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Varsani A, Krupovic M. 2024 Smacoviridae family update: 59 new species in seven genera. Arch Virol 2024; 169:184. [PMID: 39167240 DOI: 10.1007/s00705-024-06116-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
Family Smacoviridae (order Cremevirales, class Arfiviricetes, phylum Cressdnaviricota) comprises viruses with small circular genomes of ~2300-3000 nt in length that encode at least two proteins, the rolling-circle replication associated protein (Rep) and the capsid protein (CP). Smacovirids have been discovered in fecal samples of various animals and display remarkable sequence diversity. Here, we provide an overview of the genomic properties of classified smacovirids and report on the latest taxonomy update in the family Smacoviridae. The family has been expanded by 59 new species in the genera Porprismacovirus (n = 25), Inpeasmacovirus (n = 1), Felismacovirus (n = 22), Drosmacovirus (n = 4), Dragsmacovirus (n = 2), Bovismacovirus (n = 4), and Bonzesmacovirus (n = 1) and currently includes 12 genera with 143 species officially recognized 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, AZ, 85287-5001, USA.
- Structural Biology Research Unit, Department of Integrative, Biomedical Sciences, University of Cape Town, Observatory, Cape Town, 7925, South Africa.
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, Archaeal Virology Unit, 25 rue du Dr Roux, 75015, Paris, France.
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Qian L, Zhuang Z, Lu J, Wang H, Wang X, Yang S, Ji L, Shen Q, Zhang W, Shan T. Metagenomic survey of viral diversity obtained from feces of piglets with diarrhea. Heliyon 2024; 10:e25616. [PMID: 38375275 PMCID: PMC10875384 DOI: 10.1016/j.heliyon.2024.e25616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 12/02/2023] [Accepted: 01/30/2024] [Indexed: 02/21/2024] Open
Abstract
Pigs are natural host to various zoonotic pathogens including viruses. In this study, we analyzed the viral communities in the feces of 89 piglets with diarrhea under one month old which were collected from six farms in Jiangsu Province of the Eastern China, using the unbiased virus metagenomic method. A total of 89 libraries were constructed, and 46937894 unique sequence reads were generated by Illumina sequencing. Overall, the family Picornaviridae accounted for the majority of the total reads of putative mammalian viruses. Ten novel virus genomes from different family members were discovered, including Parvoviridae (n = 2), Picobirnaviridae (n = 4) and CRESS DNA viruses (n = 4). A large number of phages were identified, which mainly belonged to the order Caudovirales and the family Microviridae. Moreover, some identified viruses were closely related to viruses found in non-porcine hosts, highlighting the potential for cross-species virus dissemination. This study increased our understanding of the fecal virus communities of diarrhea piglets and provided valuable information for virus monitoring and preventing.
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Affiliation(s)
- Lingling Qian
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Zi Zhuang
- Center of Clinical Laboratory, Dushu Lake Hospital Affiliated to Soochow University, Soochow University, Suzhou, Jiangsu, 215000, China
| | - Juan Lu
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Huiying Wang
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 200062, China
| | - Xiaochun Wang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Shixing Yang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Likai Ji
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Quan Shen
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Wen Zhang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Tongling Shan
- Department of Swine Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
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Kabir A, Habib T, Chouhan CS, Hassan J, Rahman AKMA, Nazir KHMNH. Epidemiology and molecular characterization of Feline panleukopenia virus from suspected domestic cats in selected Bangladesh regions. PLoS One 2023; 18:e0282559. [PMID: 37862355 PMCID: PMC10588828 DOI: 10.1371/journal.pone.0282559] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 06/06/2023] [Indexed: 10/22/2023] Open
Abstract
