Bastroviruses (Astroviridae): genetic diversity and potential impact on human and animal health
- Authors: Roev G.V.1,2, Borisova N.I.1, Chistyakova N.V.3, Vyhodtseva A.V.1, Akimkin V.G.1, Khafizov K.F.1
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Affiliations:
- Central Research Institute for Epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing
- Moscow Institute of Physics and Technology (National Research University)
- A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences
- Issue: Vol 68, No 6 (2023)
- Pages: 505-512
- Section: ORIGINAL RESEARCH
- URL: https://journals.rcsi.science/0507-4088/article/view/249447
- DOI: https://doi.org/10.36233/0507-4088-192
- EDN: https://elibrary.ru/iqblwy
- ID: 249447
Cite item
Abstract
Introduction. Bastroviruses were discovered in the Netherlands in 2016 in human stool samples and show partial genetic similarities to astroviruses and hepatitis E viruses. Their association with disease onset has not yet been established.
Materials and methods. Metagenomic sequencing of fecal samples of Nyctalus noctula bats collected in the Russian Federation in 2023 was performed. Two almost complete genomes of bastroviruses were assembled. The zoonotic potential of these viruses was assessed using machine learning methods, their recombination was studied, and phylogenetic trees were constructed.
Results. A nearly complete bastrovirus genome was de novo assembled in one of the samples, and it was used to assemble another genome in another sample. The zoonotic potential of the virus from one of these samples was estimated as high. The existence of recombination between structural and non-structural polyproteins was demonstrated.
Conclusion. Two bastrovirus genomes were assembled, phylogenetic and recombination analyses were performed, and the zoonotic potential was evaluated.
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##article.viewOnOriginalSite##About the authors
German V. Roev
Central Research Institute for Epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing; Moscow Institute of Physics and Technology (National Research University)
Email: roevherman@gmail.com
ORCID iD: 0000-0002-2353-5222
Bioinformatician of Laboratory for Genomics Research of the Central Research Institute for Epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Moscow, Russia
Russian Federation, 111123, Moscow; 115184, DolgoprudnyNadezhda I. Borisova
Central Research Institute for Epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing
Email: borisova@cmd.su
ORCID iD: 0000-0002-9672-0648
Junior researcher of Laboratory for Genomics Research of the Central Research Institute for Epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Moscow, Russia
Russian Federation, 111123, MoscowNadezhda V. Chistyakova
A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences
Email: lanche@mail.ru
ORCID iD: 0009-0002-6034-1408
Engineer of Laboratory of comparative etology and biocommunication of A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences, Russia, Moscow, Russia
Russian Federation, 119071, MoscowAnastasia V. Vyhodtseva
Central Research Institute for Epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing
Email: vihodceva@cmd.su
ORCID iD: 0009-0005-1911-9620
Technologist of Laboratory for Genomics Research of the Central Research Institute for Epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Moscow, Russia
Russian Federation, 111123, MoscowVasiliy G. Akimkin
Central Research Institute for Epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing
Email: vgakimkin@yandex.ru
ORCID iD: 0000-0003-4228-9044
Doctor of Medicine, Professor, Director of Central Research Institute for Epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Moscow, Russia
Russian Federation, 111123, MoscowKamil F. Khafizov
Central Research Institute for Epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing
Author for correspondence.
Email: khafizov@cmd.su
ORCID iD: 0000-0001-5524-0296
PhD (Biol.), Head of Laboratory for Genomics Research of the Central Research Institute for Epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Moscow, Russia
Russian Federation, 111123, MoscowReferences
- Oude Munnink B.B., Cotten M., Canuti M., Deijs M., Jebbink M.F., van Hemert F.J., et al. A Novel astrovirus-like RNA virus detected in human stool. Virus Evol. 2016; 2(1): vew005. https://doi.org/10.1093/ve/vew005
- Dos Anjos K., Nagata T., Melo F.L. Complete genome sequence of a novel bastrovirus isolated from raw sewage. Genome Announc. 2017; 5(40): e01010–17. https://doi.org/10.1128/genomeA.01010-17
- Yinda C.K., Ghogomu S.M., Conceição-Neto N., Beller L., Deboutte W., Vanhulle E., et al. Cameroonian fruit bats harbor divergent viruses, including rotavirus H, bastroviruses, and picobirnaviruses using an alternative genetic code. Virus Evol. 2018; 4(1): vey008. https://doi.org/10.1093/ve/vey008
- Bauermann F.V., Hause B., Buysse A.R., Joshi L.R., Diel D.G. Identification and genetic characterization of a porcine hepe-astrovirus (bastrovirus) in the United States. Arch. Virol. 2019; 164(9): 2321–6. https://doi.org/10.1007/s00705-019-04313-x
