Altered TMPRSS2 usage by SARS-CoV-2 Omicron impacts infectivity and fusogenicity.
Adult
Aged
Aged, 80 and over
Angiotensin-Converting Enzyme 2
/ metabolism
Animals
Antibodies, Neutralizing
/ immunology
Antibodies, Viral
/ immunology
COVID-19
/ immunology
COVID-19 Vaccines
/ immunology
Cell Line
Cell Membrane
/ metabolism
Chlorocebus aethiops
Convalescence
Female
Humans
Immune Sera
/ immunology
Intestines
/ pathology
Lung
/ pathology
Male
Membrane Fusion
Middle Aged
Mutation
Nasal Mucosa
/ pathology
SARS-CoV-2
/ drug effects
Serine Endopeptidases
/ metabolism
Spike Glycoprotein, Coronavirus
/ genetics
Tissue Culture Techniques
Virulence
Virus Internalization
Virus Replication
Journal
Nature
ISSN: 1476-4687
Titre abrégé: Nature
Pays: England
ID NLM: 0410462
Informations de publication
Date de publication:
03 2022
03 2022
Historique:
received:
21
12
2021
accepted:
26
01
2022
pubmed:
2
2
2022
medline:
1
4
2022
entrez:
1
2
2022
Statut:
ppublish
Résumé
The SARS-CoV-2 Omicron BA.1 variant emerged in 2021
Identifiants
pubmed: 35104837
doi: 10.1038/s41586-022-04474-x
pii: 10.1038/s41586-022-04474-x
pmc: PMC8942856
doi:
Substances chimiques
Antibodies, Neutralizing
0
Antibodies, Viral
0
COVID-19 Vaccines
0
Immune Sera
0
Spike Glycoprotein, Coronavirus
0
spike protein, SARS-CoV-2
0
ACE2 protein, human
EC 3.4.17.23
Angiotensin-Converting Enzyme 2
EC 3.4.17.23
Serine Endopeptidases
EC 3.4.21.-
TMPRSS2 protein, human
EC 3.4.21.-
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
706-714Subventions
Organisme : Medical Research Council
ID : MC_PC_17230
Pays : United Kingdom
Organisme : NIAID NIH HHS
ID : DP1 AI158186
Pays : United States
Organisme : Wellcome Trust
ID : 200594/Z/16/Z
Pays : United Kingdom
Organisme : Howard Hughes Medical Institute
Pays : United States
Organisme : Medical Research Council
ID : MC_UP_1201/16
Pays : United Kingdom
Organisme : Medical Research Council
ID : MR/P008801/1
Pays : United Kingdom
Organisme : NIAID NIH HHS
ID : HHSN272201700059C
Pays : United States
Organisme : Wellcome Trust
ID : WT108082AIA
Pays : United Kingdom
Organisme : Wellcome Trust
Pays : United Kingdom
Organisme : NIGMS NIH HHS
ID : T32 GM008268
Pays : United States
Organisme : Medical Research Council
ID : MC_U105181010
Pays : United Kingdom
Organisme : NIAID NIH HHS
ID : R01 AI138546
Pays : United States
Investigateurs
Stephen Baker
(S)
Gordon Dougan
(G)
Christoph Hess
(C)
Nathalie Kingston
(N)
Paul J Lehner
(PJ)
Paul A Lyons
(PA)
Nicholas J Matheson
(NJ)
Willem H Ouwehand
(WH)
Caroline Saunders
(C)
Charlotte Summers
(C)
James E D Thaventhiran
(JED)
Mark Toshner
(M)
Michael P Weekes
(MP)
Patrick Maxwell
(P)
Ashley Shaw
(A)
Ashlea Bucke
(A)
Jo Calder
(J)
Laura Canna
(L)
Jason Domingo
(J)
Anne Elmer
(A)
Stewart Fuller
(S)
Julie Harris
(J)
Sarah Hewitt
(S)
Jane Kennet
(J)
Sherly Jose
(S)
Jenny Kourampa
(J)
