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Williams RAJ, Sánchez-Llatas CJ, Doménech A, Madrid R, Fandiño S, Cea-Callejo P, Gomez-Lucia E, Benítez L. Emerging and Novel Viruses in Passerine Birds. Microorganisms 2023; 11:2355. [PMID: 37764199 PMCID: PMC10536639 DOI: 10.3390/microorganisms11092355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/13/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
There is growing interest in emerging viruses that can cause serious or lethal disease in humans and animals. The proliferation of cloacal virome studies, mainly focused on poultry and other domestic birds, reveals a wide variety of viruses, although their pathogenic significance is currently uncertain. Analysis of viruses detected in wild birds is complex and often biased towards waterfowl because of the obvious interest in avian influenza or other zoonotic viruses. Less is known about the viruses present in the order Passeriformes, which comprises approximately 60% of extant bird species. This review aims to compile the most significant contributions on the DNA/RNA viruses affecting passerines, from traditional and metagenomic studies. It highlights that most passerine species have never been sampled. Especially the RNA viruses from Flaviviridae, Orthomyxoviridae and Togaviridae are considered emerging because of increased incidence or avian mortality/morbidity, spread to new geographical areas or hosts and their zoonotic risk. Arguably poxvirus, and perhaps other virus groups, could also be considered "emerging viruses". However, many of these viruses have only recently been described in passerines using metagenomics and their role in the ecosystem is unknown. Finally, it is noteworthy that only one third of the viruses affecting passerines have been officially recognized.
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Affiliation(s)
- Richard A. J. Williams
- Department of Genetics, Physiology, and Microbiology, School of Biology, Complutense University of Madrid (UCM), C. de José Antonio Nováis, 12, 28040 Madrid, Spain; (C.J.S.-L.); (R.M.); (P.C.-C.); (L.B.)
- “Animal Viruses” Research Group, Complutense University of Madrid, 28040 Madrid, Spain; (A.D.); (S.F.); (E.G.-L.)
| | - Christian J. Sánchez-Llatas
- Department of Genetics, Physiology, and Microbiology, School of Biology, Complutense University of Madrid (UCM), C. de José Antonio Nováis, 12, 28040 Madrid, Spain; (C.J.S.-L.); (R.M.); (P.C.-C.); (L.B.)
| | - Ana Doménech
- “Animal Viruses” Research Group, Complutense University of Madrid, 28040 Madrid, Spain; (A.D.); (S.F.); (E.G.-L.)
- Deparment of Animal Health, Veterinary Faculty, Complutense University of Madrid, Av. Puerta de Hierro, s/n, 28040 Madrid, Spain
| | - Ricardo Madrid
- Department of Genetics, Physiology, and Microbiology, School of Biology, Complutense University of Madrid (UCM), C. de José Antonio Nováis, 12, 28040 Madrid, Spain; (C.J.S.-L.); (R.M.); (P.C.-C.); (L.B.)
- “Animal Viruses” Research Group, Complutense University of Madrid, 28040 Madrid, Spain; (A.D.); (S.F.); (E.G.-L.)
| | - Sergio Fandiño
- “Animal Viruses” Research Group, Complutense University of Madrid, 28040 Madrid, Spain; (A.D.); (S.F.); (E.G.-L.)
- Deparment of Animal Health, Veterinary Faculty, Complutense University of Madrid, Av. Puerta de Hierro, s/n, 28040 Madrid, Spain
| | - Pablo Cea-Callejo
- Department of Genetics, Physiology, and Microbiology, School of Biology, Complutense University of Madrid (UCM), C. de José Antonio Nováis, 12, 28040 Madrid, Spain; (C.J.S.-L.); (R.M.); (P.C.-C.); (L.B.)
- “Animal Viruses” Research Group, Complutense University of Madrid, 28040 Madrid, Spain; (A.D.); (S.F.); (E.G.-L.)
| | - Esperanza Gomez-Lucia
- “Animal Viruses” Research Group, Complutense University of Madrid, 28040 Madrid, Spain; (A.D.); (S.F.); (E.G.-L.)
- Deparment of Animal Health, Veterinary Faculty, Complutense University of Madrid, Av. Puerta de Hierro, s/n, 28040 Madrid, Spain
| | - Laura Benítez
- Department of Genetics, Physiology, and Microbiology, School of Biology, Complutense University of Madrid (UCM), C. de José Antonio Nováis, 12, 28040 Madrid, Spain; (C.J.S.-L.); (R.M.); (P.C.-C.); (L.B.)
- “Animal Viruses” Research Group, Complutense University of Madrid, 28040 Madrid, Spain; (A.D.); (S.F.); (E.G.-L.)
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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] [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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Dolatyabi S, Peighambari SM, Razmyar J. Molecular detection and analysis of beak and feather disease viruses in Iran. Front Vet Sci 2022; 9:1053886. [PMID: 36532332 PMCID: PMC9751380 DOI: 10.3389/fvets.2022.1053886] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 11/14/2022] [Indexed: 10/25/2023] Open
Abstract
The beak and feather disease virus (BFDV) is one of the few pathogens capable of causing extinction of psittacines. To determine the prevalence and the nature of BFDV mutation, this study investigated the presence of the BFDV among 1,095 individual birds of the 17 psittacine species in Iran followed by analyzing the DNA sequences of seven replication-associated protein (rep) and 10 capsid (cap) genomes of the virus. The BFDV was found to be the foremost pathogen among more than 12 psittacine species, and phylogenetic analysis showed that the BFDV GenBank-published sequences from Poland, Saudi Arabia, South Africa, Taiwan, and Thailand were most similar to those of this study. Evolutionary analysis concluded that arginine, leucine, and glycine were the amino acids frequently involved in the least-conserved substitution patterns of BFDV, and conversely, methionine, glutamine, and tryptophan were the amino acids that exhibited ultra-high conservation through the substitution patterns. The high substitution rate of arginine to lysine and glycine to serine also made greater contribution to the BFDV gene mutation. The relative synonymous codon usage between two genes revealed that the cap genome encoded proteins frequently used fewer codons, while the rep genome encoded proteins used more codons only at moderate frequency, explaining the broader divergence of the cap compared to the rep sequence. The data analysis also introduced a new variant of BFDV that exists in the rep and cap sequences of budgerigars. While the existence of more new variants was suspected, more solid evidence is required to substantiate this suspicion.
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Epidemiology, genetic diversity, and association of canine circovirus infection in dogs with respiratory disease. Sci Rep 2022; 12:15445. [PMID: 36104425 PMCID: PMC9472715 DOI: 10.1038/s41598-022-19815-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 09/05/2022] [Indexed: 11/08/2022] Open
Abstract
AbstractAlthough canine circovirus (CanineCV)-associated with gastroenteritis has been well documented, the virus is also detectable in the respiratory discharge of dogs with respiratory disease. In this study, an epidemiological approach was used to explore the association between the presence of CanineCV and respiratory symptoms in dogs. Respiratory swabs were collected from 76 healthy dogs and 114 dogs with respiratory illness and tested for CanineCV using conventional PCR (cPCR). Furthermore, lung tissues collected from 15 necropsied dogs showing pneumonia were tested using the real-time PCR (qPCR) and in situ hybridization (ISH) technique. A total of 8.95% (17/190) of dogs were CanineCV positive, with a significant association (p = 0.013) in dogs with respiratory signs. Four necropsied dogs were qPCR positive with the CanineCV-DNA labeling localized in tracheobronchial lymphoid cells (3/4), pulmonary parenchyma, capillary endothelia, and mononuclear cells harboring in alveoli (2/4). Full-length genome sequences of seven CanineCV strains were analyzed, indicating that the detected CanineCV genome clustered in the CanineCV-4 genotype. Genetic recombination was also evident in the replicase (Rep) gene. Although the role of CanineCV primarily affecting lung lesions could not be determined from this study, the presence of CanineCV DNA in pulmonary-associated cells indicated the potential association of the virus with canine respiratory disease; thus, linking causality must be examined in further studies.
