[Emerging Microbes & Infections] Attenuated SARS-CoV-2 variants with deletions at the S1/S2 junction.

Emerging Microbes & Infections, 17 April 2020

Siu-Ying Lau, Pui Wang, Bobo Wing-Yee Mok, Anna Jinxia Zhang, Hin Chu, Andrew Chak-Yiu Lee, Shaofeng Deng, Pin Chen, Kwok-Hung Chan, Wenjun Song, Zhiwei Chen, Kelvin Kai-Wang To, Jasper Fuk-Woo Chan, Kwok-Yung Yuen & Honglin Chen

SARS-CoV-2 variants with deletions at the S1/S2 junction


  • The exact origin of SARS-CoV-2 remains elusive, but the presence of a distinct motif in the S1/S2 junction region suggests possible acquisition of cleavage site(s) in the spike protein that promoted cross-species transmission.
  • Found a series of SARS-CoV-2 variants containing 15-30 bp deletions (Del-mut) or point mutations at the S1/S2 junction
  • Hamster study shows that one of the variants (Del-mut-1), which carries deletion of 10 amino acids (30 bp), does not cause the body weight loss or more severe pathological changes in the lungs that is associated with wild type virus infection.
  • The unique cleavage motif promoting SARS-CoV-2 infection in humans may be under strong selective pressure, given that replication in permissive Vero-E6 cells leads to the loss of this adaptive function.

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