Anne Meadows
(A)
Criona O'Brien
(C)
Jane Price
(J)
Cherry Publico
(C)
Rebecca Rastall
(R)
Carla Ribeiro
(C)
Jane Rowlands
(J)
Valentina Ruffolo
(V)
Hugo Tordesillas
(H)
Ben Bullman
(B)
Benjamin J Dunmore
(BJ)
Stefan Gräf
(S)
Josh Hodgson
(J)
Christopher Huang
(C)
Kelvin Hunter
(K)
Emma Jones
(E)
Ekaterina Legchenko
(E)
Cecilia Matara
(C)
Jennifer Martin
(J)
Federica Mescia
(F)
Ciara O'Donnell
(C)
Linda Pointon
(L)
Joy Shih
(J)
Rachel Sutcliffe
(R)
Tobias Tilly
(T)
Carmen Treacy
(C)
Zhen Tong
(Z)
Jennifer Wood
(J)
Marta Wylot
(M)
Ariana Betancourt
(A)
Georgie Bower
(G)
Chiara Cossetti
(C)
Aloka De Sa
(A)
Madeline Epping
(M)
Stuart Fawke
(S)
Nick Gleadall
(N)
Richard Grenfell
(R)
Andrew Hinch
(A)
Sarah Jackson
(S)
Isobel Jarvis
(I)
Ben Krishna
(B)
Francesca Nice
(F)
Ommar Omarjee
(O)
Marianne Perera
(M)
Martin Potts
(M)
Nathan Richoz
(N)
Veronika Romashova
(V)
Luca Stefanucci
(L)
Mateusz Strezlecki
(M)
Lori Turner
(L)
Eckart M D D De Bie
(EMDD)
Katherine Bunclark
(K)
Masa Josipovic
(M)
Michael Mackay
(M)
Helen Butcher
(H)
Daniela Caputo
(D)
Matt Chandler
(M)
Patrick Chinnery
(P)
Debbie Clapham-Riley
(D)
Eleanor Dewhurst
(E)
Christian Fernandez
(C)
Anita Furlong
(A)
Barbara Graves
(B)
Jennifer Gray
(J)
Sabine Hein
(S)
Tasmin Ivers
(T)
Emma Le Gresley
(E)
Rachel Linger
(R)
Mary Kasanicki
(M)
Rebecca King
(R)
Nathalie Kingston
(N)
Sarah Meloy
(S)
Alexei Moulton
(A)
Francesca Muldoon
(F)
Nigel Ovington
(N)
Sofia Papadia
(S)
Christopher J Penkett
(CJ)
Isabel Phelan
(I)
Venkatesh Ranganath
(V)
Roxana Paraschiv
(R)
Abigail Sage
(A)
Jennifer Sambrook
(J)
Ingrid Scholtes
(I)
Katherine Schon
(K)
Hannah Stark
(H)
Kathleen E Stirrups
(KE)
Paul Townsend
(P)
Neil Walker
(N)
Jennifer Webster
(J)
Erika P Butlertanaka
(EP)
Yuri L Tanaka
(YL)
Jumpei Ito
(J)
Keiya Uriu
(K)
Yusuke Kosugi
(Y)
Mai Suganami
(M)
Akiko Oide
(A)
Miyabishara Yokoyama
(M)
Mika Chiba
(M)
Chihiro Motozono
(C)
Hesham Nasser
(H)
Ryo Shimizu
(R)
Kazuko Kitazato
(K)
Haruyo Hasebe
(H)
Takashi Irie
(T)
So Nakagawa
(S)
Jiaqi Wu
(J)
Miyoko Takahashi
(M)
Takasuke Fukuhara
(T)
Kenta Shimizu
(K)
Kana Tsushima
(K)
Haruko Kubo
(H)
Yasuhiro Kazuma
(Y)
Ryosuke Nomura
(R)
Yoshihito Horisawa
(Y)
Kayoko Nagata
(K)
Yugo Kawai
(Y)
Yohei Yanagida
(Y)
Yusuke Tashiro
(Y)
Kenzo Tokunaga
(K)
Seiya Ozono
(S)
Ryoko Kawabata
(R)
Nanami Morizako
(N)
Kenji Sadamasu
(K)
Hiroyuki Asakura
(H)
Mami Nagashima
(M)
Kazuhisa Yoshimura
(K)
Paúl Cárdenas
(P)
Erika Muñoz
(E)
Veronica Barragan
(V)
Sully Márquez
(S)
Belén Prado-Vivar
(B)
Mónica Becerra-Wong
(M)
Mateo Caravajal
(M)
Gabriel Trueba
(G)
Patricio Rojas-Silva
(P)
Michelle Grunauer
(M)
Bernardo Gutierrez
(B)
Juan José Guadalupe
(JJ)
Juan Carlos Fernández-Cadena
(JC)
Derly Andrade-Molina
(D)
Manuel Baldeon
(M)
Andrea Pinos
(A)
Commentaires et corrections
Type : UpdateOf
Type : CommentIn
Informations de copyright
© 2022. The Author(s).