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Diversity of CRESS DNA Viruses in Squamates Recapitulates Hosts Dietary and Environmental Sources of Exposure. Microbiol Spectr 2022; 10:e0078022. [PMID: 35616383 PMCID: PMC9241739 DOI: 10.1128/spectrum.00780-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [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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Wang H, Gao H, Jiang Z, Shi L, Zhao P, Zhang Y, Wang C. Molecular detection and phylogenetic analysis of pigeon circovirus from racing pigeons in Northern China. BMC Genomics 2022; 23:290. [PMID: 35410130 PMCID: PMC8995411 DOI: 10.1186/s12864-022-08425-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 02/28/2022] [Indexed: 01/20/2023] Open
Abstract
Background Pigeon circovirus (PiCV) infections in pigeons (Columba livia) have been reported worldwide. Currently, pigeon racing is becoming increasingly popular and considered to be a national sport in China, and even, the greatest competitions of racing pigeons are taking place in China. However, there are still no epidemiologic data regarding PiCV infections among racing pigeons in China. The purpose of our study was to provide information of prevalence, genetic variation and evolution of PiCV from racing pigeons in China. Results To trace the prevalence, genetic variation and evolution of PiCV in sick and healthy racing pigeons, 622 samples were collected from 11 provinces or municipalities in China from 2016 to 2019. The results showed that the positive rate of PiCV was 19.3% (120/622) at the sample level and 59.0% (23/39) at the club level, thus suggesting that the virus was prevalent in Chinese racing pigeons. A sequence analysis revealed that the cap genes of the PiCV strains identified in our study displayed a high genetic diversity and shared nucleotide homologies of 71.9%–100% and amino acid homologies of 71.7%–100%. 28 and 36 unique amino acid substitutions were observed in the Cap and Rep proteins derived from our PiCV strains, respectively. A cladogram representation of PiCV strains phylogeny based on 90 cap gene sequences showed that the strains in this study could be further divided into seven clades (A, B, C, E, G, H, and I) and some of them were closely related to worldwide strains from different types of pigeons. A large number of recombination events (31 events) were also detected in the PiCV genomes from Chinese racing pigeons. Conclusions These findings indicate that PiCV strains circulating in China exhibit a high genetic diversity and also contribute to information of prevalence, genetic variation and evolution of PiCV from racing pigeons in China. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08425-8.
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Affiliation(s)
- Haoran Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, China
| | - Hui Gao
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, China
| | - Zhiwen Jiang
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, China
| | - Leibo Shi
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, China
| | - Pengwei Zhao
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, China
| | - Yanming Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, China
| | - Chengbao Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, China.
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Blanco G, Morinha F, Carrete M, Tella JL. Apparent Lack of Circovirus Transmission from Invasive Parakeets to Native Birds. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19063196. [PMID: 35328884 PMCID: PMC8953828 DOI: 10.3390/ijerph19063196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/04/2022] [Accepted: 03/06/2022] [Indexed: 11/16/2022]
Abstract
The transmission of pathogens to native species has been highlighted as one of the most important impacts of biological invasions. In this study, we evaluated the presence of psittacine beak and feather disease virus (BFDV) and other circoviruses in native bird species cohabiting with invasive populations of wild rose-ringed (Psittacula krameri) and monk parakeets (Myiopsitta monachus) that were found positive for a particular BFDV genotype in Sevilla, southern Spain. None of the 290 individuals from the 18 native bird species captured showed typical signs of disease caused by BFDV. A sample of 79 individuals from 15 native species showed negative results for the presence of the BFDV genotype previously detected in the sympatric invasive parakeets, as well as any other of the circoviruses tested. Although preliminary, this study suggests a lack of circovirus transmission from invasive parakeets to native birds at the study site. Further research is needed to determine if this apparent absence in transmission depends on the BFDV genotype present in the parakeets, which requires additional screening in other invasive and native populations living in sympatry.
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Affiliation(s)
- Guillermo Blanco
- Department of Evolutionary Ecology, National Museum of Natural Sciences (MNCN), Spanish National Research Council (CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain
- Correspondence:
| | - Francisco Morinha
- Morinha Lab—Laboratory of Biodiversity and Molecular Genetics, 5000-562 Vila Real, Portugal;
| | - Martina Carrete
- Department of Physical, Chemical and Natural Systems, University Pablo de Olavide, Ctra. de Utrera km. 1, 41013 Sevilla, Spain;
| | - José L. Tella
- Department of Conservation Biology, Estación Biológica de Doñana (CSIC), Avda. Américo Vespucio, 41092 Sevilla, Spain;
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Fehér E, Kaszab E, Bali K, Hoitsy M, Sós E, Bányai K. Novel Circoviruses from Birds Share Common Evolutionary Roots with Fish Origin Circoviruses. Life (Basel) 2022; 12:life12030368. [PMID: 35330119 PMCID: PMC8950603 DOI: 10.3390/life12030368] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/24/2022] [Accepted: 02/28/2022] [Indexed: 11/16/2022] Open
Abstract
Circoviruses occur in a variety of animal species and are common pathogens of mammalian and avian hosts. In our study internal organ samples of wild birds were processed for screening of circoviral sequences. Two novel viruses were identified and characterized in specimens of a little bittern and a European bee-eater that suffered from wing injuries, were weakened, had liver or kidney failures, and finally succumbed at a rescue station. The 1935 nt and 1960 nt long viral DNA genomes exhibited a genomic structure typical for circoviruses and were predicted to encode replication-associated protein in the viral strand, and a capsid protein in the complementary strand of the replicative intermediate DNA form. The genome of the newly described viruses showed 37.6% pairwise identity with each other and ≤41.5% identity with circovirus sequences, and shared a common branch with fish, human and Weddel seal circoviruses in the phylogenetic tree, implying evolutionary relationship among the ancestors of these viruses. Based on the results the little bittern and European bee-eater circoviruses represent two distinct species of the Circovirus genus, Circoviridae family.
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Affiliation(s)
- Enikő Fehér
- Veterinary Medical Research Institute, H-1143 Budapest, Hungary; (E.K.); (K.B.); (K.B.)
- Correspondence:
| | - Eszter Kaszab
- Veterinary Medical Research Institute, H-1143 Budapest, Hungary; (E.K.); (K.B.); (K.B.)
| | - Krisztina Bali
- Veterinary Medical Research Institute, H-1143 Budapest, Hungary; (E.K.); (K.B.); (K.B.)
| | - Márton Hoitsy
- Conservation and Veterinary Services, Budapest Zoo and Botanical Garden, H-1164 Budapest, Hungary; (M.H.); (E.S.)
| | - Endre Sós
- Conservation and Veterinary Services, Budapest Zoo and Botanical Garden, H-1164 Budapest, Hungary; (M.H.); (E.S.)
| | - Krisztián Bányai
- Veterinary Medical Research Institute, H-1143 Budapest, Hungary; (E.K.); (K.B.); (K.B.)
- Department of Pharmacology and Toxicology, University of Veterinary Medicine, H-1078 Budapest, Hungary
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Hubálek Z. Pathogenic microorganisms associated with gulls and terns (Laridae). JOURNAL OF VERTEBRATE BIOLOGY 2021. [DOI: 10.25225/jvb.21009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Zdeněk Hubálek
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic; e-mail:
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Nath BK, Das S, Roby JA, Sarker S, Luque D, Raidal SR, Forwood JK. Structural Perspectives of Beak and Feather Disease Virus and Porcine Circovirus Proteins. Viral Immunol 2020; 34:49-59. [PMID: 33275868 DOI: 10.1089/vim.2020.0097] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Circoviruses represent a rapidly expanding group of viruses that infect both vertebrate and invertebrate hosts. Members are responsible for diseases of veterinary and economic importance, including postweaning multisystemic wasting syndrome in pigs, and beak and feather disease (BFD) in birds. These viruses are associated with lymphoid depletion and immunosuppressive conditions in infected animals leading to systemic illness. Circoviruses are small nonenveloped DNA viruses containing a single-stranded circular genome, encoding two major proteins: the capsid-associated protein (Cap), comprising the entirety of the viral capsid, and the replication-associated protein (Rep). Cap is the only protein component of the virion and plays crucial roles throughout the virus replication cycle, including viral attachment, cell entry, genome uncoating, and packaging of newly formed viral particles. Rep mediates recognition of replication origin motifs in the viral genome sequence and is responsible for endonuclease activity enabling nicking of the circular DNA and initiation of rolling-circle replication (RCR). Porcine circovirus 2 (PCV2) was the first circovirus capsid structure to be solved at atomic resolution using X-ray crystallography. The structure revealed an assembly comprising 60 monomeric subunits to form virus-like particles. Each Cap monomer harbors a canonical viral jelly roll domain composed of two, four-stranded antiparallel β-sheets. Crystal structures of two distinct macromolecular assemblies from BFD virus Cap were also resolved at high resolution. In these structures, the exposure of the N-terminal arginine-rich motif, responsible for DNA binding and nuclear localization is reversed. Additional structural investigations have also elucidated a PCV2 type-specific neutralizing epitope, and interaction between the PCV2 capsid and polymers such as heparin. In this review, we provide a snapshot of the structural and functional aspects of circovirus proteins.
