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Tuladhar ET, Shrestha S, Vernon S, Droit L, Mihindukulasuriya KA, Tamang M, Karki L, Ngono AE, Jha B, Awal BK, Chalise BS, Jha R, Shresta S, Wang D, Manandhar KD. Gemykibivirus detection in acute encephalitis patients from Nepal. medRxiv 2024:2024.02.13.24302648. [PMID: 38405898 PMCID: PMC10889008 DOI: 10.1101/2024.02.13.24302648] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Acute Encephalitis Syndrome (AES) causes significant morbidity and mortality worldwide. In Nepal, Japanese encephalitis virus (JEV) accounts for ~ 5-20% of AES cases, but ~75% of AES cases are of unknown etiology. We identified a gemykibivirus in CSF collected in 2020 from a male child with AES using metagenomic next-generation sequencing. Gemykibiviruses are single stranded, circular DNA viruses in the family Genomoviridae. The complete genome of 2211 nucleotides was sequenced which shared 98.69% nucleotide identity to its closest relative, Human associated gemykibivirus 2 isolate SAfia-449D. Two real-time PCR assays were designed, and screening of 337 CSF and 164 serum samples from AES patients in Nepal collected in 2020 and 2022 yielded 11 CSF and 1 serum sample that were positive in both PCR assays. Complete genomes of 7 of the positives were sequenced. These results identify a candidate etiologic agent of encephalitis in Nepal.
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Affiliation(s)
- Eans Tara Tuladhar
- Tribhuvan University Central Department of Biotechnology, Kathmandu, Nepal
| | - Smita Shrestha
- Tribhuvan University Central Department of Biotechnology, Kathmandu, Nepal
| | - Susan Vernon
- Washington University in St. Louis, Missouri, United States
| | - Lindsay Droit
- Washington University in St. Louis, Missouri, United States
| | | | - Mamta Tamang
- Tribhuvan University Central Department of Biotechnology, Kathmandu, Nepal
| | - Lata Karki
- Tribhuvan University Central Department of Biotechnology, Kathmandu, Nepal
| | | | - Bimlesh Jha
- National Public Health Laboratory, Kathmandu, Nepal
| | | | | | - Runa Jha
- National Public Health Laboratory, Kathmandu, Nepal
| | - Sujan Shresta
- La Jolla Institute for Immunology, California, United States
| | - David Wang
- Washington University in St. Louis, Missouri, United States
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Andrianjakarivony FH, Bettarel Y, Cecchi P, Bouchard S, Chase E, Desnues C. Decoding the DNA and RNA viromes of a tropical urban lagoon. Environ Microbiol 2023; 25:2368-2387. [PMID: 37431274 DOI: 10.1111/1462-2920.16463] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 06/19/2023] [Indexed: 07/12/2023]
Abstract
Human and livestock sewage is one of the major causes of excess nutrients, leading to the eutrophication of aquatic ecosystems and potentially to the emergence or spread of pathogenic viruses. This study aimed to investigate the composition and diversity of aquatic viromes in a highly anthropized lagoon, to identify the presence of pathogenic taxa and to explore their use as possible viral indicators of faecal contamination. For this, water and sediment samples were collected in the Ebrié Lagoon (Ivory Coast) at seven stations with contrasting levels of eutrophication. The DNA viromes of the planktonic and the benthic compartments were highly divergent, but were not influenced by the level of eutrophication. Conversely, the RNA viromes in the water column were comparable to those found in sediment, but showed significant differences between the stations. We detected the presence of viral DNA and RNA sequences we had assigned as indicators of faecal contamination (smacovirus, pecovirus and pepper mild mottle virus) as well as human pathogens (human cyclovirus, coxsackie B virus and picobirnavirus), which were all enriched in the most eutrophicated sites. These findings suggest that the examination of viromes represents a promising tool for assessing the state of human-induced contamination of aquatic ecosystems.
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Affiliation(s)
- Felana Harilanto Andrianjakarivony
- Microbes, Evolution, Phylogeny, and Infection (MEФI), IHU - Méditerranée Infection, Marseille, France
- Microbiologie Environnementale Biotechnologie (MEB), Mediterranean Institute of Oceanography (MIO), Marseille, France
| | - Yvan Bettarel
- Marine Biodiversity, Exploitation & Conservation (MARBEC), University of Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | - Philippe Cecchi
- Marine Biodiversity, Exploitation & Conservation (MARBEC), University of Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | - Sonia Bouchard
- Microbes, Evolution, Phylogeny, and Infection (MEФI), IHU - Méditerranée Infection, Marseille, France
- Microbiologie Environnementale Biotechnologie (MEB), Mediterranean Institute of Oceanography (MIO), Marseille, France
| | - Emily Chase
- Microbiologie Environnementale Biotechnologie (MEB), Mediterranean Institute of Oceanography (MIO), Marseille, France
| | - Christelle Desnues
- Microbes, Evolution, Phylogeny, and Infection (MEФI), IHU - Méditerranée Infection, Marseille, France
- Microbiologie Environnementale Biotechnologie (MEB), Mediterranean Institute of Oceanography (MIO), Marseille, France
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3
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Vidovszky MZ, Kapitány S, Gellért Á, Harrach B, Görföl T, Boldogh SA, Kohl C, Wibbelt G, Mühldorfer K, Kemenesi G, Gembu GC, Hassanin A, Tu VT, Estók P, Horváth A, Kaján GL. Detection and genetic characterization of circoviruses in more than 80 bat species from eight countries on four continents. Vet Res Commun 2023; 47:1561-1573. [PMID: 37002455 PMCID: PMC10066014 DOI: 10.1007/s11259-023-10111-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/19/2023] [Indexed: 04/03/2023]
Abstract
Several bat-associated circoviruses and circular rep-encoding single-stranded DNA (CRESS DNA) viruses have been described, but the exact diversity and host species of these viruses are often unknown. Our goal was to describe the diversity of bat-associated circoviruses and cirliviruses, thus, 424 bat samples from more than 80 species were collected on four continents. The samples were screened for circoviruses using PCR and the resulting amino acid sequences were subjected to phylogenetic analysis. The majority of bat strains were classified in the genus Circovirus and some strains in the genus Cyclovirus and the clades CRESS1 and CRESS3. Some strains, however, could only be classified at the taxonomic level of the order and were not classified in any of the accepted or proposed clades. In the family Circoviridae, 71 new species have been predicted. This screening of bat samples revealed a great diversity of circoviruses and cirliviruses. These studies underline the importance of the discovery and description of new cirliviruses and the need to establish new species and families in the order Cirlivirales.
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Affiliation(s)
| | | | - Ákos Gellért
- Veterinary Medical Research Institute, Budapest, Hungary
| | - Balázs Harrach
- Veterinary Medical Research Institute, Budapest, Hungary
| | - Tamás Görföl
- National Laboratory of Virology, University of Pécs, Pécs, Hungary
| | | | - Claudia Kohl
- Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
| | - Gudrun Wibbelt
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Kristin Mühldorfer
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Gábor Kemenesi
- National Laboratory of Virology, University of Pécs, Pécs, Hungary
| | - Guy-Crispin Gembu
- Faculté des Sciences, Université de Kisangani, Kisangani, République Démocratique du Congo
| | - Alexandre Hassanin
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Sorbonne Université, MNHN, CNRS, EPHE, UA, Paris, France
| | - Vuong Tan Tu
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Péter Estók
- Department of Zoology, Eszterházy Károly Catholic University, Eger, Hungary
| | - Anna Horváth
- QUIRÓN, Center for Equine Assisted Interventions and Training for Well-Being and Sustainability, Comitán de Domínguez, Mexico
| | - Győző L. Kaján
- Veterinary Medical Research Institute, Budapest, Hungary
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Vasinioti VI, Pellegrini F, Buonavoglia A, Capozza P, Cardone R, Diakoudi G, Desario C, Catella C, Vicenza T, Lucente MS, Di Martino B, Camero M, Elia G, Decaro N, Martella V, Lanave G. Investigating the genetic diversity of CRESS DNA viruses in cats identifies a novel feline circovirus and unveils exposure of cats to canine circovirus. Res Vet Sci 2023; 161:86-95. [PMID: 37327693 DOI: 10.1016/j.rvsc.2023.06.011] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 06/08/2023] [Accepted: 06/09/2023] [Indexed: 06/18/2023]
Abstract
Circular replication-associated protein (Rep)-encoding single stranded (CRESS) DNA viruses include Circoviruses which have been found in several animal species and in human specimens. Circoviruses are associated with severe disease in pigs and birds and with respiratory and gastrointestinal disorders and systemic disease in dogs. In cats there are only a few anecdotical studies reporting CRESS DNA viruses. In this study, a total of 530 samples (361 sera, 131 stools, and 38 respiratory swabs) from cats, were screened for the presence of CRESS DNA viruses. Overall, 48 (9.0%) of 530 samples tested positive using a pan-Rep PCR. A total of 30 Rep sequences were obtained. Ten sequences of fecal origin were tightly related to each other (82.4-100% nt identity) and more distantly related to mongoose circoviruses (68.3 to 77.2% nt identity). At genome level these circoviruses displayed the highest nt identity (74.3-78.7%) to mongoose circoviruses thus representing a novel circovirus species. Circoviruses from different animal hosts (n = 12) and from humans (n = 8) were also identified. However, six Rep sequences were obtained from serum samples, including canine circoviruses, a human cyclovirus and human and fish-associated CRESS DNA viruses. The presence of these viruses in the sera would imply, to various extent, virus replication in the animal host, able to sustain viremia. Overall, these findings indicate a wide genetic diversity of CRESS DNA viruses in cats and warrant further investigations.
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Affiliation(s)
- Violetta Iris Vasinioti
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Francesco Pellegrini
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Alessio Buonavoglia
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Paolo Capozza
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Roberta Cardone
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Georgia Diakoudi
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Costantina Desario
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Cristiana Catella
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Teresa Vicenza
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Maria Stella Lucente
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Barbara Di Martino
- Department of Veterinary Medicine, Università degli Studi di Teramo, SP18, 64100 Teramo, Italy
| | - Michele Camero
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Gabriella Elia
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Nicola Decaro
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Vito Martella
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Gianvito Lanave
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy.
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Orf GS, Olivo A, Harris B, Weiss SL, Achari A, Yu G, Federman S, Mbanya D, James L, Mampunza S, Chiu CY, Rodgers MA, Cloherty GA, Berg MG. Metagenomic Detection of Divergent Insect- and Bat-Associated Viruses in Plasma from Two African Individuals Enrolled in Blood-Borne Surveillance. Viruses 2023; 15:v15041022. [PMID: 37113001 PMCID: PMC10145552 DOI: 10.3390/v15041022] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/18/2023] [Accepted: 04/19/2023] [Indexed: 04/29/2023] Open
Abstract
Metagenomic next-generation sequencing (mNGS) has enabled the high-throughput multiplexed identification of sequences from microbes of potential medical relevance. This approach has become indispensable for viral pathogen discovery and broad-based surveillance of emerging or re-emerging pathogens. From 2015 to 2019, plasma was collected from 9586 individuals in Cameroon and the Democratic Republic of the Congo enrolled in a combined hepatitis virus and retrovirus surveillance program. A subset (n = 726) of the patient specimens was analyzed by mNGS to identify viral co-infections. While co-infections from known blood-borne viruses were detected, divergent sequences from nine poorly characterized or previously uncharacterized viruses were also identified in two individuals. These were assigned to the following groups by genomic and phylogenetic analyses: densovirus, nodavirus, jingmenvirus, bastrovirus, dicistrovirus, picornavirus, and cyclovirus. Although of unclear pathogenicity, these viruses were found circulating at high enough concentrations in plasma for genomes to be assembled and were most closely related to those previously associated with bird or bat excrement. Phylogenetic analyses and in silico host predictions suggested that these are invertebrate viruses likely transmitted through feces containing consumed insects or through contaminated shellfish. This study highlights the power of metagenomics and in silico host prediction in characterizing novel viral infections in susceptible individuals, including those who are immunocompromised from hepatitis viruses and retroviruses, or potentially exposed to zoonotic viruses from animal reservoir species.
