Identification of common deletions in the spike protein of severe acute respiratory syndrome coronavirus 2

Zhe Liu, Huanying Zheng, Huifang Lin, Mingyue Li, Runyu Yuan, Jinju Peng, Qianling Xiong, Jiufeng Sun, Baisheng Li, Jie Wu, Lina Yi, Xiaofang Peng, Huan Zhang, Wei Zhang, Ruben J.G. Hulswit, Nick Loman, Andrew Rambaut, Changwen Ke, Thomas A. Bowden, Oliver G. PybusJing Lu*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

45 Citations (Scopus)

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel coronavirus first identified in December 2019. Notable features that make SARS-CoV-2 distinct from most other previously identified betacoronaviruses include a receptor binding domain and a unique insertion of 12 nucleotides or 4 amino acids (PRRA) at the S1/S2 boundary. In this study, we identified two deletion variants of SARS-CoV-2 that either directly affect the polybasic cleavage site itself (NSPRRAR) or a flanking sequence (QTQTN). These deletions were verified by multiple sequencing methods. In vitro results showed that the deletion of NSPRRAR likely does not affect virus replication in Vero and Vero-E6 cells; however, the deletion of QTQTN may restrict late-phase viral replication. The deletion of QTQTN was detected in 3 of 68 clinical samples and 12 of 24 in vitro-isolated viruses, while the deletion of NSPRRAR was identified in 3 in vitro-isolated viruses. Our data indicate that (i) there may be distinct selection pressures on SARS-CoV-2 replication or infection in vitro and in vivo; (ii) an efficient mechanism for deleting this region from the viral genome may exist, given that the deletion variant is commonly detected after two rounds of cell passage; and (iii) the PRRA insertion, which is unique to SARS-CoV-2, is not fixed during virus replication in vitro. These findings provide information to aid further investigation of SARS-CoV-2 infection mechanisms and a better understanding of the NSPRRAR deletion variant observed here. IMPORTANCE The spike protein determines the infectivity and host range of coronaviruses. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has two unique features in its spike protein, the receptor binding domain and an insertion of 12 nucleotides at the S1/S2 boundary resulting in a furin-like cleavage site. Here, we identified two deletion variants of SARS-CoV-2 that either directly affect the furin-like cleavage site itself (NSPRRAR) or a flanking sequence (QTQTN), and we investigated these deletions in cell isolates and clinical samples. The absence of the polybasic cleavage site in SARS-CoV-2 did not affect virus replication in Vero or Vero-E6 cells. Our data indicate the PRRAR sequence and the flanking QTQTN sequence are not fixed in vitro; thus, there appears to be distinct selection pressures on SARS-CoV-2 sequences in vitro and in vivo. Further investigation of the mechanism of generating these deletion variants and their infectivity in different animal models would improve our understanding of the origin and evolution of this virus.

Original languageEnglish
Article numbere00790-20
JournalJournal of Virology
Volume94
Issue number17
DOIs
Publication statusPublished - Sep 2020
Externally publishedYes

Bibliographical note

Funding Information:
This work was supported by grants from Guangdong Provincial Novel Coronavirus Scientific and Technological Project (2020111107001) and Science and Technology Planning Project of Guangdong (2018B020207006). T.A.B. is supported by the Medical Research Council (MR/S007555/1). The Wellcome Centre for Human Genetics is supported by Wellcome Trust grant 203141/Z/16/Z. This work was supported by the European Research Council under the European Commission Seventh Framework Programme (FP7/2007-2013)/European Research Council grant agreement (614725-PATHPHYLODYN).

Publisher Copyright:
© 2020 American Society for Microbiology. All Rights Reserved.

Keywords

  • COVID-19
  • Deletion mutation
  • Replication kinetics
  • SARS-CoV-2
  • Spike protein

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