Citation: | Feng-Juan Tian, Jing Li, Wen-Li Liu, Yu-Jie Liu, Yun-Jia Hu, Qi-Hang Tu, Yang Li, Yu Bai, Mang Shi, Teng-Cheng Que, Yan-Ling Hu, Yi-Gang Tong. Virome in healthy pangolins reveals compatibility with multiple potentially zoonotic viruses. Zoological Research, 2022, 43(6): 977-988. doi: 10.24272/j.issn.2095-8137.2022.246 |
[1] |
Berg MG, Forberg K, Perez LJ, Luk KC, Meyer TV, Cloherty GA. 2021. Emergence of a distinct picobirnavirus genotype circulating in patients hospitalized with acute respiratory illness. Viruses, 13(12): 2534. doi: 10.3390/v13122534
|
[2] |
Buchfink B, Xie C, Huson DH. 2015. Fast and sensitive protein alignment using DIAMOND. Nature Methods, 12(1): 59−60. doi: 10.1038/nmeth.3176
|
[3] |
CDC. 2021. Zoonotic Diseases.
|
[4] |
Chen SF, Zhou YQ, Chen YR, Gu J. 2018. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics, 34(17): i884−i890. doi: 10.1093/bioinformatics/bty560
|
[5] |
Choo SW, Rayko M, Tan TK, Hari R, Komissarov A, Wee WY, et al. 2016. Pangolin genomes and the evolution of mammalian scales and immunity. Genome Research, 26(10): 1312−1322. doi: 10.1101/gr.203521.115
|
[6] |
Cotmore SF, Agbandje-McKenna M, Canuti M, Chiorini JA, Eis-Hubinger AM, Hughes J, et al. 2019. ICTV virus taxonomy profile: parvoviridae. Journal of General Virology, 100(3): 367−368. doi: 10.1099/jgv.0.001212
|
[7] |
Gao WH, Lin XD, Chen YM, Xie CG, Tan ZZ, Zhou JJ, et al. 2020. Newly identified viral genomes in pangolins with fatal disease. Virus Evolution, 6(1): veaa020. doi: 10.1093/ve/veaa020
|
[8] |
Ghosh S, Kobayashi N. 2014. Exotic rotaviruses in animals and rotaviruses in exotic animals. Virusdisease, 25(2): 158−172. doi: 10.1007/s13337-014-0194-z
|
[9] |
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. Systematic Biology, 59(3): 307−321. doi: 10.1093/sysbio/syq010
|
[10] |
Haley PJ. 2022. From bats to pangolins: new insights into species differences in the structure and function of the immune system. Innate Immunity, 28(3–4): 107–121.
|
[11] |
Harrison RL, Herniou EA, Jehle JA, Theilmann DA, Burand JP, Becnel JJ, et al. 2018. ICTV virus taxonomy profile: baculoviridae. Journal of General Virology, 99(9): 1185–1186.
|
[12] |
Harvey E, Holmes EC. 2022. Diversity and evolution of the animal virome. Nature Reviews Microbiology, 20(6): 321−334. doi: 10.1038/s41579-021-00665-x
|
[13] |
Hassan M, Sulaiman MH, Lian CJ. 2013. The prevalence and intensity of Amblyomma javanense infestation on Malayan pangolins (Manis javanica Desmarest) from Peninsular Malaysia. Acta Tropica, 126(2): 142−145. doi: 10.1016/j.actatropica.2013.02.001
|
[14] |
Hassanin A, Tu VT, Curaudeau M, Csorba G. 2021. Inferring the ecological niche of bat viruses closely related to SARS-CoV-2 using phylogeographic analyses of Rhinolophus species. Scientific Reports, 11(1): 14276. doi: 10.1038/s41598-021-93738-z
|
[15] |
He WT, Hou X, Zhao J, Sun JM, He HJ, Si W, et al. 2022. Virome characterization of game animals in China reveals a spectrum of emerging pathogens. Cell, 185(7): 1117−1129.E8. doi: 10.1016/j.cell.2022.02.014
|
[16] |
Heath M, Coulson I. 1997. Home range size and distribution in a wild population of Cape pangolins, Manis temminckii, in north-west Zimbabwe. African Journal of Ecology, 35(2): 94−109. doi: 10.1111/j.1365-2028.1997.080-89080.x
|
[17] |
Huaman JL, Pacioni C, Sarker S, Doyle M, Forsyth DM, Pople A, et al. 2021. Molecular epidemiology and characterization of picobirnavirus in wild deer and cattle from australia: evidence of genogroup I and II in the upper respiratory Tract. Viruses, 13(8): 1492. doi: 10.3390/v13081492
|
[18] |
Islam A, Ferdous J, Islam S, Sayeed A, Rahman K, Saha O, et al. 2021. Transmission dynamics and susceptibility patterns of SARS-CoV-2 in domestic, farmed and wild animals: Sustainable One Health surveillance for conservation and public health to prevent future epidemics and pandemics. Transboundary and Emerging Diseases,doi: 10.1111/tbed.14356.
