA
| | - Baoqing Guo
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, 1907 ISU C-Drive, VMRI#1, Ames, IA, 50011, USA
| | - Kyoung-Jin Yoon
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, 1907 ISU C-Drive, VMRI#1, Ames, IA, 50011, USA
| | - Phillip C Gauger
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, 1907 ISU C-Drive, VMRI#1, Ames, IA, 50011, USA
| | - Karen M Harmon
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, 1907 ISU C-Drive, VMRI#1, Ames, IA, 50011, USA
| | - Rodger G Main
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, 1907 ISU C-Drive, VMRI#1, Ames, IA, 50011, USA
| | - Ganwu Li
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, 1907 ISU C-Drive, VMRI#1, Ames, IA, 50011, USA.
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Abstract
A number of novel viruses have been associated with canine gastroenteritis in recent years, from viral families as diverse as Caliciviridae and Picornaviridae to Parvoviridae and Circoviridae. The ability of many of these viruses to cause disease is uncertain, but epidemiological studies are continually adding to our knowledge of these potential pathogens. This review presents a summary of the latest research and current understanding of novel viruses associated with canine gastroenteritis.
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Affiliation(s)
- S L Caddy
- Magdalene College, University of Cambridge, Cambridge, UK; Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK.
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10
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Li Y, Khalafalla AI, Paden CR, Yusof MF, Eltahir YM, Al Hammadi ZM, Tao Y, Queen K, Hosani FA, Gerber SI, Hall AJ, Al Muhairi S, Tong S. Identification of diverse viruses in upper respiratory samples in dromedary camels from United Arab Emirates. PLoS One 2017; 12:e0184718. [PMID: 28902913 PMCID: PMC5597213 DOI: 10.1371/journal.pone.0184718] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 08/29/2017] [Indexed: 02/05/2023] Open
Abstract
Camels are known carriers for many viral pathogens, including Middle East respiratory syndrome coronavirus (MERS-CoV). It is likely that there are additional, as yet unidentified viruses in camels with the potential to cause disease in humans. In this study, we performed metagenomic sequencing analysis on nasopharyngeal swab samples from 108 MERS-CoV-positive dromedary camels from a live animal market in Abu Dhabi, United Arab Emirates. We obtained a total of 846.72 million high-quality reads from these nasopharyngeal swab samples, of which 2.88 million (0.34%) were related to viral sequences while 512.63 million (60.5%) and 50.87 million (6%) matched bacterial and eukaryotic sequences, respectively. Among the viral reads, sequences related to mammalian viruses from 13 genera in 10 viral families were identified, including Coronaviridae, Nairoviridae, Paramyxoviridae, Parvoviridae, Polyomaviridae, Papillomaviridae, Astroviridae, Picornaviridae, Poxviridae, and Genomoviridae. Some viral sequences belong to known camel or human viruses and others are from potentially novel camel viruses with only limited sequence similarity to virus sequences in GenBank. A total of five potentially novel virus species or strains were identified. Co-infection of at least two recently identified camel coronaviruses was detected in 92.6% of the camels in the study. This study provides a comprehensive survey of viruses in the virome of upper respiratory samples in camels that have extensive contact with the human population.
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Affiliation(s)
- Yan Li
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | | | - Clinton R. Paden
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, United States of America
| | - Mohammed F. Yusof
- Animal Wealth Sector, Abu Dhabi Food Control Authority, Abu Dhabi, United Arab Emirates
| | - Yassir M. Eltahir
- Animal Wealth Sector, Abu Dhabi Food Control Authority, Abu Dhabi, United Arab Emirates
| | | | - Ying Tao
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Krista Queen
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, United States of America
| | | | - Susan I. Gerber
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Aron J. Hall
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Salama Al Muhairi
- Animal Wealth Sector, Abu Dhabi Food Control Authority, Abu Dhabi, United Arab Emirates
- * E-mail: (ST); (SAM)
| | - Suxiang Tong
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- * E-mail: (ST); (SAM)
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11
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Boniotti MB, Papetti A, Lavazza A, Alborali G, Sozzi E, Chiapponi C, Faccini S, Bonilauri P, Cordioli P, Marthaler D. Porcine Epidemic Diarrhea Virus and Discovery of a Recombinant Swine Enteric Coronavirus, Italy. Emerg Infect Dis 2016; 22:83-7. [PMID: 26689738 PMCID: PMC4696687 DOI: 10.3201/eid2201.150544] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Porcine epidemic diarrhea virus (PEDV) has been detected sporadically in Italy since the 1990s. We report the phylogenetic relationship of swine enteric coronaviruses collected in Italy during 2007-2014 and identify a drastic shift in PEDV strain variability and a new swine enteric coronavirus generated by recombination of transmissible gastroenteritis virus and PEDV.
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12
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Abstract
First identified in 2012 in a surveillance study in Hong Kong, porcine deltacoronavirus (PDCoV) is a proposed member of the genus Deltacoronavirus of the family Coronaviridae. In February of 2014, PDCoV was detected in pigs with clinical diarrheal symptoms for the first time in the USA. Since then, it has been detected in more than 20 states in the USA and in other countries, including Canada, South Korea, and mainland China. So far, histological lesions in the intestines of pigs naturally infected with PDCoV under field conditions have not been reported. In this report, we describe the characteristic histological lesions in the small intestine that were associated with PDCoV infection, as evidenced by detection of viral nucleic acid by RT-PCR. In addition, we performed genomic analysis to determine the genetic relationship of all PDCoV strains from the four countries. We found that PDCoV mainly caused histological lesions in the small intestines of naturally infected piglets. Sequence analysis demonstrated that the PDCoV strains of different countries are closely related and shared high nucleotide sequence similarity; however, deletion patterns in the spike and 3' untranslated regions are different among the strains from mainland China, Hong Kong, the USA, and South Korea. Our study highlights the fact that continual surveillance is needed to trace the evolution of this virus.
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Affiliation(s)
- Leyi Wang
- Animal Disease Diagnostic Laboratory, Ohio Department of Agriculture, 8995 East Main Street, Building #6, Reynoldsburg, OH, 43068, USA.
| | - Jeff Hayes
- Animal Disease Diagnostic Laboratory, Ohio Department of Agriculture, 8995 East Main Street, Building #6, Reynoldsburg, OH, 43068, USA
| | - Craig Sarver
- Animal Disease Diagnostic Laboratory, Ohio Department of Agriculture, 8995 East Main Street, Building #6, Reynoldsburg, OH, 43068, USA
| | - Beverly Byrum
- Animal Disease Diagnostic Laboratory, Ohio Department of Agriculture, 8995 East Main Street, Building #6, Reynoldsburg, OH, 43068, USA
| | - Yan Zhang
- Animal Disease Diagnostic Laboratory, Ohio Department of Agriculture, 8995 East Main Street, Building #6, Reynoldsburg, OH, 43068, USA.
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13
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Glushakova LG, Sharma N, Hoshika S, Bradley AC, Bradley KM, Yang Z, Benner SA. Detecting respiratory viral RNA using expanded genetic alphabets and self-avoiding DNA. Anal Biochem 2015; 489:62-72. [PMID: 26299645 PMCID: PMC4733849 DOI: 10.1016/j.ab.2015.08.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Revised: 08/07/2015] [Accepted: 08/13/2015] [Indexed: 11/23/2022]
Abstract
Nucleic acid (NA)-targeted tests detect and quantify viral DNA and RNA (collectively xNA) to support epidemiological surveillance and, in individual patients, to guide therapy. They commonly use polymerase chain reaction (PCR) and reverse transcription PCR. Although these all have rapid turnaround, they are expensive to run. Multiplexing would allow their cost to be spread over multiple targets, but often only with lower sensitivity and accuracy, noise, false positives, and false negatives; these arise by interactions between the multiple nucleic acid primers and probes in a multiplexed kit. Here we offer a multiplexed assay for a panel of respiratory viruses that mitigates these problems by combining several nucleic acid analogs from the emerging field of synthetic biology: (i) self-avoiding molecular recognition systems (SAMRSs), which facilitate multiplexing, and (ii) artificially expanded genetic information systems (AEGISs), which enable low-noise PCR. These are supplemented by “transliteration” technology, which converts standard nucleotides in a target to AEGIS nucleotides in a product, improving hybridization. The combination supports a multiplexed Luminex-based respiratory panel that potentially differentiates influenza viruses A and B, respiratory syncytial virus, severe acute respiratory syndrome coronavirus (SARS), and Middle East respiratory syndrome (MERS) coronavirus, detecting as few as 10 MERS virions in a 20-μl sample.
