1
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Ramos EDSF, Tozetto-Mendoza TR, Bortoletto P, Ferreira NE, Honorato L, Barbosa EMG, Luchs A, Linhares IM, Spandorfer SD, Leal E, da Costa AC, Witkin SS, Mendes-Correa MC. Characterization of CRESS-DNA viruses in human vaginal secretions: An exploratory metagenomic investigation. J Med Virol 2024; 96:e29750. [PMID: 38953413 DOI: 10.1002/jmv.29750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 05/16/2024] [Accepted: 06/09/2024] [Indexed: 07/04/2024]
Abstract
The Phylum Cressdnaviricota consists of a large number of circular Rep-encoding single-stranded (CRESS)-DNA viruses. Recently, metagenomic analyzes revealed their ubiquitous distribution in a diverse range of eukaryotes. Data relating to CRESS-DNA viruses in humans remains scarce. Our study investigated the presence and genetic diversity of CRESS-DNA viruses in human vaginal secretions. Vaginal swabs were collected from 28 women between 29 and 43 years old attending a fertility clinic in New York City. An exploratory metagenomic analysis was performed and detection of CRESS-DNA viruses was confirmed through analysis of near full-length sequences of the viral isolates. A phylogenetic tree was based on the REP open reading frame sequences of the CRESS-DNA virus genome. Eleven nearly complete CRESS-DNA viral genomes were identified in 16 (57.1%) women. There were no associations between the presence of these viruses and any demographic or clinical parameters. Phylogenetic analysis indicated that one of the sequences belonged to the genus Gemycircularvirus within the Genomoviridae family, while ten sequences represented previously unclassified species of CRESS-DNA viruses. Novel species of CRESS-DNA viruses are present in the vaginal tract of adult women. Although they be transient commensal agents, the potential clinical implications for their presence at this site cannot be dismissed.
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Affiliation(s)
- Endrya do Socorro Foro Ramos
- Laboratório de diversidade Viral, Instituto de Ciências Biológicas, Departamento de Virologia, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Tania Regina Tozetto-Mendoza
- Laboratório de Investigação Médica em Virologia (LIM52), Department of Infectology and Tropical Medicine, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Pietro Bortoletto
- Fertility department, Boston IVF-The Eugin Group, Waltham, Massachusetts, USA
- Medicine department, Harvard Medical School, Boston, Massachusetts, USA
- Department of Obstetrics and Gynecology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Noely Evangelista Ferreira
- Laboratório de Investigação Médica em Virologia (LIM52), Department of Infectology and Tropical Medicine, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Layla Honorato
- Laboratório de Investigação Médica em Virologia (LIM52), Department of Infectology and Tropical Medicine, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Erick Matheus Garcia Barbosa
- Laboratório de Investigação Médica em Virologia (LIM52), Department of Infectology and Tropical Medicine, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Adriana Luchs
- Virology department, Enteric Diseases Laboratory, Virology Center, Adolfo Lutz Institute, São Paulo, Sao Paulo, Brazil
| | - Iara M Linhares
- Department of Gynecology and Obstetrics, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Steven D Spandorfer
- Department of Gynecology and Obstetrics, Center for Reproductive Medicine and Infertility, Weill Cornell Medicine, New York City, New York, USA
| | - Elcio Leal
- Laboratório de diversidade Viral, Instituto de Ciências Biológicas, Departamento de Virologia, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Antonio Charlys da Costa
- Laboratório de Investigação Médica em Virologia (LIM52), Department of Infectology and Tropical Medicine, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Steven S Witkin
- Laboratório de Investigação Médica em Virologia (LIM52), Department of Infectology and Tropical Medicine, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York City, New York, USA
| | - Maria Cassia Mendes-Correa
- Laboratório de Investigação Médica em Virologia (LIM52), Department of Infectology and Tropical Medicine, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
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2
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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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3
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Tong P, Wang Z, Dang Y, Zhang L, Song G, Song X, Pan J, Kuang L, Li J, Lu G, Xie J. Donkey-like kirkovirus is associated with diarrhea in piglets. Virus Genes 2024; 60:314-319. [PMID: 38526778 DOI: 10.1007/s11262-024-02066-7] [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: 01/19/2024] [Accepted: 03/10/2024] [Indexed: 03/27/2024]
Abstract
Kirkovirus (kirV), a seemingly novel virus family, has been found in horses and donkeys. The study's objectives are to investigate the presence of the virus in swine. In this study, donkey-like kirV was detected in rectal swabs of piglets with diarrhea, and the positive rate was found to be 100% (149/149). However, this virus was detected in only one of 261 clinically healthy piglets, which suggested a strong relationship between the kirV and the diarrheic disease. We obtained the whole-genome sequences of three kirVs (Cj-D5, Cj-D32, and Cj-D43), with a length of 3750 nucleotides (nt) and sharing 99.9% nt identity with donkey kirVs. Furthermore, the three viruses shared 88.5-100% and 23-51% of the Rep protein sequence, similar to available reference strains of Kirkoviridae and Circoviridae, respectively. Moreover, like horse and donkey kirVs, the RCR domain and P-loop NTPase domains of Rep protein and nonanucleotide motif (CAATATTAC) of the three viruses were similar to those of Circoviruses and Cycloviruses. Phylogenetic analysis showed that these viruses could be grouped with members in the proposed family Kirkoviridae. This is the first report to describe that kirV can circulate in piglets with diarrhea, and future studies are needed to determine the pathogenesis of this virus.
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Affiliation(s)
- Panpan Tong
- Xinjiang Key Laboratory of Herbivore Drug Research and Creation, College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, 830052, China
| | - Zunbao Wang
- College of Veterinary Medicine, Jilin University, Changchun, 130062, China
- Tecon Bio-Technology Co, LTD, Urumqi, 830032, China
| | - Yueyi Dang
- Xinjiang Key Laboratory of Herbivore Drug Research and Creation, College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, 830052, China
| | - Lei Zhang
- Aksu Regional Animal Disease Control and Diagnostic Center, Aksu, 843000, China
| | | | - Xiaozhen Song
- People's Government of Ziniquanzi Town, Ziniquanzi, 831502, China
| | - Juanjuan Pan
- Xinjiang Key Laboratory of Herbivore Drug Research and Creation, College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, 830052, China
| | - Ling Kuang
- Xinjiang Key Laboratory of Herbivore Drug Research and Creation, College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, 830052, China
| | - Junhui Li
- Tecon Bio-Technology Co, LTD, Urumqi, 830032, China.
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, China.
| | - Gang Lu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.
| | - Jinxin Xie
- Xinjiang Key Laboratory of Herbivore Drug Research and Creation, College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, 830052, China.
- Institute of Western Agriculture, The Chinese Academy of Agricultural Sciences, Changji, 831100, China.
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4
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Cao X, Tang L, Song J. Circular Single-Stranded DNA: Discovery, Biological Effects, and Applications. ACS Synth Biol 2024; 13:1038-1058. [PMID: 38501391 DOI: 10.1021/acssynbio.4c00040] [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: 03/20/2024]
Abstract
The field of nucleic acid therapeutics has witnessed a significant surge in recent times, as evidenced by the increasing number of approved genetic drugs. However, current platform technologies containing plasmids, lipid nanoparticle-mRNAs, and adeno-associated virus vectors encounter various limitations and challenges. Thus, we are devoted to finding a novel nucleic acid vector and have directed our efforts toward investigating circular single-stranded DNA (CssDNA), an ancient form of nucleic acid. CssDNAs are ubiquitous, but generally ignored. Accumulating evidence suggests that CssDNAs possess exceptional properties as nucleic acid vectors, exhibiting great potential for clinical applications in genetic disorders, gene editing, and immune cell therapy. Here, we comprehensively review the discovery and biological effects of CssDNAs as well as their applications in the field of biomedical research for the first time. Undoubtedly, as an ancient form of DNA, CssDNA holds immense potential and promises novel insights for biomedical research.
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Affiliation(s)
- Xisen Cao
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Linlin Tang
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou 310022, China
| | - Jie Song
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou 310022, China
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5
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Clemons RA, Yacoub MN, Faust E, Toledo LF, Jenkinson TS, Carvalho T, Simmons DR, Kalinka E, Fritz-Laylin LK, James TY, Stajich JE. An endogenous DNA virus in an amphibian-killing fungus associated with pathogen genotype and virulence. Curr Biol 2024; 34:1469-1478.e6. [PMID: 38490202 DOI: 10.1016/j.cub.2024.02.062] [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: 04/04/2023] [Revised: 12/18/2023] [Accepted: 02/26/2024] [Indexed: 03/17/2024]
Abstract
The global panzootic lineage (GPL) of the pathogenic fungus Batrachochytrium dendrobatidis (Bd) has caused severe amphibian population declines, yet the drivers underlying the high frequency of GPL in regions of amphibian decline are unclear. Using publicly available Bd genome sequences, we identified multiple non-GPL Bd isolates that contain a circular Rep-encoding single-stranded (CRESS)-like DNA virus, which we named Bd DNA virus 1 (BdDV-1). We further sequenced and constructed genome assemblies with long read sequences to find that the virus is integrated into the nuclear genome in some strains. Attempts to cure virus-positive isolates were unsuccessful; however, phenotypic differences between naturally virus-positive and virus-negative Bd isolates suggested that BdDV-1 decreases the growth of its host in vitro but increases the virulence of its host in vivo. BdDV-1 is the first-described CRESS DNA mycovirus of zoosporic true fungi, with a distribution inversely associated with the emergence of the panzootic lineage.
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Affiliation(s)
- Rebecca A Clemons
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Mark N Yacoub
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA 92521, USA
| | - Evelyn Faust
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - L Felipe Toledo
- Laboratório de História Natural de Anfíbios Brasileiros (LaHNAB), Departamento de Biologia Animal Instituto de Biologia (IB), Universidade Estadual de Campinas, Campinas, SP 13083-862, Brazil
| | - Thomas S Jenkinson
- Department of Biological Sciences, California State University, East Bay, Hayward, CA 94592, USA
| | - Tamilie Carvalho
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - D Rabern Simmons
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Erik Kalinka
- Department of Biology, University of Massachusetts, Amherst, Amherst, MA 01003, USA
| | | | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA 92521, USA.