Feline panleukopenia (FPL) is a highly contagious cat disease and is endemic in Bangladesh. The study aims to describe the epidemiology and molecular characterization of the Feline panleukopenia virus from the suspected domestic cats in selected Bangladesh regions. Randomly, 161 rectal swabs were collected from the pet hospitals between July 2021 and December 2022. A structured questionnaire was administered through face-to-face interviews with cat owners in order to collect data on potential risk factors for FPL, such as age, sex, sharing litter boxes and every day utensils in multicat households, vaccination history, hospital visits for other diseases, and season. The rectal swabs were tested by PCR targeting the VP2 capsid protein gene, and six PCR-positive samples were further sequenced for molecular characterizations. The risk factors for FPLV were identified using multivariable logistic regression analysis. The overall prevalence of FPL among suspects was 22.9%. The mortality and case fatality were 10.6%, and 45.9%, respectively. However, mortality in kittens was significantly higher (16.4%) than younger cats. The odds of FPL were 8.83 times (95% CI: 3.14-24.85) higher among unvaccinated cats than vaccinated cats. The winter season had almost six times (95% CI: 1.38-24.40) higher odds of FPL than rainy season. In a multicat house, the odds of FPL was about five times (95% CI: 1.93-13.45) higher for cats that shared a litter box and food utensils compared to those that did not engage in such sharing. Visiting hospitals for other reasons nearly triples the odds of FPL (OR: 2.80, 95% CI: 1.04-7.54) compared to cats that do not visit hospitals. Analysis of partial sequence of the VP2 gene revealed genetic variations among the isolates from different regions. Among these isolates, four were identical to FPLV isolates from South Korea and China, while one showed complete homology with FPLV isolates from Thailand. In contrast, the remaining one was 100% identical to Carnivore protoparvovirus-1 isolated from a feline sample in Italy. Our isolates were classified into three distinct clades alongside Feline panleukopenia virus and Carnivore protoparvovirus-1. One in every three suspected cats was infected with Feline panleukopenia. Regular vaccination of the cats, especially those that share common litter box and food utensils and visit hospitals for other purposes, will help reduce the prevalence of FPL in Bangladesh. Besides, it is worth emphasizing the existence of genetic diversity among the circulating Feline panleukopenia viruses in Bangladesh.
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Affiliation(s)
- Ajran Kabir
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Tasmia Habib
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | | | - Jayedul Hassan
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | | | - K. H. M. Nazmul Hussain Nazir
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
- Mymensingh Pet Clinic and Research Center, Mymensingh, Bangladesh
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Cardoso BTM, de Deus DR, Sousa EC, Pinheiro KDC, da Costa JN, Maués MAC, Mesquita MJDF, Teixeira DM, Siqueira JAM, Resque HR, Gabbay YB, da Silva LD. Molecular analysis of canine circovirus in dogs from animal shelters in Belém, Pará, northern Brazil: first detection at the amazon region. BRAZILIAN JOURNAL OF VETERINARY MEDICINE 2023; 45:e000723. [PMID: 37859867 PMCID: PMC10583600 DOI: 10.29374/2527-2179.bjvm000723] [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: 02/17/2023] [Accepted: 08/03/2023] [Indexed: 10/21/2023] Open
Abstract
The canine circovirus (CanCV) is a single-stranded DNA virus that has become an important emerging virus associated with gastroenteritis in dogs worldwide. In the present study, the CanCV was detected by PCR in 15% (22/147) of dogs from animal shelters in Belém, between 2019 and 2020. We observed an association between the CanCV infection and the presence of diarrhea in animals younger than one year of age (p > 0.01). The Brazilian strains were grouped in Chinese genotypes, with 99.54 to 100% nucleotilde homology. The GMRF Bayesian Skyride used the molecular clock model, which was the best suited technique to plot the dataset. The most recent common ancestor (TMRCA) was estimated in 2017, with the evolution rate of 1.6 x 10-3 s/s/y. The viral family diversity was also investigated, with emphasis on the families of the enteric pathogenic viruses Parvoviridae, Picornaviridae and Astroviridae, which were detected in the CanCV positive pooled samples. This study highlights the importance of the CanCV as an emergent virus that causes diarrhea in Brazilian dogs. The results found herein contribute to the understanding of the role of CanCV in enteric diseases and in the evolutionary molecular characterization of the circulating genotypes. Furthermore, we increased the understanding of the fecal virome in dogs with diarrhea, providing data for the monitoring and prevention viral gastroenteric diseases in domestic animals.
