リケラボ論文検索は、全国の大学リポジトリにある学位論文・教授論文を一括検索できる論文検索サービスです。

リケラボ 全国の大学リポジトリにある学位論文・教授論文を一括検索するならリケラボ論文検索大学・研究所にある論文を検索できる

リケラボ 全国の大学リポジトリにある学位論文・教授論文を一括検索するならリケラボ論文検索大学・研究所にある論文を検索できる

大学・研究所にある論文を検索できる 「Hidden Viral Sequences in Public Sequencing Data and Warning for Future Emerging Diseases」の論文概要。リケラボ論文検索は、全国の大学リポジトリにある学位論文・教授論文を一括検索できる論文検索サービスです。
リケラボ

コピーが完了しました

URLをコピーしました

論文の公開元へ論文の公開元へ
書き出し

Hidden Viral Sequences in Public Sequencing Data and Warning for Future Emerging Diseases

Kawasaki, Junna Kojima, Shohei Tomonaga, Keizo Horie, Masayuki 京都大学 DOI:10.1128/mBio.01638-21

2021.08.31

概要

RNA viruses cause numerous emerging diseases, mostly due to transmission from mammalian and avian reservoirs. Large-scale surveillance of RNA viral infections in these animals is a fundamental step for controlling viral infectious diseases. Metagenomic analysis is a powerful method for virus identification with low bias and has contributed substantially to the discovery of novel viruses. Deep-sequencing data have been collected from diverse animals and accumulated in public databases, which can be valuable resources for identifying unknown viral sequences. Here, we screened for infections of 33 RNA viral families in publicly available mammalian and avian sequencing data and found approximately 900 hidden viral infections. We also discovered six nearly complete viral genomes in livestock, wild, and experimental animals: hepatovirus in a goat, hepeviruses in blind mole-rats and a galago, astrovirus in macaque monkeys, parechovirus in a cow, and pegivirus in tree shrews. Some of these viruses were phylogenetically close to human-pathogenic viruses, suggesting the potential risk of causing disease in humans upon infection. Furthermore, infections of five novel viruses were identified in several different individuals, indicating that their infections may have already spread in the natural host population. Our findings demonstrate the reusability of public sequencing data for surveying viral infections and identifying novel viral sequences, presenting a warning about a new threat of viral infectious disease to public health. IMPORTANCE Monitoring the spread of viral infections and identifying novel viruses capable of infecting humans through animal reservoirs are necessary to control emerging viral diseases. Massive amounts of sequencing data collected from various animals are publicly available, and these data may contain sequences originating from a wide variety of viruses. Here, we analyzed more than 46, 000 public sequencing data and identified approximately 900 hidden RNA viral infections in mammalian and avian samples. Some viruses discovered in this study were genetically similar to pathogens that cause hepatitis, diarrhea, or encephalitis in humans, suggesting the presence of new threats to public health. Our study demonstrates the effectiveness of reusing public sequencing data to identify known and unknown viral infections, indicating that future continuous monitoring of public sequencing data by metagenomic analyses would help prepare and mitigate future viral pandemics.

論文の公開元へ

この論文で使われている画像

関連論文

関連論文をもっと見る

参考文献

A Self-archived copy in

Kyoto University Research Information Repository

https://repository.kulib.kyoto-u.ac.jp

31. Cordey S, Vu D-L, Schibler M, L'Huillier AG, Brito F, Docquier M, PosfayBarbe KM, Petty TJ, Turin L, Zdobnov EM, Kaiser L. 2016. Astrovirus MLB2,

a new gastroenteric virus associated with meningitis and disseminated

infection. Emerg Infect Dis 22:846–853. https://doi.org/10.3201/eid2205

.151807.

32. Karlsson EA, Small CT, Freiden P, Feeroz M, Matsen FA, San S, Hasan MK,

Wang D, Jones-Engel L, Schultz-Cherry S. 2015. Non-human primates harbor diverse mammalian and avian astroviruses including those associated

with human infections. PLoS Pathog 11:e1005225. https://doi.org/10

.1371/journal.ppat.1005225.