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6
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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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Reyes NS, Spezia PG, Jara R, Filippini F, Boccia N, García G, Hermida E, Poletta FA, Pistello M, Laham G, Maggi F, Echavarria M. Torque Teno Virus (TTV) in Renal Transplant Recipients: Species Diversity and Variability. Viruses 2024; 16:432. [PMID: 38543797 PMCID: PMC10974959 DOI: 10.3390/v16030432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 02/26/2024] [Accepted: 02/28/2024] [Indexed: 05/23/2024] Open
Abstract
Torque Teno Virus (TTV) is a nonpathogenic and ubiquitous ssDNA virus, a member of the Anelloviridae family. TTV has been postulated as a biomarker in transplant patients. This study aimed to determine the TTV species diversity and variability in renal transplant recipients and to associate species diversity with the corresponding TTV viral load. From 27 recipients, 30 plasma samples were selected. Viral load was determined using two real-time PCR assays, followed by RCA-NGS and ORF1 phylogenetic analysis. The TTV diversity was determined in all samples. Variability was determined in three patients with two sequential samples (pre- and post-transplantation). Most of the samples presented multiple TTV species, up to 15 different species were detected. In the pre-transplant samples (n = 12), the most prevalent species were TTV3 (75%) and TTV13 (75%), and the median number of species per sample was 5 (IQR: 4-7.5). TTV3 was also the most prevalent (56%) in the post-transplant samples (n = 18), and the median number of species was 2 (IQR: 1.8-5.5). No significant correlation between the number of species and viral load was found. The number and type of TTV species showed total variability over time. We report high TTV species diversity in Argentinian recipients, especially in pre-transplant period, with total intra-host variability. However, we found no significant correlation between this high diversity and TTV viral load.
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Affiliation(s)
- Noelia Soledad Reyes
- Virology Unit, Centro de Educación Médica e Investigaciones Clínicas (CEMIC) University Hospital, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Galván 4102, Buenos Aires C1631FWO, Argentina; (R.J.); (E.H.); (M.E.)
| | - Pietro Giorgio Spezia
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani—IRCCS, 00149 Rome, Italy;
| | - Raquel Jara
- Virology Unit, Centro de Educación Médica e Investigaciones Clínicas (CEMIC) University Hospital, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Galván 4102, Buenos Aires C1631FWO, Argentina; (R.J.); (E.H.); (M.E.)
| | - Fabio Filippini
- Department of Translational Research, University of Pisa, 56127 Pisa, Italy; (F.F.); (M.P.)
| | - Natalia Boccia
- Department of Nephrology, Centro de Educación Médica e Investigaciones Clínicas (CEMIC) University Hospital, Buenos Aires C1631FWO, Argentina; (N.B.); (G.G.); (G.L.)
| | - Gonzalo García
- Department of Nephrology, Centro de Educación Médica e Investigaciones Clínicas (CEMIC) University Hospital, Buenos Aires C1631FWO, Argentina; (N.B.); (G.G.); (G.L.)
| | - Eliana Hermida
- Virology Unit, Centro de Educación Médica e Investigaciones Clínicas (CEMIC) University Hospital, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Galván 4102, Buenos Aires C1631FWO, Argentina; (R.J.); (E.H.); (M.E.)
| | - Fernando Adrian Poletta
- Genetic Epidemiology Laboratory, Centro de Educación Médica e Investigaciones Clínicas (CEMIC) University Hospital, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1631FWO, Argentina;
| | - Mauro Pistello
- Department of Translational Research, University of Pisa, 56127 Pisa, Italy; (F.F.); (M.P.)
| | - Gustavo Laham
- Department of Nephrology, Centro de Educación Médica e Investigaciones Clínicas (CEMIC) University Hospital, Buenos Aires C1631FWO, Argentina; (N.B.); (G.G.); (G.L.)
| | - Fabrizio Maggi
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani—IRCCS, 00149 Rome, Italy;
| | - Marcela Echavarria
- Virology Unit, Centro de Educación Médica e Investigaciones Clínicas (CEMIC) University Hospital, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Galván 4102, Buenos Aires C1631FWO, Argentina; (R.J.); (E.H.); (M.E.)
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8
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Tarján ZL, Szekeres S, Vidovszky MZ, Egyed L. Detection of circovirus in free-ranging brown rats (Rattus norvegicus). INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 118:105548. [PMID: 38176604 DOI: 10.1016/j.meegid.2023.105548] [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: 10/31/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 01/06/2024]
Abstract
Accidentally found, two poisoned brown rats from Hungary were surveyed for presence of circoviral DNA, using specific nested primers, designed against the rep gene of the virus. Both specimens were positive. The whole genomes were amplified using inverse PCR based on the Rep sequence parts and sequenced by the primer walking method. Genomic analyses revealed that these novel rat viruses, together with tawny owl-associated circovirus reported by Italian researchers in 2022, are sequence variations of the same virus from genus Circovirus. In phylogenetic reconstructions, these circovirus strains detected from brown rats clustered closest to circoviruses derived from faeces samples of various predatory mammals. Molecular data as well as the phylogenetic analyses of the complete derived replication-associated protein and the capsid protein, as well as the prey preference of the host species of the recently described tawny owl-associated virus suggest that brown rat could be the evolutionary adapted host of the viruses described in this paper (brown rat circovirus types 1 and 2) and the previously reported tawny owl-associated virus. Possible pathogenic and zoonotic role of these viruses need further studies.
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Affiliation(s)
- Z L Tarján
- HUN-REN Veterinary Medical Research Institute, Budapest, Hungary
| | - S Szekeres
- Department of Parasitology and Zoology, University of Veterinary Medicine, Budapest, Hungary; HUN-REN-UVMB Climate Change: New Blood-Sucking Parasites and Vector-Borne Pathogens Research Group, Budapest, Hungary
| | - M Z Vidovszky
- HUN-REN Veterinary Medical Research Institute, Budapest, Hungary
| | - L Egyed
- HUN-REN Veterinary Medical Research Institute, Budapest, Hungary.
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Nadeem S, Riaz Ahmed S, Luqman T, Tan DKY, Maryum Z, Akhtar KP, Muhy Ud Din Khan S, Tariq MS, Muhammad N, Khan MKR, Liu Y. A comprehensive review on Gossypium hirsutum resistance against cotton leaf curl virus. Front Genet 2024; 15:1306469. [PMID: 38440193 PMCID: PMC10909863 DOI: 10.3389/fgene.2024.1306469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 02/01/2024] [Indexed: 03/06/2024] Open
Abstract
Cotton (Gossypium hirsutum L.) is a significant fiber crop. Being a major contributor to the textile industry requires continuous care and attention. Cotton is subjected to various biotic and abiotic constraints. Among these, biotic factors including cotton leaf curl virus (CLCuV) are dominant. CLCuV is a notorious disease of cotton and is acquired, carried, and transmitted by the whitefly (Bemisia tabaci). A cotton plant affected with CLCuV may show a wide range of symptoms such as yellowing of leaves, thickening of veins, upward or downward curling, formation of enations, and stunted growth. Though there are many efforts to protect the crop from CLCuV, long-term results are not yet obtained as CLCuV strains are capable of mutating and overcoming plant resistance. However, systemic-induced resistance using a gene-based approach remained effective until new virulent strains of CLCuV (like Cotton Leaf Curl Burewala Virus and others) came into existence. Disease control by biological means and the development of CLCuV-resistant cotton varieties are in progress. In this review, we first discussed in detail the evolution of cotton and CLCuV strains, the transmission mechanism of CLCuV, the genetic architecture of CLCuV vectors, and the use of pathogen and nonpathogen-based approaches to control CLCuD. Next, we delineate the uses of cutting-edge technologies like genome editing (with a special focus on CRISPR-Cas), next-generation technologies, and their application in cotton genomics and speed breeding to develop CLCuD resistant cotton germplasm in a short time. Finally, we delve into the current obstacles related to cotton genome editing and explore forthcoming pathways for enhancing precision in genome editing through the utilization of advanced genome editing technologies. These endeavors aim to enhance cotton's resilience against CLCuD.
