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).