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Identification of a novel ephemerovirus in a water buffalo (Bubalus bubalis [Linnaeus, 1758])





Bubalus bubalis、 ephemerovirus、 water buffalo


Ephemeroviruses, belonging to the genus Ephemerovirus within the family Rhabdoviridae of the Mononegavirales, are non-segmented, negative-strand RNA viruses that infect artiodactyls and blood-sucking arthropods. Although recent advances in sequencing techniques have facilitated the identification of novel ephemeroviruses, thereby expanding our understanding of this viral genus, their diversity remains elusive, as evidenced by phylogenetic gaps. In this study, we analyzed publicly available RNA-seq data and identified a novel ephemerovirus, tentatively named Punjab virus (PBV), in a water buffalo (Bubalus bubalis [Linnaeus, 1758]). We obtained two separate PBV contigs from the RNA-seq data; the first contig covers the N, P, and M genes, while the second contig covers the G, α, β, γ, and L genes. Together, these PBV contigs represent 99% of the estimated complete viral genome. Mapping analysis revealed a typical transcriptional gradient pattern commonly observed in mononegaviruses, suggesting that the water buffalo is the authentic host for PBV. Sequence comparisons with its closest relatives indicate that the newly identified virus meets the ICTV species demarcation criteria for sequence divergence. Thus, this study contributes to a deeper understanding of the diversity of ephemeroviruses.


There is no conflict of interest.

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Bailey, T. L., Johnson, J., Grant, C. E. and Noble, W. S. 2015. The MEME Suite. Nucleic Acids Res. 43: W39–49.

Balinandi, S., Hayer, J., Cholleti, H., Wille, M., Lutwama, J. J., Malmberg, M. and Mugisha, L. 2022. Identification and molecular characterization of highly divergent RNA viruses in cattle, Uganda. Virus Res. 313: 198739.

Blasdell, K. R., Davis, S. S., Voysey, R., Bulach, D. M., Middleton, D., Williams, S., Harmsen, M. B., Weir, R. P., Crameri, S., Walsh, S. J., Peck, G. R., Tesh, R. B., Boyle, D. B., Melville, L. F. and Walker, P. J. 2020. Hayes Yard virus: a novel ephemerovirus isolated from a bull with severe clinical signs of bovine ephemeral fever is most closely related to Puchong virus. Vet. Res. 51: 58.

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.

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.

Chen, S., Zhou, Y., Chen, Y. and Gu, J. 2018. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 34: i884–i890.

Danecek, P., Bonfield, J. K., Liddle, J., Marshall, J., Ohan, V., Pollard, M. O., Whitwham, A., Keane, T., McCarthy, S. A., Davies, R. M. and Li, H. 2021. Twelve years of SAMtools and BCFtools. Gigascience. 10.:

Darriba, D., Posada, D., Kozlov, A. M., Stamatakis, A., Morel, B. and Flouri, T. 2020. ModelTest-NG: A New and Scalable Tool for the Selection of DNA and Protein Evolutionary Models. Mol. Biol. Evol. 37: 291–294.

Fu, L., Niu, B., Zhu, Z., Wu, S. and Li, W. 2012. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics. 28: 3150–3152.

Geoghegan, J. L. and Holmes, E. C. 2017. Predicting virus emergence amid evolutionary noise. Open Biol. 7.:

Golender, N., Klement, E., Ofer, L., Hoffmann, B., Wernike, K., Beer, M. and Pfaff, F. 2023. Hefer valley virus: a novel ephemerovirus detected in the blood of a cow with severe clinical signs in Israel in 2022. Arch. Virol. 168: 234.

Grabherr, M. G., Haas, B. J., Yassour, M., Levin, J. Z., Thompson, D. A., Amit, I., Adiconis, X., Fan, L., Raychowdhury, R., Zeng, Q., Chen, Z., Mauceli, E., Hacohen, N., Gnirke, A., Rhind, N., di Palma, F., Birren, B. W., Nusbaum, C., Lindblad-Toh, K., Friedman, N. and Regev, A. 2011. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 29: 644–652.

