Meta-transcriptomics and the evolutionary biology of RNA viruses

Virus Research

Volumn 243, Issue , 2018, Pages 83-90

  Shi, Mang ^a,b   Zhang, Yong Zhen ^b   Holmes, Edward C ^a,b  

^a University of Sydney   (Australia)

^b CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION   (China)

Author keywords

Classification; Evolution; Meta transcriptomics; Metagenomics; Phylogeny; Virosphere

Indexed keywords

ANIMAL VIRUS; GENE STRUCTURE; INSECT VIRUS; INVERTEBRATE; METAGENOMICS; NONHUMAN; PLANT VIRUS; PRIORITY JOURNAL; REVIEW; RNA VIRUS; SPECIES DIVERSITY; TRANSCRIPTOMICS; VERTEBRATE; VIROGENESIS; VIRUS GENOME; VIRUS IDENTIFICATION; VIRUS TRANSMISSION; ANIMAL; CLASSIFICATION; GENETICS; HUMAN; ISOLATION AND PURIFICATION; MOLECULAR EVOLUTION; PHYLOGENY; RNA VIRUS INFECTION; VIROLOGY;

ANIMALS; EVOLUTION, MOLECULAR; GENOME, VIRAL; HUMANS; METAGENOMICS; PHYLOGENY; RNA VIRUS INFECTIONS; RNA VIRUSES;

EID: 85032452649     PISSN: 01681702     EISSN: 18727492     Source Type: Journal    
DOI: 10.1016/j.virusres.2017.10.016     Document Type: Review

References (51)

