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

Oxford Nanopore Technologies is hindered by its high sequencing error rate (10-15%). We observed 31 discrepancies between MinION and Illumina sequencing. Although indels and substitutions are frequent in nanopore data, there might be other factors involved in these discrepancies, that is, the read correction, read assembly, and genome polishing methods (Loman et al., 2015; Koren et al., 2017; Xiao et al., 2017) , in addition to potential sequencing errors, which needs further investigation. Base modifications have been reported in human, prokaryotes, and viruses (Gokhale and Horner, 2017; Xiao et al., 2018) , some of which could be detected by ONT (Simpson et al., 2017; Liu et al., 2019) . Thus, base modifications may also contribute to genomic discrepancies (Greig et al., 2019) . Illumina platforms usually have very low sequencing errors, however, they are characterized by a relatively complex sample preparation procedure, a relatively long sequencing time, and high-performance computing equipment for downstream FIGURE 4 | Phylogenetic tree constructed via whole-genome sequences. All available HAdV21 and other human mastadenovirus B genomes were used. The sequence displayed in red represents the current isolate.