VP7 and VP4 genotyping approach
Nucleic acid was extracted from stool or rectal swab specimens (19). Specimens with the lowest RT-qPCR Ct value (corresponding to higher viral load) were subsequently subjected to VP7/VP4 genotyping using conventional RT-PCR and electrophoretyping with genotypes being determined by banding pattern (29) with updated G12 primers (30) (Supplemental Methods). A subset of specimens that could not be genotyped due to polymorphisms at the primer binding sites or low viral load, were subjected to an alternative sequence-based method of G/P genotyping specifically designed for low viral load samples (15) (Supplemental Methods). The sequences obtained were analyzed using MEGAv7 software and genotypes were aligned to reference sequences available in GenBank (31).