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Denison ER, Zepernick BN, McKay RML, Wilhelm SW. Metatranscriptomic analysis reveals dissimilarity in viral community activity between an ice-free and ice-covered winter in Lake Erie. mSystems 2024; 9:e0075324. [PMID: 38940524 PMCID: PMC11264689 DOI: 10.1128/msystems.00753-24] [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: 05/31/2024] [Accepted: 06/10/2024] [Indexed: 06/29/2024] Open
Abstract
Winter is a relatively under-studied season in freshwater ecology. The paucity of wintertime surveys has led to a lack of knowledge regarding microbial community activity during the winter in Lake Erie, a North American Great Lake. Viruses shape microbial communities and regulate biogeochemical cycles by acting as top-down controls, yet very few efforts have been made to examine active virus populations during the winter in Lake Erie. Furthermore, climate change-driven declines in seasonal ice cover have been shown to influence microbial community structure, but no studies have compared viral community activity between different ice cover conditions. We surveyed surface water metatranscriptomes for viral hallmark genes as a proxy for active virus populations and compared activity metrics between ice-covered and ice-free conditions from two sampled winters. Transcriptionally active viral communities were detected in both winters, spanning diverse phylogenetic clades of putative bacteriophage (Caudoviricetes), giant viruses (Nucleocytoviricota, or NCLDV), and RNA viruses (Orthornavirae). However, viral community activity metrics revealed pronounced differences between the ice-covered and ice-free winters. Viral community composition was distinct between winters and viral hallmark gene richness was reduced in the ice-covered relative to the ice-free conditions. In addition, the observed differences in viral communities correlated with microbial community activity metrics. Overall, these findings contribute to our understanding of the viral populations that are active during the winter in Lake Erie and suggest that viral community activity may be associated with ice cover extent.IMPORTANCEAs seasonal ice cover is projected to become increasingly rare on large temperate lakes, there is a need to understand how microbial communities might respond to changing ice conditions. Although it is widely recognized that viruses impact microbial community structure and function, there is little known regarding wintertime viral activity or the relationship between viral activity and ice cover extent. Our metatranscriptomic analyses indicated that viruses were transcriptionally active in the winter surface waters of Lake Erie. These findings also expanded the known diversity of viral lineages in the Great Lakes. Notably, viral community activity metrics were significantly different between the two sampled winters. The pronounced differences we observed in active viral communities between the ice-covered and ice-free samples merit further research regarding how viral communities will function in future, potentially ice-free, freshwater systems.
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Affiliation(s)
| | | | - R. Michael L. McKay
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada
| | - Steven W. Wilhelm
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
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Paietta EN, Kraberger S, Lund MC, Vargas KL, Custer JM, Ehmke E, Yoder AD, Varsani A. Diverse Circular DNA Viral Communities in Blood, Oral, and Fecal Samples of Captive Lemurs. Viruses 2024; 16:1099. [PMID: 39066262 DOI: 10.3390/v16071099] [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: 06/11/2024] [Revised: 07/01/2024] [Accepted: 07/03/2024] [Indexed: 07/28/2024] Open
Abstract
Few studies have addressed viral diversity in lemurs despite their unique evolutionary history on the island of Madagascar and high risk of extinction. Further, while a large number of studies on animal viromes focus on fecal samples, understanding viral diversity across multiple sample types and seasons can reveal complex viral community structures within and across species. Groups of captive lemurs at the Duke Lemur Center (Durham, NC, USA), a conservation and research center, provide an opportunity to build foundational knowledge on lemur-associated viromes. We sampled individuals from seven lemur species, i.e., collared lemur (Eulemur collaris), crowned lemur (Eulemur coronatus), blue-eyed black lemur (Eulemur flavifrons), ring-tailed lemur (Lemur catta), Coquerel's sifaka (Propithecus coquereli), black-and-white ruffed lemur (Varecia variegata variegata), and red ruffed lemur (Varecia rubra), across two lemur families (Lemuridae, Indriidae). Fecal, blood, and saliva samples were collected from Coquerel's sifaka and black-and-white ruffed lemur individuals across two sampling seasons to diversify virome biogeography and temporal sampling. Using viral metagenomic workflows, the complete genomes of anelloviruses (n = 4), cressdnaviruses (n = 47), caudoviruses (n = 15), inoviruses (n = 34), and microviruses (n = 537) were determined from lemur blood, feces, and saliva. Many virus genomes, especially bacteriophages, identified in this study were present across multiple lemur species. Overall, the work presented here uses a viral metagenomics approach to investigate viral communities inhabiting the blood, oral cavity, and feces of healthy captive lemurs.
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Affiliation(s)
- Elise N Paietta
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Michael C Lund
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Karla L Vargas
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Joy M Custer
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Erin Ehmke
- Duke Lemur Center, Duke University, Durham, NC 27708, USA
| | - Anne D Yoder
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town 7925, South Africa
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Wang X, Kotta-Loizou I, Coutts RHA, Deng H, Han Z, Hong N, Shafik K, Wang L, Guo Y, Yang M, Xu W, Wang G. A circular single-stranded DNA mycovirus infects plants and confers broad-spectrum fungal resistance. MOLECULAR PLANT 2024; 17:955-971. [PMID: 38745413 DOI: 10.1016/j.molp.2024.05.003] [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: 01/25/2024] [Revised: 04/15/2024] [Accepted: 05/09/2024] [Indexed: 05/16/2024]
Abstract
Circular single-stranded DNA (ssDNA) viruses have been rarely found in fungi, and the evolutionary and ecological relationships among ssDNA viruses infecting fungi and other organisms remain unclear. In this study, a novel circular ssDNA virus, tentatively named Diaporthe sojae circular DNA virus 1 (DsCDV1), was identified in the phytopathogenic fungus Diaporthe sojae isolated from pear trees. DsCDV1 has a monopartite genome (3185 nt in size) encapsidated in isometric virions (21-26 nm in diameter). The genome comprises seven putative open reading frames encoding a discrete replicase (Rep) split by an intergenic region, a putative capsid protein (CP), several proteins of unknown function (P1-P4), and a long intergenic region. Notably, the two split parts of DsCDV1 Rep share high identities with the Reps of Geminiviridae and Genomoviridae, respectively, indicating an evolutionary linkage with both families. Phylogenetic analysis based on Rep or CP sequences placed DsCDV1 in a unique cluster, supporting the establishment of a new family, tentatively named Gegemycoviridae, intermediate to both families. DsCDV1 significantly attenuates fungal growth and nearly erases fungal virulence when transfected into the host fungus. Remarkably, DsCDV1 can systematically infect tobacco and pear seedlings, providing broad-spectrum resistance to fungal diseases. Subcellular localization analysis revealed that DsCDV1 P3 is systematically localized in the plasmodesmata, while its expression in trans-complementation experiments could restore systematic infection of a movement-deficient plant virus, suggesting that P3 is a movement protein. DsCDV1 exhibits unique molecular and biological traits not observed in other ssDNA viruses, serving as a link between fungal and plant ssDNA viruses and presenting an evolutionary connection between ssDNA viruses and fungi. These findings contribute to expanding our understanding of ssDNA virus diversity and evolution, offering potential biocontrol applications for managing crucial plant diseases.
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Affiliation(s)
- Xianhong Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Key Lab of Plant Pathology of Hubei Province, Wuhan 430070, China
| | - Ioly Kotta-Loizou
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, UK; Department of Clinical, Pharmaceutical and Biological Science, School of Life and Medical Sciences, University of Hertfordshire, Hatfield AL10 9AB, UK
| | - Robert H A Coutts
- Department of Clinical, Pharmaceutical and Biological Science, School of Life and Medical Sciences, University of Hertfordshire, Hatfield AL10 9AB, UK
| | - Huifang Deng
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Key Lab of Plant Pathology of Hubei Province, Wuhan 430070, China
| | - Zhenhao Han
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Key Lab of Plant Pathology of Hubei Province, Wuhan 430070, China
| | - Ni Hong
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Key Lab of Plant Pathology of Hubei Province, Wuhan 430070, China
| | - Karim Shafik
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Key Lab of Plant Pathology of Hubei Province, Wuhan 430070, China; Department of Plant Pathology, Faculty of Agriculture, Alexandria University, Alexandria 21526, Egypt
| | - Liping Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Key Lab of Plant Pathology of Hubei Province, Wuhan 430070, China
| | - Yashuang Guo
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Key Lab of Plant Pathology of Hubei Province, Wuhan 430070, China
| | - Mengmeng Yang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Key Lab of Plant Pathology of Hubei Province, Wuhan 430070, China
| | - Wenxing Xu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Key Lab of Plant Pathology of Hubei Province, Wuhan 430070, China.
| | - Guoping Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Key Lab of Plant Pathology of Hubei Province, Wuhan 430070, China.
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Couto RDS, Abreu WU, Rodrigues LRR, Marinho LF, Morais VDS, Villanova F, Pandey RP, Deng X, Delwart E, da Costa AC, Leal E. Genomoviruses in Liver Samples of Molossus molossus Bats. Microorganisms 2024; 12:688. [PMID: 38674632 PMCID: PMC11052389 DOI: 10.3390/microorganisms12040688] [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: 02/24/2024] [Revised: 03/15/2024] [Accepted: 03/20/2024] [Indexed: 04/28/2024] Open
Abstract
CRESS-DNA encompasses a broad spectrum of viruses documented across diverse organisms such as animals, plants, diatoms, fungi, and marine invertebrates. Despite this prevalence, the full extent of these viruses' impact on the environment and their respective hosts remains incompletely understood. Furthermore, an increasing number of viruses within this category lack detailed characterization. This investigation focuses on unveiling and characterizing viruses affiliated with the Genomoviridae family identified in liver samples from the bat Molossus molossus. Leveraging viral metagenomics, we identified seven sequences (MmGmV-PA) featuring a circular DNA genome housing two ORFs encoding replication-associated protein (Rep) and capsid protein (Cap). Predictions based on conserved domains typical of the Genomoviridae family were established. Phylogenetic analysis revealed the segregation of these sequences into two clades aligning with the genera Gemycirculavirus (MmGmV-06-PA and MmGmV-07-PA) and Gemykibivirus (MmGmV-01-PA, MmGmV-02-PA, MmGmV-03-PA, MmGmV-05-PA, and MmGmV-09-PA). At the species level, pairwise comparisons based on complete nucleotide sequences indicated the potential existence of three novel species. In summary, our study significantly contributes to an enhanced understanding of the diversity of Genomoviridae within bat samples, shedding light on previously undiscovered viral entities and their potential ecological implications.
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Affiliation(s)
- Roseane da Silva Couto
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, PA, Brazil; (R.d.S.C.); (F.V.)
| | - Wandercleyson Uchôa Abreu
- Programa de Pos-Graduação REDE Bionorte, Polo Pará, Universidade Federal do Oeste do Pará, Santarém 68040-255, PA, Brazil;
| | - Luís Reginaldo Ribeiro Rodrigues
- Laboratory of Genetics & Biodiversity, Institute of Educational Sciences, Universidade Federal do Oeste do Pará, Santarém 68040-255, PA, Brazil;
| | | | - Vanessa dos Santos Morais
- Laboratory of Virology (LIM 52), Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (V.d.S.M.); (A.C.d.C.)
| | - Fabiola Villanova
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, PA, Brazil; (R.d.S.C.); (F.V.)
| | - Ramendra Pati Pandey
- School of Health Sciences & Technology, UPES University, Dehradun 248007, Uttarakhand, India;
| | - Xutao Deng
- Vitalant Research Institute, San Francisco, CA 94143, USA;
| | - Eric Delwart
- Department Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA;
| | - Antonio Charlys da Costa
- Laboratory of Virology (LIM 52), Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (V.d.S.M.); (A.C.d.C.)
| | - Elcio Leal
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, PA, Brazil; (R.d.S.C.); (F.V.)
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5
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Yadhav Y, Selvaraj K, Ramasamy S, Venkataraman S. Computational studies on rep and capsid proteins of CRESS DNA viruses. Virusdisease 2024; 35:17-26. [PMID: 38817400 PMCID: PMC11133267 DOI: 10.1007/s13337-024-00858-x] [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: 11/20/2023] [Accepted: 01/29/2024] [Indexed: 06/01/2024] Open
Abstract
The circular rep-encoding single-stranded DNA viruses (CRESS DNA viruses) are among the smallest, with 2-6 kb ssDNA genomes that encode for a coat protein (C) and a replication protein (R). To comprehend the complexity and divergence of the C and R proteins, we have created predictive structural models of representative viruses infecting unique hosts from each family using the neural network-based method AlphaFold2 and carried out molecular dynamic simulations to assess their stability. The structural characteristics indicate that differences in loops and amino-terminus may play a significant role in facilitating adaptations to multiple hosts and vectors. In comparison to the C, the Rs show a high degree of conservation and structural mimicry of the nuclease-helicase domains of plasmids. A phylogenetic analysis based on the structures and sequences of the C and R proteins reveals evolutionary variances. Our study also highlights the conservation of structural components involved in the interaction of R with the conserved intergenic region of the genome. Further, we envisage that the adaptability of R's central linker may be crucial for establishing interactions with multiple protein partners, including C. Supplementary Information The online version contains supplementary material available at 10.1007/s13337-024-00858-x.