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Affiliation(s)
- Sahar Nadeem
- Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Faisalabad, Pakistan
| | - Syed Riaz Ahmed
- Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Faisalabad, Pakistan
- Pakistan Agriculture Research Council (PARC), Horticulture Research Institute Khuzdar Baghbana, Khuzdar, Pakistan
| | - Tahira Luqman
- Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Faisalabad, Pakistan
| | - Daniel K. Y. Tan
- School of Life and Environmental Sciences, Plant Breeding Institute, Sydney Institute of Agriculture, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
| | - Zahra Maryum
- Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Faisalabad, Pakistan
| | - Khalid Pervaiz Akhtar
- Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Faisalabad, Pakistan
| | - Sana Muhy Ud Din Khan
- Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Faisalabad, Pakistan
| | - Muhammad Sayyam Tariq
- Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Faisalabad, Pakistan
| | - Nazar Muhammad
- Agriculture and Cooperative Department, Quetta, Pakistan
| | - Muhammad Kashif Riaz Khan
- Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Faisalabad, Pakistan
- Plant Breeding and Genetics Division, Cotton Group, Nuclear Institute for Agriculture and Biology, Faisalabad, Pakistan
| | - Yongming Liu
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, China
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Zhu Q, Qi S, Guo D, Li C, Su M, Wang J, Li Z, Yang D, Sun H, Wang X, Wang M, Wu H, Yu S, Bai W, Zhang Y, Yang X, Jiang L, Liu J, Zhao Y, Xing X, Shi D, Feng L, Sun D. A survey of fecal virome and bacterial community of the diarrhea-affected cattle in northeast China reveals novel disease-associated ecological risk factors. mSystems 2024; 9:e0084223. [PMID: 38108282 PMCID: PMC10804951 DOI: 10.1128/msystems.00842-23] [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] [Received: 08/10/2023] [Accepted: 11/06/2023] [Indexed: 12/19/2023] Open
Abstract
Limited information on the virome and bacterial community hampers our ability to discern systemic ecological risk factors that cause cattle diarrhea, which has become a pressing issue in the control of disease. A total of 110 viruses, 1,011 bacterial genera, and 322 complete viral genomes were identified from 70 sequencing samples mixed with 1,120 fecal samples from 58 farms in northeast China. For the diarrheic samples, the identified virome and bacterial community varied in terms of composition, abundance, diversity, and geographic distribution in relation to different disease-associated ecological factors; the abundance of identified viruses and bacteria was significantly correlated with the host factors of clinical status, cattle type, and age, and with environmental factors such as aquaculture model and geographical location (P < 0.05); a significant interaction occurred between viruses and viruses, bacteria and bacteria, as well as between bacteria and viruses (P < 0.05). The abundance of SMB53, Butyrivibrio, Facklamia, Trichococcus, and Turicibacter was significantly correlated with the health status of cattle (P < 0.05). The proportion of BRV, BCoV, BKV, BToV, BoNoV, BoNeV, BoAstV, BEV, BoPV, and BVDV in 1,120 fecal samples varied from 1.61% to 12.05%. A series of significant correlations were observed between the prevalence of individual viruses and the disease-associated ecological factors. A genome-based phylogenetic analysis revealed high variability of 10 bovine enteric viruses. The bovine hungarovirus was initially identified in both dairy and beef cattle in China. This study elucidates the fecal virome and bacterial community signatures of cattle affected by diarrhea, and reveals novel disease-associated ecological risk factors, including cattle type, cattle age, aquaculture model, and geographical location.IMPORTANCEThe lack of data on the virome and bacterial community restricts our capability to recognize ecological risk factors for bovine diarrhea disease, thereby hindering our overall comprehension of the disease's cause. In this study, we found that, for the diarrheal samples, the identified virome and bacterial community varied in terms of composition, abundance, diversity, configuration, and geographic distribution in relation to different disease-associated ecological factors. A series of significant correlations were observed between the prevalence of individual viruses and the disease-associated ecological factors. Our study aims to uncover novel ecological risk factors of bovine diarrheal disease by examining the pathogenic microorganism-host-environment disease ecology, thereby providing a new perspective on the control of bovine diarrheal diseases.
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Affiliation(s)
- Qinghe Zhu
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Shanshan Qi
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Donghua Guo
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Chunqiu Li
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Mingjun Su
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Jianfa Wang
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Zijian Li
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Dan Yang
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Haibo Sun
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Xiaoran Wang
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Meijiao Wang
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Haoyang Wu
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Shiping Yu
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Wenfei Bai
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Yongchen Zhang
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Xu Yang
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Limin Jiang
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Jiaying Liu
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Yingying Zhao
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Xiaoxu Xing
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Da Shi
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Li Feng
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Dongbo Sun
- Key Laboratory of Bovine Disease Control in Northeast China, Ministry of Agriculture and Rural affairs of the People’s Republic of China, Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
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11
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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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12
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Cui Y, Li S, Xu W, Li Y, Xie J, Wang D, Guo J, Zhou J, Feng X, Hou L, Liu J. A Receptor Integrin β1 Promotes Infection of Avian Metapneumovirus Subgroup C by Recognizing a Viral Fusion Protein RSD Motif. Int J Mol Sci 2024; 25:829. [PMID: 38255903 PMCID: PMC10815723 DOI: 10.3390/ijms25020829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 12/30/2023] [Accepted: 01/06/2024] [Indexed: 01/24/2024] Open
Abstract
Avian metapneumovirus subgroup C (aMPV/C) causes respiratory diseases and egg dropping in chickens and turkeys, resulting in severe economic losses to the poultry industry worldwide. Integrin β1 (ITGB1), a transmembrane cell adhesion molecule, is present in various cells and mediates numerous viral infections. Herein, we demonstrate that ITGB1 is essential for aMPV/C infection in cultured DF-1 cells, as evidenced by the inhibition of viral binding by EDTA blockade, Arg-Ser-Asp (RSD) peptide, monoclonal antibody against ITGB1, and ITGB1 short interfering (si) RNA knockdown in cultured DF-1 cells. Simulation of the binding process between the aMPV/C fusion (F) protein and avian-derived ITGB1 using molecular dynamics showed that ITGB1 may be a host factor benefiting aMPV/C attachment or internalization. The transient expression of avian ITGB1-rendered porcine and feline non-permissive cells (DQ cells and CRFK cells, respectively) is susceptible to aMPV/C infection. Kinetic replication of aMPV/C in siRNA-knockdown cells revealed that ITGB1 plays an important role in aMPV/C infection at the early stage (attachment and internalization). aMPV/C was also able to efficiently infect human non-small cell lung cancer (A549) cells. This may be a consequence of the similar structures of both metapneumovirus F protein-specific motifs (RSD for aMPV/C and RGD for human metapneumovirus) recognized by ITGB1. Overexpression of avian-derived ITGB1 and human-derived ITGB1 in A549 cells enhanced aMPV/C infectivity. Taken together, this study demonstrated that ITGB1 acts as an essential receptor for aMPV/C attachment and internalization into host cells, facilitating aMPV/C infection.
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Affiliation(s)
- Yongqiu Cui
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (Y.C.); (S.L.); (W.X.); (Y.L.); (J.X.); (D.W.); (J.G.); (J.Z.); (X.F.)
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Siting Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (Y.C.); (S.L.); (W.X.); (Y.L.); (J.X.); (D.W.); (J.G.); (J.Z.); (X.F.)
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Weiyin Xu
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (Y.C.); (S.L.); (W.X.); (Y.L.); (J.X.); (D.W.); (J.G.); (J.Z.); (X.F.)
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Yeqiu Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (Y.C.); (S.L.); (W.X.); (Y.L.); (J.X.); (D.W.); (J.G.); (J.Z.); (X.F.)
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Jiali Xie
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (Y.C.); (S.L.); (W.X.); (Y.L.); (J.X.); (D.W.); (J.G.); (J.Z.); (X.F.)
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Dedong Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (Y.C.); (S.L.); (W.X.); (Y.L.); (J.X.); (D.W.); (J.G.); (J.Z.); (X.F.)
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Jinshuo Guo
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (Y.C.); (S.L.); (W.X.); (Y.L.); (J.X.); (D.W.); (J.G.); (J.Z.); (X.F.)
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Jianwei Zhou
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (Y.C.); (S.L.); (W.X.); (Y.L.); (J.X.); (D.W.); (J.G.); (J.Z.); (X.F.)
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Xufei Feng
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (Y.C.); (S.L.); (W.X.); (Y.L.); (J.X.); (D.W.); (J.G.); (J.Z.); (X.F.)
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Lei Hou
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (Y.C.); (S.L.); (W.X.); (Y.L.); (J.X.); (D.W.); (J.G.); (J.Z.); (X.F.)
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Jue Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (Y.C.); (S.L.); (W.X.); (Y.L.); (J.X.); (D.W.); (J.G.); (J.Z.); (X.F.)
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
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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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Yan D, Han K, Lu Y, Peng J, Rao S, Wu G, Liu Y, Chen J, Zheng H, Yan F. The nanovirus U2 protein suppresses RNA silencing via three conserved cysteine residues. MOLECULAR PLANT PATHOLOGY 2024; 25:e13394. [PMID: 37823358 PMCID: PMC10782648 DOI: 10.1111/mpp.13394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 09/19/2023] [Accepted: 09/19/2023] [Indexed: 10/13/2023]
Abstract
Nanoviruses have multipartite, circular, single-stranded DNA genomes and cause huge production losses in legumes and other crops. No viral suppressor of RNA silencing (VSR) has yet been reported from a member of the genus Nanovirus. Here, we demonstrate that the nanovirus U2 protein is a VSR. The U2 protein of milk vetch dwarf virus (MDV) suppressed the silencing of the green fluorescent protein (GFP) gene induced by single-stranded and double-stranded RNA, and the systemic spread of the GFP silencing signal. An electrophoretic mobility shift assay showed that the U2 protein was able to bind double-stranded 21-nucleotide small interfering RNA (siRNA). The cysteine residues at positions 43, 79 and 82 in the MDV U2 protein are critical to its nuclear localization, self-interaction and siRNA-binding ability, and were essential for its VSR activity. In addition, expression of the U2 protein via a potato virus X vector induced more severe necrosis symptoms in Nicotiana benthamiana leaves. The U2 proteins of other nanoviruses also acted as VSRs, and the three conserved cysteine residues were indispensable for their VSR activity.