1. Akopyants, N.S., Lye, L.F., Dobson, D.E., Lukeš, J., Beverley, S.M., A novel bunyavirus-like virus of trypanosomatid protist parasites. Genome Announc. 4 (2016), e00715–16.
2. Allison, A.B., Ballard, J.R., Tesh, R.B., Brown, J.D., Ruder, M.G., Keel, M.K., Munk, B.A., Mickley, R.M., Travassos da Rosa, A.P.A., Ellis, J.C., Ip, H., Shern-Bochsler, V.I., Rodgers, M.B., Ghedin, E., Holmes, E.C., Parrish, C.R., Dwyer, C., Cyclic avian mass mortality in the northeastern United States is associated with a novel orthomyxovirus. J. Virol. 89 (2015), 1389–1403.
3. Angly, F.E., Felts, B., Breitbart, M., Salamon, P., Edwards, R.A., Carlson, C., Chan, A.M., Haynes, M., Kelley, S., Liu, H., Mahaffy, J.M., Mueller, J.E., Nulton, J., Olson, R., Parsons, R., Rayhawk, S., Suttle, C.A., Rohwer, F., The marine virospheres of four oceanic regions. PLoS Biol., 4, 2006, e368.
4. Anthony, S.J., Johnson, C.K., Greig, D.J., Kramer, S., Che, X., Wells, H., Hicks, A.L., Joly, D.O., Wolfe, N.D., Daszak, P., Karesh, W., Lipkin, W.I., Morse, S.S., PREDICT Consortium Mazet, J.A.K., Goldstein, T., Global patterns in coronavirus diversity. Virus Evol., 3, 2017, 10.1093/ve/vex012.
5. Bolduc, B., Shaughnessy, D.P., Wolf, Y.I., Koonin, E.V., Roberto, F.F., Young, M., Identification of novel positive-strand RNA viruses by metagenomic analysis of archaea-dominated Yellowstone hot springs. J. Virol. 86 (2012), 5562–5573.
6. Bolling, B.G., Weaver, S.C., Tesh, R.B., Vasilakis, N., Insect-specific virus discovery: significance for the arbovirus community. Viruses 7 (2015), 4911–4928.
7. Cook, S., Chung, B.Y., Bass, D., Moureau, G., Tang, S., McAlister, E., Culverwell, C.L., Glücksman, E., Wang, H., Brown, T.D., Gould, E.A., Harbach, R.E., de Lamballerie, X., Firth, A.E., Novel virus discovery and genome reconstruction from field RNA samples reveals highly divergent viruses in dipteran hosts. PLoS One, 18, 2013, e80720.
8. Culley, A.I., Lang, A.S., Suttle, C.A., Metagenomic analysis of coastal RNA virus communities. Science 312 (2006), 1795–1798.
9. Desnues, C., Rodriguez-Brito, B., Rayhawk, S., Kelley, S., Tran, T., Haynes, M., Liu, H., Furlan, M., Wegley, L., Chau, B., Ruan, Y., Hall, D., Angly, F.E., Edwards, R.A., Li, L., Thurber, R.V., Reid, R.P., Siefert, J., Souza, V., Valentine, D.L., Swan, B.K., Breitbart, M., Rohwer, F., Biodiversity and biogeography of phages in modern stromatolites and thrombolites. Nature 452 (2008), 340–343.
10. Drexler, J.F., Corman, V.M., Muller, M.A., Lukashev, A.N., Gmyl, A., Coutard, B., Adam, A., Ritz, D., Leijten, L.M., van Riel, D., Kallies, R., Klose, S.M., Gloza-Rausch, F., Binger, T., Annan, A., Adu-Sarkodie, Y., Oppong, S., Bourgarel, M., Rupp, D., Hoffmann, B., Schlegel, M., Kummerer, B.M., Kruger, D.H., Schmidt-Chanasit, J., Setien, A.A., Cottontail, V.M., Hemachudha, T., Wacharapluesadee, S., Osterrieder, K., Bartenschlager, R., Matthee, S., Beer, M., Kuiken, T., Reusken, C., Leroy, E.M., Ulrich, R.G., Drosten, C., Evidence for novel hepaciviruses in rodents. PLoS Pathog., 9, 2013, e1003438.
11. Firth, C., Lipkin, W.I., The genomics of emerging pathogens. Annu. Rev. Genom. Hum. Genet. 14 (2013), 281–300.
12. Geoghegan, J.L., Holmes, E.C., Predicting virus emergence amidst evolutionary noise. Open Biol, 7, 2017 170189.