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Affiliation(s)
- Yagavi Yadhav
- Department of Biotechnology, Anna University, Guindy, Chennai, 600025 India
| | - Karthiga Selvaraj
- Department of Biotechnology, Anna University, Guindy, Chennai, 600025 India
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Torralba B, Blanc S, Michalakis Y. Reassortments in single-stranded DNA multipartite viruses: Confronting expectations based on molecular constraints with field observations. Virus Evol 2024; 10:veae010. [PMID: 38384786 PMCID: PMC10880892 DOI: 10.1093/ve/veae010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 11/23/2023] [Accepted: 01/30/2024] [Indexed: 02/23/2024] Open
Abstract
Single-stranded DNA multipartite viruses, which mostly consist of members of the genus Begomovirus, family Geminiviridae, and all members of the family Nanoviridae, partly resolve the cost of genomic integrity maintenance through two remarkable capacities. They are able to systemically infect a host even when their genomic segments are not together in the same host cell, and these segments can be separately transmitted by insect vectors from host to host. These capacities potentially allow such viruses to reassort at a much larger spatial scale, since reassortants could arise from parental genotypes that do not co-infect the same cell or even the same host. To assess the limitations affecting reassortment and their implications in genome integrity maintenance, the objective of this review is to identify putative molecular constraints influencing reassorted segments throughout the infection cycle and to confront expectations based on these constraints with empirical observations. Trans-replication of the reassorted segments emerges as the major constraint, while encapsidation, viral movement, and transmission compatibilities appear more permissive. Confronting the available molecular data and the resulting predictions on reassortments to field population surveys reveals notable discrepancies, particularly a surprising rarity of interspecific natural reassortments within the Nanoviridae family. These apparent discrepancies unveil important knowledge gaps in the biology of ssDNA multipartite viruses and call for further investigation on the role of reassortment in their biology.
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Affiliation(s)
- Babil Torralba
- PHIM, Université Montpellier, IRD, CIRAD, INRAE, Institut Agro, Avenue du Campus d’Agropolis - ZAC de Baillarguet, Montpellier 34980, France
| | - Stéphane Blanc
- PHIM, Université Montpellier, IRD, CIRAD, INRAE, Institut Agro, Avenue du Campus d’Agropolis - ZAC de Baillarguet, Montpellier 34980, France
| | - Yannis Michalakis
- MIVEGEC, Université Montpellier, CNRS, IRD, 911, Avenue Agropolis, Montpellier 34394, France
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Zhu P, Liu C, Liu GF, Liu H, Xie KM, Zhang HS, Xu X, Xiao J, Jiang JZ. Unveiling CRESS DNA Virus Diversity in Oysters by Virome. Viruses 2024; 16:228. [PMID: 38400004 PMCID: PMC10892194 DOI: 10.3390/v16020228] [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: 01/02/2024] [Revised: 01/27/2024] [Accepted: 01/30/2024] [Indexed: 02/25/2024] Open
Abstract
Oysters that filter feed can accumulate numerous pathogens, including viruses, which can serve as a valuable viral repository. As oyster farming becomes more prevalent, concerns are mounting about diseases that can harm both cultivated and wild oysters. Unfortunately, there is a lack of research on the viruses and other factors that can cause illness in shellfish. This means that it is harder to find ways to prevent these diseases and protect the oysters. This is part of a previously started project, the Dataset of Oyster Virome, in which we further study 30 almost complete genomes of oyster-associated CRESS DNA viruses. The replication-associated proteins and capsid proteins found in CRESS DNA viruses display varying evolutionary rates and frequently undergo recombination. Additionally, some CRESS DNA viruses have the capability for cross-species transmission. A plethora of unclassified CRESS DNA viruses are detectable in transcriptome libraries, exhibiting higher levels of transcriptional activity than those found in metagenome libraries. The study significantly enhances our understanding of the diversity of oyster-associated CRESS DNA viruses, emphasizing the widespread presence of CRESS DNA viruses in the natural environment and the substantial portion of CRESS DNA viruses that remain unidentified. This study's findings provide a basis for further research on the biological and ecological roles of viruses in oysters and their environment.
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Affiliation(s)
- Peng Zhu
- College of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai 201306, China
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510000, China
- Animal and Plant Inspection and Quarantine Technology Centre, Shenzhen Customs, Shenzhen 518000, China
| | - Chang Liu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510000, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai 519000, China
| | - Guang-Feng Liu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510000, China
| | - Hong Liu
- Animal and Plant Inspection and Quarantine Technology Centre, Shenzhen Customs, Shenzhen 518000, China
| | - Ke-Ming Xie
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510000, China
- School of Life Science and Biopharmacy, Guangdong Pharmaceutical University, Guangzhou 510000, China
| | - Hong-Sai Zhang
- College of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai 201306, China
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510000, China
| | - Xin Xu
- Livestock, Aquaculture and Technology Promotion and Service Center of Conghua District, Guangzhou 510000, China
| | - Jian Xiao
- Livestock, Aquaculture and Technology Promotion and Service Center of Conghua District, Guangzhou 510000, China
| | - Jing-Zhe Jiang
- College of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai 201306, China
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510000, China
- School of Life Science and Biopharmacy, Guangdong Pharmaceutical University, Guangzhou 510000, China
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Olivo D, Khalifeh A, Custer JM, Kraberger S, Varsani A. Diverse Small Circular DNA Viruses Identified in an American Wigeon Fecal Sample. Microorganisms 2024; 12:196. [PMID: 38258021 PMCID: PMC10821283 DOI: 10.3390/microorganisms12010196] [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: 12/24/2023] [Revised: 01/13/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024] Open
Abstract
American wigeons (Mareca americana) are waterfowls that are widely distributed throughout North America. Research of viruses associated with American wigeons has been limited to orthomyxoviruses, coronaviruses, and circoviruses. To address this poor knowledge of viruses associated with American wigeons, we undertook a pilot study to identify small circular DNA viruses in a fecal sample collected in January 2021 in the city of Tempe, Arizona (USA). We identified 64 diverse circular DNA viral genomes using a viral metagenomic workflow biased towards circular DNA viruses. Of these, 45 belong to the phylum Cressdnaviricota based on their replication-associated protein sequence, with 3 from the Genomoviridae family and the remaining 42 which currently cannot be assigned to any established virus group. It is most likely that these 45 viruses infect various organisms that are associated with their diet or environment. The remaining 19 virus genomes are part of the Microviridae family and likely associated with the gut enterobacteria of American wigeons.
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Affiliation(s)
- Diego Olivo
- Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85042, USA; (D.O.)
| | - Anthony Khalifeh
- Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85042, USA; (D.O.)
| | - Joy M. Custer
- Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85042, USA; (D.O.)
| | - Simona Kraberger
- Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85042, USA; (D.O.)
| | - Arvind Varsani
- Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85042, USA; (D.O.)
- Structural Biology Research Unit, Department of Integrative, Biomedical Sciences, University of Cape Town, Observatory, Cape Town 7925, South Africa
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9
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Rodríguez-Negrete EA, Grande-Pérez A. Quantification of Virion-Sense and Complementary-Sense DNA Strands of Circular Single-Stranded DNA Viruses. Methods Mol Biol 2024; 2724:93-109. [PMID: 37987901 DOI: 10.1007/978-1-0716-3485-1_8] [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] [Indexed: 11/22/2023]
Abstract
Circular ssDNA viruses are ubiquitous and can be found in both prokaryotes and eukaryotes. To understand the interaction of ssDNA viruses with their hosts, it is important to characterize the dynamics of viral sense (VS) and complementary-sense (CS) viral strands during the infection process. Here, we present a simple and rapid protocol that allows sensitive and accurate determination of the VS and CS strands generated during viral infection.The method consists of a two-step qPCR in which the first step uses a strand-specific (CS or VS) labeled primer and T4 DNA polymerase that lacks strand displacement activity and makes a single copy per VS or CS strand. Next, the T4 DNA polymerase and unincorporated oligonucleotides are removed by a silica membrane spin column. Finally, the purified VS or CS strands are quantified by qPCR in a second step in which amplification uses a tag primer and a specific primer. Absolute quantification of VS and CS strands is obtained by extrapolating the Cq data to a standard curve of ssDNA, which can be generated by phagemid expression. Quantification of VS and CS strands of two geminiviruses in infections of Solanum lycopersicum (tomato) and Nicotiana benthamiana plants using this method is shown.
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Affiliation(s)
- Edgar A Rodríguez-Negrete
- Instituto Politécnico Nacional, CIIDIR Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave, Sinaloa, Mexico
| | - Ana Grande-Pérez
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Málaga, Spain.
- Departamento de Biología Celular, Genética y Fisiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain.
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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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Ruiz-Padilla A, Turina M, Ayllón MA. Molecular characterization of a tetra segmented ssDNA virus infecting Botrytis cinerea worldwide. Virol J 2023; 20:306. [PMID: 38114992 PMCID: PMC10731770 DOI: 10.1186/s12985-023-02256-z] [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: 07/25/2023] [Accepted: 12/02/2023] [Indexed: 12/21/2023] Open
Abstract
BACKGROUND Family Genomoviridae was recently established, and only a few mycoviruses have been described and characterized, and almost all of them (Sclerotinia sclerotiorum hypovirulence-associated DNA virus 1, Fusarium graminearum gemyptripvirus 1 and Botrytis cinerea gemydayirivirus 1) induced hypovirulence in their host. Botrytis cinerea ssDNA virus 1 (BcssDV1), a tetrasegmented single-stranded DNA virus infecting the fungus Botrytis cinerea, has been molecularly characterized in this work. METHODS BcssDV1 was detected in Spanish and Italian B. cinerea field isolates obtained from grapevine. BcssDV1 variants genomes were molecularly characterized via NGS and Sanger sequencing. Nucleotide and amino acid sequences were used for diversity and phylogenetic analysis. Prediction of protein tertiary structures and putative associated functions were performed by AlphaFold2 and DALI. RESULTS BcssDV1 is a tetrasegmented single-stranded DNA virus. The mycovirus was composed by four genomic segments of approximately 1.7 Kb each, which are DNA-A, DNA-B, and DNA-C and DNA-D, that coded, respectively, for the rolling-circle replication initiation protein (Rep), capsid protein (CP) and two hypothetical proteins. BcssDV1 was present in several Italian and Spanish regions with high incidence and low variability among the different viral variants. DNA-A and DNA-D were found to be the more conserved genomic segments among variants, while DNA-B and DNA-C segments were shown to be the most variable ones. Tertiary structures of the proteins encoded by each segment suggested specific functions associated with each of them. CONCLUSIONS This study presented the first complete sequencing and characterization of a tetrasegmented ssDNA mycovirus, its incidence in Spain and Italy, its presence in other countries and its high conservation among regions.
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Affiliation(s)
- Ana Ruiz-Padilla
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (UPM-INIA/CSIC), Pozuelo de Alarcón, Madrid, Spain
| | - Massimo Turina
- Institute for Sustainable Plant Protection, National Research Council of Italy, Torino, Italy
| | - María A Ayllón
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (UPM-INIA/CSIC), Pozuelo de Alarcón, Madrid, Spain.
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, Spain.
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12
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Boros Á, Pankovics P, László Z, Urbán P, Herczeg R, Gáspár G, Tóth F, Reuter G. The genomic and epidemiological investigations of enteric viruses of domestic caprine ( Capra hircus) revealed the presence of multiple novel viruses related to known strains of humans and ruminant livestock species. Microbiol Spectr 2023; 11:e0253323. [PMID: 37823638 PMCID: PMC10714811 DOI: 10.1128/spectrum.02533-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 09/04/2023] [Indexed: 10/13/2023] Open
Abstract
IMPORTANCE Compared with other domestic animals, the virome and viral diversity of small ruminants especially in caprine are less studied even of its zoonotic potential. In this study, the enteric virome of caprine was investigated in detail using next-generation sequencing and reverse transcription PCR techniques. The complete or nearly complete genomes of seven novel viruses were determined which show a close phylogenetic relationship to known human and ruminant viruses. The high similarity between the identified caprine tusavirus (family Parvoviridae) and an unassigned CRESS DNA virus with closely related human strains could indicate the (reverse) zoonotic potential of these viruses. Others, like astroviruses (family Astroviridae), enteroviruses, or novel caripiviruses (named after the term caprine picornavirus) of family Picornaviridae found mostly in multiple co-infections in caprine and ovine, could indicate the cross-species transmission capabilities of these viruses between small ruminants.
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Affiliation(s)
- Ákos Boros
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary
| | - Péter Pankovics
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary
| | - Zoltán László
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary
| | - Péter Urbán
- János Szentágothai Research Centre of the University of Pécs, Bioinformatics Research Group, Genomics and Bioinformatics Core Facility, Pécs, Hungary
| | - Róbert Herczeg
- János Szentágothai Research Centre of the University of Pécs, Bioinformatics Research Group, Genomics and Bioinformatics Core Facility, Pécs, Hungary
| | - Gábor Gáspár
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary
| | - Fruzsina Tóth
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary
| | - Gábor Reuter
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary
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13
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Bonnamy M, Blanc S, Michalakis Y. Replication mechanisms of circular ssDNA plant viruses and their potential implication in viral gene expression regulation. mBio 2023; 14:e0169223. [PMID: 37695133 PMCID: PMC10653810 DOI: 10.1128/mbio.01692-23] [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] [Indexed: 09/12/2023] Open
Abstract
The replication of members of the two circular single-stranded DNA (ssDNA) virus families Geminiviridae and Nanoviridae, the only ssDNA viruses infecting plants, is believed to be processed by rolling-circle replication (RCR) and recombination-dependent replication (RDR) mechanisms. RCR is a ubiquitous replication mode for circular ssDNA viruses and involves a virus-encoded Replication-associated protein (Rep) which fulfills multiple functions in the replication mechanism. Two key genomic elements have been identified for RCR in Geminiviridae and Nanoviridae: (i) short iterative sequences called iterons which determine the specific recognition of the viral DNA by the Rep and (ii) a sequence enabling the formation of a stem-loop structure which contains a conserved motif and constitutes the origin of replication. In addition, studies in Geminiviridae provided evidence for a second replication mode, RDR, which has also been documented in some double-stranded DNA viruses. Here, we provide a synthesis of the current understanding of the two presumed replication modes of Geminiviridae and Nanoviridae, and we identify knowledge gaps and discuss the possibility that these replication mechanisms could regulate viral gene expression through modulation of gene copy number.