|
[19] |
Kashnikov AY, Epifanova NV, Novikova NA. 2020. Picobirnaviruses: prevalence, genetic diversity, detection methods. Vavilov Journal of Genetics and Breeding, 24(6): 661−672. doi: 10.18699/VJ20.660
|
[20] |
Katoh K, Misawa K, Kuma KI, Miyata T. 2002. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research, 30(14): 3059−3066. doi: 10.1093/nar/gkf436
|
[21] |
Lam TTY, Jia N, Zhang YW, Shum MHH, Jiang JF, Zhu HC, et al. 2020. Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins. Nature, 583(7815): 282−285. doi: 10.1038/s41586-020-2169-0
|
[22] |
Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nature Methods, 9(4): 357−359. doi: 10.1038/nmeth.1923
|
[23] |
Li DH, Liu CM, Luo RB, 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(10): 1674–1676.
|
[24] |
Li DH, Luo RB, Liu CM, Leung CM, Ting HF, Sadakane K, et al. 2016. MEGAHIT v1.0: a fast and scalable metagenome assembler driven by advanced methodologies and community practices. Methods, 102: 3−11. doi: 10.1016/j.ymeth.2016.02.020
|
[25] |
Liu P, Chen W, Chen JP. 2019. Viral metagenomics revealed sendai virus and coronavirus infection of malayan pangolins (Manis javanica). Viruses, 11(11): 979. doi: 10.3390/v11110979
|
[26] |
Navarro R, Yibin C, Nair R, Peda A, Aung MS, Ketzis J, et al. 2017. Molecular characterization of complete genomic segment-2 of picobirnavirus strains detected in a cat and a dog. Infection, Genetics and Evolution, 54: 200−204. doi: 10.1016/j.meegid.2017.07.006
|
[27] |
Nga NTT, Latinne A, Thuy HB, Van Long N, Ngoc PTB, Anh NTL, et al. 2022. Evidence of SARS-CoV-2 related coronaviruses circulating in sunda pangolins (Manis javanica) confiscated from the illegal wildlife trade in viet nam. Frontiers in Public Health, 10: 826116. doi: 10.3389/fpubh.2022.826116
|
[28] |
Ning SY, Dai ZY, Zhao CY, Feng ZH, Jin KX, Yang SX, et al. 2022. Novel putative pathogenic viruses identified in pangolins by mining metagenomic data. Journal of Medical Virology, 94(6): 2500−2509. doi: 10.1002/jmv.27564
|
[29] |
Olendraite I, Brown K, Valles SM, Firth AE, Chen YP, Guérin DMA, et al. 2019. ICTV virus taxonomy profile: Polycipiviridae. Journal of General Virology, 100(4): 554–555.
|
[30] |
Peng MS, Li JB, Cai ZF, Liu H, Tang XL, Ying RC, et al. 2021. The high diversity of SARS-CoV-2-related coronaviruses in pangolins alerts potential ecological risks. Zoological Research, 42(6): 834−844.
|
[31] |
Que TC, Li J, He YG, Chen PY, Lin W, He MH, et al. 2022. Human parainfluenza 3 and respiratory syncytial viruses detected in pangolins. Emerging Microbes & Infections, 11(1): 1657−1663.
