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

Illumina sequencing was further employed to de novo assemble the viral genome. After quality control, a total of 133,334 reads with a GC content of 44.04% were used for downstream assembly. One scaffold with a length of 35,369 bp was obtained. A total of 31 genomic discrepancies between MinION and Illumina sequencing were identified by both MEGA and dnadiff (Phillippy et al., 2008) programs (Table 1) and further validated and confirmed by PCR coupled with Sanger sequencing. Among these discrepancies, six ones were single-nucleotide polymorphisms (SNPs), and the rest belonged to insertion and deletions (indels). All the SNPs could be classified as base transitions. Table S1 ). The dnadiff tool revealed that the pairwise nucleotide identity between the two draft sequences was 99.91%. Although sequencing errors still existed in the polished MinION genome, we are confident that the MinION output could achieve the goal of identifying pathogen at a comparable level. The corrected genome contained 35,369 bp with a GC content of 51.21%. The MinION read depth across the genome ranged from 44 X to 609 X, whereas the Illumina read depth ranged from 2 X to 125 X (Figure 2 ).