33. Britton PN, Jones CA, Macartney K, Cheng AC. 2018. Parechovirus: an important emerging infection in young infants. Med J Aust 208:365–369.

https://doi.org/10.5694/mja18.00149.

34. Zell R, Delwart E, Gorbalenya AE, Hovi T, King AMQ, Knowles NJ, Lindberg

AM, Pallansch MA, Palmenberg AC, Reuter G, Simmonds P, Skern T,

Stanway G, Yamashita T. 2017. ICTV virus taxonomy profile: Picornaviridae. J Gen Virol 98:2421–2422. https://doi.org/10.1099/jgv.0.000911.

35. Simmonds P, Becher P, Bukh J, Gould EA, Meyers G, Monath T, Muerhoff

S, Pletnev A, Rico-Hesse R, Smith DB, Stapleton JT. 2017. ICTV virus taxonomy profile: Flaviviridae. J Gen Virol 98:2–3. https://doi.org/10.1099/jgv.0

.000672.

36. Wu Z, Han Y, Liu B, Li H, Zhu G, Latinne A, Dong J, Sun L, Su H, Liu L, Du J,

Zhou S, Chen M, Kritiyakan A, Jittapalapong S, Chaisiri K, Buchy P, Duong

V, Yang J, Jiang J, Xu X, Zhou H, Yang F, Irwin DM, Morand S, Daszak P,

Wang J, Jin Q. 2021. Decoding the RNA viromes in rodent lungs provides

new insight into the origin and evolutionary patterns of rodent-borne

pathogens in Mainland Southeast Asia. Microbiome 9:18. https://doi.org/

10.1186/s40168-020-00965-z.

37. Antipov D, Raiko M, Lapidus A, Pevzner PA. 2020. MetaviralSPAdes: assembly of viruses from metagenomic data. Bioinformatics 36:4126–4129.

https://doi.org/10.1093/bioinformatics/btaa490.

38. Yahara K, Suzuki M, Hirabayashi A, Suda W, Hattori M, Suzuki Y, Okazaki Y.

2021. Long-read metagenomics using PromethION uncovers oral bacteriophages and their interaction with host bacteria. Nat Commun 12:27.

https://doi.org/10.1038/s41467-020-20199-9.

39. Dreher TW. 1999. Functions of the 39-untranslated regions of positive

strand RNA viral genomes. Annu Rev Phytopathol 37:151–174. https://doi

.org/10.1146/annurev.phyto.37.1.151.

40. Munis AM, Bentley EM, Takeuchi Y. 2020. A tool with many applications:

vesicular stomatitis virus in research and medicine. Expert Opin Biol Ther

20:1187–1201. https://doi.org/10.1080/14712598.2020.1787981.

41. Feehan BJ, Penin AA, Mukhin AN, Kumar D, Moskvina AS, Khametova

KM, Yuzhakov AG, Musienko MI, Zaberezhny AD, Aliper TI, Marthaler D,

Alekseev KP. 2019. Novel mammalian orthorubulavirus 5 discovered as

accidental cell culture contaminant. Viruses 11:777. https://doi.org/10

.3390/v11090777.

42. Wignall-Fleming E, Young DF, Goodbourn S, Davison AJ, Randall RE. 2016.

Genome sequence of the parainfluenza virus 5 strain that persistently

infects AGS cells. Genome Announc 4:e00653-16. https://doi.org/10.1128/

genomeA.00653-16.

43. Ngoi CN, Siqueira J, Li L, Deng X, Mugo P, Graham SM, Price MA, Sanders EJ,

Delwart E. 2017. Corrigendum: The plasma virome of febrile adult Kenyans

shows frequent parvovirus B19 infections and a novel arbovirus (Kadipiro virus). J Gen Virol 98:517–517. https://doi.org/10.1099/jgv.0.000762.

44. Gibb R, Albery GF, Becker DJ, Brierley L, Connor R, Dallas TA, Eskew EA,

Farrell MJ, Rasmussen AL, Ryan SJ, Sweeny A, Carlson CJ, Poisot T. 2021.