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Affiliation(s)
| | - Nidhi Sharma
- Foundation for Applied Molecular Evolution (FfAME), Alachua, FL 32615, USA
| | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution (FfAME), Alachua, FL 32615, USA
| | - Andrea C Bradley
- Foundation for Applied Molecular Evolution (FfAME), Alachua, FL 32615, USA
| | - Kevin M Bradley
- Foundation for Applied Molecular Evolution (FfAME), Alachua, FL 32615, USA
| | - Zunyi Yang
- Foundation for Applied Molecular Evolution (FfAME), Alachua, FL 32615, USA
| | - Steven A Benner
- Firebird Biomolecular Sciences, Alachua, FL 32615, USA; Foundation for Applied Molecular Evolution (FfAME), Alachua, FL 32615, USA.
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14
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Kocik J, Niemcewicz M, Winnicka I, Michalski A, Bielawska-Drózd A, Kołodziej M, Joniec J, Cieślik P, Graniak G, Mirski T, Gaweł J, Bielecka-Oder A, Kubiak L, Russell K. Diversity of influenza-like illness etiology in Polish Armed Forces in influenza epidemic season. Acta Biochim Pol 2014; 61:489-494. [PMID: 25195140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 08/12/2014] [Accepted: 08/26/2014] [Indexed: 06/03/2023]
Abstract
The aim of this study was to conduct an epidemiological and laboratory surveillance of Influenza-Like Illnesses (ILI) in Polish Armed Forces, civilian military personnel and their families in 2011/2012 epidemic season, under the United States Department of Defense-Global Emerging Infections Surveillance and Response System (DoD-GEIS). ILI incidence data were analyzed in relation to age, gender, patient category as well as pathogen patterns. Multiple viral, bacterial and viral-bacterial co-infections were identified. Nose and throat swabs of active duty soldiers in the homeland country and in the NATO peacekeeping forces KFOR (Kosovo Force), as well as members of their families were tested for the presence of viral and bacterial pathogens. From October 2011 to May 2012, 416 specimens from ILI symptoms patients were collected and analyzed for the presence of viral and bacterial pathogens. Among viruses, coronavirus was the most commonly detected. In the case of bacterial infections, the most common pathogen was Staphylococcus aureus.
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Affiliation(s)
- Janusz Kocik
- Department of Epidemiology, General Karol Kaczkowski Military Institute of Hygiene and Epidemiology, Warsaw, Poland
| | - Marcin Niemcewicz
- Biological Threat Identification and Countermeasure Center of General Karol Kaczkowski Military Institute of Hygiene and Epidemiology, Puławy, Poland
| | - Izabela Winnicka
- Department of Epidemiology, General Karol Kaczkowski Military Institute of Hygiene and Epidemiology, Warsaw, Poland
| | - Aleksander Michalski
- Biological Threat Identification and Countermeasure Center of General Karol Kaczkowski Military Institute of Hygiene and Epidemiology, Puławy, Poland
| | - Agata Bielawska-Drózd
- Biological Threat Identification and Countermeasure Center of General Karol Kaczkowski Military Institute of Hygiene and Epidemiology, Puławy, Poland
| | - Marcin Kołodziej
- Biological Threat Identification and Countermeasure Center of General Karol Kaczkowski Military Institute of Hygiene and Epidemiology, Puławy, Poland
| | - Justyna Joniec
- Biological Threat Identification and Countermeasure Center of General Karol Kaczkowski Military Institute of Hygiene and Epidemiology, Puławy, Poland
| | - Piotr Cieślik
- Biological Threat Identification and Countermeasure Center of General Karol Kaczkowski Military Institute of Hygiene and Epidemiology, Puławy, Poland
| | - Grzegorz Graniak
- Biological Threat Identification and Countermeasure Center of General Karol Kaczkowski Military Institute of Hygiene and Epidemiology, Puławy, Poland
| | - Tomasz Mirski
- Biological Threat Identification and Countermeasure Center of General Karol Kaczkowski Military Institute of Hygiene and Epidemiology, Puławy, Poland
| | - Jerzy Gaweł
- Biological Threat Identification and Countermeasure Center of General Karol Kaczkowski Military Institute of Hygiene and Epidemiology, Puławy, Poland
| | - Anna Bielecka-Oder
- Department of Epidemiology, General Karol Kaczkowski Military Institute of Hygiene and Epidemiology, Warsaw, Poland
| | - Leszek Kubiak
- Department of Epidemiology, General Karol Kaczkowski Military Institute of Hygiene and Epidemiology, Warsaw, Poland
| | - Kevin Russell
- United States Armed Forces Health Surveillance Center, Silver Spring (AFHSC), Maryland, USA
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15
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Abstract
The identification of Middle East respiratory syndrome coronavirus (MERS-CoV) in 2012 reaffirmed the importance of understanding how coronaviruses emerge, infect, and cause disease. By comparing what is known about severe acute respiratory syndrome coronavirus (SARS-CoV) to what has recently been found for MERS-CoV, researchers are discovering similarities and differences that may be important for pathogenesis. Here we discuss what is known about each virus and what gaps remain in our understanding, especially concerning MERS-CoV.
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Affiliation(s)
- Christopher M Coleman
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
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16
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Drexler JF, Corman VM, Drosten C. Ecology, evolution and classification of bat coronaviruses in the aftermath of SARS. Antiviral Res 2014; 101:45-56. [PMID: 24184128 PMCID: PMC7113851 DOI: 10.1016/j.antiviral.2013.10.013] [Citation(s) in RCA: 265] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 09/30/2013] [Accepted: 10/21/2013] [Indexed: 01/22/2023]
Abstract
In 2002/2003, a novel coronavirus (CoV) caused a pandemic, infecting more than 8000 people, of whom nearly 10% died. This virus, termed severe acute respiratory syndrome-CoV was linked to a zoonotic origin from rhinolophid bats in 2005. Since then, numerous studies have described novel bat CoVs, including close relatives of the newly emerging Middle East respiratory syndrome (MERS)-CoV. In this paper we discuss CoV genomic properties and compare different taxonomic approaches in light of the technical difficulties of obtaining full genomic sequences directly from bat specimens. We first present an overview of the available studies on bat CoVs, with details on their chiropteran hosts, then comparatively analyze the increase in bat CoV studies and novel genomic sequences obtained since the SARS pandemic. We then conduct a comprehensive phylogenetic analysis of the genera Alpha- and Betacoronavirus, to show that bats harbour more CoV diversity than other mammalian hosts and are widely represented in most, but not all parts of the tree of mammalian CoVs. We next discuss preliminary evidence for phylogenetic co-segregation of CoVs and bat hosts encompassing the Betacoronavirus clades b and d, with an emphasis on the sampling bias that exists among bat species and other mammals, then present examples of CoVs infecting different hosts on the one hand and viruses apparently confined to host genera on the other. We also demonstrate a geographic bias within available studies on bat CoVs, and identify a critical lack of information from biodiversity hotspots in Africa, Asia and Latin America. We then present evidence for a zoonotic origin of four of the six known human CoVs (HCoV), three of which likely involved bats, namely SARS-CoV, MERS-CoV and HCoV-229E; compare the available data on CoV pathogenesis in bats to that in other mammalian hosts; and discuss hypotheses on the putative insect origins of CoV ancestors. Finally, we suggest caution with conclusions on the zoonotic potential of bat viruses, based only on genomic sequence data, and emphasize the need to preserve these ecologically highly relevant animals. This paper forms part of a symposium in Antiviral Research on "from SARS to MERS: 10years of research on highly pathogenic human coronaviruses".
