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Identification of Common Deletions in the Spike Protein of Severe Acute Respiratory Syndrome Coronavirus 2.
J Virol. 2020 08 17; 94(17)JV

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.

Authors+Show Affiliations

Guangdong Provincial Institution of Public Health, Guangzhou, China. Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China.Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China.Guangdong Provincial Institution of Public Health, Guangzhou, China. Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China.Department of Rehabilitation Medicine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.Guangdong Provincial Institution of Public Health, Guangzhou, China. Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China.Guangdong Provincial Institution of Public Health, Guangzhou, China. Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China.Guangdong Provincial Institution of Public Health, Guangzhou, China. Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China.Guangdong Provincial Institution of Public Health, Guangzhou, China. Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China.Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China.Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China.Guangdong Provincial Institution of Public Health, Guangzhou, China. Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China.Guangdong Provincial Institution of Public Health, Guangzhou, China. Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China.Guangdong Provincial Institution of Public Health, Guangzhou, China. Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China.Guangdong Provincial Institution of Public Health, Guangzhou, China. Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China.Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom.Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom.Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China.Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.Department of Zoology, University of Oxford, Oxford, United Kingdom oliver.pybus@zoo.ox.ac.uk Jimlu0331@163.com. Department of Pathobiology and Population Sciences, The Royal Veterinary College, London, United Kingdom.Guangdong Provincial Institution of Public Health, Guangzhou, China oliver.pybus@zoo.ox.ac.uk Jimlu0331@163.com. Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

32571797

Citation

Liu, Zhe, et al. "Identification of Common Deletions in the Spike Protein of Severe Acute Respiratory Syndrome Coronavirus 2." Journal of Virology, vol. 94, no. 17, 2020.
Liu Z, Zheng H, Lin H, et al. Identification of Common Deletions in the Spike Protein of Severe Acute Respiratory Syndrome Coronavirus 2. J Virol. 2020;94(17).
Liu, Z., Zheng, H., Lin, H., Li, M., Yuan, R., Peng, J., Xiong, Q., Sun, J., Li, B., Wu, J., Yi, L., Peng, X., Zhang, H., Zhang, W., Hulswit, R. J. G., Loman, N., Rambaut, A., Ke, C., Bowden, T. A., ... Lu, J. (2020). Identification of Common Deletions in the Spike Protein of Severe Acute Respiratory Syndrome Coronavirus 2. Journal of Virology, 94(17). https://doi.org/10.1128/JVI.00790-20
Liu Z, et al. Identification of Common Deletions in the Spike Protein of Severe Acute Respiratory Syndrome Coronavirus 2. J Virol. 2020 08 17;94(17) PubMed PMID: 32571797.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Identification of Common Deletions in the Spike Protein of Severe Acute Respiratory Syndrome Coronavirus 2. AU - Liu,Zhe, AU - Zheng,Huanying, AU - Lin,Huifang, AU - Li,Mingyue, AU - Yuan,Runyu, AU - Peng,Jinju, AU - Xiong,Qianling, AU - Sun,Jiufeng, AU - Li,Baisheng, AU - Wu,Jie, AU - Yi,Lina, AU - Peng,Xiaofang, AU - Zhang,Huan, AU - Zhang,Wei, AU - Hulswit,Ruben J G, AU - Loman,Nick, AU - Rambaut,Andrew, AU - Ke,Changwen, AU - Bowden,Thomas A, AU - Pybus,Oliver G, AU - Lu,Jing, Y1 - 2020/08/17/ PY - 2020/04/26/received PY - 2020/06/16/accepted PY - 2020/6/24/pubmed PY - 2020/9/2/medline PY - 2020/6/24/entrez KW - COVID-19 KW - SARS-CoV-2 KW - deletion mutation KW - replication kinetics KW - spike protein JF - Journal of virology JO - J Virol VL - 94 IS - 17 N2 - 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. SN - 1098-5514 UR - https://www.unboundmedicine.com/medline/citation/32571797/Identification_of_Common_Deletions_in_the_Spike_Protein_of_Severe_Acute_Respiratory_Syndrome_Coronavirus_2_ L2 - http://jvi.asm.org/cgi/pmidlookup?view=long&pmid=32571797 DB - PRIME DP - Unbound Medicine ER -