Optimizing diagnostic strategy for novel coronavirus pneumonia, a multi-center study in Eastern China

Jing-Wen Ai; Hao-Cheng Zhang; Teng Xu; Jing Wu; Mengqi Zhu; Yi-Qi Yu; Han-Yue Zhang; Zhongliang Shen; Yang Li; Xian Zhou; Guo-Qing Zang; Jie Xu; Wen-Jing Chen; Yong-Jun Li; De-Sheng Xie; Ming-Zhe Zhou; Jing-Ying Sun; Jia-Zhen Chen; Wen-Hong Zhang

Metagenomic sequencing was the method by which SARS-COV-2 was initially identified. Despite its longer turnaround time and higher cost, mNGS demonstrated a satisfying level of sensitivity when compared to PCR assays in our study. Moreover, the nature of unbiased sequencing offers higher tolerance for genetic drift in the target pathogens, whereas certain changes in sequence can result in critical impact on the assay efficiency 21, 22 . Along with targeted assays, mNGS should serve as an indispensable tool for sensitive and close monitoring of the molecular evolution for SARS-COV-2. Such genetic information will offer valuable insights not only for public health management, but also for contentious optimization of diagnostic assays 23, 24 . Therefore, as the SARS-COV-2 epidemic is currently entering into a critical stage, both within China and over the global 25 , according to the results of our study, the following improvements in molecular diagnosis are recommended in the optimized diagnostic flow diagram [ Figure 5 ]. First of all, repeated sampling could increase the positivity, and especially during clinical situations where epidemiological history and clinical manifestations highly indicate NCP, a third or fourth sampling may be helpful when resources are available. Second, our study showed that mNGS showed reliable and stable detection ability in the NCP diagnosis, and may facilitate to solve diagnostic difficulties during important or critical clinical cases and low positive RT-PCR results. What's more, in order to circumvent possible mutations in RT-PCR primers region, more than 1 gene target was recommended to amplify when designing RT-PCR assays [25] . Whole Genome Sequencing (WGS) method can overcome the mutation problems which cause false-negative result in RT-PCR. Therefore, we used this method in all enrolled patients and should be continue using for mutation surveillance. Lastly, lower respiratory tract specimens might provide higher positivity, due to that higher viral loads may be detected there. Therefore, physicians might collect such samples through bronchoscopy or trachea cannula when under through medical protection.