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17
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18
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Lau SKP, Woo PCY, Yip CCY, Fan RYY, Huang Y, Wang M, Guo R, Lam CSF, Tsang AKL, Lai KKY, Chan KH, Che XY, Zheng BJ, Yuen KY. Isolation and characterization of a novel Betacoronavirus subgroup A coronavirus, rabbit coronavirus HKU14, from domestic rabbits. J Virol 2012; 86:5481-96. [PMID: 22398294 PMCID: PMC3347282 DOI: 10.1128/jvi.06927-11] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Accepted: 02/23/2012] [Indexed: 01/30/2023] Open
Abstract
We describe the isolation and characterization of a novel Betacoronavirus subgroup A coronavirus, rabbit coronavirus HKU14 (RbCoV HKU14), from domestic rabbits. The virus was detected in 11 (8.1%) of 136 rabbit fecal samples by reverse transcriptase PCR (RT-PCR), with a viral load of up to 10(8) copies/ml. RbCoV HKU14 was able to replicate in HRT-18G and RK13 cells with cytopathic effects. Northern blotting confirmed the production of subgenomic mRNAs coding for the HE, S, NS5a, E, M, and N proteins. Subgenomic mRNA analysis revealed a transcription regulatory sequence, 5'-UCUAAAC-3'. Phylogenetic analysis showed that RbCoV HKU14 formed a distinct branch among Betacoronavirus subgroup A coronaviruses, being most closely related to but separate from the species Betacoronavirus 1. A comparison of the conserved replicase domains showed that RbCoV HKU14 possessed <90% amino acid identities to most members of Betacoronavirus 1 in ADP-ribose 1″-phosphatase (ADRP) and nidoviral uridylate-specific endoribonuclease (NendoU), indicating that RbCoV HKU14 should represent a separate species. RbCoV HKU14 also possessed genomic features distinct from those of other Betacoronavirus subgroup A coronaviruses, including a unique NS2a region with a variable number of small open reading frames (ORFs). Recombination analysis revealed possible recombination events during the evolution of RbCoV HKU14 and members of Betacoronavirus 1, which may have occurred during cross-species transmission. Molecular clock analysis using RNA-dependent RNA polymerase (RdRp) genes dated the most recent common ancestor of RbCoV HKU14 to around 2002, suggesting that this virus has emerged relatively recently. Antibody against RbCoV was detected in 20 (67%) of 30 rabbit sera tested by an N-protein-based Western blot assay, whereas neutralizing antibody was detected in 1 of these 20 rabbits.
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Affiliation(s)
- Susanna K. P. Lau
- State Key Laboratory of Emerging Infectious Diseases
- Research Centre of Infection and Immunology
- Carol Yu Centre for Infection
- Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Patrick C. Y. Woo
- State Key Laboratory of Emerging Infectious Diseases
- Research Centre of Infection and Immunology
- Carol Yu Centre for Infection
- Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Cyril C. Y. Yip
- Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Rachel Y. Y. Fan
- Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Yi Huang
- Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Ming Wang
- Guangzhou Center for Disease Control and Prevention
| | - Rongtong Guo
- Guangzhou Center for Disease Control and Prevention
| | - Carol S. F. Lam
- Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Alan K. L. Tsang
- Department of Microbiology, The University of Hong Kong, Hong Kong
| | | | - Kwok-Hung Chan
- Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Xiao-Yan Che
- Center of Laboratory, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Bo-Jian Zheng
- State Key Laboratory of Emerging Infectious Diseases
- Research Centre of Infection and Immunology
- Carol Yu Centre for Infection
- Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases
- Research Centre of Infection and Immunology
- Carol Yu Centre for Infection
- Department of Microbiology, The University of Hong Kong, Hong Kong
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19
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Osborne C, Cryan PM, O'Shea TJ, Oko LM, Ndaluka C, Calisher CH, Berglund AD, Klavetter ML, Bowen RA, Holmes KV, Dominguez SR. Alphacoronaviruses in New World bats: prevalence, persistence, phylogeny, and potential for interaction with humans. PLoS One 2011; 6:e19156. [PMID: 21589915 PMCID: PMC3093381 DOI: 10.1371/journal.pone.0019156] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Accepted: 03/20/2011] [Indexed: 11/19/2022] Open
Abstract
Bats are reservoirs for many different coronaviruses (CoVs) as well as many other important zoonotic viruses. We sampled feces and/or anal swabs of 1,044 insectivorous bats of 2 families and 17 species from 21 different locations within Colorado from 2007 to 2009. We detected alphacoronavirus RNA in bats of 4 species: big brown bats (Eptesicus fuscus), 10% prevalence; long-legged bats (Myotis volans), 8% prevalence; little brown bats (Myotis lucifugus), 3% prevalence; and western long-eared bats (Myotis evotis), 2% prevalence. Overall, juvenile bats were twice as likely to be positive for CoV RNA as adult bats. At two of the rural sampling sites, CoV RNAs were detected in big brown and long-legged bats during the three sequential summers of this study. CoV RNA was detected in big brown bats in all five of the urban maternity roosts sampled throughout each of the periods tested. Individually tagged big brown bats that were positive for CoV RNA and later sampled again all became CoV RNA negative. Nucleotide sequences in the RdRp gene fell into 3 main clusters, all distinct from those of Old World bats. Similar nucleotide sequences were found in amplicons from gene 1b and the spike gene in both a big-brown and a long-legged bat, indicating that a CoV may be capable of infecting bats of different genera. These data suggest that ongoing evolution of CoVs in bats creates the possibility of a continued threat for emergence into hosts of other species. Alphacoronavirus RNA was detected at a high prevalence in big brown bats in roosts in close proximity to human habitations (10%) and known to have direct contact with people (19%), suggesting that significant potential opportunities exist for cross-species transmission of these viruses. Further CoV surveillance studies in bats throughout the Americas are warranted.
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Affiliation(s)
- Christina Osborne
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Paul M. Cryan
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, United States of America
| | - Thomas J. O'Shea
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, United States of America
| | - Lauren M. Oko
- Department of Microbiology, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Christina Ndaluka
- Department of Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Charles H. Calisher
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Andrew D. Berglund
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Mead L. Klavetter
- Pinon Canyon Maneuver Site, Model, Colorado, United States of America
| | - Richard A. Bowen
- Department of Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Kathryn V. Holmes
- Department of Microbiology, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Samuel R. Dominguez
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, United States of America
- Department of Microbiology, University of Colorado School of Medicine, Aurora, Colorado, United States of America
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20
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Osborne C, Cryan PM, O'Shea TJ, Oko LM, Ndaluka C, Calisher CH, Berglund AD, Klavetter ML, Bowen RA, Holmes KV, Dominguez SR. Alphacoronaviruses in New World bats: prevalence, persistence, phylogeny, and potential for interaction with humans. PLoS One 2011; 6:e19156. [PMID: 21589915 DOI: 10.1371/journal.pone.0019156pone-d-11-00052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Accepted: 03/20/2011] [Indexed: 05/24/2023] Open
Abstract
Bats are reservoirs for many different coronaviruses (CoVs) as well as many other important zoonotic viruses. We sampled feces and/or anal swabs of 1,044 insectivorous bats of 2 families and 17 species from 21 different locations within Colorado from 2007 to 2009. We detected alphacoronavirus RNA in bats of 4 species: big brown bats (Eptesicus fuscus), 10% prevalence; long-legged bats (Myotis volans), 8% prevalence; little brown bats (Myotis lucifugus), 3% prevalence; and western long-eared bats (Myotis evotis), 2% prevalence. Overall, juvenile bats were twice as likely to be positive for CoV RNA as adult bats. At two of the rural sampling sites, CoV RNAs were detected in big brown and long-legged bats during the three sequential summers of this study. CoV RNA was detected in big brown bats in all five of the urban maternity roosts sampled throughout each of the periods tested. Individually tagged big brown bats that were positive for CoV RNA and later sampled again all became CoV RNA negative. Nucleotide sequences in the RdRp gene fell into 3 main clusters, all distinct from those of Old World bats. Similar nucleotide sequences were found in amplicons from gene 1b and the spike gene in both a big-brown and a long-legged bat, indicating that a CoV may be capable of infecting bats of different genera. These data suggest that ongoing evolution of CoVs in bats creates the possibility of a continued threat for emergence into hosts of other species. Alphacoronavirus RNA was detected at a high prevalence in big brown bats in roosts in close proximity to human habitations (10%) and known to have direct contact with people (19%), suggesting that significant potential opportunities exist for cross-species transmission of these viruses. Further CoV surveillance studies in bats throughout the Americas are warranted.
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Affiliation(s)
- Christina Osborne
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, United States of America
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21
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Chandra M, Singh G, Singh B. Isolation of infectious bronchitis, infectious bursal disease and avian adenoviruses from chickens with nephritis-nephrosis syndrome. Zentralbl Veterinarmed B 2010; 27:352-9. [PMID: 6255706 DOI: 10.1111/j.1439-0450.1980.tb01702.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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22
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Abstract
Recently discovered respiratory viruses were detected in 19 (9.2%) of 205 nasal swab specimens from children in Brazil with respiratory illnesses. Five each were positive for human metapneumovirus (HMPV) alone and human bocavirus (HBoV) alone, 3 for human coronaviruses (HCoV-HKU1 or -NL63) alone, and 6 for more than 1 recently discovered virus.
