Era of molecular diagnosis for pathogen identification of unexplained pneumonia, lessons to be learned

Emerg Microbes Infect. 2020 Mar 16;9(1):597-600. doi: 10.1080/22221751.2020.1738905. eCollection 2020.


Unexplained pneumonia (UP) caused by a novel coronavirus SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) emerged in China in late December 2019 and has infected more than 9000 cases by 31 January 2020. Shanghai reported the first imported case of COVID-19 (Coronavirus Disease 2019) in 20 January 2020. A combinative approach of real-time RT-PCR, CRISPR-based assay and metagenomic next-generation sequencing (mNGS) were used to diagnose this unexplained pneumonia patient. Real-time RT-PCR and CRISPR-based assay both reported positive. This sample belonged to Betacoronavirus and shared a more than 99% nucleotide (nt) identity with the Wuhan SARS-CoV-2 isolates. We further compared pros and cons of common molecular diagnostics in UP. In this study, we illustrated the importance of combining molecular diagnostics to rule out common pathogens and performed mNGS to obtain unbiased potential pathogen result for the diagnosis of UP.

Keywords: COVID-19; SARS-CoV-2; Unexplained pneumonia; diagnosis; molecular.

Publication types

  • Letter

MeSH terms

  • Betacoronavirus / genetics
  • Betacoronavirus / isolation & purification
  • COVID-19
  • COVID-19 Testing
  • COVID-19 Vaccines
  • Clinical Laboratory Techniques*
  • Coronavirus Infections / diagnosis*
  • Coronavirus Infections / epidemiology
  • Coronavirus Infections / transmission
  • Humans
  • Molecular Diagnostic Techniques
  • Phylogeny
  • Pneumonia, Viral / diagnosis*
  • Pneumonia, Viral / epidemiology
  • Pneumonia, Viral / transmission
  • SARS-CoV-2


  • COVID-19 Vaccines
  • Covid-19 aAPC vaccine

Grant support

This study was supported by Key Technologies Research and Development Program for Infectious Diseases of China under [grant number 2018ZX10305-409-001-003].