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Affiliation(s)
- Dankan Yan
- College of Life SciencesFujian Agriculture and Forestry UniversityFuzhouChina
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐Products, Institute of Plant VirologyNingbo UniversityNingboChina
- Institute of Plant Protection and Agro‐Products SafetyAnhui Academy of Agricultural SciencesHefeiChina
| | - Kelei Han
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐Products, Institute of Plant VirologyNingbo UniversityNingboChina
- Institute of Plant Protection and Agro‐Products SafetyAnhui Academy of Agricultural SciencesHefeiChina
| | - Yuwen Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐Products, Institute of Plant VirologyNingbo UniversityNingboChina
| | - Jiejun Peng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐Products, Institute of Plant VirologyNingbo UniversityNingboChina
| | - Shaofei Rao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐Products, Institute of Plant VirologyNingbo UniversityNingboChina
| | - Guanwei Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐Products, Institute of Plant VirologyNingbo UniversityNingboChina
| | - Yong Liu
- Institute of Plant ProtectionHunan Academy of Agricultural SciencesChangshaChina
| | - Jianping Chen
- College of Life SciencesFujian Agriculture and Forestry UniversityFuzhouChina
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐Products, Institute of Plant VirologyNingbo UniversityNingboChina
| | - Hongying Zheng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐Products, Institute of Plant VirologyNingbo UniversityNingboChina
| | - Fei Yan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐Products, Institute of Plant VirologyNingbo UniversityNingboChina
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15
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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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16
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Nery FMB, Batista JG, Melo FFS, Ribeiro SG, Boiteux LS, Melo FL, Silva JGI, Reis LDNA, Pereira-Carvalho RC. Novel plant-associated genomoviruses from the Brazilian Cerrado biome. Arch Virol 2023; 168:286. [PMID: 37940763 DOI: 10.1007/s00705-023-05892-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 08/19/2023] [Indexed: 11/10/2023]
Abstract
The discovery rate of new plant viruses has increased due to studies involving high-throughput sequencing (HTS), particularly for single-stranded DNA viruses of the family Genomoviridae. We carried out an HTS-based survey of genomoviruses in a wide range of native and exotic trees grown in the Brazilian Cerrado biome, and the complete genome sequences of two novel members of the family Genomoviridae from two distinct genera were determined. Specific primers were designed to detect these genomoviruses in individual samples. A new gemykolovirus (Tecoma stans associated gemykolovirus) was detected in Tecoma stans, and a new gemykibivirus (Ouratea duparquetiana associated gemykibivirus) was detected in Ouratea duparquetiana. A gemykrogvirus related to Gila monster associated gemykrogvirus (80% pairwise identity) was also detected in foliar samples of Trembleya parviflora. Our pilot study paves the way for a better characterization of this diverse collection of genomoviruses as well as their interactions with the associated tree species.
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Affiliation(s)
- Flávia Milene B Nery
- Departamento de Fitopatologia, Universidade de Brasília (UnB), Campus Universitário Darcy Ribeiro, Brasília, DF, 70910-900, Brazil
| | - Josiane G Batista
- Departamento de Fitopatologia, Universidade de Brasília (UnB), Campus Universitário Darcy Ribeiro, Brasília, DF, 70910-900, Brazil
| | - Felipe Fochat S Melo
- Departamento de Fitopatologia, Universidade de Brasília (UnB), Campus Universitário Darcy Ribeiro, Brasília, DF, 70910-900, Brazil
| | - Simone G Ribeiro
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, 70770-017, Brazil
| | - Leonardo S Boiteux
- Embrapa Vegetable Crops (Hortaliças), National Center for Vegetable Crops Research (CNPH), Brasília, DF, 70275-970, Brazil
| | - Fernando L Melo
- Departamento de Fitopatologia, Universidade de Brasília (UnB), Campus Universitário Darcy Ribeiro, Brasília, DF, 70910-900, Brazil
| | - Juliana Gabrielle I Silva
- Departamento de Fitopatologia, Universidade de Brasília (UnB), Campus Universitário Darcy Ribeiro, Brasília, DF, 70910-900, Brazil
| | - Luciane de Nazaré A Reis
- Departamento de Fitopatologia, Universidade de Brasília (UnB), Campus Universitário Darcy Ribeiro, Brasília, DF, 70910-900, Brazil
| | - Rita C Pereira-Carvalho
- Departamento de Fitopatologia, Universidade de Brasília (UnB), Campus Universitário Darcy Ribeiro, Brasília, DF, 70910-900, Brazil.
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17
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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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18
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Gomes RAL, Zerbini FM. ConCreT, a 2D convolutional neural network for taxonomic classification applied to viruses in the phylum Cressdnaviricota. J Virol Methods 2023; 320:114789. [PMID: 37536450 DOI: 10.1016/j.jviromet.2023.114789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 07/19/2023] [Accepted: 07/31/2023] [Indexed: 08/05/2023]
Abstract
Taxonomic assignments allow scientists to communicate better with each other. In virology, taxonomy is continually improving towards a more precise and comprehensive framework. With the huge numbers of new viruses being described in metagenomic studies, automated taxonomy tools are urgently needed. A number of such tools have been proposed, and those applying machine learning (ML), mainly in the deep learning branch, stand out with accurate results. Still, there is a demand for tools that are less computationally intensive and that can classify viruses down to the ranks of genus and species. Cressdnaviruses are good subjects for testing such tools, due to their small, circular genomes and the existence of several families and genera with a highly imbalanced number of species. We developed a 2D convolutional neural network for virus taxonomy and tested it for classification of viruses from the phylum Cressdnaviricota. We obtained >98 % accuracy in the final pipeline tested, which we named ConCreT (Convolutional Neural Network for Cressdnavirus Taxonomy). The mixture of augmentation for more imbalanced groups with no augmentation for more balanced ones achieved the best score in the final test.
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Affiliation(s)
- Ruither A L Gomes
- Dep. de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil; National Institute for Science and Technology on Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - F Murilo Zerbini
- Dep. de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil; National Institute for Science and Technology on Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil.
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19
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Williams RAJ, Sánchez-Llatas CJ, Doménech A, Madrid R, Fandiño S, Cea-Callejo P, Gomez-Lucia E, Benítez L. Emerging and Novel Viruses in Passerine Birds. Microorganisms 2023; 11:2355. [PMID: 37764199 PMCID: PMC10536639 DOI: 10.3390/microorganisms11092355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/13/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
There is growing interest in emerging viruses that can cause serious or lethal disease in humans and animals. The proliferation of cloacal virome studies, mainly focused on poultry and other domestic birds, reveals a wide variety of viruses, although their pathogenic significance is currently uncertain. Analysis of viruses detected in wild birds is complex and often biased towards waterfowl because of the obvious interest in avian influenza or other zoonotic viruses. Less is known about the viruses present in the order Passeriformes, which comprises approximately 60% of extant bird species. This review aims to compile the most significant contributions on the DNA/RNA viruses affecting passerines, from traditional and metagenomic studies. It highlights that most passerine species have never been sampled. Especially the RNA viruses from Flaviviridae, Orthomyxoviridae and Togaviridae are considered emerging because of increased incidence or avian mortality/morbidity, spread to new geographical areas or hosts and their zoonotic risk. Arguably poxvirus, and perhaps other virus groups, could also be considered "emerging viruses". However, many of these viruses have only recently been described in passerines using metagenomics and their role in the ecosystem is unknown. Finally, it is noteworthy that only one third of the viruses affecting passerines have been officially recognized.
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Affiliation(s)
- Richard A. J. Williams
- Department of Genetics, Physiology, and Microbiology, School of Biology, Complutense University of Madrid (UCM), C. de José Antonio Nováis, 12, 28040 Madrid, Spain; (C.J.S.-L.); (R.M.); (P.C.-C.); (L.B.)
- “Animal Viruses” Research Group, Complutense University of Madrid, 28040 Madrid, Spain; (A.D.); (S.F.); (E.G.-L.)
| | - Christian J. Sánchez-Llatas
- Department of Genetics, Physiology, and Microbiology, School of Biology, Complutense University of Madrid (UCM), C. de José Antonio Nováis, 12, 28040 Madrid, Spain; (C.J.S.-L.); (R.M.); (P.C.-C.); (L.B.)
| | - Ana Doménech
- “Animal Viruses” Research Group, Complutense University of Madrid, 28040 Madrid, Spain; (A.D.); (S.F.); (E.G.-L.)
- Deparment of Animal Health, Veterinary Faculty, Complutense University of Madrid, Av. Puerta de Hierro, s/n, 28040 Madrid, Spain
| | - Ricardo Madrid
- Department of Genetics, Physiology, and Microbiology, School of Biology, Complutense University of Madrid (UCM), C. de José Antonio Nováis, 12, 28040 Madrid, Spain; (C.J.S.-L.); (R.M.); (P.C.-C.); (L.B.)
- “Animal Viruses” Research Group, Complutense University of Madrid, 28040 Madrid, Spain; (A.D.); (S.F.); (E.G.-L.)
| | - Sergio Fandiño
- “Animal Viruses” Research Group, Complutense University of Madrid, 28040 Madrid, Spain; (A.D.); (S.F.); (E.G.-L.)
- Deparment of Animal Health, Veterinary Faculty, Complutense University of Madrid, Av. Puerta de Hierro, s/n, 28040 Madrid, Spain
| | - Pablo Cea-Callejo
- Department of Genetics, Physiology, and Microbiology, School of Biology, Complutense University of Madrid (UCM), C. de José Antonio Nováis, 12, 28040 Madrid, Spain; (C.J.S.-L.); (R.M.); (P.C.-C.); (L.B.)
- “Animal Viruses” Research Group, Complutense University of Madrid, 28040 Madrid, Spain; (A.D.); (S.F.); (E.G.-L.)
| | - Esperanza Gomez-Lucia
- “Animal Viruses” Research Group, Complutense University of Madrid, 28040 Madrid, Spain; (A.D.); (S.F.); (E.G.-L.)
- Deparment of Animal Health, Veterinary Faculty, Complutense University of Madrid, Av. Puerta de Hierro, s/n, 28040 Madrid, Spain
| | - Laura Benítez
- Department of Genetics, Physiology, and Microbiology, School of Biology, Complutense University of Madrid (UCM), C. de José Antonio Nováis, 12, 28040 Madrid, Spain; (C.J.S.-L.); (R.M.); (P.C.-C.); (L.B.)
- “Animal Viruses” Research Group, Complutense University of Madrid, 28040 Madrid, Spain; (A.D.); (S.F.); (E.G.-L.)