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23
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Abstract
The etiologic role of recently identified respiratory viruses for acute wheezing in children is not yet clear. The purpose of this study was to investigate the prevalence of recently identified viruses, including human metapneumovirus (hMPV), human bocavirus (hBoV), human coronavirus NL63 (hCoV‐NL63), and human coronavirus HKU1 (hCoV‐HKU1) in children with acute wheezing. Viral etiology was identified in 231 children hospitalized with acute wheezing, aged from 1 month to 5 years. Viral antigens for common respiratory viruses were detected by IFA or multiplex PCR. RT‐PCR was used to detect respiratory rhinoviruses, hCoV‐NL63, hCoV‐HKU1, and hMPV. PCR assays for hBoV DNA were performed using the primer sets for noncapsid protein (NP1) and nonstructural protein (NS1) genes. Viruses were found in 61.5% (142/231) of the study population and a single virus was detected in 45.5% (105/231) of the study population. Rhinovirus (33.3%), human respiratory syncytial virus (hRSV; 13.8%), and hBoV (13.8%) were the most frequently detected viruses. hMPV and hCoV‐NL63 were detected in 7.8% and 1.3% of wheezing children, respectively. HCoV‐HKU1 was not detected. In 16.0% of the study population, more than one virus was detected. In children with acute wheezing, rhinovirus, hRSV, and hBoV were most frequently detected. Further studies including healthy control subjects are needed to define the clinical significance of hBoV in acute wheezing. J. Med. Virol. 79: 1238–1243, 2007. © 2007 Wiley‐Liss, Inc.
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Affiliation(s)
- Ju-Young Chung
- Department of Pediatrics, Sanggyepaik Hospital, Inje University College of Medicine, Seoul, Korea.
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Lau SKP, Woo PCY, Li KSM, Huang Y, Wang M, Lam CSF, Xu H, Guo R, Chan KH, Zheng BJ, Yuen KY. Complete genome sequence of bat coronavirus HKU2 from Chinese horseshoe bats revealed a much smaller spike gene with a different evolutionary lineage from the rest of the genome. Virology 2007; 367:428-39. [PMID: 17617433 PMCID: PMC7103351 DOI: 10.1016/j.virol.2007.06.009] [Citation(s) in RCA: 136] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2007] [Revised: 05/16/2007] [Accepted: 06/06/2007] [Indexed: 12/15/2022]
Abstract
Apart from bat-SARS-CoV, we have identified a novel group 1 coronavirus, bat-CoV HKU2, in Rhinolophus sinicus (Chinese horseshoe bats). Since it has been suggested that the receptor-binding motif (RBM) of SARS-CoV may have been acquired from a group 1 coronavirus, we conducted a surveillance study and identified bat-SARS-CoV and bat-CoV HKU2 in 8.7% and 7.5% respectively of R. sinicus in Hong Kong and Guangdong. Complete genome sequencing of four strains of bat-CoV HKU2 revealed the smallest coronavirus genome (27164 nucleotides) and a unique spike protein evolutionarily distinct from the rest of the genome. This spike protein, sharing similar deletions with other group 2 coronaviruses in its C-terminus, also contained a 15-amino acid peptide homologous to a corresponding peptide within the RBM of spike protein of SARS-CoV, which was absent in other coronaviruses except bat-SARS-CoV. These suggest a common evolutionary origin in the spike protein of bat-CoV HKU2, bat-SARS-CoV, and SARS-CoV.
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Affiliation(s)
- Susanna K P Lau
- State Key Laboratory of Emerging Infectious Diseases, Hong Kong
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25
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Abstract
Although many novel members of the Coronaviridae have recently been recognized in different species, the ecology of coronaviruses has not been established. Our study indicates that bats harbor a much wider diversity of coronaviruses than any other animal species. Dating of different coronavirus lineages suggests that bat coronaviruses are older than those recognized in other animals and that the human severe acute respiratory syndrome (SARS) coronavirus was directly derived from viruses from wild animals in wet markets of southern China. Furthermore, the most closely related bat and SARS coronaviruses diverged in 1986, an estimated divergence time of 17 years prior to the outbreak, suggesting that there may have been transmission via an unknown intermediate host. Analysis of lineage-specific selection pressure also indicated that only SARS coronaviruses in civets and humans were under significant positive selection, also demonstrating a recent interspecies transmission. Analysis of population dynamics revealed that coronavirus populations in bats have constant population growth, while viruses from all other hosts show epidemic-like increases in population. These results indicate that diverse coronaviruses are endemic in different bat species, with repeated introductions to other animals and occasional establishment in other species. Our findings suggest that bats are likely the natural hosts for all presently known coronavirus lineages and that all coronaviruses recognized in other species were derived from viruses residing in bats. Further surveillance of bat and other animal populations is needed to fully describe the ecology and evolution of this virus family.
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Affiliation(s)
- D Vijaykrishna
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, The University of Hong Kong, Li Ka Shing Faculty of Medicine Building, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China
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Woo PCY, Wang M, Lau SKP, Xu H, Poon RWS, Guo R, Wong BHL, Gao K, Tsoi HW, Huang Y, Li KSM, Lam CSF, Chan KH, Zheng BJ, Yuen KY. Comparative analysis of twelve genomes of three novel group 2c and group 2d coronaviruses reveals unique group and subgroup features. J Virol 2006; 81:1574-85. [PMID: 17121802 PMCID: PMC1797546 DOI: 10.1128/jvi.02182-06] [Citation(s) in RCA: 214] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Twelve complete genomes of three novel coronaviruses-bat coronavirus HKU4 (bat-CoV HKU4), bat-CoV HKU5 (putative group 2c), and bat-CoV HKU9 (putative group 2d)-were sequenced. Comparative genome analysis showed that the various open reading frames (ORFs) of the genomes of the three coronaviruses had significantly higher amino acid identities to those of other group 2 coronaviruses than group 1 and 3 coronaviruses. Phylogenetic trees constructed using chymotrypsin-like protease, RNA-dependent RNA polymerase, helicase, spike, and nucleocapsid all showed that the group 2a and 2b and putative group 2c and 2d coronaviruses are more closely related to each other than to group 1 and 3 coronaviruses. Unique genomic features distinguishing between these four subgroups, including the number of papain-like proteases, the presence or absence of hemagglutinin esterase, small ORFs between the membrane and nucleocapsid genes and ORFs (NS7a and NS7b), bulged stem-loop and pseudoknot structures downstream of the nucleocapsid gene, transcription regulatory sequence, and ribosomal recognition signal for the envelope gene, were also observed. This is the first time that NS7a and NS7b downstream of the nucleocapsid gene has been found in a group 2 coronavirus. The high Ka/Ks ratio of NS7a and NS7b in bat-CoV HKU9 implies that these two group 2d-specific genes are under high selective pressure and hence are rapidly evolving. The four subgroups of group 2 coronaviruses probably originated from a common ancestor. Further molecular epidemiological studies on coronaviruses in the bats of other countries, as well as in other animals, and complete genome sequencing will shed more light on coronavirus diversity and their evolutionary histories.
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Affiliation(s)
- Patrick C Y Woo
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, The University of Hong Kong, University Pathology Building, Queen Mary Hospital, Hong Kong
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Escutenaire S, Mohamed N, Isaksson M, Thorén P, Klingeborn B, Belák S, Berg M, Blomberg J. SYBR Green real-time reverse transcription-polymerase chain reaction assay for the generic detection of coronaviruses. Arch Virol 2006; 152:41-58. [PMID: 16941059 PMCID: PMC7087200 DOI: 10.1007/s00705-006-0840-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2006] [Accepted: 07/12/2006] [Indexed: 12/02/2022]
Abstract
Coronaviruses are etiologic agents of respiratory and enteric diseases in humans and in animals. In this study, a one-step real-time reverse transcription-polymerase chain reaction (RT-PCR) assay based on SYBR Green chemistry and degenerate primers was developed for the generic detection of coronaviruses. The primers, designed in the open reading frame 1b, enabled the detection of 32 animal coronaviruses including strains of canine coronavirus, feline coronavirus, transmissible gastroenteritis virus (TGEV), bovine coronavirus (BCoV), murine hepatitis virus (MHV) and infectious bronchitis virus (IBV). A specific amplification was also observed with the human coronaviruses (HCoV) HCoV-NL63, HCoV-OC43, HCoV-229E and severe acute respiratory syndrome coronavirus (SARS-CoV). The real-time RT-PCR detected down to 10 cRNA copies from TGEV, BCoV, SARS-CoV and IBV. In addition, the assay exhibited a high sensitivity and specificity on clinical samples from different animal species. The developed assay represents a potential tool for laboratory diagnostics and for detecting still uncharacterized coronaviruses.
