SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion.
Journal
Nature
ISSN: 1476-4687
Titre abrégé: Nature
Pays: England
ID NLM: 0410462
Informations de publication
Date de publication:
11 2021
11 2021
Historique:
received:
18
06
2021
accepted:
23
08
2021
pubmed:
7
9
2021
medline:
12
11
2021
entrez:
6
9
2021
Statut:
ppublish
Résumé
The B.1.617.2 (Delta) variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first identified in the state of Maharashtra in late 2020 and spread throughout India, outcompeting pre-existing lineages including B.1.617.1 (Kappa) and B.1.1.7 (Alpha)
Identifiants
pubmed: 34488225
doi: 10.1038/s41586-021-03944-y
pii: 10.1038/s41586-021-03944-y
pmc: PMC8566220
mid: EMS137317
doi:
Substances chimiques
Antibodies, Neutralizing
0
COVID-19 Vaccines
0
Spike Glycoprotein, Coronavirus
0
spike protein, SARS-CoV-2
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
114-119Subventions
Organisme : Medical Research Council
ID : MC_PC_17230
Pays : United Kingdom
Organisme : Medical Research Council
ID : MC_PC_19012
Pays : United Kingdom
Organisme : Wellcome Trust
ID : 108082
Pays : United Kingdom
Organisme : Wellcome Trust
ID : 200594/Z/16/Z
Pays : United Kingdom
Organisme : Medical Research Council
ID : MC_U105181010
Pays : United Kingdom
Organisme : Medical Research Council
ID : MR/W005611/1
Pays : United Kingdom
Organisme : Medical Research Council
ID : MR/V038109/1
Pays : United Kingdom
Organisme : Wellcome Trust
ID : 081772
Pays : United Kingdom
Organisme : Wellcome Trust
ID : WT108082AIA
Pays : United Kingdom
Organisme : Wellcome Trust
Pays : United Kingdom
Organisme : Medical Research Council
ID : MR/R015600/1
Pays : United Kingdom
Investigateurs
Himanshu Chauhan
(H)
Tanzin Dikid
(T)
Hema Gogia
(H)
Hemlata Lall
(H)
Kaptan Verma
(K)
Mahesh Shanker Dhar
(MS)
Manoj K Singh
(MK)
Namita Soni
(N)
Namonarayan Meena
(N)
Preeti Madan
(P)
Priyanka Singh
(P)
Ramesh Sharma
(R)
Rajeev Sharma
(R)
Sandhya Kabra
(S)
Sattender Kumar
(S)
Swati Kumari
(S)
Uma Sharma
(U)
Urmila Chaudhary
(U)
Sridhar Sivasubbu
(S)
Vinod Scaria
(V)
J K Oberoi
(JK)
Reena Raveendran
(R)
S Datta
(S)
Saumitra Das
(S)
Arindam Maitra
(A)
Sreedhar Chinnaswamy
(S)
Nidhan Kumar Biswas
(NK)
Ajay Parida
(A)
Sunil K Raghav
(SK)
Punit Prasad
(P)
Apurva Sarin
(A)
Satyajit Mayor
(S)
Uma Ramakrishnan
(U)
Dasaradhi Palakodeti
(D)
Aswin Sai Narain Seshasayee
(ASN)
K Thangaraj
(K)
Murali Dharan Bashyam
(MD)
Ashwin Dalal
(A)
Manoj Bhat
(M)
Yogesh Shouche
(Y)
Ajay Pillai
(A)
Priya Abraham
(P)
Varsha Atul Potdar
(VA)
Sarah S Cherian
(SS)
Anita Sudhir Desai
(AS)
Chitra Pattabiraman
(C)
M V Manjunatha
(MV)
Reeta S Mani
(RS)
Gautam Arunachal Udupi
(GA)
Vinay Nandicoori
(V)
Karthik Bharadwaj Tallapaka
(KB)
Divya Tej Sowpati
(DT)
Ryoko Kawabata
(R)
Nanami Morizako
(N)
Kenji Sadamasu
(K)
Hiroyuki Asakura
(H)
Mami Nagashima
(M)
Kazuhisa Yoshimura
(K)
Jumpei Ito
(J)
Izumi Kimura
(I)
Keiya Uriu
(K)
Yusuke Kosugi
(Y)
Mai Suganami
(M)
Akiko Oide
(A)
Miyabishara Yokoyama
(M)
Mika Chiba
(M)
Akatsuki Saito
(A)
Erika P Butlertanaka
(EP)
Yuri L Tanaka
(YL)
Terumasa Ikeda
(T)
Chihiro Motozono
(C)
Hesham Nasser
(H)
Ryo Shimizu
(R)
Yue Yuan
(Y)
Kazuko Kitazato
(K)
Haruyo Hasebe
(H)
So Nakagawa
(S)
Jiaqi Wu
(J)
Miyoko Takahashi
(M)
Takasuke Fukuhara
(T)
Kenta Shimizu
(K)
Kana Tsushima
(K)
Haruko Kubo
(H)
Kotaro Shirakawa
(K)
Yasuhiro Kazuma