Data proliferation, reconciliation, and synthesis in viral ecology. bioRxiv

https://doi.org/10.1101/2021.01.14.426572:2021.01.14.426572.

July/August 2021 Volume 12 Issue 4 e01638-21

45. Chen S, Zhou Y, Chen Y, Gu J. 2018. fastp: an ultra-fast all-in-one FASTQ

preprocessor. Bioinformatics 34:i884–i890. https://doi.org/10.1093/

bioinformatics/bty560.

46. Kim D, Langmead B, Salzberg SL. 2015. HISAT: a fast spliced aligner with

low memory requirements. Nat Methods 12:357–360. https://doi.org/10

.1038/nmeth.3317.

47. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G,

Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup.

2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics

25:2078–2079. https://doi.org/10.1093/bioinformatics/btp352.

48. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS,

Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV,

Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J

Comput Biol 19:455–477. https://doi.org/10.1089/cmb.2012.0021.

49. Nurk S, Meleshko D, Korobeynikov A, Pevzner PA. 2017. metaSPAdes: a

new versatile metagenomic assembler. Genome Res 27:824–834. https://

doi.org/10.1101/gr.213959.116.

50. Shen W, Le S, Li Y, Hu F. 2016. SeqKit: a cross-platform and ultrafast toolkit

for FASTA/Q file manipulation. PLoS One 11:e0163962. https://doi.org/10

.1371/journal.pone.0163962.

51. Fourie P, Kirkman W, Cook G, Steyn C, de Bruyn R, Bester R, Roberts R,

Bassimba DD, José CM, Maree HJ. 2020. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Plant

Dis 22:1658–1659.

52. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K,

Madden TL. 2009. BLAST1: architecture and applications. BMC Bioinformatics 10:421. https://doi.org/10.1186/1471-2105-10-421.

53. Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. 2016. GenBank.

Nucleic Acids Res 44:D67–D72. https://doi.org/10.1093/nar/gkv1276.

54. Barrett T, Clark K, Gevorgyan R, Gorelenkov V, Gribov E, Karsch-Mizrachi I,

Kimelman M, Pruitt KD, Resenchuk S, Tatusova T, Yaschenko E, Ostell J.

2012. BioProject and BioSample databases at NCBI: facilitating capture

and organization of metadata. Nucleic Acids Res 40:D57–D63. https://doi

.org/10.1093/nar/gkr1163.

55. Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol

30:772–780. https://doi.org/10.1093/molbev/mst010.

56. Nguyen L-T, Schmidt HA, Von Haeseler A, Minh BQ. 2015. IQ-TREE: a fast

and effective stochastic algorithm for estimating maximum-likelihood

phylogenies. Mol Biol Evol 32:268–274. https://doi.org/10.1093/molbev/

msu300.

57. Kalyaanamoorthy S, Minh BQ, Wong TKF, Von Haeseler A, Jermiin LS.

2017. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods 14:587–589. https://doi.org/10.1038/nmeth.4285.

58. Hoang DT, Chernomor O, Von Haeseler A, Minh BQ, Vinh LS. 2018. UFBoot2:

improving the ultrafast bootstrap approximation. Mol Biol Evol 35:518–522.

https://doi.org/10.1093/molbev/msx281.

59. Yu G, Smith DK, Zhu H, Guan Y, Lam TTY. 2017. ggtree: an r package for

visualization and annotation of phylogenetic trees with their covariates

and other associated data. Methods Ecol Evol 8:28–36. https://doi.org/10

.1111/2041-210X.12628.

60. Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P,

Chaisson M, Gingeras TR. 2013. STAR: ultrafast universal RNA-seq aligner.

Bioinformatics 29:15–21. https://doi.org/10.1093/bioinformatics/bts635.

61. Quinlan AR, Hall IM. 2010. BEDTools: a flexible suite of utilities for comparing

genomic features. Bioinformatics 26:841–842. https://doi.org/10.1093/

bioinformatics/btq033.

mbio.asm.org

17

Downloaded from https://journals.asm.org/journal/mbio on 17 June 2022 by 130.54.110.22.

Public Data Reusability To Identify Viral Infections

...

参考文献をもっと見る