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20
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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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21
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Kane Y, Chen J, Li L, Descorps-Declère S, Wong G, Berthet N. Diverse single-stranded DNA viruses from viral metagenomics on a cynopterus bat in China. Heliyon 2023; 9:e18270. [PMID: 37520955 PMCID: PMC10374907 DOI: 10.1016/j.heliyon.2023.e18270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/06/2023] [Accepted: 07/12/2023] [Indexed: 08/01/2023] Open
Abstract
Bats serve as reservoirs for many emerging viruses. Cressdnaviruses can infect a wide range of animals, including agricultural species, such as pigs, in which porcine circoviruses cause severe gastroenteritis. New cressdnaviruses have also attracted considerable attention recently, due to their involvement with infectious diseases. However, little is known about their host range and many cressdnaviruses remain poorly characterized. We identified and characterized 11 contigs consisting of previously unknown cressdnaviruses from a rectal swab sample of a Cynopterus bat collected in Yunnan Province, China, in 2011. Full genomes of two cressdnaviruses (OQ267680, 2069 nt; OQ351951, 2382 nt), and a nearly complete genome for a third (OQ267683, 2361 nt) were obtained. Phylogenetic analyses and the characteristics of these viral genomes suggest a high degree of ssDNA virus diversity. These results shed light on cressdnavirus diversity and the probable role of Cynopterus bats as their hosts.
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Affiliation(s)
- Yakhouba Kane
- Viral Hemorrhagic Fevers Research Unit, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinping Chen
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
| | - Linmiao Li
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
| | - Stéphane Descorps-Declère
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015 Paris, France
| | - Gary Wong
- Viral Hemorrhagic Fevers Research Unit, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
| | - Nicolas Berthet
- Centre for Microbes, Development and Health, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Discovery and Molecular Characterization of Pathogens Unit, Shanghai 200031, China
- Institut Pasteur, Unité Environnement et Risque Infectieux, Cellule D’Intervention Biologique D’Urgence, 75015 Paris, France
- Institut Pasteur, Université Paris-Cité, Unité Epidémiologie et Physiopathologie des Virus Oncogènes, 75724 Paris, France
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22
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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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23
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Fomsgaard AS, Tahas SA, Spiess K, Polacek C, Fonager J, Belsham GJ. Unbiased Virus Detection in a Danish Zoo Using a Portable Metagenomic Sequencing System. Viruses 2023; 15:1399. [PMID: 37376698 DOI: 10.3390/v15061399] [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: 05/12/2023] [Revised: 06/16/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
Metagenomic next-generation sequencing (mNGS) is receiving increased attention for the detection of new viruses and infections occurring at the human-animal interface. The ability to actively transport and relocate this technology enables in situ virus identification, which could reduce response time and enhance disease management. In a previous study, we developed a straightforward mNGS procedure that greatly enhances the detection of RNA and DNA viruses in human clinical samples. In this study, we improved the mNGS protocol with transportable battery-driven equipment for the portable, non-targeted detection of RNA and DNA viruses in animals from a large zoological facility, to simulate a field setting for point-of-incidence virus detection. From the resulting metagenomic data, we detected 13 vertebrate viruses from four major virus groups: (+)ssRNA, (+)ssRNA-RT, dsDNA and (+)ssDNA, including avian leukosis virus in domestic chickens (Gallus gallus), enzootic nasal tumour virus in goats (Capra hircus) and several small, circular, Rep-encoding, ssDNA (CRESS DNA) viruses in several mammal species. More significantly, we demonstrate that the mNGS method is able to detect potentially lethal animal viruses, such as elephant endotheliotropic herpesvirus in Asian elephants (Elephas maximus) and the newly described human-associated gemykibivirus 2, a human-to-animal cross-species virus, in a Linnaeus two-toed sloth (Choloepus didactylus) and its enclosure, for the first time.
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Affiliation(s)
- Anna S Fomsgaard
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, 5 Artillerivej, 2300 Copenhagen, Denmark
- Department of Veterinary and Animal Sciences, University of Copenhagen, 4 Stigboejlen, 1870 Frederiksberg, Denmark
| | | | - Katja Spiess
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, 5 Artillerivej, 2300 Copenhagen, Denmark
| | - Charlotta Polacek
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, 5 Artillerivej, 2300 Copenhagen, Denmark
| | - Jannik Fonager
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, 5 Artillerivej, 2300 Copenhagen, Denmark
| | - Graham J Belsham
- Department of Veterinary and Animal Sciences, University of Copenhagen, 4 Stigboejlen, 1870 Frederiksberg, Denmark
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Butkovic A, Kraberger S, Smeele Z, Martin DP, Schmidlin K, Fontenele RS, Shero MR, Beltran RS, Kirkham AL, Aleamotu’a M, Burns JM, Koonin EV, Varsani A, Krupovic M. Evolution of anelloviruses from a circovirus-like ancestor through gradual augmentation of the jelly-roll capsid protein. Virus Evol 2023; 9:vead035. [PMID: 37325085 PMCID: PMC10266747 DOI: 10.1093/ve/vead035] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 05/15/2023] [Accepted: 05/22/2023] [Indexed: 06/17/2023] Open
Abstract
Anelloviruses are highly prevalent in diverse mammals, including humans, but so far have not been linked to any disease and are considered to be part of the 'healthy virome'. These viruses have small circular single-stranded DNA (ssDNA) genomes and encode several proteins with no detectable sequence similarity to proteins of other known viruses. Thus, anelloviruses are the only family of eukaryotic ssDNA viruses currently not included in the realm Monodnaviria. To gain insights into the provenance of these enigmatic viruses, we sequenced more than 250 complete genomes of anelloviruses from nasal and vaginal swab samples of Weddell seal (Leptonychotes weddellii) from Antarctica and a fecal sample of grizzly bear (Ursus arctos horribilis) from the USA and performed a comprehensive family-wide analysis of the signature anellovirus protein ORF1. Using state-of-the-art remote sequence similarity detection approaches and structural modeling with AlphaFold2, we show that ORF1 orthologs from all Anelloviridae genera adopt a jelly-roll fold typical of viral capsid proteins (CPs), establishing an evolutionary link to other eukaryotic ssDNA viruses, specifically, circoviruses. However, unlike CPs of other ssDNA viruses, ORF1 encoded by anelloviruses from different genera display remarkable variation in size, due to insertions into the jelly-roll domain. In particular, the insertion between β-strands H and I forms a projection domain predicted to face away from the capsid surface and function at the interface of virus-host interactions. Consistent with this prediction and supported by recent experimental evidence, the outermost region of the projection domain is a mutational hotspot, where rapid evolution was likely precipitated by the host immune system. Collectively, our findings further expand the known diversity of anelloviruses and explain how anellovirus ORF1 proteins likely diverged from canonical jelly-roll CPs through gradual augmentation of the projection domain. We suggest assigning Anelloviridae to a new phylum, 'Commensaviricota', and including it into the kingdom Shotokuvirae (realm Monodnaviria), alongside Cressdnaviricota and Cossaviricota.
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Affiliation(s)
- Anamarija Butkovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, 25 rue du Dr Roux, Paris 75015, France
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ 85287, USA
| | - Zoe Smeele
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ 85287, USA
| | - Darren P Martin
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ 85287, USA
| | - Kara Schmidlin
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, 1001 S. McAllister Ave, 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, 1001 S. McAllister Ave, Tempe, AZ 85287, USA
| | - Michelle R Shero
- Biology Department, Woods Hole Oceanographic Institution, 266 Woods Hole Rd, Woods Hole, MA 02543, USA
| | - Roxanne S Beltran
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, 130 McAllister Way, Santa Cruz, CA 95060, USA
| | - Amy L Kirkham
- U.S. Fish and Wildlife Service, Marine Mammals Management, 1011 E, Tudor Road, Anchorage, AK 99503, USA
| | - Maketalena Aleamotu’a
- School of Environmental and Life Sciences, The University of Newcastle, University Drive, Callaghan, NSW 2308, Australia
| | - Jennifer M Burns
- Department of Biological Sciences, Texas Tech University, 2500 Broadway, Lubbock, TX 79409, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ 85287, USA
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory, 1 Anzio Road, Cape Town 7925, South Africa
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, 25 rue du Dr Roux, Paris 75015, France
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25
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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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26
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Discovery and comparative genomic analysis of a novel equine anellovirus, representing the first complete Mutorquevirus genome. Sci Rep 2023; 13:3703. [PMID: 36878942 PMCID: PMC9988894 DOI: 10.1038/s41598-023-30875-7] [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: 09/30/2022] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
The complete genome of a novel torque teno virus species (Torque teno equus virus 2 (TTEqV2) isolate Alberta/2018) was obtained by high-throughput sequencing (HTS) of nucleic acid extracted from the lung and liver tissue of a Quarter Horse gelding that died of nonsuppurative encephalitis in Alberta, Canada. The 2805 nucleotide circular genome is the first complete genome from the Mutorquevirus genus and has been approved as a new species by the International Committee on Taxonomy of Viruses. The genome contains several characteristic features of torque teno virus (TTV) genomes, including an ORF1 encoding a putative 631 aa capsid protein with an arginine-rich N-terminus, several rolling circle replication associated amino acid motifs, and a downstream polyadenylation signal. A smaller overlapping ORF2 encodes a protein with an amino acid motif (WX7HX3CXCX5H) which, in general, is highly conserved in TTVs and anelloviruses. The UTR contains two GC-rich tracts, two highly conserved 15 nucleotide sequences, and what appears to be an atypical TATA-box sequence also observed in two other TTV genera. Codon usage analysis of TTEqV2 and 11 other selected anelloviruses from five host species revealed a bias toward adenine ending (A3) codons in the anelloviruses, while in contrast, A3 codons were observed at a low frequency in horse and the four other associated host species examined. Phylogenetic analysis of TTV ORF1 sequences available to date shows TTEqV2 clusters with the only other currently reported member of the Mutorquevirus genus, Torque teno equus virus 1 (TTEqV1, KR902501). Genome-wide pairwise alignment of TTEqV2 and TTEqV1 shows the absence of several highly conserved TTV features within the UTR of TTEqV1, suggesting it is incomplete and TTEqV2 is the first complete genome within the genus Mutorquevirus.