13. Geoghegan, J.L., Duchêne, S., Holmes, E.C., Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families. PLoS Pathog., 13, 2017, e1006215.
14. Hall, R.A., Bielefeldt-Ohmann, H., McLean, B.J., O'Brien, C.A., Colmant, A.M., Piyasena, T.B., Harrison, J.J., Newton, N.D., Barnard, R.T., Prow, N.A., Deerain, J.M., Mah, M.G., Hobson-Peters, J., Commensal viruses of mosquitoes: host restriction, transmission, and interaction with arboviral pathogens. Evol. Bioinform. Online 12 (2017), 35–44.
15. Holmes, E.C., Harvey, P.H., May, R.M., (eds.) The Evolution and Emergence of RNA Viruses. Oxford Series in Ecology and Evolution (OSEE), 2009, Oxford University Press, Oxford.
16. Iranzo, J., Krupovic, M., Koonin, E.V., The double-stranded DNA virosphere as a modular hierarchical network of gene sharing. mBio 7 (2016), e00978–16.
17. Junglen, S., Drosten, C., Virus discovery and recent insights into virus diversity in arthropods. Curr. Opin. Microbiol. 16 (2013), 507–513.
18. Koonin, E.V., Dolja, V.V., Virus world as an evolutionary network of viruses and capsidless selfish elements. Microbiol. Mol. Biol. Rev. 78 (2014), 278–303.
19. Koonin, E.V., Dolja, V.V., Krupovic, M., Origins and evolution of viruses of eukaryotes: the ultimate modularity. Virology 479–480 (2015), 2–25.
20. Krupovic, M., Dolja, V.V., Koonin, E.V., Plant viruses of the Amalgaviridae family evolved via recombination between viruses with double-stranded and negative-strand RNA genomes. Biol. Direct, 10, 2012, 12.
21. Kuhn, J.H., Bekal, S., Caì, Y., Clawson, A.N., Domier, L.L., Herrel, M., Jahrling, P.B., Kondo, H., Lambert, K.N., Mihindukulasuriya, K.A., Nowotny, N., Radoshitzky, S.R., Schneider, U., Staeheli, P., Suzuki, N., Tesh, R.B., Wang, D., Wang, L.F., Dietzgen, R.G., Nyamiviridae: proposal for a new family in the order Mononegavirales. Arch. Virol. 158 (2013), 1621–1629.
22. Kumar, A., Murthy, S., Kapoor, A., Evolution of selective-sequencing approaches for virus discovery and virome analysis. Virus Res. 239 (2017), 172–179.
23. Ladner, J.T., Wiley, M.R., Beitzel, B., Auguste, A.J., Dupuis A.P.2nd Lindquist, M.E., Sibley, S.D., Kota, K.P., Fetterer, D., Eastwood, G., Kimmel, D., Prieto, K., Guzman, H., Aliota, M.T., Reyes, D., Brueggemann, E.E., St John, L., Hyeroba, D., Lauck, M., Friedrich, T.C., O'Connor, D.H., Gestole, M.C., Cazares, L.H., Popov, V.L., Castro-Llanos, F., Kochel, T.J., Kenny, T., White, B., Ward, M.D., Loaiza, J.R., Goldberg, T.L., Weaver, S.C., Kramer, L.D., Tesh, R.B., Palacios, G., A multicomponent animal virus isolated from mosquitoes. Cell Host Microbe 20 (2016), 357–367.
24. Leland, D.S., Ginocchio, C.C., Role of cell culture for virus detection in the age of technology. Clin. Microbiol. Rev. 20 (2007), 49–59.
25. Li, C.-X., Shi, M., Tian, J.-H., Lin, X.-D., Kang, Y.-J., Qin, X.-C., Chen, L.-J., Xu, J., Holmes, E.C., Zhang, Y.-Z., Unprecedented RNA virus diversity in arthropods reveals the ancestry of negative-sense RNA viruses. eLife, 4, 2015, e05378.
26. Luis, A.D., Hayman, D.T., O'Shea, T.J., Cryan, P.M., Gilbert, A.T., Pulliam, J.R., Mills, J.N., Timonin, M.E., Willis, C.K., Cunningham, A.A., Fooks, A.R., Rupprecht, C.E., Wood, J.L., Webb, C.T., A comparison of bats and rodents as reservoirs of zoonotic viruses: are bats special?. Proc. Biol. Sci., 280, 2013, 20122753.
