To study the application of nanopore sequencing technology in pathogen detection for an adenovirus outbreak in Tangshan in February, 2019, and to report the results of sequencing and analysis of samples processed with different methods.

Nasopharyngeal swabs from 16 severe cases and 16 mild cases were randomly selected. These samples were mixed and enriched for direct sequencing on the MinION sequencer. Real-time PCR was performed to detect adenovirus. The positive sample with the lowest Ct value was further sequenced directly using MnION.

Eight severe cases and 15 mild cases were positive for adenovirus. The nanopore sequencing identified the first reads of adenovirus type 7 in 14 and 22 minutes on the mixed sample and single sample, respectively. Within 3 h of sequencing, 99% of the reference genome were covered. Phylogenetic analysis revealed that the strains in the outbreak had a close genetic relation with a strain isolated in Beijing.

Nanopore sequencing technology can be used for rapid adenovirus identification in epidemics and obtaining genome sequences. The results proved the potential value of MinION in real-time detection of novel emerging or unknown or mutated pathogens.

Adenovirus type 7; Nanopore sequencing technology; MinION sequencer