(Y)
Ryosuke Nomura
(R)
Yoshihito Horisawa
(Y)
Akifumi Takaori-Kondo
(A)
Kenzo Tokunaga
(K)
Seiya Ozono
(S)
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 Owehand
(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)
Stuart Fawke
(S)
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)
Nicole Pond
(N)
Joy Shih
(J)
Rachel Sutcliffe
(R)
Tobias Tilly
(T)
Carmen Treacy
(C)
Zhen Tong
(Z)
Jennifer Wood
(J)
Marta Wylot
(M)
Laura Bergamaschi
(L)
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)
Oisin Huhn
(O)
Sarah Jackson
(S)
Isobel Jarvis
(I)
Ben Krishna
(B)
Daniel Lewis
(D)
Joe Marsden
(J)
Francesca Nice
(F)
Georgina Okecha
(G)
Ommar Omarjee
(O)
Marianne Perera
(M)
Martin Potts
(M)
Nathan Richoz
(N)
Veronika Romashova
(V)
Natalia Savinykh Yarkoni
(NS)
Rahul Sharma
(R)
Luca Stefanucci
(L)
Jonathan Stephens
(J)
Mateusz Strezlecki
(M)
Lori Turner
(L)
Eckart M D D De Bie
(EMDD)
Katherine Bunclark
(K)
Masa Josipovic
(M)
Michael Mackay
(M)
Sabrina Rossi
(S)
Mayurun Selvan
(M)
Sarah Spencer
(S)
Cissy Yong
(C)
John Allison
(J)
Helen Butcher
(H)
Daniela Caputo
(D)
Debbie Clapham-Riley
(D)
Eleanor Dewhurst
(E)
Anita Furlong
(A)
Barbara Graves
(B)
Jennifer Gray
(J)
Tasmin Ivers
(T)
Mary Kasanicki
(M)
Emma Le Gresley
(E)
Rachel Linger
(R)
Sarah Meloy
(S)
Francesca Muldoon
(F)
Nigel Ovington
(N)
Sofia Papadia
(S)
Isabel Phelan
(I)
Hannah Stark
(H)
Kathleen E Stirrups
(KE)
Paul Townsend
(P)
Neil Walker
(N)
Jennifer Webster
(J)
Ingrid Scholtes
(I)
Sabine Hein
(S)
Rebecca King
(R)
Informations de copyright
© 2021. The Author(s).
Références
Ferreira, I. et al. SARS-CoV-2 B.1.617 mutations L452 and E484Q are not synergistic for antibody evasion. J. Infect. Dis. https://doi.org/10.1093/infdis/jiab368 (2021).
Volz, E. et al. Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England. Nature https://doi.org/10.1038/s41586-021-03470-x (2021).
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).
doi: 10.1038/s41586-021-03412-7
Cherian, S. et al. Convergent evolution of SARS-CoV-2 spike mutations, L452R, E484Q and P681R, in the second wave of COVID-19 in Maharashtra, India. Preprint at https://doi.org/10.1101/2021.04.22.440932 (2021).
Deng, X. et al. Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation. Preprint at https://doi.org/10.1101/2021.03.07.21252647 (2021).
McCallum, M. et al. SARS-CoV-2 immune evasion by variant B.1.427/B.1.429. Preprint at https://doi.org/10.1101/2021.03.31.437925 (2021).
Motozono, C. et al. An emerging SARS-CoV-2 mutant evading cellular immunity and increasing viral infectivity. Preprint at https://doi.org/10.1101/2021.04.02.438288 (2021).
Weinreich, D. M. et al. REGN-COV2, a neutralizing antibody cocktail, in outpatients with Covid-19. N. Engl. J. Med. 384, 238–251 (2020).
doi: 10.1056/NEJMoa2035002
Peacock, T. P. et al. The furin cleavage site in the SARS-CoV-2 spike protein is required for transmission in ferrets. Nat. Microbiol. https://doi.org/10.1038/s41564-021-00908-w (2021).
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).
doi: 10.1016/j.stem.2020.10.004
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).
doi: 10.1371/journal.ppat.1009246
Cattin-Ortolá, J. et al. Sequences in the cytoplasmic tail of SARS-CoV-2 Spike facilitate expression at the cell surface and syncytia formation. Preprint at https://doi.org/10.1101/2020.10.12.335562 (2021).
