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Analysis of genetic information of an insect picorna-like virus, infectious flacherie virus of silkworm: evidence for evolutionary relationships among insect, mammalian and plant picorna(-like) viruses

Isawa, H., Asano, S., Sahara, K., Iizuka, T., Bando, H.
Archives of virology 1998 v.143 no.1 pp. 127-143
DNA-directed RNA polymerase, Infectious flacherie virus, Picornaviridae, RNA, amino acid sequences, codons, complementary DNA, computer analysis, genetic techniques and protocols, genome, mammals, nucleotides, open reading frames, phylogeny, plant viruses, plasmids, proteinases, silkworms, structural proteins
We synthesized the cDNAs of an insect picornavirus, infectious flacherie virus of silkworm (IFV), genomic RNA and inserted it into a bacterial plasmid (pUC119). The 9 650 nucleotides (nts) sequence except for the poly(A) tail was obtained from the cloned cDNAs, and the sequence integrity was confirmed by primer extension and direct RNA sequencing. The sequence has a large open reading frame (ORF) of 9 255 nts (3 085 codons) flanked by the short 5′ non-coding region (156 nts) and by the rather long 3′ non-coding (239 nts). The structural proteins VP3, 4, 1 and 2 were located at the N-terminus of the polyprotein in this order and were preceded by a tentative small peptide. Computer analysis identified the sequences similar to the consensus sequences of 2C (helicase?), 3C (protease), and 3D (RNA polymerase) conserved among mammalian and plant picorna(-like) viruses. In addition, the predicted genome organization of IFV was quite similar to those of picornaviruses. Further analyses of the characteristics of the genome structure and a tentative phylogenetic tree constructed on the basis of the amino acid sequence similarity emphasized the evolutionary relationships among the insect and plant viruses.