When compared to the A22/Iraq vaccine, these viruses had more than 40 aa changes SB431542 chemical structure in the capsid region, whilst about 35% of these had r1 values above 0.3 indicating a good match. This indicates that a large proportion of the substitutions are neutral and only a few, located at particular capsid positions impact on the antigenic nature of the virus. Similar analyses were also carried out to study if the r1-values correlated with the number of aa changes in
each of the individual structural proteins (VP1-4); however no linear correlation was observed (data not shown). In vitro testing of viruses belonging to the BAR-08 sub-lineage with either A22/Iraq or A/TUR/2006 antisera generated low r1-values indicating lower expected protection. The capsid aa sequences of these viruses, including sequences for two isolates previously reported , were analysed further to understand the changes in the antigenicity of these viruses. As most of these viruses do not cross-react with the antisera of either of the v/s, we specifically looked for aa residues in the field
isolates which were different from those of both the v/s ( Fig. 4). A total of 11 aa residues were identified; three residues (VP1-45, 65 Afatinib and VP3-59) were indicated in a similar study . Three residues were eliminated as being either completely (VP1-28) or partly (VP2-98) on the internal surface of the virion ( Fig. 5C), or completely (VP1-65) buried in the structure; though Jamal and colleagues indicated substitution of VP1-65 may change the surface structure . The remaining GBA3 eight residues (VP1-45, 83, 141; VP2-65, 79; VP3-59, 65, 220) were surface-exposed ( Fig. 5B) and are therefore good candidates to explain the inability of the antisera to cross-react with the field isolates. The substitutions in VP2-65 and 79 were recorded in nine out of 10 isolates studied. We excluded VP1-45 because (i) both the residues are hydrophobic; (ii) this/adjacent residues were reported to be part of antigenic site-3 in case of serotype O viruses  and SAT 1 , however this has never been reported in serotype A mar-mutant studies;
(iii) this residue is also picked up by epitope prediction software, however, mutation of this residue in a cDNA clone did not have much impact on the antigenicity of the virus (F. Bari and M. Mahapatra, unpublished results). Three residues VP1-83, 141 and VP3-59 (shown in cyan in Fig. 5B) have been reported to be critical in serotype A mar-mutant studies , ,  and . A change in these residues may affect the overall conformation of the viral capsid and thereby alter the antigenicity of the virus. VP3-220 is located in close proximity to the C-terminus of VP1 of an adjacent protomer, and in close vicinity to residue VP3-218, which was recently reported to be critical in serotype Asia 1 . In addition, all these residues were highly variable among the A-Iran-05 viruses ( Fig.