The D614G Mutation Redirects SARS-CoV-2 Spike to Lysosomes and Suppresses Deleterious Traits of the Furin Cleavage Site Insertion Mutation

Overview

Journal Sci Adv

Specialties Biology
Science

Date 2022 Dec 23

PMID 36563151

Authors

Chenxu Guo

Shang-Jui Tsai

Yiwei Ai

Maggie Li

Eduardo Anaya

Andrew Pekosz

Andrea Cox

Stephen J Gould

Affiliations

Soon will be listed here.

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) egress occurs by lysosomal exocytosis. We show that the Spike D614G mutation enhances Spike trafficking to lysosomes, drives Spike-mediated reprogramming of lysosomes, and reduces cell surface Spike expression by ~3-fold. D614G is not a human-specific adaptation. Rather, it is an adaptation to the earlier furin cleavage site insertion (FCSI) mutation that occurred at the genesis of SARS-CoV-2. While advantageous to the virus, furin cleavage of spike has deleterious effects on spike structure and function, inhibiting its trafficking to lysosomes and impairing its infectivity by the transmembrane serine protease 2(TMPRSS2)-independent, endolysosomal pathway. D614G restores spike trafficking to lysosomes and enhances the earliest events in SARS-CoV-2 infectivity, while spike mutations that restore SARS-CoV-2's TMPRSS2-independent infectivity restore spike's trafficking to lysosomes. Together, these and other results show that D614G is an intragenic suppressor of deleterious traits linked to the FCSI and lend additional support to the endolysosomal model of SARS-CoV-2 egress and entry.

Citing Articles

Application of machine learning algorithms to identify serological predictors of COVID-19 severity and outcomes.

Dhakal S, Yin A, Escarra-Senmarti M, Demko Z, Pisanic N, Johnston T Commun Med (Lond). 2024; 4(1):249.

PMID: 39592832 PMC: 11599591. DOI: 10.1038/s43856-024-00658-w.

Virion morphology and on-virus spike protein structures of diverse SARS-CoV-2 variants.

Ke Z, Peacock T, Brown J, Sheppard C, Croll T, Kotecha A EMBO J. 2024; 43(24):6469-6495.

PMID: 39543395 PMC: 11649927. DOI: 10.1038/s44318-024-00303-1.

Inhibition of protein kinase D and its substrate phosphatidylinositol-4 kinase III beta blocks common human coronavirus replication.

Han H, Liu H, Steiner R, Zhao Z, Jin Z Microbiol Spectr. 2024; :e0150124.

PMID: 39540754 PMC: 11619529. DOI: 10.1128/spectrum.01501-24.

Strengths and limitations of SARS-CoV-2 virus-like particle systems.

Sultana R, Stahelin R Virology. 2024; 601:110285.

PMID: 39536645 PMC: 11624109. DOI: 10.1016/j.virol.2024.110285.

CD81 fusion alters SARS-CoV-2 Spike trafficking.

Cone A, Zhou Y, McNamara R, Eason A, Arias G, Landis J mBio. 2024; 15(9):e0192224.

PMID: 39140770 PMC: 11389398. DOI: 10.1128/mbio.01922-24.

References

Volz E, Hill V, McCrone J, Price A, Jorgensen D, OToole A . Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity. Cell. 2020; 184(1):64-75.e11. PMC: 7674007. DOI: 10.1016/j.cell.2020.11.020. View

Peacock T, Goldhill D, Zhou J, Baillon L, Frise R, Swann O . The furin cleavage site in the SARS-CoV-2 spike protein is required for transmission in ferrets. Nat Microbiol. 2021; 6(7):899-909. DOI: 10.1038/s41564-021-00908-w. View

Klein S, Pekosz A, Park H, Ursin R, Shapiro J, Benner S . Sex, age, and hospitalization drive antibody responses in a COVID-19 convalescent plasma donor population. J Clin Invest. 2020; 130(11):6141-6150. PMC: 7598041. DOI: 10.1172/JCI142004. View

Baravalle G, Schober D, Huber M, Bayer N, Murphy R, Fuchs R . Transferrin recycling and dextran transport to lysosomes is differentially affected by bafilomycin, nocodazole, and low temperature. Cell Tissue Res. 2005; 320(1):99-113. DOI: 10.1007/s00441-004-1060-x. View