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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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28
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Yan T, Zhao M, Sun Y, Zhang S, Zhang X, Liu Q, Li Y, Cheng Z. Molecular evolution analysis of three species gyroviruses in China from 2018 to 2019. Virus Res 2023; 326:199058. [PMID: 36731631 DOI: 10.1016/j.virusres.2023.199058] [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: 10/24/2022] [Revised: 01/26/2023] [Accepted: 01/29/2023] [Indexed: 02/04/2023]
Abstract
Gyrovirus (GyV) is a widespread ssDNA virus with a high population diversity, and several of its species, including the chicken anemia virus (CAV), gyrovirus galga 1 (GyG1), and gyrovirus homsa 1 (GyH1), have been shown to be pathogenic to poultry. The evolution of these viruses, however, is still unclear. Our study analyzed epidemiology and molecular evolution of three species of GyVs (CAV, GyG1, and GyH1) from 2018 to 2019 in China. The survey results indicated that GyV was widespread in China. It is vital to consider the coinfections among the three species of GyV. The phylogenetic analysis showed that CAV was divided into three clades and GyG1 and GyH1 were divided into two clades. Based on the recombination analysis, CAV and GyG1 had similar recombination regions associated with viral replication and transcription. Furthermore, the substitution rates for CAV and GyG1 were approximately 6.09 × 10-4 and 2.784 × 10-4 nucleotides per site per year, respectively. The high substitution rate and recombination were the main factors for the high diversity of GyVs. Unfortunately, GyH1 strains have not been discovered in enough numbers to allow evolutionary analysis. The GyVs had several positively selected sites, possibly related to their potential to escape the host immune response. In summary, our study provides insights into the time of origin, evolution rate, and recombination of GyV for assessing their evolutionary process and genetic diversity.
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Affiliation(s)
- Tianxing Yan
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an, 271018, China
| | - Manda Zhao
- Department of Animal Science and Technology, Vocational-technical school of Husbandry and Veterinary Medicine, Weifang, 261061, China
| | - Yufeng Sun
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an, 271018, China
| | - Shicheng Zhang
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an, 271018, China
| | - Xianwen Zhang
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an, 271018, China
| | - Qing Liu
- Service center of Jinan Zoo, Jinan, 250032, China
| | - Yubao Li
- Liaocheng University, Liaocheng, 252059, China
| | - Ziqiang Cheng
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an, 271018, China.
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Smiley AT, Tompkins KJ, Pawlak MR, Krueger AJ, Evans RL, Shi K, Aihara H, Gordon WR. Watson-Crick Base-Pairing Requirements for ssDNA Recognition and Processing in Replication-Initiating HUH Endonucleases. mBio 2023; 14:e0258722. [PMID: 36541758 PMCID: PMC9973303 DOI: 10.1128/mbio.02587-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
Replication-initiating HUH endonucleases (Reps) are sequence-specific nucleases that cleave and rejoin single-stranded DNA (ssDNA) during rolling-circle replication. These functions are mediated by covalent linkage of the Rep to its substrate post cleavage. Here, we describe the structures of the endonuclease domain from the Muscovy duck circovirus Rep in complex with its cognate ssDNA 10-mer with and without manganese in the active site. Structural and functional analyses demonstrate that divalent cations play both catalytic and structural roles in Reps by polarizing and positioning their substrate. Further structural comparisons highlight the importance of an intramolecular substrate Watson-Crick (WC) base pairing between the -4 and +1 positions. Subsequent kinetic and functional analyses demonstrate a functional dependency on WC base pairing between these positions regardless of the pair's identity (i.e., A·T, T·A, G·C, or C·G), highlighting a structural specificity for substrate interaction. Finally, considering how well WC swaps were tolerated in vitro, we sought to determine to what extent the canonical -4T·+1A pairing is conserved in circular Rep-encoding single-stranded DNA viruses and found evidence of noncanonical pairings in a minority of these genomes. Altogether, our data suggest that substrate intramolecular WC base pairing is a universal requirement for separation and reunion of ssDNA in Reps. IMPORTANCE Circular Rep-encoding single-stranded DNA (CRESS-DNA) viruses are a ubiquitous group of viruses that infect organisms across all domains of life. These viruses negatively impact both agriculture and human health. All members of this viral family employ a multifunctional nuclease (Rep) to initiate replication. Reps are structurally similar throughout this family, making them targets of interest for viral inhibition strategies. Here, we investigate the functional dependencies of the Rep protein from Muscovy duck circovirus for ssDNA interaction. We demonstrate that this Rep requires an intramolecular Watson-Crick base pairing for origin of replication (Ori) recognition and interaction. We show that noncognate base pair swaps are well tolerated, highlighting a local structural specificity over sequence specificity. Bioinformatic analysis found that the vast majority of CRESS-DNA Oris form base pairs in conserved positions, suggesting this pairing is a universal requirement for replication initiation in the CRESS-DNA virus family.
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Affiliation(s)
- Adam T. Smiley
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Kassidy J. Tompkins
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Matthew R. Pawlak
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - August J. Krueger
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Robert L. Evans
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Ke Shi
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Wendy R. Gordon
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
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30
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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: 0] [Impact Index Per Article: 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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31
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Cerna GM, Serieys LEK, Riley SPD, Richet C, Kraberger S, Varsani A. A circovirus and cycloviruses identified in feces of bobcats (Lynx rufus) in California. Arch Virol 2023; 168:23. [PMID: 36593430 DOI: 10.1007/s00705-022-05656-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 09/25/2022] [Indexed: 01/04/2023]
Abstract
Viruses in the family Circoviridae have small circular single-stranded DNA (ssDNA) genomes. Circoviruses are known to infect a wide variety of animals, with notable disease pathology in psittacine (psittacine beak and feather disease) and porcine (postweaning multisystemic wasting syndrome) species. There is still a dearth of research investigating circoviruses associated with felid species. In six fecal samples collected from bobcats (Lynx rufus) in California from 2010 to 2011, we identified six viruses belonging to the genera Circovirus (n = 1) and Cyclovirus (n = 5), using a high-throughput-sequencing-based approach. Of these, the virus in the genus Circovirus represents a new species, as it shares only 54-60% genome-wide sequence identity with the other members of this genus. The five viruses in the genus Cyclovirus represent three new species, sharing <73% genome-wide sequence identity with all other cycloviruses. Three of the cycloviruses belong to a single putative species and were obtained from the feces of three individual bobcats, sharing 95.7-99.9% sequence identity, whereas the other two unique cycloviruses were identified in a single fecal sample. At present, it is unknown whether the identified viruses infect bobcats, their prey, or their gut parasites.
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Affiliation(s)
- Gabriella M Cerna
- 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
| | | | - Seth P D Riley
- National Park Service, Santa Monica Mountains National Recreation Area, 401 W. Hillcrest Dr, Thousand Oaks, CA, 91360, USA
| | - Cécile Richet
- 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
| | - 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
| | - 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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Abstract
Anelloviruses are the most common viruses infecting humans. Every human carries a nonpathogenic personal anellovirus virome (anellome), yet it is unknown which mechanisms contribute to its stability. Here, we assessed the dynamics and impact of a host antiviral defense mechanism-cytidine deaminase activity leading to C to U editing in anelloviruses-on the stability of the anellome. We investigated anellome sequence data obtained from serum samples collected every 6 months from two healthy subjects followed for more than 30 years. The subjects were infected by a total of 64 anellovirus lineages. Minus-stranded C to U editing was observed in lineages belonging to the Alpha-, Beta-, and Gammatorquevirus genera. The edited genomes were present within virus particles, therefore editing must have occurred at the late stages of the virus life cycle. Editing was favored by 5'-TC contexts in the virus genome, indicating that apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like, catalytic subunit 3 or A3 (APOBEC3) proteins are involved. Within a lineage, mutational dynamics varied over time and few fixations of mutations were detected, indicating that C to U editing is a dead end for a virus genome. We detected an editing coldspot in the GC-rich regions, suggesting that the GC-rich region is crucial for genome packaging, since only packaged virus particles were included in the analysis. Finally, we noticed a lineage-specific reduced concentration after an editing event, yet no clearance. In conclusion, cytidine deaminase activity does not clear anelloviruses, nor does it play a major role in virus evolution, but it does contribute to the stability of the anellome. IMPORTANCE Despite significant attention on anellovirus research, the interaction between the anellovirus virome and the human host remains unknown. We show the dynamics of APOBEC3-mediated cytidine deaminase activity on anelloviruses during a 30-year period of chronic infection and postulate that this antiviral mechanism controls anelloviruses. These results expand our knowledge of anellovirus-host interactions, which may be important for the design of gene therapies.
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Yang S, Zhang D, Zhang Y, Fan Z, Jiang L, Wang Y, Zhang W. Multiple novel smaco-like viruses identified in chicken cloaca swabs. Arch Virol 2022; 167:2703-2708. [PMID: 36125556 DOI: 10.1007/s00705-022-05577-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 07/13/2022] [Indexed: 12/14/2022]
Abstract
Viral metagenomics has been used in numerous animal virus discoveries. Recently, an unprecedented diversity of CRESS DNA viruses was identified using this method, and this has expanded our understanding of the environmental distribution and host range of CRESS DNA viruses. In this study, using an unbiased viral metagenomics approach, we investigated the fecal virome of chickens collected from two farms of Anhui Province, China. Five novel CRESS DNA viruses were obtained and characterized. The genome of the five viruses is 2,401-2,742 bp in length, containing two ORFs in the same orientation. Phylogenetic analysis indicated that all five viruses have a closer genetic relationship to smacoviruses than to other viruses in the order Cremevirales. Pairwise comparison of Rep amino acid sequences showed that these five viruses had only low amino acid sequence identity (8.9%-30.6%) to members of the family Smacoviridae, and the sequence identity among the five smaco-like viruses and other unclassified smacovirus strains was 70.3-95.8%. These findings broaden our knowledge of the genetic diversity of CRESS DNA viruses and provide a basis for classification of unclassified smacoviruses.