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Affiliation(s)
- Gregory S Orf
- Infectious Disease Research, Abbott Diagnostics, Abbott Park, IL 60004, USA
- Abbott Pandemic Defense Coalition, Abbott Park, IL 60004, USA
| | - Ana Olivo
- Infectious Disease Research, Abbott Diagnostics, Abbott Park, IL 60004, USA
- Abbott Pandemic Defense Coalition, Abbott Park, IL 60004, USA
| | - Barbara Harris
- Infectious Disease Research, Abbott Diagnostics, Abbott Park, IL 60004, USA
- Abbott Pandemic Defense Coalition, Abbott Park, IL 60004, USA
| | - Sonja L Weiss
- Infectious Disease Research, Abbott Diagnostics, Abbott Park, IL 60004, USA
- Abbott Pandemic Defense Coalition, Abbott Park, IL 60004, USA
| | - Asmeeta Achari
- Abbott Pandemic Defense Coalition, Abbott Park, IL 60004, USA
- Department of Laboratory Medicine, University of California-San Francisco, San Francisco, CA 94143, USA
| | - Guixia Yu
- Abbott Pandemic Defense Coalition, Abbott Park, IL 60004, USA
- Department of Laboratory Medicine, University of California-San Francisco, San Francisco, CA 94143, USA
| | - Scot Federman
- Abbott Pandemic Defense Coalition, Abbott Park, IL 60004, USA
- Department of Laboratory Medicine, University of California-San Francisco, San Francisco, CA 94143, USA
| | - Dora Mbanya
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé P.O. Box 1364, Cameroon
| | - Linda James
- School of Medicine, Université Protestante au Congo, Kinshasa P.O. Box 4745, Democratic Republic of the Congo
| | - Samuel Mampunza
- School of Medicine, Université Protestante au Congo, Kinshasa P.O. Box 4745, Democratic Republic of the Congo
| | - Charles Y Chiu
- Abbott Pandemic Defense Coalition, Abbott Park, IL 60004, USA
- Department of Laboratory Medicine, University of California-San Francisco, San Francisco, CA 94143, USA
- Department of Medicine, University of California-San Francisco, San Francisco, CA 94143, USA
| | - Mary A Rodgers
- Infectious Disease Research, Abbott Diagnostics, Abbott Park, IL 60004, USA
- Abbott Pandemic Defense Coalition, Abbott Park, IL 60004, USA
| | - Gavin A Cloherty
- Infectious Disease Research, Abbott Diagnostics, Abbott Park, IL 60004, USA
- Abbott Pandemic Defense Coalition, Abbott Park, IL 60004, USA
| | - Michael G Berg
- Infectious Disease Research, Abbott Diagnostics, Abbott Park, IL 60004, USA
- Abbott Pandemic Defense Coalition, Abbott Park, IL 60004, USA
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Jiang JZ, Fang YF, Wei HY, Zhu P, Liu M, Yuan WG, Yang LL, Guo YX, Jin T, Shi M, Yao T, Lu J, Ye LT, Shi SK, Wang M, Duan M, Zhang DC. A remarkably diverse and well-organized virus community in a filter-feeding oyster. Microbiome 2023; 11:2. [PMID: 36611217 PMCID: PMC9825006 DOI: 10.1186/s40168-022-01431-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 11/17/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Viruses play critical roles in the marine environment because of their interactions with an extremely broad range of potential hosts. Many studies of viruses in seawater have been published, but viruses that inhabit marine animals have been largely neglected. Oysters are keystone species in coastal ecosystems, yet as filter-feeding bivalves with very large roosting numbers and species co-habitation, it is not clear what role they play in marine virus transmission and coastal microbiome regulation. RESULTS Here, we report a Dataset of Oyster Virome (DOV) that contains 728,784 nonredundant viral operational taxonomic unit contigs (≥ 800 bp) and 3473 high-quality viral genomes, enabling the first comprehensive overview of both DNA and RNA viral communities in the oyster Crassostrea hongkongensis. We discovered tremendous diversity among novel viruses that inhabit this oyster using multiple approaches, including reads recruitment, viral operational taxonomic units, and high-quality virus genomes. Our results show that these viruses are very different from viruses in the oceans or other habitats. In particular, the high diversity of novel circoviruses that we found in the oysters indicates that oysters may be potential hotspots for circoviruses. Notably, the viruses that were enriched in oysters are not random but are well-organized communities that can respond to changes in the health state of the host and the external environment at both compositional and functional levels. CONCLUSIONS In this study, we generated a first "knowledge landscape" of the oyster virome, which has increased the number of known oyster-related viruses by tens of thousands. Our results suggest that oysters provide a unique habitat that is different from that of seawater, and highlight the importance of filter-feeding bivalves for marine virus exploration as well as their essential but still invisible roles in regulating marine ecosystems. Video Abstract.
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Affiliation(s)
- Jing-Zhe Jiang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, Guangdong, China.
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China.
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, 510006, Guangdong, China.
- Tianjin Agricultural University, Tianjin, 300384, China.
| | - Yi-Fei Fang
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
- Shanghai Majorbio Bio-Pharm Technology Co Ltd, Shanghai, 201203, China
| | - Hong-Ying Wei
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
- Guangdong Magigene Biotechnology Co Ltd, Guangzhou, 510000, Guangdong, China
| | - Peng Zhu
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Min Liu
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Wen-Guang Yuan
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, 510006, Guangdong, China
| | - Li-Ling Yang
- Tianjin Agricultural University, Tianjin, 300384, China
| | | | - Tao Jin
- Guangdong Magigene Biotechnology Co Ltd, Guangzhou, 510000, Guangdong, China
| | - Mang Shi
- School of Medicine, Sun Yat-Sen University, Shenzhen, 518107, Guangdong, China
| | - Tuo Yao
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, Guangdong, China
| | - Jie Lu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, Guangdong, China
| | - Ling-Tong Ye
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, Guangdong, China
| | - Shao-Kun Shi
- Shenzhen Fisheries Development Research Center, Shenzhen, 518067, Guangdong, China
| | - Meng Wang
- Bureau of Agriculture and Rural Affairs of Conghua District, Guangzhou, 510925, Guangdong, China
| | - Ming Duan
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China, Hubei.
| | - Dian-Chang Zhang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, Guangdong, China.
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Capozza P, Lanave G, Diakoudi G, Pellegrini F, Cardone R, Vasinioti VI, Decaro N, Elia G, Catella C, Alberti A, Bányai K, Mendoza-Roldan JA, Otranto D, Buonavoglia C, Martella V. Diversity of CRESS DNA Viruses in Squamates Recapitulates Hosts Dietary and Environmental Sources of Exposure. Microbiol Spectr 2022;:e0078022. [PMID: 35616383 DOI: 10.1128/spectrum.00780-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Replication-associated protein (Rep)-encoding single-stranded (CRESS) DNA viruses comprise viruses with covalently closed, circular, single-stranded DNA (ssDNA) genomes, and are considered the smallest known autonomously replicating, capsid-encoding animal pathogens. CRESS DNA viruses (phylum Cressdnaviricota) encompass several viral families including Circoviridae. Circoviruses are classified into two genera, Circovirus and Cyclovirus, and they are known to cause fatal diseases in birds and pigs. Circoviruses have also been identified in human stools, blood, and cerebrospinal fluid (CSF), as well as in various wild and domestic vertebrates, including reptiles. The synanthropic presence of Squamata reptiles has increased in the last century due to the anthropic pressure, which has shifted forested animal behavior to an urban and peri-urban adaptation. In this paper, we explored the diversity of CRESS DNA viruses in Squamata reptiles from different Italian areas representative of the Mediterranean basin. CRESS DNA viruses were detected in 31.7% (33/104) of sampled lizards and geckoes. Different CRESS DNA viruses likely reflected dietary composition or environmental contamination and included avian-like (n = 3), dog (n = 4), bat-like (n = 1), goat-like (n = 1), rodent-like (n = 4), and insect-like (n = 2) viruses. Rep sequences of at least two types of human-associated cycloviruses (CyV) were identified consistently, regardless of geographic location, namely, TN9-like (n = 11) and TN12-like (n = 6). A third human-associated CyV, TN25-like, was detected in a single sample. The complete genome of human-like CyVs, of a rodent-like, insect-like, and of a bat-like virus were generated. Collectively, the results recapitulate hosts dietary and environmental sources of exposure and may suggest unexpected ecological niches for some CRESS DNA viruses. IMPORTANCE CRESS DNA viruses are significant pathogens of birds and pigs and have been detected repeatedly in human samples (stools, serum, and cerebrospinal fluid), both from healthy individuals and from patients with neurological disease, eliciting in 2013 a risk assessment by the European Centre for Disease Prevention and Control (ECDC). Sequences of CRESS DNA viruses previously reported in humans (TN9, TN12, and TN25), and detected in different animal species (e.g., birds, dogs, and bats) were herein detected in fecal samples of synanthropic squamates (geckos and lizards). The complete genome sequence of six viruses was generated. This study extends the information on the genetic diversity and ecology of CRESS DNA viruses. Because geckos and lizards are synanthropic animals, a role in sustaining CRESS DNA virus circulation and increasing viral pressure in the environment is postulated.
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Allali I, Abotsi RE, Tow LA, Thabane L, Zar HJ, Mulder NM, Nicol MP. Human microbiota research in Africa: a systematic review reveals gaps and priorities for future research. Microbiome 2021; 9:241. [PMID: 34911583 PMCID: PMC8672519 DOI: 10.1186/s40168-021-01195-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 11/14/2021] [Indexed: 05/11/2023]
Abstract
BACKGROUND The role of the human microbiome in health and disease is an emerging and important area of research; however, there is a concern that African populations are under-represented in human microbiome studies. We, therefore, conducted a systematic survey of African human microbiome studies to provide an overview and identify research gaps. Our secondary objectives were: (i) to determine the number of peer-reviewed publications; (ii) to identify the extent to which the researches focused on diseases identified by the World Health Organization [WHO] State of Health in the African Region Report as being the leading causes of morbidity and mortality in 2018; (iii) to describe the extent and pattern of collaborations between researchers in Africa and the rest of the world; and (iv) to identify leadership and funders of the studies. METHODOLOGY We systematically searched Medline via PubMed, Scopus, CINAHL, Academic Search Premier, Africa-Wide Information through EBSCOhost, and Web of Science from inception through to 1st April 2020. We included studies that characterized samples from African populations using next-generation sequencing approaches. Two reviewers independently conducted the literature search, title and abstract, and full-text screening, as well as data extraction. RESULTS We included 168 studies out of 5515 records retrieved. Most studies were published in PLoS One (13%; 22/168), and samples were collected from 33 of the 54 African countries. The country where most studies were conducted was South Africa (27/168), followed by Kenya (23/168) and Uganda (18/168). 26.8% (45/168) focused on diseases of significant public health concern in Africa. Collaboration between scientists from the United States of America and Africa was most common (96/168). The first and/or last authors of 79.8% of studies were not affiliated with institutions in Africa. Major funders were the United States of America National Institutes of Health (45.2%; 76/168), Bill and Melinda Gates Foundation (17.8%; 30/168), and the European Union (11.9%; 20/168). CONCLUSIONS There are significant gaps in microbiome research in Africa, especially those focusing on diseases of public health importance. There is a need for local leadership, capacity building, intra-continental collaboration, and national government investment in microbiome research within Africa. Video Abstract.
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Affiliation(s)
- Imane Allali
- Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
- Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, and Genomic Centre of Human Pathologies, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, Rabat, Morocco
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Regina E Abotsi
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Department of Molecular and Cell Biology, Faculty of Science, University of Cape Town, Cape Town, South Africa
- Department of Pharmaceutical Microbiology, School of Pharmacy, University of Health and Allied Sciences, Ho, Ghana
| | - Lemese Ah Tow
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Lehana Thabane
- Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, Ontario, Canada
- Biostatistics Unit, Father Sean O'Sullivan Research Centre, St Joseph's Healthcare, Hamilton, Ontario, Canada
- Departments of Paediatrics and Anaesthesia, McMaster University, Hamilton, Ontario, Canada
- Centre for Evaluation of Medicine, St Joseph's Healthcare, Hamilton, Ontario, Canada
- Population Health Research Institute, Hamilton Health Sciences, Hamilton, Ontario, Canada
- Centre for Evidence-based Health Care, Faculty of Health Sciences, Stellenbosch University, Tygerberg, South Africa
- Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Heather J Zar
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, Cape Town, South Africa
- MRC Unit on Child & Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Nicola M Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Mark P Nicol
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
- School of Biomedical Sciences, University of Western Australia, M504, Perth, WA, 6009, Australia.
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9
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Gainor K, Malik YS, Ghosh S. Novel Cyclovirus Species in Dogs with Hemorrhagic Gastroenteritis. Viruses 2021; 13:2155. [PMID: 34834961 DOI: 10.3390/v13112155] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 11/21/2022] Open
Abstract
Nested PCRs with circovirus/cyclovirus pan-rep (replicase gene) primers detected eukaryotic circular Rep-encoding single-stranded DNA (CRESS DNA) viruses in three (samples CN9E, CN16E and CN34) of 18 canine parvovirus-2-positive fecal samples from household dogs with hemorrhagic gastroenteritis on the Caribbean island of Nevis. The complete genomes of CRESS DNA virus CN9E, CN16E and CN34 were determined by inverse nested PCRs. Based on (i) genome organization, (ii) location of the putative origin of replication, (iii) pairwise genome-wide sequence identities, (iv) the presence of conserved motifs in the putative replication-associated protein (Rep) and the arginine-rich region in the amino terminus of the putative capsid protein (Cp) and (v) a phylogenetic analysis, CN9E, CN16E and CN34 were classified as cycloviruses. Canine-associated cycloviruses CN16E and CN34 were closely related to each other and shared low genome-wide nucleotide (59.642–59.704%), deduced Rep (35.018–35.379%) and Cp (26.601%) amino acid sequence identities with CN9E. All the three canine-associated cycloviruses shared < 80% genome-wide pairwise nucleotide sequence identities with cycloviruses from other animals/environmental samples, constituting two novel species (CN9E and CN16E/34) within the genus Cyclovirus. Considering the feeding habits of dogs, we could not determine whether the cycloviruses were of dietary origin or infected the host. Interestingly, the CN9E putative Rep-encoding open reading frame was found to use the invertebrate mitochondrial genetic code with an alternative initiation codon (ATA) for translation, corroborating the hypothesis that cycloviruses are actually arthropod-infecting viruses. To our knowledge, this is the first report on the detection and complete genome analysis of cycloviruses from domestic dogs.