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Affiliation(s)
- Babu Kanti Nath
- School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, Australia
| | - Shubhagata Das
- School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, Australia
| | - Justin A Roby
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, Australia
| | - Subir Sarker
- Department of Physiology, Anatomy and Microbiology, School of Life Sciences, La Trobe University, Melbourne, Australia
| | - Daniel Luque
- Centro Nacional de Microbiología/ISCIII, Majadahonda, Madrid, Spain
| | - Shane R Raidal
- School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, Australia
| | - Jade K Forwood
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, Australia
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Liu H, Li LX, Sun WC, Shi N, Sun XT, Jin NY, Si XK. Molecular survey of duck circovirus infection in poultry in southern and southwestern China during 2018 and 2019. BMC Vet Res 2020; 16:80. [PMID: 32138728 PMCID: PMC7059369 DOI: 10.1186/s12917-020-02301-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Accepted: 02/28/2020] [Indexed: 12/22/2022] Open
Abstract
Background Duck circovirus (DuCV) is a potential immunosuppressive virus that causes feather disorders in young ducks. In this study, DuCV obtained from various species of ducks was investigated by polymerase chain reaction (PCR) in southern and southwestern China (Guangdong, Guangxi and Yunnan provinces) from 2018 to 2019. Results A total of 848 bursa samples were collected from dead Mulard, Cherry Valley Pekin, Muscovy and Mallard ducks from duck farms. The positivity rate of DuCV in the total sample was approximately 36.91%. We found that the prevalence of DuCV in Yunnan (43.09%) was higher than those in Guangxi (34.38%) and Guangdong (34.4%). However, the positivity rates of DuCV in the four duck species were not significantly different (P > 0.05). Nineteen randomly selected complete viral genomes were sequenced. The complete genomes of the DuCV were 1987 to 1995 nt in length, and were 81.7–99.3% homologous to the other 57 sequences in GenBank. Phylogenetic analyses based on the complete genomes of 76 DuCVs showed that the 19 novel DuCV sequences from Guangdong and Guangxi provinces mainly belonged to the DuCV-1 and DuCV-2 genetic groups, respectively. However, the two genotype groups coexisted in Yunnan Province. In addition, recombination analysis showed putative recombination sites in 3 strains in Yunnan that originated from strains Guangdong and Guangxi. Interestingly, the epidemiological investigation showed that Mulard ducks, Cherry Valley Pekin ducks and Muscovy ducks more than 4 weeks old were more susceptible to infection with the novel DuCV than ducks less than 4 weeks old. Conclusions These data provide insight into the molecular epidemiology and genetic diversity of DuCVs circulating in southern and southwestern China for the first time.
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Affiliation(s)
- Hao Liu
- School of Life Sciences and Engineering, Foshan University, Foshan, 528000, China
| | - Li Xia Li
- School of Life Sciences and Engineering, Foshan University, Foshan, 528000, China.,Jilin Wildlife Rescue and Rehabilitation Center, Forestry Department of Jilin Province, Changchun, 130122, China
| | - Wen Chao Sun
- Institute of Virology, Wenzhou University, Wenzhou, 325035, China
| | - Ning Shi
- School of Life Sciences and Engineering, Foshan University, Foshan, 528000, China
| | - Xiu Tao Sun
- Honghe Animal Disease Prevention and Control Center, Mengzi, 661000, China
| | - Ning Yi Jin
- Military Veterinary Institute, Academy of Military Medical Sciences, Changchun, 130122, China
| | - Xing Kui Si
- School of Life Sciences and Engineering, Foshan University, Foshan, 528000, China.
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12
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Landrau-Giovannetti N, Subramaniam K, Brown MA, Ng TFF, Rotstein DS, West K, Frasca S, Waltzek TB. Genomic characterization of a novel circovirus from a stranded Longman's beaked whale (Indopacetus pacificus). Virus Res 2019; 277:197826. [PMID: 31790774 DOI: 10.1016/j.virusres.2019.197826] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 11/26/2019] [Accepted: 11/26/2019] [Indexed: 11/28/2022]
Abstract
Tissues from a juvenile Longman's beaked whale that stranded in Hawaii in 2010 were screened for viruses using a Next-Generation Sequencing (NGS) approach. From the NGS data, the full genome (1,849 bp) of a novel beaked whale circovirus (BWCV) was determined. Two open reading frames (ORF) were annotated, including ORF1 that encodes the capsid gene, ORF2 that encodes the replication-associated gene, and a 9-bp conserved nonamer on the apex of the open loop found in all circoviruses. Independent phylogenetic analyses based on amino acid sequence alignments of the two CV proteins supported the BWCV as a member of the genus Circovirus, branching as the sister species to the recently discovered canine circovirus. A sequence identity matrix generated from complete genome alignments revealed the BWCV displays between from 51.1 to 56.7% nucleotide identity to other circoviruses, which is lower than the 80% threshold proposed for species demarcation. Considering the genetic and phylogenetic analyses, we propose the formal species designation of beaked whale circovirus. An endpoint PCR assay targeting the BWCV genome confirmed the presence of the BWCV DNA in every tissue from which DNA was extracted, including spleen, muscle, left ventricle, left adrenal gland, liver, lung, cerebrum, cerebellum, and lymph node. An automated in situ hybridization assay utilizing RNAscope® technology and targeting the replication-associated gene resulted in labeling of individual cells morphologically resembling mononuclear leukocytes and cells of blood vessels in diaphragm, liver, lymph nodes, lung, pericardium, oral mucosa and tongue, adrenal gland, testis, aorta, intestine, stomach and heart. The clinical or pathologic significance of BWCV is undetermined, as are its host range, prevalence, and pathogenicity in cetaceans of Hawaiian waters and elsewhere.
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Affiliation(s)
- Nelmarie Landrau-Giovannetti
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States
| | - Kuttichantran Subramaniam
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States
| | - Melissa Ann Brown
- Molecular Histotechnology Laboratory, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States
| | - Terry Fei Fan Ng
- College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | | | - Kristi West
- Hawaii Institute of Marine Biology, University of Hawaii at Manoa, PO Box 1346, Kaneohe, HI, United States; Department of Human Nutrition Food and Animal Science, College of Tropical Agriculture and Human Resources, 1955 East-West Road, University of Hawaii at Manoa Ag Sci 216, Honolulu, HI 96822, United States
| | - Salvatore Frasca
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States
| | - Thomas B Waltzek
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States.
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Canuti M, Munro HJ, Robertson GJ, Kroyer ANK, Roul S, Ojkic D, Whitney HG, Lang AS. New Insight Into Avian Papillomavirus Ecology and Evolution From Characterization of Novel Wild Bird Papillomaviruses. Front Microbiol 2019; 10:701. [PMID: 31031718 PMCID: PMC6473165 DOI: 10.3389/fmicb.2019.00701] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 03/20/2019] [Indexed: 11/24/2022] Open
Abstract
Viruses in the family Papillomaviridae have circular dsDNA genomes of approximately 5.7–8.6 kb that are packaged within non-enveloped, icosahedral capsids. The known papillomavirus (PV) representatives infect vertebrates, and there are currently more than 130 recognized PV species in more than 50 genera. We identified 12 novel avian papillomavirus (APV) types in wild birds that could represent five distinct species and two genera. Viruses were detected in paired oropharyngeal/cloacal swabs collected from six bird species, increasing the number of avian species known to harbor PVs by 40%. A new duck PV (DuPV-3) was found in mallard and American black duck (27.6% estimated prevalence) that was monophyletic with other known DuPVs. A single viral type was identified in Atlantic puffin (PuPV-1, 9.8% estimated prevalence), while a higher genetic diversity was found in other Charadriiformes. Specifically, three types [gull PV-1 (GuPV-1), -2, and -3] were identified in two gull species (estimated prevalence of 17% and 2.6% in American herring and great black-backed gull, respectively), and seven types [kittiwake PV-1 (KiPV-1) through -7] were found in black-legged kittiwake (81.3% estimated prevalence). Significantly higher DuPV-3 circulation was observed in spring compared to fall and in adults compared to juveniles. The studied host species’ tendencies to be in crowded environments likely affect infection rates and their migratory behaviors could explain the high viral diversity, illustrating how host behavior can influence viral ecology and distribution. For DuPV-3, GuPV-1, PuPV-1, and KiPV-2, we obtained the complete genomic sequences, which showed the same organization as other known APVs. Phylogenetic analyses showed evidence for virus–host co-divergence at the host taxonomic levels of family, order, and inter-order, but we also observed that host-specificity constraints are relaxed among highly related hosts as we found cross-species transmission within ducks and within gulls. Furthermore, the phylogeny of viruses infecting the Charadriiformes did not match the host phylogeny and gull viruses formed distinct monophyletic clades with kittiwake viruses, possibly reflecting past host-switching events. Considering the vast PV genotype diversity in other hosts and the large number of bird species, many more APVs likely remain to be discovered.
