Identifying the pathogens of one patient with upper respiratory infection using high throughput sequencing technology

Abstract

Objective To identify the possible pathogens of a patient with upper respiratory infection using high throughput sequencing technology and to optimize the methods for sample pre-treatment. Methods After pre-treating the sample with Benzonase Nuclease and/or ribosomal RNA (rRNA) probes, RNA was amplified with sequence independent single primer amplification (SISPA). The amplicons were used to prepare the sequencing library. Then the high throughput sequencing and bioinformatics analysis were performed. Results After resembled reads were blast against viruses library, we found the presence of influenza B virus sequences. Furthurmore, phylogenetic analysis showed that the influenza B virus belonged to Yamagat linage. Treatment with nuclease and ribosomal RNA (rRNA) probes provided more target sequences and higher coverage for the high throughput sequencing. Conclusions Combination of using nuclease and ribosomal RNA (rRNA) probes to treat sample and high throughput sequencing can rapidly identify the pathogen of unknown infection. Key words: Influenza B virus; high throughput sequencing; nuclease; ribosomal RNA