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Affiliation(s)
- Bruna Trindade Moreira Cardoso
- Biomedical Scientist, Programa de Pós-graduação em Biologia Parasitária da Amazônia (PPGBPA), Centro de Ciências Biológicas e da Saúde (CCBS), Universidade do Estado do Pará, Belém, PA, Brazil.
| | - Danielle Rodrigues de Deus
- Biologist, MSc., Programa de Pós-graduação em Virologia, Instituto Evandro Chagas, Ananindeua, PA, Brazil.
| | - Edivaldo Costa Sousa
- Biomedical Scientist, DSc., Seção de Parasitologia, Instituto Evandro Chagas, Ananindeua, PA, Brazil.
| | - Kenny da Costa Pinheiro
- Biomedical Scientist, DSc., Seção de Virologia, Instituto Evandro Chagas, Ananindeua, PA, Brazil.
| | - Jonaia Novaes da Costa
- Biomedical Scientist, Programa de Pós-graduação em Biologia Parasitária da Amazônia (PPGBPA), Centro de Ciências Biológicas e da Saúde (CCBS), Universidade do Estado do Pará, Belém, PA, Brazil.
| | | | | | - Dielle Monteiro Teixeira
- Biomedical Scientist, DSc., Seção de Virologia, Instituto Evandro Chagas, Ananindeua, PA, Brazil.
| | | | - Hugo Reis Resque
- Biomedical Scientist, DSc., Seção de Virologia, Instituto Evandro Chagas, Ananindeua, PA, Brazil.
| | - Yvone Benchimol Gabbay
- Biomedical Scientist, DSc., Seção de Virologia, Instituto Evandro Chagas, Ananindeua, PA, Brazil.
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Chen D, Guo X, Wang K, Zhao W, Chang Z, Wang Q, Xu C. Multi-Omics Analysis Reveals the Pathogenesis of Growth-Disordered Raccoon Dog. Int J Mol Sci 2023; 24:14237. [PMID: 37762538 PMCID: PMC10531513 DOI: 10.3390/ijms241814237] [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: 08/07/2023] [Revised: 09/08/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Microorganisms of the genus Eperythrozoon are a zoonotic chronic infectious disease with wide distribution. We found that raccoons infected with Eperythrozoon showed obvious stunting, which seriously affected the economic benefits of raccoon dogs. To investigate the pathogenesis of the raccoon dog, we used transcriptome and proteome sequencing to analyze the changes in mRNA, miRNA, and protein expression in raccoon dogs infected with Eperythrozoon and normal raccoons. The results showed that the expression levels of genes related to immunity, metabolism, and enzyme activity were significantly changed. Among these, ERLIN1, IGF1R, CREB3L1, TNS1, TENC1, and mTOR play key roles. Additionally, the miR-1268, miR-125b, miR-10-5p, and miR-10 as central miRNAs regulate the expression of these genes. Integrated transcriptomic and proteomic analyses revealed consistent trends in mRNA and protein changes in MYH9, FKBP1A, PRKCA, and CYP11B2. These results suggest that Eperythrozoon may contribute to the slow development of raccoons by affecting the expression of mRNAs and miRNAs, reducing their immunity and causing metabolic abnormalities.
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Affiliation(s)
- Danyang Chen
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, 4899 Juye Street, Changchun 130112, China; (D.C.); (X.G.); (K.W.); (W.Z.); (Z.C.)
- Innovation Center for Feeding and Utilization of Special Animals in Jilin Province and Research Center for Microbial Feed Engineering of Special Animals in Jilin Province, 4899 Juye Street, Changchun 130112, China
| | - Xiaolan Guo
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, 4899 Juye Street, Changchun 130112, China; (D.C.); (X.G.); (K.W.); (W.Z.); (Z.C.)
- Innovation Center for Feeding and Utilization of Special Animals in Jilin Province and Research Center for Microbial Feed Engineering of Special Animals in Jilin Province, 4899 Juye Street, Changchun 130112, China
| | - Kaiying Wang
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, 4899 Juye Street, Changchun 130112, China; (D.C.); (X.G.); (K.W.); (W.Z.); (Z.C.)