27. Marklewitz, M., Zirkel, F., Kurth, A., Drosten, C., Junglen, S., Evolutionary and phenotypic analysis of live virus isolates suggests arthropod origin of a pathogenic RNA virus family. Proc. Natl. Acad. Sci. U. S. A. 112 (2015), 7536–7541.
28. May, F.J., Clark, D.C., Pham, K., Diviney, S.M., Williams, D.T., Field, E.J., Kuno, G., Chang, G.J., Cheah, W.Y., Setoh, Y.X., Prow, N.A., Hobson-Peters, J., Hall, R.A., Genetic divergence among members of the Kokobera group of flaviviruses supports their separation into distinct species. J. Gen. Virol. 94 (2013), 1462–1467.
29. Mokili, J.L., Rohwer, F., Dutilh, B.E., Metagenomics and future perspectives in virus discovery. Curr. Opin. Virol. 2 (2012), 63–77.
30. Nga, P.T., Parquet Mdel, C., Lauber, C., Parida, M., Nabeshima, T., Yu, F., Thuy, N.T., Inoue, S., Ito, T., Okamoto, K., Ichinose, A., Snijder, E.J., Morita, K., Gorbalenya, A.E., Discovery of the first insect nidovirus, a missing evolutionary link in the emergence of the largest RNA virus genomes. PLoS Pathog., 7, 2011, e1002215.
31. Olival, K.J., Hosseini, P.R., Zambrana-Torrelio, C., Ross, N., Bogich, T.L., Daszak, P., Host and viral traits predict zoonotic spillover from mammals. Nature 546 (2017), 646–650, 10.1038/nature22975.
32. Paez-Espino, D., Eloe-Fadrosh, E.A., Pavlopoulos, G.A., Thomas, A.D., Huntemann, M., Mikhailova, N., Rubin, E., Ivanova, N.N., Kyrpides, N.C., Uncovering earth's virome. Nature 536 (2016), 425–430.
33. Palacios, G., Druce, J., Du, L., Tran, T., Birch, C., Briese, T., Conlan, S., Quan, P.L., Hui, J., Marshall, J., Simons, J.F., Egholm, M., Paddock, C.D., Shieh, W.J., Goldsmith, C.S., Zaki, S.R., Catton, M., Lipkin, W.I., A new arenavirus in a cluster of fatal transplant-associated diseases. N. Engl. J. Med. 358 (2008), 991–998.
34. Parrish, C.R., Holmes, E.C., Morens, D.M., Park, E.-C., Burke, D.S., Calisher, C.H., Laughlin, C.A., Saif, L.J., Daszak, P., Cross-species viral transmission and the emergence of new epidemic diseases. Microbiol. Mol. Biol. Rev. 72 (2008), 457–470.
35. Philosof, A., Yutin, N., Flores-Uribe, J., Sharon, I., Koonin, E.V., Béjà, O., Novel abundant oceanic viruses of uncultured marine group II euryarchaeota. Curr. Biol. 27 (2017), 1362–1368.
36. Plowright, R.K., Parrish, C.R., McCallum, H., Hudson, P.J., Ko, A.I., Graham, A.L., Lloyd-Smith, J.O., Pathways to zoonotic spillover. Nat. Rev. Micro 15 (2017), 502–510.
37. Presti, R.M., Zhao, G., Beatty, W.L., Mihindukulasuriya, K.A., da Rosa, A.P., Popov, V.L., Tesh, R.B., Virgin, H.W., Wang, D., Quaranfil, Johnston Atoll, and Lake Chad viruses are novel members of the family Orthomyxoviridae. J. Virol. 83 (2009), 11599–11606.
38. Qin, X.-C., Shi, M., Tian, J.-H., Lin, X.-D., Gao, D.-Y., He, J.-R., Wang, J.-B., Li, C.-X., Kang, Y.-J., Yu, B., Zhou, D.-J., Xu, J., Plyusnin, A., Holmes, E.C., Zhang, Y.-Z., A tick-borne segmented RNA virus contains genome segments derived from unsegmented viral ancestors. Proc. Natl. Acad. Sci. U. S. A. 111 (2014), 6744–6749.
39. Sasaya, T., Ishikawa, K., Koganezawa, H., The nucleotide sequence of RNA1 of Lettuce big-vein virus, genus Varicosavirus, reveals its relation to nonsegmented negative-strand RNA viruses. Virology 297 (2002), 289–297.
40. Shi, M., Lin, X.-D., Tian, J.-H., Chen, L.-J., Chen, X., Li, C.-X., Qin, X.-C., Li, J., Cao, J.-P., Eden, J.-S., Buchmann, J.P., Wang, W., Xu, J., Holmes, E.C., Zhang, Y.-Z., Redefining the invertebrate virosphere. Nature 540 (2016), 539–543.