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Carbo EC, Blankenspoor I, Goeman JJ, Kroes ACM, Claas ECJ, De Vries JJC. Viral metagenomic sequencing in the diagnosis of meningoencephalitis: a review of technical advances and diagnostic yield. Expert Rev Mol Diagn 2021; 21:1139-1146. [PMID: 34607520 DOI: 10.1080/14737159.2021.1985467] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
INTRODUCTION Meningoencephalitis patients are often severely impaired and benefit from early etiological diagnosis, though many cases remain without identified cause. Metagenomics as pathogen agnostic approach can result in additional etiological findings; however, the exact diagnostic yield when used as a secondary test remains unknown. AREAS COVERED This review aims to highlight recent advances with regard to wet and dry lab methodologies of metagenomic testing and technical milestones that have been achieved. A selection of procedures currently applied in accredited diagnostic laboratories is described in more detail to illustrate best practices. Furthermore, a meta-analysis was performed to assess the additional diagnostic yield utilizing metagenomic sequencing in meningoencephalitis patients. Finally, the remaining challenges for successful widespread implementation of metagenomic sequencing for the diagnosis of meningoencephalitis are addressed in a future perspective. EXPERT OPINION The last decade has shown major advances in technical possibilities for using mNGS in diagnostic settings including cloud-based analysis. An additional advance may be the current established infrastructure of platforms for bioinformatic analysis of SARS-CoV-2, which may assist to pave the way for global use of clinical metagenomics.
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Affiliation(s)
- Ellen C Carbo
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ivar Blankenspoor
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Jelle J Goeman
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Aloys C M Kroes
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Eric C J Claas
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Jutte J C De Vries
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
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Gainor K, Becker AAMJ, Malik YS, Ghosh S. Detection and Complete Genome Analysis of Circoviruses and Cycloviruses in the Small Indian Mongoose ( Urva auropunctata): Identification of Novel Species. Viruses 2021; 13:1700. [PMID: 34578282 DOI: 10.3390/v13091700] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 02/06/2023] Open
Abstract
Fecal samples from 76 of 83 apparently healthy small Indian mongooses (Urva auropunctata) were PCR positive with circovirus/cyclovirus pan-rep (replicase gene) primers. In this case, 30 samples yielded high quality partial rep sequences (~400 bp), of which 26 sequences shared maximum homology with cycloviruses from an arthropod, bats, humans or a sheep. Three sequences exhibited maximum identities with a bat circovirus, whilst a single sequence could not be assigned to either genus. Using inverse nested PCRs, the complete genomes of mongoose associated circoviruses (Mon-1, -29 and -66) and cycloviruses (Mon-20, -24, -32, -58, -60 and -62) were determined. Mon-1, -20, -24, -29, -32 and -66 shared <80% maximum genome-wide pairwise nucleotide sequence identities with circoviruses/cycloviruses from other animals/sources, and were assigned to novel circovirus, or cyclovirus species. Mon-58, -60 and -62 shared maximum pairwise identities of 79.90–80.20% with human and bat cycloviruses, which were borderline to the cut-off identity value for assigning novel cycloviral species. Despite high genetic diversity, the mongoose associated circoviruses/cycloviruses retained the various features that are conserved among members of the family Circoviridae, such as presence of the putative origin of replication (ori) in the 5′-intergenic region, conserved motifs in the putative replication-associated protein and an arginine rich region in the amino terminus of the putative capsid protein. Since only fecal samples were tested, and mongooses are polyphagous predators, we could not determine whether the mongoose associated circoviruses/cycloviruses were of dietary origin, or actually infected the host. To our knowledge, this is the first report on detection and complete genome analysis of circoviruses/cycloviruses in the small Indian mongoose, warranting further studies in other species of mongooses.
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Dimkić I, Fira D, Janakiev T, Kabić J, Stupar M, Nenadić M, Unković N, Grbić ML. The microbiome of bat guano: for what is this knowledge important? Appl Microbiol Biotechnol 2021; 105:1407-1419. [PMID: 33512572 PMCID: PMC7845282 DOI: 10.1007/s00253-021-11143-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/15/2021] [Accepted: 01/25/2021] [Indexed: 12/17/2022]
Abstract
Bats as flying mammals are potent vectors and natural reservoir hosts for many infectious viruses, bacteria, and fungi, also detected in their excreta such as guano. Accelerated deforestation, urbanization, and anthropization hastily lead to overpopulation of the bats in urban areas allowing easy interaction with other animals, expansion, and emergence of new zoonotic disease outbreaks potentially harmful to humans. Therefore, getting new insights in the microbiome of bat guano from different places represents an imperative for the future. Furthermore, the use of novel high-throughput sequencing technologies allows better insight in guano microbiome and potentially indicated that some species could be typical guano-dwelling members. Bats are well known as a natural reservoir of many zoonotic viruses such as Ebola, Nipah, Marburg, lyssaviruses, rabies, henipaviruses, and many coronaviruses which caused a high number of outbreaks including ongoing COVID-19 pandemic. Additionally, many bacterial and fungal pathogens were identified as common guano residents. Thus, the presence of multi-drug-resistant bacteria as environmental reservoirs of extended spectrum β-lactamases and carbapenemase-producing strains has been confirmed. Bat guano is the most suitable substrate for fungal reproduction and dissemination, including pathogenic yeasts and keratinophilic and dimorphic human pathogenic fungi known as notorious causative agents of severe endemic mycoses like histoplasmosis and fatal cryptococcosis, especially deadly in immunocompromised individuals. This review provides an overview of bat guano microbiota diversity and the significance of autochthonous and pathogenic taxa for humans and the environment, highlighting better understanding in preventing emerging diseases. KEY POINTS: Bat guano as reservoir and source for spreading of autochthonous and pathogenic microbiota Bat guano vs. novel zoonotic disease outbreaks Destruction of bat natural habitats urgently demands increased human awareness.
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Affiliation(s)
- Ivica Dimkić
- Faculty of Biology, University of Belgrade, Studentski Trg 16, Belgrade, 11000, Serbia.
| | - Djordje Fira
- Faculty of Biology, University of Belgrade, Studentski Trg 16, Belgrade, 11000, Serbia
| | - Tamara Janakiev
- Faculty of Biology, University of Belgrade, Studentski Trg 16, Belgrade, 11000, Serbia
| | - Jovana Kabić
- Faculty of Medicine, University of Belgrade, dr Subotića starijeg 1, Belgrade, 11000, Serbia
| | - Miloš Stupar
- Faculty of Biology, University of Belgrade, Studentski Trg 16, Belgrade, 11000, Serbia
| | - Marija Nenadić
- Institute for Biological Research "Siniša Stanković", Bulevar despota Stefana 142, Belgrade, 11060, Serbia
| | - Nikola Unković
- Faculty of Biology, University of Belgrade, Studentski Trg 16, Belgrade, 11000, Serbia
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Perlejewski K, Bukowska-Ośko I, Rydzanicz M, Dzieciątkowski T, Zakrzewska-Pniewska B, Podlecka-Piętowska A, Filipiak A, Barć K, Caraballo Cortés K, Pawełczyk A, Radkowski M, Laskus T. Search for viral agents in cerebrospinal fluid in patients with multiple sclerosis using real-time PCR and metagenomics. PLoS One 2020; 15:e0240601. [PMID: 33112911 PMCID: PMC7592794 DOI: 10.1371/journal.pone.0240601] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 03/29/2020] [Accepted: 09/29/2020] [Indexed: 12/21/2022] Open
Abstract
Multiple sclerosis (MS) is a chronic, immune-mediated demyelinating disease of the central nervous system of unclear etiology, but there is some evidence that viral infections could be responsible for triggering autoimmune mechanisms against myelin. We searched for viral RNA and DNA in cerebrospinal fluid (CSF) of 34 MS patients and 13 controls using RT-PCR/PCR against common neurotropic viruses. In addition, shotgun DNA- and RNA-based metagenomics were done in 13 MS patients and 4 controls. Specific quantitative real-time RT-PCR/PCR testing revealed the presence of viral nucleic acid in seven (20.59%) MS patients and in one (7.69%) control patient. In MS patients the most frequently detected was human herpesvirus type 6 (HHV-6; 3 cases; 8.82%); followed by Epstein-Barr virus (EBV; 2 cases; 5.88%), varicella zoster virus (VZV; 1 case; 2.94%) and Enterovirus (EV; 1 case; 2.94%). The single identified virus among controls was EBV (7.69%). DNA and RNA metagenomic assays did not identify any known eukaryotic viruses even though three of the analyzed samples were low-level positive by specific quantitative real-time PCR. In conclusion, we detected the presence of Herpesviridae and occasionally Enteroviridae in CSF from patients with MS but their prevalence was not significantly higher than among controls. Metagenomic analysis seems to be less sensitive than real-time RT-PCR/PCR and it did not detect any potential viral pathogens.
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Affiliation(s)
- Karol Perlejewski
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
- * E-mail:
| | - Iwona Bukowska-Ośko
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Małgorzata Rydzanicz
- Department of the Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | | | | | | | - Agata Filipiak
- University Clinical Center of Medical University of Warsaw, Medical University of Warsaw, Warsaw, Poland
| | - Krzysztof Barć
- University Clinical Center of Medical University of Warsaw, Medical University of Warsaw, Warsaw, Poland
| | - Kamila Caraballo Cortés
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Agnieszka Pawełczyk
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Marek Radkowski
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Tomasz Laskus
- Department of Adult Infectious Diseases, Medical University of Warsaw, Warsaw, Poland
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Yan T, Li G, Zhou D, Yang X, Hu L, Cheng Z. Novel Cyclovirus Identified in Broiler Chickens With Transmissible Viral Proventriculitis in China. Front Vet Sci 2020; 7:569098. [PMID: 33134354 PMCID: PMC7550471 DOI: 10.3389/fvets.2020.569098] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 08/18/2020] [Indexed: 11/30/2022] Open
Abstract
In October 2018, an outbreak of transmissible viral proventriculitis (TVP) occurred in 30-day-old commercial broiler chickens on a farm in Weifang, China. TVP, an infectious viral disease characterized by runting and stunting, is associated with many viruses, and has a significant economic impact on the global poultry industry. TVP is diagnosed according to clinical symptoms, gross and histological lesions, and negative PCR results for pathogenic bacteria, avian leukosis virus subgroup J, Marek's disease virus, reticuloendotheliosis virus, infectious bursa disease virus, avian reovirus, chicken anemia virus, infectious bronchitis virus, chicken proventricular necrosis virus, gyrovirus 3 and chicken circovirus. To further detect the possible causative pathogens of TVP, we used PacBio third-generation sequencing to examine proventricular samples. A dominant abundance of the novel cyclovirus (CyCV), chCyCV-SDAU-1, was identified in broilers with TVP. The complete chCyCV-SDAU-1 genome was verified via inverse PCR, was 1936 bp long, and consisted of Rep, Cp, and two intergenic regions. Phylogenetic tree analysis showed that chCyCV-SDAU-1 formed an independent branch with other cycloviruses. The homology of chCyCV-SDAU-1 with 20 others known cycloviruses was < 40%. Retrospective investigation showed that the CyCV infection rate in the broilers with TVP was 80% (16/20), while no CyCV was found in healthy chickens. In conclusion, a novel CyCV was identified in chickens with TVP, though its role in this disease is unclear.
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Affiliation(s)
- Tianxing Yan
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an, China
| | - Gen Li
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an, China.,College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Defang Zhou
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an, China
| | - Xiaoxia Yang
- Hospital of Shandong Agricultural University, Tai'an, China
| | - Liping Hu
- Animal Epidemic Prevention and Control Center of Shandong Province, Jinan, China
| | - Ziqiang Cheng
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an, China
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Thi Kha Tu N, Thi Thu Hong N, Thi Han Ny N, My Phuc T, Thi Thanh Tam P, van Doorn HR, Dang Trung Nghia H, Thao Huong D, An Han D, Thi Thu Ha L, Deng X, Thwaites G, Delwart E, Virtala AMK, Vapalahti O, Baker S, Van Tan L. The Virome of Acute Respiratory Diseases in Individuals at Risk of Zoonotic Infections. Viruses 2020; 12:E960. [PMID: 32872469 PMCID: PMC7552073 DOI: 10.3390/v12090960] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 07/06/2020] [Revised: 08/19/2020] [Accepted: 08/26/2020] [Indexed: 12/11/2022] Open
Abstract
The ongoing coronavirus disease 2019 (COVID-19) pandemic emphasizes the need to actively study the virome of unexplained respiratory diseases. We performed viral metagenomic next-generation sequencing (mNGS) analysis of 91 nasal-throat swabs from individuals working with animals and with acute respiratory diseases. Fifteen virus RT-PCR-positive samples were included as controls, while the other 76 samples were RT-PCR negative for a wide panel of respiratory pathogens. Eukaryotic viruses detected by mNGS were then screened by PCR (using primers based on mNGS-derived contigs) in all samples to compare viral detection by mNGS versus PCR and assess the utility of mNGS in routine diagnostics. mNGS identified expected human rhinoviruses, enteroviruses, influenza A virus, coronavirus OC43, and respiratory syncytial virus (RSV) A in 13 of 15 (86.7%) positive control samples. Additionally, rotavirus, torque teno virus, human papillomavirus, human betaherpesvirus 7, cyclovirus, vientovirus, gemycircularvirus, and statovirus were identified through mNGS. Notably, complete genomes of novel cyclovirus, gemycircularvirus, and statovirus were genetically characterized. Using PCR screening, the novel cyclovirus was additionally detected in 5 and the novel gemycircularvirus in 12 of the remaining samples included for mNGS analysis. Our studies therefore provide pioneering data of the virome of acute-respiratory diseases from individuals at risk of zoonotic infections. The mNGS protocol/pipeline applied here is sensitive for the detection of a variety of viruses, including novel ones. More frequent detections of the novel viruses by PCR than by mNGS on the same samples suggests that PCR remains the most sensitive diagnostic test for viruses whose genomes are known. The detection of novel viruses expands our understanding of the respiratory virome of animal-exposed humans and warrant further studies.