- Innovation Center for Feeding and Utilization of Special Animals in Jilin Province and Research Center for Microbial Feed Engineering of Special Animals in Jilin Province, 4899 Juye Street, Changchun 130112, China
| | - Weigang Zhao
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, 4899 Juye Street, Changchun 130112, China; (D.C.); (X.G.); (K.W.); (W.Z.); (Z.C.)
- Innovation Center for Feeding and Utilization of Special Animals in Jilin Province and Research Center for Microbial Feed Engineering of Special Animals in Jilin Province, 4899 Juye Street, Changchun 130112, China
| | - Zhongjuan Chang
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, 4899 Juye Street, Changchun 130112, China; (D.C.); (X.G.); (K.W.); (W.Z.); (Z.C.)
- Innovation Center for Feeding and Utilization of Special Animals in Jilin Province and Research Center for Microbial Feed Engineering of Special Animals in Jilin Province, 4899 Juye Street, Changchun 130112, China
| | - Quankai Wang
- College of Animal Science and Technology, Jilin Agriculture University, Changchun 130118, China;
| | - Chao Xu
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, 4899 Juye Street, Changchun 130112, China; (D.C.); (X.G.); (K.W.); (W.Z.); (Z.C.)
- Innovation Center for Feeding and Utilization of Special Animals in Jilin Province and Research Center for Microbial Feed Engineering of Special Animals in Jilin Province, 4899 Juye Street, Changchun 130112, China
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Chae SB, Jeong CG, Park JS, Na EJ, Oem JK. Detection and Genetic Characterization of Astroviruses in Brain Tissues of Wild Raccoon Dogs. Viruses 2023; 15:1488. [PMID: 37515175 PMCID: PMC10384943 DOI: 10.3390/v15071488] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 06/26/2023] [Accepted: 06/29/2023] [Indexed: 07/30/2023] Open
Abstract
Astroviruses (AstVs) have been detected in a wide range of animal species, including mammals and birds. Recently, a novel AstV associated with neurological symptoms has been detected in the brains of some mammals. Raccoon dog AstV has been reported recently in China. However, there have been no reports in South Korea. Therefore, the present study aimed to detect and genetically characterize AstVs in the intestine and brain tissues of 133 wild raccoon dogs collected in Korea between 2017 and 2019. Of the seven raccoon dogs, AstVs were detected in six intestinal tissues and four brain tissues. Analysis of the capsid protein amino acid sequences of raccoon dog AstVs detected in Korea revealed a high similarity to canine AstVs, suggesting possible interspecies transmission between raccoon dogs and dogs. Phylogenetic and capsid protein amino acid sequence analysis of raccoon dog AstVs detected in the brain the 17-148B strain belonging to the HMO clade and exhibiting conserved sequences found in neurotropic AstVs (NT-AstVs), indicating their potential as NT-AstVs. However, the pathogenicity and transmission routes of the raccoon dog AstV detected in Korea have not yet been elucidated, so further research and continued surveillance for AstV in wild raccoon dogs are needed.
