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Arhab Y, Pestova TV, Hellen CUT. Translation of Overlapping Open Reading Frames Promoted by Type 2 IRESs in Avian Calicivirus Genomes. Viruses 2024; 16:1413. [PMID: 39339889 PMCID: PMC11436067 DOI: 10.3390/v16091413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2024] [Revised: 08/30/2024] [Accepted: 08/31/2024] [Indexed: 09/30/2024] Open
Abstract
Caliciviruses have positive-sense RNA genomes, typically with short 5'-untranslated regions (5'UTRs) that precede the long open reading frame 1 (ORF1). Exceptionally, some avian caliciviruses have long 5'UTRs containing a picornavirus-like internal ribosomal entry site (IRES), which was likely acquired by horizontal gene transfer. Here, we identified numerous additional avian calicivirus genomes with IRESs, predominantly type 2, and determined that many of these genomes contain a ~200-300 codon-long ORF (designated ORF1*) that overlaps the 5'-terminal region of ORF1. The activity of representative type 2 IRESs from grey teal calicivirus (GTCV) and Caliciviridae sp. isolate yc-13 (RaCV1) was confirmed by in vitro translation. Toeprinting showed that in cell-free extracts and in vitro reconstituted reactions, ribosomal initiation complexes assembled on the ORF1* initiation codon and at one or two AUG codons in ORF1 at the 3'-border and/or downstream of the IRES. Initiation at all three sites required eIF4A and eIF4G, which bound to a conserved region of the IRES; initiation on the ORF1* and principal ORF1 initiation codons involved eIF1/eIF1A-dependent scanning from the IRES's 3'-border. Initiation on these IRESs was enhanced by the IRES trans-acting factors (ITAFs) Ebp1/ITAF45, which bound to the apical subdomain Id of the IRES, and PTB (GTCV) or PCBP2 (RaCV1).
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Affiliation(s)
- Yani Arhab
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, NY 11203, USA
| | - Tatyana V Pestova
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, NY 11203, USA
| | - Christopher U T Hellen
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, NY 11203, USA
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2
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Dai Z, Lu Q, Sun M, Chen H, Zhu R, Wang H. Identification of a Novel Parvovirus in the Arctic Wolf ( Canis lupus arctos). Pol J Microbiol 2024; 73:395-401. [PMID: 39268953 PMCID: PMC11395419 DOI: 10.33073/pjm-2024-035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Accepted: 08/06/2024] [Indexed: 09/15/2024] Open
Abstract
A novel virus, temporarily named "Arctic wolf parvovirus" (AWPV), was discovered in a pharyngeal metagenomic library derived from an Arctic wolf (Canis lupus arctos) in China. The genome sequence was assigned GenBase accession number C_AA071902.1. AWPV has a genome comprised of 4,920 base pairs with a nucleotide composition of 36.4% A, 23.4% T, 18.2% G, and 22.0% C, with a GC content of 40.2%. Its structure resembles parvoviruses, containing two open reading frames: the nonstructural (NS) region encoding replication enzymes and the structural (VP) region encoding capsid protein. Pairwise sequence comparison and phylogenetic analysis suggest AWPV may represent a novel species within the genus Protoparvovirus. This discovery enhances our understanding of mammalian virus ecology and potential future infectious diseases.
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Affiliation(s)
- Ziyuan Dai
- Department of Clinical Laboratory, Affiliated Hospital 6 of Nantong University, Yancheng Third People’s Hospital, Yancheng, China
| | - Qiang Lu
- Department of Clinical Laboratory, Affiliated Hospital 6 of Nantong University, Yancheng Third People’s Hospital, Yancheng, China
| | - Mingzhong Sun
- Department of Clinical Laboratory, Affiliated Hospital 6 of Nantong University, Yancheng Third People’s Hospital, Yancheng, China
| | - Hongmei Chen
- Department of Clinical Laboratory, Affiliated Hospital 6 of Nantong University, Yancheng Third People’s Hospital, Yancheng, China
| | - Rong Zhu
- Department of Clinical Laboratory, Affiliated Hospital 6 of Nantong University, Yancheng Third People’s Hospital, Yancheng, China
| | - Huiqing Wang
- Department of Clinical Laboratory, Affiliated Hospital 6 of Nantong University, Yancheng Third People’s Hospital, Yancheng, China
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Peng L, Yang F, Shi J, Liu Y, Pan L, Mao D, Luo Y. Insights into the panorama of multiple DNA viruses in municipal wastewater and recycled sludge in Tianjin, China. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 355:124215. [PMID: 38797349 DOI: 10.1016/j.envpol.2024.124215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 05/06/2024] [Accepted: 05/23/2024] [Indexed: 05/29/2024]
Abstract
Environmental viruses in wastewater and sludge are widely recognized for their roles in waterborne diseases. However, previous studies mainly focused on RNA viruses, and little is known about the diversity of DNA viral communities and their driving factors in municipal wastewater treatment environments. Herein, we conducted a pilot study to explore DNA virus profiles in municipal wastewater and recycled sludge by metagenomics method, and track their temporal changes in northern China. Results showed that 467 viral species were co-shared among all the samples. We identified six families of human viruses with a prevalence of 0.1%, which were rare but relatively stable in wastewater and sludge for six months. Adenoviridae, Parvoviridae, and Herpersviridae were the most dominant human viral families in municipal wastewater and recycled sludge. A time series of samples revealed that the dynamic changes of human DNA viruses were stable based on qPCR results, particularly for high-risk fecal-oral transmission viruses of adenovirus, bocavirus, polyomavirus, human gamma herpesvirus, human papillomavirus, and hepatitis B virus. Concentrations of Adenovirus (5.39-7.48 log10 copies/L) and bocavirus (4.36-7.48 log10 copies/L) were observed to be the highest in these samples compared to other viruses. Our findings demonstrated the DNA viruses' high prevalence and persistence in municipal wastewater treatment environments, highlighting the value of enhancing public health responses based on wastewater-based epidemiology.
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Affiliation(s)
- Liang Peng
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin, 300071, China
| | - Fengxia Yang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Jingliang Shi
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin, 300071, China
| | - YiXin Liu
- School of Medicine, Nankai University, Tianjin, 300071, China
| | - Liuzhu Pan
- School of Medicine, Nankai University, Tianjin, 300071, China
| | - Daqing Mao
- School of Medicine, Nankai University, Tianjin, 300071, China
| | - Yi Luo
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin, 300071, China; State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210093, China.
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4
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Baril C, Cassone BJ. Metatranscriptomic analysis of common mosquito vector species in the Canadian Prairies. mSphere 2024; 9:e0020324. [PMID: 38912793 PMCID: PMC11288045 DOI: 10.1128/msphere.00203-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 05/05/2024] [Indexed: 06/25/2024] Open
Abstract
The microbiome plays vital roles in the life history of mosquitoes, including their development, immunity, longevity, and vector competence. Recent advances in sequencing technologies have allowed for detailed exploration into the diverse microorganisms harbored by these medically important insects. Although these meta-studies have cataloged the microbiomes of mosquitoes in several continents, much of the information currently available for North America is limited to the state of California. In this study, we collected >35,000 mosquitoes throughout Manitoba, Canada, over a 3-year period and then harnessed RNA sequencing and targeted reverse transcriptase-PCR to characterize the microbiomes of the eight most pervasive and important vector and pest species. The consensus microbiome of each species was overwhelmingly composed of viruses but also included fungi, bacteria, protozoa, and parasitic invertebrates. The microbial assemblages were heterogeneous between species, even within the same genus. We detected notable pathogens, including the causal agents of Cache Valley Fever, avian malaria, and canine heartworm. The remaining microbiome consisted largely of putatively insect-specific viruses that are not well characterized, including 17 newly discovered viruses from 10 different families. Future research should focus on evaluating the potential application of these viruses in biocontrol, as biomarkers, and/or in disrupting mosquito vectorial capacity. Interestingly, we also detected viruses that naturally infect honeybees and thrips, which were presumably acquired indirectly through nectar foraging behaviors. Overall, we provide the first comprehensive catalog of the microorganisms harbored by the most common and important mosquito vectors and pests in the Canadian Prairies. IMPORTANCE Mosquitoes are the most dangerous animals on the planet, responsible for over 800,000 deaths per year globally. This is because they carry and transmit a plethora of human disease-causing microorganisms, such as West Nile virus and the malaria parasite. Recent innovations in nucleic acid sequencing technologies have enabled researchers unparalleled opportunities to characterize the suite of microorganisms harbored by different mosquito species, including the causal agents of disease. In our study, we carried out 3 years of intensive mosquito surveillance in Canada. We collected and characterized the microorganisms harbored by >35,000 mosquitoes, including the identification of the agents of Cache Valley fever, avian malaria, and canine heartworm. We also detected insect-specific viruses and discovered 17 new viruses that have never been reported. This study, which is the first of its kind in Canada and one of only a handful globally, will greatly aid in future infectious disease research.
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Affiliation(s)
- Cole Baril
- Department of Biology, Brandon University, Brandon, Manitoba, Canada
| | - Bryan J. Cassone
- Department of Biology, Brandon University, Brandon, Manitoba, Canada
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Zhang Y, Talukder S, Bhuiyan MSA, He L, Sarker S. Opportunistic sampling of yellow canary (Crithagra flaviventris) has revealed a high genetic diversity of detected parvoviral sequences. Virology 2024; 595:110081. [PMID: 38599030 DOI: 10.1016/j.virol.2024.110081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 03/18/2024] [Accepted: 04/03/2024] [Indexed: 04/12/2024]
Abstract
Parvoviruses are known to be significant viral pathogens that infect a wide range of species globally. However, little is known about the parvoviruses circulating in Australian birds, including yellow canaries. Here, we present four parvoviral sequences including three novel parvoviruses detected from 10 yellow canaries (Crithagra flaviventris), named canary chaphamaparvovirus 1 and -2 (CaChPV1 and CaChPV2), canary dependoparvovirus 1 and -2 (CaDePV1 and CaDePV2). The whole genome sequences of CaChPV1, CaChPV2, CaDePV1, and CaDePV2 showed the highest identity with other parvoviruses at 76.4%, 75.9%, 84.0%, and 59.1%, respectively. Phylogenetic analysis demonstrated that CaChPV1 and CaChPV2 were clustered within the genus Chaphamaparvovirus. Meanwhile, CaDePV1 and CaDePV2 fall within the genus Dependoparvovirus and have the closest evolutionary relationship to the bird-associated dependoparvoviruses. Overall, this study enriched our understanding of the genetic diversity among avian parvoviruses within the Parvoviridae family.
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Affiliation(s)
- Yuhao Zhang
- The Key Lab of Animal Disease and Public Health /Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, Henan University of Science and Technology, Luoyang, 471023, Henan, China
| | - Saranika Talukder
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, 4811, Australia
| | - Md Safiul Alam Bhuiyan
- Faculty of Sustainable Agriculture, Livestock Production, Universiti Malaysia Sabah, Sandakan, Sabah, Malaysia
| | - Lei He
- The Key Lab of Animal Disease and Public Health /Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, Henan University of Science and Technology, Luoyang, 471023, Henan, China.
| | - Subir Sarker
- Biomedical Sciences & Molecular Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD 4811, Australia.
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Li Y, Zhang L, Wang L, Li J, Zhao Y, Liu F, Wang Q. Structure and function of type IV IRES in picornaviruses: a systematic review. Front Microbiol 2024; 15:1415698. [PMID: 38855772 PMCID: PMC11157119 DOI: 10.3389/fmicb.2024.1415698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 05/13/2024] [Indexed: 06/11/2024] Open
Abstract
The Picornaviridae is a family of icosahedral viruses with single-stranded, highly diverse positive-sense RNA genomes. Virions consist of a capsid, without envelope, surrounding a core of RNA genome. A typical genome of picornavirus harbors a well-conserved and highly structured RNA element known as the internal ribosome entry site (IRES), functionally essential for viral replication and protein translation. Based on differences in their structures and mechanisms of action, picornaviral IRESs have been categorized into five types: type I, II, III, IV, and V. Compared with the type IV IRES, the others not only are structurally complicated, but also involve multiple initiation factors for triggering protein translation. The type IV IRES, often referred to as hepatitis C virus (HCV)-like IRES due to its structural resemblance to the HCV IRES, exhibits a simpler and more compact structure than those of the other four. The increasing identification of picornaviruses with the type IV IRES suggests that this IRES type seems to reveal strong retention and adaptation in terms of viral evolution. Here, we systematically reviewed structural features and biological functions of the type IV IRES in picornaviruses. A comprehensive understanding of the roles of type IV IRESs will contribute to elucidating the replication mechanism and pathogenesis of picornaviruses.
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Affiliation(s)
- Yan Li
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
- Qingdao Center for Animal Disease Control and Prevention, Qingdao, China
| | - Lei Zhang
- Shandong New Hope Liuhe Group Co., Ltd., Qingdao, China
| | - Ling Wang
- University Hospital, Qingdao Agricultural University, Qingdao, China
| | - Jing Li
- Market Supervision Administration of Huangdao District, Qingdao, China
| | - Yanwei Zhao
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Fuxiao Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Qianqian Wang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
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de Moraes Pires WM, Cruz ACR, de Souza AJS, Silva SP, Souza Barbosa Coelho TF, Dias DD, Rosa Júnior JW, Mendes SB, da Costa Fraga E, Barros MC, Sampaio I. Genomic characterization of a novel Hepatovirus identified in Maranhão state, Brazil. Sci Rep 2024; 14:7981. [PMID: 38575654 PMCID: PMC10995186 DOI: 10.1038/s41598-024-58171-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 03/26/2024] [Indexed: 04/06/2024] Open
Abstract
Bats are efficient reservoirs of a number of viruses with zoonotic potential, and are involved directly in the transmission cycle of many zoonoses. In the present study, which is part of a larger project that is documenting the viromes of the bat species found in the Mid-North states of Maranhão and Piauí, we analyzed 16 pooled samples obtained from four species of bat of the genus Artibeus-Artibeus obscurus, Artibeus cinereus, Artibeus lituratus and Artibeus planirostris. We describe and identify a Hepatovirus, denominated Hepatovirus H isolate sotense, which was found in a pool of internal organs (liver and lungs) extracted from a specimen of A. planirostris, a frugivorous bat, collected in the Cerrado biome of Maranhão state. This material was analyzed using new generation sequencing, which produced a contig of 7390 nucleotides and presented a degree of identity with a number of existing Hepatovirus sequences available for bats (amino acid identity of 61.5% with Bat hepatovirus C of Miniopterus cf. manavi, 66.6% with Bat hepatovirus G of Coleura afra, 67.4% with Hepatovirus G2 of Rhinolophus landeri, and 75.3% with Hepatovirus H2 of Rhinolophus landeri). The analysis of the functional domains of this contig confirmed a pattern consistent with the characteristics of the genus Hepatovirus (Picornaviridae). In the phylogenetic tree with several other Hepatovirus species, this genome also grouped in a monophyletic clade with Hepatovirus H (HepV-H1; HepV-H2, and HepV-H3) albeit on an external branch, which suggests that it may be a distinct genotype within this species. This is the first isolate of Hepatovirus H identified in bats from South America, and represents an important discovery, given that most studies of viruses associated with bats in the state of Maranhão have focused on the family Rhabdoviridae.