- Mishra N., Fagbo S.F., Alagaili A.N., Nitido A., Williams S.H., Ng J., et al. A viral metagenomic survey identifies known and novel mammalian viruses in bats from Saudi Arabia. PLoS One. 2019; 14(4): e0214227. https://doi.org/10.1371/journal.pone.0214227
- Nagai M., Okabayashi T., Akagami M., Matsuu A., Fujimoto Y., Hashem M.A., et al. Metagenomic identification, sequencing, and genome analysis of porcine hepe-astroviruses (bastroviruses) in porcine feces in Japan. Infect. Genet. Evol. 2021; 88: 104664. https://doi.org/10.1016/j.meegid.2020.104664
- Chen Z., Zhao H., Li Z., Huang M., Si N., Zhao H., et al. First discovery of phenuiviruses within diverse RNA viromes of Asiatic toad (Bufo gargarizans) by metagenomics sequencing. Viruses. 2023; 15(3): 750. https://doi.org/10.3390/v15030750
- Bolger A.M., Lohse M., Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014; 30(15): 2114–20. https://doi.org/10.1093/bioinformatics/btu170
- Bushnell B., Rood J., Singer E. BBMerge – accurate paired shotgun read merging via overlap. PLoS One. 2017; 12(10): e0185056. https://doi.org/10.1371/journal.pone.0185056
- Menzel P., Ng K.L., Krogh A. Fast and sensitive taxonomic classification for metagenomics with Kaiju. Nat. Commun. 2016; 7: 11257. https://doi.org/10.1038/ncomms11257
- Li D., Liu C.M., Luo R., Sadakane K., Lam T.W. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics. 2015; 31(10): 1674–6. https://doi.org/10.1093/bioinformatics/btv033
- Buchfink B., Reuter K., Drost H.G. Sensitive protein alignments at tree-of-life scale using DIAMOND. Nat. Methods. 2021; 18(4): 366–8. https://doi.org/10.1038/s41592-021-01101-x
- Langmead B., Wilks C., Antonescu V., Charles R. Scaling read aligners to hundreds of threads on general-purpose processors. Bioinformatics. 2019; 35(3): 421–32. https://doi.org/10.1093/bioinformatics/bty648
- Danecek P., Bonfield J.K., Liddle J., Marshall J., Ohan V., Pollard M.O., et al. Twelve years of SAMtools and BCFtools. Gigascience. 2021; 10(2): giab008. https://doi.org/10.1093/gigascience/giab008
- Wheeler D.L., Church D.M., Federhen S., Lash A.E., Madden T.L., Pontius J.U., et al. Database resources of the National Center for Biotechnology. Nucleic. Acids Res. 2003; 31(1): 28–33. https://doi.org/10.1093/nar/gkg033
- Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 1990; 215(3): 403–10. https://doi.org/10.1016/S0022-2836(05)80360-2
- Katoh K., Standley D.M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 2013; 30(4): 772–80. https://doi.org/10.1093/molbev/mst010
- Nguyen L.T., Schmidt H.A., von Haeseler A., Minh B.Q. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 2015; 32(1): 268–74. https://doi.org/10.1093/molbev/msu300
- Kalyaanamoorthy S., Minh B.Q., Wong T.K.F., von Haeseler A., Jermiin L.S. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat. Methods. 2017; 14(6): 587–9. https://doi.org/10.1038/nmeth.4285
- Letunic I., Bork P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic. Acids Res. 2021; 49(W1): W293–6. https://doi.org/10.1093/nar/gkab301
- Suyama M., Torrents D., Bork P. PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res. 2006; 34(Web Server issue): W609–12. https://doi.org/10.1093/nar/gkl315
- Martin D.P., Murrell B., Golden M., Khoosal A., Muhire B. RDP4: Detection and analysis of recombination patterns in virus genomes. Virus Evol. 2015; 1(1): vev003. https://doi.org/10.1093/ve/vev003
- Mollentze N., Babayan S.A., Streicker D.G. Identifying and prioritizing potential human-infecting viruses from their genome sequences. PLoS Biol. 2021; 19(9): e3001390. https://doi.org/10.1371/journal.pbio.3001390
- Wolfaardt M., Kiulia N.M., Mwenda J.M., Taylor M.B. Evidence of a recombinant wild-type human astrovirus strain from a Kenyan child with gastroenteritis. J. Clin. Microbiol. 2011; 49(2): 728–31. https://doi.org/10.1128/JCM.01093-10
- Wohlgemuth N., Honce R., Schultz-Cherry S. Astrovirus evolution and emergence. Infect. Genet. Evol. 2019; 69: 30–7. https://doi.org/10.1016/j.meegid.2019.01.009
- Worobey M., Holmes E.C. Evolutionary aspects of recombination in RNA viruses. J. Gen. Virol. 1999; 80(Pt. 10): 2535–43. https://doi.org/10.1099/0022-1317-80-10-2535
- van Dijk E.L., Auger H., Jaszczyszyn Y., Thermes C. Ten years of next-generation sequencing technology. Trends Genet. 2014; 30(9): 418–26. https://doi.org/10.1016/j.tig.2014.07.001
- Kiselev D., Matsvay A., Abramov I., Dedkov V., Shipulin G., Khafizov K. Current trends in diagnostics of viral infections of unknown etiology. Viruses. 2020; 12(2): 211. https://doi.org/10.3390/v12020211
- Radford A.D., Chapman D., Dixon L., Chantrey J., Darby A.C., Hall N. Application of next-generation sequencing technologies in virology. J. Gen. Virol. 2012; 93(Pt. 9): 1853–68. https://doi.org/10.1099/vir.0.043182-0
- Bassi C., Guerriero P., Pierantoni M., Callegari E., Sabbioni S. Novel virus identification through metagenomics: a systematic review. Life (Basel). 2022; 12(12): 2048. https://doi.org/10.3390/life12122048
- Li W., Shi Z., Yu M., Ren W., Smith C., Epstein J.H., et al. Bats are natural reservoirs of SARS-like coronaviruses. Science. 2005; 310(5748): 676–9. https://doi.org/10.1126/science.1118391