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Affiliation(s)
- Su-Beom Chae
- Laboratory of Veterinary Infectious Disease, College of Veterinary of Medicine, Jeonbuk National University, Iksan 54596, Republic of Korea
| | - Chang-Gi Jeong
- Laboratory of Veterinary Infectious Disease, College of Veterinary of Medicine, Jeonbuk National University, Iksan 54596, Republic of Korea
| | - Jun-Soo Park
- Laboratory of Veterinary Infectious Disease, College of Veterinary of Medicine, Jeonbuk National University, Iksan 54596, Republic of Korea
| | - Eun-Jee Na
- Laboratory of Veterinary Infectious Disease, College of Veterinary of Medicine, Jeonbuk National University, Iksan 54596, Republic of Korea
| | - Jae-Ku Oem
- Laboratory of Veterinary Infectious Disease, College of Veterinary of Medicine, Jeonbuk National University, Iksan 54596, Republic of Korea
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Zhuang Z, Qian L, Lu J, Zhang X, Mahmood A, Cui L, Wang H, Wang X, Yang S, Ji L, Shan T, Shen Q, Zhang W. Comparison of viral communities in the blood, feces and various tissues of wild brown rats ( Rattus norvegicus). Heliyon 2023; 9:e17222. [PMID: 37389044 PMCID: PMC10300334 DOI: 10.1016/j.heliyon.2023.e17222] [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: 02/04/2023] [Revised: 06/08/2023] [Accepted: 06/10/2023] [Indexed: 07/01/2023] Open
Abstract
Viral diseases caused by new outbreaks of viral infections pose a serious threat to human health. Wild brown rats (Rattus norvegicus), considered one of the world's largest and most widely distributed rodents, are host to various zoonotic pathogens. To further understand the composition of the virus community in wild brown rats and explore new types of potentially pathogenic viruses, viral metagenomics was conducted to investigate blood, feces, and various tissues of wild brown rats captured from Zhenjiang, China. Results indicated that the composition of the virus community in different samples showed significant differences. In blood and tissue samples, members of the Parvoviridae and Anelloviridae form the main body of the virus community. Picornaviridae, Picobirnaviridae, and Astroviridae made up a large proportion of fecal samples. Several novel genome sequences from members of different families, including Anelloviridae, Parvoviridae, and CRESS DNA viruses, were detected in both blood and other samples, suggesting that they have the potential to spread across organs to cause viremia. These viruses included not only strains closely related to human viruses, but also a potential recombinant virus. Multiple dual-segment picornaviruses were obtained from fecal samples, as well as virus sequences from the Astroviridae and Picornaviridae. Phylogenetic analysis showed that these viruses belonged to different genera, with multiple viruses clustered with other animal viruses. Whether they have pathogenicity and the ability to spread across species needs further study.
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Affiliation(s)
- Zi Zhuang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Lingling Qian
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Juan Lu
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Xiaodan Zhang
- Department of Clinical Laboratory, Zhenjiang Center for Disease Prevention and Control, Zhenjiang, 212002, China
| | - Asif Mahmood
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Lei Cui
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 200062, China
| | - Huiying Wang
- Department of Swine Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Xiaochun Wang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Shixing Yang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Likai Ji
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Tongling Shan
- Department of Swine Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Quan Shen
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Wen Zhang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
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Viral Metagenomic Analysis of the Fecal Samples in Domestic Dogs (Canis lupus familiaris). Viruses 2023; 15:v15030685. [PMID: 36992396 PMCID: PMC10058366 DOI: 10.3390/v15030685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/24/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
Canine diarrhea is a common intestinal illness that is usually caused by viruses, bacteria, and parasites, and canine diarrhea may induce morbidity and mortality of domestic dogs if treated improperly. Recently, viral metagenomics was applied to investigate the signatures of the enteric virome in mammals. In this research, the characteristics of the gut virome in healthy dogs and dogs with diarrhea were analyzed and compared using viral metagenomics. The alpha diversity analysis indicated that the richness and diversity of the gut virome in the dogs with diarrhea were much higher than the healthy dogs, while the beta diversity analysis revealed that the gut virome of the two groups was quite different. At the family level, the predominant viruses in the canine gut virome were certified to be Microviridae, Parvoviridae, Siphoviridae, Inoviridae, Podoviridae, Myoviridae, and others. At the genus level, the predominant viruses in the canine gut virome were certified to be Protoparvovirus, Inovirus, Chlamydiamicrovirus, Lambdavirus, Dependoparvovirus, Lightbulbvirus, Kostyavirus, Punavirus, Lederbergvirus, Fibrovirus, Peduovirus, and others. However, the viral communities between the two groups differed significantly. The unique viral taxa identified in the healthy dogs group were Chlamydiamicrovirus and Lightbulbvirus, while the unique viral taxa identified in the dogs with diarrhea group were Inovirus, Protoparvovirus, Lambdavirus, Dependoparvovirus, Kostyavirus, Punavirus, and other viruses. Phylogenetic analysis based on the near-complete genome sequences showed that the CPV strains collected in this study together with other CPV Chinese isolates clustered into a separate branch, while the identified CAV-2 strain D5-8081 and AAV-5 strain AAV-D5 were both the first near-complete genome sequences in China. Moreover, the predicted bacterial hosts of phages were certified to be Campylobacter, Escherichia, Salmonella, Pseudomonas, Acinetobacter, Moraxella, Mediterraneibacter, and other commensal microbiota. In conclusion, the enteric virome of the healthy dogs group and the dogs with diarrhea group was investigated and compared using viral metagenomics, and the viral communities might influence canine health and disease by interacting with the commensal gut microbiome.