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Affiliation(s)
| | - Ana Cecília Ribeiro Cruz
- Department of Arbovirology and Hemorrhagic Fevers, Instituto Evandro Chagas IEC/SVS/MS, Ananindeua, Pará, 67030-000, Brazil
| | - Alex Junior Souza de Souza
- Department of Pathology, School of Veterinary Medicine and Animal Science, University of São Paulo (USP), São Paulo, Brazil
| | - Sandro Patroca Silva
- Department of Arbovirology and Hemorrhagic Fevers, Instituto Evandro Chagas IEC/SVS/MS, Ananindeua, Pará, 67030-000, Brazil
| | | | - Daniel Damous Dias
- Laboratory of Medical Entomology, Instituto Evandro Chagas IEC/SVS/MS, Ananindeua, Pará, 67030-000, Brazil
| | - José Wilson Rosa Júnior
- Department of Arbovirology and Hemorrhagic Fevers, Instituto Evandro Chagas IEC/SVS/MS, Ananindeua, Pará, 67030-000, Brazil
| | - Samira Brito Mendes
- Graduate Program in Biodiversity and Biotechnology-Bionorte Network, Laboratory of Genetics and Molecular Biology, Universidade Estadual do Maranhão, São Luís, Maranhão, 65055-310, Brazil
| | - Elmary da Costa Fraga
- Laboratory of Genetics and Molecular Biology-GENBIMOL, Universidade Estadual Do Maranhão-Campus Caxias, Caxias, Maranhão, 65604-380, Brazil
| | - Maria Claudene Barros
- Laboratory of Genetics and Molecular Biology-GENBIMOL, Universidade Estadual Do Maranhão-Campus Caxias, Caxias, Maranhão, 65604-380, Brazil
| | - Iracilda Sampaio
- Laboratory of Evolution, Institute of Coastal Studies, Universidade Federal do Pará-UFPA-UFPA, Bragança, Pará, 68600-000, Brazil
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Li S, Huo X, Mu Y, Liu X, Wu J, Chen Y, Wang Y. TaqMan-based real-time polymerase chain reaction for the detection of feline chaphamaparvovirus. 3 Biotech 2024; 14:61. [PMID: 38344284 PMCID: PMC10850043 DOI: 10.1007/s13205-024-03917-8] [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: 03/20/2023] [Accepted: 01/03/2024] [Indexed: 03/10/2024] Open
Abstract
Feline chaphamaparvovirus (FeChPV) is a new viral strain detected in Chinese Mainland in recent years. The symptoms mainly include diarrhea and bloody stool in young cats, which can lead to death in severe cases. In this study, a TaqMan-based real-time quantitative PCR (qPCR) with specific primers and TaqMan probes based on the VP1 gene sequence of FeChPV was performed to detect the virus. The established qPCR indicated that there is no cross-reaction of FeChPV with other common feline viruses. The minimum detection limit of the established qPCR method is 3.75 × 10 copies/µL, while conventional PCR is 3.75 × 103 copies/µL. The result that the proposed qPCR protocol was shown to be 100 times more sensitive than conventional PCR. The correlation coefficients exceeded 0.995, and the amplification efficiency was 98%. The difference within and between groups is less than 5%, indicating that the established method has good repeatability. The results of clinical sample detection shown that 16 positive samples were detected from 45 stool samples by the established qPCR method. The conventional PCR method only detected 3 positive samples. In conclusion, the established qPCR method is fast and effective in identifying FeChPV, with higher specificity and sensitivity. It could be used as a diagnostic tool to quantitatively detect the virus content, which is conducive to disease monitoring and epidemiological investigation.
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Affiliation(s)
- Shuyan Li
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036 People’s Republic of China
| | - Xinrui Huo
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036 People’s Republic of China
| | - Yuanyuan Mu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036 People’s Republic of China
| | - Xuan Liu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036 People’s Republic of China
| | - Jing Wu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036 People’s Republic of China
| | - Yumeng Chen
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036 People’s Republic of China
| | - Yong Wang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036 People’s Republic of China
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Cui N, Yang X, Sui H, Tan L, Wang W, Su S, Qi L, Huang Q, Hrabchenko N, Xu C. Virome characterization of diarrheic red-crowned crane (G. japonensis). Anim Microbiome 2024; 6:8. [PMID: 38419121 PMCID: PMC10902971 DOI: 10.1186/s42523-024-00299-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 02/26/2024] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND The red-crowned crane is one of the vulnerable bird species. Although the captive population has markedly increased over the last decade, infectious diseases can lead to the death of young red-crowned cranes while few virological studies have been conducted. METHODS Using a viral metagenomics approach, we analyzed the virome of tissues of the dead captive red-crowned crane with diarrhea symptoms in Dongying Biosphere Reserve, Shandong Province, China and feces of individual birds breeding at the corresponding captive breeding center, which were pooled separately. RESULTS There is much more DNA and RNA viruses in the feces than that of the tissues. RNA virus belonging to the families Picornaviridae, and DNA viruses belonging to the families Parvoviridae, associated with enteric diseases were detected in the tissues and feces. Genomes of the picornavirus, genomovirus, and parvovirus identified in the study were fully characterized, which further suggested that infectious viruses of these families were possibly presented in the diseased red-crowned crane. CONCLUSION RNA virus belonging to the families Picornaviridae, and DNA viruses belonging to the families Genomoviridae and Parvoviridae were possibly the causative agent for diarrhea of red-crowned crane. This study has expanded our understanding of the virome of red-crowned crane and provides a baseline for elucidating the etiology for diarrhea of the birds.
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Affiliation(s)
- Ning Cui
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Jinan, China
| | - Xiao Yang
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Jinan, China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Veterinary Medicine, Shandong Agricultural University, Tai'an, China
| | - Hong Sui
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Jinan, China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Veterinary Medicine, Shandong Agricultural University, Tai'an, China
| | - Liugang Tan
- Dongying Animal Husbandry and Veterinary Station, Dongying, China
| | - Weihua Wang
- National Nature Reserve Management Committee of Shandong Yellow River Triangle, Dongying, China
| | - Shuai Su
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Veterinary Medicine, Shandong Agricultural University, Tai'an, China
| | - Lihong Qi
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Jinan, China
| | - Qinghua Huang
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China.
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Jinan, China.
| | - Nataliia Hrabchenko
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China.
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Jinan, China.
| | - Chuantian Xu
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China.
- Key Laboratory of Livestock and Poultry Multi-omics of MARA, Jinan, China.
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10
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Hess SC, Weiss KCB, Custer JM, Lewis JS, Kraberger S, Varsani A. Identification of small circular DNA viruses in coyote fecal samples from Arizona (USA). Arch Virol 2023; 169:12. [PMID: 38151635 DOI: 10.1007/s00705-023-05937-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 11/22/2023] [Indexed: 12/29/2023]
Abstract
Coyotes (Canis latrans) have a broad geographic distribution across North and Central America. Despite their widespread presence in urban environments in the USA, there is limited information regarding viruses associated with coyotes in the USA and in particular the state of Arizona. To explore viruses associated with coyotes, particularly small DNA viruses, 44 scat samples were collected (April-June 2021 and November 2021-January 2022) along the Salt River near Phoenix, Arizona (USA), along 43 transects (500 m). From these samples, we identified 11 viral genomes: two novel circoviruses, six unclassified cressdnaviruses, and two anelloviruses. One of the circoviruses is most closely related to a circovirus sequence identified from an aerosolized dust sample in Arizona, USA. The second circovirus is most closely related to a rodent-associated circovirus and canine circovirus. Of the unclassified cressdnaviruses, three encode replication-associated proteins that are similar to those found in protists (Histomonas meleagridis and Monocercomonoides exilis), implying an evolutionary relationship with or a connection to similar unidentified protist hosts. The two anelloviruses are most closely related to those found in rodents, and this suggests a diet-related identification.
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Affiliation(s)
- Savage C Hess
- The School of Life Sciences, Arizona State University, 427 E Tyler Mall, Tempe, AZ, 85281, USA
| | - Katherine C B Weiss
- The School of Life Sciences, Arizona State University, 427 E Tyler Mall, Tempe, AZ, 85281, USA
| | - Joy M Custer
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ, 85287, USA
| | - Jesse S Lewis
- College of Integrative Sciences and Arts, Arizona State University, Polytechnic Campus, 6073 South Backus Mall, Mesa, AZ, 85212, USA
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ, 85287, USA
| | - Arvind Varsani
- The School of Life Sciences, Arizona State University, 427 E Tyler Mall, Tempe, AZ, 85281, USA.
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ, 85287, USA.
- Center of Evolution and Medicine, Arizona State University, 427 E Tyler Mall, Tempe, AZ, 85281, USA.
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, 7925, South Africa.
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11
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Piewbang C, Lohavicharn P, Nguyen TV, Punyathi P, Kasantikul T, Techangamsuwan S. Carnivore chaphamaparvovirus-1 (CaChPV-1) infection in diarrheic dogs reveals viral endotheliotropism in intestine and lung. Vet Q 2023; 43:1-10. [PMID: 36846895 PMCID: PMC10013547 DOI: 10.1080/01652176.2023.2185696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
BACKGROUND Carnivore chaphamaparvovirus-1 (CaChPV-1) is a parvovirus identified in dogs and association of infection with diarrhea is controversial. Information on whether tissue tropism persists is lacking. OBJECTIVES To determine the disease association of CaChPV-1 in dogs with diarrhea and to investigate viral tropism and genetic diversity. ANIMALS AND METHODS CaChPV-1 infection was investigated in five recently deceased puppies and designed a retrospective study to determine whether the presence of CaChPV-1 is associated with diarrhea. The retrospective study was conducted in 137 intestinal tissue samples and 168 fecal samples obtained from 305 dogs. CaChPV-1 tissue localization was determined using in situ hybridization, and CaChPV-1 complete genomes obtained from dead puppies and retrospective study were sequenced and analyzed. RESULTS CaChPV-1 was detected in 6.56% (20/305) of tested dogs, including 14 diarrheic- and 6 non-diarrheic dogs, and was significant in puppies with diarrhea (p = 0.048). Among the CaChPV-1-positive diarrheic dogs, one sample was obtained from intestinal tissue and 13 samples were fecal samples. However, six CaChPV-1 positive non-diarrheic dogs were based on fecal samples but not on intestinal tissue. Within the age range, the presence of CaChPV-1 was significant in puppies (p < 0.00001) and was mainly localized in the stromal and endothelial cells of intestinal villi and pulmonary alveoli. Phylogenetic analysis indicated genetic diversity of CaChPV-1 Thai strains that were mostly clustered within the sequences found in China. CONCLUSIONS Although definitive pathogenesis of CaChPV-1 remains undetermined, this study provides evidence supporting that CaChPV-1 localizes in canine cells and could play a potential role as an enteric pathogen.
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Affiliation(s)
- Chutchai Piewbang
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.,Animal Virome and Diagnostic Development Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Pattiya Lohavicharn
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.,Animal Virome and Diagnostic Development Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Tin Van Nguyen
- Animal Virome and Diagnostic Development Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.,The International Graduate Course of Veterinary Science and Technology (VST), Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Panitnan Punyathi
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Tanit Kasantikul
- Clemson Veterinary Diagnostic Center, Clemson University, Columbia, South Carolina, USA
| | - Somporn Techangamsuwan
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.,Animal Virome and Diagnostic Development Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
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12
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Zhao Q, Zhao R, Sun Y, Ji L, Xi Y, Wang X, Shen Q, Ji L, Wang Y, You Z, Yang S, Zhang W. Identification of Multiple Novel Viruses in Fecal Samples of Black-Necked Cranes Using Viral Metagenomic Methods. Viruses 2023; 15:2068. [PMID: 37896845 PMCID: PMC10612090 DOI: 10.3390/v15102068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/04/2023] [Accepted: 10/07/2023] [Indexed: 10/29/2023] Open
Abstract
The black-necked crane is the only species of crane that lives in the high-altitude region of the Tibet Plateau. At present, there is little research on viral diseases of the black-necked crane (Grus nigricollis). In this study, a viral metagenomic approach was employed to investigate the fecal virome of black-necked cranes in Saga County, Shigatse City, Tibet, China. The identified virus families carried by black-necked cranes mainly include Genomoviridae, Parvoviridae, and Picornaviridae. The percentages of sequence reads belonging to these three virus families were 1.6%, 3.1%, and 93.7%, respectively. Among them, one genome was characterized as a novel species in the genus Grusopivirus of the family Picornaviridae, four new parvovirus genomes were obtained and classified into four different novel species within the genus Chaphamaparvovirus of the subfamily Hamaparvovirinae, and four novel genomovirus genomes were also acquired and identified as members of three different species, including Gemykroznavirus haeme1, Gemycircularvirus ptero6, and Gemycircularvirus ptero10. All of these viruses were firstly detected in fecal samples of black-necked cranes. This study provides valuable information for understanding the viral community composition in the digestive tract of black-necked cranes in Tibet, which can be used for monitoring, preventing, and treating potential viral diseases in black-necked cranes.
