Identification of a novel filovirus in a common lancehead (Bothrops atrox (Linnaeus, 1758))
I performed metaviromic analysis of publicly available RNA-seq data from reptiles to understand the diversity of filoviruses (family Filoviridae). I identified a coding-complete sequence of a filovirus from the common lancehead (Bothrops atrox (Linnaeus, 1758)), tentatively named Tapajós virus (TAPV...
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Published in | Journal of Veterinary Medical Science Vol. 83; no. 9; pp. 1485 - 1488 |
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Format | Journal Article |
Language | English |
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JAPANESE SOCIETY OF VETERINARY SCIENCE
2021
The Japanese Society of Veterinary Science |
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Abstract | I performed metaviromic analysis of publicly available RNA-seq data from reptiles to understand the diversity of filoviruses (family Filoviridae). I identified a coding-complete sequence of a filovirus from the common lancehead (Bothrops atrox (Linnaeus, 1758)), tentatively named Tapajós virus (TAPV). Although the genome organization of TAPV is similar to mammalian filoviruses, our phylogenetic analysis showed that TAPV forms a cluster with a fish filovirus. However, TAPV is still distantly related to all the known filoviruses, suggesting that TAPV can be assigned as a species of a novel genus in Filoviridae. To our knowledge, this is the first report identifying a filovirus in reptiles, and thus contributes to a deeper understanding of the diversity and evolution of filoviruses. |
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AbstractList | I performed metaviromic analysis of publicly available RNA-seq data from reptiles to understand the diversity of filoviruses (family Filoviridae). I identified a coding-complete sequence of a filovirus from the common lancehead (Bothrops atrox (Linnaeus, 1758)), tentatively named Tapajós virus (TAPV). Although the genome organization of TAPV is similar to mammalian filoviruses, our phylogenetic analysis showed that TAPV forms a cluster with a fish filovirus. However, TAPV is still distantly related to all the known filoviruses, suggesting that TAPV can be assigned as a species of a novel genus in Filoviridae. To our knowledge, this is the first report identifying a filovirus in reptiles, and thus contributes to a deeper understanding of the diversity and evolution of filoviruses.I performed metaviromic analysis of publicly available RNA-seq data from reptiles to understand the diversity of filoviruses (family Filoviridae). I identified a coding-complete sequence of a filovirus from the common lancehead (Bothrops atrox (Linnaeus, 1758)), tentatively named Tapajós virus (TAPV). Although the genome organization of TAPV is similar to mammalian filoviruses, our phylogenetic analysis showed that TAPV forms a cluster with a fish filovirus. However, TAPV is still distantly related to all the known filoviruses, suggesting that TAPV can be assigned as a species of a novel genus in Filoviridae. To our knowledge, this is the first report identifying a filovirus in reptiles, and thus contributes to a deeper understanding of the diversity and evolution of filoviruses. I performed metaviromic analysis of publicly available RNA-seq data from reptiles to understand the diversity of filoviruses (family Filoviridae). I identified a coding-complete sequence of a filovirus from the common lancehead (Bothrops atrox (Linnaeus, 1758)), tentatively named Tapajós virus (TAPV). Although the genome organization of TAPV is similar to mammalian filoviruses, our phylogenetic analysis showed that TAPV forms a cluster with a fish filovirus. However, TAPV is still distantly related to all the known filoviruses, suggesting that TAPV can be assigned as a species of a novel genus in Filoviridae. To our knowledge, this is the first report identifying a filovirus in reptiles, and thus contributes to a deeper understanding of the diversity and evolution of filoviruses. I performed metaviromic analysis of publicly available RNA-seq data from reptiles to understand the diversity of filoviruses (family Filoviridae ). I identified a coding-complete sequence of a filovirus from the common lancehead ( Bothrops atrox (Linnaeus, 1758)), tentatively named Tapajós virus (TAPV). Although the genome organization of TAPV is similar to mammalian filoviruses, our phylogenetic analysis showed that TAPV forms a cluster with a fish filovirus. However, TAPV is still distantly related to all the known filoviruses, suggesting that TAPV can be assigned as a species of a novel genus in Filoviridae . To our knowledge, this is the first report identifying a filovirus in reptiles, and thus contributes to a deeper understanding of the diversity and evolution of filoviruses. |