|
[32] |
Schweizer M, Peterhans E. 2014. Pestiviruses. Annual Review of Animal Biosciences, 2: 141−163. doi: 10.1146/annurev-animal-022513-114209
|
[33] |
Shi WQ, Shi M, Que TC, Cui XM, Ye RZ, Xia LY, et al. 2022. Trafficked Malayan pangolins contain viral pathogens of humans. Nature Microbiology, 7(8): 1259−1269. doi: 10.1038/s41564-022-01181-1
|
[34] |
Simmonds P, Becher P, Bukh J, Gould EA, Meyers G, Monath T, et al. 2017. ICTV virus taxonomy profile: Flaviviridae. Journal of General Virology, 98(1): 2–3.
|
[35] |
Stoltz DB, Krell P, Summers MD, Vinson SB. 1984. Polydnaviridae - a proposed family of insect viruses with segmented, double-stranded, circular DNA genomes. Intervirology, 21(1): 1−4. doi: 10.1159/000149497
|
[36] |
Valles SM, Chen Y, Firth AE, Guérin DMA, Hashimoto Y, Herrero S, et al. 2017. ICTV virus taxonomy profile: Dicistroviridae. Journal of General Virology, 98(3): 355–356.
|
[37] |
Walker PJ, Blasdell KR, Calisher CH, Dietzgen RG, Kondo H, Kurath G, et al. 2018. ICTV virus taxonomy profile: Rhabdoviridae. Journal of General Virology, 99(4): 447–448.
|
[38] |
Wang SL, Tu YC, Lee MS, Wu LH, Chen TY, Wu CH, et al. 2020. Fatal canine parvovirus-2 (CPV-2) infection in a rescued free-ranging Taiwanese pangolin (Manis pentadactyla pentadactyla). Transboundary and Emerging Diseases, 67(3): 1074−1081. doi: 10.1111/tbed.13469
|
[39] |
Wang XH, Chen W, Xiang R, Li LM, Chen J, Zhong RQ, et al. 2019. Complete genome sequence of parainfluenza virus 5 (PIV5) from a sunda pangolin (Manis javanica) in China. Journal of Wildlife Diseases, 55(4): 947−950. doi: 10.7589/2018-09-211
|
[40] |
Xiao KP, Zhai JQ, Feng YY, Zhou N, Zhang X, Zou JJ, et al. 2020. Isolation of SARS-CoV-2-related coronavirus from Malayan pangolins. Nature, 583(7815): 286−289. doi: 10.1038/s41586-020-2313-x
|
[41] |
Yang SX, Shan TL, Xiao YQ, Zhang HT, Wang XC, Shen Q, et al. 2021. Digging metagenomic data of pangolins revealed SARS-CoV-2 related viruses and other significant viruses. Journal of Medical Virology, 93(3): 1786−1791. doi: 10.1002/jmv.26524
|
[42] |
Ye RZ, Que TC, Xia LY, Cui XM, Zhang YW, Jiang JF, et al. 2022. Natural infection of pangolins with human respiratory syncytial viruses. Current Biology, 32(7): R307−R308. doi: 10.1016/j.cub.2022.02.057
|
[43] |
Zhai SL, Lu SS, Wei WK, Lv DH, Wen XH, Zhai Q, et al. 2019. Reservoirs of porcine circoviruses: a mini review. Frontiers in Veterinary Science, 6: 319. doi: 10.3389/fvets.2019.00319
|
[44] |
Zhang YZ, Shi M, Holmes EC. 2018. Using metagenomics to characterize an expanding virosphere. Cell, 172(6): 1168−1172. doi: 10.1016/j.cell.2018.02.043
|
[45] |
Zhao M, Yue CJ, Yang ZJ, Li YL, Zhang DS, Zhang J, et al. 2022. Viral metagenomics unveiled extensive communications of viruses within giant pandas and their associated organisms in the same ecosystem. Science of the Total Environment, 820: 153317. doi: 10.1016/j.scitotenv.2022.153317
|
![]() |
![]() |