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Affiliation(s)
- Qifan Zhao
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang 212013, China; (Q.Z.); (Y.S.); (L.J.); (Y.X.); (X.W.); (Q.S.); (L.J.); (Y.W.)
| | - Ran Zhao
- Department of Prevention and Control, Xiamen Animal Disease Prevention and Control Center, Xiamen 361009, China;
| | - Yijie Sun
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang 212013, China; (Q.Z.); (Y.S.); (L.J.); (Y.X.); (X.W.); (Q.S.); (L.J.); (Y.W.)
| | - Li Ji
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang 212013, China; (Q.Z.); (Y.S.); (L.J.); (Y.X.); (X.W.); (Q.S.); (L.J.); (Y.W.)
| | - Yuan Xi
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang 212013, China; (Q.Z.); (Y.S.); (L.J.); (Y.X.); (X.W.); (Q.S.); (L.J.); (Y.W.)
| | - Xiaochun Wang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang 212013, China; (Q.Z.); (Y.S.); (L.J.); (Y.X.); (X.W.); (Q.S.); (L.J.); (Y.W.)
| | - Quan Shen
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang 212013, China; (Q.Z.); (Y.S.); (L.J.); (Y.X.); (X.W.); (Q.S.); (L.J.); (Y.W.)
| | - Likai Ji
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang 212013, China; (Q.Z.); (Y.S.); (L.J.); (Y.X.); (X.W.); (Q.S.); (L.J.); (Y.W.)
| | - Yan Wang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang 212013, China; (Q.Z.); (Y.S.); (L.J.); (Y.X.); (X.W.); (Q.S.); (L.J.); (Y.W.)
| | - Zhenqiang You
- School of Public Health, Hangzhou Medical College, Hangzhou 310013, China;
| | - Shixing Yang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang 212013, China; (Q.Z.); (Y.S.); (L.J.); (Y.X.); (X.W.); (Q.S.); (L.J.); (Y.W.)
| | - Wen Zhang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang 212013, China; (Q.Z.); (Y.S.); (L.J.); (Y.X.); (X.W.); (Q.S.); (L.J.); (Y.W.)
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13
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Liu H, Huang J, Lu ZS, Li LX, Liang XT, Tang T, Sun WC, Lu HJ, Jin NY, Bai X, Si XK. Isolation and characterization of a novel parvovirus from a red-crowned crane, China, 2021. BMC Vet Res 2023; 19:169. [PMID: 37735392 PMCID: PMC10512598 DOI: 10.1186/s12917-023-03683-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 08/02/2023] [Indexed: 09/23/2023] Open
Abstract
BACKGROUND Parvoviruses are icosahedral, nonenveloped viruses with single-stranded DNA genomes of approximately 5 kb in length. In recent years, parvoviruses have frequently mutated and expanded their host range to cause disease in many wild animals by altering their tissue tropism. Animal infection mainly results in acute enteritis and inflammation of other organs. In this study, we used a viral metagenomic method to detect a novel parvovirus species in a red-crowned crane that died due to severe diarrhea in China. RESULTS The presence of the viral genome in the kidney, lung, heart, liver, and intestine were confirmed by PCR. Histopathological examination of the intestine showed a large number of infiltrated inflammatory cells. The JL21/10 strain of the red-crowned crane parvovirus was first isolated from the intestine. Whole-genome sequence analysis showed that JL21/10 shared high identity with the red-crowned crane Parvovirinae strains yc-8 at the nucleotide level (96.61%). Phylogenetic analysis of the complete genome and NS1 gene revealed that the JL21/10 strain clustered with strains in chicken and revealed a close genetic relationship with the red-crowned crane parvovirus strains.The complete of VP2 gene analysis showed that JL21/10 shared identity with the red-crowned crane yc-8 strains (97.7%), chicken (55.4%),ducks(31.0%) and geese(30.1%) at the amino acid level. The result showed that red-crowned crane parvovirus may be cross-species transmission to chicken. However, There is little possibility of transmission to ducks and geese. CONCLUSION This is the first isolation and identification of a parvovirus in red-crowned crane that was associated with severe diarrhea.
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Affiliation(s)
- Hao Liu
- School of Life Sciences and Engineering, Foshan University, Foshan, Guangdong Province, China
| | - Jie Huang
- School of Life Sciences and Engineering, Foshan University, Foshan, Guangdong Province, China
| | - Zi-Shuo Lu
- School of Life Sciences and Engineering, Foshan University, Foshan, Guangdong Province, China
| | - Li-Xia Li
- School of Life Sciences and Engineering, Foshan University, Foshan, Guangdong Province, China
| | - Xiao-Tong Liang
- School of Life Sciences and Engineering, Foshan University, Foshan, Guangdong Province, China
| | - Tian Tang
- School of Life Sciences and Engineering, Foshan University, Foshan, Guangdong Province, China
| | - Wen-Chao Sun
- Institute of Virology, Wenzhou University, 325035, Wenzhou, China
| | - Hui-Jun Lu
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, Jilin Province, China
| | - Ning-Yi Jin
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, Jilin Province, China
| | - Xue Bai
- Institute of Special Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, Jilin Province, China.
- Key Laboratory of Special Animal Epidemic Disease of Ministry of Agriculture and Rural Affairs, Institute of Special Animals and Plants, Chinese Academy of Agricultural Sciences, No. 4899 Juye Street, 130112, Changchun, Jilin province, China.
| | - Xing-Kui Si
- School of Life Sciences and Engineering, Foshan University, Foshan, Guangdong Province, China.
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14
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Li N, Bai Y, Yan X, Guo Z, Xiang K, Yang Z, Shangguan H, Ge J, Zhao L. The prevalence, genetic diversity and evolutionary analysis of cachavirus firstly detected in northeastern China. Front Vet Sci 2023; 10:1233972. [PMID: 37771946 PMCID: PMC10527371 DOI: 10.3389/fvets.2023.1233972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 08/25/2023] [Indexed: 09/30/2023] Open
Abstract
Canine cachavirus is a novel parvovirus belonging to the genus Chaphamaparvovirus that was first detected in dogs in the United States. However, our knowledge of the prevalence and genetic characteristics of cachavirus is relatively limited. In this study, 325 canine fecal specimens collected from healthy and diarrheic dogs in northeastern China were screened with PCR. Twenty-two of the 325 (6.8%) samples were positive for cachavirus. The diarrhea samples showed high viral coinfection rates, and we detected coinfections with canine astrovirus (CaAstV) and cachavirus for the first time. A sequence analysis revealed that the Chinese cachavirus strains have point mutations in four consecutive amino acid codons relative to the original American strain. A codon usage analysis of the VP1 gene showed that most preferred codons in cachavirus were A- or T-ending codons, as in traditional canine parvovirus 2. A co-evolutionary analysis showed that cachavirus has undergone cospeciation with its hosts and has been transmitted among different host species. Our findings extend the limited cachavirus sequences available, and provide detailed molecular characterization of the strains in northeastern China. Further epidemiological surveillance is required to determine the significance and evolution of cachavirus.
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Affiliation(s)
- Nuowa Li
- State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Yue Bai
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Xin Yan
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Zhiyuan Guo
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Kongrui Xiang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Zaixing Yang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Haikun Shangguan
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Junwei Ge
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
- Heilongjiang Provincial Key Laboratory of Zoonosis, Harbin, China
| | - Lili Zhao
- State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
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15
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Wang Y, Sun Y, Li X, Chen R, Li W, Ji L, Zhao Q, Ji L, Yang S, Zhang W. Molecular detection and characterization of three novel parvoviruses belonging to two different subfamilies in zoo birds. Arch Virol 2023; 168:163. [PMID: 37198283 DOI: 10.1007/s00705-023-05785-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 04/18/2023] [Indexed: 05/19/2023]
Abstract
Birds carry a large number of viruses that may cause diseases in animals or humans. At present, information about the virome of zoo birds is limited. In this study, using viral metagenomics, we investigated the fecal virome of zoo birds collected from a zoo in Nanjing, Jiangsu Province, China. Three novel parvoviruses were obtained and characterized. The genomes of the three viruses are 5,909, 4,411, and 4,233 nt in length, respectively, and contain four or five ORFs. Phylogenetic analysis showed that these three novel parvoviruses clustered with other strains and formed three different clades. Pairwise comparison of NS1 amino acid sequences showed that Bir-01-1 shared 44.30-74.92% aa sequence identity with other parvoviruses belonging to the genus Aveparvovirus, while Bir-03-1 and Bir-04-1 shared less than 66.87% and 53.09% aa sequence identity, respectively, with other parvoviruses belonging to the genus Chaphamaparvovirus. Each of these three viruses was identified as a member of a novel species based on the species demarcation criteria for parvoviruses. These findings broaden our knowledge of the genetic diversity of parvoviruses and provide epidemiological data regarding potential outbreaks of parvovirus disease in birds.
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Affiliation(s)
- Yan Wang
- School of Medicine, Jiangsu University, 301 Xuefu Road, 212013, Zhenjiang, Jiangsu, People's Republic of China
| | - Yijie Sun
- School of Medicine, Jiangsu University, 301 Xuefu Road, 212013, Zhenjiang, Jiangsu, People's Republic of China
| | - Xin Li
- The Affiliated Taizhou People's Hospital of Nanjing Medical University, 225300, Taizhou, Jiangsu, People's Republic of China
| | - Rong Chen
- Nanjing Hongshan Forest Zoo, 210000, Nanjing, Jiangsu, People's Republic of China
| | - Wang Li
- The Affiliated Taizhou People's Hospital of Nanjing Medical University, 225300, Taizhou, Jiangsu, People's Republic of China
| | - Li Ji
- School of Medicine, Jiangsu University, 301 Xuefu Road, 212013, Zhenjiang, Jiangsu, People's Republic of China
| | - Qifan Zhao
- School of Medicine, Jiangsu University, 301 Xuefu Road, 212013, Zhenjiang, Jiangsu, People's Republic of China
| | - Likai Ji
- School of Medicine, Jiangsu University, 301 Xuefu Road, 212013, Zhenjiang, Jiangsu, People's Republic of China
| | - Shixing Yang
- School of Medicine, Jiangsu University, 301 Xuefu Road, 212013, Zhenjiang, Jiangsu, People's Republic of China.
| | - Wen Zhang
- School of Medicine, Jiangsu University, 301 Xuefu Road, 212013, Zhenjiang, Jiangsu, People's Republic of China.
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16
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Molecular Characterization of Feline Chaphamaparvovirus (Carnivore chaphamaparvovirus 2) Firstly Detected in Dogs from China. Transbound Emerg Dis 2023. [DOI: 10.1155/2023/5882871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
A new type of parvovirus known as feline chaphamaparvovirus (FeChPV) was discovered in the feces of shelter cats in Canada in 2019, and >50% of cats were reported to be infected with this virus. In this study, two FeChPV-positive samples were identified from the rectal swabs of 285 dogs with diarrhea but none in 50 healthy dogs. Whole genome sequences of these two FeChPV strains (OQ162042 and OQ162043) were amplified and compared with those of the two viruses originally discovered in Canada (IDEXX-1 and VRI849). The whole genome, NS1, and VP1 of the two FeChPV strains shared a high identity of 95.0%–97.8% nucleotide, 96.9%–98.6% amino acid (aa), and 97.2%–98.8% aa with the reported FeChPV strains, respectively. The phylogenetic tree of NS1 and VP1 revealed that two FeChPV strains, namely, CHN20201025 and CHN20201226, were closely clustered with the two FeChPV prototypes detected in Canada in a group. Moreover, CHN20201025 and CHN20201226 were obviously different from Carnivore chaphamaparvovirus 1 and were classified as Carnivore chaphamaparvovirus 2. This is the first study to report the identification of FeChPV in fecal samples from dogs in China, and the genetic analysis of the FeChPV, which was previously detected in Canadian cats, would improve our understanding of its host spectrum.
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17
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Miranda TDS, Schiffler FB, D'arc M, Moreira FRR, Cosentino MAC, Coimbra A, Mouta R, Medeiros G, Girardi DL, Wanderkoke V, Soares CFA, Francisco TM, Henry MD, Afonso BC, Soffiati FL, Ferreira SS, Ruiz-Miranda CR, Soares MA, Santos AFA. Metagenomic analysis reveals novel dietary-related viruses in the gut virome of marmosets hybrids (Callithrix jacchus x Callithrix penicillata), Brazil. Virus Res 2023; 325:199017. [PMID: 36565815 DOI: 10.1016/j.virusres.2022.199017] [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: 10/13/2022] [Revised: 12/02/2022] [Accepted: 12/04/2022] [Indexed: 12/24/2022]
Abstract
Viral metagenomics has contributed enormously to the characterization of a wide range of viruses infecting animals of all phyla in the last decades. Among Neotropical primates, especially those introduced, knowledge about viral diversity remains poorly studied. Therefore, using metagenomics based on virus enrichment, we explored the viral microbiota present in the feces of introduced common marmosets (Callithrix sp.) in three locations from the Silva Jardim region in the State of Rio de Janeiro, Brazil. Fecal samples were collected from nine marmosets, pooled into three sample pools, and sequenced on Illumina MiSeq platform. Sequence reads were analyzed using a viral metagenomic analysis pipeline and two novel insect viruses belonging to the Parvoviridae and Baculoviridae families were identified. The complete genome of a densovirus (Parvoviridae family) of 5,309 nucleotides (nt) was obtained. The NS1 and VP1 proteins share lower than 32% sequence identity with the corresponding proteins of known members of the subfamily Densovirinae. Phylogenetic analysis suggests that this virus represents a new genus, provisionally named Afoambidensovirus due to its discovery in the Brazilian Atlantic Forest. The novel species received the name Afoambidensovirus incertum 1. The complete circular genome of a baculovirus of 107,191 nt was also obtained, showing 60.8% sequence identity with the most closely related member of the Baculoviridae family. Phylogenetic analysis suggests that this virus represents a new species in the Betabaculovirus genus, provisionally named Betabaculovirus incertum 1. In addition, sequences from several families of arthropods in the three pools evaluated were characterized (contigs ranging from 244 to 6,750 nt), corroborating the presence of possible insect hosts with which these new viruses may be associated. Our study expands the knowledge about two viral families known to infect insects, an important component of the marmosets' diet. This identification in hosts' feces samples demonstrates one of the many uses of this type of data and could serve as a basis for future research characterizing viruses in wildlife using noninvasive samples.
