Analysis of new aphid lethal paralysis virus (ALPV) isolates suggests evolution of two ALPV species

Journal of General Virology

Volumn 95, Issue , 2014, Pages 2809-2819

  Liu, Sijun ^a   Vijayendran, Diveena ^a   Carrillo Tripp, Jimena ^a   Allen Miller, W ^a   Bonning, Bryony C ^a  

^a IOWA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; AMINO ACID SEQUENCE; APHID LETHAL PARALYSIS VIRUS; APIS MELLIFERA; ARTICLE; DIABROTICA VIRGIFERA; DICISTROVIRIDAE; EXPRESSED SEQUENCE TAG; GENOME ANALYSIS; HOST RANGE; INTERNAL RIBOSOME ENTRY SITE; MAXIMUM LIKELIHOOD METHOD; MOLECULAR CLONING; MOLECULAR EVOLUTION; MOLECULAR WEIGHT; NONHUMAN; NUCLEOTIDE SEQUENCE; PEA APHID; PHYLOGENETIC TREE; PHYLOGENY; POINT MUTATION; POLYACRYLAMIDE GEL ELECTROPHORESIS; PROTEIN SECONDARY STRUCTURE; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA SEQUENCE; SEQUENCE ANALYSIS; SPAIN; STOP CODON; VIRUS ASSEMBLY; VIRUS GENOME; VIRUS ISOLATION; VIRUS PARTICLE; ANIMAL; APHID; CLASSIFICATION; EVOLUTION; GENETICS; MOLECULAR GENETICS; MOTH; SPECIES DIFFERENCE; VIROLOGY;

VIRUS DNA;

ANIMALS; APHIDS; BASE SEQUENCE; BIOLOGICAL EVOLUTION; DICISTROVIRIDAE; DNA, VIRAL; MOLECULAR SEQUENCE DATA; MOTHS; SPECIES SPECIFICITY;

EID: 84910605748     PISSN: 00221317     EISSN: 14652099     Source Type: Journal    
DOI: 10.1099/vir.0.069765-0     Document Type: Article

References (25)