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Affiliation(s)
- Marta Canuti
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Hannah J Munro
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Gregory J Robertson
- Wildlife Research Division, Environment and Climate Change Canada, Mount Pearl, NL, Canada
| | - Ashley N K Kroyer
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Sheena Roul
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Davor Ojkic
- Animal Health Laboratory, University of Guelph, Guelph, ON, Canada
| | - Hugh G Whitney
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Andrew S Lang
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada
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Abstract
The red-crowned crane is one of the rarest crane species, and its population is decreasing due to loss of habitat, poisoning, and infections. Using a viral metagenomics approach, we analyzed the virome of feces from wild and captive red-crowned cranes, which were pooled separately. Vertebrate viruses belonging to the families Picornaviridae, Parvoviridae, Circoviridae, and Caliciviridae were detected. Among the members of the family Picornaviridae, we found three that appear to represent new genera. Six nearly complete genomes from members of the family Parvoviridae were also obtained, including four new members of the proposed genus “Chapparvovirus”, and two members of the genus Aveparvovirus. Six small circular DNA genomes were also characterized. One nearly complete genome showing a low level of sequence identity to caliciviruses was also characterized. Numerous viruses believed to infect insects, plants, and crustaceans were also identified, which were probably derived from the diet of red-crowned cranes. This study increases our understanding of the enteric virome of red-crowned cranes and provides a baseline for comparison to those of other birds or following disease outbreaks.
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Sheykhi A, Sheikhi N, Charkhkar S, Brujeni GN. Detection and Characterization of Circovirus in Canary Flocks. Avian Dis 2018; 62:137-142. [PMID: 29944404 DOI: 10.1637/11776-120417-regr] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Circovirus infections have been documented in adult and nestling canaries (Fringillidae) but the distribution of the virus in the world is not yet known. In captive canary flocks, Circovirus infections have been reported based on the clinical observations. In this study, the presence of both canary circovirus (CaCV) and chicken anemia virus (CAV) in canary flocks was investigated. Virus strains were detected by PCR and direct sequencing of amplified products. Nucleotide sequences were aligned and compared with existing data in GenBank. PCR identified CaCV-positive birds, giving an overall positivity rate of 25%, but all samples were negative for CAV. According to the sequencing data, three distinct strains were identified. Our results indicated a relationship between genetic variation in the replicase gene ( rep) and the geographic regions as well as the feasibility of using the rep gene for virus detection and molecular epidemiology investigations. We are reporting detection and characterization of canary circovirus based on the rep gene. Sequencing results and sequence identity analysis revealed that the rep gene could be used for detecting and discriminating the members of family Circoviridae. This manuscript is the first report of canary circovirus in Iran and of three new strains in the world.
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Affiliation(s)
- Abdulmajid Sheykhi
- A Department of Clinical Science, College of Veterinary, Tehran Science and Research Branch, Islamic Azad University, Tehran, Iran, Post code: 1477893855
| | - Nariman Sheikhi
- A Department of Clinical Science, College of Veterinary, Tehran Science and Research Branch, Islamic Azad University, Tehran, Iran, Post code: 1477893855
| | - Saeid Charkhkar
- A Department of Clinical Science, College of Veterinary, Tehran Science and Research Branch, Islamic Azad University, Tehran, Iran, Post code: 1477893855
| | - Gholamreza Nikbakht Brujeni
- B Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran: 1417614418
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16
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Portas T, Jackson B, Das S, Shamsi S, Raidal SR. Beak and feather disease virus carriage by Knemidocoptes pilae in a sulphur-crested cockatoo (Cacatua galerita). Aust Vet J 2018; 95:486-489. [PMID: 29243237 DOI: 10.1111/avj.12649] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Revised: 05/01/2017] [Accepted: 05/14/2017] [Indexed: 01/23/2023]
Abstract
BACKGROUND This paper describes the pathology associated with psittacine beak and feather disease in a wild sulphur-crested cockatoo with concurrent knemidocoptic mange, cestodiasis and mycotic encephalitis. METHODS & RESULTS Large numbers of Knemidocoptes pilae Lavoipierre and Griffiths, 1951 (Acari: Epidermoptidae, Knemidokoptinae) were identified in affected skin associated with enhanced expression of beak and feather disease virus (BFDV) determined by immunohistochemistry. Also, BFDV antigen was demonstrated in high concentration in the gut and faecal sacs of mites, raising the possibility of ectoparasites as fomites and vectors of BFDV transmission. Large numbers of Raillietina spp. cestodes were present in the intestines. Within the brain there was a focally extensive region of necrosis and inflammation associated with branching, septate, pigmented hyphae consistent with zygomycete fungal infection. CONCLUSION This case highlights the potential immunosuppressive effects of BFDV infection and its potential as a keystone pathogen in the Australian environment.
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Affiliation(s)
- T Portas
- RSPCA Queensland Wildlife Hospital, Wacol, Queensland, Australia
| | - B Jackson
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia, Australia
| | - S Das
- School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia
| | - S Shamsi
- School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia
| | - S R Raidal
- School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia
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17
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Niu X, Liu L, Han C, Li J, Zeng X. First findings of duck circovirus in migrating wild ducks in China. Vet Microbiol 2018. [DOI: 10.1016/j.vetmic.2018.02.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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18
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Shehata AA, Gerry DM, Heenemann K, Halami MY, Tokarzewski S, Wencel P, Vahlenkamp TW. Goose Parvovirus and Circovirus Coinfections in Ornamental Ducks. Avian Dis 2017; 60:516-22. [PMID: 27309298 DOI: 10.1637/11335-112615-case] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Clinical observations and diagnostic procedures carried out to elucidate the cause of high mortality in 2-8-wk-old ornamental ducks (mandarin, wood, falcated, and silver teal ducks) are described. At necropsy, ducklings showed general pallor of skeletal and heart muscles, subcutaneous gelatinous transudates, pericarditis, ascites, and severe edema and hyperemia of lungs. Histopathologic examination revealed that the most important changes were located in the crop, bursa of Fabricius, and lungs with presence of amorphic basic intracytoplasmic inclusions. No bacteria or fungi could be detected from affected organs and ascitic fluid. Viral diagnosis included molecular detection for the presence of goose parvovirus (GPV), circovirus, avian influenza, herpesviruses, paramyxovirus, reovirus, and polyomavirus. Both GPV and circovirus could be detected by real-time PCR and nested broad-spectrum PCR, respectively. Phylogenetically, full-length nucleotide sequence of GPV showed a close similarity ranging from 95.6% to 97.9% with European and Asian pathogenic GPV. On the other hand, the detected circovirus showed nucleotide identity of 90% to 98% with goose circoviruses (GoCVs). This is the first report of GoCVs and GPV in ornamental ducks. The concurrence of GPV and GoCV infections is thought to contribute to the high mortality.
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Affiliation(s)
- Awad A Shehata
- A Center for Infectious Diseases, Institute of Virology, Faculty of Veterinary Medicine, University of Leipzig, An den Tierkliniken 29, 04103 Leipzig, Germany.,B Avian and Rabbit Diseases Department, Faculty of Veterinary Medicine, Sadat City University, 22857 Minoufiya, Egypt
| | - Dorrestein M Gerry
- C Pathology Laboratory NOIVBD, Wintelresedijk 51, 5507 PP Veldhoven, the Netherlands
| | - Kristin Heenemann
- A Center for Infectious Diseases, Institute of Virology, Faculty of Veterinary Medicine, University of Leipzig, An den Tierkliniken 29, 04103 Leipzig, Germany
| | - Mohammed Y Halami
- A Center for Infectious Diseases, Institute of Virology, Faculty of Veterinary Medicine, University of Leipzig, An den Tierkliniken 29, 04103 Leipzig, Germany
| | | | - Peter Wencel
- D AviExpert S.P.W.C.P, ul. Gajowa 1, 20-827 Lublin, Poland
| | - Thomas W Vahlenkamp
- A Center for Infectious Diseases, Institute of Virology, Faculty of Veterinary Medicine, University of Leipzig, An den Tierkliniken 29, 04103 Leipzig, Germany
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GENETIC CHARACTERIZATION OF H13 AND H16 INFLUENZA A VIRUSES IN GULLS (LARUS SPP.) WITH CLINICALLY SEVERE DISEASE AND CONCURRENT CIRCOVIRUS INFECTION. J Wildl Dis 2017; 53:561-571. [PMID: 28384060 DOI: 10.7589/2016-09-212] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Influenza A viruses (IAVs) of the subtypes H13 and H16 are primarily found in gulls ( Larus spp., order Charadriiformes). Although the gull-adapted subtypes replicate efficiently during infection, gulls usually remain apparently healthy during infection. Avian influenza virus isolates are generally separated into two distinct populations, North American and Eurasian, because of the limited gene flow between the continents. Reassortment between these lineages does occur occasionally; however, direct intercontinental transmission of all eight gene segments is rare. Extensive research has been done to understand the ecology of IAV subtypes that naturally circulate in ducks (order Anseriformes), but the ecology of H13 and H16 IAVs in gulls remains far less studied. In Finland, gulls were screened for IAVs for passive (dead and diseased gulls) and active (clinically healthy gulls) surveillance purposes during the years 2005-10. During that period, 11 H13, two H16 viruses, and one H3N8 IAV were detected. We sequenced partial and full-length hemagglutinin genes of these gull-origin IAVs for phylogenetic assessments. All but one of the H13 genes clustered together with northern European and northeastern Asian viruses, whereas one virus clustered with North American viruses. Interestingly, a high rate (10/14) of these low-pathogenic IAVs was detected in dead or diseased gulls. The atypical clinical status of the IAV-positive gulls and previous observations of circovirus-like inclusion bodies in diseased gulls during autopsies, led us to screen for concurrent circovirus infections in our samples. The DNA of circovirus, an immunosuppressive pathogen of both birds and mammals, was detected in 54% (7/13) of the tested IAV-positive gulls, whereas only 25% (14/56) of our panel of IAV-negative gulls tested positive by circovirus PCR.