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Affiliation(s)
- Thamiris Dos Santos Miranda
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | | | - Mirela D'arc
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Filipe Romero Rebello Moreira
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil; Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | | | - Amanda Coimbra
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Ricardo Mouta
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Gabriel Medeiros
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Déa Luiza Girardi
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Victor Wanderkoke
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Caique Ferreira Amaral Soares
- Associação Mico-Leão-Dourado, Silva Jardim, Rio de Janeiro, RJ, Brazil; Laboratório de Ciências Ambientais, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, Brazil
| | - Talitha Mayumi Francisco
- Associação Mico-Leão-Dourado, Silva Jardim, Rio de Janeiro, RJ, Brazil; Laboratório de Ciências Ambientais, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, Brazil
| | - Malinda Dawn Henry
- Laboratório de Ciências Ambientais, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, Brazil
| | - Bianca Cardozo Afonso
- Associação Mico-Leão-Dourado, Silva Jardim, Rio de Janeiro, RJ, Brazil; Laboratório de Ciências Ambientais, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, Brazil
| | | | | | - Carlos Ramon Ruiz-Miranda
- Associação Mico-Leão-Dourado, Silva Jardim, Rio de Janeiro, RJ, Brazil; Laboratório de Ciências Ambientais, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, Brazil
| | - Marcelo Alves Soares
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil; Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, RJ, Brazil
| | - André Felipe Andrade Santos
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil.
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18
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Dai Z, Wang H, Wu H, Zhang Q, Ji L, Wang X, Shen Q, Yang S, Ma X, Shan T, Zhang W. Parvovirus dark matter in the cloaca of wild birds. Gigascience 2022; 12:giad001. [PMID: 36734170 PMCID: PMC9896142 DOI: 10.1093/gigascience/giad001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/28/2022] [Accepted: 01/03/2023] [Indexed: 02/04/2023] Open
Abstract
With the development of viral metagenomics and next-generation sequencing technology, more and more novel parvoviruses have been identified in recent years, including even entirely new lineages. The Parvoviridae family includes a different group of viruses that can infect a wide variety of animals. In this study, systematic analysis was performed to identify the "dark matter" (datasets that cannot be easily attributed to known viruses) of parvoviruses and to explore their genetic diversity from wild birds' cloacal swab samples. We have tentatively defined this parvovirus "dark matter" as a highly divergent lineage in the Parvoviridae family. All parvoviruses showed several characteristics, including 2 major protein-coding genes and similar genome lengths. Moreover, we observed that the novel parvo-like viruses share similar genome organizations to most viruses in Parvoviridae but could not clustered with the established subfamilies in phylogenetic analysis. We also found some new members associated with the Bidnaviridae family, which may be derived from parvovirus. This suggests that systematic analysis of domestic and wild animal samples is necessary to explore the genetic diversity of parvoviruses and to mine for more of this potential dark matter.
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Affiliation(s)
- Ziyuan Dai
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
- Department of Clinical Laboratory, The Sixth Affiliated Hospital of Nantong University, Yancheng Third People's Hospital, Yancheng, Jiangsu 224001, China
| | - Haoning Wang
- School of Geography and Tourism, Harbin University, Harbin, Heilongjiang 150076, China
| | - Haisheng Wu
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
- Qinghai Institute of Endemic Disease Prevention and Control, Xining, Qinghai 810099, China
| | - Qing Zhang
- Qinghai Institute of Endemic Disease Prevention and Control, Xining, Qinghai 810099, China
| | - Likai Ji
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Xiaochun Wang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Quan Shen
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Shixing Yang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Xiao Ma
- Qinghai Institute of Endemic Disease Prevention and Control, Xining, Qinghai 810099, China
| | - Tongling Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 810099, China
| | - Wen Zhang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
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Hao X, Li Y, Chen B, Wang H, Wang X, Xiao X, Zhou P, Li S. Detection of FeChPV in a cat shelter outbreak of upper respiratory tract disease in China. Front Microbiol 2022; 13:1064747. [PMID: 36569076 PMCID: PMC9773189 DOI: 10.3389/fmicb.2022.1064747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 11/14/2022] [Indexed: 12/14/2022] Open
Abstract
Feline parvovirus often causes a fatal infectious disease and has a serious impact on domestic cats and wild felines. Feline chaphamaparvovirus (FeChPV) is a novel type of feline parvovirus that has been successively identified in Canada, Italy, and Turkey. The prevalence and pathogenicity of FeChPV in other regions is still unknown. In this study, we recorded the detection of FeChPV in a cat shelter in China. A high prevalence (81.08%, 30/37) of FeChPV was detected in cats with symptoms of upper respiratory tract disease (URTD) in this cat shelter. Multiple pathogen testing indicated high coinfection rates of 80% (24/30) with other common viruses in FeChPV-positive cats. Analyses of the necropsy and histopathological findings revealed severe lymphadenitis, encephalitis, and viral DNA in several tissues (including brain) of the deceased cat. Finally, we obtained nearly full-length genomes of four strains with 98.4%~98.6% homology with previously reported genomes. Notably, VP1 proteins showed seven unique amino acid mutations, while NS1 proteins carried eight mutations. In the evolutionary tree based on VP1 and NS1, the sequences clustered in a large branch with Italian and Canadian FeChPV strains. Given the possible association of FeChPV with URTD, further studies are necessary to evaluate the pathogenicity and epidemiological characteristics of this novel feline pathogen.
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Affiliation(s)
- Xiangqi Hao
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China,Guangdong Provincial Pet Engineering Technology Research Center, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Yanchao Li
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China,Guangdong Provincial Pet Engineering Technology Research Center, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Bo Chen
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China,Guangdong Provincial Pet Engineering Technology Research Center, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Hanhong Wang
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China,Guangdong Provincial Pet Engineering Technology Research Center, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xinrui Wang
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China,Guangdong Provincial Pet Engineering Technology Research Center, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xiangyu Xiao
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China,Guangdong Provincial Pet Engineering Technology Research Center, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Pei Zhou
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China,Guangdong Provincial Pet Engineering Technology Research Center, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China,*Correspondence: Pei Zhou,
| | - Shoujun Li
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China,Guangdong Provincial Pet Engineering Technology Research Center, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China,Shoujun Li,
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20
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Bassi C, Guerriero P, Pierantoni M, Callegari E, Sabbioni S. Novel Virus Identification through Metagenomics: A Systematic Review. LIFE (BASEL, SWITZERLAND) 2022; 12:life12122048. [PMID: 36556413 PMCID: PMC9784588 DOI: 10.3390/life12122048] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/25/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]
Abstract
Metagenomic Next Generation Sequencing (mNGS) allows the evaluation of complex microbial communities, avoiding isolation and cultivation of each microbial species, and does not require prior knowledge of the microbial sequences present in the sample. Applications of mNGS include virome characterization, new virus discovery and full-length viral genome reconstruction, either from virus preparations enriched in culture or directly from clinical and environmental specimens. Here, we systematically reviewed studies that describe novel virus identification through mNGS from samples of different origin (plant, animal and environment). Without imposing time limits to the search, 379 publications were identified that met the search parameters. Sample types, geographical origin, enrichment and nucleic acid extraction methods, sequencing platforms, bioinformatic analytical steps and identified viral families were described. The review highlights mNGS as a feasible method for novel virus discovery from samples of different origins, describes which kind of heterogeneous experimental and analytical protocols are currently used and provides useful information such as the different commercial kits used for the purification of nucleic acids and bioinformatics analytical pipelines.
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Affiliation(s)
- Cristian Bassi
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
- Laboratorio per Le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, 44121 Ferrara, Italy
| | - Paola Guerriero
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
- Laboratorio per Le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, 44121 Ferrara, Italy
| | - Marina Pierantoni
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
| | - Elisa Callegari
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
| | - Silvia Sabbioni
- Laboratorio per Le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, 44121 Ferrara, Italy
- Department of Life Science and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
- Correspondence: ; Tel.: +39-053-245-5319
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21
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Yang S, Mao Q, Wang Y, He J, Yang J, Chen X, Xiao Y, He Y, Zhao M, Lu J, Yang Z, Dai Z, Liu Q, Yao Y, Lu X, Li H, Zhou R, Zeng J, Li W, Zhou C, Wang X, Shen Q, Xu H, Deng X, Delwart E, Shan T, Zhang W. Expanding known viral diversity in plants: virome of 161 species alongside an ancient canal. ENVIRONMENTAL MICROBIOME 2022; 17:58. [PMID: 36437477 PMCID: PMC9703751 DOI: 10.1186/s40793-022-00453-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 11/17/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Since viral metagenomic approach was applied to discover plant viruses for the first time in 2006, many plant viruses had been identified from cultivated and non-cultivated plants. These previous researches exposed that the viral communities (virome) of plants have still largely uncharacterized. Here, we investigated the virome in 161 species belonging to 38 plant orders found in a riverside ecosystem. RESULTS We identified 245 distinct plant-associated virus genomes (88 DNA and 157 RNA viruses) belonging to 27 known viral families, orders, or unclassified virus groups. Some viral genomes were sufficiently divergent to comprise new species, genera, families, or even orders. Some groups of viruses were detected that currently are only known to infect organisms other than plants. It indicates a wider host range for members of these clades than previously recognized theoretically. We cannot rule out that some viruses could be from plant contaminating organisms, although some methods were taken to get rid of them as much as possible. The same viral species could be found in different plants and co-infections were common. CONCLUSIONS Our data describe a complex viral community within a single plant ecosystem and expand our understanding of plant-associated viral diversity and their possible host ranges.
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Affiliation(s)
- Shixing Yang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
- International Genome Center, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Qingqing Mao
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Yan Wang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Jingxian He
- Suzhou Medical College of Soochow University, Suzhou, 215123, China
| | - Jie Yang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Xu Chen
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Yuqing Xiao
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Yumin He
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Min Zhao
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Juan Lu
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Zijun Yang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Ziyuan Dai
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Qi Liu
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Yuxin Yao
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Xiang Lu
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Hong Li
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Rui Zhou
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Jian Zeng
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Wang Li
- Department of Laboratory Medicine, Jiangsu Taizhou People's Hospital, Taizhou, 225300, Jiangsu, China
| | - Chenglin Zhou
- Department of Laboratory Medicine, Jiangsu Taizhou People's Hospital, Taizhou, 225300, Jiangsu, China
| | - Xiaochun Wang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Quan Shen
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Hui Xu
- The Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, Jiangsu, China
| | - Xutao Deng
- Vitalant Research Institute, San Francisco, CA, 94118, USA
| | - Eric Delwart
- Vitalant Research Institute, San Francisco, CA, 94118, USA
- Department of Laboratory Medicine, University of California, San Francisco, CA, 94118, USA
| | - Tongling Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China.
| | - Wen Zhang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
- International Genome Center, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
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22
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Cloacal virome of an ancient host lineage – The tuatara (Sphenodon punctatus) – Reveals abundant and diverse diet-related viruses. Virology 2022; 575:43-53. [DOI: 10.1016/j.virol.2022.08.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/11/2022] [Accepted: 08/23/2022] [Indexed: 11/23/2022]
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23
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Fu X, Luo M, Zheng G, Liang H, Liu L, Lin Q, Niu Y, Luo X, Li N. Determination and Characterization of a Novel Birnavirus Associated with Massive Mortality in Largemouth Bass. Microbiol Spectr 2022; 10:e0171621. [PMID: 35319246 PMCID: PMC9045220 DOI: 10.1128/spectrum.01716-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 02/06/2022] [Indexed: 11/20/2022] Open
Abstract
Largemouth bass (Micropterus salmoides) is an important and fast-growing aquaculture species in China. In 2017, an epidemic associated with severe mortality occurred in fingerlings of largemouth bass in Guangdong, China. The causative pathogen was identified and named as largemouth bass Birnavirus (LBBV) by virome analysis, viral isolation, electron microscopy, genome sequencing, Western blot, indirect immunofluorescence, experimental challenge, and so on. Virome sequencing results showed that the relative abundance reads related to the family Birnaviridae were the highest, occupied ∼25% of the total viral reads. Electron microscopy revealed large numbers of nonenveloped virus particles in the spleen of diseased fish with a diameter of about 53 nm. LBBV was isolated and propagated in Chinese perch brain cells and induced a typical cytopathic effect. LBBV was stable to chloroform, heat, and 5-bromo-2'-deoxyuridine, but sensitive to acid (pH 3.0). The complete genome of LBBV was comprised of segment A with a size 3525 bp and segment B with a size 2737 bp. Phylogenetic analysis basing on RdRp and VP2 protein sequences revealed that LBBV were clustered into one clade with Lates calcarifer Birnavirus (LCBV), sharing 98.7% or 91.9% sequence identity with LCBV, respectively, but only sharing 59.7% and 52.7% sequence identity with Blosnavirus, suggesting that LBBV and LCBV probably belonged to a new genus. Challenge experiments results indicated that clinical disease symptoms similar to those observed naturally were replicated and the cumulative mortality reached 100% at 3 dpi by i.p. injection. The investigation of prevalence of LBBV infection showed that 41.5% (17/41) sample pools collected from diseased ponds was positive during 2017-2020, indicating that an emerging outbreak of this disease may be spreading within the largemouth bass in China. Above results confirmed that LBBV is a novel Birnavirus associated with massive mortality for fingerlings of largemouth bass. This provides a basis for prevention and control of this emerging viral disease. IMPORTANCE Pathogen isolation and identification are vital for emerging infectious outbreaks. Here we report the isolation, determination and characterization of a novel largemouth bass Birnavirus (LBBV) associated with massive mortality in largemouth bass. And genome of LBBV is determined and analyzed. Based on phylogenetic and alignment analysis of genome, we suggest LBBV belongs to a new genus (designated as Perbirnavirus genus) in Birnaviridae family. Our findings will provide a basis for the further study on prevention and control of this emerging viral disease.
