The Pearson correlation coefficient was calculated by Pearson chi square test for crosstab tables using SPSS software. The sensitivity and specificity of the peptide-ELISA versus HI test was determined by ROC curve analysis using SPSS software. Figure S1 Localization comparison between the identified peptides and the classical five antigenic sites in stereo view. The HA monomer surface view of influenza virus A/PR/8/34 (PDB ID:1RU7) is shown and colored to illustrate the five antigenic sites (Sa, Sb, Ca1, Ca2, and Cb) and the identified peptides. From most membrane distal to proximal: P3 (blue), P31 (red), P5 (black), Cb (green), Ca1 (magenta), Ca2 (rainbow), Sa (yellow), and Sb (cyan). (TIF) Stimulation of stop codon readthrough: frequent presence of an extended 3′ RNA structural element In Sindbis, Venezuelan equine encephalitis and related alphaviruses, the polymerase is translated as a fusion with other non-structural proteins via readthrough of a UGA stop codon. Surprisingly, earlier work reported that the signal for efficient readthrough comprises a single cytidine residue 3′-adjacent to the UGA. However, analysis of variability at synonymous sites revealed strikingly enhanced conservation within the ∼150 nt 3′-adjacent to the UGA, and RNA folding algorithms revealed the potential for a phylogenetically conserved stem–loop structure in the same region. Mutational analysis of the predicted structure demonstrated that the stem–loop increases readthrough by up to 10-fold. The same computational analysis indicated that similar RNA structures are likely to be relevant to readthrough in certain plant virus genera, notably Furovirus, Pomovirus, Tobravirus, Pecluvirus and Benyvirus, as well as the Drosophilia gene kelch. These results suggest that 3′ RNA stimulatory structures feature in a much larger proportion of readthrough cases than previously anticipated, and provide a new criterion for assessing the large number of cellular readthrough candidates that are currently being revealed by comparative sequence analysis. There are two types of exceptions to universality of the genetic code. In one, the meaning of a codon is globally reassigned in a context independent manner (1) . In the other, codon redefinition is in competition with standard decoding and it is codon context dependent (2) . Though there is an example where the meaning of a sense codon is redefined (3) , most cases of codon redefinition involve one of the three stop codons of the standard code (UGA, UAG or UAA) specifying an amino acid at least a proportion of the time that it is decoded. Where the significant feature of stop codon redefinition is to allow ribosomes to continue translation into a downstream open reading frame (ORF), rather than the identity of the amino acid specified, then it is generally termed stop codon readthrough (RT) (4) . In contrast, when selenocysteine or pyrrolysine are specified by UGA or UAG, respectively, then the important features are the special properties of these non-universal amino acids (5) (6) (7) . Both types of non-global codon redefinition are just one aspect of the variety of ways (collectively referred to as 'recoding') in which genetic readout can be dynamically altered in a site-or mRNA-specific manner (8, 9) .