Whole genome sequencing and phylogenetic analysis
Whole genome sequencing was carried out using the same library preparation kit and technology for the three most prevalent genotypes, HRV A47, A49, and A101. Adapters were removed using Porechop (v.0.2.4) (36) and low quality reads were filtered out with Filtlong (v.0.2.1) (37). Raw sequence reads were mapped to reference sequences (GenBank accession numbers KY369890.1, OM001351.1, and KY369891.1) using the Burrows-Wheeler Aligner (BWA) tool (v.0.7.17) (38) and processed using samtools (v.1.15.1) (39). Sequences generated in this study are available in NCBI GenBank (OR116985 – OR117139).
All available whole genome sequences of HRV A47, A49, and A101 were retrieved from GenBank. Sequences were aligned using MAFFT (v7.487) (34), and time-scaled phylogenetic trees were constructed based on sample collection dates using the least square dating (LSD2) (40) method integrated in IQ-TREE (v.2.0.3) with 100 replicates to obtain confidence intervals. Trees were visualized with FigTree (v1.4.4).