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Affiliation(s)
- Nguyen Thi Kha Tu
- Doctoral School in Health Sciences, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland;
- Oxford University Clinical Research Unit, Ho Chi Minh City 7000, Vietnam; (N.T.T.H.); (N.T.H.N.); (T.M.P.); (P.T.T.T.); (H.D.T.N.); (D.T.H.); (G.T.)
- Dong Thap Provincial Center for Disease Control, Cao Lanh City 660273, Dong Thap Province, Vietnam; (D.A.H.); (L.T.T.H.)
| | - Nguyen Thi Thu Hong
- Oxford University Clinical Research Unit, Ho Chi Minh City 7000, Vietnam; (N.T.T.H.); (N.T.H.N.); (T.M.P.); (P.T.T.T.); (H.D.T.N.); (D.T.H.); (G.T.)
| | - Nguyen Thi Han Ny
- Oxford University Clinical Research Unit, Ho Chi Minh City 7000, Vietnam; (N.T.T.H.); (N.T.H.N.); (T.M.P.); (P.T.T.T.); (H.D.T.N.); (D.T.H.); (G.T.)
| | - Tran My Phuc
- Oxford University Clinical Research Unit, Ho Chi Minh City 7000, Vietnam; (N.T.T.H.); (N.T.H.N.); (T.M.P.); (P.T.T.T.); (H.D.T.N.); (D.T.H.); (G.T.)
| | - Pham Thi Thanh Tam
- Oxford University Clinical Research Unit, Ho Chi Minh City 7000, Vietnam; (N.T.T.H.); (N.T.H.N.); (T.M.P.); (P.T.T.T.); (H.D.T.N.); (D.T.H.); (G.T.)
| | - H. Rogier van Doorn
- Oxford University Clinical Research Unit, Ha Noi 8000, Vietnam;
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LG, UK
| | - Ho Dang Trung Nghia
- Oxford University Clinical Research Unit, Ho Chi Minh City 7000, Vietnam; (N.T.T.H.); (N.T.H.N.); (T.M.P.); (P.T.T.T.); (H.D.T.N.); (D.T.H.); (G.T.)
| | - Dang Thao Huong
- Oxford University Clinical Research Unit, Ho Chi Minh City 7000, Vietnam; (N.T.T.H.); (N.T.H.N.); (T.M.P.); (P.T.T.T.); (H.D.T.N.); (D.T.H.); (G.T.)
| | - Duong An Han
- Dong Thap Provincial Center for Disease Control, Cao Lanh City 660273, Dong Thap Province, Vietnam; (D.A.H.); (L.T.T.H.)
| | - Luu Thi Thu Ha
- Dong Thap Provincial Center for Disease Control, Cao Lanh City 660273, Dong Thap Province, Vietnam; (D.A.H.); (L.T.T.H.)
| | - Xutao Deng
- Department of Laboratory Medicine, University of California, San Francisco, CA 94143, USA; (X.D.); (E.D.)
- Vitalant Research Institute, San Francisco, CA 94118, USA
| | - Guy Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City 7000, Vietnam; (N.T.T.H.); (N.T.H.N.); (T.M.P.); (P.T.T.T.); (H.D.T.N.); (D.T.H.); (G.T.)
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LG, UK
| | - Eric Delwart
- Department of Laboratory Medicine, University of California, San Francisco, CA 94143, USA; (X.D.); (E.D.)
- Vitalant Research Institute, San Francisco, CA 94118, USA
| | - Anna-Maija K. Virtala
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, 00014 Helsinki, Finland;
| | - Olli Vapalahti
- Doctoral School in Health Sciences, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland;
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, 00014 Helsinki, Finland;
- Virology and Immunology, HUSLAB, Helsinki University Hospital, 00029 Helsinki, Finland
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK;
| | - Le Van Tan
- Oxford University Clinical Research Unit, Ho Chi Minh City 7000, Vietnam; (N.T.T.H.); (N.T.H.N.); (T.M.P.); (P.T.T.T.); (H.D.T.N.); (D.T.H.); (G.T.)
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Zanella MC, Cordey S, Kaiser L. Beyond Cytomegalovirus and Epstein-Barr Virus: a Review of Viruses Composing the Blood Virome of Solid Organ Transplant and Hematopoietic Stem Cell Transplant Recipients. Clin Microbiol Rev 2020; 33:e00027-20. [PMID: 32847820 DOI: 10.1128/CMR.00027-20] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Viral primary infections and reactivations are common complications in patients after solid organ transplantation (SOT) and hematopoietic stem cell transplantation (HSCT) and are associated with high morbidity and mortality. Among these patients, viral infections are frequently associated with viremia. Beyond the usual well-known viruses that are part of the routine clinical management of transplant recipients, numerous other viral signatures or genomes can be identified in the blood of these patients. The identification of novel viral species and variants by metagenomic next-generation sequencing has opened up a new field of investigation and new paradigms. Thus, there is a need to thoroughly describe the state of knowledge in this field with a review of all viral infections that should be scrutinized in high-risk populations. Here, we review the eukaryotic DNA and RNA viruses identified in blood, plasma, or serum samples of pediatric and adult SOT/HSCT recipients and the prevalence of their detection, with a particular focus on recently identified viruses and those for which their potential association with disease remains to be investigated, such as members of the Polyomaviridae, Anelloviridae, Flaviviridae, and Astroviridae families. Current knowledge of the clinical significance of these viral infections with associated viremia among transplant recipients is also discussed. To ensure a comprehensive description in these two populations, individuals described as healthy (mostly blood donors) are considered for comparative purposes. The list of viruses that should be on the clinicians' radar is certainly incomplete and will expand, but the challenge is to identify those of possible clinical significance.
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Zijlstra EE, van Hellemond JJ, Moes AD, de Boer C, Boeschoten SA, van Blijswijk CEM, van der Vuurst de Vries RM, Bailey PAB, Kampondeni S, van Lieshout L, Smits SL, Katchanov J, Mkandawire NM, Rothe C. Nontraumatic Myelopathy in Malawi: A Prospective Study in an Area with High HIV Prevalence. Am J Trop Med Hyg 2020; 102:451-457. [PMID: 31837130 DOI: 10.4269/ajtmh.19-0209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Nontraumatic myelopathy causes severe morbidity and is not uncommon in Africa. Clinically, patients often present with paraplegia, and extrinsic cord compression and transverse myelitis are most common causes. Data on exact pathogenesis are scanty because of limitations in diagnostic methods. In Queen Elizabeth Central Hospital, Blantyre, Malawi, we recorded consecutive patients presenting with nontraumatic paraplegia for maximally 6 months between January and July 2010 and from March to December 2011. The diagnostic workup included imaging and examining blood, stool, urine, sputum, and cerebrospinal fluid (CSF) samples for infection. After discharge, additional diagnostic tests, including screening for virus infections, borreliosis, syphilis, and schistosomiasis, were carried out in the Netherlands. The clinical diagnosis was, thus, revised in retrospect with a more accurate final differential diagnosis. Of 58 patients included, the mean age was 41 years (range, 12-83 years) and the median time between onset and presentation was 18 days (range, 0-121 days), and of 55 patients tested, 23 (42%) were HIV positive. Spinal tuberculosis (n = 24, 41%), tumors (n = 16, 28%), and transverse myelitis (n = 6, 10%) were most common; in six cases (10%), no diagnosis could be made. The additional tests yielded evidence for CSF infection with Schistosoma, Treponema pallidum, Epstein-Barr virus (EBV), HHV-6, HIV, as well as a novel cyclovirus. The diagnosis of the cause of paraplegia is complex and requires access to an magnetic resonance imaging (MRI) scan and other diagnostic (molecular) tools to demonstrate infection. The major challenge is to confirm the role of detected pathogens in the pathophysiology and to design an effective and affordable diagnostic approach.
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Affiliation(s)
| | - Jaap J van Hellemond
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Arthur D Moes
- Division of Nephrology, Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Christa de Boer
- Infectious Disease Control, Municipal Health Service Zuid-Holland Zuid, Dordrecht, The Netherlands
| | - Shelley A Boeschoten
- Erasmus University Medical Center - Sophia Children's Hospital, Rotterdam, The Netherlands
| | | | | | | | | | - Lisette van Lieshout
- Department of Parasitology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Saskia L Smits
- Viroclinics Biosciences BV, Rotterdam Science Tower, Rotterdam, The Netherlands
| | - Juri Katchanov
- Department of Hematology and Oncology, LMU University of Munich, Munich, Germany.,Department of Medicine, College of Medicine, Blantyre, Malawi
| | | | - Camilla Rothe
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Munich, Germany.,Department of Medicine, College of Medicine, Blantyre, Malawi
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18
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Caesar L, Cibulski SP, Canal CW, Blochtein B, Sattler A, Haag KL. The virome of an endangered stingless bee suffering from annual mortality in southern Brazil. J Gen Virol 2019; 100:1153-1164. [PMID: 31169486 DOI: 10.1099/jgv.0.001273] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Meliponiculture - the management of stingless bee colonies - is an expanding activity in Brazil with economic, social and environmental potential. However, unlike in apiculture, the pathogens that impact on meliponiculture remain largely unknown. In southern Brazil, every year at the end of the summer, managed colonies of the stingless bee Melipona quadrifasciata manifest a syndrome that eventually leads to collapse. Here we characterize the M. quadrifasciata virome using high-throughput sequencing, with the aim of identifying potentially pathogenic viruses, and test whether they are related to the syndrome outbreaks. Two paired viromes are explored, one from healthy bees and another from unhealthy ones. Each virome is built from metagenomes assembled from sequencing reads derived either from RNA or DNA. A total of 40 621 reads map to viral contigs of the unhealthy bees' metagenomes, whereas only 11 reads map to contigs identified as viruses of healthy bees. The viruses showing the largest copy numbers in the virome of unhealthy bees belong to the family Dicistroviridae - common pathogenic honeybee viruses - as well as Parvoviridae and Circoviridae, which have never been reported as being pathogenic in insects. Our analyses indicate that they represent seven novel viruses associated with stingless bees. PCR-based detection of these viruses in individual bees (healthy or unhealthy) from three different localities revealed a statistically significant association between viral infection and symptom manifestation in one meliponary. We conclude that although viral infections may contribute to colony collapses in the annual syndrome in some meliponaries, viruses spread opportunistically during the outbreak, perhaps due to colony weakness.
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Affiliation(s)
- Lílian Caesar
- 1 Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, CEP 91501-970, Porto Alegre, RS, Brazil
| | - Samuel Paulo Cibulski
- 2 Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9090, CEP 91540-000, Porto Alegre, RS, Brazil
| | - Cláudio Wageck Canal
- 2 Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9090, CEP 91540-000, Porto Alegre, RS, Brazil
| | - Betina Blochtein
- 3 Escola de Ciências, Pontifícia Universidade Católica do Rio Grande do Sul, Av. Ipiranga 6681, CEP 90619-900, Porto Alegre, RS, Brazil
| | - Aroni Sattler
- 4 Laboratório de Apicultura, Departamento de Fitossanidade, Faculdade de Agronomia, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 7712, CEP 91540-000, Porto Alegre, RS, Brazil
| | - Karen Luisa Haag
- 1 Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, CEP 91501-970, Porto Alegre, RS, Brazil
- 5 Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, CEP 91501-970, Porto Alegre, RS, Brazil
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19
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Ling Y, Zhang X, Qi G, Yang S, Jingjiao L, Shen Q, Wang X, Cui L, Hua X, Deng X, Delwart E, Zhang W. Viral metagenomics reveals significant viruses in the genital tract of apparently healthy dairy cows. Arch Virol 2019; 164:1059-67. [PMID: 30783771 DOI: 10.1007/s00705-019-04158-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Accepted: 01/03/2019] [Indexed: 01/03/2023]
Abstract
The virome in genital tract secretion samples collected from 80 dairy cattle in Shanghai, China, was characterized. Viruses detected included members of the families Papillomaviridae, Polyomaviridae, Hepeviridae, Parvoviridae, Astroviridae, Picornaviridae, and Picobirnaviridae. A member of a new species within the genus Dyoxipapillomavirus and six circular Rep-encoding single-stranded DNA (ssDNA) (CRESS-DNA) viral genomes were fully sequenced and phylogenetically analyzed. The prevalence of bovine polyomaviruses 1 and 2 was measured by PCR to be 10% (8/80) and 6.25% (5/80), respectively. PCR screening also indicated that the novel papillomavirus ujs-21015 and bovine herpesvirus 6 were present in three and two out of the 80 samples, respectively.
