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

According to the QIASTAT and metagenomic sequencing results, we found 11 co-infection cases among 20 NCP cases, including viruses such as influenza A/B, rhino/enterovirus, respiratory syncytial viral and etc., and other atypical pathogen, fungi and bacteria synchronously ( Figure 3 ). Among the 33 laboratory-confirmed non-NCP patients, QIASTAT and metagenomic sequencing reported positive in 7 and 23 patients, respectively. Pathogen distribution of non-NCP cases was shown in Figure 3 . Phylogenetic analysis was performed to investigate the genetic relationship between SARS-COV-2 and other pathogenic coronavirus, as well as the diversity among our SARS-COV-2 strains. Consistent with previous reports, SARS-COV-2 was identified as a new species that's most similar to SARS-CoV. The SARS-COV-2 strains sequenced in our cases were highly conserved with the original Wuhan strain. Genetic variations were further analyzed in 10 cases with sufficient coverage and depth of the N gene. Among which, only one single nucleotide mutation (g605a) was identified in two of the samples which resulted in a non-synonymous S203N change in the N gene, suggesting a relatively low level of genetic polymorphism in our SARS-COV-2 cases (Figure 4 ).