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Affiliation(s)
- Shixing Yang
- School of Medicine, Jiangsu University, 301 Xuefu Road, 212013, Zhenjiang, Jiangsu, People's Republic of China
| | - Dianqi Zhang
- School of Medicine, Jiangsu University, 301 Xuefu Road, 212013, Zhenjiang, Jiangsu, People's Republic of China
| | - Yuyang Zhang
- School of Medicine, Jiangsu University, 301 Xuefu Road, 212013, Zhenjiang, Jiangsu, People's Republic of China
| | - Zhaobin Fan
- College of Pharmacy, Heze University, 274015, Heze, Shandong, People's Republic of China
| | - Lili Jiang
- College of Pharmacy, Heze University, 274015, Heze, Shandong, People's Republic of China
| | - Yan Wang
- School of Medicine, Jiangsu University, 301 Xuefu Road, 212013, Zhenjiang, Jiangsu, People's Republic of China.
| | - Wen Zhang
- School of Medicine, Jiangsu University, 301 Xuefu Road, 212013, Zhenjiang, Jiangsu, People's Republic of China.
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34
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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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35
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Wang J, Xiao J, Zhu Z, Wang S, Zhang L, Fan Z, Deng Y, Hu Z, Peng F, Shen S, Deng F. Diverse viromes in polar regions: A retrospective study of metagenomic data from Antarctic animal feces and Arctic frozen soil in 2012-2014. Virol Sin 2022; 37:883-893. [PMID: 36028202 PMCID: PMC9797369 DOI: 10.1016/j.virs.2022.08.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 08/17/2022] [Indexed: 01/01/2023] Open
Abstract
Antarctica and the Arctic are the coldest places, containing a high diversity of microorganisms, including viruses, which are important components of polar ecosystems. However, owing to the difficulties in obtaining access to animal and environmental samples, the current knowledge of viromes in polar regions is still limited. To better understand polar viromes, this study performed a retrospective analysis using metagenomic sequencing data of animal feces from Antarctica and frozen soil from the Arctic collected during 2012-2014. The results reveal diverse communities of DNA and RNA viruses from at least 23 families from Antarctic animal feces and 16 families from Arctic soils. Although the viral communities from Antarctica and the Arctic show a large diversity, they have genetic similarities with known viruses from different ecosystems and organisms with similar viral proteins. Phylogenetic analysis of Microviridae, Parvoviridae, and Larvidaviridae was further performed, and complete genomic sequences of two novel circular replication-associated protein (rep)-encoding single-stranded (CRESS) DNA viruses closely related to Circoviridae were identified. These results reveal the high diversity, complexity, and novelty of viral communities from polar regions, and suggested the genetic similarity and functional correlations of viromes between the Antarctica and Arctic. Variations in viral families in Arctic soils, Arctic freshwater, and Antarctic soils are discussed. These findings improve our understanding of polar viromes and suggest the importance of performing follow-up in-depth investigations of animal and environmental samples from Antarctica and the Arctic, which would reveal the substantial role of these viruses in the global viral community.
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Affiliation(s)
- Jun Wang
- State Key Laboratory of Virology and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Jian Xiao
- State Key Laboratory of Virology and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Zheng Zhu
- State Key Laboratory of Virology and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Siyuan Wang
- State Key Laboratory of Virology and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China,Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, 830046, China
| | - Lei Zhang
- State Key Laboratory of Virology and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Zhaojun Fan
- State Key Laboratory of Virology and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Yali Deng
- State Key Laboratory of Virology and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Zhihong Hu
- State Key Laboratory of Virology and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Fang Peng
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan, 430072, China,Corresponding authors.
| | - Shu Shen
- State Key Laboratory of Virology and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China,Corresponding authors.
| | - Fei Deng
- State Key Laboratory of Virology and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China,Corresponding authors.
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36
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Gainor K, Castillo Fortuna Y, Alakkaparambil AS, González W, Malik YS, Ghosh S. Detection and Complete Genome Analysis of Porcine Circovirus 2 (PCV2) and an Unclassified CRESS DNA Virus from Diarrheic Pigs in the Dominican Republic: First Evidence for Predominance of PCV2d from the Caribbean Region. Viruses 2022; 14:v14081799. [PMID: 36016421 PMCID: PMC9415081 DOI: 10.3390/v14081799] [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: 06/27/2022] [Revised: 08/08/2022] [Accepted: 08/15/2022] [Indexed: 11/16/2022] Open
Abstract
We report here high rates (47.5%, 48/101) of detection of porcine circovirus 2 (PCV2) in diarrheic pigs from three pig farms in the Dominican Republic. Seventeen of the PCV2 positive samples, representing the three pig farms, different age groups and sampling periods (2020–2021), were amplified for the complete PCV2 genome. Based on analysis of open reading frame 2 and complete genome sequences, the 17 PCV2 strains were assigned to the PCV2d genotype. Significant differences were observed in PCV2 detection rates between the vaccinated (20% (10/50)) and unvaccinated (62.5% (10/16) and 80% (28/35)) farms, corroborating previous observations that PCV2a-based vaccines confer protection against heterologous PCV2 genotypes. The present study is the first to report detection and molecular characterization of PCV2 from the Dominican Republic, warranting large-scale molecular epidemiological studies on PCV2 in pig farms and backyard systems across the country. For the first time, PCV2d was identified as the predominant PCV2 genotype in a study from the Caribbean region, suggesting that a genotype shift from PCV2b to PCV2d might be happening in the Caribbean region, which mirrored the current PCV2 genotype scenario in many other parts of the world. Besides PCV2, we also identified a pigeon circovirus-like virus, and a circular Replication-associated protein (Rep)-encoding single-stranded (CRESS) DNA virus, which was characterized for the complete genome. The CRESS DNA virus shared a similar genomic organization and was related to unclassified CRESSV2 DNA viruses (belonging to the Order Cirlivirales) from porcine feces in Hungary, indicating that related unclassified CRESS DNA viruses are circulating among pigs in different geographical regions, warranting further studies on the epidemiology and biology of these novel viruses.
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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
| | - Yussaira Castillo Fortuna
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre P.O. Box 334, Saint Kitts and Nevis
| | - Angeline Steny Alakkaparambil
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre P.O. Box 334, Saint Kitts and Nevis
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632014, India
| | - Wendy González
- Epidemiological Surveillance Division, Dirección General de Ganadería, Santo Domingo 10410, Dominican Republic
- School of Veterinary Medicine, Faculty of Agronomic and Veterinary Sciences, Autonomous University of Santo Domingo, Calle Camino de Engombe 10904, Dominican Republic
| | - 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
- Correspondence: or ; Tel.: +1-(869)-4654161 (ext. 401-1202)
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37
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Taylo LJ, Keeler EL, Bushman FD, Collman RG. The enigmatic roles of Anelloviridae and Redondoviridae in humans. Curr Opin Virol 2022; 55:101248. [PMID: 35870315 DOI: 10.1016/j.coviro.2022.101248] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/06/2022] [Accepted: 06/09/2022] [Indexed: 12/26/2022]
Abstract
Anelloviridae and Redondoviridae are virus families with small, circular, single-stranded DNA genomes that are common components of the human virome. Despite their small genome size of less than 5000 bases, they are remarkably successful - anelloviruses colonize over 90% of adult humans, while the recently discovered redondoviruses have been found at up to 80% prevalence in some populations. Anelloviruses are present in blood and many organs, while redondoviruses are found mainly in the ororespiratory tract. Despite their high prevalence, little is known about their biology or pathogenic potential. In this review, we discuss anelloviruses and redondoviruses and explore their enigmatic roles in human health and disease.
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Affiliation(s)
- Louis J Taylo
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Emma L Keeler
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Frederic D Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ronald G Collman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Medicine, Pulmonary, Allergy and Critical Care Division, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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38
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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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39
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Witt AA, Alves RS, do Canto Olegário J, de Camargo LJ, Weber MN, da Silva MS, Canova R, Mosena ACS, Cibulski SP, Varela APM, Mayer FQ, Canal CW, da Fontoura Budaszewski R. The virome of the white-winged vampire bat Diaemus youngi is rich in circular DNA viruses. Virus Genes 2022; 58:214-226. [PMID: 35366197 PMCID: PMC8976263 DOI: 10.1007/s11262-022-01897-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 03/17/2022] [Indexed: 11/13/2022]
Abstract
In the Neotropical region, the white-winged vampire bat (Diaemus youngi) is the rarest of the three species of vampire bats. This bat species feeds preferentially on bird blood, and there is limited information on the viruses infecting D. youngi. Hence, this study aimed to expand the knowledge about the viral diversity associated with D. youngi by sampling and pooling the lungs, liver, kidneys, heart, and intestines of all animals using high-throughput sequencing (HTS) on the Illumina MiSeq platform. A total of three complete and 10 nearly complete circular virus genomes were closely related to gemykrogvirus (Genomoviridae family), smacovirus (Smacoviridae family), and torque teno viruses (TTVs) (Anelloviridae family). In addition, three sequences of bat paramyxovirus were detected and found to be closely related to viruses reported in Pomona roundleaf bats and rodents. The present study provides a snapshot of the viral diversity associated with white-winged vampire bats and provides a baseline for comparison to viruses detected in future outbreaks.
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Affiliation(s)
- André Alberto Witt
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil.,Secretaria Estadual de Agricultura, Pecuária e Desenvolvimento Rural (SEAPDR), Porto Alegre, Rio Grande do Sul, Brazil
| | - Raquel Silva Alves
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Juliana do Canto Olegário
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Laura Junqueira de Camargo
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Matheus Nunes Weber
- Laboratório de Microbiologia Molecular, Instituto de Ciências da Saúde, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Mariana Soares da Silva
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil.,Laboratório de Microbiologia Molecular, Instituto de Ciências da Saúde, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Raíssa Canova
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Ana Cristina Sbaraini Mosena
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Samuel Paulo Cibulski
- Centro de Biotecnologia (Cbiotec), Universidade Federal da Paraíba, João Pessoa, Paraíba, Brazil
| | - Ana Paula Muterle Varela
- Laboratório de Biologia Molecular, Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Secretaria da Agricultura, Pecuária e Desenvolvimento Rural (SEAPDR), Eldorado Do Sul, Rio Grande do Sul, Brazil
| | - Fabiana Quoos Mayer
- Laboratório de Biologia Molecular, Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Secretaria da Agricultura, Pecuária e Desenvolvimento Rural (SEAPDR), Eldorado Do Sul, Rio Grande do Sul, Brazil
| | - Cláudio Wageck Canal
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Renata da Fontoura Budaszewski
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil.
