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SARS-CoV-2 Lambda variant exhibits higher infectivity and immune resistance

Izumi Kimura, Yusuke Kosugi, Jiaqi Wu, Daichi Yamasoba, Erika P Butlertanaka, Yuri L Tanaka, Yafei Liu, Kotaro Shirakawa, Yasuhiro Kazuma, Ryosuke Nomura, Yoshihito Horisawa, View ORCID ProfileKenzo Tokunaga, Akifumi Takaori-Kondo, View ORCID ProfileHisashi Arase, The Genotype to Phenotype Japan (G2P-Japan) Consortium, Akatsuki Saito, View ORCID ProfileSo Nakagawa, View ORCID ProfileKei Sato
doi: https://doi.org/10.1101/2021.07.28.454085
Izumi Kimura
1Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
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Yusuke Kosugi
1Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
2Laboratory of Systems Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 6068507, Japan
3Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 6068501, Japan
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Jiaqi Wu
4Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa 2591193, Japan
5CREST, Japan Science and Technology Agency, Saitama 3220012, Japan
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Daichi Yamasoba
1Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
6Faculty of Medicine, Kobe University, Hyogo 6500017, Japan
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Erika P Butlertanaka
7Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki 8892192, Japan
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Yuri L Tanaka
7Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki 8892192, Japan
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Yafei Liu
8Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, Osaka 5650871, Japan
9Laboratory of Immunochemistry, World Premier International Immunology Frontier Research Centre, Osaka University, Osaka 5650871, Japan
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Kotaro Shirakawa
10Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto 6068507, Japan
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Yasuhiro Kazuma
10Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto 6068507, Japan
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Ryosuke Nomura
10Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto 6068507, Japan
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Yoshihito Horisawa
10Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto 6068507, Japan
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Kenzo Tokunaga
11Department of Pathology, National Institute of Infectious Diseases, Tokyo 1628640, Japan
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  • ORCID record for Kenzo Tokunaga
Akifumi Takaori-Kondo
10Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto 6068507, Japan
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Hisashi Arase
8Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, Osaka 5650871, Japan
9Laboratory of Immunochemistry, World Premier International Immunology Frontier Research Centre, Osaka University, Osaka 5650871, Japan
12Center for Infectious Disease Education and Research, Osaka University, Osaka 5650871, Japan
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Akatsuki Saito
7Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki 8892192, Japan
13Center for Animal Disease Control, University of Miyazaki, Miyazaki 8892192, Japan
14Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki 8892192, Japan
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So Nakagawa
4Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa 2591193, Japan
5CREST, Japan Science and Technology Agency, Saitama 3220012, Japan
15Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka 4118540, Japan
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  • For correspondence: so@tokai.ac.jp KeiSato@g.ecc.u-tokyo.ac.jp
Kei Sato
1Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
5CREST, Japan Science and Technology Agency, Saitama 3220012, Japan
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  • ORCID record for Kei Sato
  • For correspondence: so@tokai.ac.jp KeiSato@g.ecc.u-tokyo.ac.jp
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Summary

SARS-CoV-2 Lambda, a new variant of interest, is now spreading in some South American countries; however, its virological features and evolutionary trait remain unknown. Here we reveal that the spike protein of the Lambda variant is more infectious and it is attributed to the T76I and L452Q mutations. The RSYLTPGD246-253N mutation, a unique 7-amino-acid deletion mutation in the N-terminal domain of the Lambda spike protein, is responsible for evasion from neutralizing antibodies. Since the Lambda variant has dominantly spread according to the increasing frequency of the isolates harboring the RSYLTPGD246-253N mutation, our data suggest that the insertion of the RSYLTPGD246-253N mutation is closely associated with the massive infection spread of the Lambda variant in South America.

Highlights

  • Lambda S is highly infectious and T76I and L452Q are responsible for this property

  • Lambda S is more susceptible to an infection-enhancing antibody

  • RSYLTPGD246-253N, L452Q and F490S confer resistance to antiviral immunity

Figure

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • ↵16 Twitter: @SystemsVirology

  • ↵18 Lead Contact

  • Conflict of interest: The authors declare that no competing interests exist.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted July 28, 2021.
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SARS-CoV-2 Lambda variant exhibits higher infectivity and immune resistance
Izumi Kimura, Yusuke Kosugi, Jiaqi Wu, Daichi Yamasoba, Erika P Butlertanaka, Yuri L Tanaka, Yafei Liu, Kotaro Shirakawa, Yasuhiro Kazuma, Ryosuke Nomura, Yoshihito Horisawa, Kenzo Tokunaga, Akifumi Takaori-Kondo, Hisashi Arase, The Genotype to Phenotype Japan (G2P-Japan) Consortium, Akatsuki Saito, So Nakagawa, Kei Sato
bioRxiv 2021.07.28.454085; doi: https://doi.org/10.1101/2021.07.28.454085
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SARS-CoV-2 Lambda variant exhibits higher infectivity and immune resistance
Izumi Kimura, Yusuke Kosugi, Jiaqi Wu, Daichi Yamasoba, Erika P Butlertanaka, Yuri L Tanaka, Yafei Liu, Kotaro Shirakawa, Yasuhiro Kazuma, Ryosuke Nomura, Yoshihito Horisawa, Kenzo Tokunaga, Akifumi Takaori-Kondo, Hisashi Arase, The Genotype to Phenotype Japan (G2P-Japan) Consortium, Akatsuki Saito, So Nakagawa, Kei Sato
bioRxiv 2021.07.28.454085; doi: https://doi.org/10.1101/2021.07.28.454085

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