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Affiliation(s)
- S Escutenaire
- Department of Virology, National Veterinary Institute, Uppsala, Sweden
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Woo PC, Lau SK, Li KS, Poon RW, Wong BH, Tsoi HW, Yip BC, Huang Y, Chan KH, Yuen KY. Molecular diversity of coronaviruses in bats. Virology 2006; 351:180-7. [PMID: 16647731 PMCID: PMC7111821 DOI: 10.1016/j.virol.2006.02.041] [Citation(s) in RCA: 202] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2006] [Revised: 02/23/2006] [Accepted: 02/28/2006] [Indexed: 11/24/2022]
Abstract
The existence of coronaviruses in bats is unknown until the recent discovery of bat-SARS-CoV in Chinese horseshoe bats and a novel group 1 coronavirus in other bat species. Among 309 bats of 13 species captured from 20 different locations in rural areas of Hong Kong over a 16-month period, coronaviruses were amplified from anal swabs of 37 (12%) bats by RT-PCR. Phylogenetic analysis of RNA-dependent-RNA-polymerase (pol) and helicase genes revealed six novel coronaviruses from six different bat species, in addition to the two previously described coronaviruses. Among the six novel coronaviruses, four were group 1 coronaviruses (bat-CoV HKU2 from Chinese horseshoe bat, bat-CoV HKU6 from rickett's big-footed bat, bat-CoV HKU7 from greater bent-winged bat and bat-CoV HKU8 from lesser bent-winged bat) and two were group 2 coronaviruses (bat-CoV HKU4 from lesser bamboo bats and bat-CoV HKU5 from Japanese pipistrelles). An astonishing diversity of coronaviruses was observed in bats.
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Affiliation(s)
- Patrick C.Y. Woo
- Department of Microbiology, The University of Hong Kong, University Pathology Building, Queen Mary Hospital, Hong Kong
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong
| | - Susanna K.P. Lau
- Department of Microbiology, The University of Hong Kong, University Pathology Building, Queen Mary Hospital, Hong Kong
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong
| | - Kenneth S.M. Li
- Department of Microbiology, The University of Hong Kong, University Pathology Building, Queen Mary Hospital, Hong Kong
| | - Rosana W.S. Poon
- Department of Microbiology, The University of Hong Kong, University Pathology Building, Queen Mary Hospital, Hong Kong
| | - Beatrice H.L. Wong
- Department of Microbiology, The University of Hong Kong, University Pathology Building, Queen Mary Hospital, Hong Kong
| | - Hoi-wah Tsoi
- Department of Microbiology, The University of Hong Kong, University Pathology Building, Queen Mary Hospital, Hong Kong
| | - Bethanie C.K. Yip
- Department of Microbiology, The University of Hong Kong, University Pathology Building, Queen Mary Hospital, Hong Kong
| | - Yi Huang
- Department of Microbiology, The University of Hong Kong, University Pathology Building, Queen Mary Hospital, Hong Kong
| | - Kwok-hung Chan
- Department of Microbiology, The University of Hong Kong, University Pathology Building, Queen Mary Hospital, Hong Kong
| | - Kwok-yung Yuen
- Department of Microbiology, The University of Hong Kong, University Pathology Building, Queen Mary Hospital, Hong Kong
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong
- Corresponding author. Department of Microbiology, The University of Hong Kong, University Pathology Building, Queen Mary Hospital, Hong Kong. Fax: +852 28551241.
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Vabret A, Dina J, Gouarin S, Petitjean J, Corbet S, Freymuth F. Detection of the new human coronavirus HKU1: a report of 6 cases. Clin Infect Dis 2006; 42:634-9. [PMID: 16447108 PMCID: PMC7107802 DOI: 10.1086/500136] [Citation(s) in RCA: 146] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2005] [Accepted: 10/04/2005] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Human coronavirus HKU1 (HCoV-HKU1), a new group 2 coronavirus, was first characterized in 2005 from 2 adults with pneumonia in Hong Kong, China. To the best of our knowledge, there is no other report to date about the detection of this new virus. We report a molecular method allowing for the detection of HCoV-HKU1 and also report the clinical presentation of 6 infected patients. METHODS We screened 141 specimens (135 nasal samples and 6 stool samples) received in February and March 2005 in our laboratory and obtained from 135 hospitalized patients (61.5% of whom were <5 years old and 34.1% of whom were >20 years old) for HCoV-HKU1. RESULTS HCoV-HKU1 was detected in 6 (4.4%) of the 135 nasal specimens and in 2 (33.3%) of the 6 stool samples; the positive samples were obtained from 6 patients (5 children and 1 adult). The clinical presentation of these 6 patients was as follows: 3 were admitted to the hospital for acute enteric disease resulting in severe dehydration associated with upper respiratory symptoms; 1 had fever, otitis, and febrile seizure; 1 had a sample obtained to investigate failure to thrive; and 1 had a sample obtained for exploration of X-linked agammaglobulinemia and hyperleucocytosis. CONCLUSION HCoV-HKU1 can be detected in respiratory and stool samples from children and adults in a part of the world other than Hong Kong. Our results suggest that HCoV-HKU1 could be associated with respiratory and enteric diseases, and its detection can be related to a persistent asymptomatic infection in patients with poor underlying conditions.
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Affiliation(s)
- Astrid Vabret
- Laboratory of Virology, University Hospital of Caen, Caen, France.
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Song DS, Kang BK, Lee SS, Yang JS, Moon HJ, Oh JS, Ha GW, Jang YS, Park BK. Use of an internal control in a quantitative RT-PCR assay for quantitation of porcine epidemic diarrhea virus shedding in pigs. J Virol Methods 2005; 133:27-33. [PMID: 16300838 DOI: 10.1016/j.jviromet.2005.10.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2005] [Revised: 10/03/2005] [Accepted: 10/06/2005] [Indexed: 11/23/2022]
Abstract
Porcine epidemic diarrhea virus (PEDV), a member of the family Coronaviridae, has caused a devastating enteric disease in the Korean swine industry. Previously, the differences between virulent field PEDV strains and a Vero cell culture adapted PEDV DR13 strain were determined using restriction fragment length polymorphism analysis (RFLP), and PEDV shedding patterns in pigs were reported. In an extension to these studies, an internal control was constructed and quantitative analysis of virus shedding after oral inoculation was established. A parent field PEDV and a cell culture adapted PEDV DR13 were inoculated orally to colostrum-deprived 1-day-old piglets, commercial 2-week-old pigs, and sows (1-5 ml dose, 10(5.8)-10(6.0) TCID(50)/0.1 ml). PEDV shedding was monitored every day and virus levels were measured using a quantitative reverse transcriptase polymerase chain reaction (RT-PCR) method. In fecal samples from experimentally-inoculated pigs, the level of virus excreted peaked at 2 days after oral inoculation and gradually decreased thereafter. In addition, PEDV from field specimens was quantified using the same RT-PCR assay to determine shedding viral load. This suggests that measurement of PEDV shedding viral load in pigs, by quantitative RT-PCR, may be a useful tool for estimating the transmission potential of PEDV in the swine population.