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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] [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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Rinder M, Schmitz A, Peschel A, Wörle B, Gerlach H, Korbel R. Molecular characterization of a recently identified circovirus in zebra finches (Taeniopygia guttata) associated with immunosuppression and opportunistic infections. Avian Pathol 2016; 46:106-116. [DOI: 10.1080/03079457.2016.1223272] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Monika Rinder
- Clinic for Birds, Reptiles, Amphibians and Ornamental Fish, Center for Clinical Veterinary Medicine, LMU Munich, Munich, Germany
| | - Anna Schmitz
- Clinic for Birds, Reptiles, Amphibians and Ornamental Fish, Center for Clinical Veterinary Medicine, LMU Munich, Munich, Germany
| | - Andrea Peschel
- Clinic for Birds, Reptiles, Amphibians and Ornamental Fish, Center for Clinical Veterinary Medicine, LMU Munich, Munich, Germany
| | - Barbara Wörle
- Max Planck Institute for Ornithology, Pöcking, Germany
| | | | - Rüdiger Korbel
- Clinic for Birds, Reptiles, Amphibians and Ornamental Fish, Center for Clinical Veterinary Medicine, LMU Munich, Munich, Germany
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Evidence of a deep viral host switch event with beak and feather disease virus infection in rainbow bee-eaters (Merops ornatus). Sci Rep 2015; 5:14511. [PMID: 26411487 PMCID: PMC4585972 DOI: 10.1038/srep14511] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 09/02/2015] [Indexed: 11/27/2022] Open
Abstract
Since the characterization of psittacine beak and feather disease (PBFD) in 1984, a wide range of avian circoviruses have been discovered with varying pathogenic effects amongst a diverse range of avian hosts. Until recently these circovirus species were thought to be restricted to within avian Orders such as the Psittaciformes for beak and feather disease virus (BFDV) and Columbiformes for pigeon circovirus with little evidence of cross-family transmission or replication. We report evidence of a naturally occurring novel host switch event with self-limiting BFDV infection in a group of rainbow bee-eaters (Merops ornatus) a species of Coraciiformes unrelated to parrots and not previously known to be susceptible to any avian circovirus. The outbreak highlights important and unexpected aspects of disease emergence and host-switching pertinent to other situations when viruses might cross species boundaries as well as the potential of avian circoviruses to infect disparate host species.
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Matczuk AK, Krawiec M, Wieliczko A. A new duck circovirus sequence, detected in velvet scoter (Melanitta fusca) supports great diversity among this species of virus. Virol J 2015; 12:121. [PMID: 26253134 PMCID: PMC4528844 DOI: 10.1186/s12985-015-0352-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 07/28/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The aim of this study was to investigate the presence of circoviruses in wild bird populations, in Poland. Circoviruses possess immuno-suppressive properties and might interfere with the health of wild birds. METHOD 83 birds, which belonged to 23 species, were tested with broad-range, nested PCR. The obtained PCR products were sequenced and new primers designed, to analyse the full-length, viral genome. A phylogenetic analysis was conducted, to find any relationship to known circoviruses. RESULTS The circovirus DNA sequence was found in 4 birds. All samples originated from the velvet scoter (Melanitta fusca) a marine duck from the Merginae sub-family. Birds which tested positive for the circovirus were found dead in fishing nets, off the Baltic coast. During post-mortem examination, carcasses of two of the scoters showed only light emaciation, while the two other birds appeared healthy. The obtained, full-length, circovirus sequence revealed 1,988 nucleotides and the presence of typical features (i.e. Cap, Rep and ORF3). Nucleotide similarity to other duck circoviruses was 84 to 86 %. Phylogenetic analysis of the complete genome and cap gene, indicated that the new circovirus is related to known duck circoviruses, especially to sub-types sometimes referred to as duck circovirus genotype 1, but not genotype 2. CONCLUSIONS In this study, we have reported a new duck circovirus sequence detected in the velvet scoter, a species of marine duck. Sequence comparison and phylogenetic analysis of the new virus sequence support previous reports that duck circovirus (DuCV) is a species with a high degree of diversity. The viral sequence obtained from the velvet scoter suggests that DuCV may infect birds from the Anatinae sub-family. More studies are needed to prove if the velvet scoter and other marine ducks act as a reservoir for DuCV.
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Affiliation(s)
- Anna Karolina Matczuk
- Department of Pathology, Division of Microbiology, The Faculty of Veterinary Medicine, Wrocław University of Environmental and Life Sciences, Norwida 31, 50-375, Wrocław, Poland.
| | - Marta Krawiec
- Department of Epizootiology and Clinic of Bird and Exotic Animals, The Faculty of Veterinary Medicine, Wrocław University of Environmental and Life Sciences, Pl. Grunwaldzki 45, 50-366, Wrocław, Poland.
| | - Alina Wieliczko
- Department of Epizootiology and Clinic of Bird and Exotic Animals, The Faculty of Veterinary Medicine, Wrocław University of Environmental and Life Sciences, Pl. Grunwaldzki 45, 50-366, Wrocław, Poland.
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Complete genome sequence of a novel circovirus from zebra finch. GENOME ANNOUNCEMENTS 2015; 3:3/3/e00560-15. [PMID: 26021933 PMCID: PMC4447918 DOI: 10.1128/genomea.00560-15] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
A novel circovirus was identified in zebra finches (Taeniopygia guttata). The genome of the circovirus strain, designated 8454V25-1, comprised 1,982 nucleotides with two major open reading frames encoding a replication-associated protein and a viral capsid protein.
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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] [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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26
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Mahzounieh M, Heidari Khoei H, Ghasemi Shamsabadi M, Dastjerdi A. Detection and phylogenetic characterization of Columbid circoviruses in Chaharmahal va Bakhtiari province, Iran. Avian Pathol 2014; 43:524-8. [DOI: 10.1080/03079457.2014.966648] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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27
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Höfle U, Van de Bildt MWG, Leijten LM, Van Amerongen G, Verhagen JH, Fouchier RAM, Osterhaus ADME, Kuiken T. Tissue tropism and pathology of natural influenza virus infection in black-headed gulls (Chroicocephalus ridibundus). Avian Pathol 2014; 41:547-53. [PMID: 23237367 DOI: 10.1080/03079457.2012.744447] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Black-headed gulls (Chroicocephalus ridibundus) are a suitable host species to study the epidemiology of low-pathogenic avian influenza virus (LPAIV) infection in wild waterbirds because they are a common colony-breeding species in which LPAIV infection is detected frequently, limited mainly to the H13 and H16 subtypes. However, the sites of virus replication and associated lesions are poorly understood. We therefore performed virological and pathological analyses on tissues of black-headed gulls naturally infected with LPAIV. We found that 24 of 111 black-headed gulls collected from breeding colonies were infected with LPAIV (10 birds with H16N3, one bird with H13N8, 13 birds undetermined), based on virus and viral genome detection in pharyngeal and cloacal swabs. Of these 24 gulls, 15 expressed virus antigen in their tissues. Virus antigen expression was limited to epithelial cells of intestine and cloacal bursa. No histological lesions were detected in association with virus antigen expression. Our findings show that LPAIV replication in the intestinal tract of black-headed gulls is mainly a superficial infection in absence of detectable lesions, as determined recently for natural LPAIV infection in free-living mallards (Anas platyrhynchos). These findings imply that LPAIV in black-headed gulls has adapted to minimal pathogenicity to its host and that potentially the primary transmission route is faecal-oral.