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20
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Klaumann F, Correa-Fiz F, Franzo G, Sibila M, Núñez JI, Segalés J. Current Knowledge on Porcine circovirus 3 (PCV-3): A Novel Virus With a Yet Unknown Impact on the Swine Industry. Front Vet Sci 2018; 5:315. [PMID: 30631769 PMCID: PMC6315159 DOI: 10.3389/fvets.2018.00315] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 11/28/2018] [Indexed: 12/21/2022] Open
Abstract
Porcine circovirus 3 (PCV-3) is a recently described virus belonging to the family Circoviridae. It represents the third member of genus Circovirus able to infect swine, together with PCV-1, considered non-pathogenic, and PCV-2, one of the most economically relevant viruses for the swine worldwide industry. PCV-3 was originally found by metagenomics analyses in 2015 in tissues of pigs suffering from porcine dermatitis and nephropathy syndrome, reproductive failure, myocarditis and multisystemic inflammation. The lack of other common pathogens as potential infectious agents of these conditions prompted the suspicion that PCV-3 might etiologically be involved in disease occurrence. Subsequently, viral genome was detected in apparently healthy pigs, and retrospective studies indicated that PCV-3 was already present in pigs by early 1990s. In fact, current evidence suggests that PCV-3 is a rather widespread virus worldwide. Recently, the virus DNA has also been found in wild boar, expanding the scope of infection susceptibility among the Suidae family; also, the potential reservoir role of this species for the domestic pig has been proposed. Phylogenetic studies with available PCV-3 partial and complete sequences from around the world have revealed high nucleotide identity (>96%), although two main groups and several subclusters have been described as well. Moreover, it has been proposed the existence of a most common ancestor dated around 50 years ago. Taking into account the economic importance and the well-known effects of PCV-2 on the swine industry, a new member of the same family like PCV-3 should not be neglected. Studies on epidemiology, pathogenesis, immunity and diagnosis are guaranteed in the next few years. Therefore, the present review will update the current knowledge and future trends of research on PCV-3.
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Affiliation(s)
- Francini Klaumann
- CAPES Foundation, Ministry of Education of Brazil, Brasília, Brazil.,IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Florencia Correa-Fiz
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Giovanni Franzo
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, Padua, Italy
| | - Marina Sibila
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, Barcelona, Spain
| | - José I Núñez
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Joaquim Segalés
- UAB, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, Barcelona, Spain.,Departament de Sanitat i Anatomia Animals, Facultat de Veterinària, Universitat Autònoma de Barcelona, Barcelona, Spain
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21
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Zhao L, Rosario K, Breitbart M, Duffy S. Eukaryotic Circular Rep-Encoding Single-Stranded DNA (CRESS DNA) Viruses: Ubiquitous Viruses With Small Genomes and a Diverse Host Range. Adv Virus Res 2018; 103:71-133. [PMID: 30635078 DOI: 10.1016/bs.aivir.2018.10.001] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
While single-stranded DNA (ssDNA) was once thought to be a relatively rare genomic architecture for viruses, modern metagenomics sequencing has revealed circular ssDNA viruses in most environments and in association with diverse hosts. In particular, circular ssDNA viruses encoding a homologous replication-associated protein (Rep) have been identified in the majority of eukaryotic supergroups, generating interest in the ecological effects and evolutionary history of circular Rep-encoding ssDNA viruses (CRESS DNA) viruses. This review surveys the explosion of sequence diversity and expansion of eukaryotic CRESS DNA taxonomic groups over the last decade, highlights similarities between the well-studied geminiviruses and circoviruses with newly identified groups known only through their genome sequences, discusses the ecology and evolution of eukaryotic CRESS DNA viruses, and speculates on future research horizons.
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Affiliation(s)
- Lele Zhao
- Department of Ecology, Evolution and Natural Resources, Rutgers, the State University of New Jersey, New Brunswick, NJ, United States
| | - Karyna Rosario
- College of Marine Science, University of South Florida, Saint Petersburg, FL, United States
| | - Mya Breitbart
- College of Marine Science, University of South Florida, Saint Petersburg, FL, United States
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, Rutgers, the State University of New Jersey, New Brunswick, NJ, United States.
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22
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Sauvage V, Gomez J, Barray A, Vandenbogaert M, Boizeau L, Tagny CT, Rakoto O, Bizimana P, Guitteye H, Ciré BB, Soumana H, Tchomba JBS, Caro V, Laperche S. High prevalence of cyclovirus Vietnam (CyCV-VN) in plasma samples from Madagascan healthy blood donors. Infection, Genetics and Evolution 2018; 66:9-12. [DOI: 10.1016/j.meegid.2018.09.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 09/03/2018] [Accepted: 09/06/2018] [Indexed: 10/28/2022]
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23
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Takano T, Yanai Y, Hiramatsu K, Doki T, Hohdatsu T. Novel single-stranded, circular DNA virus identified in cats in Japan. Arch Virol 2018; 163:3389-3393. [PMID: 30218220 PMCID: PMC7087140 DOI: 10.1007/s00705-018-4020-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 09/05/2018] [Indexed: 12/03/2022]
Abstract
We detected a novel feline stool-associated circular DNA virus (FeSCV) in fecal samples from cats with diarrhea using consensus primers matching those of circovirus and cyclovirus. FeSCV is a circular DNA virus containing a genome with a total length of 2,046 nt encoding 2 open reading frames. Phylogenetic analyses indicated that FeSCV is classified into a clade different from that of circovirus and cyclovirus. Since the FeSCVs detected in several cats in the same household had genetically similar genomes, these viruses are most likely derived from the same origin.
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Affiliation(s)
- Tomomi Takano
- Laboratory of Veterinary Infectious Disease, School of Veterinary Medicine, Kitasato University, Towada, Japan
| | - Yoshitomo Yanai
- Laboratory of Veterinary Infectious Disease, School of Veterinary Medicine, Kitasato University, Towada, Japan
| | - Kanae Hiramatsu
- Laboratory of Veterinary Infectious Disease, School of Veterinary Medicine, Kitasato University, Towada, Japan
| | - Tomoyoshi Doki
- Laboratory of Veterinary Infectious Disease, School of Veterinary Medicine, Kitasato University, Towada, Japan
| | - Tsutomu Hohdatsu
- Laboratory of Veterinary Infectious Disease, School of Veterinary Medicine, Kitasato University, Towada, Japan.
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24
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Dennis TPW, Flynn PJ, de Souza WM, Singer JB, Moreau CS, Wilson SJ, Gifford RJ. Insights into Circovirus Host Range from the Genomic Fossil Record. J Virol 2018; 92:e00145-18. [PMID: 29875243 PMCID: PMC6069186 DOI: 10.1128/jvi.00145-18] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [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: 03/12/2018] [Accepted: 05/24/2018] [Indexed: 11/30/2022] Open
Abstract
A diverse range of DNA sequences derived from circoviruses (family Circoviridae) has been identified in samples obtained from humans and domestic animals, often in association with pathological conditions. In the majority of cases, however, little is known about the natural biology of the viruses from which these sequences are derived. Endogenous circoviral elements (CVe) are DNA sequences derived from circoviruses that occur in animal genomes and provide a useful source of information about circovirus-host relationships. In this study, we screened genome assemblies of 675 animal species and identified numerous circovirus-related sequences, including the first examples of CVe derived from cycloviruses. We confirmed the presence of these CVe in the germ line of the elongate twig ant (Pseudomyrmex gracilis), thereby establishing that cycloviruses infect insects. We examined the evolutionary relationships between CVe and contemporary circoviruses, showing that CVe from ants and mites group relatively closely with cycloviruses in phylogenies. Furthermore, the relatively random interspersion of CVe from insect genomes with cyclovirus sequences recovered from vertebrate samples suggested that contamination might be an important consideration in studies reporting these viruses. Our study demonstrates how endogenous viral sequences can inform metagenomics-based virus discovery. In addition, it raises doubts about the role of cycloviruses as pathogens of humans and other vertebrates.IMPORTANCE Advances in DNA sequencing have dramatically increased the rate at which new viruses are being identified. However, the host species associations of most virus sequences identified in metagenomic samples are difficult to determine. Our analysis indicates that viruses proposed to infect vertebrates (in some cases being linked to human disease) may in fact be restricted to arthropod hosts. The detection of these sequences in vertebrate samples may reflect their widespread presence in the environment as viruses of parasitic arthropods.
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Affiliation(s)
- Tristan P W Dennis
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Peter J Flynn
- Field Museum of Natural History, Department of Science and Education, Chicago, Illinois, USA
- University of Chicago, Committee on Evolutionary Biology, Chicago, Illinois, USA
| | - William Marciel de Souza
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
- Virology Research Center, School of Medicine of Ribeirão Preto of University of São Paulo, Ribeirão Preto, Brazil
| | - Joshua B Singer
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Corrie S Moreau
- Field Museum of Natural History, Department of Science and Education, Chicago, Illinois, USA
| | - Sam J Wilson
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Robert J Gifford
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
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25
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Islam SU, Lin W, Wu R, Lin C, Islam W, Arif M, Du Z, Wu Z. Complete genome sequences of three novel cycloviruses identified in a dragonfly (Odonata: Anisoptera) from China. Arch Virol 2018; 163:2569-2573. [PMID: 29774431 DOI: 10.1007/s00705-018-3876-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Accepted: 05/02/2018] [Indexed: 11/27/2022]
Abstract
Three cycloviruses (genus Cyclovirus, family Circoviridae) were recovered from a dragonfly (Odonata: Anisoptera) captured in Fuzhou, China. The three cycloviruses, named dragonfly associated cyclovirus 9, 10 and 11 (DfCyV-9, -10, -11), respectively, show 56.1-79.6% genome-wide identity to known cycloviruses and 61.6-65.1% among themselves. Thus, according to the current species demarcation criteria, they represent three novel cycloviruses. Notably, DfCyV-10 has a predicted replication-associated protein (Rep) that is most similar to that of bat associated cyclovirus 2 (BatACyV-2), a cyclovirus discovered in China, with 79.4% amino acid sequence identity, but a putative capsid protein (Cp) most similar to that of BatACyV-10, a cyclovirus discovered in Brazil, with 71.7% amino acid sequence identity. These data are useful for understanding the diversity and evolution of cycloviruses, especially those found in insects.
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Affiliation(s)
- Saif Ul Islam
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fuzhou, 350002, China.,College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wenzhong Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fuzhou, 350002, China.,College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ran Wu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fuzhou, 350002, China.,College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chen Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fuzhou, 350002, China.,College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Waqar Islam
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fuzhou, 350002, China.,College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Muhammad Arif
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fuzhou, 350002, China.,College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhenguo Du
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fuzhou, 350002, China. .,College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Zujian Wu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fuzhou, 350002, China. .,College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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26
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Wang H, Li S, Mahmood A, Yang S, Wang X, Shen Q, Shan T, Deng X, Li J, Hua X, Cui L, Delwart E, Zhang W. Plasma virome of cattle from forest region revealed diverse small circular ssDNA viral genomes. Virol J 2018; 15:11. [PMID: 29334978 PMCID: PMC5769433 DOI: 10.1186/s12985-018-0923-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 01/04/2018] [Indexed: 11/12/2022] Open
Abstract
Background Free-range cattle are common in the Northeast China area, which have close contact with farmers and may carry virus threatening to cattle and farmers. Methods Using viral metagenomics we analyzed the virome in plasma samples collected from 80 cattle from the forested region of Northeast China. Results The virome of cattle plasma is composed of the viruses belonging to the families including Parvoviridae, Papillomaviridae, Picobirnaviridae, and divergent viral genomes showing sequence similarity to circular Rep-encoding single stranded (CRESS) DNA viruses. Five such CRESS-DNA genomes were full characterized, with Rep sequences related to circovirus and gemycircularvirus. Three bovine parvoviruses belonging to two different genera were also characterized. Conclusion The virome in plasma samples of cattle from the forested region of Northeast China was revealed, which further characterized the diversity of viruses in cattle plasma. Electronic supplementary material The online version of this article (10.1186/s12985-018-0923-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hao Wang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, 212013, China.,Department of Swine Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Shouxin Li
- College of Wildlife Resources, Northeast Forestry University, Harbin, Heilongjiang, 150040, China.,College of Life Science, Shenyang Normal University, Shenyang, Liaoning, 110034, China
| | - Asif Mahmood
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, 212013, China
| | - Shixing Yang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, 212013, China
| | - Xiaochun Wang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, 212013, China
| | - Quan Shen
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, 212013, China
| | - Tongling Shan
- Department of Swine Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China.
| | - Xutao Deng
- Blood Systems Research Institute, Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, 94118, USA
| | - Jingjiao Li
- School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, 200240, China
| | - Xiuguo Hua
- School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, 200240, China
| | - Li Cui
- School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, 200240, China
| | - Eric Delwart
- Blood Systems Research Institute, Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, 94118, USA
| | - Wen Zhang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, 212013, China.
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27
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Boddu RS, Divakar K. Metagenomic Insights into Environmental Microbiome and Their Application in Food/Pharmaceutical Industry. Microb Biotechnol 2018. [DOI: 10.1007/978-981-10-7140-9_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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28
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Abstract
Applying high-throughput sequencing to pathogen discovery is a relatively new field, the objective of which is to find disease-causing agents when little or no background information on disease is available. Key steps in the process are the generation of millions of sequence reads from an infected tissue sample, followed by assembly of these reads into longer, contiguous stretches of nucleotide sequences, and then identification of the contigs by matching them to known databases, such as those stored at GenBank or Ensembl. This technique, that is, de novo metagenomics, is particularly useful when the pathogen is viral and strong discriminatory power can be achieved. However, recently, we found that striking differences in results can be achieved when different assemblers were used. In this study, we test formally the impact of five popular assemblers (MIRA, VELVET, METAVELVET, SPADES, and OMEGA) on the detection of a novel virus and assembly of its whole genome in a data set for which we have confirmed the presence of the virus by empirical laboratory techniques, and compare the overall performance between assemblers. Our results show that if results from only one assembler are considered, biologically important reads can easily be overlooked. The impacts of these results on the field of pathogen discovery are considered.