ArticleNumber | 21-0285 |
Author | HORIE, Masayuki |
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Cites_doi | 10.1055/s-0028-1106144 10.1093/bioinformatics/btp348 10.1128/mBio.01360-14 10.1093/nar/gkp335 10.1007/s11262-020-01803-y 10.1016/j.biochi.2015.08.006 10.1101/gr.849004 10.1093/bioinformatics/btz305 10.1038/s41586-018-0012-7 10.1093/molbev/mst010 10.1007/s00705-014-2197-x 10.1186/1471-2105-10-421 10.3390/v9050106 10.1093/ve/veab005 |
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References | 1. Bailey, T. L., Boden, M., Buske, F. A., Frith, M., Grant, C. E., Clementi, L., Ren, J., Li, W. W. and Noble, W. S. 2009. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 37: W202-8. 16. Siegert, R., Shu, H. L., Slenczka, W., Peters, D. and Müller, G. 1967. On the etiology of an unknown human infection originating from monkeys. Dtsch. Med. Wochenschr. 92: 2341–2343. (in German) 2. Bao, Y., Chetvernin, V. and Tatusova, T. 2014. Improvements to pairwise sequence comparison (PASC): a genome-based web tool for virus classification. Arch. Virol. 159: 3293–3304. 3. Bào, Y., Amarasinghe, G. K., Basler, C. F., Bavari, S., Bukreyev, A., Chandran, K., Dolnik, O., Dye, J. M., Ebihara, H., Formenty, P., Hewson, R., Kobinger, G. P., Leroy, E. M., Mühlberger, E., Netesov, S. V., Patterson, J. L., Paweska, J. T., Smither, S. J., Takada, A., Towner, J. S., Volchkov, V. E., Wahl-Jensen, V. and Kuhn, J. H. 2017. Implementation of objective PASC-derived taxon demarcation criteria for official classification of filoviruses. Viruses 9: 9. 13. Kuhn, J., Amarasinghe, G., Perry, D., Howley, P., Knipe, D. and Whelan, S. 2020. Fields virology: emerging viruses. pp. 449–503. In: Wolters Kluwer, Lippincott Williams & Wilkins, Philadelphia. 8. Freitas-de-Sousa, L. A., Amazonas, D. R., Sousa, L. F., Sant’Anna, S. S., Nishiyama, M. Y. Jr., Serrano, S. M., Junqueira-de-Azevedo, I. L., Chalkidis, H. M., Moura-da-Silva, A. M. and Mourão, R. H. 2015. Comparison of venoms from wild and long-term captive Bothrops atrox snakes and characterization of Batroxrhagin, the predominant class PIII metalloproteinase from the venom of this species. Biochimie 118: 60–70. 9. Geoghegan, J. L., Di Giallonardo, F., Wille, M., Ortiz-Baez, A. S., Costa, V. A., Ghaly, T., Mifsud, J. C. O., Turnbull, O. M. H., Bellwood, D. R., Williamson, J. E. and Holmes, E. C. 2021. Virome composition in marine fish revealed by meta-transcriptomics. Virus Evol. 7: veab005. 10. Horie, M., Akashi, H., Kawata, M. and Tomonaga, K. 2020. Identification of a reptile lyssavirus in Anolis allogus provided novel insights into lyssavirus evolution. Virus Genes. 57: 40–49 15. Shi, M., Lin, X. D., Chen, X., Tian, J. H., Chen, L. J., Li, K., Wang, W., Eden, J. S., Shen, J. J., Liu, L., Holmes, E. C. and Zhang, Y. Z. 2018. The evolutionary history of vertebrate RNA viruses. Nature 556: 197–202. 14. Ladner, J. T., Beitzel, B., Chain, P. S., Davenport, M. G., Donaldson, E. F., Frieman, M., Kugelman, J. R., Kuhn, J. H., O’Rear, J., Sabeti, P. C., Wentworth, D. E., Wiley, M. R., Yu, G. Y., Sozhamannan, S., Bradburne, C., Palacios, G., Threat Characterization Consortium. 2014. Standards for sequencing viral genomes in the era of high-throughput sequencing. MBio 5: e01360–e14. 6. Coordinators, N. R.NCBI Resource Coordinators. 2018. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 46 D1: D8–D13. 4. Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K. and Madden, T. L. 2009. BLAST+: architecture and applications. BMC Bioinformatics 10: 421. 11. Katoh, K. and Standley, D. M. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30: 772–780. 5. Capella-Gutiérrez, S., Silla-Martínez, J. M. and Gabaldón, T. 2009. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25: 1972–1973. 7. Crooks, G. E., Hon, G., Chandonia, J. M. and Brenner, S. E. 2004. WebLogo: a sequence logo generator. Genome Res. 14: 1188–1190. 12. Kozlov, A. M., Darriba, D., Flouri, T., Morel, B. and Stamatakis, A. 2019. RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics 35: 4453–4455. 11 12 13 14 15 16 1 2 3 4 5 6 7 8 9 10 |
