Genome analysis of gyroviruses identified in waterfowl in Arizona (USA).
Journal
Archives of virology
ISSN: 1432-8798
Titre abrégé: Arch Virol
Pays: Austria
ID NLM: 7506870
Informations de publication
Date de publication:
16 May 2024
16 May 2024
Historique:
received:
01
03
2024
accepted:
29
04
2024
medline:
16
5
2024
pubmed:
16
5
2024
entrez:
16
5
2024
Statut:
epublish
Résumé
Gyroviruses are small single-stranded DNA (ssDNA) viruses that are largely associated with birds. Chicken anemia virus is the most extensively studied gyrovirus due to its disease impact on the poultry industry. However, we know much less about gyroviruses infecting other avian species. To investigate gyroviruses infecting waterfowl, we determined six complete genome sequences that fall into three gyrovirus groups, referred to as waterfowl gyrovirus 1 (n = 3), 2 (n = 2), and 3 (n = 1), in organs from hunter-harvested waterfowl from Arizona (USA). The waterfowl gyrovirus 1 variants were identified in multiple organs of a single American wigeon and represent a tentative new species. The waterfowl gyrovirus 2 variants were identified in the livers of two American wigeons and share >70% VP1 nucleotide sequence identity with gyrovirus 9, previously identified in the spleen of a Brazilian Pekin duck (MT318123) and a human fecal sample (KP742975). Waterfowl gyrovirus 3 was identified in a northern pintail spleen sample, and it shares >73% VP1 nucleotide sequence identity with two gyrovirus 13 sequences previously identified in Brazilian Pekin duck spleens (MT318125 and MT318127). These gyroviruses are the first to be identified in waterfowl in North America, as well as in American wigeons and northern pintails.
Identifiants
pubmed: 38753261
doi: 10.1007/s00705-024-06049-9
pii: 10.1007/s00705-024-06049-9
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
120Informations de copyright
© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Austria, part of Springer Nature.
Références
Niu J-T, Yi S-S, Dong G-Y, Guo Y-B, Zhao Y-L, Huang H-L, Wang K, Hu G-X, Dong H (2019) Genomic Characterization of Diverse Gyroviruses Identified in the Feces of Domestic Cats. Sci Rep 9:13303
doi: 10.1038/s41598-019-49955-8
pubmed: 31527770
pmcid: 6746754
Kraberger S, Opriessnig T, Celer V, Maggi F, Okamoto H, Blomstrom AL, Cadar D, Harrach B, Biagini P, Varsani A (2021) Taxonomic updates for the genus Gyrovirus (family Anelloviridae): recognition of several new members and establishment of species demarcation criteria. Arch Virol 166:2937–2942
doi: 10.1007/s00705-021-05194-9
pubmed: 34347169
Varsani A, Kraberger S, Opriessnig T, Maggi F, Celer V, Okamoto H, Biagini P (2023) Anelloviridae taxonomy update 2023. Arch Virol 168:277
doi: 10.1007/s00705-023-05903-6
pubmed: 37864606
Fatoba AJ, Adeleke MA (2019) Chicken anemia virus: A deadly pathogen of poultry. Acta Virol 63:19–25
doi: 10.4149/av_2019_110
pubmed: 30879309
Schat KA, Skinner MA (2014) Avian Immunosuppressive Diseases and Immunoevasion. Avian Immunology, 2nd edn. pp 275–297
Li G, Zhou D, Zhao M, Liu Q, Hao X, Yan T, Yuan S, Zhang S, Cheng Z (2021) Kinetic analysis of pathogenicity and tissue tropism of gyrovirus 3 in experimentally infected chickens. Vet Res 52:120
doi: 10.1186/s13567-021-00990-2
pubmed: 34526128
pmcid: 8442313
Zhang W, Li L, Deng X, Kapusinszky B, Delwart E (2014) What is for dinner? Viral metagenomics of US store bought beef, pork, and chicken. Virology 468–470:303–310
doi: 10.1016/j.virol.2014.08.025
pubmed: 25217712
Gia Phan T, Phung Vo N, Sdiri-Loulizi K, Aouni M, Pothier P, Ambert-Balay K, Deng X, Delwart E (2013) Divergent gyroviruses in the feces of Tunisian children. Virology 446:346–348
doi: 10.1016/j.virol.2013.08.020
pubmed: 24074598
Feher E, Pazar P, Kovacs E, Farkas SL, Lengyel G, Jakab F, Martella V, Banyai K (2014) Molecular detection and characterization of human gyroviruses identified in the ferret fecal virome. Arch Virol 159:3401–3406
doi: 10.1007/s00705-014-2203-3
pubmed: 25119678
pmcid: 7087032
