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Breno Zampieri Lima M, Giovana Pereira Daniel T, Tayaná Oliveira Bitencourt H, Carlos Junior Alcantara L, Haddad R, Kashima S, Carolina Elias M, Giovanetti M, Coccuzzo Sampaio S, Nanev Slavov S. Molecular frequency of human gemycircularvirus (GCYV) dna among blood donors from the Brazilian Amazon. Transfus Clin Biol 2024; 31:123-126. [PMID: 38280666 DOI: 10.1016/j.tracli.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 01/29/2024]
Affiliation(s)
- Marlon Breno Zampieri Lima
- Blood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Thuany Giovana Pereira Daniel
- Blood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | | | - Luiz Carlos Junior Alcantara
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil; Climate Amplified Diseases And Epidemics (CLIMADE), Americas, Brazil
| | - Rodrigo Haddad
- Campus Ceilandia, University of Brasília, Brasília, Federal District, Brazil
| | - Simone Kashima
- Blood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | | | - Marta Giovanetti
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil; Sciences and Technologies for Sustainable Development and One Health, Universitá Campus Bio-Medico di Roma, Rome, Italy
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König MT, Frölich K, Jandowsky A, Knauf-Witzens T, Langner C, Dietrich R, Märtlbauer E, Didier A. First Insights into the Occurrence of Circular Single-Stranded DNA Genomes in Asian and African Cattle. Animals (Basel) 2023; 13:ani13091492. [PMID: 37174530 PMCID: PMC10177065 DOI: 10.3390/ani13091492] [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: 03/17/2023] [Revised: 04/21/2023] [Accepted: 04/23/2023] [Indexed: 05/15/2023] Open
Abstract
Circular replicase-encoding single-stranded (CRESS) DNA viruses and other circular DNA agents are increasingly found in various samples and animals. A specific class of these agents-termed bovine meat and milk factors (BMMF)-has been supposed to act as a factor in indirect carcinogenesis in humans. Initial observations attributed the BMMF to European cattle breeds and foodstuffs produced thereof. In the present study, blood and fecal samples from African and Asian cattle were examined. BMMF molecules and genomoviruses were detected in all bovids under study. The majority (79%) of the 29 circular elements could be assigned to BMMF groups 1 and 2, whereas CRESS viruses of the family Genomoviridae accounted for the smaller part (21%). Two genomoviruses belong to the genus Gemykibivirus and one to the genus Gemykrogvirus. The remaining three might be considered as novel species within the genus Gemycircularvirus. The majority of all isolated molecules originated from fecal samples, whereas only three derived from blood. The results from this study expand our knowledge on the diversity and presence of circular DNA in different ruminants that serve for food production in many countries over the world.
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Affiliation(s)
- Marie-Thérèse König
- Department of Veterinary Sciences, Institute of Food Science, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität München, Schönleutnerstraße 8, 85764 Oberschleißheim, Germany
| | - Kai Frölich
- Tierpark Arche Warder, Zentrum für Seltene Nutztierrassen e. V., Langwedeler Weg 11, 24646 Warder, Germany
| | - Anabell Jandowsky
- Tierpark Arche Warder, Zentrum für Seltene Nutztierrassen e. V., Langwedeler Weg 11, 24646 Warder, Germany
| | - Tobias Knauf-Witzens
- Wilhelma Zoological-Botanical Gardens Stuttgart, Wilhelma 13, 70376 Stuttgart, Germany
| | - Christoph Langner
- Stralsund Zoological Garden, Grünhufer Bogen 2, 18437 Stralsund, Germany
| | - Richard Dietrich
- Department of Veterinary Sciences, Institute of Food Science, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität München, Schönleutnerstraße 8, 85764 Oberschleißheim, Germany
| | - Erwin Märtlbauer
- Department of Veterinary Sciences, Institute of Food Science, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität München, Schönleutnerstraße 8, 85764 Oberschleißheim, Germany
| | - Andrea Didier
- Department of Veterinary Sciences, Institute of Food Science, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität München, Schönleutnerstraße 8, 85764 Oberschleißheim, Germany