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Affiliation(s)
- Ursula Höfle
- Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ciudad Real, 13005, Ciudad Real, Spain.
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28
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Circella E, Legretto M, Pugliese N, Caroli A, Bozzo G, Accogli G, Lavazza A, Camarda A. Psittacine Beak and Feather Disease–like Illness in Gouldian Finches (Chloebia gouldiae). Avian Dis 2014; 58:482-7. [DOI: 10.1637/10745-121113case.1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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29
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Tarján Z, Pénzes J, Tóth R, Benkő M. First detection of circovirus-like sequences in amphibians and novel putative circoviruses in fishes. Acta Vet Hung 2014; 62:134-44. [PMID: 24334078 DOI: 10.1556/avet.2013.061] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The negative samples of a collection, established originally for seeking new adeno- and herpesviruses in lower vertebrates, were screened for the pres-ence of circoviruses by a consensus nested PCR targeting the gene coding for the replication-associated protein. Six fish samples representing five species, namely asp (Aspius aspius), roach (Rutilus rutilus), common bream (Abramis brama), round goby (Neogobius melanostomus) and monkey goby (Neogobius fluviatilis), as well as three frog samples were found positive for circoviral DNA. Sequence analysis of the amplicons indicated the presence of three novel putative circo-like viruses and a circovirus in Hungarian fishes and one novel circovirus in a common toad (Bufo bufo), and another one in a dead and an alive specimen of green tree frog (Litoria caerulea), respectively. In phylogeny reconstruction, the putative bream circovirus clustered together with circoviruses discovered in other cyprinid fishes recently. Three other piscine circoviral sequences appeared closest to sequences derived from different environmental samples. Surprisingly, the nucleotide sequence derived from two fish samples (a bream and a monkey goby) proved to be from porcine circovirus 2 (PCV2), almost identical to a sequence detected in Sweden previously. This is the first report on the detection of PCV2 in fish and circoviral DNA in amphibian hosts.
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Affiliation(s)
- Zoltán Tarján
- 1 Hungarian Academy of Sciences Institute for Veterinary Medical Research, Centre for Agricultural Research P.O. Box 18 Budapest H-1581 Hungary
| | - Judit Pénzes
- 1 Hungarian Academy of Sciences Institute for Veterinary Medical Research, Centre for Agricultural Research P.O. Box 18 Budapest H-1581 Hungary
| | - Róza Tóth
- 1 Hungarian Academy of Sciences Institute for Veterinary Medical Research, Centre for Agricultural Research P.O. Box 18 Budapest H-1581 Hungary
| | - Mária Benkő
- 1 Hungarian Academy of Sciences Institute for Veterinary Medical Research, Centre for Agricultural Research P.O. Box 18 Budapest H-1581 Hungary
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30
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Gholami-Ahangaran M, Fathi-Hafshejani E, Seyed-Hosseini R. Seromolecular study of chicken infectious anemia in chickens, ostriches, and turkeys in Iran. J APPL POULTRY RES 2013. [DOI: 10.3382/japr.2012-00567] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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31
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He B, Li Z, Yang F, Zheng J, Feng Y, Guo H, Li Y, Wang Y, Su N, Zhang F, Fan Q, Tu C. Virome profiling of bats from Myanmar by metagenomic analysis of tissue samples reveals more novel Mammalian viruses. PLoS One 2013; 8:e61950. [PMID: 23630620 PMCID: PMC3632529 DOI: 10.1371/journal.pone.0061950] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Accepted: 03/11/2013] [Indexed: 02/07/2023] Open
Abstract
Bats are reservoir animals harboring many important pathogenic viruses and with the capability of transmitting these to humans and other animals. To establish an effective surveillance to monitor transboundary spread of bat viruses between Myanmar and China, complete organs from the thorax and abdomen from 853 bats of six species from two Myanmar counties close to Yunnan province, China, were collected and tested for their virome through metagenomics by Solexa sequencing and bioinformatic analysis. In total, 3,742,314 reads of 114 bases were generated, and over 86% were assembled into 1,649,512 contigs with an average length of 114 bp, of which 26,698 (2%) contigs were recognizable viral sequences belonging to 24 viral families. Of the viral contigs 45% (12,086/26,698) were related to vertebrate viruses, 28% (7,443/26,698) to insect viruses, 27% (7,074/26,698) to phages and 95 contigs to plant viruses. The metagenomic results were confirmed by PCR of selected viruses in all bat samples followed by phylogenetic analysis, which has led to the discovery of some novel bat viruses of the genera Mamastrovirus, Bocavirus, Circovirus, Iflavirus and Orthohepadnavirus and to their prevalence rates in two bat species. In conclusion, the present study aims to present the bat virome in Myanmar, and the results obtained further expand the spectrum of viruses harbored by bats.
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Affiliation(s)
- Biao He
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, Jilin, China
| | - Zuosheng Li
- Center for Disease Control and Prevention, Chengdu Military Region of the People’s Liberation Army, Kunming, Yunnan, China
| | - Fanli Yang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, Jilin, China
| | - Junfeng Zheng
- Center for Disease Control and Prevention, Chengdu Military Region of the People’s Liberation Army, Kunming, Yunnan, China
| | - Ye Feng
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, Jilin, China
| | - Huancheng Guo
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, Jilin, China
| | - Yingying Li
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, Jilin, China
| | - Yiyin Wang
- Center for Disease Control and Prevention, Chengdu Military Region of the People’s Liberation Army, Kunming, Yunnan, China
| | - Nan Su
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, Jilin, China
| | - Fuqiang Zhang
- Center for Disease Control and Prevention, Chengdu Military Region of the People’s Liberation Army, Kunming, Yunnan, China
| | - Quanshui Fan
- Center for Disease Control and Prevention, Chengdu Military Region of the People’s Liberation Army, Kunming, Yunnan, China
- * E-mail: (QF); (CT)
| | - Changchun Tu
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, Jilin, China
- * E-mail: (QF); (CT)
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32
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Molecular characterisation of beak and feather disease virus (BFDV) in New Zealand and its implications for managing an infectious disease. Arch Virol 2012; 157:1651-63. [PMID: 22638639 DOI: 10.1007/s00705-012-1336-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Accepted: 04/03/2012] [Indexed: 10/28/2022]
Abstract
Beak and feather disease virus (BFDV) infections are often fatal to both captive and wild parrot populations. Its recent discovery in a wild population of native red-fronted parakeets has raised concerns for the conservation of native parrots, all of which are threatened or endangered. The question of a recent introduction versus a native genotype of the virus poses different conservation-management challenges, and thus, a clear understanding of the molecular phylogeny of BDFV is a crucial step towards integrated management planning. This study represents the first comprehensive attempt to screen New Zealand's endangered and threatened psittacines systematically for BFDV. We sampled and screened kakapos (Strigops habroptilus), kakas (Nestor meridionalis), keas (N. notabilis), Chatham parakeets (Cyanoramphus forbesi), Malherbe's parakeets (Cyanoramphus malherbi), yellow-crowned parakeets (C. auriceps) and red-fronted parakeets (Cyanoramphus novaezelandiae), as well as eastern rosellas (Platycercus eximius), an introduced species that is now common throughout the North Island, for BFDV. Out of all species and populations sampled (786 individuals), we found 16 BFDV-positive red-fronted parakeets from Little Barrier Island/Hauturu, seven eastern rosellas from the Auckland region, and eight yellow-crowned parakeets from the Eglinton Valley in the South Island. The full genomes of the viral isolates from the red-fronted parakeets share 95-97 % sequence identity to those from the invasive eastern rosellas and 92.7-93.4 % to those isolates from the South Island yellow-crowned parakeets. The yellow-crowned parakeet BFDV isolates share 92-94 % sequence identity with those from eastern rosellas. The low level of diversity among all BFDV isolates from red-fronted parakeets could suggest a more recent infection among these birds compared to the yellow-crowned parakeets, whereas the diversity in the eastern rosellas indicates a much more established infection. Pro-active screening and monitoring of BFDV infection rates in aviaries as well as in wild populations are necessary to limit the risk of transmission among threatened and endangered parrot populations in New Zealand.