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MESH Headings
- Animals
- Chlorocebus aethiops
- Coronaviridae/genetics
- Coronaviridae/isolation & purification
- Coronaviridae Infections/diagnosis
- Coronaviridae Infections/veterinary
- Coronaviridae Infections/virology
- DNA, Complementary
- Feces/virology
- Gastroenteritis, Transmissible, of Swine/diagnosis
- Gastroenteritis, Transmissible, of Swine/genetics
- Gastroenteritis, Transmissible, of Swine/virology
- Polymorphism, Restriction Fragment Length
- RNA, Viral/analysis
- RNA, Viral/genetics
- Reference Standards
- Reverse Transcriptase Polymerase Chain Reaction/veterinary
- Swine
- Swine Diseases/diagnosis
- Swine Diseases/virology
- Vero Cells
- Viral Load
- Virus Shedding
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Affiliation(s)
- Dae-Sub Song
- Research Unit, Green Cross Veterinary Products, Yong-In 449-903, Korea
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31
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Sampath R, Hofstadler SA, Blyn LB, Eshoo MW, Hall TA, Massire C, Levene HM, Hannis JC, Harrell PM, Neuman B, Buchmeier MJ, Jiang Y, Ranken R, Drader JJ, Samant V, Griffey RH, McNeil JA, Crooke ST, Ecker DJ. Rapid identification of emerging pathogens: coronavirus. Emerg Infect Dis 2005; 11:373-9. [PMID: 15757550 PMCID: PMC3298233 DOI: 10.3201/eid1103.040629] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
New surveillance approach can analyze >900 polymerase chain reactions per day. We describe a new approach for infectious disease surveillance that facilitates rapid identification of known and emerging pathogens. The process uses broad-range polymerase chain reaction (PCR) to amplify nucleic acid targets from large groupings of organisms, electrospray ionization mass spectrometry for accurate mass measurements of PCR products, and base composition signature analysis to identify organisms in a sample. We demonstrate this principle by using 14 isolates of 9 diverse Coronavirus spp., including the severe acute respiratory syndrome–associated coronavirus (SARS-CoV). We show that this method could identify and distinguish between SARS and other known CoV, including the human CoV 229E and OC43, individually and in a mixture of all 3 human viruses. The sensitivity of detection, measured by using titered SARS-CoV spiked into human serum, was ≈1 PFU/mL. This approach, applicable to the surveillance of bacterial, viral, fungal, or protozoal pathogens, is capable of automated analysis of >900 PCR reactions per day.
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Abstract
PURPOSE OF REVIEW Since Kapakian first identified a virus in the stool of a patient with diarrhoea in 1972, many viruses have been described that cause diarrhoea directly or indirectly. It is now appreciated that viruses are the most common cause of diarrhoeal illness worldwide. Although bacteria and other pathogens cause significant numbers of gastroenteritis, it is the viruses that are dealt with in this review. The viruses responsible will be discussed individually. RECENT FINDINGS Rotavirus remains the leading cause of diarrhoeal disease overall, with the newly designated calicivirus family causing the most outbreaks in the industrialized nations. As diagnostic techniques improve, however, the importance of astrovirus and other previously under-reported pathogens is becoming more apparent and the number of viruses associated with gastroenteritis continues to increase. The emergence of severe acute respiratory syndrome coronavirus, arguably the most important emerging infection of recent years and a cause of significant gastrointestinal disease, is also discussed. SUMMARY No effective treatments have been developed for viral gastroenteritis. Current efforts are targeted at the development of suitable vaccines and the implementation of infection control measures.
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Affiliation(s)
- Benjamin Clark
- Department of Infection and Tropical Medicine, Royal Hallamshire Hospital, Sheffield S10 2JF, UK.
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McIntosh K. Commentary: McIntosh K, Chao RK, Krause HE, Wasil R, Mocega HE, Mufson MA. Coronavirus infection in acute lower respiratory tract disease of infants. J Infect Dis 1974; 130:502-7. J Infect Dis 2004; 190:1033-41. [PMID: 15295713 PMCID: PMC7110017 DOI: 10.1086/422851] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Kenneth McIntosh
- Division of Infectious Diseases, Children's Hospital Boston, Harvard Medical School, Massachusetts 02115, USA.
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Abstract
OBJECTIVE To determine whether viable White Spot Syndrome virus (WSSV) or Yellowhead virus (YHV) were present in prawn products imported into Australia. PROCEDURE A sample of fourteen uncooked prawns was obtained from a consignment imported from southeast Asia. Each of the prawns was examined for WSSV by polymerase chain reaction (PCR), and then a bioassay was conducted in which a 10% homogenate of cuticular epithelium from each of the prawns was inoculated intramuscularly into healthy challenge prawns (Penaeus monodon) from Australia. The latter were then monitored for clinical signs of disease, and tissue samples were processed for electron microscopy, histological examination and for detection of WSSV by in situ hybridization (ISH) using a commercial kit. Limited numbers of haemolymph samples from inoculated challenge prawns were also examined by PCR for the presence of WSSV and YHV. All work was carried out under microbiologically secure conditions. RESULTS Results of the initial PCR examination for WSSV on the imported prawns were not definitive. However, in the bioassay, several of the challenge prawns inoculated with homogenates from the imported prawns showed clinical signs of disease (inappetence and lethargy) within 24 h post inoculation (pi) and died at 1 to 4 days pi. Tissue samples from a number of moribund prawns demonstrated lesions typical of White Spot Disease (WSD), and the presence of the virus was confirmed by electron microscopy, ISH and PCR. YHV was also demonstrated by PCR in two challenge prawns inoculated with homogenates. CONCLUSION Viable WSSV and YHV were present in frozen prawn products imported into Australia for human consumption from southeast Asia. Importation of frozen infected products may present a risk of transferring virus to wild and farmed populations of crustaceans in this country. To date, WSD and Yellowhead Disease remain exotic to Australia.
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Affiliation(s)
- K A McColl
- CSIRO Livestock Industries, Australian Animal Health Laboratory, PO Bag 24, Geelong, Victoria 3220
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Sasaki I, Kazusa Y, Shirai J, Taniguchi T, Honda E. Neutralizing test of hemagglutinating encephalomyelitis virus (HEV) in FS-L3 cells cultured without serum. J Vet Med Sci 2003; 65:381-3. [PMID: 12679570 DOI: 10.1292/jvms.65.381] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
FS-L3 cells, originating from porcine kidney, were used for propagation of Hemagglutinating encephalomyelitis virus (HEV) and development of a virus neutralizing (VN) test. Sera of pigs, rats, cows and dogs had VN activities to HEV. On the other hand, sera of mice, rabbits, goats, sheep, horses, cats, chickens, hamsters and human did not have measurable VN activities, although these sera had high HI activities. Our results support the idea that the VN is a more reliable measure of HEV infection than the conventionally used HI test.
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Affiliation(s)
- Ikuko Sasaki
- Veterinary Microbiology, Department of Veterinary Medicine, Tokyo University of Agriculture and Technology, Tokyo, Japan
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Eiros Bouza J, Bachiller Luque M, Ortiz De Lejarazu R. [Emergent riboviruses implicated in gastroenteritis]. An Esp Pediatr 2001; 54:136-44. [PMID: 11181210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
Viral agents are one of the main causes of acute diarrhea, particularly in infants and young children. Astrovirus, coronavirus, torovirus, and picobirnavirus are increasingly being identified as causative agents of gastroenteritis. Astroviruses have been detected in the stools of between 1.2% and 20% of children with diarrhea requiring medical care in a variety of geographical areas. Outbreaks have been described in schools, day care settings and pediatric wards. Children younger than 3 years old are the most frequently affected. In temperate climates incidence is greater in winter whereas in tropical areas infection occurs throughout the year. Transmission is mainly through the fecaloral route. At least seven serotypes of human astroviruses have been recognized and serotype 1 is more common than the other serotypes. Astroviruses are often shed in stools during long periods and can be detected by electron microscopy. An enzymeimmunoassay technique that detects the astrovirus group antigen has been widely used in epidemiological studies. Nucleic acid hybridization and polymerase chain reactionbased techniques have also been used. Enteric coronaviruses have most frequently been associated with gastrointestinal disease in neonates and children younger than 12 years old. The role of toroviruses and picobirnaviruses as causative agents of gastroenteritis is still emerging. Further epidemiological studies to determine the frequency of these viruses in the community and to identify their mechanisms of transmission are needed, as are further studies to elucidate the pathophysiology of diseases due to these agents.
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Affiliation(s)
- J Eiros Bouza
- Departamentos de aMicrobiología y bPediatría. Facultad de Medicina. Universidad de Valladolid.