Références
Viana, R. et al. Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa. Nature https://doi.org/10.1038/s41586-022-04411-y (2022).
Cele, S. et al. Omicron extensively but incompletely escapes Pfizer BNT162b2 neutralization. Nature https://doi.org/10.1038/s41586-021-04387-1 (2021).
Hoffmann, M. et al. SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor. Cell 181, 271–280 (2020).
pubmed: 32142651
pmcid: 7102627
Mlcochova, P. et al. SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion. Nature 599, 114–119 (2021).
pubmed: 34488225
pmcid: 8566220
doi: 10.1038/s41586-021-03944-y
Meng, B. et al. Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. Cell Rep. 35, 109292 (2021).
pubmed: 34166617
pmcid: 8185188
doi: 10.1016/j.celrep.2021.109292
Saito, A. et al. Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. Nature 602, 300–306 (2021).
pubmed: 34823256
pmcid: 8828475
Peacock, T. P. et al. The furin cleavage site in the SARS-CoV-2 spike protein is required for transmission in ferrets. Nat. Microbiol. 6, 899–909 (2021).
pubmed: 33907312
doi: 10.1038/s41564-021-00908-w
Dejnirattisai, W. et al. Reduced neutralisation of SARS-COV-2 Omicron-B.1.1.529 variant by post-immunisation serum. Lancet 399, 234–236 (2021).
pubmed: 34942101
pmcid: 8687667
doi: 10.1016/S0140-6736(21)02844-0
Wolter, N. et al. Early assessment of the clinical severity of the SARS-CoV-2 Omicron variant in South Africa: a data linkage study. Lancet https://doi.org/10.1016/S0140-6736(22)00017-4 (2022).
Walls, A. C. et al. Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein. Cell 181, 281–292 (2020).
pubmed: 32155444
pmcid: 7102599
doi: 10.1016/j.cell.2020.02.058
Cameroni, E. et al. Broadly neutralizing antibodies overcome SARS-CoV-2 Omicron antigenic shift. Nature https://doi.org/10.1038/s41586-021-04386-2 (2021).
Starr, T. N. et al. Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding. Cell 182, 1295–1310 (2020).
pubmed: 32841599
pmcid: 7418704
doi: 10.1016/j.cell.2020.08.012
McCallum, M. et al. Molecular basis of immune evasion by the Delta and Kappa SARS-CoV-2 variants. Science 374, 1621–1626 (2021).
pubmed: 34751595
doi: 10.1126/science.abl8506
Collier, D. A. et al. SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. Nature 593, 136–141 (2021).
pubmed: 33706364
doi: 10.1038/s41586-021-03412-7
McCallum, M. et al. Structural basis of SARS-CoV-2 Omicron immune evasion and receptor engagement. Science https://doi.org/10.1126/science.abn8652 (2021).
Barnes, C. O. et al. SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies. Nature 588, 682–687 (2020).
pubmed: 33045718
pmcid: 8092461
doi: 10.1038/s41586-020-2852-1
Naldini, L. et al. In vivo gene delivery and stable transduction of non-dividing cells by a lentiviral vector. Science 272, 263–267 (1996).
pubmed: 8602510
doi: 10.1126/science.272.5259.263
Mlcochova, P. et al. Combined point of care nucleic acid and antibody testing for SARS-CoV-2 following emergence of D614G spike variant. Cell Rep. Med. 1, 100099 (2020).
pubmed: 32905045
pmcid: 7462534
doi: 10.1016/j.xcrm.2020.100099
Pommerenke, C. et al. Identification of cell lines CL-14, CL-40 and CAL-51 as suitable models for SARS-CoV-2 infection studies. PLoS ONE 16, e0255622 (2021).
pubmed: 34339474
pmcid: 8328321
doi: 10.1371/journal.pone.0255622
Youk, J. et al. Three-dimensional human alveolar stem cell culture models reveal infection response to SARS-CoV-2. Cell Stem Cell 27, 905–919 (2020).