References_xml | – reference: 10. Horie, M., Akashi, H., Kawata, M. and Tomonaga, K. 2020. Identification of a reptile lyssavirus in Anolis allogus provided novel insights into lyssavirus evolution. Virus Genes. 57: 40–49 – reference: 9. Geoghegan, J. L., Di Giallonardo, F., Wille, M., Ortiz-Baez, A. S., Costa, V. A., Ghaly, T., Mifsud, J. C. O., Turnbull, O. M. H., Bellwood, D. R., Williamson, J. E. and Holmes, E. C. 2021. Virome composition in marine fish revealed by meta-transcriptomics. Virus Evol. 7: veab005. – reference: 6. Coordinators, N. R.NCBI Resource Coordinators. 2018. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 46 D1: D8–D13. – reference: 13. Kuhn, J., Amarasinghe, G., Perry, D., Howley, P., Knipe, D. and Whelan, S. 2020. Fields virology: emerging viruses. pp. 449–503. In: Wolters Kluwer, Lippincott Williams & Wilkins, Philadelphia. – reference: 3. Bào, Y., Amarasinghe, G. K., Basler, C. F., Bavari, S., Bukreyev, A., Chandran, K., Dolnik, O., Dye, J. M., Ebihara, H., Formenty, P., Hewson, R., Kobinger, G. P., Leroy, E. M., Mühlberger, E., Netesov, S. V., Patterson, J. L., Paweska, J. T., Smither, S. J., Takada, A., Towner, J. S., Volchkov, V. E., Wahl-Jensen, V. and Kuhn, J. H. 2017. Implementation of objective PASC-derived taxon demarcation criteria for official classification of filoviruses. Viruses 9: 9. – reference: 7. Crooks, G. E., Hon, G., Chandonia, J. M. and Brenner, S. E. 2004. WebLogo: a sequence logo generator. Genome Res. 14: 1188–1190. – reference: 2. Bao, Y., Chetvernin, V. and Tatusova, T. 2014. Improvements to pairwise sequence comparison (PASC): a genome-based web tool for virus classification. Arch. Virol. 159: 3293–3304. – reference: 14. Ladner, J. T., Beitzel, B., Chain, P. S., Davenport, M. G., Donaldson, E. F., Frieman, M., Kugelman, J. R., Kuhn, J. H., O’Rear, J., Sabeti, P. C., Wentworth, D. E., Wiley, M. R., Yu, G. Y., Sozhamannan, S., Bradburne, C., Palacios, G., Threat Characterization Consortium. 2014. Standards for sequencing viral genomes in the era of high-throughput sequencing. MBio 5: e01360–e14. – reference: 15. Shi, M., Lin, X. D., Chen, X., Tian, J. H., Chen, L. J., Li, K., Wang, W., Eden, J. S., Shen, J. J., Liu, L., Holmes, E. C. and Zhang, Y. Z. 2018. The evolutionary history of vertebrate RNA viruses. Nature 556: 197–202. – reference: 5. Capella-Gutiérrez, S., Silla-Martínez, J. M. and Gabaldón, T. 2009. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25: 1972–1973. – reference: 4. Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K. and Madden, T. L. 2009. BLAST+: architecture and applications. BMC Bioinformatics 10: 421. – reference: 16. Siegert, R., Shu, H. L., Slenczka, W., Peters, D. and Müller, G. 1967. On the etiology of an unknown human infection originating from monkeys. Dtsch. Med. Wochenschr. 92: 2341–2343. (in German) – reference: 11. Katoh, K. and Standley, D. M. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30: 772–780. – reference: 8. Freitas-de-Sousa, L. A., Amazonas, D. R., Sousa, L. F., Sant’Anna, S. S., Nishiyama, M. Y. Jr., Serrano, S. M., Junqueira-de-Azevedo, I. L., Chalkidis, H. M., Moura-da-Silva, A. M. and Mourão, R. H. 2015. Comparison of venoms from wild and long-term captive Bothrops atrox snakes and characterization of Batroxrhagin, the predominant class PIII metalloproteinase from the venom of this species. Biochimie 118: 60–70. – reference: 1. Bailey, T. L., Boden, M., Buske, F. A., Frith, M., Grant, C. E., Clementi, L., Ren, J., Li, W. W. and Noble, W. S. 2009. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 37: W202-8. – reference: 12. Kozlov, A. M., Darriba, D., Flouri, T., Morel, B. and Stamatakis, A. 2019. RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics 35: 4453–4455. – ident: 16 doi: 10.1055/s-0028-1106144 – ident: 5 doi: 10.1093/bioinformatics/btp348 – ident: 14 doi: 10.1128/mBio.01360-14 – ident: 1 doi: 10.1093/nar/gkp335 – ident: 10 doi: 10.1007/s11262-020-01803-y – ident: 8 doi: 10.1016/j.biochi.2015.08.006 – ident: 7 doi: 10.1101/gr.849004 – ident: 12 doi: 10.1093/bioinformatics/btz305 – ident: 13 – ident: 15 doi: 10.1038/s41586-018-0012-7 – ident: 11 doi: 10.1093/molbev/mst010 – ident: 2 doi: 10.1007/s00705-014-2197-x – ident: 4 doi: 10.1186/1471-2105-10-421 – ident: 3 doi: 10.3390/v9050106 – ident: 6 – ident: 9 doi: 10.1093/ve/veab005 |
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Snippet | I performed metaviromic analysis of publicly available RNA-seq data from reptiles to understand the diversity of filoviruses (family Filoviridae). I identified... I performed metaviromic analysis of publicly available RNA-seq data from reptiles to understand the diversity of filoviruses (family Filoviridae ). I... |
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SubjectTerms | Bothrops atrox common lancehead Filoviridae filovirus Virology virome |
Title | Identification of a novel filovirus in a common lancehead (Bothrops atrox (Linnaeus, 1758)) |
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