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Affiliation(s)
| | - Jing Wang
- Institute of Environmental Science and Research at the National Centre for Biosecurity and Infectious Disease, Upper Hutt, New Zealand
| | - Richard J. Hall
- Animal Health Laboratory, Investigation and Diagnostic Centres and Response, Ministry for Primary Industries—Manatū Ahu Matua, Upper Hutt, New Zealand
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Cui L, Wu B, Zhu X, Guo X, Ge Y, Zhao K, Qi X, Shi Z, Zhu F, Sun L, Zhou M. Identification and genetic characterization of a novel circular single-stranded DNA virus in a human upper respiratory tract sample. Arch Virol 2017; 162:3305-3312. [PMID: 28707271 DOI: 10.1007/s00705-017-3481-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 06/26/2017] [Indexed: 12/22/2022]
Abstract
Metagenomic analysis through high-throughput sequencing is a tool for detecting both known and novel viruses. Using this technique, a novel circular single-stranded DNA (ssDNA) virus genome was discovered in respiratory secretions from a febrile traveler. The virus, named human respiratory-associated PSCV-5-like virus (HRAPLV), has a genome comprising 3,018 bases, with two major putative ORFs inversely encoding capsid (Cap) and replicase (Rep) protein and separated by two intergenic regions. One stem-loop structure was predicted in the larger intergenic region (LIR). The predicted amino acid sequences of the Cap and Rep proteins of HRAPLV showed highest identity to those of porcine stool-associated circular virus 5 isolate CP3 (PoSCV 5) (53.0% and 48.9%, respectively). The host tropism of the virus is unknown, and further study is warranted to determine whether this novel virus is associated with human disease.
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Affiliation(s)
- Lunbiao Cui
- Institute of Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Key Laboratories of Enteric Pathogenic Microbiology (Ministry of Health), Nanjing, China
| | - Binyao Wu
- Jiangsu International Travel Healthcare Center, Nanjing, China
| | - Xiaojuan Zhu
- Institute of Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Key Laboratories of Enteric Pathogenic Microbiology (Ministry of Health), Nanjing, China
| | - Xiling Guo
- Institute of Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Key Laboratories of Enteric Pathogenic Microbiology (Ministry of Health), Nanjing, China
| | - Yiyue Ge
- Institute of Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Key Laboratories of Enteric Pathogenic Microbiology (Ministry of Health), Nanjing, China
| | - Kangchen Zhao
- Institute of Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Key Laboratories of Enteric Pathogenic Microbiology (Ministry of Health), Nanjing, China
| | - Xian Qi
- Institute of Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Key Laboratories of Enteric Pathogenic Microbiology (Ministry of Health), Nanjing, China
| | - Zhiyang Shi
- Institute of Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Key Laboratories of Enteric Pathogenic Microbiology (Ministry of Health), Nanjing, China
| | - Fengcai Zhu
- Institute of Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Key Laboratories of Enteric Pathogenic Microbiology (Ministry of Health), Nanjing, China
| | - Lixin Sun
- Jiangsu International Travel Healthcare Center, Nanjing, China.
| | - Minghao Zhou
- Institute of Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Key Laboratories of Enteric Pathogenic Microbiology (Ministry of Health), Nanjing, China.
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Abstract
Viruses rapidly evolve and can emerge in unpredictable ways. Transmission pathways by which foodborne viruses may enter human populations and evolutionary mechanisms by which viruses can become virulent are discussed in this chapter. A majority of viruses emerge from zoonotic animal reservoirs, often by adapting and infecting intermediate hosts, such as domestic animals and livestock. Viruses that are known foodborne threats include hepatitis E virus, tick-borne encephalitis virus, enteroviruses, adenovirus, and astroviruses, among others. Viruses may potentially evolve and emerge as a result of modern agricultural practices which can concentrate livestock and bring them into contact with wild animals. Examples of viruses that have emerged in this manner are influenza, coronaviruses such as severe acute respiratory syndrome and Middle East respiratory syndrome, and the Nipah virus. The role of bats, bush meat, rodents, pigs, cattle, and poultry as reservoirs from which infectious pathogenic viruses emerge are discussed.
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31
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Kemenesi G, Kurucz K, Zana B, Tu VT, Görföl T, Estók P, Földes F, Sztancsik K, Urbán P, Fehér E, Jakab F. Highly divergent cyclo-like virus in a great roundleaf bat (Hipposideros armiger) in Vietnam. Arch Virol 2017; 162:2403-2407. [PMID: 28447216 DOI: 10.1007/s00705-017-3377-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 04/07/2017] [Indexed: 11/27/2022]
Abstract
Members of the viral family Circoviridae are increasingly recognized worldwide. Bats seem to be natural reservoirs or dietary-related dispensers of these viruses. Here, we report a distantly related member of the genus Cyclovirus detected in the faeces of a great roundleaf bat (Hipposideros armiger). Interestingly, the novel virus lacks a Circoviridae-specific stem-loop structure, although a Geminiviridae-like nonamer sequence was detected in the large intergenic region. Based on these differences and its phylogenetic position, we propose that our new virus represents a distant and highly divergent member of the genus Cyclovirus. However it is lacking several characteristics of members of the genus, which raises a challenge in its taxonomic classification.
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Affiliation(s)
- Gábor Kemenesi
- Virological Research Group, Szentágothai Research Centre, University of Pécs, Ifjúság út 20, 7624, Pécs, Hungary.,Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Kornélia Kurucz
- Virological Research Group, Szentágothai Research Centre, University of Pécs, Ifjúság út 20, 7624, Pécs, Hungary
| | - Brigitta Zana
- Virological Research Group, Szentágothai Research Centre, University of Pécs, Ifjúság út 20, 7624, Pécs, Hungary.,Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Vuong Tan Tu
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Tamás Görföl
- Department of Zoology, Hungarian Natural History Museum, Budapest, Hungary
| | - Péter Estók
- Department of Zoology, Eszterházy Károly University, Eger, Hungary
| | - Fanni Földes
- Virological Research Group, Szentágothai Research Centre, University of Pécs, Ifjúság út 20, 7624, Pécs, Hungary.,Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Katalin Sztancsik
- Virological Research Group, Szentágothai Research Centre, University of Pécs, Ifjúság út 20, 7624, Pécs, Hungary.,Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Péter Urbán
- Microbial Biotechnology Research Group, Szentágothai Reasearch Centre, University of Pécs, Pécs, Hungary.,Department of General and Environmental Microbiology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Enikő Fehér
- Institute for Veterinary Medical Research Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Ferenc Jakab
- Virological Research Group, Szentágothai Research Centre, University of Pécs, Ifjúság út 20, 7624, Pécs, Hungary. .,Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary.
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Han HJ, Wen HL, Zhao L, Liu JW, Luo LM, Zhou CM, Qin XR, Zhu YL, Liu MM, Qi R, Li WQ, Yu H, Yu XJ. Novel coronaviruses, astroviruses, adenoviruses and circoviruses in insectivorous bats from northern China. Zoonoses Public Health 2017; 64:636-646. [PMID: 28371451 PMCID: PMC7165899 DOI: 10.1111/zph.12358] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Indexed: 11/29/2022]
Abstract
Bats are considered as the reservoirs of several emerging infectious disease, and novel viruses are continually found in bats all around the world. Studies conducted in southern China found that bats carried a variety of viruses. However, few studies have been conducted on bats in northern China, which harbours a diversity of endemic insectivorous bats. It is important to understand the prevalence and diversity of viruses circulating in bats in northern China. In this study, a total of 145 insectivorous bats representing six species were collected from northern China and screened with degenerate primers for viruses belonging to six families, including coronaviruses, astroviruses, hantaviruses, paramyxoviruses, adenoviruses and circoviruses. Our study found that four of the viruses screened for were positive and the overall detection rates for astroviruses, coronaviruses, adenoviruses and circoviruses in bats were 21.4%, 15.9%, 20% and 37.2%, respectively. In addition, we found that bats in northern China harboured a diversity of novel viruses. Common Serotine (Eptesicus serotinu), Fringed long‐footed Myotis (Myotis fimriatus) and Peking Myotis (Myotis pequinius) were investigated in China for the first time. Our study provided new information on the ecology and phylogeny of bat‐borne viruses.
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Affiliation(s)
- H-J Han
- School of Public Health, Shandong University, Jinan, Shandong, China
| | - H-L Wen
- School of Public Health, Shandong University, Jinan, Shandong, China
| | - L Zhao
- School of Public Health, Shandong University, Jinan, Shandong, China
| | - J-W Liu
- School of Public Health, Shandong University, Jinan, Shandong, China
| | - L-M Luo
- Shandong Center for Disease Control and Prevention, Jinan, Shandong, China
| | - C-M Zhou
- School of Public Health, Shandong University, Jinan, Shandong, China
| | - X-R Qin
- School of Public Health, Shandong University, Jinan, Shandong, China
| | - Y-L Zhu
- School of Public Health, Shandong University, Jinan, Shandong, China
| | - M-M Liu
- School of Public Health, Shandong University, Jinan, Shandong, China
| | - R Qi
- School of Public Health, Shandong University, Jinan, Shandong, China
| | - W-Q Li
- School of Public Health, Shandong University, Jinan, Shandong, China
| | - H Yu
- Schools of Medicine, Fudan University, Shanghai, China
| | - X-J Yu
- Wuhan University School of Health Sciences, Wuhan, Hubei, China.,Departments of Pathology and Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
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33
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Rosario K, Breitbart M, Harrach B, Segalés J, Delwart E, Biagini P, Varsani A. Revisiting the taxonomy of the family Circoviridae: establishment of the genus Cyclovirus and removal of the genus Gyrovirus. Arch Virol 2017; 162:1447-1463. [PMID: 28155197 DOI: 10.1007/s00705-017-3247-y] [Citation(s) in RCA: 240] [Impact Index Per Article: 34.3] [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: 12/09/2016] [Accepted: 12/29/2016] [Indexed: 12/19/2022]
Abstract
The family Circoviridae contains viruses with covalently closed, circular, single-stranded DNA (ssDNA) genomes, including the smallest known autonomously replicating, capsid-encoding animal pathogens. Members of this family are known to cause fatal diseases in birds and pigs and have been historically classified in one of two genera: Circovirus, which contains avian and porcine pathogens, and Gyrovirus, which includes a single species (Chicken anemia virus). However, over the course of the past six years, viral metagenomic approaches as well as degenerate PCR detection in unconventional hosts and environmental samples have elucidated a broader host range, including fish, a diversity of mammals, and invertebrates, for members of the family Circoviridae. Notably, these methods have uncovered a distinct group of viruses that are closely related to members of the genus Circovirus and comprise a new genus, Cyclovirus. The discovery of new viruses and a re-evaluation of genomic features that characterize members of the Circoviridae prompted a revision of the classification criteria used for this family of animal viruses. Here we provide details on an updated Circoviridae taxonomy ratified by the International Committee on the Taxonomy of Viruses in 2016, which establishes the genus Cyclovirus and reassigns the genus Gyrovirus to the family Anelloviridae, a separate lineage of animal viruses that also contains circular ssDNA genomes. In addition, we provide a new species demarcation threshold of 80% genome-wide pairwise identity for members of the family Circoviridae, based on pairwise identity distribution analysis, and list guidelines to distinguish between members of this family and other eukaryotic viruses with circular, ssDNA genomes.
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Affiliation(s)
- Karyna Rosario
- College of Marine Science, University of South Florida, Saint Petersburg, FL, 33701, USA.
| | - Mya Breitbart
- College of Marine Science, University of South Florida, Saint Petersburg, FL, 33701, USA
| | - Balázs Harrach
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Joaquim Segalés
- Departament de Sanitat i Anatomia Animals, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
- UAB, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, California, USA
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Philippe Biagini
- Viral Emergence and Co-evolution Unit, ADES, UMR 7268, Aix-Marseille University, CNRS, EFS, 27 Bd. Jean Moulin, 13005, Marseille, France
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life sciences, Arizona State University, Tempe, AZ, 85287-5001, USA.
- Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory, Cape Town, South Africa.
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35
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Macera L, Focosi D, Vatteroni ML, Manzin A, Antonelli G, Pistello M, Maggi F. Cyclovirus Vietnam DNA in immunodeficient patients. J Clin Virol 2016; 81:12-5. [PMID: 27270127 DOI: 10.1016/j.jcv.2016.05.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Revised: 05/18/2016] [Accepted: 05/19/2016] [Indexed: 10/21/2022]
Abstract
BACKGROUND Cyclovirus Vietnam (CyCV-VN) is a CyCV detected in 2013 from cerebrospinal fluid (CSF) samples of patients with neurological disorders. Information on prevalence, pathogenesis and disease association of CyCV-VN is still very patchy. OBJECTIVES AND STUDY DESIGN In this study, we have used a PCR assay targeting the Rep gene to investigate the prevalence of CyCV-VN infection in blood and CSF samples of 346 Italian subjects. RESULTS Overall, 7% of blood samples were positive for CyCV-VN while the virus was not detected in any of the CSF samples. The prevalence of CyCV-VN was relatively high in HIV positive patients (21%), modest in patients with HBV or HCV infection (6%), and low in transplant recipient patients (2%). Positive patients showed low levels of CyCV-VN viremia. The virus was not detected in serum samples from healthy individuals. Longitudinal analysis of serum samples obtained from selected patients showed a stable or transient presence of circulating CyCV-VN. CONCLUSIONS The present study is the first to demonstrate CyCV-VN DNA circulation in Italy and to cast light on some biological aspects of this novel virus of men.