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Affiliation(s)
- Mélia Bonnamy
- PHIM, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
- MIVEGEC, CNRS, IRD, Univ Montpellier, Montpellier, France
| | - Stéphane Blanc
- PHIM, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
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14
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Vidovszky MZ, Kapitány S, Gellért Á, Harrach B, Görföl T, Boldogh SA, Kohl C, Wibbelt G, Mühldorfer K, Kemenesi G, Gembu GC, Hassanin A, Tu VT, Estók P, Horváth A, Kaján GL. Detection and genetic characterization of circoviruses in more than 80 bat species from eight countries on four continents. Vet Res Commun 2023; 47:1561-1573. [PMID: 37002455 PMCID: PMC10066014 DOI: 10.1007/s11259-023-10111-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/19/2023] [Indexed: 04/03/2023]
Abstract
Several bat-associated circoviruses and circular rep-encoding single-stranded DNA (CRESS DNA) viruses have been described, but the exact diversity and host species of these viruses are often unknown. Our goal was to describe the diversity of bat-associated circoviruses and cirliviruses, thus, 424 bat samples from more than 80 species were collected on four continents. The samples were screened for circoviruses using PCR and the resulting amino acid sequences were subjected to phylogenetic analysis. The majority of bat strains were classified in the genus Circovirus and some strains in the genus Cyclovirus and the clades CRESS1 and CRESS3. Some strains, however, could only be classified at the taxonomic level of the order and were not classified in any of the accepted or proposed clades. In the family Circoviridae, 71 new species have been predicted. This screening of bat samples revealed a great diversity of circoviruses and cirliviruses. These studies underline the importance of the discovery and description of new cirliviruses and the need to establish new species and families in the order Cirlivirales.
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Affiliation(s)
| | | | - Ákos Gellért
- Veterinary Medical Research Institute, Budapest, Hungary
| | - Balázs Harrach
- Veterinary Medical Research Institute, Budapest, Hungary
| | - Tamás Görföl
- National Laboratory of Virology, University of Pécs, Pécs, Hungary
| | | | - Claudia Kohl
- Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
| | - Gudrun Wibbelt
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Kristin Mühldorfer
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Gábor Kemenesi
- National Laboratory of Virology, University of Pécs, Pécs, Hungary
| | - Guy-Crispin Gembu
- Faculté des Sciences, Université de Kisangani, Kisangani, République Démocratique du Congo
| | - Alexandre Hassanin
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Sorbonne Université, MNHN, CNRS, EPHE, UA, Paris, France
| | - Vuong Tan Tu
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Péter Estók
- Department of Zoology, Eszterházy Károly Catholic University, Eger, Hungary
| | - Anna Horváth
- QUIRÓN, Center for Equine Assisted Interventions and Training for Well-Being and Sustainability, Comitán de Domínguez, Mexico
| | - Győző L. Kaján
- Veterinary Medical Research Institute, Budapest, Hungary
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15
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Paietta EN, Kraberger S, Custer JM, Vargas KL, Espy C, Ehmke E, Yoder AD, Varsani A. Characterization of Diverse Anelloviruses, Cressdnaviruses, and Bacteriophages in the Human Oral DNA Virome from North Carolina (USA). Viruses 2023; 15:1821. [PMID: 37766228 PMCID: PMC10537320 DOI: 10.3390/v15091821] [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: 07/08/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023] Open
Abstract
The diversity of viruses identified from the various niches of the human oral cavity-from saliva to dental plaques to the surface of the tongue-has accelerated in the age of metagenomics. This rapid expansion demonstrates that our understanding of oral viral diversity is incomplete, with only a few studies utilizing passive drool collection in conjunction with metagenomic sequencing methods. For this pilot study, we obtained 14 samples from healthy staff members working at the Duke Lemur Center (Durham, NC, USA) to determine the viral diversity that can be identified in passive drool samples from humans. The complete genomes of 3 anelloviruses, 9 cressdnaviruses, 4 Caudoviricetes large bacteriophages, 29 microviruses, and 19 inoviruses were identified in this study using high-throughput sequencing and viral metagenomic workflows. The results presented here expand our understanding of the vertebrate-infecting and microbe-infecting viral diversity of the human oral virome in North Carolina (USA).
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Affiliation(s)
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Joy M. Custer
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Karla L. Vargas
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Claudia Espy
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Erin Ehmke
- Duke Lemur Center, Duke University, Durham, NC 27705, USA;
| | - Anne D. Yoder
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town 7925, South Africa
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16
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da Silva JPH, de Resende FMP, da Silva JCF, de Breuil S, Nome C, Bejerman N, Zerbini FM. Amesuviridae: a new family of plant-infecting viruses in the phylum Cressdnaviricota, realm Monodnaviria. Arch Virol 2023; 168:223. [PMID: 37561218 DOI: 10.1007/s00705-023-05852-0] [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: 08/11/2023]
Abstract
The phylum Cressdnaviricota comprises viruses with single-stranded, circular DNA genomes that encode an HUH-type endonuclease (known as Rep). The phylum includes two classes, eight orders, and 11 families. Here, we report the creation of a twelfth family in the order Mulpavirales, class Arfiviricetes of the phylum Cressdnaviricota. The family Amesuviridae comprises viruses that infect plants and is divided into two genera: Temfrudevirus, including the species Temfrudevirus temperatum (with temperate fruit decay-associated virus as a member), and Yermavirus, including the species Yermavirus ilicis (with yerba mate-associated circular DNA virus as a member). Both viruses encode Rep proteins with HUH endonuclease and SH3 superfamily helicase domains. Phylogenetic analysis indicates that the replicative module of amesuviruses constitutes a well-supported monophyletic clade related to Rep proteins from viruses in the order Mulpavirales. Furthermore, both viruses encode a single capsid protein (CP) related to geminivirus CPs. Phylogenetic incongruence between the replicative and structural modules of amesuviruses suggests a chimeric origin resulting from remote recombination events between ancestral mulpavirales and geminivirids. The creation of the family Amesuviridae has been ratified by the International Committee on Taxonomy of Viruses (ICTV).
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Affiliation(s)
| | | | | | - Soledad de Breuil
- Instituto de Patología Vegetal, Centro de Investigaciones, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Camino 60 Cuadras Km 5.5, X5020ICA, Agropecuarias, Córdoba, Argentina
| | - Claudia Nome
- Instituto de Patología Vegetal, Centro de Investigaciones, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Camino 60 Cuadras Km 5.5, X5020ICA, Agropecuarias, Córdoba, Argentina
| | - Nicolas Bejerman
- Instituto de Patología Vegetal, Centro de Investigaciones, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Camino 60 Cuadras Km 5.5, X5020ICA, Agropecuarias, Córdoba, Argentina
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17
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Vasinioti VI, Pellegrini F, Buonavoglia A, Capozza P, Cardone R, Diakoudi G, Desario C, Catella C, Vicenza T, Lucente MS, Di Martino B, Camero M, Elia G, Decaro N, Martella V, Lanave G. Investigating the genetic diversity of CRESS DNA viruses in cats identifies a novel feline circovirus and unveils exposure of cats to canine circovirus. Res Vet Sci 2023; 161:86-95. [PMID: 37327693 DOI: 10.1016/j.rvsc.2023.06.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 06/08/2023] [Accepted: 06/09/2023] [Indexed: 06/18/2023]
Abstract
Circular replication-associated protein (Rep)-encoding single stranded (CRESS) DNA viruses include Circoviruses which have been found in several animal species and in human specimens. Circoviruses are associated with severe disease in pigs and birds and with respiratory and gastrointestinal disorders and systemic disease in dogs. In cats there are only a few anecdotical studies reporting CRESS DNA viruses. In this study, a total of 530 samples (361 sera, 131 stools, and 38 respiratory swabs) from cats, were screened for the presence of CRESS DNA viruses. Overall, 48 (9.0%) of 530 samples tested positive using a pan-Rep PCR. A total of 30 Rep sequences were obtained. Ten sequences of fecal origin were tightly related to each other (82.4-100% nt identity) and more distantly related to mongoose circoviruses (68.3 to 77.2% nt identity). At genome level these circoviruses displayed the highest nt identity (74.3-78.7%) to mongoose circoviruses thus representing a novel circovirus species. Circoviruses from different animal hosts (n = 12) and from humans (n = 8) were also identified. However, six Rep sequences were obtained from serum samples, including canine circoviruses, a human cyclovirus and human and fish-associated CRESS DNA viruses. The presence of these viruses in the sera would imply, to various extent, virus replication in the animal host, able to sustain viremia. Overall, these findings indicate a wide genetic diversity of CRESS DNA viruses in cats and warrant further investigations.
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Affiliation(s)
- Violetta Iris Vasinioti
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Francesco Pellegrini
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Alessio Buonavoglia
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Paolo Capozza
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Roberta Cardone
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Georgia Diakoudi
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Costantina Desario
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Cristiana Catella
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Teresa Vicenza
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Maria Stella Lucente
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Barbara Di Martino
- Department of Veterinary Medicine, Università degli Studi di Teramo, SP18, 64100 Teramo, Italy
| | - Michele Camero
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Gabriella Elia
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Nicola Decaro
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Vito Martella
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Gianvito Lanave
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy.
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18
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Chen XM, Zhao YY, Liu XC, Han YY, Zhang YH, Hou CY, Zheng LL, Ma SJ, Chen HY. Molecular detection and genetic characteristics of a novel porcine circovirus (porcine circovirus 4) and porcine reproductive and respiratory syndrome virus in Shaanxi and Henan Provinces of China. Comp Immunol Microbiol Infect Dis 2023; 98:102009. [PMID: 37390696 DOI: 10.1016/j.cimid.2023.102009] [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: 05/23/2023] [Revised: 06/18/2023] [Accepted: 06/19/2023] [Indexed: 07/02/2023]
Abstract
Porcine circovirus 4 (PCV4) is a recently discovered circovirus that was first reported in 2019 in several pigs with severe clinical disease in Hunan province of China, and also identified in pigs infected with porcine reproductive and respiratory syndrome virus (PRRSV). To further investigate the epidemic profile and genetic characteristics of the two viruses, 150 clinical samples were collected from 9 swine farms in Shaanxi and Henan provinces of China, and a SYBR Green I-based duplex quantitative real-time polymerase chain reaction (qPCR) was developed for detecting PCV4 and PRRSV simultaneously. The results showed the limits of detection were 41.1 copies/μL and 81.5 copies/μL for PCV4 and PRRSV, respectively. The detection rates of PCV4 and PRRSV were 8.00% (12/150) and 12.00% (18/150) respectively, and a case of co-infection with PCV4 and PRRSV was found in the lung tissue of a suckling pig with respiratory symptom. Subsequently, the complete genomic sequences of five PCV4 strains were obtained, of which one PCV4 strain (SX-ZX) was from Shaanxi province, and these strains were 1770 nucleotides in length and had 97.7%-99.4% genomic identity with 59 PCV4 reference strains. The genome characteristic of the SX-ZX strain was evaluated from three aspects, a "stem-loop" structure, ORF1 and ORF2. As essential elements for the replication, the 17-bp iterative sequence was predicted as the stem structure, in which three non-tandem hexamers were found at downstream with H1/H2 (12-CGGCACACTTCGGCAC-27) as the minimal binding site. Three of the five PCV4 strains were clustered into PCV4b, which was composed of Suidae, fox, dairy cow, dog and raccoon dog. Phylogenetic analysis revealed that seven PRRSV strains from the present study were clustered into the PRRSV-2 genotype. Collectively, these data extend our understanding of the genome characteristic of PCV4 as well as the molecular epidemiology and the genetic profile of PCV4 and PRRSV.
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Affiliation(s)
- Xi-Meng Chen
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengdong New District Longzi Lake 15#, Zhengzhou 450046, People's Republic of China
| | - You-Yi Zhao
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengdong New District Longzi Lake 15#, Zhengzhou 450046, People's Republic of China
| | - Xiao-Chen Liu
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengdong New District Longzi Lake 15#, Zhengzhou 450046, People's Republic of China
| | - Ying-Ying Han
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengdong New District Longzi Lake 15#, Zhengzhou 450046, People's Republic of China
| | - Yuan-Hang Zhang
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengdong New District Longzi Lake 15#, Zhengzhou 450046, People's Republic of China
| | - Cheng-Yao Hou
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengdong New District Longzi Lake 15#, Zhengzhou 450046, People's Republic of China
| | - Lan-Lan Zheng
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengdong New District Longzi Lake 15#, Zhengzhou 450046, People's Republic of China
| | - Shi-Jie Ma
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengdong New District Longzi Lake 15#, Zhengzhou 450046, People's Republic of China.
| | - Hong-Ying Chen
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengdong New District Longzi Lake 15#, Zhengzhou 450046, People's Republic of China.
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19
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Ding Y, Wan M, Li Z, Ma X, Zhang W, Xu M. Comparison of the gut virus communities between patients with Crohn's disease and healthy individuals. Front Microbiol 2023; 14:1190172. [PMID: 37396350 PMCID: PMC10311494 DOI: 10.3389/fmicb.2023.1190172] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 05/18/2023] [Indexed: 07/04/2023] Open
Abstract
Introduction The escalating incidence of Crohn's disease (CD), a debilitating ailment that ravages individuals and their families, has become a formidable issue over recent decades. Method In this study, fecal samples from patients with CD and healthy individuals were investigated by means of viral metagenomics. Results The fecal virome was analyzed and some suspected disease-causing viruses were described. A polyomavirus named HuPyV with 5,120 base pairs (bp) was found in the disease group. In a preliminary analysis employing large T region-specific primers, it was found that HuPyV was present in 3.2% (1/31) of healthy samples and 43.2% (16/37) of disease samples. Additionally, two other viruses from the anellovirus and CRESS-DNA virus families were found in fecal samples from CD patients. The complete genome sequences of these two viruses were described respectively, and the phylogenetic trees have been built using the anticipated amino acid sequences of the viral proteins. Discussion Further research is required to elucidate the relationship between these viruses and the onset and development of Crohn's disease.