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Liu Y, Guo L, Wang G, Gao F, Tu Z, Xu D, Sun L, Yi L, Zhu G, Tu C, He B. DNA virome of ticks in the Northeast and Hubei provinces of China reveals diverse single-stranded circular DNA viruses. Parasit Vectors 2023; 16:61. [PMID: 36759895 PMCID: PMC9912487 DOI: 10.1186/s13071-023-05684-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 01/25/2023] [Indexed: 02/11/2023] Open
Abstract
BACKGROUND Ticks are medically important vectors capable of transmitting a variety of pathogens to and between host species. Although the spectrum of tick-borne RNA viruses has been frequently investigated, the diversity of tick-borne DNA viruses remains largely unknown. METHODS A total of 1571 ticks were collected from forests and infested animals, and the diversity of the viruses they harbored was profiled using a DNA-specific virome method. The viromic data were phylogenetically analyzed and validated by PCR assays. RESULTS Although diverse and abundant prokaryotic viruses were identified in the collected ticks, only eukaryotic DNA viruses with single-stranded circular genomes covering the anelloviruses and circular replication-associated (Rep) protein-encoding single-stranded (CRESS) DNA viruses were recovered from ticks. Anelloviruses were detected only in two tick pools, but CRESS DNA viruses were prevalent across these ticks except in one pool of Dermacentor spp. ticks. Phylogenetic analyses revealed that these tick-borne CRESS DNA viruses were related to viruses recovered from animal feces, tissues and even environmental samples, suggesting that their presence may be largely explained by environmental factors rather than by tick species and host blood meals. CONCLUSIONS Based on the results, tick-borne eukaryotic DNA viruses appear to be much less common than eukaryotic RNA viruses. Investigations involving a wider collection area and more diverse tick species are required to further support this speculation.
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Affiliation(s)
- Yuhang Liu
- grid.268415.cJiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, Jiangsu China ,grid.410727.70000 0001 0526 1937Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin China
| | - Lei Guo
- grid.454880.50000 0004 0596 3180Division of Wildlife and Plant Conservation, State Forestry and Grassland Administration, Changchun, Jilin China
| | - Guoshuai Wang
- grid.410727.70000 0001 0526 1937Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin China
| | - Fei Gao
- Section of Wildlife Conservation, Greater Xing’an Mountains Forestry Group Corporation, Jiagedaqi, Heilongjiang China
| | - Zhongzhong Tu
- grid.410727.70000 0001 0526 1937Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin China
| | - Deming Xu
- Forestry Bureau of Linjiang City, Linjiang, Jilin China
| | - Lanshun Sun
- Provincial Wildlife Disease Monitoring Station of Shuanghe, Xunke, Heilongjiang China
| | - Le Yi
- grid.410727.70000 0001 0526 1937Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin China
| | - Guoqiang Zhu
- grid.268415.cJiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, Jiangsu China
| | - Changchun Tu
- grid.268415.cJiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, Jiangsu China ,grid.410727.70000 0001 0526 1937Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin China
| | - Biao He
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China. .,Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin, China.
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4
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Li X, Liu Q, Chen X, Xiao Y, Yang S, Zhang W, Chen J. The virome of bronchoalveolar lavage fluid from patients with fever of unknown origin. Future Virol 2022. [DOI: 10.2217/fvl-2020-0027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Background: Viral metagenomics, a high-throughput sequencing combined with virus sequence-independent amplification by random PCR, allows for unbiased detection of virtually any viruses present in samples. Materials & methods: In order to investigate the virome of bronchoalveolar lavage fluid from patients with fever of unknown origin, 58 samples collected from diseased patients were characterized and compared. Results: Some representatives of Anelloviridae were identified, we found the torque teno virus (TTV) accounts for the majority of virus communities and were more prevalent in the specimens of febrile patients. Phylogenetic analysis suggested that these anellovirus isolates were close to the previous TTV available in GenBank®. Conclusion: All these data indicate that the human anellovirus species TTV may associated with fever of unknown origin.