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Azevedo LSD, França Y, Viana E, Medeiros RS, Morillo SG, Guiducci R, Ribeiro CD, Vieira HR, Barrio-Nuevo KM, Cunha MS, Guerra JM, Silva DDMCE, Filho VBD, Araújo ELL, Ferreira SRS, Batista CF, Silva GCDD, Nogueira ML, Ahagon CM, Moreira RC, Cunha L, Morais VS, da Costa AC, Luchs A. Lack of molecular evidence of fecal-borne viruses in capybaras from São Paulo state, Brazil, 2018-2020: a minor public health issue. Braz J Microbiol 2023; 54:543-551. [PMID: 36342660 PMCID: PMC9640885 DOI: 10.1007/s42770-022-00859-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 10/24/2022] [Indexed: 11/09/2022] Open
Abstract
Capybara (Hydrochoerus hydrochaeris) is the world's largest rodent species distributed throughout South America. These animals are incredibly tolerant to anthropogenic environments and are occupying large urban centers. Capybaras are known to carry potentially zoonotic agents, including R. rickettsia, Leishmania spp., Leptospira spp., Trypanosoma spp., Salmonella spp., Toxoplasma gondii, and rabies virus. Focusing on the importance of monitoring potential sources of emerging zoonotic viruses and new viral reservoirs, the aim of the present study was to assess the presence of fecal-borne viruses in the feces of capybaras living in urban parks in São Paulo state, Brazil. A total of 337 fecal samples were collected between 2018 and 2020 and screened for the following: (i) Rotavirus group A (RVA) by ELISA; (ii) non-RVA species and Picobirnavirus (PBV) using PAGE; (iii) Human Bocaparvovirus (HBoV), Bufavirus (BuV), Tusavirus (TuV), and Cutavirus (CuV) qPCR; (iv) Human Enterovirus (EV), Norovirus GII (NoV), and Hantavirus by in houses RT-qPCR; (v) SARS-CoV-2 via commercial RT-qPCR kit assay; and (vi) Astrovirus (AstV) and Adenovirus (AdV) using conventional nested (RT)-PCRs. All fecal samples tested were negative for fecal-borne viruses. This study adds further evidence that the fecal-borne viruses is a minor public health issue in Brazilian capybaras, at least during the surveillance period and surveyed areas. Continuous monitoring of sylvatic animals is essential to prevent and control the emergence or re-emergence of newly discovered virus as well as viruses with known zoonotic potential.
