Author: Valeria Lulla; Andrew E. Firth
Title: A hidden gene in astroviruses encodes a cell-permeabilizing protein involved in virus release Document date: 2019_6_6
ID: avq3zwmc_4
Snippet: We repeated the synonymous site conservation analysis using clades, sequence alignments and phylogenetic trees based on only ORF2 in order to rule out potential artefacts as a result of possible recombination between the nonstructural and structural modules of the virus genome, and to include additional part-genome sequences (total 415 sequences with ORF2 coverage; Fig. 1D; Fig. S4 ). This analysis revealed conserved regions overlapping the 5′ .....
Document: We repeated the synonymous site conservation analysis using clades, sequence alignments and phylogenetic trees based on only ORF2 in order to rule out potential artefacts as a result of possible recombination between the nonstructural and structural modules of the virus genome, and to include additional part-genome sequences (total 415 sequences with ORF2 coverage; Fig. 1D; Fig. S4 ). This analysis revealed conserved regions overlapping the 5′ end of ORF2 throughout genogroup I, III and IV astroviruses but, generally, not in genogroup II or VI astroviruses (Fig. S5 ). Those clades with synonymous site conservation also contain a conserved overlapping +1 frame ORF, whereas those sequences without synonymous site conservation generally also lacked a conserved overlapping +1 frame ORF (Fig. S5) .
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