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Affiliation(s)
- Yuzhu Ding
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Mengtian Wan
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Zheng Li
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Xiao Ma
- Qinghai Institute for Endemic Disease Prevention and Control, Xining, Qinghai, China
| | - Wen Zhang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Min Xu
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, Jiangsu, China
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20
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Lund MC, Larsen BB, Rowsey DM, Otto HW, Gryseels S, Kraberger S, Custer JM, Steger L, Yule KM, Harris RE, Worobey M, Van Doorslaer K, Upham NS, Varsani A. Using archived and biocollection samples towards deciphering the DNA virus diversity associated with rodent species in the families cricetidae and heteromyidae. Virology 2023; 585:42-60. [PMID: 37276766 DOI: 10.1016/j.virol.2023.05.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/15/2023] [Accepted: 05/19/2023] [Indexed: 06/07/2023]
Abstract
Rodentia is the most speciose order of mammals, and they are known to harbor a wide range of viruses. Although there has been significant research on zoonotic viruses in rodents, research on the diversity of other viruses has been limited, especially for rodents in the families Cricetidae and Heteromyidae. In fecal and liver samples of nine species of rodents, we identify 346 distinct circular DNA viral genomes. Of these, a large portion are circular, single-stranded DNA viruses in the families Anelloviridae (n = 3), Circoviridae (n = 5), Genomoviridae (n = 7), Microviridae (n = 297), Naryaviridae (n = 4), Vilyaviridae (n = 15) and in the phylum Cressdnaviricota (n = 13) that cannot be assigned established families. We also identified two large bacteriophages of 36 and 50 kb that are part of the class Caudoviricetes. Some of these viruses are clearly those that infect rodents, however, most of these likely infect various organisms associated with rodents, their environment or their diet.
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Affiliation(s)
- Michael C Lund
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287-5001, USA; The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA
| | - Brendan B Larsen
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA; Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98102, USA
| | - Dakota M Rowsey
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287-5001, USA; Biodiversity Knowledge Integration Center, Arizona State University, Tempe, AZ, 85287, USA
| | - Hans W Otto
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Sophie Gryseels
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA; Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000, Leuven, Belgium; Department of Biology, University of Antwerp, 2000, Antwerp, Belgium; OD Taxonomy and Phylogeny, Royal Belgian Museum of Natural Sciences, 1000, Brussels, Belgium
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA
| | - Joy M Custer
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA
| | - Laura Steger
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287-5001, USA; Biodiversity Knowledge Integration Center, Arizona State University, Tempe, AZ, 85287, USA
| | - Kelsey M Yule
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287-5001, USA; Biodiversity Knowledge Integration Center, Arizona State University, Tempe, AZ, 85287, USA
| | - Robin E Harris
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287-5001, USA
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Koenraad Van Doorslaer
- School of Animal and Comparative Biomedical Sciences, The BIO5 Institute, Department of Immunobiology, Cancer Biology Graduate Interdisciplinary Program, UA Cancer Center, University of Arizona Tucson, AZ, 85724, USA
| | - Nathan S Upham
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287-5001, USA; Biodiversity Knowledge Integration Center, Arizona State University, Tempe, AZ, 85287, USA
| | - Arvind Varsani
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287-5001, USA; The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA; Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Observatory, Cape Town, 7701, South Africa.
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21
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Gainor K, Stewart KM, Picknell A, Russ M, Makela N, Watson K, Mancuso DM, Malik YS, Ghosh S. First Report on Detection and Complete Genomic Analysis of a Novel CRESS DNA Virus from Sea Turtles. Pathogens 2023; 12:pathogens12040601. [PMID: 37111487 PMCID: PMC10142553 DOI: 10.3390/pathogens12040601] [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: 03/13/2023] [Revised: 04/10/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023] Open
Abstract
To date, only a handful of viruses have been identified in sea turtles. Although eukaryotic circular Rep (replication initiation protein)-encoding single-stranded DNA (CRESS DNA) viruses have been reported from a wide variety of terrestrial species, and some of these viruses have been associated with clinical conditions in certain animals, limited information is available on CRESS DNA viruses from marine life. The present study aimed to investigate the presence of CRESS DNA viruses in sea turtles. In the present study, two (samples T3 and T33) of the 34 cloacal samples from 31 sea turtles (found in ocean waters around the Caribbean Islands of St. Kitts and Nevis) tested positive for CRESS DNA viruses by a pan-rep nested PCR assay. The partial Rep sequence of T3 shared 75.78% of a deduced amino acid (aa) identity with that of a CRESS DNA virus (classified under family Circoviridae) from a mollusk. On the other hand, the complete genome (2428 bp) of T33 was determined by an inverse nested PCR assay. The genomic organization of T33 mirrored those of type II CRESS DNA viral genomes of cycloviruses, characterized by the putative "origin of replication" in the 5'-intergenic region, and the putative Capsid (Cap)- and Rep-encoding open reading frame on the virion-sense- and antisense-strand, respectively. The putative Rep (322 aa) of T33 retained the conserved "HUH endonuclease" and the "super 3 family helicase" domains and shared pairwise aa identities of ~57% with unclassified CRESS DNA viruses from benthic sediment and mollusks. Phylogenetically, the T33 Rep formed a distinct branch within an isolated cluster of unclassified CRESS DNA viruses. The putative Cap (370 aa) of T33 shared maximum pairwise aa identity of 30.51% with an unclassified CRESS DNA virus from a capybara. Except for a blood sample from T33 that tested negative for CRESS DNA viruses, other tissue samples were not available from the sea turtles. Therefore, we could not establish whether the T3 and T33 viral strains infected the sea turtles or were of dietary origin. To our knowledge, this is the first report on the detection of CRESS DNA viruses from sea turtles, adding yet another animal species to the rapidly expanding host range of these viruses. Complete genome analysis of T33 identified a novel, unclassified CRESS DNA virus, providing insights into the high genetic diversity between viruses within the phylum Cressdnaviricota. Considering that sea turtles are an at-risk species, extensive studies on virus discovery, surveillance, and pathogenesis in these marine animals are of the utmost importance.
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Affiliation(s)
- Kerry Gainor
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre P.O. Box 334, Saint Kitts and Nevis
| | - Kimberly M Stewart
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre P.O. Box 334, Saint Kitts and Nevis
- St. Kitts Sea Turtle Monitoring Network, Basseterre P.O. Box 2298, Saint Kitts and Nevis
| | - Angela Picknell
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre P.O. Box 334, Saint Kitts and Nevis
- St. Kitts Sea Turtle Monitoring Network, Basseterre P.O. Box 2298, Saint Kitts and Nevis
| | - Morgan Russ
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre P.O. Box 334, Saint Kitts and Nevis
- St. Kitts Sea Turtle Monitoring Network, Basseterre P.O. Box 2298, Saint Kitts and Nevis
| | - Noah Makela
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre P.O. Box 334, Saint Kitts and Nevis
- St. Kitts Sea Turtle Monitoring Network, Basseterre P.O. Box 2298, Saint Kitts and Nevis
| | - Kierra Watson
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre P.O. Box 334, Saint Kitts and Nevis
- St. Kitts Sea Turtle Monitoring Network, Basseterre P.O. Box 2298, Saint Kitts and Nevis
| | - Diana M Mancuso
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre P.O. Box 334, Saint Kitts and Nevis
| | - Yashpal Singh Malik
- College of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Science University, Ludhiana 141012, India
| | - Souvik Ghosh
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre P.O. Box 334, Saint Kitts and Nevis
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22
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Harding C, Larsen BB, Otto HW, Potticary AL, Kraberger S, Custer JM, Suazo C, Upham NS, Worobey M, Van Doorslaer K, Varsani A. Diverse DNA virus genomes identified in fecal samples of Mexican free-tailed bats (Tadarida brasiliensis) captured in Chiricahua Mountains of southeast Arizona (USA). Virology 2023; 580:98-111. [PMID: 36801670 DOI: 10.1016/j.virol.2023.02.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 02/08/2023] [Accepted: 02/09/2023] [Indexed: 02/14/2023]
Abstract
Bats (order Chiroptera) are some of the most abundant mammals on earth and their species ecology strongly influences zoonotic potential. While substantial research has been conducted on bat-associated viruses, particularly on those that can cause disease in humans and/or livestock, globally, limited research has focused on endemic bats in the USA. The southwest region of the US is of particular interest because of its high diversity of bat species. We identified 39 single-stranded DNA virus genomes in the feces of Mexican free-tailed bats (Tadarida brasiliensis) sampled in the Rucker Canyon (Chiricahua Mountains) of southeast Arizona (USA). Twenty-eight of these belong to the virus families Circoviridae (n = 6), Genomoviridae (n = 17), and Microviridae (n = 5). Eleven viruses cluster with other unclassified cressdnaviruses. Most of the viruses identified represent new species. Further research on identification of novel bat-associated cressdnaviruses and microviruses is needed to provide greater insights regarding their co-evolution and ecology relative to bats.
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Affiliation(s)
- Ciara Harding
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, Tempe, AZ, 85287, USA; School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Brendan B Larsen
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA; Howard Hughes Medical Institute, Seattle, WA, 98109, USA
| | - Hans W Otto
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Ahva L Potticary
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA; University of Georgia in the Department of Entomology, Athens, GA, 30602, USA
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, Tempe, AZ, 85287, USA
| | - Joy M Custer
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, Tempe, AZ, 85287, USA
| | - Crystal Suazo
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, Tempe, AZ, 85287, USA; School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Nathan S Upham
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Koenraad Van Doorslaer
- School of Animal and Comparative Biomedical Sciences, The BIO5 Institute, Department of Immunobiology, Cancer Biology Graduate Interdisciplinary Program, Genetics Graduate Interdisciplinary Program, UA Cancer Center, University of Arizona Tucson, AZ, 85724, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, Tempe, AZ, 85287, USA; School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA; Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Observatory, Cape Town, 7701, South Africa.
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23
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Genetic Diversity and Characterization of Circular Replication (Rep)-Encoding Single-Stranded (CRESS) DNA Viruses. Microbiol Spectr 2022; 10:e0105722. [PMID: 36346238 PMCID: PMC9769708 DOI: 10.1128/spectrum.01057-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The CRESS-DNA viruses are the ubiquitous virus detected in almost all eukaryotic life trees and play an essential role in the maintaining ecosystem of the globe. Still, their genetic diversity is not fully understood. Here, we bring to light the genetic diversity of replication (Rep) and capsid (Cap) proteins of CRESS-DNA viruses. We divided the Rep protein of the CRESS-DNA virus into 10 clusters using CLANS and phylogenetic analyses. Also, most of the Rep protein in Rep cluster 1 (R1) and R2 (Circoviridae, Smacoviridae, Nanoviridae, and CRESSV1-5) contain the Viral_Rep superfamily and P-loop_NTPase superfamily domains, while the Rep protein of viruses in other clusters has no such characterized functional domain. The Circoviridae, Nanoviridae, and CRESSV1-3 viruses contain two domains, such as Viral_Rep and P-loop_NTPase; the CRESSV4 and CRESSV5 viruses have only the Viral_Rep domain; most of the sequences in the pCRESS-related group have only P-loop_NTPase; and Smacoviridae do not have these two domains. Further, we divided the Cap protein of the CRESS-DNA virus into 20 clusters using CLANS and phylogenetic analyses. The Rep and Cap proteins of Circoviridae and Smacoviridae are grouped into a specific cluster. Cap protein of CRESS-DNA viruses grouped with one cluster and Rep protein with another cluster. Further, our study reveals that selection pressure plays a significant role in the evolution of CRESS-DNA viruses' Rep and Cap genes rather than mutational pressure. We hope this study will help determine the genetic diversity of CRESS-DNA viruses as more sequences are discovered in the future. IMPORTANCE The genetic diversity of CRESS-DNA viruses is not fully understood. CRESS-DNA viruses are classified as CRESSV1 to CRESSV6 using only Rep protein. This study revealed that the Rep protein of the CRESS-DNA viruses is classified as CRESSV1 to CRESSV6 groups and the new Smacoviridae-related, CRESSV2-related, pCRESS-related, Circoviridae-related, and 1 to 4 outgroups, according to the Viral_Rep and P-loop_NTPase domain organization, CLANS, and phylogenetic analysis. Furthermore, for the first time in this study, the Cap protein of CRESS-DNA viruses was classified into 20 distinct clusters by CLANS and phylogenetic analysis. Through this classification, the genetic diversity of CRESS-DNA viruses clarifies the possibility of recombinations in Cap and Rep proteins. Finally, it has been shown that selection pressure plays a significant role in the evolution and genetic diversity of Cap and Rep proteins. This study explains the genetic diversity of CRESS-DNA viruses and hopes that it will help classify future detected viruses.
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24
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Krupovic M, Varsani A. Naryaviridae, Nenyaviridae, and Vilyaviridae: three new families of single-stranded DNA viruses in the phylum Cressdnaviricota. Arch Virol 2022; 167:2907-2921. [PMID: 36098801 DOI: 10.1007/s00705-022-05557-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 07/19/2022] [Indexed: 12/14/2022]
Abstract
The phylum Cressdnaviricota includes viruses with circular single-stranded DNA (ssDNA) genomes and icosahedral capsids. These viruses display global environmental distribution and infect diverse eukaryotic hosts, including animals, plants, and fungi. Here, we report on the formal creation of two new orders, Rivendellvirales and Rohanvirales, and three new families, Naryaviridae, Nenyaviridae, and Vilyaviridae, of ssDNA viruses associated with protozoan parasites belonging to the genera Entamoeba and Giardia. We describe a sequence-based taxonomic framework, which was used to classify 60 ssDNA viruses into 12 genera (with 18 species) within the family Vilyaviridae; four genera (with five species) within the family Naryaviridae; and five genera (with six species) within the family Nenyaviridae. We also highlight the challenges associated with the classification of chimeric virus genomes, such as those in the families Naryaviridae and Nenyaviridae, where the replication initiation and capsid protein genes have undergone several independent non-orthologous replacements. The described taxonomic changes have been ratified by the International Committee on Taxonomy of Viruses (ICTV) and expand the phylum Cressdnaviricota to eight orders and 11 families.
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Affiliation(s)
- Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, F-75015, Paris, France.
| | - 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.