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Delwart E, Li L. Rapidly expanding genetic diversity and host range of the Circoviridae viral family and other Rep encoding small circular ssDNA genomes. Virus Res 2012; 164:114-21. [PMID: 22155583 PMCID: PMC3289258 DOI: 10.1016/j.virusres.2011.11.021] [Citation(s) in RCA: 121] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2011] [Revised: 11/22/2011] [Accepted: 11/23/2011] [Indexed: 11/30/2022]
Abstract
The genomes of numerous circoviruses and distantly related circular ssDNA viruses encoding a rolling circle replication initiator protein (Rep) have been characterized from the tissues of mammals, fish, insects, plants (geminivirus and nanovirus), in human and animal feces, in an algae cell, and in diverse environmental samples. We review the genome organization, phylogenetic relationships and initial prevalence studies of cycloviruses, a proposed new genus in the Circoviridae family. Viral fossil rep sequences were also recently identified integrated on the chromosomes of mammals, frogs, lancelets, crustaceans, mites, gastropods, roundworms, placozoans, hydrozoans, protozoans, land plants, fungi, algae, and phytoplasma bacterias and their plasmids, reflecting the very wide past host range of rep bearing viruses. An ancient origin for viruses with Rep-encoding small circular ssDNA genomes, predating the diversification of eukaryotes, is discussed. The cellular hosts and pathogenicity of many recently described rep-containing circular ssDNA genomes remain to be determined. Future studies of the virome of single cell and multi-cellular eukaryotes are likely to further extend the known diversity and host-range of small rep-containing circular ssDNA viral genomes.
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Affiliation(s)
- Eric Delwart
- Blood Systems Research Institute, San Francisco, CA, USA.
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34
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Patterson EI, Forwood JK, Raidal SR. Homology Modelling and Structural Comparisons of Capsid-Associated Proteins from Circoviruses Reveal Important Virus-Specific Surface Antigens. ACTA ACUST UNITED AC 2012. [DOI: 10.4236/csta.2012.12002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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35
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Molecular study of porcine circovirus type 2 circulating in Portugal. INFECTION GENETICS AND EVOLUTION 2011; 11:2162-72. [DOI: 10.1016/j.meegid.2011.08.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Revised: 08/23/2011] [Accepted: 08/25/2011] [Indexed: 11/19/2022]
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36
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Ge X, Li J, Peng C, Wu L, Yang X, Wu Y, Zhang Y, Shi Z. Genetic diversity of novel circular ssDNA viruses in bats in China. J Gen Virol 2011; 92:2646-2653. [DOI: 10.1099/vir.0.034108-0] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Novel circular ssDNA genomes have recently been detected in animals and in the environment using metagenomic and high-throughput sequencing approaches. In this study, five full-length circular ssDNA genomes were recovered from bat faecal samples using inverse PCR with sequences designed based on circovirus-related sequences obtained from Solexa sequencing data derived from a random amplification method. These five sequences shared a similar genomic organization to circovirus or the recently proposed cyclovirus of the family Circoviridae. The newly obtained circovirus/cyclovirus-like genomes ranged from 1741 to 2177 bp, and each consisted of two major ORFs, ORF1 and ORF2, encoding putative replicase (Rep) and capsid (Cap) proteins, respectively. The potential stem–loop region was predicted in all five genomes, and three of them had the typical conserved nonanucleotide motif of cycloviruses. A set of primers targeting the conserved Rep region was designed and used to detect the prevalence of circovirus/cyclovirus sequences in individual bats. Among 199 samples tested, 47 were positive (23.6 %) for the circovirus genome and two (1.0 %) were positive for the cyclovirus genome. In total, 48 partial Rep sequences plus the five full-length genomes were obtained in this study. Detailed analysis indicated that these sequences are distantly related to known circovirus/cyclovirus genomes and may represent 22 novel species that belong to the family Circoviridae.
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Affiliation(s)
- Xingyi Ge
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, PR China
| | - Jialu Li
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, PR China
| | - Cheng Peng
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, PR China
| | - Lijun Wu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, PR China
| | - Xinglou Yang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, PR China
| | - Yongquan Wu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, PR China
| | - Yunzhi Zhang
- Yunnan Institute of Endemic Diseases Control and Prevention, Dali, PR China
| | - Zhengli Shi
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, PR China
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37
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Wan C, Huang Y, Cheng L, Fu G, Shi SH, Chen H, Peng C, Lin F, Lin J. The development of a rapid SYBR Green I-based quantitative PCR for detection of Duck circovirus. Virol J 2011; 8:465. [PMID: 21978576 PMCID: PMC3198713 DOI: 10.1186/1743-422x-8-465] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Accepted: 10/07/2011] [Indexed: 11/10/2022] Open
Abstract
This report describes a one-step real-time polymerase chain reaction assay based on SYBR Green I for detection of a broad range of duck circovirus (DuCV). Align with all DuCV complete genome sequences and other Genus Circovirus download from the GenBank (such as goose circovirus, pigeon circovirus), the primers targets to the replicate gene of DuCV were designed. The detection assay was linear in the range of 1.31 × 102-1.31 × 107 copies/μL. The reaction efficiency of the assay using the slope (the slope was -3.349) and the Y-intercept was 37.01 from the linear equation was estimated to be 0.99 and the correlation coefficient (R2) was 0.993. A series of experiments were carried out to assess the reproducibility, sensitivity, and specificity of the assay, following by the low intra-assay and inter-assay CVs for CT values obtained with the standard plasmids. The intra-assay CVs were equal or less than 1.89% and the inter-assay CVs were equal or less than 1.26%. There was no cross-reaction occurred with nucleic acids extracted from RA (Riemerella anatipestifer), E. coli (Escherichia coli), Duck Cholera (Pasteurella multocida), Avian influenza virus, avian paramyxovirus, Muscovy duck parvovirus, Duck reovirus, Duck hepatitis A virus as control templates. The nucleic acids extracted from samples of healthy ducks were used as negative controls. The assay was specific and reproducible. The established real time PCR was used to detect 45 DuCV-negative samples, which were tested using conventional PCR under the developed optimal conditions, each 15 for embryonated eggs, non-embryonated budgerigar eggs, newly hatched duck, the mixture of the lung, liver, spleen which were analysis for the presence of DuCV DNA, to conform that whether the DuCV can be transmitted vertically. Meanwhile, no positive result was shown by the real-time PCR method. The SYBR Green I-based quantitative PCR can therefore be practically used as an alternative diagnostic tool and a screening method for ducks infected with duck circovirus.
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Affiliation(s)
- Chunhe Wan
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
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38
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Epidemiological investigation and genome analysis of duck circovirus in Southern China. Virol Sin 2011; 26:289-96. [PMID: 21979568 DOI: 10.1007/s12250-011-3192-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2011] [Accepted: 08/03/2011] [Indexed: 10/17/2022] Open
Abstract
Duck circovirus (DuCV), a potential immunosuppressive virus, was investigated in Southern China from March 2006 to December 2009 by using a polymerase chain reaction (PCR) based method. In this study, a total of 138 sick or dead duck samples from 18 different farms were examined with an average DuCV infection rate of ∼35%. It was found that ducks between the ages of 40∼60 days were more susceptible to DuCV. There was no evidence showing that the DuCV virus was capable of vertical transmission. Farms with positive PCR results exhibited no regularly apparent clinical abnormalities such as feathering disorders, growth retardation or lower-than-average weight. The complete genomes of 9 strains from Fujian Province and 1 from Zhejiang Province were sequenced and analyzed. The 10 DuCV genomes, compared with others genomes downloaded from GenBank, ranged in size from 1988 to 1996 base pairs, with sequence identities ranging from 83.2% to 99.8%. Phylogenetic analysis based on genome sequences demonstrated that DuCVs can be divided into two distinct genetic genotypes, Group I (the Euro-USA lineage) and Group II (the Taiwan lineage), with approximately 10.0% genetic difference between the two types. Molecular epidemiological data suggest there is no obvious difference among DuCV strains isolated from different geographic locations or different species, including Duck, Muscovy duck, Mule duck, Cheery duck, Mulard duck and Pekin duck.
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39
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Li L, Shan T, Soji OB, Alam MM, Kunz TH, Zaidi SZ, Delwart E. Possible cross-species transmission of circoviruses and cycloviruses among farm animals. J Gen Virol 2010; 92:768-72. [PMID: 21177928 DOI: 10.1099/vir.0.028704-0] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Circoviruses consist of highly prevalent and genetically diverse porcine and avian pathogens. The genomes of cycloviruses, a proposed new genus in the family Circoviridae, were recently identified in human and chimpanzee faeces. Here, six cyclovirus and four circovirus genomes from the tissues of chickens, goats, cows, and a bat were amplified and sequenced using rolling-circle amplification and inverse PCR. A goat cyclovirus was nearly identical to a cyclovirus from a cow. USA beef contained circoviruses with >99% similarity to porcine circovirus 2b. Circoviruses in chicken were related to those of pigeons. The close genetic similarity of a subset of cycloviruses and circoviruses replicating in distinct animal species may reflect recent cross-species transmissions. Further studies will be required to determine the impact of these highly prevalent infections on the health of farm animals.