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Affiliation(s)
| | - Yasmin França
- Enteric Disease Laboratory, Virology Center, Adolfo Lutz Institute, Sao Paulo, Brazil
| | - Ellen Viana
- Enteric Disease Laboratory, Virology Center, Adolfo Lutz Institute, Sao Paulo, Brazil
| | | | | | - Raquel Guiducci
- Enteric Disease Laboratory, Virology Center, Adolfo Lutz Institute, Sao Paulo, Brazil
| | - Cibele Daniel Ribeiro
- Enteric Disease Laboratory, Virology Center, Adolfo Lutz Institute, Sao Paulo, Brazil
| | - Heloisa Rosa Vieira
- Enteric Disease Laboratory, Virology Center, Adolfo Lutz Institute, Sao Paulo, Brazil
| | | | - Mariana Sequetin Cunha
- Vector Borne Diseases Laboratory, Virology Center, Adolfo Lutz Institute, Sao Paulo, Brazil
| | - Juliana Mariotti Guerra
- Quantitative Pathology Laboratory, Pathology Center, Adolfo Lutz Institute, Sao Paulo, Brazil
| | | | | | - Emerson Luiz Lima Araújo
- General Coordination of Public Health, Laboratories of the Strategic Articulation, Department of the Health, Surveillance Secretariat, Ministry of Health (CGLAB/DAEVS/SVS-MS), Brasília, Brazil
| | | | | | | | | | - Cintia Mayumi Ahagon
- Blood and Sexual Diseases - Retrovirus Laboratory, Virology Center, Adolfo Lutz Institute, Sao Paulo, Brazil
| | | | - Lia Cunha
- Hepatitis Laboratory, Virology Center, Adolfo Lutz Institute, Sao Paulo, Brazil
| | - Vanessa Santos Morais
- Medical Parasitology Laboratory (LIM/46), Institute of Tropical Medicine, University of Sao Paulo, Sao Paulo, Brazil
| | - Antonio Charlys da Costa
- Medical Parasitology Laboratory (LIM/46), Institute of Tropical Medicine, University of Sao Paulo, Sao Paulo, Brazil
| | - Adriana Luchs
- Enteric Disease Laboratory, Virology Center, Adolfo Lutz Institute, Sao Paulo, Brazil.
- Centro de Virologia, Núcleo de Doenças Entéricas, Instituto Adolfo Lutz, Av. Dr Arnaldo, nº 355, São Paulo, SP, 01246-902, Brasil.
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Yang S, Zhang D, Zhang Y, Fan Z, Jiang L, Wang Y, Zhang W. Multiple novel smaco-like viruses identified in chicken cloaca swabs. Arch Virol 2022; 167:2703-2708. [PMID: 36125556 DOI: 10.1007/s00705-022-05577-6] [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: 05/23/2022] [Accepted: 07/13/2022] [Indexed: 12/14/2022]
Abstract
Viral metagenomics has been used in numerous animal virus discoveries. Recently, an unprecedented diversity of CRESS DNA viruses was identified using this method, and this has expanded our understanding of the environmental distribution and host range of CRESS DNA viruses. In this study, using an unbiased viral metagenomics approach, we investigated the fecal virome of chickens collected from two farms of Anhui Province, China. Five novel CRESS DNA viruses were obtained and characterized. The genome of the five viruses is 2,401-2,742 bp in length, containing two ORFs in the same orientation. Phylogenetic analysis indicated that all five viruses have a closer genetic relationship to smacoviruses than to other viruses in the order Cremevirales. Pairwise comparison of Rep amino acid sequences showed that these five viruses had only low amino acid sequence identity (8.9%-30.6%) to members of the family Smacoviridae, and the sequence identity among the five smaco-like viruses and other unclassified smacovirus strains was 70.3-95.8%. These findings broaden our knowledge of the genetic diversity of CRESS DNA viruses and provide a basis for classification of unclassified smacoviruses.
