Introduction
The epidemic of emerging infectious diseases worldwide poses a great threat to public health. It is noted that most epidemic is caused by viral cross-species transmission from animals to human. Surveillance by fast and accurate diagnostic methods is crucial for the disease control and patient treatment. Thanks to the development of metagenomic next-generation sequencing (mNGS) methodology, the direct investigation of infectious microorganism from original clinical samples is currently achievable [1]. Particularly, RNA based mNGS approach could simultaneously reveal the entire “infectome” (i.e. RNA viruses, DNA viruses, bacteria and eukaryotes) present within an organism, because all except for prion express RNA [2]. Furthermore, RNA sequencing goes beyond pathogen identification to reveal relevant data on pathogen abundance, genome sequence, and gene expression, providing important insight into the cause of disease such that it represents an avant-guard diagnostic tool in the information age. Recently, in December 2019, an outbreak of unusual pneumonia caused by unknown infection was reported in Wuhan, China [3]. The earlier cases (before January) were all linked to Huanan Seafood Market in Wuhan before the disease was further spread to other cities of China and even overseas. Since this is an outbreak with unknown etiology, we report the use of RNA based mNGS approach for a rapid identification and characterization of a potential pathogen, which is therefore of great importance for disease control and prevention.