41. Shi, M., Lin, X.-D., Vasilakis, N., Tian, J.-H., Li, C.-X., Chen, L.-J., Eastwood, J., Diao, X.-N., Chen, M.-H., Chen, X., Qin, X.-X., Widen, S.G., Wood, T.G., Tesh, R.B., Xu, J., Holmes, E.C., Zhang, Y.-Z., Divergent viruses discovered in arthropods and vertebrates revise the evolutionary history of the Flaviviridae and related viruses. J. Virol. 90 (2016), 659–669.
42. Shi, M., Neville, P., Nicholson, J., Eden, J.-S., Imrie, A., Holmes, E.C., High-resolution metatranscriptomics reveals the ecological dynamics of mosquito-associated RNA viruses in Western Australia. J. Virol. 91 (2017), e00680–17, 10.1128/JVI.00680-17.
43. Simmonds, P., Adams, M.J., Benkő, M., Breitbart, M., Brister, J.R., Carstens, E.B., Davison, A.J., Delwart, E., Gorbalenya, A.E., Harrach, B., Hull, R., King, A.M., Koonin, E.V., Krupovic, M., Kuhn, J.H., Lefkowitz, E.J., Nibert, M.L., Orton, R., Roossinck, M.J., Sabanadzovic, S., Sullivan, M.B., Suttle, C.A., Tesh, R.B., van der Vlugt, R.A., Varsani, A., Zerbini, F.M., Consensus statement: virus taxonomy in the age of metagenomics. Nat. Rev. Microbiol. 15 (2017), 161–168.
44. Simmonds, P., Becher, P., Bukh, J., Gould, E.A., Meyers, G., Monath, T., Muerhoff, S., Pletnev, A., Rico-Hesse, R., Smith, D.B., Stapleton, J.T., ICTV Report Consortium, ICTV virus taxonomy profile: Flaviviridae. J. Gen. Virol. 98 (2017), 2–3.
45. Smith, I., Wang, L.F., Bats and their virome: an important source of emerging viruses capable of infecting humans. Curr. Opin. Virol. 3 (2013), 84–91.
46. Stenglein, M.D., Jacobson, E.R., Wozniak, E.J., Wellehan, J.F., Kincaid, A., Gordon, M., Porter, B.F., Baumgartner, W., Stahl, S., Kelley, K., Towner, J.S., DeRisi, J.L., Ball python nidovirus: a candidate etiologic agent for severe respiratory disease in Python regius. mBio 5 (2014), e01484–14.
47. Tong, S., Li, Y., Rivailler, P., Conrardy, C., Castillo, D.A., Chen, L.M., Recuenco, S., Ellison, J.A., Davis, C.T., York, I.A., Turmelle, A.S., Moran, D., Rogers, S., Shi, M., Tao, Y., Weil, M.R., Tang, K., Rowe, L.A., Sammons, S., Xu, X., Frace, M., Lindblade, K.A., Cox, N.J., Anderson, L.J., Rupprecht, C.E., Donis, R.O., A distinct lineage of influenza A virus from bats. Proc. Natl. Acad. Sci. U. S. A. 109 (2012), 4269–4274.
48. Vasilakis, N., Tesh, R.B., Insect-specific viruses and their potential impact on arbovirus transmission. Curr. Opin. Virol. 15 (2015), 69–74.
49. Webster, C.L., Waldron, F.M., Robertson, S., Crowson, D., Ferrari, G., Quintana, J.F., Brouqui, J.M., Bayne, E.H., Longdon, B., Buck, A.H., Lazzaro, B.P., Akorli, J., Haddrill, P.R., Obbard, D.J., The discovery, distribution, and evolution of viruses associated with Drosophila melanogaster. PLoS Biol., 13, 2015, e1002210.
50. Wilson, M.R., Naccache, S.N., Samayoa, E., Biagtan, M., Bashir, H., Yu, G., Salamat, S.M., Somasekar, S., Federman, S., Miller, S., Sokolic, R., Garabedian, E., Candotti, F., Buckley, R.H., Reed, K.D., Meyer, T.L., Seroogy, C.M., Galloway, R., Henderson, S.L., Gern, J.E., DeRisi, J.L., Chiu, C.Y., Actionable diagnosis of neuroleptospirosis by next-generation sequencing. N. Engl. J. Med. 370 (2014), 2408–2417.
51. Zanotto, P.M. de A., Gibbs, M.J., Gould, E.A., Holmes, E.C., A reevaluation of the higher taxonomy of viruses based on RNA polymerases. J. Virol. 70 (1996), 6083–6096.