A SARS-CoV-2 variant with the 12-bp deletion at E gene

Emerg Microbes Infect. 2020 Dec;9(1):2361-2367. doi: 10.1080/22221751.2020.1837017.


The coronavirus disease 2019 (COVID-19) pandemic is still ongoing and has become an important public health threat. This disease is caused by a new coronavirus named severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection, and so far, little is known about this virus. In this study, by using plaque purification, we purified two SARS-CoV-2 virus strains from the same specimen, one named F8 containing a 12-bp deletion in the E gene and the other named 8X containing the wild-type E gene. There was no significant difference in the viral titer and infectivity of these two strains. The S protein content of the F8 viral culture was 0.39 μg/ml, much higher than that of 8X. An inactivated vaccine made from the F8 strain could trigger high levels of the IgG titer and neutralizing antibody titer, which could last for at least 6 weeks and were significantly higher than those from the 8X strain at 1 and 3 weeks post vaccination, respectively. In conclusion, we reported that both the E gene mutant and wild-type SARS-CoV-2 strains were isolated from the same clinical sample by plaque purification. A 12-bp deletion in the E gene was important for SARS-CoV-2 replication and immunogenicity.

Keywords: COVID-19; E gene mutant; SARS-CoV-2; immunogenicity; virus replication.

MeSH terms

  • Animals
  • Antibodies, Neutralizing / immunology
  • Antibodies, Viral / immunology
  • Betacoronavirus / genetics*
  • Betacoronavirus / immunology
  • Betacoronavirus / pathogenicity
  • COVID-19
  • Coronavirus Envelope Proteins
  • Coronavirus Infections / epidemiology
  • Coronavirus Infections / virology*
  • Female
  • Humans
  • Immunization
  • Male
  • Mice
  • Mice, Inbred BALB C
  • Pandemics
  • Pneumonia, Viral / epidemiology
  • Pneumonia, Viral / virology*
  • SARS-CoV-2
  • Sequence Deletion
  • Spike Glycoprotein, Coronavirus / administration & dosage
  • Spike Glycoprotein, Coronavirus / genetics
  • Spike Glycoprotein, Coronavirus / immunology
  • Viral Envelope Proteins / administration & dosage
  • Viral Envelope Proteins / genetics*
  • Viral Envelope Proteins / immunology
  • Virulence


  • Antibodies, Neutralizing
  • Antibodies, Viral
  • Coronavirus Envelope Proteins
  • Spike Glycoprotein, Coronavirus
  • Viral Envelope Proteins
  • envelope protein, SARS-CoV-2

Grants and funding

This work was supported by the Major Science and Technology Project of the Science and Technology Department of Zhejiang Province (2018C03070).