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Affiliation(s)
- Shixing Yang
- School of Medicine, Jiangsu University, 301 Xuefu Road, 212013, Zhenjiang, Jiangsu, People's Republic of China
| | - Dianqi Zhang
- School of Medicine, Jiangsu University, 301 Xuefu Road, 212013, Zhenjiang, Jiangsu, People's Republic of China
| | - Yuyang Zhang
- School of Medicine, Jiangsu University, 301 Xuefu Road, 212013, Zhenjiang, Jiangsu, People's Republic of China
| | - Zhaobin Fan
- College of Pharmacy, Heze University, 274015, Heze, Shandong, People's Republic of China
| | - Lili Jiang
- College of Pharmacy, Heze University, 274015, Heze, Shandong, People's Republic of China
| | - Yan Wang
- 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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11
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Lan T, Li H, Yang S, Shi M, Han L, Sahu SK, Lu Y, Wang J, Zhou M, Liu H, Huang J, Wang Q, Zhu Y, Wang L, Xu Y, Lin C, Liu H, Hou Z. The chromosome-scale genome of the raccoon dog: Insights into its evolutionary characteristics. iScience 2022; 25:105117. [PMID: 36185367 PMCID: PMC9523411 DOI: 10.1016/j.isci.2022.105117] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 07/07/2022] [Accepted: 09/08/2022] [Indexed: 11/28/2022] Open
Affiliation(s)
- Tianming Lan
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin 150040, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Haimeng Li
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shangchen Yang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Minhui Shi
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Han
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Yaxian Lu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Jiangang Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Mengchao Zhou
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Hui Liu
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), College of Forestry, Hainan University, Haikou 570228, China
| | - Junxuan Huang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Qing Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yixin Zhu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Wang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yanchun Xu
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin 150040, China
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
- Corresponding author
| | - Chuyu Lin
- Shenzhen Zhong Nong Jing Yue Biotech Company Limited, Shenzhen 518120, China
- Corresponding author
| | - Huan Liu
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin 150040, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, China
- Corresponding author
| | - Zhijun Hou
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin 150040, China
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
- Corresponding author
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12
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Canuti M, Pénzes JJ, Lang AS. A new perspective on the evolution and diversity of the genus Amdoparvovirus (family Parvoviridae) through genetic characterization, structural homology modeling, and phylogenetics. Virus Evol 2022; 8:veac056. [PMID: 35783582 PMCID: PMC9242002 DOI: 10.1093/ve/veac056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 05/13/2022] [Accepted: 06/13/2022] [Indexed: 12/11/2022] Open
Abstract
Amdoparvoviruses (genus Amdoparvovirus, family Parvoviridae) are primarily viruses of carnivorans, but recent studies have indicated that their host range might also extend to rodents and chiropterans. While their classification is based on the full sequence of the major nonstructural protein (NS1), several studies investigating amdoparvoviral diversity have been focused on partial sequences, leading to difficulties in accurately determining species demarcations and leaving several viruses unclassified. In this study, while reporting the complete genomic sequence of a novel amdoparvovirus identified in an American mink (British Columbia amdoparvovirus, BCAV), we studied the phylogenetic relationships of all amdoparvovirus-related sequences and provide a comprehensive reevaluation of their diversity and evolution. After excluding recombinant sequences, phylogenetic and pairwise sequence identity analyses allowed us to define fourteen different viruses, including the five currently classified species, BCAV, and four additional viruses that fulfill the International Committee on Taxonomy of Viruses criteria to be classified as species. We show that the group of viruses historically known as Aleutian mink disease virus (species Carnivore amdoparvovirus 1) should be considered as a cluster of at least four separate viral species that have been co-circulating in mink farms, facilitating the occurrence of inter-species recombination. Genome organization, splicing donor and acceptor sites, and protein sequence motifs were surprisingly conserved within the genus. The sequence of the major capsid protein virus protein 2 (VP2) was significantly more conserved between and within species compared to NS1, a phenomenon possibly linked to antibody-dependent enhancement (ADE). Homology models suggest a remarkably high degree of conservation of the spikes located near the icosahedral threefold axis of the capsid, comprising the surface region associated with ADE. A surprisingly high number of divergent amino acid positions were found in the luminal threefold and twofold axes of the capsid, regions of hitherto unknown function. We emphasize the importance of complete genome analyses and, given the marked phylogenetic inconsistencies across the genome, advise to obtain the complete coding sequences of divergent strains. Further studies on amdoparvovirus biology and structure as well as epidemiological and virus discovery investigations are required to better characterize the ecology and evolution of this important group of viruses.
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Affiliation(s)
- Marta Canuti
- Department of Biology, Memorial University of Newfoundland, 45 Arctic Ave., St. John’s NL A1C 5S7, Canada
| | - Judit J Pénzes
- Institute for Quantitative Biomedicine, Rutgers the State University of New Jersey, 174 Frelinghuysen Rd, Piscataway, NJ 08854, USA
| | - Andrew S Lang
- Department of Biology, Memorial University of Newfoundland, 45 Arctic Ave., St. John’s NL A1C 5S7, Canada
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