RV1 genome constellation analysis and phylogenetics
Illumina short read sequences were quality filtered using Trimmomatic v0.39 software (32). Quality-filtered reads were classified against all rotavirus sequence information from NCBI (downloaded 2019-12-02; n=76,138) with Kraken 2.0.8-beta (33). Consensus genomes were constructed by first finding the closest matching segments against all full-length rotavirus segments from NCBI (n=54,005 sequences from all files downloaded above on 2019-12-02) using Mash 2.2.2 screen (34). The sequence with the closest mash-distance was used as a reference, where the Kraken2-classified sequences were mapped using BWA MEM 0.7.17-r1188 (arXiv:1303.3997v2). Consensus sequences for each segment were generated using SAMtools v1.9 (35) and iVar v1.0 (36). Rotavirus genome depth and coverage were plotted using SAMtools, R 3.6.1 (R Core Team; https://www.R-project.org), ggplot2 v3.2.1 (Wickham; 2016; https://ggplot2.tidyverse.org) and viridis v0.5.1. RV1 whole genome sequences from the four specimens were uploaded to the Viral Pathogen Resource (ViPR) website to determine the genome constellation of the strains and results were compared to RV1 constellation (accessed in May 2022, now available at the Bacterial and Viral Bioinformatics Resource Center https://www.bv-brc.org).