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25
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Detection of human feces pecovirus in newly diagnosed HIV patients in Brazil. PLoS One 2022; 17:e0272067. [PMID: 36067165 PMCID: PMC9447917 DOI: 10.1371/journal.pone.0272067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 07/12/2022] [Indexed: 12/04/2022] Open
Abstract
Circular single stranded DNA viruses (CRESS DNA) encoding a homologous replication-associated protein (REP) have been identified in most of eukaryotic groups. It is not clear yet the role in human diseases or details of the life cycle of these viruses. Recently, much interest has been raised in the evolutionary history of CRESS DNA owing to the increasing number of new sequences obtained by Next-Generation Sequencing (NGS) in distinct host species. In this study we describe two full-length CRESS DNA genomes obtained of two newly diagnosed HIV patients from São Paulo State, Brazil. The initial BLASTx search indicated that both sequences (named SP-FFB/2020 and SP-MJMS/2020) are highly similar (98%) to a previous CRESS DNA sequence detected in human fecal sample from Peru in 2016 and designated as pecovirus (Peruvian stool-associated circo-like virus). This study reported for the first time the Human feces pecovirus in the feces of two newly diagnosed HIV patients in Brazil. Our comparative analysis showed that although pecoviruses in South America share an identical genome structure they diverge and form distinct clades. Thus, we suggest the circulation of different species of pecoviruses in Latin America. Nevertheless, further studies must be done to examine the pathogenicity of this virus.
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Villanova F, Milagres FADP, Brustulin R, Araújo ELL, Pandey RP, Raj VS, Deng X, Delwart E, Luchs A, da Costa AC, Leal É. A New Circular Single-Stranded DNA Virus Related with Howler Monkey Associated Porprismacovirus 1 Detected in Children with Acute Gastroenteritis. Viruses 2022; 14:v14071472. [PMID: 35891454 PMCID: PMC9319269 DOI: 10.3390/v14071472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/17/2022] [Accepted: 06/30/2022] [Indexed: 12/04/2022] Open
Abstract
Putative replication-associated protein (REP) and capsid-like (CAP) proteins are encoded by circular single-stranded DNA viruses (CRESS DNA), which have been found in samples from most eukaryotic groups. However, the details of these viruses’ life cycles and their significance in diseases have yet to be established. We presented and analyzed two full-length CRESS DNA genomes acquired from two children diagnosed with acute gastroenteritis (GI) in the northeast state of Tocantins, Brazil, using next-generation sequencing and a virus-like filtration approach. Both sequences (named SmaCV3BR08 and SmaCV3BR291) are closely similar to a prior CRESS DNA sequence discovered in the feces of a new world monkey (Alouatta caraya) from the United States in 2009 and termed Howler monkey-associated porprismacovirus 1 (Genbank ID: NC 026317). According to our comparative study, these porprismacovirus genomes deviate by 10% at the nucleotide level. For comparative reasons, the divergence between our sequences (SmaCV3BR08 and SmaCV3BR291) and a porprismacovirus recently identified in a human fecal sample from Peru is 37%. These data suggest that there is a great diversity of porprismacoviruses in South America, perhaps more than two species. In addition, the finding of closely related sequences of porprismacoviruses in humans and native monkeys highlights the zoonotic potential of these viruses.
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Affiliation(s)
- Fabiola Villanova
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, Pará, Brazil;
| | - Flávio Augusto de Padua Milagres
- Secretary of Health of Tocantins, Palmas 77453-000, Tocantins, Brazil; (F.A.d.P.M.); (R.B.)
- Public Health Laboratory of Tocantins State (LACEN/TO), Palmas 77016-330, Tocantins, Brazil
| | - Rafael Brustulin
- Secretary of Health of Tocantins, Palmas 77453-000, Tocantins, Brazil; (F.A.d.P.M.); (R.B.)
| | - Emerson Luiz Lima Araújo
- General Coordination of Public Health Laboratories of the Strategic Articulation Department of the Health Surveillance Secretariat of the Ministry of Health (CGLAB/DAEVS/SVS-MS), Brasília 70719-040, Distrito Federal, Brazil;
| | - Ramendra Pati Pandey
- Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi-NCR, Rajiv Gandhi Education City, Sonepat 131029, Haryana, India; (R.P.P.); (V.S.R.)
| | - V. Samuel Raj
- Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi-NCR, Rajiv Gandhi Education City, Sonepat 131029, Haryana, India; (R.P.P.); (V.S.R.)
| | - Xutao Deng
- Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA 94118, USA; (X.D.); (E.D.)
- Department Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Eric Delwart
- Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA 94118, USA; (X.D.); (E.D.)
- Department Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Adriana Luchs
- Enteric Disease Laboratory, Virology Center, Adolfo Lutz Institute, São Paulo 01246-000, São Paulo, Brazil;
| | - Antonio Charlys da Costa
- Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-000, São Paulo, Brazil;
| | - Élcio Leal
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, Pará, Brazil;
- Correspondence:
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Abstract
Microviruses encompass an astonishing array of small, single-stranded DNA phages that, due to the surge in metagenomic surveys, are now known to be prevalent in most environments. Current taxonomy concedes the considerable diversity within this lineage to a single family (the Microviridae), which has rendered it difficult to adequately and accurately assess the amount of variation that actually exists within this group. We amassed and curated the largest collection of microviral genomes to date and, through a combination of protein-sharing networks and phylogenetic analysis, discovered at least three meaningful taxonomic levels between the current ranks of family and genus. When considering more than 13,000 microviral genomes from recognized lineages and as-yet-unclassified microviruses in metagenomic samples, microviral diversity is better understood by elevating microviruses to the level of an order that consists of three suborders and at least 19 putative families, each with their respective subfamilies. These revisions enable fine-scale assessment of microviral dynamics: for example, in the human gut, there are considerable differences in the abundances of microviral families both between urban and rural populations and in individuals over time. In addition, our analysis of genome contents and gene exchange shows that microviral families carry no recognizable accessory metabolic genes and rarely, if ever, engage in horizontal gene transfer across microviral families or with their bacterial hosts. These insights bring microviral taxonomy in line with current developments in the taxonomy of other phages and increase the understanding of microvirus biology.
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A Structural Perspective of Reps from CRESS-DNA Viruses and Their Bacterial Plasmid Homologues. Viruses 2021; 14:v14010037. [PMID: 35062241 PMCID: PMC8780604 DOI: 10.3390/v14010037] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/14/2021] [Accepted: 12/15/2021] [Indexed: 11/17/2022] Open
Abstract
Rolling circle replication (RCR) is ubiquitously used by cellular and viral systems for genome and plasmid replication. While the molecular mechanism of RCR has been described, the structural mechanism is desperately lacking. Circular-rep encoded single stranded DNA (CRESS-DNA) viruses employ a viral encoded replicase (Rep) to initiate RCR. The recently identified prokaryotic homologues of Reps may also be responsible for initiating RCR. Reps are composed of an endonuclease, oligomerization, and ATPase domain. Recent structural studies have provided structures for all these domains such that an overall mechanism of RCR initiation can begin to be synthesized. However, structures of Rep in complex with its various DNA substrates and/or ligands are lacking. Here we provide a 3D bioinformatic review of the current structural information available for Reps. We combine an excess of 1590 sequences with experimental and predicted structural data from 22 CRESS-DNA groups to identify similarities and differences between Reps that lead to potentially important functional sites. Experimental studies of these sites may shed light on how Reps execute their functions. Furthermore, we identify Rep-substrate or Rep-ligand structures that are urgently needed to better understand the structural mechanism of RCR.
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Tochetto C, Cibulski SP, Muterle Varela AP, Cerva C, Alves de Lima D, Fumaco Teixeira T, Quoos Mayer F, Roehe PM. A variety of highly divergent eukaryotic ssDNA viruses in sera of pigs. J Gen Virol 2021; 102. [PMID: 34928204 DOI: 10.1099/jgv.0.001706] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Over the last decade, viral metagenomics has been established as a non-targeted approach for identifying viruses in stock animals, including pigs. This has led to the identification of a vast diversity of small circular ssDNA viruses. The present study focuses on the investigation of eukaryotic circular Rep-encoding single-stranded (CRESS) DNA viral genomes present in serum of commercially reared pigs from southern Brazil. Several CRESS DNA viral genomes were detected, including representatives of the families Smacoviridae (n=5), Genomoviridae (n=3), Redondoviridae (n=1), Nenyaviridae (n=1) and other yet unclassified genomes (n=9), plus a circular DNA molecule, which probably belongs to the phylum Cressdnaviricota. A novel genus within the family Smacoviridae, tentatively named 'Suismacovirus', comprising 21 potential new species, is proposed. Although the reported genomes were recovered from pigs with clinical signs of respiratory disease, further studies should examine their potential role as pathogens. Nonetheless, these findings highlight the diversity of circular ssDNA viruses in serum of domestic pigs, expand the knowledge on CRESS DNA viruses' genetic diversity and distribution and contribute to the global picture of the virome of commercially reared pigs.
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Affiliation(s)
- Caroline Tochetto
- Laboratório de Virologia, Departamento de Microbiologia Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
| | - Samuel Paulo Cibulski
- Centro de Biotecnologia - CBiotec, Laboratório de Biotecnologia Celular e Molecular, Universidade Federal da Paraíba - UFPB, João Pessoa, Paraíba, Brazil
| | - Ana Paula Muterle Varela
- Laboratório de Virologia, Departamento de Microbiologia Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
| | - Cristine Cerva
- Centro de Pesquisa em Saúde Animal, Instituto de Pesquisas Veterinárias Desidério Finamor(IPVDF), Departamento de Diagnóstico e Pesquisa Agropecuária, Secretaria de Agricultura, Pecuária e Desenvolvimento Rural, Eldorado do Sul, Rio Grande do Sul, Brazil
| | - Diane Alves de Lima
- Laboratório de Microbiologia do Centro Clínico Veterinário, Centro Universitário da Serra Gaúcha - FSG, Caxias do Sul, Rio Grande do Sul, Brazil
| | - Thais Fumaco Teixeira
- Centro de Pesquisa em Saúde Animal, Instituto de Pesquisas Veterinárias Desidério Finamor(IPVDF), Departamento de Diagnóstico e Pesquisa Agropecuária, Secretaria de Agricultura, Pecuária e Desenvolvimento Rural, Eldorado do Sul, Rio Grande do Sul, Brazil
| | - Fabiana Quoos Mayer
- Centro de Pesquisa em Saúde Animal, Instituto de Pesquisas Veterinárias Desidério Finamor(IPVDF), Departamento de Diagnóstico e Pesquisa Agropecuária, Secretaria de Agricultura, Pecuária e Desenvolvimento Rural, Eldorado do Sul, Rio Grande do Sul, Brazil
| | - Paulo Michel Roehe
- Laboratório de Virologia, Departamento de Microbiologia Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
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Diverse Single-Stranded DNA Viruses Identified in Chicken Buccal Swabs. Microorganisms 2021; 9:microorganisms9122602. [PMID: 34946202 PMCID: PMC8703526 DOI: 10.3390/microorganisms9122602] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/11/2021] [Accepted: 12/13/2021] [Indexed: 11/18/2022] Open
Abstract
High-throughput sequencing approaches offer the possibility to better understand the complex microbial communities associated with animals. Viral metagenomics has facilitated the discovery and identification of many known and unknown viruses that inhabit mucosal surfaces of the body and has extended our knowledge related to virus diversity. We used metagenomics sequencing of chicken buccal swab samples and identified various small DNA viruses with circular genome organization. Out of 134 putative circular viral-like circular genome sequences, 70 are cressdnaviruses and 26 are microviruses, whilst the remaining 38 most probably represent sub-genomic molecules. The cressdnaviruses found in this study belong to the Circoviridae, Genomoviridae and Smacoviridae families as well as previously described CRESS1 and naryavirus groups. Among these, genomoviruses and smacoviruses were the most prevalent across the samples. Interestingly, we also identified 26 bacteriophages that belong to the Microviridae family, whose members are known to infect enterobacteria.
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Diverse single-stranded DNA viruses identified in New Zealand (Aotearoa) South Island robin (Petroica australis) fecal samples. Virology 2021; 565:38-51. [PMID: 34715607 DOI: 10.1016/j.virol.2021.10.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/16/2021] [Accepted: 10/18/2021] [Indexed: 12/12/2022]
Abstract
The South Island robin (Petroica australis) is a small passerine bird endemic to New Zealand (Aotearoa). Although its population has declined recently and it is considered 'at risk,' little research has been done to identify viruses in this species. This study aimed to survey the diversity of single-stranded DNA viruses associated with South Island robins in a small, isolated population on Nukuwaiata Island. In total, 108 DNA viruses were identified from pooled fecal samples collected from 38 individual robins sampled. These viruses belong to the Circoviridae (n = 10), Genomoviridae (n = 12), and Microviridae (n = 73) families. A number of genomes that belong to the phylum Cressdnaviricota but are otherwise unclassified (n = 13) were also identified. These results greatly expand the known viral diversity associated with South Island robins, and we identify a novel group of viruses most closely related genomoviruses.
