First Identification of Human Adenovirus Subtype 21a in China With MinION and Illumina Sequencers

Ye, Fuqiang; Han, Yifang; Zhu, Juanjuan; Li, Peng; Zhang, Qi; Lin, Yanfeng; Wang, Taiwu; Lv, Heng; Wang, Changjun; Wang, Chunhui; Zhang, Jinhai

The multiple alignments of genome sequences of HAdV21p (KF528688.1), HAdV3 (AY599834.1), HAdV66 (JN860676.1), and current genome were performed using ClustalW method in MEGA X. The alignment file in fasta format was used as the input of bootscan analysis of SimPlot (V3.5.1) 2 with the following parameters: window = 1,000 bp, step = 20 bp, GapStrip = on, reps = 500, distance model = Kimura, T/t = 2.0, and tree model = neighbor-joining. To detect a subtype-wide recombinant event related to E4 gene, multiple alignment of gene sequences 1 https://www.drive5.com/usearch/download.html 2 https://sray.med.som.jhmi.edu/SCRoftware/simplot/ FIGURE 1 | Investigation of the minimal read number to identify the current isolate. (A) The overall genome coverage distribution when 5-5,000 reads were randomly selected. The x axis denotes pseudosequencing depth, and the y axis, the corresponding genome coverages. (B) Genome coverage distribution decomposed by the maximal aligned read length. The dashed line corresponds to 69.10%. (C) Hit ratio distribution decomposed by the maximal aligned read length. The dashed line corresponds to 16.92%. "Y" represents read length being more than 25 kb, and "N" indicates less than 25 kb. Boxes represent the interquartile range (IQR) between the first and third quartiles (25th and 75th percentiles, respectively). Lines inside denote the median, and whiskers denote the most extreme values within 1.5 times IQR from the first and third quartiles. Outlier values are represented as points.