Wu Q, Xu X, Chen Q, Ji J, Kan Y, Yao L, Xie Q (2019) Genetic analysis of avian gyrovirus 2 variant-related gyrovirus detected in farmed king ratsnake (Elaphe carinata): The first report from China. Pathogens 8:185
doi: 10.3390/pathogens8040185
pubmed: 31614719
pmcid: 6963503
Rijsewijk FA, Dos Santos HF, Teixeira TF, Cibulski SP, Varela AP, Dezen D, Franco AC, Roehe PM (2011) Discovery of a genome of a distant relative of chicken anemia virus reveals a new member of the genus Gyrovirus. Arch Virol 156:1097–1100
doi: 10.1007/s00705-011-0971-6
pubmed: 21442232
Li L, Pesavento PA, Gaynor AM, Duerr RS, Phan TG, Zhang W, Deng X, Delwart E (2015) A gyrovirus infecting a sea bird. Arch Virol 160:2105–2109
doi: 10.1007/s00705-015-2468-1
pubmed: 26036564
pmcid: 4657940
Truchado DA, Diaz-Piqueras JM, Gomez-Lucia E, Domenech A, Mila B, Perez-Tris J, Schmidt-Chanasit J, Cadar D, Benitez L (2019) A Novel and divergent gyrovirus with unusual genomic features detected in wild passerine birds from a remote rainforest in French Guiana. Viruses 11:1148
doi: 10.3390/v11121148
pubmed: 31835740
pmcid: 6950609
Waits K, Bradley RW, Warzybok P, Kraberger S, Fontenele RS, Varsani A (2018) Genome Sequence of a Gyrovirus Associated with Ashy Storm-Petrel. Microbiol Resour Announc 7:e00958-18
Cibulski S, Weber MN, de Sales Lima FE, Lima DAd, Fernandes Dos Santos H, Teixeira TF, Varela APM, Tochetto C, Mayer FQ, Roehe PM (2020) Viral metagenomics in Brazilian Pekin ducks identifies two gyrovirus, including a new species, and the potentially pathogenic duck circovirus. Virology 548:101–108
doi: 10.1016/j.virol.2020.05.013
pubmed: 32838930
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 (2023) Evolution of anelloviruses from a circovirus-like ancestor through gradual augmentation of the jelly-roll capsid protein. Virus Evol 9:vead035
doi: 10.1093/ve/vead035
pubmed: 37325085
pmcid: 10266747
Hatcher EL, Zhdanov SA, Bao Y, Blinkova O, Nawrocki EP, Ostapchuck Y, Schaffer AA, Brister JR (2017) Virus Variation Resource - improved response to emergent viral outbreaks. Nucleic Acids Res 45:D482–D490
doi: 10.1093/nar/gkw1065
pubmed: 27899678
van Santen VL, Toro H, Hoerr FJ (2007) Biological characteristics of chicken anemia virus regenerated from clinical specimen by PCR. Avian Dis 51:66–77
doi: 10.1637/0005-2086(2007)051[0066:BCOCAV]2.0.CO;2
pubmed: 17461269
Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120
doi: 10.1093/bioinformatics/btu170
pubmed: 24695404
pmcid: 4103590
Li D, Liu CM, Luo R, Sadakane K, Lam TW (2015) MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 31:1674–1676
doi: 10.1093/bioinformatics/btv033
pubmed: 25609793
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410
doi: 10.1016/S0022-2836(05)80360-2
pubmed: 2231712
Muhire BM, Varsani A, Martin DP (2014) SDT: a virus classification tool based on pairwise sequence alignment and identity calculation. PLoS ONE 9:e108277
doi: 10.1371/journal.pone.0108277
pubmed: 25259891
pmcid: 4178126
Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30:772–780
doi: 10.1093/molbev/mst010
pubmed: 23329690
pmcid: 3603318
Darriba D, Taboada GL, Doallo R, Posada D (2011) ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics 27:1164–1165
doi: 10.1093/bioinformatics/btr088
pubmed: 21335321
Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 59:307–321
doi: 10.1093/sysbio/syq010
pubmed: 20525638
Gouy M, Guindon S, Gascuel O (2010) SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol Biol Evol 27:221–224
doi: 10.1093/molbev/msp259
pubmed: 19854763
Stover BC, Muller KF (2010) TreeGraph 2: combining and visualizing evidence from different phylogenetic analyses. BMC Bioinformatics 11:7
doi: 10.1186/1471-2105-11-7
pubmed: 20051126
pmcid: 2806359
Letunic I, Bork P (2021) Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res 49:W293–W296
doi: 10.1093/nar/gkab301
pubmed: 33885785
pmcid: 8265157
Phan TG, da Costa AC, Zhang W, Pothier P, Ambert-Balay K, Deng X, Delwart E (2015) A new gyrovirus in human feces. Virus Genes 51:132–135
doi: 10.1007/s11262-015-1210-0
pubmed: 26013257
pmcid: 4519424