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Ortega-Del Campo S, Grigoras I, Timchenko T, Gronenborn B, Grande-Pérez A. Twenty years of evolution and diversification of digitaria streak virus in Digitaria setigera. Virus Evol 2021; 7:veab083. [PMID: 34659796 PMCID: PMC8516820 DOI: 10.1093/ve/veab083] [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: 03/08/2021] [Revised: 09/09/2021] [Accepted: 09/20/2021] [Indexed: 11/21/2022] Open
Abstract
Within the family Geminiviridae, the emergence of new species results from their high mutation and recombination rates. In this study, we report the variability and evolution of digitaria streak virus (DSV), a mastrevirus isolated in 1986 from the grass Digitaria setigera in an island of the Vanuatu archipelago. Viral DNA of DSV samples was amplified from D. setigera specimens, derived from the naturally infected original plant, which were propagated in different laboratories in France and Italy for more than 20 years. From the consensus sequences, the nucleotide substitution rate was estimated for the period between a sample and the original sequence published in 1987, as well as for the period between samples. In addition, the intra-host genetic complexity and diversity of 8 DSV populations with a total of 165 sequenced haplotypes was characterized. The evolutionary rate of DSV was estimated to be between 1.13 × 10−4 and 9.87 × 10−4 substitutions/site/year, within the ranges observed in other single-stranded DNA viruses and RNA viruses. Bioinformatic analyses revealed high variability and heterogeneity in DSV populations, which confirmed that mutant spectra are continuously generated and are organized as quasispecies. The analysis of polymorphisms revealed nucleotide substitution biases in viral genomes towards deamination and oxidation of single-stranded DNA. The differences in variability in each of the genomic regions reflected a dynamic and modular evolution in the mutant spectra that was not reflected in the consensus sequences. Strikingly, the most variable region of the DSV genome, encoding the movement protein, showed rapid fixation of the mutations in the consensus sequence and a concomitant dN/dS ratio of 6.130, which suggests strong positive selection in this region. Phylogenetic analyses revealed a possible divergence in three genetic lineages from the original Vanuatu DSV isolate.
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Affiliation(s)
| | - Ioana Grigoras
- CNRS, Institut des Sciences du Végétal, Gif-sur-Yvette 91198, France
| | - Tatiana Timchenko
- CNRS, Institut des Sciences du Végétal, Gif-sur-Yvette 91198, France
| | - Bruno Gronenborn
- CNRS, Institut des Sciences du Végétal, Gif-sur-Yvette 91198, France
| | - Ana Grande-Pérez
- Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora' (IHSM-UMA-CSIC), Área de Genética, Facultad de Ciencias, Campus de Teatinos, Málaga 29071, Spain
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Abstract
Redondoviridae is a newly established family of circular Rep-encoding single-stranded (CRESS) DNA viruses found in the human ororespiratory tract. Redondoviruses were previously found in ∼15% of respiratory specimens from U.S. urban subjects; levels were elevated in individuals with periodontitis or critical illness. Here, we report higher redondovirus prevalence in saliva samples: four rural African populations showed 61 to 82% prevalence, and an urban U.S. population showed 32% prevalence. Longitudinal, limiting-dilution single-genome sequencing revealed diverse strains of both redondovirus species (Brisavirus and Vientovirus) in single individuals, persistence over time, and evidence of intergenomic recombination. Computational analysis of viral genomes identified a recombination hot spot associated with a conserved potential DNA stem-loop structure. To assess the possible role of this site in recombination, we carried out in vitro studies which showed that this potential stem-loop was cleaved by the virus-encoded Rep protein. In addition, in reconstructed reactions, a Rep-DNA covalent intermediate was shown to mediate DNA strand transfer at this site. Thus, redondoviruses are highly prevalent in humans, found in individuals on multiple continents, heterogeneous even within individuals and encode a Rep protein implicated in facilitating recombination. IMPORTANCE Redondoviridae is a recently established family of DNA viruses predominantly found in the human respiratory tract and associated with multiple clinical conditions. In this study, we found high redondovirus prevalence in saliva from urban North American individuals and nonindustrialized African populations in Botswana, Cameroon, Ethiopia, and Tanzania. Individuals on both continents harbored both known redondovirus species. Global prevalence of both species suggests that redondoviruses have long been associated with humans but have remained undetected until recently due to their divergent genomes. By sequencing single redondovirus genomes in longitudinally sampled humans, we found that redondoviruses persisted over time within subjects and likely evolve by recombination. The Rep protein encoded by redondoviruses catalyzes multiple reactions in vitro, consistent with a role in mediating DNA replication and recombination. In summary, we identify high redondovirus prevalence in humans across multiple continents, longitudinal heterogeneity and persistence, and potential mechanisms of redondovirus evolution by recombination.
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Zhao L, Lavington E, Duffy S. Truly ubiquitous CRESS DNA viruses scattered across the eukaryotic tree of life. J Evol Biol 2021; 34:1901-1916. [PMID: 34498333 DOI: 10.1111/jeb.13927] [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: 06/30/2019] [Revised: 07/05/2021] [Accepted: 08/18/2021] [Indexed: 11/29/2022]
Abstract
Until recently, most viruses detected and characterized were of economic significance, associated with agricultural and medical diseases. This was certainly true for the eukaryote-infecting circular Rep (replication-associated protein)-encoding single-stranded DNA (CRESS DNA) viruses, which were thought to be a relatively small group of viruses. With the explosion of metagenomic sequencing over the past decade and increasing use of rolling-circle replication for sequence amplification, scientists have identified and annotated copious numbers of novel CRESS DNA viruses - many without known hosts but which have been found in association with eukaryotes. Similar advances in cellular genomics have revealed that many eukaryotes have endogenous sequences homologous to viral Reps, which not only provide 'fossil records' to reconstruct the evolutionary history of CRESS DNA viruses but also reveal potential host species for viruses known by their sequences alone. The Rep protein is a conserved protein that all CRESS DNA viruses use to assist rolling-circle replication that is known to be endogenized in a few eukaryotic species (notably tobacco and water yam). A systematic search for endogenous Rep-like sequences in GenBank's non-redundant eukaryotic database was performed using tBLASTn. We utilized relaxed search criteria for the capture of integrated Rep sequence within eukaryotic genomes, identifying 93 unique species with an endogenized fragment of Rep in their nuclear, plasmid (one species), mitochondrial (six species) or chloroplast (eight species) genomes. These species come from 19 different phyla, scattered across the eukaryotic tree of life. Exogenous and endogenous CRESS DNA viral Rep tree topology suggested potential hosts for one family of uncharacterized viruses and supports a primarily fungal host range for genomoviruses.
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Affiliation(s)
- Lele Zhao
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers, the State University of New Jersey, New Brunswick, New Jersey, USA.,Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Erik Lavington
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers, the State University of New Jersey, New Brunswick, New Jersey, USA
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers, the State University of New Jersey, New Brunswick, New Jersey, USA
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35
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Analysis of chronic inflammatory lesions of the colon for BMMF Rep antigen expression and CD68 macrophage interactions. Proc Natl Acad Sci U S A 2021; 118:2025830118. [PMID: 33723077 PMCID: PMC8000208 DOI: 10.1073/pnas.2025830118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Bovine meat and milk factors (BMMF) are routinely found in bovine sera and dairy products, predominantly of Eurasian dairy cattle. BMMF DNA and proteins are demonstrated in tissues of colon cancer patients, specifically interstitial macrophages of peritumor tissues. BMMF represent plasmid-like, zoonotic infectious agents with an indirect role in cancer formation by inducing chronic inflammation leading to oxidative stress and DNA mutation in nearby replicating cells, which may develop into polyps as progenitors for colon cancer. Detection of BMMF during long latency periods prior to symptoms developing allows for specific preventive and early therapeutic measures. Detection of BMMF might offer a prognostic tool for prediction of patient survival, preventive approaches, and therapy success. Consumption of Eurasian bovine meat and milk has been associated with cancer development, in particular with colorectal cancer (CRC). In addition, zoonotic infectious agents from bovine products were proposed to cause colon cancer (zur Hausen et al., 2009). Bovine meat and milk factors (BMMF) are small episomal DNA molecules frequently isolated from bovine sera and milk products, and recently, also from colon cancer (de Villiers et al., 2019). BMMF are bioactive in human cells and were proposed to induce chronic inflammation in precancerous tissue leading to increased radical formation: for example, reactive oxygen and reactive nitrogen species and elevated levels of DNA mutations in replicating cells, such as cancer progenitor cells (zur Hausen et al., 2018). Mouse monoclonal antibodies against the replication (Rep) protein of H1MSB.1 (BMMF1) were used to analyze BMMF presence in different cohorts of CRC peritumor and tumor tissues and cancer-free individuals by immunohistochemistry and Western blot. BMMF DNA was isolated by laser microdissection from immunohistochemistry-positive tissue regions. We found BMMF Rep protein present specifically in close vicinity of CD68+ macrophages in the interstitial lamina propria adjacent to CRC tissues, suggesting the presence of local chronic inflammation. BMMF1 (modified H1MSB.1) DNA was isolated from the same tissue regions. Rep and CD68+ detection increased significantly in peritumor cancer tissues when compared to tissues of cancer-free individuals. This strengthens previous postulations that BMMF function as indirect carcinogens by inducing chronic inflammation and DNA damage in replicating cells, which represent progress to progenitor cells for adenoma (polyps) formation and cancer.
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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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Smith K, Fielding R, Schiavone K, Hall KR, Reid VS, Boyea D, Smith EL, Schmidlin K, Fontenele RS, Kraberger S, Varsani A. Circular DNA viruses identified in short-finned pilot whale and orca tissue samples. Virology 2021; 559:156-164. [PMID: 33892449 DOI: 10.1016/j.virol.2021.04.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/10/2021] [Accepted: 04/12/2021] [Indexed: 12/15/2022]
Abstract
Members of the Delphinidae family are widely distributed across the world's oceans. We used a viral metagenomic approach to identify viruses in orca (Orcinus orca) and short-finned pilot whale (Globicephala macrorhynchus) muscle, kidney, and liver samples from deceased animals. From orca tissue samples (muscle, kidney, and liver), we identified a novel polyomavirus (Polyomaviridae), three cressdnaviruses, and two genomoviruses (Genomoviridae). In the short-finned pilot whale we were able to identify one genomovirus in a kidney sample. The presence of unclassified cressdnavirus within two samples (muscle and kidney) of the same animal supports the possibility these viruses might be widespread within the animal. The orca polyomavirus identified here is the first of its species and is not closely related to the only other dolphin polyomavirus previously discovered. The identification and verification of these viruses expands the current knowledge of viruses that are associated with the Delphinidae family.
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Affiliation(s)
- Kendal Smith
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Russell Fielding
- HTC Honors College, Coastal Carolina University, Conway, SC, 29528, USA.
| | - Kelsie Schiavone
- Department of Earth and Environmental Systems, The University of the South, Sewanee, TN, 37383, USA
| | - Katharine R Hall
- Department of Earth and Environmental Systems, The University of the South, Sewanee, TN, 37383, USA
| | - Vincent S Reid
- Barrouallie Whaler's Project, Saint Vincent and the Grenadines
| | | | - Emma L Smith
- Department of Chemical & Biological Sciences, University of the West Indies-Cave Hill, Barbados
| | - Kara Schmidlin
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Rafaela S Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - 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, USA; Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Rondebosch, 7700, Cape Town, South Africa.
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38
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Nguyen VG, Do HQ, Huynh TML, Park YH, Park BK, Chung HC. Molecular-based detection, genetic characterization and phylogenetic analysis of porcine circovirus 4 from Korean domestic swine farms. Transbound Emerg Dis 2021; 69:538-548. [PMID: 33529468 DOI: 10.1111/tbed.14017] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 01/26/2021] [Accepted: 01/31/2021] [Indexed: 01/18/2023]
Abstract
Porcine circovirus 4 (PCV4), a novel and unclassified member of the genus Circovirus, was first reported in China in 2019. Aiming to provide more evidence about the active circulation of PCV4, this study screened 335 pooled internal organs and detected the virus (i) at a rate of 3.28%, (ii) from both clinically healthy and clinically sick pigs of various age groups, and (iii) in six out of nine provinces of Korea. The complete genomic sequence of the Korean PCV4 strain (E115) was 1,770 nucleotides in length and had 98.5%-98.9% identity to three PCV4 strains currently available at GenBank. Utilizing a set of bioinformatic programs, it was revealed that the Korean PCV4 strain contained several genomic features of (i) a palindrome stem-loop structure with a conserved nonanucleotide, (ii) packed overlapping ORFs oriented in different directions and (iii) two intergenic regions in between genes encoding the putative replication-associated protein (Rep) and capsid (Cap) proteins. This study also predicted the presence of essential elements for the replication of circoviruses in all PCV4 strains, for example the origin of DNA replication, endonuclease and helicase domains of Rep, and the nuclear localization signal on the putative Cap protein. Finally, based on the phylogeny inferred from sequences of the putative Rep protein, this study further clarified the genetic relationships between PCV4 and other CRESS DNA viruses in general and circoviruses in particular.
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Affiliation(s)
- Van-Giap Nguyen
- Department of Veterinary Microbiology and Infectious Diseases, Faculty of Veterinary Medicine, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Hai-Quynh Do
- Department of Veterinary Medicine Virology Lab, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, Korea.,Department of Veterinary Microbiology, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, Korea
| | - Thi-My-Le Huynh
- Department of Veterinary Microbiology and Infectious Diseases, Faculty of Veterinary Medicine, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Yong-Ho Park
- Department of Veterinary Microbiology, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, Korea
| | - Bong-Kyun Park
- Department of Veterinary Medicine Virology Lab, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, Korea
| | - Hee-Chun Chung
- Department of Veterinary Medicine Virology Lab, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, Korea
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Cibulski S, Alves de Lima D, Fernandes Dos Santos H, Teixeira TF, Tochetto C, Mayer FQ, Roehe PM. A plate of viruses: Viral metagenomics of supermarket chicken, pork and beef from Brazil. Virology 2021; 552:1-9. [PMID: 33032031 PMCID: PMC7521440 DOI: 10.1016/j.virol.2020.09.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/12/2020] [Accepted: 09/13/2020] [Indexed: 02/08/2023]
Abstract
A viral metagenomics study was conducted in beef, pork, and chicken sold in supermarkets from Southern Brazil. From chicken, six distinct gyroviruses (GyV) were detected, including GyV3 and GyV6, which for the first time were detected in samples from avian species, plus a novel smacovirus species and two highly divergent circular Rep-encoding ssDNA (CRESS-DNA) viruses. From pork, genomes of numerous anelloviruses, porcine parvovirus 5 (PPV5) and 6 (PPV6), two new genomoviruses and two new CRESS-DNA viruses were found. Finally, two new CRESS-DNA genomes were recovered from beef. Although none of these viruses have history of transmission to humans, the findings reported here reveal that such agents are inevitably consumed in diets that include these types of meat.