pubmed: 33142113
pmcid: 7577700
doi: 10.1016/j.stem.2020.10.004
Sachs, N. et al. Long-term expanding human airway organoids for disease modeling. EMBO J. 38, e100300 (2019).
pubmed: 30643021
pmcid: 6376275
doi: 10.15252/embj.2018100300
Papa, G. et al. Furin cleavage of SARS-CoV-2 Spike promotes but is not essential for infection and cell-cell fusion. PLoS Pathog. 17, e1009246 (2021).
pubmed: 33493182
pmcid: 7861537
doi: 10.1371/journal.ppat.1009246
Ou, T. et al. Hydroxychloroquine-mediated inhibition of SARS-CoV-2 entry is attenuated by TMPRSS2. PLoS Pathog. 17, e1009212 (2021).
pubmed: 33465165
pmcid: 7845965
doi: 10.1371/journal.ppat.1009212
Madissoon, E. et al. A spatial multi-omics atlas of the human lung reveals a novel immune cell survival niche. Preprint at https://doi.org/10.1101/2021.11.26.470108 (2021).
Salahudeen, A. A. et al. Progenitor identification and SARS-CoV-2 infection in human distal lung organoids. Nature 588, 670–675 (2020).
pubmed: 33238290
pmcid: 8003326
doi: 10.1038/s41586-020-3014-1
Brevini, T. et al. FXR inhibition reduces ACE2 expression, SARS-CoV-2 infection and may improve COVID-19 outcome. Preprint at https://doi.org/10.1101/2021.06.06.446781 (2021).
Buchrieser, J. et al. Syncytia formation by SARS-CoV-2-infected cells. EMBO J. 40, e107405 (2021).
pubmed: 33522642
pmcid: 7849166
doi: 10.15252/embj.2020107405
Cattin-Ortolá, J. et al. Sequences in the cytoplasmic tail of SARS-CoV-2 Spike facilitate expression at the cell surface and syncytia formation. Nat. Commun. 12, 5333 (2021).
Li, W. et al. Angiotensin-converting enzyme 2 is a functional receptor for the SARS coronavirus. Nature 426, 450–454 (2003).
pubmed: 14647384
pmcid: 7095016
doi: 10.1038/nature02145
Braga, L. et al. Drugs that inhibit TMEM16 proteins block SARS-CoV-2 Spike-induced syncytia. Nature 594, 88–93 (2021).
pubmed: 33827113
pmcid: 7611055
doi: 10.1038/s41586-021-03491-6
Bussani, R. et al. Persistence of viral RNA, pneumocyte syncytia and thrombosis are hallmarks of advanced COVID-19 pathology. eBioMedicine 61, 103104 (2020).
pubmed: 33158808
pmcid: 7677597
doi: 10.1016/j.ebiom.2020.103104
Ferreira, I. et al. SARS-CoV-2 B.1.617 mutations L452R and E484Q are not synergistic for antibody evasion. J. Infect. Dis. 224, 989–994 (2021).
pubmed: 34260717
pmcid: 8420622
doi: 10.1093/infdis/jiab368
Meng, B. et al. Recurrent emergence and transmission of a SARS-CoV-2 spike deletion H69/V70 and role in Alpha variant B.1.1.7. Cell Rep. 35, 109292 (2021).
pubmed: 34166617
pmcid: 8185188
doi: 10.1016/j.celrep.2021.109292
Cabantous, S., Terwilliger, T. C. & Waldo, G. S. Protein tagging and detection with engineered self-assembling fragments of green fluorescent protein. Nat. Biotechnol. 23, 102–107 (2005).
pubmed: 15580262
doi: 10.1038/nbt1044
Cathcart, A. L. et al. The dual function monoclonal antibodies VIR-7831 and VIR-7832 demonstrate potent in vitro and in vivo activity against SARS-CoV-2. Preprint at https://doi.org/10.1101/2021.03.09.434607 (2021).