Gurao, A., Vasisth, R., Singh, R., Dige, M. S., Vohra, V., Mukesh, M., Kumar, S. and Kataria, R. S. 2022. Identification of differential methylome signatures of white pigmented skin patches in Nili Ravi buffalo of India. Environ. Mol. Mutagen. 63: 408–417.

Karabatsos, N. 1978. Supplement to International Catalogue of Arboviruses including certain other viruses of vertebrates. Am. J. Trop. Med. Hyg. 27: 372–440.

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.

Kawasaki, J., Kojima, S., Tomonaga, K. and Horie, M. 2021. Hidden Viral Sequences in Public Sequencing Data and Warning for Future Emerging Diseases. MBio. 12: e0163821.

Kawasaki, J., Tomonaga, K. and Horie, M. 2023. Large-scale investigation of zoonotic viruses in the era of high-throughput sequencing. Microbiol. Immunol. 67: 1–13.

Kim, D., Paggi, J. M., Park, C., Bennett, C. and Salzberg, S. L. 2019. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat. Biotechnol. 37: 907–915.

Kircher, M., Sawyer, S. and Meyer, M. 2012. Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Res. 40: e3.

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.

Muhire, B. M., Varsani, A. and Martin, D. P. 2014. SDT: a virus classification tool based on pairwise sequence alignment and identity calculation. PLoS One. 9: e108277.

Nurk, S., Meleshko, D., Korobeynikov, A. and Pevzner, P. A. 2017. metaSPAdes: a new versatile metagenomic assembler. Genome Res. 27: 824–834.

Prjibelski, A., Antipov, D., Meleshko, D., Lapidus, A. and Korobeynikov, A. 2020. Using SPAdes De Novo Assembler. Curr. Protoc. Bioinformatics. 70: e102.

Sayers, E. W., Bolton, E. E., Brister, J. R., Canese, K., Chan, J., Comeau, D. C., Connor, R., Funk, K., Kelly, C., Kim, S., Madej, T., Marchler-Bauer, A., Lanczycki, C., Lathrop, S., Lu, Z., Thibaud-Nissen, F., Murphy, T., Phan, L., Skripchenko, Y., Tse, T., Wang, J., Williams, R., Trawick, B. W., Pruitt, K. D. and Sherry, S. T. 2022. Database resources of the national center for biotechnology information. Nucleic Acids Res. 50: D20–D26.

Shen, W., Le, S., Li, Y. and Hu, F. 2016. SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation. PLoS One. 11: e0163962.

Shi, M., Zhang, Y.-Z. and Holmes, E. C. 2018. Meta-transcriptomics and the evolutionary biology of RNA viruses. Virus Res. 243: 83–90.

Souvorov, A., Agarwala, R. and Lipman, D. J. 2018. SKESA: strategic k-mer extension for scrupulous assemblies. Genome Biol. 19: 153.

Steinegger, M. and Söding, J. 2017. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nat. Biotechnol. 35: 1026–1028.

Walker, P. J., Freitas-Astúa, J., Bejerman, N., Blasdell, K. R., Breyta, R., Dietzgen, R. G., Fooks, A. R., Kondo, H., Kurath, G., Kuzmin, I. V., Ramos-González, P. L., Shi, M., Stone, D. M., Tesh, R. B., Tordo, N., Vasilakis, N., Whitfield, A. E. and Ictv Report Consortium 2022. ICTV Virus Taxonomy Profile: Rhabdoviridae 2022. J. Gen. Virol. 103.:

Walker, P. J. and Klement, E. 2015. Epidemiology and control of bovine ephemeral fever. Vet. Res. 46: 124.

Wright, E. S. and Vetsigian, K. H. 2016. Quality filtering of Illumina index reads mitigates sample cross-talk. BMC Genomics. 17: 876.


投稿日時: 2023-09-01 14:31:16 UTC

公開日時: 2023-09-05 23:19:15 UTC