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Affiliation(s)
- Samuel Cibulski
- Centro de Biotecnologia - CBiotec, Laboratório de Biotecnologia Celular e Molecular, Universidade Federal da Paraíba - UFPB, João Pessoa, Paraíba, Brazil.
| | - Diane Alves de Lima
- Departamento de Microbiologia Imunologia e Parasitologia, Laboratório de Virologia, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil; Centro Universitário da Serra Gaúcha - FSG, Caxias do Sul, Grande do Sul, Brazil
| | - Helton Fernandes Dos Santos
- Departamento de Medicina Veterinária Preventiva, Universidade Federal de Santa Maria - UFSM, Santa Maria, Rio Grande do Sul, Brazil
| | - Thais Fumaco Teixeira
- Centro de Pesquisa em Saúde Animal, Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Departamento de Diagnóstico e Pesquisa Agropecuária, Secretaria de Agricultura, Pecuária e Desenvolvimento Rural, Eldorado do Sul, RS, Brazil
| | - Caroline Tochetto
- Departamento de Microbiologia Imunologia e Parasitologia, Laboratório de Virologia, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil
| | - Fabiana Quoos Mayer
- Centro de Pesquisa em Saúde Animal, Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Departamento de Diagnóstico e Pesquisa Agropecuária, Secretaria de Agricultura, Pecuária e Desenvolvimento Rural, Eldorado do Sul, RS, Brazil
| | - Paulo Michel Roehe
- Departamento de Microbiologia Imunologia e Parasitologia, Laboratório de Virologia, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil
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40
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Hufsky F, Beerenwinkel N, Meyer IM, Roux S, Cook GM, Kinsella CM, Lamkiewicz K, Marquet M, Nieuwenhuijse DF, Olendraite I, Paraskevopoulou S, Young F, Dijkman R, Ibrahim B, Kelly J, Le Mercier P, Marz M, Ramette A, Thiel V. The International Virus Bioinformatics Meeting 2020. Viruses 2020; 12:E1398. [PMID: 33291220 PMCID: PMC7762161 DOI: 10.3390/v12121398] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 12/01/2020] [Indexed: 12/16/2022] Open
Abstract
The International Virus Bioinformatics Meeting 2020 was originally planned to take place in Bern, Switzerland, in March 2020. However, the COVID-19 pandemic put a spoke in the wheel of almost all conferences to be held in 2020. After moving the conference to 8-9 October 2020, we got hit by the second wave and finally decided at short notice to go fully online. On the other hand, the pandemic has made us even more aware of the importance of accelerating research in viral bioinformatics. Advances in bioinformatics have led to improved approaches to investigate viral infections and outbreaks. The International Virus Bioinformatics Meeting 2020 has attracted approximately 120 experts in virology and bioinformatics from all over the world to join the two-day virtual meeting. Despite concerns being raised that virtual meetings lack possibilities for face-to-face discussion, the participants from this small community created a highly interactive scientific environment, engaging in lively and inspiring discussions and suggesting new research directions and questions. The meeting featured five invited and twelve contributed talks, on the four main topics: (1) proteome and RNAome of RNA viruses, (2) viral metagenomics and ecology, (3) virus evolution and classification and (4) viral infections and immunology. Further, the meeting featured 20 oral poster presentations, all of which focused on specific areas of virus bioinformatics. This report summarizes the main research findings and highlights presented at the meeting.
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Affiliation(s)
- Franziska Hufsky
- European Virus Bioinformatics Center, 07743 Jena, Germany; (N.B.); (I.M.M.); (G.M.C.); (C.M.K.); (K.L.); (M.M.); (D.F.N.); (I.O.); (S.P.); (R.D.); (B.I.); (J.K.); (P.L.M.); (M.M.); (A.R.); (V.T.)
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Niko Beerenwinkel
- European Virus Bioinformatics Center, 07743 Jena, Germany; (N.B.); (I.M.M.); (G.M.C.); (C.M.K.); (K.L.); (M.M.); (D.F.N.); (I.O.); (S.P.); (R.D.); (B.I.); (J.K.); (P.L.M.); (M.M.); (A.R.); (V.T.)
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - Irmtraud M. Meyer
- European Virus Bioinformatics Center, 07743 Jena, Germany; (N.B.); (I.M.M.); (G.M.C.); (C.M.K.); (K.L.); (M.M.); (D.F.N.); (I.O.); (S.P.); (R.D.); (B.I.); (J.K.); (P.L.M.); (M.M.); (A.R.); (V.T.)
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, 10115 Berlin, Germany
- Department of Biology, Chemistry and Pharmacy, Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
| | - Simon Roux
- Lawrence Berkeley National Laboratory, DOE Joint Genome Institute, Berkeley, CA 94720, USA;
| | - Georgia May Cook
- European Virus Bioinformatics Center, 07743 Jena, Germany; (N.B.); (I.M.M.); (G.M.C.); (C.M.K.); (K.L.); (M.M.); (D.F.N.); (I.O.); (S.P.); (R.D.); (B.I.); (J.K.); (P.L.M.); (M.M.); (A.R.); (V.T.)
- Department of Pathology, Division of Virology, University of Cambridge, Cambridge CB2 1TN, UK
| | - Cormac M. Kinsella
- European Virus Bioinformatics Center, 07743 Jena, Germany; (N.B.); (I.M.M.); (G.M.C.); (C.M.K.); (K.L.); (M.M.); (D.F.N.); (I.O.); (S.P.); (R.D.); (B.I.); (J.K.); (P.L.M.); (M.M.); (A.R.); (V.T.)
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Kevin Lamkiewicz
- European Virus Bioinformatics Center, 07743 Jena, Germany; (N.B.); (I.M.M.); (G.M.C.); (C.M.K.); (K.L.); (M.M.); (D.F.N.); (I.O.); (S.P.); (R.D.); (B.I.); (J.K.); (P.L.M.); (M.M.); (A.R.); (V.T.)
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Mike Marquet
- European Virus Bioinformatics Center, 07743 Jena, Germany; (N.B.); (I.M.M.); (G.M.C.); (C.M.K.); (K.L.); (M.M.); (D.F.N.); (I.O.); (S.P.); (R.D.); (B.I.); (J.K.); (P.L.M.); (M.M.); (A.R.); (V.T.)
- CaSe Group, Institut für Infektionsmedizin und Krankenhaushygiene, Universitätsklinikum Jena, 07743 Jena, Germany
| | - David F. Nieuwenhuijse
- European Virus Bioinformatics Center, 07743 Jena, Germany; (N.B.); (I.M.M.); (G.M.C.); (C.M.K.); (K.L.); (M.M.); (D.F.N.); (I.O.); (S.P.); (R.D.); (B.I.); (J.K.); (P.L.M.); (M.M.); (A.R.); (V.T.)
- Viroscience Department, Erasmus MC, 3015 GD Rotterdam, The Netherlands
| | - Ingrida Olendraite
- European Virus Bioinformatics Center, 07743 Jena, Germany; (N.B.); (I.M.M.); (G.M.C.); (C.M.K.); (K.L.); (M.M.); (D.F.N.); (I.O.); (S.P.); (R.D.); (B.I.); (J.K.); (P.L.M.); (M.M.); (A.R.); (V.T.)
- Department of Pathology, Division of Virology, University of Cambridge, Cambridge CB2 1TN, UK
| | - Sofia Paraskevopoulou
- European Virus Bioinformatics Center, 07743 Jena, Germany; (N.B.); (I.M.M.); (G.M.C.); (C.M.K.); (K.L.); (M.M.); (D.F.N.); (I.O.); (S.P.); (R.D.); (B.I.); (J.K.); (P.L.M.); (M.M.); (A.R.); (V.T.)
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Francesca Young
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK;
| | - Ronald Dijkman
- European Virus Bioinformatics Center, 07743 Jena, Germany; (N.B.); (I.M.M.); (G.M.C.); (C.M.K.); (K.L.); (M.M.); (D.F.N.); (I.O.); (S.P.); (R.D.); (B.I.); (J.K.); (P.L.M.); (M.M.); (A.R.); (V.T.)
- Institute of Virology and Immunology, University of Bern, 3012 Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
- Institute for Infectious Diseases, University of Bern, 3012 Bern, Switzerland
| | - Bashar Ibrahim
- European Virus Bioinformatics Center, 07743 Jena, Germany; (N.B.); (I.M.M.); (G.M.C.); (C.M.K.); (K.L.); (M.M.); (D.F.N.); (I.O.); (S.P.); (R.D.); (B.I.); (J.K.); (P.L.M.); (M.M.); (A.R.); (V.T.)
- Centre for Applied Mathematics and Bioinformatics, Hawally 32093, Kuwait
- Department of Mathematics and Natural Sciences Gulf University for Science and Technology, Hawally 32093, Kuwait
| | - Jenna Kelly
- European Virus Bioinformatics Center, 07743 Jena, Germany; (N.B.); (I.M.M.); (G.M.C.); (C.M.K.); (K.L.); (M.M.); (D.F.N.); (I.O.); (S.P.); (R.D.); (B.I.); (J.K.); (P.L.M.); (M.M.); (A.R.); (V.T.)
- Institute of Virology and Immunology, University of Bern, 3012 Bern, Switzerland
| | - Philippe Le Mercier
- European Virus Bioinformatics Center, 07743 Jena, Germany; (N.B.); (I.M.M.); (G.M.C.); (C.M.K.); (K.L.); (M.M.); (D.F.N.); (I.O.); (S.P.); (R.D.); (B.I.); (J.K.); (P.L.M.); (M.M.); (A.R.); (V.T.)
- Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, 1205 Geneva, Switzerland
| | - Manja Marz
- European Virus Bioinformatics Center, 07743 Jena, Germany; (N.B.); (I.M.M.); (G.M.C.); (C.M.K.); (K.L.); (M.M.); (D.F.N.); (I.O.); (S.P.); (R.D.); (B.I.); (J.K.); (P.L.M.); (M.M.); (A.R.); (V.T.)
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Alban Ramette
- European Virus Bioinformatics Center, 07743 Jena, Germany; (N.B.); (I.M.M.); (G.M.C.); (C.M.K.); (K.L.); (M.M.); (D.F.N.); (I.O.); (S.P.); (R.D.); (B.I.); (J.K.); (P.L.M.); (M.M.); (A.R.); (V.T.)
- Institute for Infectious Diseases, University of Bern, 3012 Bern, Switzerland
| | - Volker Thiel
- European Virus Bioinformatics Center, 07743 Jena, Germany; (N.B.); (I.M.M.); (G.M.C.); (C.M.K.); (K.L.); (M.M.); (D.F.N.); (I.O.); (S.P.); (R.D.); (B.I.); (J.K.); (P.L.M.); (M.M.); (A.R.); (V.T.)
- Institute of Virology and Immunology, University of Bern, 3012 Bern, Switzerland
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Kinsella CM, Bart A, Deijs M, Broekhuizen P, Kaczorowska J, Jebbink MF, van Gool T, Cotten M, van der Hoek L. Entamoeba and Giardia parasites implicated as hosts of CRESS viruses. Nat Commun 2020; 11:4620. [PMID: 32934242 PMCID: PMC7493932 DOI: 10.1038/s41467-020-18474-w] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 08/25/2020] [Indexed: 12/13/2022] Open
Abstract
Metagenomic techniques have enabled genome sequencing of unknown viruses without isolation in cell culture, but information on the virus host is often lacking, preventing viral characterisation. High-throughput methods capable of identifying virus hosts based on genomic data alone would aid evaluation of their medical or biological relevance. Here, we address this by linking metagenomic discovery of three virus families in human stool samples with determination of probable hosts. Recombination between viruses provides evidence of a shared host, in which genetic exchange occurs. We utilise networks of viral recombination to delimit virus-host clusters, which are then anchored to specific hosts using (1) statistical association to a host organism in clinical samples, (2) endogenous viral elements in host genomes, and (3) evidence of host small RNA responses to these elements. This analysis suggests two CRESS virus families (Naryaviridae and Nenyaviridae) infect Entamoeba parasites, while a third (Vilyaviridae) infects Giardia duodenalis. The trio supplements five CRESS virus families already known to infect eukaryotes, extending the CRESS virus host range to protozoa. Phylogenetic analysis implies CRESS viruses infecting multicellular life have evolved independently on at least three occasions.
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Affiliation(s)
- Cormac M Kinsella
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.
| | - Aldert Bart
- Laboratory of Clinical Parasitology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Martin Deijs
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Patricia Broekhuizen
- Laboratory of Clinical Parasitology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Joanna Kaczorowska
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Maarten F Jebbink
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Tom van Gool
- Laboratory of Clinical Parasitology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Matthew Cotten
- MRC/UVRI & LSHTM Uganda Research Unit, 3FC6+Q3, Entebbe, Uganda.,MRC-University of Glasgow Centre for Virus Research, G61 1QH, Glasgow, UK
| | - Lia van der Hoek
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.
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Abstract
Viruses are the most abundant biological entities on Earth. In addition to their impact on animal and plant health, viruses have important roles in ecosystem dynamics as well as in the evolution of the biosphere. Circular Rep-encoding single-stranded (CRESS) DNA viruses are ubiquitous in nature, many are agriculturally important, and they appear to have multiple origins from prokaryotic plasmids. A subset of CRESS-DNA viruses, the cruciviruses, have homologues of capsid proteins encoded by RNA viruses. The genetic structure of cruciviruses attests to the transfer of capsid genes between disparate groups of viruses. However, the evolutionary history of cruciviruses is still unclear. By collecting and analyzing cruciviral sequence data, we provide a deeper insight into the evolutionary intricacies of cruciviruses. Our results reveal an unexpected diversity of this virus group, with frequent recombination as an important determinant of variability. The discovery of cruciviruses revealed the most explicit example of a common protein homologue between DNA and RNA viruses to date. Cruciviruses are a novel group of circular Rep-encoding single-stranded DNA (ssDNA) (CRESS-DNA) viruses that encode capsid proteins that are most closely related to those encoded by RNA viruses in the family Tombusviridae. The apparent chimeric nature of the two core proteins encoded by crucivirus genomes suggests horizontal gene transfer of capsid genes between DNA and RNA viruses. Here, we identified and characterized 451 new crucivirus genomes and 10 capsid-encoding circular genetic elements through de novo assembly and mining of metagenomic data. These genomes are highly diverse, as demonstrated by sequence comparisons and phylogenetic analysis of subsets of the protein sequences they encode. Most of the variation is reflected in the replication-associated protein (Rep) sequences, and much of the sequence diversity appears to be due to recombination. Our results suggest that recombination tends to occur more frequently among groups of cruciviruses with relatively similar capsid proteins and that the exchange of Rep protein domains between cruciviruses is rarer than intergenic recombination. Additionally, we suggest members of the stramenopiles/alveolates/Rhizaria supergroup as possible crucivirus hosts. Altogether, we provide a comprehensive and descriptive characterization of cruciviruses.
