Deduced amino acids analysis of PEDV variants in China
In this study, the S-INDEL like strains were identified in seven samples. The deduced amino acid sequences of S proteins in the identified S-INDEL like strains were used to compare with the reference S-INDEL strains. A sequence alignment showed that four amio acid deletions (58QGVN61) were observed in the attenuated CV777 strain (GI-b) and S-INDEL like strains as compared with the vaccine strain AJ1102 (GII-b). In addition, three mutations and one deletion of the deduced S protein were found in the identified S-INDEL like strains as compared with the reference S-INDEL strains (Figure 2A).
A new amino acid insertion relative to the prototype in the S protein were found in five samples.The CH/GDMM/202012 had continuous 5 amino acid insertions (360QGRKS364) in the S1 domain. CH/GXDX/202010, CH/AHBZ/202010, CH/AHLA/202010, and CH/HNLY/202003 had 3 or 4 amino acid insertions (1279DVF1281 or 1278VDVF1281) in the S2 domain (Figure 2B).