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Affiliation(s)
- Xiaozhe Fu
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of fishery Drug Development, Ministry of Agriculture and Rural Affairs, Guangdong Province Key Laboratory of Aquatic Animal Immune Technology, Guangzhou, China
| | - Mingju Luo
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of fishery Drug Development, Ministry of Agriculture and Rural Affairs, Guangdong Province Key Laboratory of Aquatic Animal Immune Technology, Guangzhou, China
| | - Guo Zheng
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of fishery Drug Development, Ministry of Agriculture and Rural Affairs, Guangdong Province Key Laboratory of Aquatic Animal Immune Technology, Guangzhou, China
| | - Hongru Liang
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of fishery Drug Development, Ministry of Agriculture and Rural Affairs, Guangdong Province Key Laboratory of Aquatic Animal Immune Technology, Guangzhou, China
| | - Lihui Liu
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of fishery Drug Development, Ministry of Agriculture and Rural Affairs, Guangdong Province Key Laboratory of Aquatic Animal Immune Technology, Guangzhou, China
| | - Qiang Lin
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of fishery Drug Development, Ministry of Agriculture and Rural Affairs, Guangdong Province Key Laboratory of Aquatic Animal Immune Technology, Guangzhou, China
| | - Yinjie Niu
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of fishery Drug Development, Ministry of Agriculture and Rural Affairs, Guangdong Province Key Laboratory of Aquatic Animal Immune Technology, Guangzhou, China
| | - Xia Luo
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of fishery Drug Development, Ministry of Agriculture and Rural Affairs, Guangdong Province Key Laboratory of Aquatic Animal Immune Technology, Guangzhou, China
| | - Ningqiu Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of fishery Drug Development, Ministry of Agriculture and Rural Affairs, Guangdong Province Key Laboratory of Aquatic Animal Immune Technology, Guangzhou, China
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24
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Shan T, Yang S, Wang H, Wang H, Zhang J, Gong G, Xiao Y, Yang J, Wang X, Lu J, Zhao M, Yang Z, Lu X, Dai Z, He Y, Chen X, Zhou R, Yao Y, Kong N, Zeng J, Ullah K, Wang X, Shen Q, Deng X, Zhang J, Delwart E, Tong G, Zhang W. Virome in the cloaca of wild and breeding birds revealed a diversity of significant viruses. MICROBIOME 2022; 10:60. [PMID: 35413940 PMCID: PMC9001828 DOI: 10.1186/s40168-022-01246-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 02/16/2022] [Indexed: 06/01/2023]
Abstract
BACKGROUND Wild birds may harbor and transmit viruses that are potentially pathogenic to humans, domestic animals, and other wildlife. RESULTS Using the viral metagenomic approach, we investigated the virome of cloacal swab specimens collected from 3182 birds (the majority of them wild species) consisting of > 87 different species in 10 different orders within the Aves classes. The virus diversity in wild birds was higher than that in breeding birds. We acquired 707 viral genomes from 18 defined families and 4 unclassified virus groups, with 265 virus genomes sharing < 60% protein sequence identities with their best matches in GenBank comprising new virus families, genera, or species. RNA viruses containing the conserved RdRp domain with no phylogenetic affinity to currently defined virus families existed in different bird species. Genomes of the astrovirus, picornavirus, coronavirus, calicivirus, parvovirus, circovirus, retrovirus, and adenovirus families which include known avian pathogens were fully characterized. Putative cross-species transmissions were observed with viruses in wild birds showing > 95% amino acid sequence identity to previously reported viruses in domestic poultry. Genomic recombination was observed for some genomes showing discordant phylogenies based on structural and non-structural regions. Mapping the next-generation sequencing (NGS) data respectively against the 707 genomes revealed that these viruses showed distribution pattern differences among birds with different habitats (breeding or wild), orders, and sampling sites but no significant differences between birds with different behavioral features (migratory and resident). CONCLUSIONS The existence of a highly diverse virome highlights the challenges in elucidating the evolution, etiology, and ecology of viruses in wild birds. Video Abstract.
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Affiliation(s)
- Tongling Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Shixing Yang
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Haoning Wang
- School of Geography and Tourism, Harbin University, Harbin, 150886, Heilongjiang, China
- Key Laboratory of Wildlife diseases and Biosecurity Management of Heilongjiang Province, Harbin, 150886, Heilongjiang, China
| | - Hao Wang
- Department of Clinical Laboratory, The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, 223002, Jiangsu, China
| | - Ju Zhang
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Ga Gong
- Animal Science College, Tibet Agriculture and Animal Husbandry University, Nyingchi, 860000, Tibet, China
| | - Yuqing Xiao
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Jie Yang
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Xiaolong Wang
- Wildlife and Protected Area College/Center of Conservation Medicine and Ecological Safety Northeast Forestry University, Harbin, 150006, Heilongjiang, China
| | - Juan Lu
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Min Zhao
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Zijun Yang
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Xiang Lu
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Ziyuan Dai
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Yumin He
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Xu Chen
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Rui Zhou
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Yuxin Yao
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Ning Kong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Jian Zeng
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Kalim Ullah
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Xiaochun Wang
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Quan Shen
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Xutao Deng
- Vitalant Research Institute, San Francisco, CA, 94118, USA
| | - Jianmin Zhang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Eric Delwart
- Vitalant Research Institute, San Francisco, CA, 94118, USA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, 94118, USA
| | - Guangzhi Tong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China.
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, 225009, Jiangsu, China.
| | - Wen Zhang
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China.
- International Center for Genomics Research, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
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25
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Arhab Y, Miścicka A, Pestova TV, Hellen CUT. Horizontal gene transfer as a mechanism for the promiscuous acquisition of distinct classes of IRES by avian caliciviruses. Nucleic Acids Res 2021; 50:1052-1068. [PMID: 34928389 PMCID: PMC8789048 DOI: 10.1093/nar/gkab1243] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 11/17/2021] [Accepted: 12/15/2021] [Indexed: 02/05/2023] Open
Abstract
In contrast to members of Picornaviridae which have long 5'-untranslated regions (5'UTRs) containing internal ribosomal entry sites (IRESs) that form five distinct classes, members of Caliciviridae typically have short 5'UTRs and initiation of translation on them is mediated by interaction of the viral 5'-terminal genome-linked protein (VPg) with subunits of eIF4F rather than by an IRES. The recent description of calicivirus genomes with 500-900nt long 5'UTRs was therefore unexpected and prompted us to examine them in detail. Sequence analysis and structural modelling of the atypically long 5'UTRs of Caliciviridae sp. isolate yc-13 and six other caliciviruses suggested that they contain picornavirus-like type 2 IRESs, whereas ruddy turnstone calicivirus (RTCV) and Caliciviridae sp. isolate hwf182cal1 calicivirus contain type 4 and type 5 IRESs, respectively. The suggestion that initiation on RTCV mRNA occurs by the type 4 IRES mechanism was confirmed experimentally using in vitro reconstitution. The high sequence identity between identified calicivirus IRESs and specific picornavirus IRESs suggests a common evolutionary origin. These calicivirus IRESs occur in a single phylogenetic branch of Caliciviridae and were likely acquired by horizontal gene transfer.
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Affiliation(s)
- Yani Arhab
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn NY 11203, USA
| | - Anna Miścicka
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn NY 11203, USA
| | - Tatyana V Pestova
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn NY 11203, USA
| | - Christopher U T Hellen
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn NY 11203, USA
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26
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Chang WS, Rose K, Holmes EC. Meta-transcriptomic analysis of the virome and microbiome of the invasive Indian myna ( Acridotheres tristis) in Australia. One Health 2021; 13:100360. [PMID: 34917744 PMCID: PMC8666354 DOI: 10.1016/j.onehlt.2021.100360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/03/2021] [Accepted: 12/05/2021] [Indexed: 11/03/2022] Open
Abstract
Invasive species exert a serious impact on native fauna and flora and have become the target of eradication and management efforts worldwide. Invasive avian species can also be important pathogen reservoirs, although their viromes and microbiomes have rarely been studied. As one of the top 100 invasive pest species globally, the expansion of Indian mynas (Acridotheres tristis) into peri-urban and rural environments, in conjunction with increasing free-ranging avian agricultural practices, may increase the risk of microbial pathogens jumping species boundaries. Herein, we used a meta-transcriptomic approach to explore the microbes present in brain, liver and large intestine of 16 invasive Indian myna birds in Sydney, Australia. From this, we discovered seven novel viruses from the families Adenoviridae, Caliciviridae, Flaviviridae, Parvoviridae and Picornaviridae. Interestingly, each of the novel viruses identified shared less than 80% genomic similarity with their closest relatives from other avian species, indicative of a lack of detectable virus transmission between invasive mynas to native or domestic species. Of note, we also identified two coccidian protozoa, Isospora superbusi and Isospora greineri, from the liver and gut tissues of mynas. Overall, these data demonstrate that invasive mynas can harbor a diversity of viruses and other microorganisms such that ongoing pathogen surveillance in this species is warranted.
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Affiliation(s)
- Wei-Shan Chang
- School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia.,Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Karrie Rose
- Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia.,Australian Registry of Wildlife Health, Taronga Conservation Society Australia, Mosman, NSW 2088, Australia
| | - Edward C Holmes
- School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia.,Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
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27
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Ullah K, Mehmood A, Chen X, Dar MA, Yang S, Zhang W. Detection and molecular characterization of picobirnaviruses in the wild birds: Identification of a novel picobirnavirus possessing yeast mitochondrial genetic code. Virus Res 2021; 308:198624. [PMID: 34762993 DOI: 10.1016/j.virusres.2021.198624] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 11/04/2021] [Accepted: 11/05/2021] [Indexed: 12/11/2022]
Abstract
Picobirnaviruses (PBVs) are bi-segmented dsRNA viruses that have been detected in various animal species including vertebrates and invertebrates. In this study, 17 complete or incomplete PBV segment-2 and one unsegmented PBV-like virus sequence were identified in fecal samples from different bird species using viral metagenomic approach. The bird PBV and PBV-like virus retained the conservative motifs that are conserved in dsRNA2 of common PBVs. The RdRp of these 17 PBVs shared the highest Amino acid (aa) identity of 45.90%∼94.19% with previous animal and human PBVs, while the RdRp of the unsegment PBV-like virus shared the highest aa sequence identity of 31.93% with one chicken PBV (GenBank No. MW837829). The unsegmented PBV-like virus unexpectedly used the yeast mitochondrial genetic code (transl_table=3) for all ORFs translation. In addition, the prokaryotic RBS sequence was not only detected upstream to ORF2 at position 360AGGAGG365 of this unsegmented PBV-like virus, but also found upstream to ORF of bird PBV dsRNA2. The presence of the prokaryotic ribosomal binding site in the bird PBV genomes, and the finding of one novel unsegmented PBV-like virus using the yeast mitochondrial genetic code for translation supported recent speculations that PBVs may actually infect prokaryotic or fungal host cells. This study enhanced our understanding of PBVs and provided data support for exploring the real host of PBVs.
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Affiliation(s)
- Kalim Ullah
- School of medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Asif Mehmood
- School of medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Xu Chen
- School of medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Mudasir A Dar
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Shixing Yang
- School of medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China.
| | - Wen Zhang
- School of medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China.
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Jager MC, Tomlinson JE, Lopez-Astacio RA, Parrish CR, Van de Walle GR. Small but mighty: old and new parvoviruses of veterinary significance. Virol J 2021; 18:210. [PMID: 34689822 PMCID: PMC8542416 DOI: 10.1186/s12985-021-01677-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 10/08/2021] [Indexed: 12/14/2022] Open
Abstract
In line with the Latin expression "sed parva forti" meaning "small but mighty," the family Parvoviridae contains many of the smallest known viruses, some of which result in fatal or debilitating infections. In recent years, advances in metagenomic viral discovery techniques have dramatically increased the identification of novel parvoviruses in both diseased and healthy individuals. While some of these discoveries have solved etiologic mysteries of well-described diseases in animals, many of the newly discovered parvoviruses appear to cause mild or no disease, or disease associations remain to be established. With the increased use of animal parvoviruses as vectors for gene therapy and oncolytic treatments in humans, it becomes all the more important to understand the diversity, pathogenic potential, and evolution of this diverse family of viruses. In this review, we discuss parvoviruses infecting vertebrate animals, with a special focus on pathogens of veterinary significance and viruses discovered within the last four years.
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Affiliation(s)
- Mason C Jager
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Joy E Tomlinson
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Robert A Lopez-Astacio
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Colin R Parrish
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Gerlinde R Van de Walle
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA.
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First detection of feline bocaparvovirus 2 and feline chaphamaparvovirus in healthy cats in Turkey. Vet Res Commun 2021; 46:127-136. [PMID: 34553342 PMCID: PMC8457779 DOI: 10.1007/s11259-021-09836-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 09/17/2021] [Indexed: 02/06/2023]
Abstract
The pet cat’s population and the number of viruses that infect them are increasing worldwide. Recently, feline chaphamaparvovirus (FeChPV, also called fechavirus) and feline bocaparvovirus (FBoV) infections, which are novel parvovirus species, have been reported in cats from different geographic regions. Here, we investigated FBoV 1–3 and FeChPVs in healthy cats in Turkey using PCR, where nuclear phosphoprotein 1 (NP1) is targeted for FBoV and NP for FeChPV. For this purpose, oropharygeal swabs were obtained from 70 healthy cats with different housing status from June 15 to December 1, 2020. After PCR screening tests, six out of 70 cats (5/47 shelter cats; 1/23 domestic cats) were found to be positive for FBOV, while two were positive for FeChPV (1/47 shelter cats; 1/23 domestic cats). No cat was found in which both viruses were detected. The nucleotide (nt) sequence comparison in the 310 base pair (bp) NP gene of the two FeChPVs identified in this study shared a high identity with each other (95.0% nt and 99% aa identities) and with previously reported FeChPVs (92.4–97.1% nt and 98.1–99.0% aa identities), including 313R/2019/ITA, 49E/2019/ITA, VRI_849, 284R/2019/ITA, and IDEXX-1. Here, the near-full length (1489 nt, 495 amino acids-aa) of the VP2 gene of the FechaV/Tur-2020/68 isolate obtained from the study was also sequenced. The nt and aa identity ratio of this isolate with other FeChPVs was 98.0–98.5%-96–96.5%, respectively. Sequences of the 465 bp NP1 gene of the six Turkish FBoV strains shared high identities with each other (99.6–100% nt and 99.3–100% aa identities) and with those of FBoV-2 strains (97.8–99.1% nt and 98.0–100% aa identities), including 16SY0701, 17CC0505-BoV2, HFXA-6, and POR1. All FBoVs detected in this study were classified as genotype 2, similar to the study conducted in Japan and Portugal. Here, the NS1 (partial), NP1, VP1 and VP2 gene of the FBoV-2/TUR/2020–14 strain obtained from the study were also sequenced and the nt and aa sequences showed high identities to the above-mentioned FBoV-2 strain/isolates (> 96%, except for the aa ratio of strain 16SY0701). In conclusion, this study shows that FBoV and FeChPV are present in healthy cats in Turkey, and these viruses can be detected from oropharyngeal swabs. Our findings contribute to further investigation of the prevalence, genotype distribution, and genetic diversity of Turkish FBoVs and FeChPVs, adding to the molecular epidemiology of FBoV and FeChPVs worldwide.