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Affiliation(s)
- Xinlin Li
- Department of Clinical Laboratory, The Affiliated People’s Hospital of Jiangsu University, No. 8 Dian Li Road, Zhenjiang, China
- School of Medicine, Jiangsu University, No. 301 Xue Fu Road, Zhenjiang, China
| | - Qi Liu
- School of Medicine, Jiangsu University, No. 301 Xue Fu Road, Zhenjiang, China
| | - Xu Chen
- School of Medicine, Jiangsu University, No. 301 Xue Fu Road, Zhenjiang, China
| | - Yuqing Xiao
- School of Medicine, Jiangsu University, No. 301 Xue Fu Road, Zhenjiang, China
| | - Shixing Yang
- School of Medicine, Jiangsu University, No. 301 Xue Fu Road, Zhenjiang, China
| | - Wen Zhang
- School of Medicine, Jiangsu University, No. 301 Xue Fu Road, Zhenjiang, China
| | - Jianguo Chen
- Department of Clinical Laboratory, The Affiliated People’s Hospital of Jiangsu University, No. 8 Dian Li Road, Zhenjiang, China
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Abstract
Anelloviruses are small negative-sense single-stranded DNA viruses with genomes ranging in size from 1.6 to 3.9 kb. The family Anelloviridae comprised 14 genera before the present changes. However, in the last five years, a large number of diverse anelloviruses have been identified in various organisms. Here, we undertake a global analysis of mammalian anelloviruses whose full genome sequences have been determined and have an intact open reading frame 1 (ORF1). We established new criteria for the classification of anelloviruses, and, based on our analyses, we establish new genera and species to accommodate the unclassified anelloviruses. We also note that based on the updated species demarcation criteria, some previously assigned species (n = 10) merge with other species. Given the rate at which virus sequence data are accumulating, and with the identification of diverse anelloviruses, we acknowledge that the taxonomy will have to be dynamic and continuously evolve to accommodate new members.
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Feng C, Feng J, Wang Z, Pedersen C, Wang X, Saleem H, Domier L, Marzano SYL. Identification of the Viral Determinant of Hypovirulence and Host Range in Sclerotiniaceae of a Genomovirus Reconstructed from the Plant Metagenome. J Virol 2021; 95:e0026421. [PMID: 34132570 PMCID: PMC8354332 DOI: 10.1128/jvi.00264-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 06/09/2021] [Indexed: 12/14/2022] Open
Abstract
Uncharacterized viral genomes that encode circular replication-associated proteins of single-stranded DNA viruses have been discovered by metagenomics/metatranscriptomics approaches. Some of these novel viruses are classified in the newly formed family Genomoviridae. Here, we determined the host range of a novel genomovirus, SlaGemV-1, through the transfection of Sclerotinia sclerotiorum with infectious clones. Inoculating with the rescued virions, we further transfected Botrytis cinerea and Monilinia fructicola, two economically important members of the family Sclerotiniaceae, and Fusarium oxysporum. SlaGemV-1 causes hypovirulence in S. sclerotiorum, B. cinerea, and M. fructicola. SlaGemV-1 also replicates in Spodoptera frugiperda insect cells but not in Caenorhabditis elegans or plants. By expressing viral genes separately through site-specific integration, the replication protein alone was sufficient to cause debilitation. Our study is the first to demonstrate the reconstruction of a metagenomically discovered genomovirus without known hosts with the potential of inducing hypovirulence, and the infectious clone allows for studying mechanisms of genomovirus-host interactions that are conserved across genera. IMPORTANCE Little is known about the exact host range of widespread genomoviruses. The genome of soybean leaf-associated gemygorvirus-1 (SlaGemV-1) was originally assembled from a metagenomic/metatranscriptomic study without known hosts. Here, we rescued SlaGemV-1 and found that it could infect three important plant-pathogenic fungi and fall armyworm (S. frugiperda Sf9) insect cells but not a model nematode, C. elegans, or model plant species. Most importantly, SlaGemV-1 shows promise for inducing hypovirulence of the tested fungal species in the family Sclerotiniaceae, including Sclerotinia sclerotiorum, Botrytis cinerea, and Monilinia fructicola. The viral determinant of hypovirulence was further identified as replication initiation protein. As a proof of concept, we demonstrate that viromes discovered in plant metagenomes can be a valuable genetic resource when novel viruses are rescued and characterized for their host range.