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Kim O, Choi C, Kim B, Chae C. Detection and differentiation of porcine epidemic diarrhoea virus and transmissible gastroenteritis virus in clinical samples by multiplex RT-PCR. Vet Rec 2000; 146:637-40. [PMID: 10872784 DOI: 10.1136/vr.146.22.637] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
A multiplex reverse-transcriptase-PCR (RT-PCR) procedure was developed for the simultaneous detection of porcine epidemic diarrhoea virus (PEDV) and transmissible gastroenteritis virus (TGEV) in preweaning pigs with diarrhoea. The membrane gene of PEDV and the nucleocapsid gene of TGEV were chosen as targets. The PCR products of PEDV and TGEV had molecular sizes of 412 and 612 base pairs, respectively. Primers from PEDV did not react with any TGEV tested and vice versa. In addition, the primers did not react with other pig viruses. The multiplex RT-PCR was able to detect 10 tissue culture-infective doses 50 per cent (TCID50)/ml of PEDV or TGEV with each of the primer sets for PEDV and TGEV, respectively. The RNAS of PEDV and TGEV were detected directly in intestinal and faecal samples from pigs infected experimentally with either virus. The results of the assay correlated well with the results of virus isolation. None of the five control specimens was positive. PEDV was detected in 10 intestinal and nine faecal samples, and among the nine positive faecal samples two were culture-negative. TGEV was also detected in 10 intestinal and nine faecal samples, and among the nine positive faecal samples, three were culture-negative.
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Affiliation(s)
- O Kim
- Department of Veterinary Pathology, College of Veterinary Medicine and School of Agricultural Biotechnology, Seoul National University, Suwon, Republic of Korea
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Shibata I, Tsuda T, Mori M, Ono M, Sueyoshi M, Uruno K. Isolation of porcine epidemic diarrhea virus in porcine cell cultures and experimental infection of pigs of different ages. Vet Microbiol 2000; 72:173-82. [PMID: 10727829 PMCID: PMC7117361 DOI: 10.1016/s0378-1135(99)00199-6] [Citation(s) in RCA: 91] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
This paper describes the isolation of porcine epidemic diarrhea (PED) virus in Vero and porcine cell cultures, and the influence of age on disease in experimental infection. PED virus was isolated from the small intestine of piglets inoculated with PED samples and cultured in Vero, porcine bladder and kidney cells propagated in collagen-coated tissue culture plates in maintenance medium (MM) containing trypsin. In porcine bladder and kidney cell cultures inoculated with isolated PED virus, cytopathic effects (CPE) including cell fusion were detected. Specific brilliant fluorescence was observed in the cytoplasm of these cells. Two- and 7-day old, and 2-, 4-, 8- and 12-week old specific pathogen-free (SPF) pigs were orally inoculated with PED virus isolated from an outbreak. All 2- and 7-day old pigs inoculated developed severe watery diarrhea from post-inoculation day (PID) 1 and died between PID 3 and 4. Although three of five 2-week old pigs developed diarrhea on PID 1-4, they eventually recovered. In the 4-week old group, three of five pigs had mild diarrhea for 1-2 days. None of the 8- and 12-week old pigs showed any clinical signs. Antibodies against PED virus were detected in all surviving pigs by virus neutralization (VN) test and immunofluorescence assay (IFA). Therefore, there is an age-dependent resistance to pathogenic PED virus infection in pigs.
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Affiliation(s)
- I Shibata
- Zen-noh Institute of Animal Health, 7 Ohja-machi, Sakura, Chiba, Japan.
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Cowley JA, Dimmock CM, Spann KM, Walker PJ. Detection of Australian gill-associated virus (GAV) and lymphoid organ virus (LOV) of Penaeus monodon by RT-nested PCR. Dis Aquat Organ 2000; 39:159-167. [PMID: 10768283 DOI: 10.3354/dao039159] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A highly sensitive test based on reverse transcription followed by nested polymerase chain reaction (RT-nPCR) was developed to detect the Australian yellow-head-like viruses, gill-associated virus (GAV) and lymphoid organ virus (LOV) of Penaeus monodon. The RT-nPCR detected viral RNA in as little as 10 fg lymphoid organ total RNA isolated from GAV-infected P. monodon. Amplification of serial dilutions of a GAV cDNA clone showed that the nested PCR was sufficiently sensitive to detect a single genome equivalent using a DNA template. The specificity and sensitivity of the RT-nPCR was also demonstrated using experimentally infected P. (Marsupenaeus) japonicus, where GAV sequences could be amplified from lymphoid organ and haemocyte RNA as early as 6 h post infection (p.i.), and from gills by 24 h p.i. In contrast, transmission electron microscopy (TEM) identified nucleocapsids and virions in lymphoid organ cells and haemocytes from Days 3 and 6 p.i., respectively, while there was no evidence of infection in gill cells at any time. The practical application of the RT-nPCR was demonstrated by screening healthy wild-caught P. monodon broodstock. The high prevalence (>98%) of broodstock that were positive by RT-nPCR suggests that LOV is endemic in northern Queensland. In addition, results with lymphoid organ, gill and haemocyte RNA suggest that small gill biopsies may be best suited to the non-sacrificial testing of valuable broodstock. The speed and sensitivity of the RT-nPCR make it a useful adjunct to TEM for diagnosing LOV/GAV infection of P. monodon, with the additional benefit that screening of gill biopsies may facilitate selection of LOV-free broodstock.
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Affiliation(s)
- J A Cowley
- Cooperative Research Centre for Aquaculture, CSIRO Tropical Agriculture, Indooroopilly, Australia.
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Kim O, Chae C. In situ hybridization for the detection and localization of porcine epidemic diarrhea virus in the intestinal tissues from naturally infected piglets. Vet Pathol 2000; 37:62-7. [PMID: 10643982 DOI: 10.1354/vp.37-1-62] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Detection and localization of porcine epidemic diarrhea virus (PEDV) was studied by in situ hybridization with a nonradioactive digoxigenin-labeled probe in formalin-fixed, paraffin-embedded tissues from 10 naturally infected piglets. A 377-base pair cDNA probe for viral RNA encoding the membrane proteins of PEDV cell-culture-adapted strain V215/78 was generated by the reverse transcription polymerase chain reaction. In the retrospective study of pigs from herds with diarrhea, the 10 piglets naturally infected with PEDV had positive signals for PEDV by in situ hybridization. When intestinal tissues were hybridized with the PEDV probe, a strong signal was seen in the villus enterocytes of jejunum and ileum but not in the cecum and colon. Positive cells typically had dark brown reaction products in the cytoplasm. Scattered epithelial cells along the ileal Peyer's patches dome areas contained viral RNA. In one piglet, hybridization signal was also found in the duodenum. PEDV was not demonstrated in tissues outside of the intestinal tract. These findings indicate that jejunal and ileal villus enterocytes are the main target of PEDV replication during epizootic outbreaks of the disease.
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Affiliation(s)
- O Kim
- Department of Veterinary Pathology, College of Veterinary Medicine, Seoul National University, Suwon, Kyounggi-Do, Republic of Korea
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McDonough SP, Stull CL, Osburn BI. Enteric pathogens in intensively reared veal calves. Am J Vet Res 1994; 55:1516-20. [PMID: 7879973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Observations were made on development of diarrhea in special-fed calves (n = 460) on 8 commercial facilities during 2 successive 16-week production cycles at weeks 0, 2, 4, 8, 12, and 16. A total of 23% were affected, with peak number of calves with diarrhea observed at week 0. Suspected enteropathogens were identified in 86% of these calves, most commonly cryptosporidia, coronavirus, and rotavirus. Identified potential zoonotic pathogens included Giardia and Salmonella spp and verotoxigenic Escherichia coli. Noncytopathic bovine viral diarrhea virus was isolated from 6 calves that had repeated bouts of illness. Only 22% of calves entering the veal facilities had adequate transfer of passive immunity. At week 0, serum IgG concentration in calves that subsequently died or had diarrhea was lower (P < 0.001) than that in healthy calves. All calves that died (n = 6) during the first 4 weeks of production had complete failure of transfer of passive immunity.
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Affiliation(s)
- S P McDonough
- Department of Pathology, School of Veterinary Medicine, University of California, Davis 95616
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Abstract
Plaque assays under Sephadex or agarose overlays are described for rat coronaviruses (RCVs) grown in L2 mouse fibroblasts. A plaque assay using Sephadex was simple; however, viable plaques could not be collected for propagation, and fixation was necessary before evaluation. Plaque formation under agarose was optimized using diethylaminoethyl-dextran (DEAE-D) in the pre-treatment and absorption media and trypsin added to the absorption media and agarose overlay. The use of DEAE-D alone, trypsin alone or trypsin combined with DEAE-D significantly increased plaque numbers and visibility. Plaque numbers were highest when pre-treatment media contained DEAE-D, absorption media contained DEAE-D and trypsin, and the agarose overlay contained trypsin. The assay was useful for plaque isolation and quantification of sialodacryoadenitis virus (SDA), Parker's rat coronavirus (PRCV) and other coronavirus isolates from rats and its specificity was demonstrated by plaque-reduction neutralization testing. These methods will facilitate production of cloned virus stocks for study of RCV biology and virus quantification for in vitro and in vivo studies of RCVs.