Koyama H, Goodpasture C, Miller M, TEPLITZ R, Riggs A . Establishment and characterization of a cell line from the American opossum (Didelphys virginiana). In Vitro. 1978; 14(3):239-46. DOI: 10.1007/BF02616032. View

Hoffmann M, Kleine-Weber H, Schroeder S, Kruger N, Herrler T, Erichsen S . SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor. Cell. 2020; 181(2):271-280.e8. PMC: 7102627. DOI: 10.1016/j.cell.2020.02.052. View

Ozono S, Zhang Y, Ode H, Sano K, Tan T, Imai K . SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity. Nat Commun. 2021; 12(1):848. PMC: 7870668. DOI: 10.1038/s41467-021-21118-2. View

Braulke T, Bonifacino J . Sorting of lysosomal proteins. Biochim Biophys Acta. 2008; 1793(4):605-14. DOI: 10.1016/j.bbamcr.2008.10.016. View

Zhou P, Yang X, Wang X, Hu B, Zhang L, Zhang W . A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature. 2020; 579(7798):270-273. PMC: 7095418. DOI: 10.1038/s41586-020-2012-7. View

10.

Ghosh S, Dellibovi-Ragheb T, Kerviel A, Pak E, Qiu Q, Fisher M . β-Coronaviruses Use Lysosomes for Egress Instead of the Biosynthetic Secretory Pathway. Cell. 2020; 183(6):1520-1535.e14. PMC: 7590812. DOI: 10.1016/j.cell.2020.10.039. View

11.

Wrapp D, Wang N, Corbett K, Goldsmith J, Hsieh C, Abiona O . Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science. 2020; 367(6483):1260-1263. PMC: 7164637. DOI: 10.1126/science.abb2507. View

12.

Sasaki M, Uemura K, Sato A, Toba S, Sanaki T, Maenaka K . SARS-CoV-2 variants with mutations at the S1/S2 cleavage site are generated in vitro during propagation in TMPRSS2-deficient cells. PLoS Pathog. 2021; 17(1):e1009233. PMC: 7853460. DOI: 10.1371/journal.ppat.1009233. View

13.

King J, Jukes T . Non-Darwinian evolution. Science. 1969; 164(3881):788-98. DOI: 10.1126/science.164.3881.788. View

14.

Lorenzo-Redondo R, Nam H, Roberts S, Simons L, Jennings L, Qi C . A clade of SARS-CoV-2 viruses associated with lower viral loads in patient upper airways. EBioMedicine. 2020; 62:103112. PMC: 7655495. DOI: 10.1016/j.ebiom.2020.103112. View

15.

Zhang L, Jackson C, Mou H, Ojha A, Peng H, Quinlan B . SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity. Nat Commun. 2020; 11(1):6013. PMC: 7693302. DOI: 10.1038/s41467-020-19808-4. View

16.

Bloom J, Chan Y, Baric R, Bjorkman P, Cobey S, Deverman B . Investigate the origins of COVID-19. Science. 2021; 372(6543):694. PMC: 9520851. DOI: 10.1126/science.abj0016. View

17.

Ruch T, Machamer C . The coronavirus E protein: assembly and beyond. Viruses. 2012; 4(3):363-82. PMC: 3347032. DOI: 10.3390/v4030363. View

18.

Guo C, Fordjour F, Tsai S, Morrell J, Gould S . Choice of selectable marker affects recombinant protein expression in cells and exosomes. J Biol Chem. 2021; 297(1):100838. PMC: 8258971. DOI: 10.1016/j.jbc.2021.100838. View

19.

Mykytyn A, Breugem T, Riesebosch S, Schipper D, van den Doel P, Rottier R . SARS-CoV-2 entry into human airway organoids is serine protease-mediated and facilitated by the multibasic cleavage site. Elife. 2021; 10. PMC: 7806259. DOI: 10.7554/eLife.64508. View

20.

Cantuti-Castelvetri L, Ojha R, Pedro L, Djannatian M, Franz J, Kuivanen S . Neuropilin-1 facilitates SARS-CoV-2 cell entry and infectivity. Science. 2020; 370(6518):856-860. PMC: 7857391. DOI: 10.1126/science.abd2985. View