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. https://doi.org/10.1016/j.celrep.2021.109292 (2021).
Bhoyar, R. C. et al. High throughput detection and genetic epidemiology of SARS-CoV-2 using COVIDSeq next-generation sequencing. PLoS ONE 16, e0247115 (2021).
doi: 10.1371/journal.pone.0247115
Lopez Bernal, J. et al. Effectiveness of Covid-19 vaccines against the B.1.617.2 (Delta) variant. N. Engl. J. Med. https://doi.org/10.1056/NEJMoa2108891 (2021).
Bernal, J. L. et al. Effectiveness of COVID-19 vaccines against the B.1.617.2 variant. Preprint at https://doi.org/10.1101/2021.05.22.21257658 (2021).
Dhar, M. S. et al. Genomic characterization and epidemiology of an emerging SARS-CoV-2 variant in Delhi, India. Science https://www.science.org/doi/10.1126/science.abj9932 (2021).
Kemp, S. A. et al. SARS-CoV-2 evolution during treatment of chronic infection. Nature 592, 277–282 (2021).
doi: 10.1038/s41586-021-03291-y
Zeng, C. et al. SARS-CoV-2 spreads through cell-to-cell transmission. Preprint at bioRxiv https://doi.org/10.1101/2021.06.01.446579 (2021).
Jackson, L. et al. SARS-CoV-2 cell-to-cell spread occurs rapidly and is insensitive to antibody neutralization. Preprint at https://doi.org/10.1101/2021.06.01.446516 (2021).
Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013).
doi: 10.1093/molbev/mst010
Rambaut, A. et al. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat. Microbiol. 5, 1403–1407 (2020).
doi: 10.1038/s41564-020-0770-5
Minh, B. Q. et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Preprint at https://doi.org/10.1101/849372 (2019).
Yu, G., Smith, D. K., Zhu, H., Guan, Y. & Lam, T. T. Y. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods Ecol. Evol. 8, 28–36 (2017).
doi: 10.1111/2041-210X.12628
Wrobel, A. G. et al. SARS-CoV-2 and bat RaTG13 spike glycoprotein structures inform on virus evolution and furin-cleavage effects. Nat. Struct. Mol. Biol. 27, 763–767 (2020).
doi: 10.1038/s41594-020-0468-7
McFadden, D. in Frontiers in Econometrics 105–142 (ed. Zarembka, P.) (Academic, 1974).
Rihn, S. J. et al. A plasmid DNA-launched SARS-CoV-2 reverse genetics system and coronavirus toolkit for COVID-19 research. PLoS Biol. 19, e3001091 (2021).
doi: 10.1371/journal.pbio.3001091
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).
doi: 10.1371/journal.pone.0050859
Matsuyama, S. et al. Enhanced isolation of SARS-CoV-2 by TMPRSS2-expressing cells. Proc. Natl Acad. Sci. USA 117, 7001–7003 (2020).
doi: 10.1073/pnas.2002589117
Reed, L. J. & Muench, H. A simple method of estimating fifty percent endpoints. Am. J. Hyg. 27, 493–497 (1938).
Motozono, C. et al. SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Cell Host Microbe https://doi.org/10.1016/j.chom.2021.06.006 (2021).
Shema Mugisha, C. et al. A simplified quantitative real-time PCR assay for monitoring SARS-CoV-2 growth in cell culture. mSphere https://doi.org/10.1128/mSphere.00658-20 (2020).
Corman, V. M. et al. Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Euro Surveill. 25, 2000045 (2020).
Schmidt, F. et al. Measuring SARS-CoV-2 neutralizing antibody activity using pseudotyped and chimeric viruses. Preprint at https://doi.org/10.1101/2020.06.08.140871 (2020).
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. https://doi.org/10.1016/j.xcrm.2020.100099 (2020).
Ou, X. et al. Characterization of spike glycoprotein of SARS-CoV-2 on virus entry and its immune cross-reactivity with SARS-CoV. Nat. Commun. 11, 1620 (2020).
doi: 10.1038/s41467-020-15562-9
Kodaka, M. et al. A new cell-based assay to evaluate myogenesis in mouse myoblast C2C12 cells. Exp. Cell Res. 336, 171–181 (2015).
doi: 10.1016/j.yexcr.2015.06.015
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).
doi: 10.1371/journal.ppat.1009246
Buchrieser, J. et al. Syncytia formation by SARS‐CoV‐2‐infected cells. EMBO J. 39, e106267 (2020).
doi: 10.15252/embj.2020106267