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Abstract
The family Genomoviridae (phylum Cressdnaviricota, class Repensiviricetes, order Geplafuvirales) includes viruses with circular single-stranded DNA genomes encoding two proteins, the capsid protein and the rolling-circle replication initiation protein. The genomes of the vast majority of members in this family have been sequenced directly from diverse environmental or animal- and plant-associated samples, but two genomoviruses have been identified infecting fungi. Since the last taxonomic update of the Genomoviridae, a number of new members of this family have been sequenced. Here, we report on the most recent taxonomic update, including the creation of one new genus, Gemytripvirus, and classification of ~420 new genomoviruses into 164 new species. We also announce the adoption of the "Genus + freeform epithet" binomial system for the naming of all 236 officially recognized species in the family Genomoviridae. The updated taxonomy presented in this article has been accepted by the International Committee on Taxonomy of Viruses (ICTV).
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Affiliation(s)
- Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, Arizona, USA.
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa.
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Paris, France.
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Hayer J, Wille M, Font A, González-Aravena M, Norder H, Malmberg M. Four novel picornaviruses detected in Magellanic Penguins (Spheniscus magellanicus) in Chile. Virology 2021; 560:116-123. [PMID: 34058706 DOI: 10.1016/j.virol.2021.05.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 05/19/2021] [Accepted: 05/19/2021] [Indexed: 10/21/2022]
Abstract
Members of the Picornaviridae family comprise a significant burden on the poultry industry, causing diseases such as gastroenteritis and hepatitis. However, with the advent of metagenomics, a number of picornaviruses have now been revealed in apparently healthy wild birds. In this study, we identified four novel viruses belonging to the family Picornaviridae in healthy Magellanic penguins, a near threatened species. All samples were subsequently screened by RT-PCR for these new viruses, and approximately 20% of the penguins were infected with at least one of these viruses. The viruses were distantly related to members of the genera Hepatovirus, Tremovirus, Gruhelivirus and Crahelvirus. Further, they had more than 60% amino acid divergence from other picornaviruses, and therefore likely constitute novel genera. Our results demonstrate the vast undersampling of wild birds for viruses, and we expect the discovery of numerous avian viruses that are related to hepatoviruses and tremoviruses in the future.
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Affiliation(s)
- Juliette Hayer
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.
| | - Michelle Wille
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, Australia; Department of Microbiology and Immunology, At the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia
| | - Alejandro Font
- nstituto Antártico Chileno, Plaza Muñoz Gamero, 1055, Punta Arenas, Chile
| | | | - Helene Norder
- Department of Infectious Diseases/Virology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Sweden; Region Västra Götaland, Sahlgrenska University Hospital, Department of Clinical Microbiology, Gothenburg, Sweden
| | - Maja Malmberg
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden; Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden.
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Genomic characterization and phylogenetic analysis of a new canine picornavirus variant in the mainland of China. Virus Res 2021; 296:198351. [PMID: 33639222 DOI: 10.1016/j.virusres.2021.198351] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 02/10/2021] [Accepted: 02/19/2021] [Indexed: 11/21/2022]
Abstract
A new canine picornavirus (CanPV) variant, designated as dog/SH1901/CHN/2019, was detected in a pool of various canine fecal samples in the mainland of China using a viral metagenomic analysis, and its nearly complete genome sequence was determined and analyzed. Sequence analyses revealed that it had a standard picornavirus genome organization, a type I internal ribosome entry site (IRES) in the 5'UTR. However, dog/SH1901/CHN/2019 has generated a serial of unique aa mutations and 7aa insertion when compared with the closely related CanPVs. Phylogenetic analysis and pairwise sequence comparisons based on the P1, 2C, 3C, and 3D protein sequences showed that dog/SH1901/ CHN/2019 was closely related to CanPV strains 244 F, 325 F and 6D, which clustered into an independent evolutionary clade and distantly related to CanPV strain A128thr of the genus Mischivirus, which indicated the unclassified CanPV strains may belong to a novel species or genus in the family Picornaviridae. This study extends our knowledge on the evolution and genetic diversity of CanPVs.
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Investigating the Diversity and Host Range of Novel Parvoviruses from North American Ducks Using Epidemiology, Phylogenetics, Genome Structure, and Codon Usage Analysis. Viruses 2021; 13:v13020193. [PMID: 33525386 PMCID: PMC7912424 DOI: 10.3390/v13020193] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/22/2021] [Accepted: 01/26/2021] [Indexed: 01/03/2023] Open
Abstract
Parvoviruses are small single-stranded DNA viruses that can infect both vertebrates and invertebrates. We report here the full characterization of novel viruses we identified in ducks, including two viral species within the subfamily Hamaparvovirinae (duck-associated chapparvovirus, DAC) and a novel species within the subfamily Densovirinae (duck-associated ambidensovirus, DAAD). Overall, 5.7% and 21.1% of the 123 screened ducks (American black ducks, mallards, northern pintail) were positive for DAC and DAAD, respectively, and both viruses were more frequently detected in autumn than in winter. Genome organization and predicted transcription profiles of DAC and DAAD were similar to viruses of the genera Chaphamaparvovirus and Protoambidensovirus, respectively. Their association to these genera was also demonstrated by subfamily-wide phylogenetic and distance analyses of non-structural protein NS1 sequences. While DACs were included in a highly supported clade of avian viruses, no definitive conclusions could be drawn about the host type of DAAD because it was phylogenetically close to viruses found in vertebrates and invertebrates and analyses of codon usage bias and nucleotide frequencies of viruses within the family Parvoviridae showed no clear host-based viral segregation. This study highlights the high parvoviral diversity in the avian reservoir with many avian-associated parvoviruses likely yet to be discovered.
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Comparative Metagenomics of Palearctic and Neotropical Avian Cloacal Viromes Reveal Geographic Bias in Virus Discovery. Microorganisms 2020; 8:microorganisms8121869. [PMID: 33256173 PMCID: PMC7761369 DOI: 10.3390/microorganisms8121869] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/20/2020] [Accepted: 11/24/2020] [Indexed: 01/11/2023] Open
Abstract
Our understanding about viruses carried by wild animals is still scarce. The viral diversity of wildlife may be best described with discovery-driven approaches to the study of viral diversity that broaden research efforts towards non-canonical hosts and remote geographic regions. Birds have been key organisms in the transmission of viruses causing important diseases, and wild birds are threatened by viral spillovers associated with human activities. However, our knowledge of the avian virome may be biased towards poultry and highly pathogenic diseases. We describe and compare the fecal virome of two passerine-dominated bird assemblages sampled in a remote Neotropical rainforest in French Guiana (Nouragues Natural Reserve) and a Mediterranean forest in central Spain (La Herrería). We used metagenomic data to quantify the degree of functional and genetic novelty of viruses recovered by examining if the similarity of the contigs we obtained to reference sequences differed between both locations. In general, contigs from Nouragues were significantly less similar to viruses in databases than contigs from La Herrería using Blastn but not for Blastx, suggesting that pristine regions harbor a yet unknown viral diversity with genetically more singular viruses than more studied areas. Additionally, we describe putative novel viruses of the families Picornaviridae, Reoviridae and Hepeviridae. These results highlight the importance of wild animals and remote regions as sources of novel viruses that substantially broaden the current knowledge of the global diversity of viruses.
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Ji J, Hu W, Liu Q, Zuo K, Zhi G, Xu X, Kan Y, Yao L, Xie Q. Genetic Analysis of Cachavirus-Related Parvoviruses Detected in Pet Cats: The First Report From China. Front Vet Sci 2020; 7:580836. [PMID: 33330704 PMCID: PMC7719813 DOI: 10.3389/fvets.2020.580836] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 10/29/2020] [Indexed: 02/05/2023] Open
Abstract
In this study, members of the Carnivore chaphamaparvovirus species 1, closely related to a virus previously reported in dog feces named cachavirus was identified for the first time in feces of Chinese cats. Screening tests using rectal swabs from 171 diarrheic and 378 healthy cats collected from Henan, Anhui, and Zhejiang provinces in China revealed two samples from diarrheic cats that were positive for cachavirus, but statistical analysis indicated no association between the presence of the virus and clinical signs (p > 0.05). Subsequently, two partial genome sequences [from nucleotides 479–4123, according to the strains from dogs (cachavirus)] of the two strains from cats (cachavirus-cat1 and -cat2) were amplified. The NS1 and VP1 sites of cachavirus-cat1 and -cat2 shared a high identity of 91.9 and 97.0% with reported cachaviruses, respectively, but lower identity of 74.8 and 73.2% with another carnivore chaphamaparvovirus named fechaviruses detected in cats, respectively, indicated the two strains might origin from dogs. These findings improve our understanding of the diversity and tropism of viruses in Carnivore chaphamaparvovirus species 1 which now include both dogs and now cats viruses.
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Affiliation(s)
- Jun Ji
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang Normal University, Nanyang, China
| | - Wen Hu
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang Normal University, Nanyang, China
| | - Qiang Liu
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang Normal University, Nanyang, China
| | - Kejing Zuo
- Veterinary Laboratory, Guangzhou Zoo, Guangzhou, China
| | - Guanglin Zhi
- Veterinary Laboratory, Guangzhou Zoo, Guangzhou, China
| | - Xin Xu
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang Normal University, Nanyang, China
| | - Yunchao Kan
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang Normal University, Nanyang, China
| | - Lunguang Yao
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang Normal University, Nanyang, China
| | - Qingmei Xie
- College of Animal Science, South China Agricultural University, Guangzhou, China
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Detection and genetic characterization of a novel parvovirus (family Parvoviridae) in barn owls (Tyto alba) in Hungary. Arch Virol 2020; 166:231-236. [PMID: 33136208 DOI: 10.1007/s00705-020-04862-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 09/16/2020] [Indexed: 10/23/2022]
Abstract
In this study, a novel parvovirus (gyb-MR02/2015/HUN, MT580795) was detected in barn owls (Tyto alba) and genetically characterized using viral metagenomics and PCR methods. The NS1 and VP1 proteins of gyb-MR02/2015/HUN share only 45.4% and 50.1% amino acid sequence identity, respectively, to the corresponding proteins of peafowl parvovirus 2 (MK988620), the closest relative. Out of 11 faecal specimens from owls (six from little owls, three from barn owls, and two from long-eared owls), two barn owl samples were positive for the novel parvovirus, which is distantly related to members of the recently established genus Chaphamaparvovirus in the subfamily Hamaparvovirinae. Systematic investigation is necessary to explore the diversity of parvoviruses.
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Hu W, Liu Q, Chen Q, Ji J. Molecular characterization of Cachavirus firstly detected in dogs in China. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2020; 85:104529. [PMID: 32890765 PMCID: PMC7468343 DOI: 10.1016/j.meegid.2020.104529] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 08/14/2020] [Accepted: 08/31/2020] [Indexed: 12/11/2022]
Abstract
Canine Cachavirus was novel parvovirus species has been firstly identified in dogs in USA and was classified within the proposed Chaphamaparvovirus genus. To investigate Cachavirus infection in dogs in China, 408 rectal swabs from healthy and diarrheic dogs obtained during 2018-2019 were screened. The rate of Cachavirus positivity was 0% and 1.55% in healthy or diarrheic dogs, respectively. However, statistical analysis suggested no association between the presence of the virus and clinical signs (p > 0.05). Nucleotide identity was 98.2%-98.9% for NS1 and 98.6%-99.1% for VP1, and amino acid identity was 97.9%-98.7% for NS1 and 98.8%-99.6% for VP1 between the five Chinese strains and Cachavirus-1A and Cachavirus-1B detected in the United States. Phylogenetic analysis also indicated that these Cachavirus strains are genetically related to Cachavirus-1A and Cachavirus-1B. This study confirms the presence of Cachavirus in pet dogs in China and provides novel findings on its molecular characteristics.
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Affiliation(s)
- Wen Hu
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang Normal University, Nanyang 473061, PR China
| | - Qiang Liu
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang Normal University, Nanyang 473061, PR China
| | - Qinxi Chen
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang Normal University, Nanyang 473061, PR China
| | - Jun Ji
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Nanyang Normal University, Nanyang 473061, PR China.
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Metatranscriptomic Analysis of Virus Diversity in Urban Wild Birds with Paretic Disease. J Virol 2020; 94:JVI.00606-20. [PMID: 32581107 PMCID: PMC7459558 DOI: 10.1128/jvi.00606-20] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 06/16/2020] [Indexed: 02/08/2023] Open
Abstract
Wildlife naturally harbor a diverse array of infectious microorganisms and can be a source of novel diseases in domestic animals and human populations. Using unbiased RNA sequencing, we identified highly diverse viruses in native birds from Australian urban environments presenting with paresis. This research included the clinical investigation and description of poorly understood recurring syndromes of unknown etiology: clenched claw syndrome and black and white bird disease. As well as identifying a range of potentially disease-causing viral pathogens, this study describes methods that can effectively and efficiently characterize emergent disease syndromes in free-ranging wildlife and promotes further surveillance for specific pathogens of potential conservation and zoonotic concern. Wild birds are major natural reservoirs and potential dispersers of a variety of infectious diseases. As such, it is important to determine the diversity of viruses they carry and use this information to help understand the potential risks of spillover to humans, domestic animals, and other wildlife. We investigated the potential viral causes of paresis in long-standing, but undiagnosed, disease syndromes in wild Australian birds. RNA from diseased birds was extracted and pooled based on tissue type, host species, and clinical manifestation for metagenomic sequencing. Using a bulk and unbiased metatranscriptomic approach, combined with clinical investigation and histopathology, we identified a number of novel viruses from the families Astroviridae, Adenoviridae, Picornaviridae, Polyomaviridae, Paramyxoviridae, Parvoviridae, and Circoviridae in common urban wild birds, including Australian magpies, magpie larks, pied currawongs, Australian ravens, and rainbow lorikeets. In each case, the presence of the virus was confirmed by reverse transcription (RT)-PCR. These data revealed a number of candidate viral pathogens that may contribute to coronary, skeletal muscle, vascular, and neuropathology in birds of the Corvidae and Artamidae families and neuropathology in members of the Psittaculidae. The existence of such a diverse virome in urban avian species highlights the importance and challenges in elucidating the etiology and ecology of wildlife pathogens in urban environments. This information will be increasingly important for managing disease risks and conducting surveillance for potential viral threats to wildlife, livestock, and human health. IMPORTANCE Wildlife naturally harbor a diverse array of infectious microorganisms and can be a source of novel diseases in domestic animals and human populations. Using unbiased RNA sequencing, we identified highly diverse viruses in native birds from Australian urban environments presenting with paresis. This research included the clinical investigation and description of poorly understood recurring syndromes of unknown etiology: clenched claw syndrome and black and white bird disease. As well as identifying a range of potentially disease-causing viral pathogens, this study describes methods that can effectively and efficiently characterize emergent disease syndromes in free-ranging wildlife and promotes further surveillance for specific pathogens of potential conservation and zoonotic concern.