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Affiliation(s)
- Chenchen Feng
- Department of Horticulture, Agronomy, and Plant Sciences, South Dakota State University, Brookings, South Dakota, USA
| | - Jiuhuan Feng
- Department of Horticulture, Agronomy, and Plant Sciences, South Dakota State University, Brookings, South Dakota, USA
| | - Ziyi Wang
- Department of Horticulture, Agronomy, and Plant Sciences, South Dakota State University, Brookings, South Dakota, USA
| | - Connor Pedersen
- Department of Biology and Microbiology, South Dakota State University, Brookings, South Dakota, USA
| | - Xiuqing Wang
- Department of Biology and Microbiology, South Dakota State University, Brookings, South Dakota, USA
| | - Huma Saleem
- Department of Biology and Microbiology, South Dakota State University, Brookings, South Dakota, USA
| | - Leslie Domier
- United States Department of Agriculture/Agricultural Research Service, Urbana, Illinois, USA
| | - Shin-Yi Lee Marzano
- Department of Horticulture, Agronomy, and Plant Sciences, South Dakota State University, Brookings, South Dakota, USA
- Department of Biology and Microbiology, South Dakota State University, Brookings, South Dakota, USA
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7
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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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8
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Xu X, Bei J, Xuan Y, Chen J, Chen D, Barker SC, Kelava S, Zhang X, Gao S, Chen Z. Full-length genome sequence of segmented RNA virus from ticks was obtained using small RNA sequencing data. BMC Genomics 2020; 21:641. [PMID: 32938401 PMCID: PMC7493057 DOI: 10.1186/s12864-020-07060-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 09/10/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In 2014, a novel tick-borne virus of the Flaviviridae family was first reported in the Mogiana region of Brazil and named the Mogiana tick virus (MGTV). Thereafter, the Jingmen tick virus (JMTV), Kindia tick virus (KITV), and Guangxi tick virus (GXTV)-evolutionarily related to MGTV-were reported. RESULTS In the present study, we used small RNA sequencing (sRNA-seq) to detect viruses in ticks and discovered a new MGTV strain in Amblyomma testudinarium ticks collected in China's Yunnan Province in 2016. We obtained the full-length genome sequence of this MGTV strain Yunnan2016 (GenBank: MT080097, MT080098, MT080099 and MT080100) and recommended it for its inclusion in the NCBI RefSeq database for future studies on MGTV, JMTV, KITV and GXTV. Phylogenetic analysis showed that MGTV, JMTV, KITV and GXTV are monophyletic and belong to a MGTV group. Furthermore, this MGTV group of viruses may be phylogenetically related to geographical regions that were formerly part of the supercontinents Gondwana and Laurasia. CONCLUSIONS To the best of our knowledge, this is the first study in which 5' and 3' sRNAs were used to generate full-length genome sequences of, but not limited to, RNA viruses. We also demonstrated the feasibility of using the sRNA-seq based method for the detection of viruses in pooled two and even possible one small ticks. MGTV may preserve the characteristic of ancient RNA viruses, which can be used to study the origin and evolution of RNA viruses. In addition, MGTV can be used as novel species for studies in phylogeography.
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Affiliation(s)
- Xiaofeng Xu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, 050024, People's Republic of China
| | - Jinlong Bei
- Guangdong Provincial Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, People's Republic of China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong, 510642, People's Republic of China
| | - Yibo Xuan
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, 050024, People's Republic of China
| | - Jiayuan Chen
- College of Life Sciences, Nankai University, Tianjin, Tianjin, 300071, People's Republic of China
| | - Defu Chen
- College of Life Sciences, Nankai University, Tianjin, Tianjin, 300071, People's Republic of China
| | - Stephen C Barker
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Samuel Kelava
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Xiaoai Zhang
- Guangdong Provincial Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, People's Republic of China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong, 510642, People's Republic of China
| | - Shan Gao
- College of Life Sciences, Nankai University, Tianjin, Tianjin, 300071, People's Republic of China.
| | - Ze Chen
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, 050024, People's Republic of China.