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Affiliation(s)
- Lisa Macera
- Virology Unit, Pisa University Hospital, Pisa, Italy; Department of Biomedical Sciences, Microbiology and Virology Unit, University of Cagliari, Italy; Retrovirus Center and Virology Section, Department of Translational Research, University of Pisa, Italy
| | - Daniele Focosi
- Division of Transfusion Medicine and Transplant Biology, Pisa University Hospital, Pisa, Italy
| | | | - Aldo Manzin
- Department of Biomedical Sciences, Microbiology and Virology Unit, University of Cagliari, Italy
| | - Guido Antonelli
- Pasteur Institute-Cenci Bolognetti Foundation, Department of Molecular Medicine, Laboratory of Virology, Sapienza University of Rome, Italy
| | - Mauro Pistello
- Virology Unit, Pisa University Hospital, Pisa, Italy; Retrovirus Center and Virology Section, Department of Translational Research, University of Pisa, Italy
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Abstract
Studies of marine viromes (viral metagenomes) have revealed that DNA viruses are highly diverse and exhibit biogeographic patterns. However, little is known about the diversity of RNA viruses, which are mostly composed of eukaryotic viruses, and their biogeographic patterns in the oceans. A growth in global commerce and maritime traffic may accelerate spread of diverse and non-cosmopolitan DNA viruses and potentially RNA viruses from one part of the world to another. Here, we demonstrated through metagenomic analyses that failure to comply with mid-ocean ballast water exchange regulation could result in movement of viromes including both DNA viruses and RNA viruses (including potential viral pathogens) unique to geographic and environmental niches. Furthermore, our results showed that virus richness (known and unknown viruses) in ballast water is associated with distance between ballast water exchange location and its nearest shoreline as well as length of water storage time in ballast tanks (voyage duration). However, richness of only known viruses is governed by local environmental conditions and different viral groups have different responses to environmental variation. Overall, these results identified ballast water as a factor contributing to ocean virome transport and potentially increased exposure of the aquatic bioshpere to viral invasion.
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Affiliation(s)
- Yiseul Kim
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
- * E-mail:
| | - Tiong Gim Aw
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, Michigan, United States of America
| | - Joan B. Rose
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, Michigan, United States of America
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Bexton S, Wiersma LC, Getu S, van Run PR, Verjans GMGM, Schipper D, Schapendonk CME, Bodewes R, Oldroyd L, Haagmans BL, Koopmans MMP, Smits SL. Detection of Circovirus in Foxes with Meningoencephalitis, United Kingdom, 2009-2013. Emerg Infect Dis 2016; 21:1205-8. [PMID: 26079061 PMCID: PMC4480402 DOI: 10.3201/eid2107.150228] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [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: 12/17/2022] Open
Abstract
A fox circovirus was identified in serum samples from foxes with unexplained neurologic signs by using viral metagenomics. Fox circovirus nucleic acid was localized in histological lesions of the cerebrum by in situ hybridization. Viruses from the family Circoviridae may have neurologic tropism more commonly than previously anticipated.
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Male MF, Kraberger S, Stainton D, Kami V, Varsani A. Cycloviruses, gemycircularviruses and other novel replication-associated protein encoding circular viruses in Pacific flying fox (Pteropus tonganus) faeces. Infect Genet Evol 2016; 39:279-292. [PMID: 26873064 DOI: 10.1016/j.meegid.2016.02.009] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 01/27/2016] [Accepted: 02/06/2016] [Indexed: 12/13/2022]
Abstract
Viral metagenomic studies have demonstrated that animal faeces can be a good sampling source for exploring viral diversity associated with the host and its environment. As part of an continuing effort to identify novel circular replication-associated protein encoding single-stranded (CRESS) DNA viruses circulating in the Tongan archipelago, coupled with the fact that bats are a reservoir species of a large number of viruses, we used a metagenomic approach to investigate the CRESS DNA virus diversity in Pacific flying fox (Pteropus tonganus) faeces. Faecal matter from four roosting sites located in Ha'avakatolo, Kolovai, Ha'ateiho and Lapaha on Tongatapu Island was collected in April 2014 and January 2015. From these samples we identified five novel cycloviruses representing three putative species, 25 gemycircularviruses representing at least 14 putative species, 17 other CRESS DNA viruses (15 putative species), two circular DNA molecules and a putative novel multi-component virus for which we have identified three cognate molecules. This study demonstrates that there exists a large diversity of CRESS DNA viruses in Pacific flying fox faeces.
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Affiliation(s)
- Maketalena F Male
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Simona Kraberger
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Daisy Stainton
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | | | - Arvind Varsani
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand; Structural Biology Research Unit, Division of Medical Biochemistry, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory 7700, South Africa; Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, USA.
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Sydler T, Brägger S, Handke M, Hartnack S, Lewis FI, Sidler X, Brugnera E. Latent porcine circovirus type 2-infected domestic pigs: A potential infection model for the effective development of vaccines against latent or chronic virus induced diseases. Vaccine 2016; 34:1047-53. [PMID: 26795369 DOI: 10.1016/j.vaccine.2016.01.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 12/22/2015] [Accepted: 01/05/2016] [Indexed: 09/30/2022]
Abstract
Until recently, knowledge of the pathogenicity of Circoviridae and Anelloviridae family members was limited. Our previous discoveries provided clues toward resolving this issue based on studies of the latent nature of porcine circovirus type 2 (PCV2) genotype group members. We developed a conventional pig infection model that indicated that weaners already harbored latent PCV2 infection in the thymus, which enabled the viruses to specifically modulate the maturation of T-helper cells. This finding raised the possibility that the thymi of normal fetuses were already infected with PCV2. The present findings further substantiate our hypothesis that PCV2 masquerades as the host by infecting fetuses before they acquire immune-competence. We provide the first demonstration that all domestic pig fetuses preferentially harbor latent PCV2-infected cells in their thymi. These PCV2-infected cells are different from thymocytes and are located in the medulla of the fetal thymus. These latent PCV2-infected cells in fetuses are found at the same location and share characteristics with the infected cells observed in adolescent pigs. Moreover, fetuses also harbor these infected cells in other lymph system organs. We provide the first demonstration that the fetal thymus virus pools are minimally affected by sow vaccination, highlighting the immune-privileged character of this organ. Furthermore, we found a striking reduction in virus-infected cells in the fetal spleen and an increase in PCV2-infected cells in the fetal intestine of anti-PCV2-vaccinated mothers. These data indicate that specific immune response interactions occur between mothers and their progeny that are not dependent on the humoral immunity of the mother and cannot be attributed to the rudimentary humoral responses of the fetuses because these pig fetuses do not have any PCV2-specific antibodies. These shifts in our understanding of the PCV2-infected cell pool will lead to different avenues in the search for effective vaccination strategies against latent and chronic pathogens.
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Affiliation(s)
- Titus Sydler
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Stefanie Brägger
- Division of Swine Medicine of the Department for Farm Animals, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Martin Handke
- Division of Swine Medicine of the Department for Farm Animals, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Sonja Hartnack
- Division of Veterinary Epidemiology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Fraser I Lewis
- Division of Veterinary Epidemiology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Xaver Sidler
- Division of Swine Medicine of the Department for Farm Animals, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Enrico Brugnera
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland; Division of Swine Medicine of the Department for Farm Animals, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland.
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40
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Abstract
Background Recently, a diverse group of viruses with circular, replication initiator protein(Rep) encoding, single stranded DNA (CRESS-DNA) genomes, were discovered from wide range of eukaryotic organisms ranging from mammals to fungi. Gemycircularvirus belongs to a distinct group of CRESS-DNA genomes and is classified under the genus name of Gemycircularvirus. Findings Here, a novel gemycircularvirus named GeTz1 from cerebrospinal fluid sample of a child with unexplainable encephalitis was characterized. The novel gemycircularvirus encodes two major proteins, including a capsid protein (Cap) and a replication-associated protein (Rep). Phylogenetic analysis based on the amino acid sequence of Rep indicated that GeTz1 clusters with one gemycircularvirus discovered from bird (KF371633), sharing 46.6 % amino acid sequence identity with each other. Conclusion A novel gemycircularvirus was discovered from cerebrospinal fluid sample of a child with unexplainable encephalitis. Further studies, such as testing human sera for specific antibodies, should be performed to investigate whether gemycircularvirus infects human and is associated with encephalitis.
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Affiliation(s)
- Chenglin Zhou
- Department of Laboratory Medicine, Jiangsu Taizhou People's Hospital, Taizhou, Jiangsu, 225300, China.
| | - Shibing Zhang
- Department of Laboratory Medicine, the First People's Hospital of Suqian, Suqian, Jiangsu, 223800, China.
| | - Qin Gong
- Jiangsu Taizhou People's Hospital, Taizhou, Jiangsu, 225300, China.
| | - Aimin Hao
- Department of Laboratory Medicine, the Second People's Hospital of Wuxi, Wuxi, Jiangsu, 214002, China.
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41
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Rosario K, Schenck RO, Harbeitner RC, Lawler SN, Breitbart M. Novel circular single-stranded DNA viruses identified in marine invertebrates reveal high sequence diversity and consistent predicted intrinsic disorder patterns within putative structural proteins. Front Microbiol 2015. [PMID: 26217327 PMCID: PMC4498126 DOI: 10.3389/fmicb.2015.00696] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Viral metagenomics has recently revealed the ubiquitous and diverse nature of single-stranded DNA (ssDNA) viruses that encode a conserved replication initiator protein (Rep) in the marine environment. Although eukaryotic circular Rep-encoding ssDNA (CRESS-DNA) viruses were originally thought to only infect plants and vertebrates, recent studies have identified these viruses in a number of invertebrates. To further explore CRESS-DNA viruses in the marine environment, this study surveyed CRESS-DNA viruses in various marine invertebrate species. A total of 27 novel CRESS-DNA genomes, with Reps that share less than 60.1% identity with previously reported viruses, were recovered from 21 invertebrate species, mainly crustaceans. Phylogenetic analysis based on the Rep revealed a novel clade of CRESS-DNA viruses that included approximately one third of the marine invertebrate associated viruses identified here and whose members may represent a novel family. Investigation of putative capsid proteins (Cap) encoded within the eukaryotic CRESS-DNA viral genomes from this study and those in GenBank demonstrated conserved patterns of predicted intrinsically disordered regions (IDRs), which can be used to complement similarity-based searches to identify divergent structural proteins within novel genomes. Overall, this study expands our knowledge of CRESS-DNA viruses associated with invertebrates and explores a new tool to evaluate divergent structural proteins encoded by these viruses.
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Affiliation(s)
- Karyna Rosario
- College of Marine Science, University of South Florida St. Petersburg, FL, USA
| | - Ryan O Schenck
- College of Marine Science, University of South Florida St. Petersburg, FL, USA
| | - Rachel C Harbeitner
- College of Marine Science, University of South Florida St. Petersburg, FL, USA
| | - Stephanie N Lawler
- College of Marine Science, University of South Florida St. Petersburg, FL, USA
| | - Mya Breitbart
- College of Marine Science, University of South Florida St. Petersburg, FL, USA
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Abstract
A long-established epidemic of enteritis, caused by an unidentified pathogen distinct from parvovirus, has now been recognized in mink. In 2013, we identified a novel circovirus by degenerate PCR and fully sequenced its genome. This virus differs substantially from currently known members of the genus Circovirus and represents a new species.
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Li L, Giannitti F, Low J, Keyes C, Ullmann LS, Deng X, Aleman M, Pesavento PA, Pusterla N, Delwart E. Exploring the virome of diseased horses. J Gen Virol 2015; 96:2721-2733. [PMID: 26044792 DOI: 10.1099/vir.0.000199] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Metagenomics was used to characterize viral genomes in clinical specimens of horses with various organ-specific diseases of unknown aetiology. A novel parvovirus as well as a previously described hepacivirus closely related to human hepatitis C virus and equid herpesvirus 2 were identified in the cerebrospinal fluid of horses with neurological signs. Four co-infecting picobirnaviruses, including an unusual genome with fused RNA segments, and a divergent anellovirus were found in the plasma of two febrile horses. A novel cyclovirus genome was characterized from the nasal secretion of another febrile animal. Lastly, a small circular DNA genome with a Rep gene, from a virus we called kirkovirus, was identified in the liver and spleen of a horse with fatal idiopathic hepatopathy. This study expands the number of viruses found in horses, and characterizes their genomes to assist future epidemiological studies of their transmission and potential association with various equine diseases.
