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).