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40
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Tong P, Deng H, Duan L, Ren M, Song X, Wang H, Gulimire D, Kuang L, Xie J. First detection of the occurrence and study of the genetic diversity of novel putative kirkoviruses in donkey in China. Virus Genes 2022; 58:146-149. [DOI: 10.1007/s11262-022-01891-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 02/25/2022] [Indexed: 11/28/2022]
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41
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Fehér E, Kaszab E, Bali K, Hoitsy M, Sós E, Bányai K. Novel Circoviruses from Birds Share Common Evolutionary Roots with Fish Origin Circoviruses. Life (Basel) 2022; 12:life12030368. [PMID: 35330119 PMCID: PMC8950603 DOI: 10.3390/life12030368] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/24/2022] [Accepted: 02/28/2022] [Indexed: 11/16/2022] Open
Abstract
Circoviruses occur in a variety of animal species and are common pathogens of mammalian and avian hosts. In our study internal organ samples of wild birds were processed for screening of circoviral sequences. Two novel viruses were identified and characterized in specimens of a little bittern and a European bee-eater that suffered from wing injuries, were weakened, had liver or kidney failures, and finally succumbed at a rescue station. The 1935 nt and 1960 nt long viral DNA genomes exhibited a genomic structure typical for circoviruses and were predicted to encode replication-associated protein in the viral strand, and a capsid protein in the complementary strand of the replicative intermediate DNA form. The genome of the newly described viruses showed 37.6% pairwise identity with each other and ≤41.5% identity with circovirus sequences, and shared a common branch with fish, human and Weddel seal circoviruses in the phylogenetic tree, implying evolutionary relationship among the ancestors of these viruses. Based on the results the little bittern and European bee-eater circoviruses represent two distinct species of the Circovirus genus, Circoviridae family.
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Affiliation(s)
- Enikő Fehér
- Veterinary Medical Research Institute, H-1143 Budapest, Hungary; (E.K.); (K.B.); (K.B.)
- Correspondence:
| | - Eszter Kaszab
- Veterinary Medical Research Institute, H-1143 Budapest, Hungary; (E.K.); (K.B.); (K.B.)
| | - Krisztina Bali
- Veterinary Medical Research Institute, H-1143 Budapest, Hungary; (E.K.); (K.B.); (K.B.)
| | - Márton Hoitsy
- Conservation and Veterinary Services, Budapest Zoo and Botanical Garden, H-1164 Budapest, Hungary; (M.H.); (E.S.)
| | - Endre Sós
- Conservation and Veterinary Services, Budapest Zoo and Botanical Garden, H-1164 Budapest, Hungary; (M.H.); (E.S.)
| | - Krisztián Bányai
- Veterinary Medical Research Institute, H-1143 Budapest, Hungary; (E.K.); (K.B.); (K.B.)
- Department of Pharmacology and Toxicology, University of Veterinary Medicine, H-1078 Budapest, Hungary
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42
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Legnardi M, Grassi L, Franzo G, Menandro ML, Tucciarone CM, Minichino A, Dipineto L, Borrelli L, Fioretti A, Cecchinato M. Detection and Molecular Characterization of a Novel Species of Circovirus in a Tawny Owl (Strix aluco) in Southern Italy. Animals (Basel) 2022; 12:ani12020135. [PMID: 35049758 PMCID: PMC8772546 DOI: 10.3390/ani12020135] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 11/23/2022] Open
Abstract
Simple Summary The genus Circovirus groups some of the smallest viruses capable of autonomous replication, including some notable swine and avian pathogens. Among domestic and wild birds, circoviruses are often associated with immunosuppression and integumental disorders, but, despite their relevance, nothing is known about their circulation in birds of prey. By conducting molecular analyses on samples from birds of prey recovered by a wildlife rescue centre in Italy, we identified a new viral species in the spleen of a tawny owl (Strix aluco). However, there is contrasting evidence regarding its definitive host. On one hand, the virus was discovered to be phylogenetically closer to mammalian rather than avian circoviruses, which allows speculations on its host being a micromammal preyed by the tawny owl, rather than the bird itself. On the other hand, its detection in the spleen, a lymphoid organ in which other avian circoviruses are often detected, supports the tawny owl being its actual host, perhaps following a spillover event associated with predation. Adding to the growing number of circoviruses found in recent years in a diverse range of hosts, this discovery represents another step forward in the characterization of this genus of remarkable veterinary importance. Abstract Thanks to recent developments in molecular methods, many new species have been discovered within the genus Circovirus, which comprises viruses of veterinary relevance found in a broad range of hosts. In particular, several circoviruses are known to infect birds, often causing immunosuppression and feathering disorders. Nonetheless, nothing is known about their circulation in birds of prey. In this study, samples from 61 birds of prey representing ten different species, recovered by a wildlife rescue centre in Southern Italy, were taken at necropsy and analysed by PCR with pan-Circovirus primers. Only one sample, collected from a tawny owl (Strix aluco), tested positive. Its genome, sequenced by primer walking, displays the typical features of circoviruses. Based on demarcation criteria, the detected strain qualifies as a novel species, which was named “tawny owl-associated circovirus” (ToCV). Phylogenetically, ToCV clustered with mammalian rather than avian circoviruses, and its closeness to a rodent circovirus suggests that its host may have been a micromammal eaten by the tawny owl. On the other hand, its detection in the spleen fits with the tropism of other avian circoviruses. Little can be therefore said on its biology and pathogenicity, and further efforts are needed to better characterize its epidemiology.
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Affiliation(s)
- Matteo Legnardi
- Dipartimento di Medicina Animale, Produzione e Salute, Università di Padova, Viale dell’Università 16, 35020 Legnaro, Italy; (L.G.); (G.F.); (M.L.M.); (C.M.T.); (M.C.)
- Correspondence:
| | - Laura Grassi
- Dipartimento di Medicina Animale, Produzione e Salute, Università di Padova, Viale dell’Università 16, 35020 Legnaro, Italy; (L.G.); (G.F.); (M.L.M.); (C.M.T.); (M.C.)
| | - Giovanni Franzo
- Dipartimento di Medicina Animale, Produzione e Salute, Università di Padova, Viale dell’Università 16, 35020 Legnaro, Italy; (L.G.); (G.F.); (M.L.M.); (C.M.T.); (M.C.)
| | - Maria Luisa Menandro
- Dipartimento di Medicina Animale, Produzione e Salute, Università di Padova, Viale dell’Università 16, 35020 Legnaro, Italy; (L.G.); (G.F.); (M.L.M.); (C.M.T.); (M.C.)
| | - Claudia Maria Tucciarone
- Dipartimento di Medicina Animale, Produzione e Salute, Università di Padova, Viale dell’Università 16, 35020 Legnaro, Italy; (L.G.); (G.F.); (M.L.M.); (C.M.T.); (M.C.)
| | - Adriano Minichino
- Dipartimento di Medicina Veterinaria e Produzioni Animali, Università di Napoli Federico II, Via F. Delpino 1, 80137 Napoli, Italy; (A.M.); (L.D.); (L.B.); (A.F.)
| | - Ludovico Dipineto
- Dipartimento di Medicina Veterinaria e Produzioni Animali, Università di Napoli Federico II, Via F. Delpino 1, 80137 Napoli, Italy; (A.M.); (L.D.); (L.B.); (A.F.)
| | - Luca Borrelli
- Dipartimento di Medicina Veterinaria e Produzioni Animali, Università di Napoli Federico II, Via F. Delpino 1, 80137 Napoli, Italy; (A.M.); (L.D.); (L.B.); (A.F.)
| | - Alessandro Fioretti
- Dipartimento di Medicina Veterinaria e Produzioni Animali, Università di Napoli Federico II, Via F. Delpino 1, 80137 Napoli, Italy; (A.M.); (L.D.); (L.B.); (A.F.)
| | - Mattia Cecchinato
- Dipartimento di Medicina Animale, Produzione e Salute, Università di Padova, Viale dell’Università 16, 35020 Legnaro, Italy; (L.G.); (G.F.); (M.L.M.); (C.M.T.); (M.C.)
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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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Identification and Characterization of Circular Single-Stranded DNA Genomes in Sheep and Goat Milk. Viruses 2021; 13:v13112176. [PMID: 34834982 PMCID: PMC8621823 DOI: 10.3390/v13112176] [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: 10/07/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 12/21/2022] Open
Abstract
In recent years, a variety of circular replicase-encoding single-stranded (CRESS) DNA viruses and unclassified virus-like DNA elements have been discovered in a broad range of animal species and environmental samples. Key questions to be answered concern their presence in the human diet and their potential impact on disease emergence. Especially DNA elements termed bovine meat and milk factors (BMMF) are suspected to act as co-factors in the development of colon and breast cancer. To expand our knowledge on the occurrence of these potential pathogens in human nutrition, a total of 73 sheep and 40 goat milk samples were assayed by combining rolling circle amplification (RCA), PCR and Sanger sequencing. The present study further includes retail milk from the aforementioned species. We recovered 15 single stranded (ss) circular genomes. Of those, nine belong to the family Genomoviridae and six are members of the unclassified group of BMMF. Thus, dairy sheep and goats add to dispersal of CRESS viruses and circular ssDNA elements, which enter the food chain via milk. The presence of these entities is therefore more widespread in Bovidae than initially assumed and seems to be part of the common human nutrition.
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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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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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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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