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Kraberger S, Schmidlin K, Fontenele RS, Walters M, Varsani A. Unravelling the Single-Stranded DNA Virome of the New Zealand Blackfly. Viruses 2019; 11:E532. [PMID: 31181730 PMCID: PMC6630596 DOI: 10.3390/v11060532] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 06/01/2019] [Accepted: 06/04/2019] [Indexed: 01/23/2023] Open
Abstract
Over the last decade, arthropods have been shown to harbour a rich diversity of viruses. Through viral metagenomics a large diversity of single-stranded (ss) DNA viruses have been identified. Here we examine the ssDNA virome of the hematophagous New Zealand blackfly using viral metagenomics. Our investigation reveals a plethora of novel ssDNA viral genomes, some of which cluster in the viral families Genomoviridae (n = 9), Circoviridae (n = 1), and Microviridae (n = 108), others in putative families that, at present, remain unclassified (n = 20) and one DNA molecule that only encodes a replication associated protein. Among these novel viruses, two putative multi-component virus genomes were recovered, and these are most closely related to a Tongan flying fox faeces-associated multi-component virus. Given that the only other known multi-component circular replication-associated (Rep) protein encoding single-stranded (CRESS) DNA viruses infecting plants are in the families Geminiviridae (members of the genus Begomovirus) and Nanoviridae, it appears these are likely a new multi-component virus group which may be associated with animals. This study reiterates the diversity of ssDNA viruses in nature and in particular with the New Zealand blackflies.
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Affiliation(s)
- Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA.
| | - Kara Schmidlin
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, 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 85287-5001, USA.
| | - Matthew Walters
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand.
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA.
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand.
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Rondebosch, Cape Town 7700, South Africa.
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10
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Pak D, Jacobs SB, Sakamoto JM. A 117-year retrospective analysis of Pennsylvania tick community dynamics. Parasit Vectors 2019; 12:189. [PMID: 31036065 PMCID: PMC6489237 DOI: 10.1186/s13071-019-3451-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 04/20/2019] [Indexed: 11/29/2022] Open
Abstract
Background Tick-borne diseases have been increasing at the local, national, and global levels. Researchers studying ticks and tick-borne diseases need a thorough knowledge of the pathogens, vectors, and epidemiology of disease spread. Both active and passive surveillance approaches are typically used to estimate tick population size and risk of tick encounter. Our data consists of a composite of active and long-term passive surveillance, which has provided insight into spatial variability and temporal dynamics of ectoparasite communities and identified rarer tick species. We present a retrospective analysis on compiled data of ticks from Pennsylvania over the last 117 years. Methods We compiled data from ticks collected during tick surveillance research, and from citizen-based submissions. The majority of the specimens were submitted by citizens. However, a subset of the data was collected through active methods (flagging or dragging, or removal of ticks from wildlife). We analyzed all data from 1900–2017 for tick community composition, host associations, and spatio-temporal dynamics. Results In total there were 4491 submission lots consisting of 7132 tick specimens. Twenty-four different species were identified, with the large proportion of submissions represented by five tick species. We observed a shift in tick community composition in which the dominant species of tick (Ixodes cookei) was overtaken in abundance by Dermacentor variabilis in the early 1990s and then replaced in abundance by I. scapularis. We analyzed host data and identified overlaps in host range amongst tick species. Conclusions We highlight the importance of long-term passive tick surveillance in investigating the ecology of both common and rare tick species. Information on the geographical distribution, host-association, and seasonality of the tick community can help researchers and health-officials to identify high-risk areas. Electronic supplementary material The online version of this article (10.1186/s13071-019-3451-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Damie Pak
- Department of Biology, Pennsylvania State University, W-234A, Millennium Science Complex, University Park, PA, 16802, USA
| | - Steven B Jacobs
- Department of Entomology, Pennsylvania State University, 501 ASI Building, University Park, PA, 16802, USA
| | - Joyce M Sakamoto
- Department of Entomology, Pennsylvania State University, W-104 Millennium Science Complex, University Park, PA, 16802, USA.
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11
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Abstract
Termites have a unique ability to effectively digest lignocellulose with the help of mutualistic symbionts. While gut bacteria and protozoa have been relatively well characterized in termites, the virome remains largely unexplored. Here, we report two genomes of microviruses (termite-associated microvirus-1 [TaMV-1] and termite-associated microvirus-2 [TaMV-2]) associated with the gut of Coptotermes formosanus.