1. Bonaldo, M. F., Lennon, G. & Soares, M. B. (1996). Normalization and subtraction: two approaches to facilitate gene discovery. Genome Res 6, 791-806.
2. Bonning, B. C. & Miller, W. A. (2010). Dicistroviruses. Annu Rev Entomol 55, 129-150.
3. Chen, Y. P., Nakashima, N., Christian, P. D., Bakonyi, T., Bonning, B. C., Valles, S. M. & Lightner, D. (2012). Family Dicistroviridae. In Virus Taxonomy, Ninth Report of the International Committee on Taxonomy of Viruses, pp. 840-845. Edited by A. M. Q. King, M. J. Adams, E. B. Carstens & E. J. Lefkowitz. London: Academic Press.
4. Cox-Foster, D. L., Conlan, S., Holmes, E. C., Palacios, G., Evans, J. D., Moran, N. A., Quan, P. L., Briese, T., Hornig, M. & other authors (2007). A metagenomic survey of microbes in honey bee colony collapse disorder. Science 318, 283-287.
5. D’Arcy, C. J., Burnett, P. A., Hewings, A. D. & Goodman, R. M. (1981). Purification and characterization of a virus from the aphid Rhopalosiphum padi. Virology 112, 346-349.
6. Dombrovsky, A. & Luria, N. (2013). The Nerium oleander aphid Aphis nerii is tolerant to a local isolate of Aphid lethal paralysis virus (ALPV). Virus Genes 46, 354-361.
7. Domingo, E., Baranowski, E., Ruiz-Jarabo, C. M., Martín-Hernández, A. M., Sáiz, J. C. & Escarmís, C. (1998). Quasispecies structure and persistence of RNA viruses. Emerg Infect Dis 4, 521-527.
8. Ge, X., Li, Y., Yang, X., Zhang, H., Zhou, P., Zhang, Y. & Shi, Z. (2012). Metagenomic analysis of viruses from bat fecal samples reveals many novel viruses in insectivorous bats in China. J Virol 86, 4620-4630.
9. Granberg, F., Vicente-Rubiano, M., Rubio-Guerri, C., Karlsson, O. E., Kukielka, D., Belák, S. & Sánchez-Vizcaíno, J. M. (2013). Metagenomic detection of viral pathogens in Spanish honeybees: co-infection by Aphid Lethal Paralysis, Israel Acute Paralysis and Lake Sinai Viruses. PLoS ONE 8, e57459.
10. Haas, B. J., Papanicolaou, A., Yassour, M., Grabherr, M., Blood, P. D., Bowden, J., Couger, M. B., Eccles, D., Li, B. & other authors (2013). De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc 8, 1494-1512.
11. Hyde, J. L., Gardner, C. L., Kimura, T., White, J. P., Liu, G., Trobaugh, D. W., Huang, C., Tonelli, M., Paessler, S. & other authors (2014). A viral RNA structural element alters host recognition of nonself RNA. Science 343, 783-787.
12. Jehle, J. A., Lange, M., Wang, H., Hu, Z., Wang, Y. & Hauschild, R. (2006). Molecular identification and phylogenetic analysis of baculoviruses from Lepidoptera. Virology 346, 180-193.
13. Leitmeyer, K. C., Vaughn, D. W., Watts, D. M., Salas, R., Villalobos, I., de Chacon, Ramos, C. & Rico-Hesse, R. (1999). Dengue virus structural differences that correlate with pathogenesis. J Virol 73, 4738-4747.
14. Liu, S., Vijayendran, D. & Bonning, B. C. (2011). Next generation sequencing technologies for insect virus discovery. Viruses 3, 1849-1869.
15. Liu, S., Chougule, N. P., Vijayendran, D. & Bonning, B. C. (2012). Deep sequencing of the transcriptomes of soybean aphid and associated endosymbionts. PLoS ONE 7, e45161.
16. Murakami, R., Suetsugu, Y., Kobayashi, T. & Nakashima, N. (2013). The genome sequence and transmission of an iflavirus from the brown planthopper, Nilaparvata lugens. Virus Res 176, 179-187.
17. Oteng-Frimpong, R., Levy, Y., Torkpo, S. K., Danquah, E. Y., Offei, S. K. & Gafni, Y. (2012). Complete genome sequencing of two causative viruses of cassava mosaic disease in Ghana. Acta Virol 56, 305-314.
18. Ravoet, J., Maharramov, J., Meeus, I., De Smet, L., Wenseleers, T., Smagghe, G. & de Graaf, D. C. (2013). Comprehensive bee pathogen screening in Belgium reveals Crithidia mellificae as a new contributory factor to winter mortality. PLoS ONE 8, e72443.
19. Runckel, C., Flenniken, M. L., Engel, J. C., Ruby, J. G., Ganem, D., Andino, R. & DeRisi, J. L. (2011). Temporal analysis of the honey bee microbiome reveals four novel viruses and seasonal prevalence of known viruses, Nosema, and Crithidia. PLoS ONE 6, e20656.
20. Schnettler, E., Sterken, M. G., Leung, J. Y., Metz, S. W., Geertsema, C., Goldbach, R. W., Vlak, J. M., Kohl, A., Khromykh, A. A. & Pijlman, G. P. (2012). Noncoding flavivirus RNA displays RNA interference suppressor activity in insect and mammalian cells. J Virol 86, 13486-13500.
21. Tamura, K., Stecher, G., Peterson, D., Filipski, A. & Kumar, S. (2013). MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol 30, 2725-2729.
22. Van Munster, M., Dullemans, A. M., Verbeek, M., Van Den Heuvel, J. F., Clé rivet, A. & Van Der Wilk, F. (2002). Sequence analysis and genomic organization of aphid lethal paralysis virus: a new member of the family Dicistroviridae. J Gen Virol 83, 3131-3138.
23. Will, S., Joshi, T., Hofacker, I. L., Stadler, P. F. & Backofen, R. (2012). LocARNA-P: accurate boundary prediction and improved detection of structural RNAs. RNA 18, 900-914.
24. Williamson, C., Rybicki, E. P., Kasdorf, G. F. & Von Wechmar, M. B. (1988). Characterization of a new picorna-like virus isolated from aphids. J Gen Virol 69, 787-795.
25. Zerbino, D. R. & Birney, E. (2008). Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18, 821-829.