Abstract
Posaviruses and posa-like viruses are unclassified viruses with sequence similarity to viruses of the order Picornavirales. They have been reported in various vertebrates and invertebrates. We identified 11 posavirus-like sequences in porcine feces and performed phylogenic analysis. Previously reported Japanese posaviruses and those identified in this study clustered with posavirus 1, 4, and 7 and husavirus 1, while five viruses branched into three independent lineages, tentatively named posavirus 10, 11, and 12. Interestingly, posaviruses, except for posavirus 8 and 9, husaviruses, and rasaviruses, formed a cluster consisting of viruses only from pigs, humans, and rats, while posavirus 8 and 9, fisavirus, and basaviruses clustered with posa-like viruses from invertebrates.
References
Le Gall O, Christian P, Fauquet CM, King AM, Knowles NJ, Nakashima N, Stanway G, Gorbalenya AE (2008) Picornavirales, a proposed order of positive-sense single-stranded RNA viruses with a pseudo-T = 3 virion architecture. Arch Virol 153:715–727. https://doi.org/10.1007/s00705-008-0041-x
Shan T, Li L, Simmonds P, Wang C, Moeser A, Delwart E (2011) The fecal virome of pigs on a high-density farm. J Virol 85:11697–11708. https://doi.org/10.1128/JVI.05217-11
Wang J, Czech B, Crunk A, Wallace A, Mitreva M, Hannon GJ, Davis RE (2011) Deep small RNA sequencing from the nematode Ascaris reveals conservation, functional diversification, and novel developmental profiles. Genome Res 21:1462–1477. https://doi.org/10.1101/gr.121426.111
Zhang B, Tang C, Yue H, Ren Y, Song Z (2014) Viral metagenomics analysis demonstrates the diversity of viral flora in piglet diarrhoeic faeces in China. J Gen Virol 95:1603–1611
Hause BM, Hesse RA, Anderson GA (2015) Identification of a novel Picornavirales virus distantly related to posavirus in swine feces. Virus Genes 51:144–147. https://doi.org/10.1007/s11262-015-1215-8
Hause BM, Palinski R, Hesse R, Anderson G (2016) Highly diverse posaviruses in swine faeces are aquatic in origin. J Gen Virol 97:1362–1367. https://doi.org/10.1099/jgv.0.000461
Sano K, Naoi Y, Kishimoto M, Masuda T, Tanabe H, Ito M, Niira K, Haga K, Asano K, Tsuchiaka S, Omatsu T, Furuya T, Katayama Y, Oba M, Ouchi Y, Yamasato H, Ishida M, Shirai J, Katayama K, Mizutani T, Nagai M (2016) Identification of further diversity among posaviruses. Arch Virol 161:3541–3548
Oude Munnink BB, Cotten M, Deijs M, Jebbink MF, Bakker M, Farsani SM, Canuti M, Kellam P, van der Hoek L (2015) A novel genus in the order Picornavirales detected in human stool. J Gen Virol 96:3440–3443
Oude Munnink BB, Phan MVT, VIZIONS Consortium, Simmonds P, Koopmans MPG, Kellam P, van der Hoek L, Cotten M (2017) Characterization of posa and posa-like virus genomes in fecal samples from humans, pigs, rats, and bats collected from a single location in Vietnam. Virus Evol 3(2):vex022. https://doi.org/10.1093/ve/vex022
Siqueira JD, Dominguez-Bello MG, Contreras M, Lander O, Caballero-Arias H, Xutao D, Noya-Alarcon O, Delwart E (2018) Complex virome in feces from Amerindian children in isolated Amazonian villages. Nat Commun 9(1):4270. https://doi.org/10.1038/s41467-018-06502-9
Reuter G, Pankovics P, Delwart E, Boros Á (2015) A novel posavirus-related single-stranded RNA virus from fish (Cyprinus carpio). Arch Virol 160:565–568. https://doi.org/10.1007/s00705-014-2304-z
Zhang W, Yang S, Shan T, Hou R, Liu Z, Li W, Guo L, Wang Y, Chen P, Wang X, Feng F, Wang H, Chen C, Shen Q, Zhou C, Hua X, Cui L, Deng X, Zhang Z, Qi D, Delwart E (2017) Virome comparisons in wild-diseased and healthy captive giant pandas. Microbiome 5(1):90. https://doi.org/10.1186/s40168-017-0308-0
Duraisamy R, Akiana J, Davoust B, Mediannikov O, Michelle C, Robert C, Parra HJ, Raoult D, Biagini P, Desnues C (2018) Detection of novel RNA viruses from free-living gorillas, Republic of the Congo: genetic diversity of picobirnaviruses. Virus Genes 54:256–271. https://doi.org/10.1007/s11262-018-1543-6
Webster CL, Longdon B, Lewis SH, Obbard DJ (2016) Twenty-five new viruses associated with the Drosophilidae (Diptera). Evol Bioinform Online 12(Suppl 2):13–25. https://doi.org/10.4137/ebo.s39454
Shi M, Lin XD, Tian JH, Chen LJ, Chen X, Li CX, Qin XC, Li J, Cao JP, Eden JS, Buchmann J, Wang W, Xu J, Holmes EC, Zhang YZ (2016) Redefining the invertebrate RNA virosphere. Nature 540:539–543. https://doi.org/10.1038/nature20167
Nagai M, Omatsu T, Aoki H, Otomaru K, Uto T, Koizumi M, Minami-Fukuda F, Takai H, Murakami T, Masuda T, Yamasato H, Shiokawa M, Tsuchiaka S, Naoi Y, Sano K, Okazaki S, Katayama Y, Oba M, Furuya T, Shirai J, Mizutani T (2015) Full genome analysis of bovine astrovirus from fecal samples of cattle in Japan: identification of possible interspecies transmission of bovine astrovirus. Arch Virol 160:2491–2501. https://doi.org/10.1007/s00705-015-2543-7
Oka T, Takagi H, Tohya Y (2014) Development of a novel single step reverse genetics system for feline calicivirus. J Virol Methods 207:178–181. https://doi.org/10.1016/j.jviromet.2014.07.004
Oka T, Lu Z, Phan T, Delwart EL, Saif LJ, Wang Q (2016) Genetic characterization and classification of human and animal sapoviruses. PLoS One 11(5):e0156373. https://doi.org/10.1371/journal.pone.0156373
Oka T, Doan YH, Haga K, Mori K, Ogawa T, Yamazaki A (2017) Genetic characterization of rare genotype GII.5 sapovirus strain detected from a suspected food-borne gastroenteritis outbreak among adults in Japan in 2010. Jpn J Infect Dis 70:223–224. https://doi.org/10.7883/yoken.JJID.2016.468
Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882
Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874
Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791
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This work was supported by JSPS KAKENHI (Grant numbers: 15K07718 and 18K05977).
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Supplementary Fig.
Genome structure of Ishi-Im7/JPN/2016 with the putative conserved domains identified using the CCD search. (PPTX 37 kb)
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Aoki, H., Sunaga, F., Ochiai, H. et al. Phylogenetic analysis of novel posaviruses detected in feces of Japanese pigs with posaviruses and posa-like viruses of vertebrates and invertebrates. Arch Virol 164, 2147–2151 (2019). https://doi.org/10.1007/s00705-019-04289-8
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DOI: https://doi.org/10.1007/s00705-019-04289-8