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Affiliation(s)
- Linlin Li
- Blood Systems Research Institute, San Francisco, CA 94118, USA
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40
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Henriques AM, Fagulha T, Duarte M, Ramos F, Barros S, Luís T, Bernardino R, Fevereiro M. Phylogenetic analysis of six isolates of beak and feather disease virus from African grey parrots in Portugal. Avian Dis 2010; 54:1066-71. [PMID: 20945789 DOI: 10.1637/9120-110309-resnote.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Beak and feather disease virus (BFDV), a member of the genus Circovirus, was detected in six dead African grey parrots (Psittacus erithacus) in Portugal. The complete nucleotide sequences of these six BFDVs (PT05, PT08, PT08-2, PT08-3, PT09, and PT09-2) were determined and analyzed. The seven open reading frames (ORFs) described for other BFDVs were detected in all strains, except for PT05 and PT08, in which ORFs 4 and 7 are absent. Bayesian inference of phylogeny based on complete genomes of BFDVs isolated in Portugal and 32 other BFDVs found in other parts of the world revealed that PT05 is included in lineage IV, whereas the others form a new proposed genotype lineage IX. The nucleotide diversity ranged from 2% to 12% between the BFDV strains isolated in Portugal and other BFDVs found worldwide.
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Affiliation(s)
- A M Henriques
- Laboratório Nacional de Investigação Veterinária, Departamento de Virologia, Estrada de Benfica 701, 1549-011 Lisboa, Portugal
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41
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DNA-binding specificity determinants of replication proteins encoded by eukaryotic ssDNA viruses are adjacent to widely separated RCR conserved motifs. Arch Virol 2010; 155:1033-46. [PMID: 20422235 DOI: 10.1007/s00705-010-0674-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2009] [Accepted: 03/22/2010] [Indexed: 10/19/2022]
Abstract
Eukaryotic ssDNA viruses encode a rolling-circle replication (RCR) initiation protein, Rep, which binds to iterated DNA elements functioning as essential elements for virus-specific replication. By using the iterons of all known circoviruses, nanoviruses and nanovirus-like satellites as heuristic devices, we have identified certain amino acid residues that presumably determine the DNA-binding specificity of their Rep proteins. These putative "specificity determinants" (SPDs) cluster in two discrete protein regions, which are adjacent to distinct conserved motifs. A comparable distribution of SPDs was uncovered in the Rep protein of geminiviruses. Modeling of the tertiary structure of diverse Rep proteins showed that SPD regions interact to form a small beta-sheet element that has been proposed to be critical for high-affinity DNA-binding of Rep. Our findings indicate that eukaryotic circular ssDNA viruses have a common ancestor and suggest that SPDs present in replication initiators from a huge variety of viral and plasmid RCR systems are associated with the same conserved motifs.
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Multiple diverse circoviruses infect farm animals and are commonly found in human and chimpanzee feces. J Virol 2009; 84:1674-82. [PMID: 20007276 DOI: 10.1128/jvi.02109-09] [Citation(s) in RCA: 289] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Circoviruses are known to infect birds and pigs and can cause a wide range of severe symptoms with significant economic impact. Using viral metagenomics, we identified circovirus-like DNA sequences and characterized 15 circular viral DNA genomes in stool samples from humans in Pakistan, Nigeria, Tunisia, and the United States and from wild chimpanzees. Distinct genomic features and phylogenetic analysis indicate that some viral genomes were part of a previously unrecognized genus in the Circoviridae family we tentatively named "Cyclovirus" whose genetic diversity is comparable to that of all the known species in the Circovirus genus. Circoviridae detection in the stools of U.S. adults was limited to porcine circoviruses which were also found in most U.S. pork products. To determine whether the divergent cycloviruses found in non-U.S. human stools were of dietary origin, we genetically compared them to the cycloviruses in muscle tissue samples of commonly eaten farm animals in Pakistan and Nigeria. Limited genetic overlap between cycloviruses in human stool samples and local cow, goat, sheep, camel, and chicken meat samples indicated that the majority of the 25 Cyclovirus species identified might be human viruses. We show that the genetic diversity of small circular DNA viral genomes in various mammals, including humans, is significantly larger than previously recognized, and frequent exposure through meat consumption and contact with animal or human feces provides ample opportunities for cyclovirus transmission. Determining the role of cycloviruses, found in 7 to 17% of non-U.S. human stools and 3 to 55% of non-U.S. meat samples tested, in both human and animal diseases is now facilitated by knowledge of their genomes.
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Duchatel JP, Todd D, Willeman C, Losson B. Quantification of pigeon circovirus in serum, blood, semen and different tissues of naturally infected pigeons using a real-time polymerase chain reaction. Avian Pathol 2009; 38:143-8. [PMID: 19322713 DOI: 10.1080/03079450902737805] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The development of a real-time polymerase chain reaction (PCR) based on SYBR Green chemistry is described for the quantification of pigeon circovirus (PiCV) DNA in various samples. Plasmid containing a fragment of the PiCV genome was used to create a standard curve and to estimate the viral DNA copies in analysed samples. Both primers were designed in highly conserved regions to avoid false negatives, and amplified a 139-base-pair amplicon. When the amplifications were performed in the presence of cellular DNA extracted from PCR-negative liver, bursa and spleen samples, the detection limits were respectively 20, 20 and 60 copies of genome per milligram of tissue. These limits were 10, 160 and 25 copies/microl for control blood, sera and semen, respectively. For cloacal swab, the detection limit was 200 copies. The assay showed a linear detection over a six-log range (R(2)>0.99) and displayed reliable inter-assay and intra-assay reproducibility. Application of the test to sera samples indicated the presence of the virus in Belgium in 1991, 6 years before PiCV infections were histologically diagnosed. Testing of samples from pigeons with "young pigeon sickness" showed that the viral loads were high in the bursa of Fabricius (up to 2.07 x 10(9) copies/mg), the liver (up to 2.88 x 10(8) copies/mg) and spleen (up to 5.57 x 10(8) copies/mg). For liver, the viral load was significantly higher in sick pigeons than in apparently healthy pigeons. Detection of high quantities of PiCV DNA (up to 1.6 x 10(9) copies/microl) in the sera or blood of some young healthy pigeons indicated that the viral load in this sample type would not be useful as predictive indicator of disease. This work also showed that PiCV DNA can be detected in relatively large amounts in semen (up to 1.0 x 10(7) copies/ejaculate) and cloacal swabs (up to 3.6 x 10(10) copies/swab), confirming that PiCV may be transmitted by vertical and horizontal routes.
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Affiliation(s)
- J P Duchatel
- Faculty of Veterinary Medicine, Department of Infections and Parasitic Diseases, University of Liège, Liège, Belgium.
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Detection of a novel circovirus in mute swans (Cygnus olor) by using nested broad-spectrum PCR. Virus Res 2008; 132:208-12. [DOI: 10.1016/j.virusres.2007.11.001] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2007] [Revised: 10/31/2007] [Accepted: 11/01/2007] [Indexed: 11/24/2022]
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Todd D, Fringuelli E, Scott ANJ, Borghmans BJ, Duchatel JP, Shivaprasad HL, Raidal SR, Abadie JX, Franciosini MP, Smyth JA. Sequence comparison of pigeon circoviruses. Res Vet Sci 2007; 84:311-9. [PMID: 17493647 DOI: 10.1016/j.rvsc.2007.03.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2006] [Revised: 01/24/2007] [Accepted: 03/18/2007] [Indexed: 10/23/2022]
Abstract
The genome sequences of eight pigeon circoviruses (PiCV) were determined and compared with four previously published sequences. The viruses compared were from the USA, five European countries, China and Australia and included PiCVs from racing, feral, ornamental and meat pigeons and a Senegal dove (Streptopelia senegalensis). The 12 PiCV genomes, ranging from 2032 to 2040 nucleotides in length, displayed similar organizations. Pairwise comparisons showed that the genome nucleotide sequence identities ranged from 85.1% to 97.8% and that the amino acid identities of the putative replication associated (Rep) and putative capsid (Cap) proteins displayed ranges of 91.5-99.1% and 73.0-99.3%, respectively. Comparative analyses identified conserved nucleotide sequences within the Rep gene and 3' intergenic regions, which would be suitable for diagnostic PCR primers, and variable amino acid sequences within the capsid proteins, which should be considered when selecting virus isolates for vaccine development.
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Affiliation(s)
- D Todd
- Veterinary Sciences Division, Agri-Food and Biosciences Institute, Stormont, Belfast, UK.
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