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Pénzes JJ, Söderlund-Venermo M, Canuti M, Eis-Hübinger AM, Hughes J, Cotmore SF, Harrach B. Reorganizing the family Parvoviridae: a revised taxonomy independent of the canonical approach based on host association. Arch Virol 2020; 165:2133-2146. [PMID: 32533329 DOI: 10.1007/s00705-020-04632-4] [Citation(s) in RCA: 132] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Parvoviridae, a diverse family of small single-stranded DNA viruses was established in 1975. It was divided into two subfamilies, Parvovirinae and Densovirinae, in 1993 to accommodate parvoviruses that infect vertebrate and invertebrate animals, respectively. This relatively straightforward segregation, using host association as the prime criterion for subfamily-level classification, has recently been challenged by the discovery of divergent, vertebrate-infecting parvoviruses, dubbed "chapparvoviruses", which have proven to be more closely related to viruses in certain Densovirinae genera than to members of the Parvovirinae. Viruses belonging to these genera, namely Brevi-, Hepan- and Penstyldensovirus, are responsible for the unmatched heterogeneity of the subfamily Densovirinae when compared to the Parvovirinae in matters of genome organization, protein sequence homology, and phylogeny. Another genus of Densovirinae, Ambidensovirus, has challenged traditional parvovirus classification, as it includes all newly discovered densoviruses with an ambisense genome organization, which introduces genus-level paraphyly. Lastly, current taxon definition and virus inclusion criteria have significantly limited the classification of certain long-discovered parvoviruses and impedes the classification of some potential family members discovered using high-throughput sequencing methods. Here, we present a new and updated system for parvovirus classification, which includes the introduction of a third subfamily, Hamaparvovirinae, resolves the paraphyly within genus Ambidensovirus, and introduces new genera and species into the subfamily Parvovirinae. These proposals were accepted by the ICTV in 2020 March.
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Affiliation(s)
- Judit J Pénzes
- Center for Structural Biology, Department of Biochemistry and Molecular Biology, The McKnight Brain Institute, University of Florida, Gainesville, FL, USA.
| | | | - Marta Canuti
- Department of Biology, Memorial University of Newfoundland, St John's, NL, Canada
| | | | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, Glasgow, G61 1QH, UK
| | - Susan F Cotmore
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, 06520-8035, USA
| | - Balázs Harrach
- Centre for Agricultural Research, Institute for Veterinary Medical Research, Budapest, Hungary
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Metagenomic characterisation of avian parvoviruses and picornaviruses from Australian wild ducks. Sci Rep 2020; 10:12800. [PMID: 32733035 PMCID: PMC7393117 DOI: 10.1038/s41598-020-69557-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 07/14/2020] [Indexed: 12/26/2022] Open
Abstract
Ducks can shed and disseminate viruses and thus play a role in cross-species transmission. In the current study, we detected and characterised various avian parvoviruses and picornaviruses from wild Pacific black ducks, Chestnut teals, Grey teals and Wood ducks sampled at multiple time points from a single location using metagenomics. We characterised 46 different avian parvoviruses belonging to three different genera Dependoparvovirus, Aveparvovirus and Chaphamaparvovirus, and 11 different avian picornaviruses tentatively belonging to four different genera Sicinivirus, Anativirus, Megrivirus and Aalivirus. Most of these viruses were genetically different from other currently known viruses from the NCBI dataset. The study showed that the abundance and number of avian picornaviruses and parvoviruses varied considerably throughout the year, with the high number of virus reads in some of the duck samples highly suggestive of an active infection at the time of sampling. The detection and characterisation of several parvoviruses and picornaviruses from the individual duck samples also suggests co-infection, which may lead to the emergence of novel viruses through possible recombination. Therefore, as new and emerging diseases evolve, it is relevant to explore and monitor potential animal reservoirs in their natural habitat.
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Arhab Y, Bulakhov AG, Pestova TV, Hellen CU. Dissemination of Internal Ribosomal Entry Sites (IRES) Between Viruses by Horizontal Gene Transfer. Viruses 2020; 12:E612. [PMID: 32512856 PMCID: PMC7354566 DOI: 10.3390/v12060612] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/01/2020] [Accepted: 06/02/2020] [Indexed: 12/19/2022] Open
Abstract
Members of Picornaviridae and of the Hepacivirus, Pegivirus and Pestivirus genera of Flaviviridae all contain an internal ribosomal entry site (IRES) in the 5'-untranslated region (5'UTR) of their genomes. Each class of IRES has a conserved structure and promotes 5'-end-independent initiation of translation by a different mechanism. Picornavirus 5'UTRs, including the IRES, evolve independently of other parts of the genome and can move between genomes, most commonly by intratypic recombination. We review accumulating evidence that IRESs are genetic entities that can also move between members of different genera and even between families. Type IV IRESs, first identified in the Hepacivirus genus, have subsequently been identified in over 25 genera of Picornaviridae, juxtaposed against diverse coding sequences. In several genera, members have either type IV IRES or an IRES of type I, II or III. Similarly, in the genus Pegivirus, members contain either a type IV IRES or an unrelated type; both classes of IRES also occur in members of the genus Hepacivirus. IRESs utilize different mechanisms, have different factor requirements and contain determinants of viral growth, pathogenesis and cell type specificity. Their dissemination between viruses by horizontal gene transfer has unexpectedly emerged as an important facet of viral evolution.
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Affiliation(s)
| | | | | | - Christopher U.T. Hellen
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, NY 11203, USA; (Y.A.); (A.G.B.); (T.V.P.)
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Fur Seal Feces-Associated Circular DNA Virus Identified in Pigs in Anhui, China. Virol Sin 2020; 36:25-32. [PMID: 32488409 PMCID: PMC7973343 DOI: 10.1007/s12250-020-00232-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 03/07/2020] [Indexed: 11/08/2022] Open
Abstract
Fur seal feces-associated circular DNA virus (FSfaCV) is an unclassified circular replication-associated protein (Rep)-encoding single-stranded (CRESS) DNA virus that has been detected in mammals (fur seals and pigs). The biology and epidemiology of the virus remain largely unknown. To investigate the virus diversity among pigs in Anhui Province, China, we pooled 600 nasal samples in 2017 and detected viruses using viral metagenomic methods. From the assembled contigs, 12 showed notably high nucleotide acid sequence similarities to the genome sequences of FSfaCVs. Based on these sequences, a full-length genome sequence of the virus was then obtained using overlapping PCR and sequencing, and the virus was designated as FSfaCV-CHN (GenBank No. MK462122). This virus shared 91.3% and 90.9% genome-wide nucleotide sequence similarities with the New Zealand fur seal strain FSfaCV-as50 and the Japanese pig strain FSfaCV-JPN1, respectively. It also clustered with the two previously identified FSfaCVs in a unique branch in the phylogenetic tree based on the open reading frame 2 (ORF2), Rep-coding gene, and the genome of the reference CRESS DNA viruses. Further epidemiological investigation using samples collected in 2018 showed that the overall positive rate for the virus was 56.4% (111/197) in Anhui Province. This is the first report of FSfaCVs identified in pigs in China, and further epidemiological studies are warranted to evaluate the influence of the virus on pigs.
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Li Y, Gordon E, Idle A, Altan E, Seguin MA, Estrada M, Deng X, Delwart E. Virome of a Feline Outbreak of Diarrhea and Vomiting Includes Bocaviruses and a Novel Chapparvovirus. Viruses 2020; 12:v12050506. [PMID: 32375386 PMCID: PMC7291048 DOI: 10.3390/v12050506] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/30/2020] [Accepted: 05/01/2020] [Indexed: 12/16/2022] Open
Abstract
An unexplained outbreak of feline diarrhea and vomiting, negative for common enteric viral and bacterial pathogens, was subjected to viral metagenomics and PCR. We characterized from fecal samples the genome of a novel chapparvovirus we named fechavirus that was shed by 8/17 affected cats and identified three different feline bocaviruses shed by 9/17 cats. Also detected were nucleic acids from attenuated vaccine viruses, members of the normal feline virome, viruses found in only one or two cases, and viruses likely derived from ingested food products. Epidemiological investigation of disease signs, time of onset, and transfers of affected cats between three facilities support a possible role for this new chapparvovirus in a highly contagious feline diarrhea and vomiting disease.
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Affiliation(s)
- Yanpeng Li
- Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA 94118, USA; (Y.L.); (E.A.); (X.D.)
- Department of Laboratory Medicine, University of California, San Francisco, CA 94118, USA
| | - Emilia Gordon
- The British Columbia Society for the Prevention of Cruelty to Animals, Vancouver, BC V5T1R1, Canada; (E.G.); (A.I.)
| | - Amanda Idle
- The British Columbia Society for the Prevention of Cruelty to Animals, Vancouver, BC V5T1R1, Canada; (E.G.); (A.I.)
| | - Eda Altan
- Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA 94118, USA; (Y.L.); (E.A.); (X.D.)
- Department of Laboratory Medicine, University of California, San Francisco, CA 94118, USA
| | - M. Alexis Seguin
- IDEXX Reference Laboratories, Inc., West Sacramento, CA 95605, USA; (M.A.S.); (M.E.)
| | - Marko Estrada
- IDEXX Reference Laboratories, Inc., West Sacramento, CA 95605, USA; (M.A.S.); (M.E.)
| | - Xutao Deng
- Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA 94118, USA; (Y.L.); (E.A.); (X.D.)
- Department of Laboratory Medicine, University of California, San Francisco, CA 94118, USA
| | - Eric Delwart
- Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA 94118, USA; (Y.L.); (E.A.); (X.D.)
- Department of Laboratory Medicine, University of California, San Francisco, CA 94118, USA
- Correspondence: ; Tel.: +1-(415)-531-0763
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45
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Fahsbender E, Charlys da-Costa A, Elise Gill D, Augusto de Padua Milagres F, Brustulin R, Julio Costa Monteiro F, Octavio da Silva Rego M, Soares D’Athaide Ribeiro E, Cerdeira Sabino E, Delwart E. Plasma virome of 781 Brazilians with unexplained symptoms of arbovirus infection include a novel parvovirus and densovirus. PLoS One 2020; 15:e0229993. [PMID: 32134963 PMCID: PMC7058308 DOI: 10.1371/journal.pone.0229993] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 02/19/2020] [Indexed: 12/16/2022] Open
Abstract
Plasma from patients with dengue-like symptoms was collected in 2013 to 2016 from the Brazilian states of Tocantins and Amapa. 781 samples testing negative for IgM against Dengue, Zika, and Chikungunya viruses and for flaviviruses, alphaviruses and enteroviruses RNA using RT-PCRs were analyzed using viral metagenomics. Viral particles-associated nucleic acids were enriched, randomly amplified, and deep sequenced in 102 mini-pools generating over 2 billion reads. Sequence data was analyzed for the presence of known and novel eukaryotic viral reads. Anelloviruses were detected in 80%, human pegivirus 1 in 19%, and parvovirus B19 in 17% of plasma pools. HIV and enteroviruses were detected in two pools each. Previously uncharacterized viral genomes were also identified, and their presence in single plasma samples confirmed by PCR. Chapparvovirus and ambidensovirus genomes, both in the Parvoviridae family, were partially characterized showing 33% and 34% identity in their NS1 sequences to their closest relative. Molecular surveillance using pre-existing plasma from febrile patients provides a readily scalable approach for the detection of novel, potentially emerging, viruses.
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Affiliation(s)
- Elizabeth Fahsbender
- Vitalant Research Institute, San Francisco, CA, United States of America
- UCSF Dept. of Laboratory Medicine, University of California–San Francisco, San Francisco, CA, United States of America
| | - Antonio Charlys da-Costa
- School of Medicine & Institute of Tropical Medicine, University of Sao Paulo, Infectious Disease, Sao Paulo, Brazil
| | - Danielle Elise Gill
- School of Medicine & Institute of Tropical Medicine, University of Sao Paulo, Infectious Disease, Sao Paulo, Brazil
| | - Flavio Augusto de Padua Milagres
- Public Health Laboratory State (LACEN/TO), Secretary of Health of Tocantins, Palmas, TO, Brazil
- Federal University of Tocantins, Palmas, Tocantins, Brazil
| | - Rafael Brustulin
- Public Health Laboratory State (LACEN/TO), Secretary of Health of Tocantins, Palmas, TO, Brazil
- Federal University of Tocantins, Palmas, Tocantins, Brazil
| | | | | | | | - Ester Cerdeira Sabino
- School of Medicine & Institute of Tropical Medicine, University of Sao Paulo, Infectious Disease, Sao Paulo, Brazil
| | - Eric Delwart
- Vitalant Research Institute, San Francisco, CA, United States of America
- UCSF Dept. of Laboratory Medicine, University of California–San Francisco, San Francisco, CA, United States of America
- * E-mail:
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46
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Lee Q, Padula MP, Pinello N, Williams SH, O'Rourke MB, Fumagalli MJ, Orkin JD, Song R, Shaban B, Brenner O, Pimanda JE, Weninger W, de Souza WM, Melin AD, Wong JJL, Crim MJ, Monette S, Roediger B, Jolly CJ. Murine and related chapparvoviruses are nephro-tropic and produce novel accessory proteins in infected kidneys. PLoS Pathog 2020; 16:e1008262. [PMID: 31971979 PMCID: PMC6999912 DOI: 10.1371/journal.ppat.1008262] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 02/04/2020] [Accepted: 12/08/2019] [Indexed: 12/21/2022] Open
Abstract
Mouse kidney parvovirus (MKPV) is a member of the provisional genus Chapparvovirus that causes renal disease in immune-compromised mice, with a disease course reminiscent of polyomavirus-associated nephropathy in immune-suppressed kidney transplant patients. Here we map four major MKPV transcripts, created by alternative splicing, to a common initiator region, and use mass spectrometry to identify “p10” and “p15” as novel chapparvovirus accessory proteins produced in MKPV-infected kidneys. p15 and the splicing-dependent putative accessory protein NS2 are conserved in all near-complete amniote chapparvovirus genomes currently available (from mammals, birds and a reptile). In contrast, p10 may be encoded only by viruses with >60% amino acid identity to MKPV. We show that MKPV is kidney-tropic and that the bat chapparvovirus DrPV-1 and a non-human primate chapparvovirus, CKPV, are also found in the kidneys of their hosts. We propose, therefore, that many mammal chapparvoviruses are likely to be nephrotropic. Parvoviruses are small, genetically simple single-strand DNA viruses that remain viable outside their hosts for very long periods of time. They cause disease in several domesticated species and in humans. Mouse kidney parvovirus (MKPV) is a causative agent of kidney failure in immune-compromised mice and is the only member of the provisional Chapparvovirus genus for which the complete genome including telomeres is known. Here, we show that MKPV propagates almost exclusively in the kidneys of mice infected naturally, wherein it produces novel accessory proteins whose coding regions are conserved in amniote-associated chapparvovirus sequences. We assemble a closely related complete viral genome present in DNA extracted from the kidney of a wild Cebus imitator monkey, and show that another related chapparvovirus is preferentially found in kidneys of the vampire bat Desmodus rotundus. We conclude that many mammal-hosted chapparvovirus are adapted to the kidney niche and may therefore cause disease following kidney stress in multiple species.