V’Kovski, P., Kratzel, A., Steiner, S., Stalder, H. & Thiel, V. Coronavirus biology and replication: implications for SARS-CoV-2. Nat. Rev. Microbiol. 19, 155–170 (2021).
pubmed: 33116300
doi: 10.1038/s41579-020-00468-6
Bugge, T. H., Antalis, T. M. & Wu, Q. Type II transmembrane serine proteases. J. Biol. Chem. 284, 23177–23181 (2009).
pubmed: 19487698
pmcid: 2749090
doi: 10.1074/jbc.R109.021006
Park, J. E. et al. Proteolytic processing of Middle East respiratory syndrome coronavirus spikes expands virus tropism. Proc. Natl Acad. Sci. USA 113, 12262–12267 (2016).
pubmed: 27791014
pmcid: 5086990
doi: 10.1073/pnas.1608147113
Shuai, H. et al. Attenuated replication and pathogenesis of SARS-CoV-2 B.1.1.529 Omicron. Nature https://doi.org/10.1038/s41586-022-04442-5 (2021).
Heurich, A. et al. TMPRSS2 and ADAM17 cleave ACE2 differentially and only proteolysis by TMPRSS2 augments entry driven by the severe acute respiratory syndrome coronavirus spike protein. J. Virol. 88, 1293–1307 (2014).
pubmed: 24227843
pmcid: 3911672
doi: 10.1128/JVI.02202-13
Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013).
pubmed: 23329690
pmcid: 3603318
doi: 10.1093/molbev/mst010
Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).
pubmed: 34265844
pmcid: 8371605
doi: 10.1038/s41586-021-03819-2
Goddard, T. D. et al. UCSF ChimeraX: meeting modern challenges in visualization and analysis. Protein Sci. 27, 14–25 (2018).
pubmed: 28710774
Motozono, C. et al. SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Cell Host Microbe 29, 1124–1136 (2021).
pubmed: 34171266
pmcid: 8205251
doi: 10.1016/j.chom.2021.06.006
Matsuyama, S. et al. Enhanced isolation of SARS-CoV-2 by TMPRSS2-expressing cells. Proc. Natl Acad. Sci. USA 117, 7001–7003 (2020).
pubmed: 32165541
pmcid: 7132130
doi: 10.1073/pnas.2002589117
Dejnirattisai, W. et al. SARS-CoV2 Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses. Cell 185, 467–484.e15 (2022).
Dejnirattisai, W. et al. Reduced neutralisation of SARS-CoV-2 omicron B.1.1.529 variant by post-immunisation serum. Lancet 399, 234–236 (2022).
pubmed: 34942101
doi: 10.1016/S0140-6736(21)02844-0
Itokawa, K., Sekizuka, T., Hashino, M., Tanaka, R. & Kuroda, M. Disentangling primer interactions improves SARS-CoV-2 genome sequencing by multiplex tiling PCR. PLoS ONE 15, e0239403 (2020).
pubmed: 32946527
pmcid: 7500614
doi: 10.1371/journal.pone.0239403
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).
pubmed: 24695404
pmcid: 4103590
doi: 10.1093/bioinformatics/btu170
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
pubmed: 22388286
pmcid: 3322381
Chen, S. et al. Gencore: an efficient tool to generate consensus reads for error suppressing and duplicate removing of NGS data. BMC Bioinform. 20, 606 (2019).
doi: 10.1186/s12859-019-3280-9
Thorvaldsdottir, H., Robinson, J. T. & Mesirov, J. P. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief. Bioinform. 14, 178–192 (2013).
pubmed: 22517427
doi: 10.1093/bib/bbs017
Kimura, I. et al. The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. Cell Rep 38, 110218 (2021).
pubmed: 34968415
pmcid: 8683271
doi: 10.1016/j.celrep.2021.110218
Vermeire, J. et al. Quantification of reverse transcriptase activity by real-time PCR as a fast and accurate method for titration of HIV, lenti- and retroviral vectors. PLoS ONE 7, e50859 (2012).
pubmed: 23227216
pmcid: 3515444
doi: 10.1371/journal.pone.0050859
Gerber, P. P. et al. A protease-activatable luminescent biosensor and reporter cell line for authentic SARS-CoV-2 infection. PLoS Pathog. https://doi.org/10.1371/journal.ppat.1010265 (2022).
French, A. P., Mills, S., Swarup, R., Bennett, M. J. & Pridmore, T. P. Colocalization of fluorescent markers in confocal microscope images of plant cells. Nat. Protoc. 3, 619–628 (2008).
pubmed: 18388944
doi: 10.1038/nprot.2008.31