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Dolja VV, Krupovic M, Koonin EV. Deep Roots and Splendid Boughs of the Global Plant Virome. ANNUAL REVIEW OF PHYTOPATHOLOGY 2020; 58:23-53. [PMID: 32459570 DOI: 10.1146/annurev-phyto-030320-041346] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Land plants host a vast and diverse virome that is dominated by RNA viruses, with major additional contributions from reverse-transcribing and single-stranded (ss) DNA viruses. Here, we introduce the recently adopted comprehensive taxonomy of viruses based on phylogenomic analyses, as applied to the plant virome. We further trace the evolutionary ancestry of distinct plant virus lineages to primordial genetic mobile elements. We discuss the growing evidence of the pivotal role of horizontal virus transfer from invertebrates to plants during the terrestrialization of these organisms, which was enabled by the evolution of close ecological associations between these diverse organisms. It is our hope that the emerging big picture of the formation and global architecture of the plant virome will be of broad interest to plant biologists and virologists alike and will stimulate ever deeper inquiry into the fascinating field of virus-plant coevolution.
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Affiliation(s)
- Valerian V Dolja
- Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331-2902, USA;
| | - Mart Krupovic
- Archaeal Virology Unit, Department of Microbiology, Institut Pasteur, 75015 Paris, France
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
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Krupovic M, Varsani A, Kazlauskas D, Breitbart M, Delwart E, Rosario K, Yutin N, Wolf YI, Harrach B, Zerbini FM, Dolja VV, Kuhn JH, Koonin EV. Cressdnaviricota: a Virus Phylum Unifying Seven Families of Rep-Encoding Viruses with Single-Stranded, Circular DNA Genomes. J Virol 2020; 94:e00582-20. [PMID: 32269128 PMCID: PMC7307096 DOI: 10.1128/jvi.00582-20] [Citation(s) in RCA: 112] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
MESH Headings
- Animals
- DNA Viruses/classification
- DNA Viruses/genetics
- DNA, Circular/chemistry
- DNA, Circular/genetics
- DNA, Circular/metabolism
- DNA, Single-Stranded/chemistry
- DNA, Single-Stranded/genetics
- DNA, Single-Stranded/metabolism
- DNA, Viral/chemistry
- DNA, Viral/genetics
- DNA, Viral/metabolism
- Diatoms/virology
- Genome Size
- Genome, Viral
- Insecta/virology
- Phylogeny
- Plants/virology
- Terminology as Topic
- Viral Proteins/genetics
- Viral Proteins/metabolism
- Virus Replication
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Affiliation(s)
- Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Paris, France
| | - 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
| | - Darius Kazlauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Mya Breitbart
- University of South Florida, College of Marine Science, St. Petersburg, Florida, USA
| | - Eric Delwart
- Vitalant Research Institute, San Francisco, California, USA
- UCSF Department of Laboratory Medicine, University of California-San Francisco, San Francisco, California, USA
| | - Karyna Rosario
- University of South Florida, College of Marine Science, St. Petersburg, Florida, USA
| | - Natalya Yutin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Balázs Harrach
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest, Hungary
| | - F Murilo Zerbini
- Departamento de Fitopatologia/Bioagro, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Valerian V Dolja
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
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Koonin EV, Dolja VV, Krupovic M, Varsani A, Wolf YI, Yutin N, Zerbini FM, Kuhn JH. Global Organization and Proposed Megataxonomy of the Virus World. Microbiol Mol Biol Rev 2020; 84:e00061-19. [PMID: 32132243 PMCID: PMC7062200 DOI: 10.1128/mmbr.00061-19] [Citation(s) in RCA: 295] [Impact Index Per Article: 73.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Viruses and mobile genetic elements are molecular parasites or symbionts that coevolve with nearly all forms of cellular life. The route of virus replication and protein expression is determined by the viral genome type. Comparison of these routes led to the classification of viruses into seven "Baltimore classes" (BCs) that define the major features of virus reproduction. However, recent phylogenomic studies identified multiple evolutionary connections among viruses within each of the BCs as well as between different classes. Due to the modular organization of virus genomes, these relationships defy simple representation as lines of descent but rather form complex networks. Phylogenetic analyses of virus hallmark genes combined with analyses of gene-sharing networks show that replication modules of five BCs (three classes of RNA viruses and two classes of reverse-transcribing viruses) evolved from a common ancestor that encoded an RNA-directed RNA polymerase or a reverse transcriptase. Bona fide viruses evolved from this ancestor on multiple, independent occasions via the recruitment of distinct cellular proteins as capsid subunits and other structural components of virions. The single-stranded DNA (ssDNA) viruses are a polyphyletic class, with different groups evolving by recombination between rolling-circle-replicating plasmids, which contributed the replication protein, and positive-sense RNA viruses, which contributed the capsid protein. The double-stranded DNA (dsDNA) viruses are distributed among several large monophyletic groups and arose via the combination of distinct structural modules with equally diverse replication modules. Phylogenomic analyses reveal the finer structure of evolutionary connections among RNA viruses and reverse-transcribing viruses, ssDNA viruses, and large subsets of dsDNA viruses. Taken together, these analyses allow us to outline the global organization of the virus world. Here, we describe the key aspects of this organization and propose a comprehensive hierarchical taxonomy of viruses.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Valerian V Dolja
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Mart Krupovic
- Institut Pasteur, Archaeal Virology Unit, Department of Microbiology, Paris, France
| | - 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 Clinical Laboratory Sciences, University of Cape Town, Observatory, Cape Town, South Africa
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Natalya Yutin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - F Murilo Zerbini
- Departamento de Fitopatologia/Bioagro, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland, USA
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46
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Li P, Wang S, Zhang L, Qiu D, Zhou X, Guo L. A tripartite ssDNA mycovirus from a plant pathogenic fungus is infectious as cloned DNA and purified virions. SCIENCE ADVANCES 2020; 6:eaay9634. [PMID: 32284975 PMCID: PMC7138691 DOI: 10.1126/sciadv.aay9634] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 01/09/2020] [Indexed: 05/27/2023]
Abstract
Here, we describe a tripartite circular single-stranded (ss) DNA mycovirus, named Fusarium graminearum gemytripvirus 1 (FgGMTV1). The genome of FgGMTV1 comprises three circular ssDNA segments (DNA-A, DNA-B, and DNA-C). Sequence alignments and phylogenetic analyses showed that FgGMTV1 is nested within the family Genomoviridae. We also constructed the first infectious DNA clones of a DNA mycovirus. Our results show that DNA-A and DNA-B are mutually interdependent for their replication and are associated with severely reduced colony growth and hypovirulence. DNA-C relies on DNA-A and DNA-B for replication and is necessary for the recovery of abnormal fungal phenotypes. DNA-C also enhances the accumulation of viral DNA in infected fungi and permits stable colonization and easy transmission via conidia. This is the first multipartite DNA virus isolated from a fungus. Our phylogenetic analyses also suggest that the multipartite genome of FgGMTV1 may have evolved from a monopartite genome of an ancient genomovirus.
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47
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Multiple origins of prokaryotic and eukaryotic single-stranded DNA viruses from bacterial and archaeal plasmids. Nat Commun 2019; 10:3425. [PMID: 31366885 PMCID: PMC6668415 DOI: 10.1038/s41467-019-11433-0] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Accepted: 07/10/2019] [Indexed: 02/07/2023] Open
Abstract
Single-stranded (ss) DNA viruses are a major component of the earth virome. In particular, the circular, Rep-encoding ssDNA (CRESS-DNA) viruses show high diversity and abundance in various habitats. By combining sequence similarity network and phylogenetic analyses of the replication proteins (Rep) belonging to the HUH endonuclease superfamily, we show that the replication machinery of the CRESS-DNA viruses evolved, on three independent occasions, from the Reps of bacterial rolling circle-replicating plasmids. The CRESS-DNA viruses emerged via recombination between such plasmids and cDNA copies of capsid genes of eukaryotic positive-sense RNA viruses. Similarly, the rep genes of prokaryotic DNA viruses appear to have evolved from HUH endonuclease genes of various bacterial and archaeal plasmids. Our findings also suggest that eukaryotic polyomaviruses and papillomaviruses with dsDNA genomes have evolved via parvoviruses from CRESS-DNA viruses. Collectively, our results shed light on the complex evolutionary history of a major class of viruses revealing its polyphyletic origins. Most single-stranded DNA viruses have small genomes replicated by rolling circle mechanism which is initiated by the Rep protein. Here, using sequence similarity network and phylogenetic analyses, Kazlauskas et al. show that viral Reps evolved from Reps of bacterial and archaeal plasmids on multiple independent occasions.
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48
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Rosario K, Mettel KA, Greco AM, Breitbart M. Prevalence of a vertically transmitted single-stranded DNA virus in spinybacked orbweavers (Gasteracantha cancriformis) from Florida, USA. J Gen Virol 2019; 100:1253-1265. [PMID: 31210632 DOI: 10.1099/jgv.0.001293] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Spiders (order Araneae, class Arachnida) are an important group of predatory arthropods in terrestrial ecosystems that have been recently identified as an untapped reservoir of single-stranded (ss)DNA viruses. Specifically, spiders harbour a diversity of ssDNA viruses encoding a replication-associated protein (Rep) within a circular genome. However, little is known about the ecology of novel circular Rep-encoding ssDNA (CRESS DNA) viruses. Here we investigated two CRESS DNA viruses recently identified in spinybacked orbweavers (Gasteracantha cancriformis), namely spinybacked orbweaver circular virus (SpOrbCV) 1 and 2. SpOrbCV-1 was detected in the majority (> 65 %) of spider specimens from all life stages, including eggs, spiderlings and adults, demonstrating that this virus is active within spinybacked orbweavers. In contrast, SpOrbCV-2 was only detected in adults at a lower (36 %) prevalence. Since we also detected SpOrbCV-2 in other spider species and this virus has been reported from a dragonfly, we suggest that SpOrbCV-2 is accumulated in these predators through common insect prey. The prevalence of SpOrbCV-1 in collected specimens allowed us to design assays to characterize this virus, which represents a new group of CRESS DNA viruses, the 'circularisviruses'. To our knowledge, SpOrbCV-1 is the first example of a vertically transmitted virus in spiders, which may explain its high prevalence in spinybacked orbweavers. Since vertically transmitted viruses infecting insects (class Insecta) can manipulate their host's behaviour and physiology, future studies should investigate the ecological role of vertically transmitted viruses in spiders.
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Affiliation(s)
- Karyna Rosario
- College of Marine Science, University of South Florida, 140 7th Avenue South, Saint Petersburg, FL, 33701, USA
| | - Kaitlin A Mettel
- College of Marine Science, University of South Florida, 140 7th Avenue South, Saint Petersburg, FL, 33701, USA
| | - Anthony M Greco
- College of Marine Science, University of South Florida, 140 7th Avenue South, Saint Petersburg, FL, 33701, USA
| | - Mya Breitbart
- College of Marine Science, University of South Florida, 140 7th Avenue South, Saint Petersburg, FL, 33701, USA
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49
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Abstract
Single-stranded (ss)DNA viruses are extremely widespread, infect diverse hosts from all three domains of life and include important pathogens. Most ssDNA viruses possess small genomes that replicate by the rolling-circle-like mechanism initiated by a distinct virus-encoded endonuclease. High throughput genome sequencing and improved bioinformatics tools have yielded vast information on presence of ssDNA viruses in diverse habitats. The simple genome of ssDNA viruses have high propensity to undergo mutation and recombination often emerging as threat to human civilization. Interestingly their genome is found embedded in fossils dating back to million years. The unusual evolutionary history of ssDNA viruses reveal evidences of horizontal gene transfer, sometimes between different species and genera.
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Discovery and genetic characterization of diverse smacoviruses in Zambian non-human primates. Sci Rep 2019; 9:5045. [PMID: 30962460 PMCID: PMC6453971 DOI: 10.1038/s41598-019-41358-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 03/07/2019] [Indexed: 11/12/2022] Open
Abstract
The Smacoviridae has recently been classified as a family of small circular single-stranded DNA viruses. An increasing number of smacovirus genomes have been identified exclusively in faecal matter of various vertebrate species and from insect body parts. However, the genetic diversity and host range of smacoviruses remains to be fully elucidated. Herein, we report the genetic characterization of eleven circular replication-associated protein (Rep) encoding single-stranded (CRESS) DNA viruses detected in the faeces of Zambian non-human primates. Based on pairwise genome-wide and amino acid identities with reference smacovirus species, ten of the identified CRESS DNA viruses are assigned to the genera Porprismacovirus and Huchismacovirus of the family Smacoviridae, which bidirectionally encode two major open reading frames (ORFs): Rep and capsid protein (CP) characteristic of a type IV genome organization. The remaining unclassified CRESS DNA virus was related to smacoviruses but possessed a genome harbouring a unidirectionally oriented CP and Rep, assigned as a type V genome organization. Moreover, phylogenetic and recombination analyses provided evidence for recombination events encompassing the 3′-end of the Rep ORF in the unclassified CRESS DNA virus. Our findings increase the knowledge of the known genetic diversity of smacoviruses and highlight African non-human primates as carrier animals.
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