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12
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Zhao L, Rosario K, Breitbart M, Duffy S. Eukaryotic Circular Rep-Encoding Single-Stranded DNA (CRESS DNA) Viruses: Ubiquitous Viruses With Small Genomes and a Diverse Host Range. Adv Virus Res 2018; 103:71-133. [PMID: 30635078 DOI: 10.1016/bs.aivir.2018.10.001] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
While single-stranded DNA (ssDNA) was once thought to be a relatively rare genomic architecture for viruses, modern metagenomics sequencing has revealed circular ssDNA viruses in most environments and in association with diverse hosts. In particular, circular ssDNA viruses encoding a homologous replication-associated protein (Rep) have been identified in the majority of eukaryotic supergroups, generating interest in the ecological effects and evolutionary history of circular Rep-encoding ssDNA viruses (CRESS DNA) viruses. This review surveys the explosion of sequence diversity and expansion of eukaryotic CRESS DNA taxonomic groups over the last decade, highlights similarities between the well-studied geminiviruses and circoviruses with newly identified groups known only through their genome sequences, discusses the ecology and evolution of eukaryotic CRESS DNA viruses, and speculates on future research horizons.
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Affiliation(s)
- Lele Zhao
- Department of Ecology, Evolution and Natural Resources, Rutgers, the State University of New Jersey, New Brunswick, NJ, United States
| | - Karyna Rosario
- College of Marine Science, University of South Florida, Saint Petersburg, FL, United States
| | - Mya Breitbart
- College of Marine Science, University of South Florida, Saint Petersburg, FL, United States
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, Rutgers, the State University of New Jersey, New Brunswick, NJ, United States.
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Rosario K, Mettel KA, Benner BE, Johnson R, Scott C, Yusseff-Vanegas SZ, Baker CCM, Cassill DL, Storer C, Varsani A, Breitbart M. Virus discovery in all three major lineages of terrestrial arthropods highlights the diversity of single-stranded DNA viruses associated with invertebrates. PeerJ 2018; 6:e5761. [PMID: 30324030 PMCID: PMC6186406 DOI: 10.7717/peerj.5761] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 09/16/2018] [Indexed: 11/20/2022] Open
Abstract
Viruses encoding a replication-associated protein (Rep) within a covalently closed, single-stranded (ss)DNA genome are among the smallest viruses known to infect eukaryotic organisms, including economically valuable agricultural crops and livestock. Although circular Rep-encoding ssDNA (CRESS DNA) viruses are a widespread group for which our knowledge is rapidly expanding, biased sampling toward vertebrates and land plants has limited our understanding of their diversity and evolution. Here, we screened terrestrial arthropods for CRESS DNA viruses and report the identification of 44 viral genomes and replicons associated with specimens representing all three major terrestrial arthropod lineages, namely Euchelicerata (spiders), Hexapoda (insects), and Myriapoda (millipedes). We identified virus genomes belonging to three established CRESS DNA viral families (Circoviridae, Genomoviridae, and Smacoviridae); however, over half of the arthropod-associated viral genomes are only distantly related to currently classified CRESS DNA viral sequences. Although members of viral and satellite families known to infect plants (Geminiviridae, Nanoviridae, Alphasatellitidae) were not identified in this study, these plant-infecting CRESS DNA viruses and replicons are transmitted by hemipterans. Therefore, members from six out of the seven established CRESS DNA viral families circulate among arthropods. Furthermore, a phylogenetic analysis of Reps, including endogenous viral sequences, reported to date from a wide array of organisms revealed that most of the known CRESS DNA viral diversity circulates among invertebrates. Our results highlight the vast and unexplored diversity of CRESS DNA viruses among invertebrates and parallel findings from RNA viral discovery efforts in undersampled taxa.