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Affiliation(s)
- D J Gaertner
- Section of Comparative Medicine, Yale University School of Medicine, New Haven, CT 06510
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Halbur PG, Paul PS, Vaughn EM, Andrews JJ. Experimental reproduction of pneumonia in gnotobiotic pigs with porcine respiratory coronavirus isolate AR310. J Vet Diagn Invest 1993; 5:184-8. [PMID: 8389599 DOI: 10.1177/104063879300500207] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The pathogenicity of porcine respiratory coronavirus (PRCV) isolate AR310 was determined for gnotobiotic pigs. PRCV-AR310 was isolated from the intestines of a nursery pig from a herd with endemic transmissible gastroenteritis. The AR310 isolate was plaque purified and cell culture propagated, passed once in a gnotobiotic pig, then used as inoculum for a gnotobiotic pig pathogenicity study. Eight pigs were inoculated oronasally with 2 x 10(6) plaque-forming units of PRCV-AR310. Eight pigs served as controls and received cell culture medium. Two pigs from each group were necropsied at 3, 5, 10, and 15 days postinoculation (DPI). There was moderate multifocal to coalescing reddish tan consolidation of 60% of the lung by 10 DPI. Microscopic examination revealed a necrotizing and proliferative bronchointerstitial pneumonia characterized by necrosis, squamous metaplasia, dysplasia, proliferation of airway epithelium, mononuclear cell infiltration of alveolar septa, mild type II pneumocyte proliferation, and lymphohistiocytic alveolar exudation. The microscopic lesions were mild by 3 DPI, moderate by 5 DPI, severe by 10 DPI, and mostly resolved by 15 DPI. No lesions were observed in the intestines of these pigs. There was no clinical respiratory disease. Control pigs remained normal and had no lesions. PRCV was isolated from the lungs but not from the intestines of inoculated pigs. PRCV was not isolated from the lungs or intestines of control pigs. PRCV was also isolated from the nasal and rectal swabs of inoculated but not of control pigs.
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Affiliation(s)
- P G Halbur
- Iowa State University, College of Veterinary Medicine, Veterinary Medical Research Institute, Ames 50011
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Abstract
A porcine respiratory coronavirus (PRCV), antigenically closely related to transmissible gastroenteritis virus (TGEV), appeared in the European swine population in 1984. The present serological study was performed to obtain insight into the epizootiology of PRCV and of TGEV. PRCV-induced neutralizing antibodies were found in 90.6 per cent of the 160 sera collected from sows at slaughter, demonstrating the enzootic appearance of PRCV in the Belgian swine population. A serological study of fattening swine on 33 farms revealed that 11 farms situated in an area with a high farm density (all farms within 4 km2) and 11 on 22 closed breeding-fattening farms situated in areas with a low farm density (only one to four farms per 12 km2) were infected with PRCV throughout the year, whereas the other 11 closed breeding-fattening farms were temporarily free of PRCV. PRCV disappeared from the farms mainly in spring and summer. All the 11 farms became reinfected in autumn or winter, indicating that PRCV is regularly reintroduced in farms in the colder seasons. There was no correlation between the herd size and the temporary disappearance of PRCV from farms. It was observed on some farms that PRCV could infect pigs shortly after weaning in the presence of declining maternal antibodies, indicating that PRCV can persist on a farm by regularly infecting newly weaned pigs. TGEV-specific antibodies were found in 7.6 per cent of the 160 sera from the slaughterhouse sows. TGEV-specific antibodies were also detected in sera from fattening swine of 5 of the above mentioned 33 farms. TGEV-outbreaks were not observed on these farms.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- M Pensaert
- Laboratory of Virology and Immunology, Faculty of Veterinary Medicine, State University of Ghent, Belgium
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Thea DM, Glass R, Grohmann GS, Perriens J, Ngoy B, Kapita B, Atido U, Mabaluku M, Keusch GT. Prevalence of enteric viruses among hospital patients with AIDS in Kinshasa, Zaire. Trans R Soc Trop Med Hyg 1993; 87:263-6. [PMID: 8236386 PMCID: PMC7107222 DOI: 10.1016/0035-9203(93)90119-b] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Diarrhoea is the most common manifestation of acquired immunodeficiency syndrome (AIDS) in Africa. Numerous parasitic or bacterial agents have been implicated, but a pathogen-specific aetiology has not been found. Enteric viruses (i.e., rotavirus, small round structured viruses, coronavirus, and adenovirus) were detected by enzyme-linked immunosorbent assay or electron microscopy in faecal specimens of 17% of 198 consecutive adult admissions to a general medical ward of an urban hospital in Kinshasa, Zaire. Overall, 57% of patients were seropositive for infection with human immunodeficiency virus (HIV) 1; of these, 50% were classified as World Health Organization AIDS stage IV. The prevalence of enteric viruses in stool specimens did not differ significantly between patients with and without HIV infection, and was not associated with acute or chronic diarrhoea, or constitutional symptoms. However, a trend (P = 0.14) towards greater frequency of virus in stools from patients in the lower 3 quintiles of the CD4/CD8 T cell ratio was seen. This trend approached statistical significance (P = 0.07) with stratification by HIV infection. Although we found no evidence in this population to support a major pathogenic role for these viruses alone in the enteropathy of AIDS, increased viral shedding was weakly associated with immunodeficiency.
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Affiliation(s)
- D M Thea
- International Co-operation in AIDS Research (ICAR) Unit, Project SIDA, Mama Yemo Hospital, Kinshasa, Zaire
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Abstract
Combinations of porcine respiratory coronavirus (PRCV) and either of two swine influenza viruses (H1N1 or H3N2) were administered intranasally and by aerosol to six- to eight-week-old specific pathogen-free pigs. The clinical responses, gross respiratory lesions and growth performances of these pigs were studied and compared with those of single (PRCV, H1N1 or H3N2) and mock-infected animals. PRCV infection caused fever, growth retardation and lung lesions, but no respiratory symptoms. Infection with swine influenza viruses caused rather similar, mild symptoms of disease, with H1N1 infection being the least severe. Combined infections with influenza viruses and PRCV did not appear to enhance the pathogenicity of these viruses. Furthermore, viruses were isolated more frequently from tissues and nasal swabs taken from 'single' than 'dual' infected animals, suggesting a possible in vivo interference between replication of PRCV and swine influenza virus.
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Affiliation(s)
- I Lanza
- Ministry of Agriculture, Fisheries and Food, Central Veterinary Laboratory, New Haw, Addlestone, Surrey
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Abstract
Total RNA extracted from both white and gray matter of brain tissue from multiple sclerosis (MS) patients and controls was analyzed using a reverse transcription-polymerase chain reaction for the presence of the nucleic acid of human coronavirus (HCV) 229E and OC43, the two strains characterized to date and associated with respiratory infections. HCV-229E viral RNA was detectable in the central nervous system tissue of 4 of 11 MS patients and in none of 6 neurological and 5 normal controls. No HCV-OC43 nucleic acid was detected in any of the specimens. These results suggest a neurotropism on the part of the 229E strain of human coronavirus and underline the importance of further studies on its tissue distribution. The fact that it was detected only in tissue from MS patients illustrates the need for continued studies on the possible role of coronaviruses in the etiology of MS.
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Affiliation(s)
- J N Stewart
- Virology Research Center, Institut Armand-Frappier, Université du Québec, Laval, Canada
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Kuljić-Kapulica N, Budisin A. [Coronaviruses]. SRP ARK CELOK LEK 1992; 120:215-8. [PMID: 1339074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Corona viruses belong to a group of not yet well known viruses isolated in patients with infections of the upper respiratory organs, especially in winter months. It is presumed that they provoke about 15% - 20% of all infections. However, in the last years more attention has been paid to the role of human corona viruses in the provocation of sickness in man and they are becoming a special field of interest in scientific studies.
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Affiliation(s)
- N Kuljić-Kapulica
- Institute for Preventive Medicine, Military Medical Academy, Belgrade
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