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Affiliation(s)
- Quintin Lee
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Matthew P. Padula
- Proteomics Core Facility, University of Technology Sydney, Sydney, NSW, Australia
| | - Natalia Pinello
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Simon H. Williams
- Center for Infection & Immunity, Mailman School of Public Health, Columbia University, New York, NY, United States of America
| | - Matthew B. O'Rourke
- Kolling Institute of Medical Research, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Marcilio Jorge Fumagalli
- Virology Research Center, School of Medicine of Ribeirão Preto of the University of São Paulo, Ribeirão Preto, Brazil
| | - Joseph D. Orkin
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
- Department of Anthropology and Archaeology, University of Calgary, Alberta, Canada
| | - Renhua Song
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Babak Shaban
- Melbourne Integrative Genomics, University of Melbourne, Melbourne, Victoria, Australia
| | - Ori Brenner
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - John E. Pimanda
- Lowy Cancer Research Centre, University of New South Wales Sydney, Sydney, NSW, Australia
| | - Wolfgang Weninger
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - William Marciel de Souza
- Virology Research Center, School of Medicine of Ribeirão Preto of the University of São Paulo, Ribeirão Preto, Brazil
| | - Amanda D. Melin
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
- Department of Medical Genetics and Alberta Children’s Hospital Research Institute, Cumming School of Medicine, University of Calgary, Alberta, Canada
| | - Justin J.-L. Wong
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Marcus J. Crim
- Microbiology and Aquatic Diagnostics, IDEXX BioAnalytics, Discovery Drive, Columbia, MO, United States of America
| | - Sébastien Monette
- Laboratory of Comparative Pathology, Center of Comparative Medicine and Pathology, Memorial Sloan Kettering Cancer Center, The Rockefeller University, Weill Cornell Medicine, New York, NY, United States of America
| | - Ben Roediger
- Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Autoimmunity, Transplantation, Inflammation (ATI) Disease Area, Novartis Institutes for Biomedical Research, Basel, Switzerland
- * E-mail: (BR); (CJJ)
| | - Christopher J. Jolly
- Lowy Cancer Research Centre, University of New South Wales Sydney, Sydney, NSW, Australia
- * E-mail: (BR); (CJJ)
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Tsoleridis T, Chappell JG, Monchatre-Leroy E, Umhang G, Shi M, Bennett M, Tarlinton RE, McClure CP, Holmes EC, Ball JK. Discovery and Prevalence of Divergent RNA Viruses in European Field Voles and Rabbits. Viruses 2019; 12:E47. [PMID: 31906044 PMCID: PMC7019641 DOI: 10.3390/v12010047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 12/24/2019] [Accepted: 12/27/2019] [Indexed: 12/13/2022] Open
Abstract
The advent of unbiased metagenomic virus discovery has revolutionized studies of virus biodiversity and evolution. Despite this, our knowledge of the virosphere, including in mammalian species, remains limited. We used unbiased metagenomic sequencing to identify RNA viruses in European field voles and rabbits. Accordingly, we identified a number of novel RNA viruses including astrovirus, rotavirus A, picorna-like virus and a morbilli-like paramyxovirus. In addition, we identified a sobemovirus and a novel luteovirus that likely originated from the rabbit diet. These newly discovered viruses were often divergent from those previously described. The novel astrovirus was most closely related to a virus sampled from the rodent-eating European roller bird (Coracias garrulous). PCR screening revealed that the novel morbilli-like paramyxovirus in the UK field vole had a prevalence of approximately 4%, and shared common ancestry with other rodent morbilli-like viruses sampled globally. Two novel rotavirus A sequences were detected in a UK field vole and a French rabbit, the latter with a prevalence of 5%. Finally, a highly divergent picorna-like virus found in the gut of the French rabbit virus was only ~35% similar to an arilivirus at the amino acid level, suggesting the presence of a novel viral genus within the Picornaviridae.
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Affiliation(s)
- Theocharis Tsoleridis
- School of Life Sciences, The University of Nottingham, Nottingham NG7 2UH, UK; (J.G.C.); (C.P.M.)
- Wolfson Centre for Global Virus Infections, The University of Nottingham, Nottingham NG7 2UH, UK
| | - Joseph G. Chappell
- School of Life Sciences, The University of Nottingham, Nottingham NG7 2UH, UK; (J.G.C.); (C.P.M.)
- Wolfson Centre for Global Virus Infections, The University of Nottingham, Nottingham NG7 2UH, UK
| | - Elodie Monchatre-Leroy
- Anses, Laboratoire de la Rage et de la Faune Sauvage, 54220 Malzeville, France; (E.M.-L.); (G.U.)
| | - Gérald Umhang
- Anses, Laboratoire de la Rage et de la Faune Sauvage, 54220 Malzeville, France; (E.M.-L.); (G.U.)
| | - Mang Shi
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia; (M.S.); (E.C.H.)
| | - Malcolm Bennett
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK; (M.B.); (R.E.T.)
| | - Rachael E. Tarlinton
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK; (M.B.); (R.E.T.)
| | - C. Patrick McClure
- School of Life Sciences, The University of Nottingham, Nottingham NG7 2UH, UK; (J.G.C.); (C.P.M.)
- Wolfson Centre for Global Virus Infections, The University of Nottingham, Nottingham NG7 2UH, UK
| | - Edward C. Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia; (M.S.); (E.C.H.)
| | - Jonathan K. Ball
- School of Life Sciences, The University of Nottingham, Nottingham NG7 2UH, UK; (J.G.C.); (C.P.M.)
- Wolfson Centre for Global Virus Infections, The University of Nottingham, Nottingham NG7 2UH, UK
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48
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Liu X, Wang H, Liu X, Li Y, Chen J, Zhang J, Wang X, Shen S, Wang H, Deng F, Wang M, Guan W, Hu Z. Genomic and transcriptional analyses of novel parvoviruses identified from dead peafowl. Virology 2019; 539:80-91. [PMID: 31706163 DOI: 10.1016/j.virol.2019.10.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 09/30/2019] [Accepted: 10/26/2019] [Indexed: 01/20/2023]
Abstract
To identify potential pathogens responsible for a disease outbreak of cultured peafowls in China in 2013, metagenomic sequencing was conducted. The genomes of two closely related parvoviruses, namely peafowl parvovirus 1 (PePV1) and PePV2, were identified with size of 4428 bp and 4348 bp, respectively. Phylogenetic analysis revealed that both viruses are novel parvoviruses, belonging to the proposed genus Chapparvovirus of Parvoviridae. The transcriptional profile of PePV1 was analyzed by transfecting a nearly complete PePV1 genome into HEK-293T cells. Results revealed that PePV1 employs one promoter and two polyadenylation sites to start and terminate its transcriptions, with one donor site and two acceptor sites for pre-mRNA splicing. PePV1 DNA and structural protein were detected in several tissues of a dead peafowl, which appeared to have suffered enteritis, pneumonia and viremia. These results provide novel information of chapparvoviruses, and call for attention to the potential pathogens.
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Affiliation(s)
- Xiaoping Liu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hanzhong Wang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Xiaoqian Liu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yong Li
- Hubei Wildlife Rescue Center, China
| | | | | | - Xi Wang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shu Shen
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Hualin Wang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Fei Deng
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Manli Wang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Wuxiang Guan
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China.
| | - Zhihong Hu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China.
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49
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A Duarte M, F Silva JM, R Brito C, S Teixeira D, L Melo F, M Ribeiro B, Nagata T, S Campos F. Faecal Virome Analysis of Wild Animals from Brazil. Viruses 2019; 11:E803. [PMID: 31480274 PMCID: PMC6784175 DOI: 10.3390/v11090803] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 08/27/2019] [Accepted: 08/28/2019] [Indexed: 12/15/2022] Open
Abstract
The Brazilian Cerrado fauna shows very wide diversity and can be a potential viral reservoir. Therefore, the animal's susceptibility to some virus can serve as early warning signs of potential human virus diseases. Moreover, the wild animal virome of this biome is unknown. Based on this scenario, high-throughput sequencing contributes a robust tool for the identification of known and unknown virus species in this environment. In the present study, faeces samples from cerrado birds (Psittacara leucophthalmus, Amazona aestiva, and Sicalis flaveola) and mammals (Didelphis albiventris, Sapajus libidinosus, and Galictis cuja) were collected at the Veterinary Hospital, University of Brasília. Viral nucleic acid was extracted, submitted to random amplification, and sequenced by Illumina HiSeq platform. The reads were de novo assembled, and the identities of the contigs were evaluated by Blastn and tblastx searches. Most viral contigs analyzed were closely related to bacteriophages. Novel archaeal viruses of the Smacoviridae family were detected. Moreover, sequences of members of Adenoviridae, Anelloviridae, Circoviridae, Caliciviridae, and Parvoviridae families were identified. Complete and nearly complete genomes of known anelloviruses, circoviruses, and parvoviruses were obtained, as well as putative novel species. We demonstrate that the metagenomics approach applied in this work was effective for identification of known and putative new viruses in faeces samples from Brazilian Cerrado fauna.
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Affiliation(s)
- Matheus A Duarte
- Faculdade de Agronomia e Veterinária, Universidade de Brasília, Brasília-DF 70.910-900, Brazil
- Departamento de Biologia Celular, Instituto de Biologia, Universidade de Brasília, Brasília-DF 70.910-900, Brazil
| | - João M F Silva
- Departamento de Biologia Celular, Instituto de Biologia, Universidade de Brasília, Brasília-DF 70.910-900, Brazil
| | - Clara R Brito
- Faculdade de Agronomia e Veterinária, Universidade de Brasília, Brasília-DF 70.910-900, Brazil
| | - Danilo S Teixeira
- Núcleo de Atendimento e Pesquisa de Animais Silvestres, Universidade Estadual de Santa Cruz, Ilhéus-BA 45.662-900, Brazil
| | - Fernando L Melo
- Departamento de Fitopatologia, Instituto de Biologia, Universidade de Brasília, Brasília-DF 70.910-900, Brazil
| | - Bergmann M Ribeiro
- Departamento de Biologia Celular, Instituto de Biologia, Universidade de Brasília, Brasília-DF 70.910-900, Brazil
| | - Tatsuya Nagata
- Departamento de Biologia Celular, Instituto de Biologia, Universidade de Brasília, Brasília-DF 70.910-900, Brazil
| | - Fabrício S Campos
- Laboratório de Bioinformática e Biotecnologia, Campus de Gurupi, Universidade Federal do Tocantins, Tocantins-TO 77.410-570, Brazil.
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50
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Canuti M, Kroyer ANK, Ojkic D, Whitney HG, Robertson GJ, Lang AS. Discovery and Characterization of Novel RNA Viruses in Aquatic North American Wild Birds. Viruses 2019; 11:E768. [PMID: 31438486 PMCID: PMC6784231 DOI: 10.3390/v11090768] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/16/2019] [Accepted: 08/18/2019] [Indexed: 12/25/2022] Open
Abstract
Wild birds are recognized viral reservoirs but our understanding about avian viral diversity is limited. We describe here three novel RNA viruses that we identified in oropharyngeal/cloacal swabs collected from wild birds. The complete genome of a novel gull metapneumovirus (GuMPV B29) was determined. Phylogenetic analyses indicated that this virus could represent a novel avian metapneumovirus (AMPV) sub-group, intermediate between AMPV-C and the subgroup of the other AMPVs. This virus was detected in an American herring (1/24, 4.2%) and great black-backed (4/26, 15.4%) gulls. A novel gull coronavirus (GuCoV B29) was detected in great black-backed (3/26, 11.5%) and American herring (2/24, 8.3%) gulls. Phylogenetic analyses of GuCoV B29 suggested that this virus could represent a novel species within the genus Gammacoronavirus, close to other recently identified potential novel avian coronaviral species. One GuMPV-GuCoV co-infection was detected. A novel duck calicivirus (DuCV-2 B6) was identified in mallards (2/5, 40%) and American black ducks (7/26, 26.9%). This virus, of which we identified two different types, was fully sequenced and was genetically closest to other caliciviruses identified in Anatidae, but more distant to other caliciviruses from birds in the genus Anas. These discoveries increase our knowledge about avian virus diversity and host distributions.
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Affiliation(s)
- Marta Canuti
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave., St. John's, NL A1B 3X9, Canada.
| | - Ashley N K Kroyer
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave., St. John's, NL A1B 3X9, Canada
| | - Davor Ojkic
- Animal Health Laboratory, Laboratory Services Division, University of Guelph, 419 Gordon St., Guelph, ON N1H 6R8, Canada
| | - Hugh G Whitney
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave., St. John's, NL A1B 3X9, Canada
| | - Gregory J Robertson
- Wildlife Research Division, Environment and Climate Change Canada, 6 Bruce Street, Mount Pearl, NL A1N 4T3, Canada
| | - Andrew S Lang
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave., St. John's, NL A1B 3X9, Canada.
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