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Affiliation(s)
- Karyna Rosario
- College of Marine Science, University of South Florida, Saint Petersburg, FL, USA
| | - Kaitlin A Mettel
- College of Marine Science, University of South Florida, Saint Petersburg, FL, USA
| | - Bayleigh E Benner
- College of Marine Science, University of South Florida, Saint Petersburg, FL, USA
| | - Ryan Johnson
- College of Marine Science, University of South Florida, Saint Petersburg, FL, USA
| | - Catherine Scott
- Department of Biological Sciences, University of Toronto, Scarborough, Scarborough, ON, Canada
| | | | - Christopher C M Baker
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Deby L Cassill
- Department of Biological Sciences, University of South Florida Saint Petersburg, Saint Petersburg, FL, USA
| | - Caroline Storer
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA.,Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town, South Africa
| | - Mya Breitbart
- College of Marine Science, University of South Florida, Saint Petersburg, FL, USA
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Kraberger S, Hofstetter RW, Potter KA, Farkas K, Varsani A. Genomoviruses associated with mountain and western pine beetles. Virus Res 2018; 256:17-20. [DOI: 10.1016/j.virusres.2018.07.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 07/23/2018] [Accepted: 07/26/2018] [Indexed: 11/30/2022]
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15
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Nishizawa T, Sugimoto Y, Takeda T, Kodera Y, Hatano Y, Takahashi M, Okamoto H. Identification and whole genome characterization of novel anelloviruses in masked palm civets (Paguma larvata): Segregation into four distinct clades. Virus Res 2018; 256:183-191. [PMID: 30149046 DOI: 10.1016/j.virusres.2018.08.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 08/16/2018] [Accepted: 08/20/2018] [Indexed: 10/28/2022]
Abstract
The members of the family Anelloviridae are small and single-stranded DNA viruses with marked diversity in sequence and length, which ubiquitously infect many vertebrates, including mammals, birds and reptiles. The anelloviruses isolated from mammals are currently classified into 11 assigned and four proposed genera; some anelloviruses remain unassigned. The present study was conducted to identify anelloviruses in wild-caught masked palm civets (Paguma larvata) in Japan using a rolling-circle amplification method. Thirteen novel anellovirus strains were identified from 8 of 10 masked palm civets and their entire genomic sequences (2039-2535 nucleotides) were determined; they were classifiable into four distinct clades. Comparative analyses of all reported anelloviruses for which the entire or near-entire genomic sequences have been determined, including the 13 strains obtained in the present study, revealed that anelloviruses can provisionally be classified into 20 clades, which may correspond to 20 genera (including 11 assigned and four proposed genera) by a >70% amino acid sequence difference in open reading frame 1 (ORF1). This study suggested that novel anelloviruses of marked diversity are circulating in animals worldwide, and that the rolling-circle amplification method would be useful for identifying novel anelloviruses and other viruses with a circular DNA genome.
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Affiliation(s)
- Tsutomu Nishizawa
- Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, Shimotsuke, Tochigi, 329-0498, Japan
| | - Yuji Sugimoto
- Nikko Branch, Tochigi Hunter Association, Nikko, Tochigi, 321-2522, Japan
| | - Tsutomu Takeda
- Center for Weeds and Wildlife Management, Utsunomiya University, Utsunomiya, Tochigi, 321-8505, Japan
| | - Yuuji Kodera
- Center for Weeds and Wildlife Management, Utsunomiya University, Utsunomiya, Tochigi, 321-8505, Japan
| | - Yumi Hatano
- Sakakibara Heart Institute Clinic, Shinjuku-ku, Tokyo, 163-0804, Japan
| | - Masaharu Takahashi
- Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, Shimotsuke, Tochigi, 329-0498, Japan
| | - Hiroaki Okamoto
- Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, Shimotsuke, Tochigi, 329-0498, Japan.
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Genome Sequences of Two Single-Stranded DNA Viruses Identified in Varroa destructor. GENOME ANNOUNCEMENTS 2018; 6:6/9/e00107-18. [PMID: 29496833 PMCID: PMC5834324 DOI: 10.1128/genomea.00107-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Varroa destructor is a ubiquitous and parasitic mite of honey bees, infecting them with pathogenic viruses having a major impact on apiculture. We identified two novel circular replication-associated protein (Rep)-encoding single-stranded (CRESS) DNA viruses from V. destructor sampled from a honey bee hive near Christchurch in New Zealand.
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