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Affiliation(s)
- Linlin Li
- Blood Systems Research Institute, San Francisco, CA, USA.,Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Federico Giannitti
- California Animal Health and Food Safety Laboratory, School of Veterinary Medicine, University of California, Davis, CA, USA.,Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, USA.,Instituto Nacional de Investigación Agropecuaria, La Estanzuela, Colonia, Uruguay
| | - Jason Low
- Department of Bioengineering, University of California, Los Angeles, CA, USA
| | - Casey Keyes
- Department of Biology, University of San Francisco, San Francisco, CA, USA
| | - Leila S Ullmann
- Department of Microbiology and Immunology, UNESP Sao Paulo State University, Sao Paulo, Brazil
| | - Xutao Deng
- Blood Systems Research Institute, San Francisco, CA, USA.,Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Monica Aleman
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Patricia A Pesavento
- Department of Pathology, Microbiology and Immunology, University of California, Davis, CA, USA
| | - Nicola Pusterla
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, CA, USA.,Department of Laboratory Medicine, University of California, San Francisco, CA, USA
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44
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Chan MCW, Kwok SWY, Chan PKS. False-positive PCR detection of cyclovirus Malawi strain VS5700009 in human cerebrospinal fluid. J Clin Virol 2015; 68:76-8. [PMID: 26071341 DOI: 10.1016/j.jcv.2015.05.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 05/07/2015] [Accepted: 05/08/2015] [Indexed: 11/29/2022]
Abstract
BACKGROUND Cyclovirus (CyCV) Malawi strain VS5700009 has recently been discovered and reported in clinical cerebrospinal fluid (CSF) samples. Further epidemiological and case-control studies are warranted. The availability of a highly sensitive and specific detection assay for this new virus is thus crucial. OBJECTIVES To evaluate the performance of the first and the only available PCR assay for CyCV-VS5700009. STUDY DESIGN A total of 100 CSF samples collected during January-December 2010 were selected for PCR detection of CyCV-VS5700009. Positive PCR amplicons were subjected to sequencing confirmation and BLAST analysis. RESULTS Initial PCR screening for CyCV-VS5700009 identified one sample, showing a PCR band of expected size (380 bp). Sequencing and BLAST analysis, however, indicated that the band was 364 bp in length and showed >99% nucleotide homology to a human gene known as nuclear receptor coactivator 6 (NCOA6). Pairwise sequence alignment confirmed that both the forward and reverse PCR primers used had significant homology (>70%) to NCOA6. None of the CSF samples tested were positive for CyCV-VS5700009. CONCLUSIONS The original PCR assay for CyCV-VS5700009 detection may have potential cross-reactivity with contaminating human genomic DNA. The assay may be of little diagnostic use on clinical specimens that are rich in host DNA such as biopsy tissues.
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Affiliation(s)
- Martin C W Chan
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Serena W Y Kwok
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Paul K S Chan
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China.
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45
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Phan TG, Mori D, Deng X, Rajindrajith S, Ranawaka U, Fan Ng TF, Bucardo-Rivera F, Orlandi P, Ahmed K, Delwart E. Small circular single stranded DNA viral genomes in unexplained cases of human encephalitis, diarrhea, and in untreated sewage. Virology 2015; 482:98-104. [PMID: 25839169 DOI: 10.1016/j.virol.2015.03.011] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 02/16/2015] [Accepted: 03/03/2015] [Indexed: 01/02/2023]
Abstract
Viruses with small circular ssDNA genomes encoding a replication initiator protein can infect a wide range of eukaryotic organisms ranging from mammals to fungi. The genomes of two such viruses, a cyclovirus (CyCV-SL) and gemycircularvirus (GemyCV-SL) were detected by deep sequencing of the cerebrospinal fluids of Sri Lankan patients with unexplained encephalitis. One and three out of 201 CSF samples (1.5%) from unexplained encephalitis patients tested by PCR were CyCV-SL and GemyCV-SL DNA positive respectively. Nucleotide similarity searches of pre-existing metagenomics datasets revealed closely related genomes in feces from unexplained cases of diarrhea from Nicaragua and Brazil and in untreated sewage from Nepal. Whether the tropism of the cyclovirus and gemycircularvirus reported here include humans or other cellular sources in or on the human body remains to be determined.
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Affiliation(s)
- Tung Gia Phan
- Blood Systems Research Institute, San Francisco, CA 94118, USA; Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA 94118, USA
| | - Daisuke Mori
- Department of Microbiology, Faculty of Medicine, Oita University, Yufu 879-5593, Japan
| | - Xutao Deng
- Blood Systems Research Institute, San Francisco, CA 94118, USA
| | - Shaman Rajindrajith
- Department of Pediatrics, Faculty of Medicine, University of Kelaniya, Ragama, Sri Lanka
| | - Udaya Ranawaka
- Department of Medicine, Faculty of Medicine, University of Kelaniya, Ragama, Sri Lanka
| | - Terry Fei Fan Ng
- Blood Systems Research Institute, San Francisco, CA 94118, USA; Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA 94118, USA
| | | | | | - Kamruddin Ahmed
- Department of Microbiology, Faculty of Medicine, Oita University, Yufu 879-5593, Japan; Research Promotion Institute, Oita University, Yufu 879-5593, Oita, Japan; Department of Pathobiology and Medical Diagnostics, Faculty of Medicine, Universiti Malaysia Sabah, 88400 Kota Kinabalu, Sabah, Malaysia
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, CA 94118, USA; Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA 94118, USA.
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46
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Klausmann S, Sydler T, Summerfield A, Lewis FI, Weilenmann R, Sidler X, Brugnera E. T-cell reprogramming through targeted CD4-coreceptor and T-cell receptor expression on maturing thymocytes by latent Circoviridae family member porcine circovirus type 2 cell infections in the thymus. Emerg Microbes Infect 2015; 4:e15. [PMID: 26038767 DOI: 10.1038/emi.2015.15] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 10/20/2014] [Accepted: 01/31/2015] [Indexed: 02/07/2023]
Abstract
Although porcine circovirus type 2 (PCV2)-associated diseases have been evaluated for known immune evasion strategies, the pathogenicity of these viruses remained concealed for decades. Surprisingly, the same viruses that cause panzootics in livestock are widespread in young, unaffected animals. Recently, evidence has emerged that circovirus-like viruses are also linked to complex diseases in humans, including children. We detected PCV2 genome-carrying cells in fetal pig thymi. To elucidate virus pathogenicity, we developed a new pig infection model by in vivo transfection of recombinant PCV2 and the immunosuppressant cofactor cyclosporine A. Using flow cytometry, immunofluorescence and fluorescence in situ hybridization, we found evidence that PCV2 dictates positive and negative selection of maturing T cells in the thymus. We show for the first time that PCV2-infected cells reside at the corticomedullary junction of the thymus. In diseased animals, we found polyclonal deletion of single positive cells (SPs) that may result from a loss of major histocompatibility complex class-II expression at the corticomedullary junction. The percentage of PCV2 antigen-presenting cells correlated with the degree of viremia and, in turn, the severity of the defect in thymocyte maturation. Moreover, the reversed T-cell receptor/CD4-coreceptor expression dichotomy on thymocytes at the CD4+CD8interm and CD4SP cell stage is viremia-dependent, resulting in a specific hypo-responsiveness of T-helper cells. We compare our results with the only other better-studied member of Circoviridae, chicken anemia virus. Our data show that PCV2 infection leads to thymocyte selection dysregulation, adding a valuable dimension to our understanding of virus pathogenicity.
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47
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Dayaram A, Potter KA, Pailes R, Marinov M, Rosenstein DD, Varsani A. Identification of diverse circular single-stranded DNA viruses in adult dragonflies and damselflies (Insecta: Odonata) of Arizona and Oklahoma, USA. Infection, Genetics and Evolution 2015; 30:278-287. [DOI: 10.1016/j.meegid.2014.12.037] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 12/17/2014] [Accepted: 12/31/2014] [Indexed: 12/16/2022]
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48
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Marton S, Ihász K, Lengyel G, Farkas S, Dán Á, Paulus P, Bányai K, Fehér E. Ubiquiter circovirus sequences raise challenges in laboratory diagnosis: the case of honey bee and bee mite, reptiles, and free living amoebae. Acta Microbiol Immunol Hung 2015; 62:57-73. [PMID: 25823454 DOI: 10.1556/amicr.62.2015.1.5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Circoviruses of pigs and birds are established pathogens, however, the exact role of other, recently described circoviruses and circovirus-like viruses remains to be elucidated. The aim of this study was the detection of circoviruses in neglected host species, including honey bees, exotic reptiles and free-living amoebae by widely used broad-spectrum polymerase chain reaction (PCR) assays specific for the replication initiation protein coding gene of these viruses. The majority of sequences obtained from honey bees were highly similar to canine and porcine circoviruses, or, were distantly related to dragonfly cycloviruses. Other rep sequences detected in some honey bees, reptiles and amoebae showed similarities to various rep sequences deposited in the GenBank. Back-to-back PCR primers designed for the amplification of whole viral genomes failed to work that suggested the existence of integrated rep-like elements in many samples. Rolling circle amplification and exonuclease treatment confirmed the absence of small circular DNA genomes in the specimens analysed. In case of honey bees Varroa mite DNA contamination might be a source of the identified endogenous rep-like elements. The reptile and amoebae rep-like sequences were nearly identical with each other and with sequences detected in chimpanzee feces raising the possibility that detection of novel or unusual rep-like elements in some host species might originate from the microbial community of the host. Our results indicate that attention is needed when broad-spectrum rep gene specific polymerase chain reaction is chosen for laboratory diagnosis of circovirus infections.
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Affiliation(s)
- Szilvia Marton
- 1 Hungarian Academy of Sciences Institute for Veterinary Medical Research, Centre for Agricultural Research Budapest Hungary
| | - Katalin Ihász
- 1 Hungarian Academy of Sciences Institute for Veterinary Medical Research, Centre for Agricultural Research Budapest Hungary
| | - György Lengyel
- 2 Hungarian Defence Forces Military Medical Centre Budapest Hungary
| | - Szilvia Farkas
- 1 Hungarian Academy of Sciences Institute for Veterinary Medical Research, Centre for Agricultural Research Budapest Hungary
| | - Ádám Dán
- 3 National Food Chain Safety Office Veterinary Diagnostic Directorate Budapest Hungary
| | - Petra Paulus
- 3 National Food Chain Safety Office Veterinary Diagnostic Directorate Budapest Hungary
| | - Krisztián Bányai
- 1 Hungarian Academy of Sciences Institute for Veterinary Medical Research, Centre for Agricultural Research Budapest Hungary
| | - Enikő Fehér
- 1 Hungarian Academy of Sciences Institute for Veterinary Medical Research, Centre for Agricultural Research Budapest Hungary
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Furuta RA, Sakamoto H, Kuroishi A, Yasiui K, Matsukura H, Hirayama F. Metagenomic profiling of the viromes of plasma collected from blood donors with elevated serum alanine aminotransferase levels. Transfusion 2015; 55:1889-99. [DOI: 10.1111/trf.13057] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 12/10/2014] [Accepted: 01/17/2015] [Indexed: 12/11/2022]
Affiliation(s)
- Rika A. Furuta
- Japanese Red Cross Kinki Block Blood Center; Osaka Japan
| | | | - Ayumu Kuroishi
- Japanese Red Cross Kinki Block Blood Center; Osaka Japan
| | - Kazuta Yasiui
- Japanese Red Cross Kinki Block Blood Center; Osaka Japan
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50
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Lima FEDS, Cibulski SP, dos Santos HF, Teixeira TF, Varela APM, Roehe PM, Delwart E, Franco AC. Genomic characterization of novel circular ssDNA viruses from insectivorous bats in Southern Brazil. PLoS One 2015; 10:e0118070. [PMID: 25688970 PMCID: PMC4331541 DOI: 10.1371/journal.pone.0118070] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [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: 09/11/2014] [Accepted: 01/04/2015] [Indexed: 11/18/2022] Open
Abstract
Circoviruses are highly prevalent porcine and avian pathogens. In recent years, novel circular ssDNA genomes have recently been detected in a variety of fecal and environmental samples using deep sequencing approaches. In this study the identification of genomes of novel circoviruses and cycloviruses in feces of insectivorous bats is reported. Pan-reactive primers were used targeting the conserved rep region of circoviruses and cycloviruses to screen DNA bat fecal samples. Using this approach, partial rep sequences were detected which formed five phylogenetic groups distributed among the Circovirus and the recently proposed Cyclovirus genera of the Circoviridae. Further analysis using inverse PCR and Sanger sequencing led to the characterization of four new putative members of the family Circoviridae with genome size ranging from 1,608 to 1,790 nt, two inversely arranged ORFs, and canonical nonamer sequences atop a stem loop.
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Affiliation(s)
- Francisco Esmaile de Sales Lima
- Virology Laboratory, Department of Microbiology, Immunology and Parasitology, Institute of Basic Health Sciences, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul (RS), Brazil
- * E-mail:
| | - Samuel Paulo Cibulski
- Virology Laboratory, Department of Microbiology, Immunology and Parasitology, Institute of Basic Health Sciences, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul (RS), Brazil
- FEPAGRO Animal Health, Institute of Veterinary Research "Desidério Finamor" (IPVDF), Eldorado do Sul, Rio Grande do Sul (RS), Brazil
| | - Helton Fernandes dos Santos
- FEPAGRO Animal Health, Institute of Veterinary Research "Desidério Finamor" (IPVDF), Eldorado do Sul, Rio Grande do Sul (RS), Brazil
| | - Thais Fumaco Teixeira
- FEPAGRO Animal Health, Institute of Veterinary Research "Desidério Finamor" (IPVDF), Eldorado do Sul, Rio Grande do Sul (RS), Brazil
| | - Ana Paula Muterle Varela
- FEPAGRO Animal Health, Institute of Veterinary Research "Desidério Finamor" (IPVDF), Eldorado do Sul, Rio Grande do Sul (RS), Brazil
| | - Paulo Michel Roehe
- Virology Laboratory, Department of Microbiology, Immunology and Parasitology, Institute of Basic Health Sciences, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul (RS), Brazil
- FEPAGRO Animal Health, Institute of Veterinary Research "Desidério Finamor" (IPVDF), Eldorado do Sul, Rio Grande do Sul (RS), Brazil
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, California, United States of America; University of California, Department of Laboratory Medicine, San Francisco, California, United States of America
| | - Ana Cláudia Franco
- Virology Laboratory, Department of Microbiology, Immunology and Parasitology, Institute of Basic Health Sciences, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul (RS), Brazil
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