Evidence for increased breakthrough rates of SARS-CoV-2 variants of concern in BNT162b2-mRNA-vaccinated individuals.


Journal

Nature medicine
ISSN: 1546-170X
Titre abrégé: Nat Med
Pays: United States
ID NLM: 9502015

Informations de publication

Date de publication:
08 2021
Historique:
received: 30 04 2021
accepted: 26 05 2021
pubmed: 16 6 2021
medline: 28 8 2021
entrez: 15 6 2021
Statut: ppublish

Résumé

The BNT162b2 mRNA vaccine is highly effective against SARS-CoV-2. However, apprehension exists that variants of concern (VOCs) may evade vaccine protection, due to evidence of reduced neutralization of the VOCs B.1.1.7 and B.1.351 by vaccine sera in laboratory assays. We performed a matched cohort study to examine the distribution of VOCs in infections of BNT162b2 mRNA vaccinees from Clalit Health Services (Israel) using viral genomic sequencing, and hypothesized that if vaccine effectiveness against a VOC is reduced, its proportion among breakthrough cases would be higher than in unvaccinated controls. Analyzing 813 viral genome sequences from nasopharyngeal swabs, we showed that vaccinees who tested positive at least 7 days after the second dose were disproportionally infected with B.1.351, compared with controls. Those who tested positive between 2 weeks after the first dose and 6 days after the second dose were disproportionally infected by B.1.1.7. These findings suggest reduced vaccine effectiveness against both VOCs within particular time windows. Our results emphasize the importance of rigorously tracking viral variants, and of increasing vaccination to prevent the spread of VOCs.

Identifiants

pubmed: 34127854
doi: 10.1038/s41591-021-01413-7
pii: 10.1038/s41591-021-01413-7
pmc: PMC8363499
doi:

Substances chimiques

COVID-19 Vaccines 0
RNA, Messenger 0
BNT162 Vaccine N38TVC63NU

Types de publication

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

Langues

eng

Sous-ensembles de citation

IM

Pagination

1379-1384

Subventions

Organisme : EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)
ID : 852223

Informations de copyright

© 2021. The Author(s).

Références

Dagan, N. et al. BNT162b2 mRNA Covid-19 vaccine in a nationwide mass vaccination setting. N. Engl. J. Med. 384, 1412–1423 (2021).
doi: 10.1056/NEJMoa2101765
Polack, F. P. et al. Safety and efficacy of the BNT162b2 mRNA Covid-19 vaccine. N. Engl. J. Med. 383, 2603–2615 (2020).
doi: 10.1056/NEJMoa2034577
Davies, N. G. et al. Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England. Science 372, eabg3055 (2021).
doi: 10.1126/science.abg3055
Davies, N. G. et al. Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7. Nature 593, 270–274 (2021).
doi: 10.1038/s41586-021-03426-1
Tegally, H. et al. Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa. Preprint at medRxiv https://doi.org/10.1101/2020.12.21.20248640 (2020).
Naveca, F. et al. Phylogenetic relationship of SARS-CoV-2 sequences from Amazonas with emerging Brazilian variants harboring mutations E484K and N501Y in the Spike protein. Virological.org https://virological.org/t/phylogenetic-relationship-of-sars-cov-2- sequences-from-amazonas-with-emerging- brazilian-variants-harboring-mutations- e484k-and-n501y-in-the-spike-protein/585 (2021).
Liu, Y. et al. Neutralizing activity of BNT162b2-elicited serum. N. Engl. J. Med. 384, 1466–1468 (2021).
doi: 10.1056/NEJMc2102017
Xie, X. et al. Neutralization of SARS-CoV-2 spike 69/70 deletion E484K and N501Y variants by BNT162b2 vaccine-elicited sera. Nat. Med. 27, 620–621 (2021).
doi: 10.1038/s41591-021-01270-4
Collier, D. A. et al. Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies. Nature 593, 136–141 (2021).
doi: 10.1038/s41586-021-03412-7
Zhou, D. et al. Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera. Cell 184, 2348–2361.e6 (2021).
doi: 10.1016/j.cell.2021.02.037
Wang, P. et al. Antibody resistance of SARS-CoV-2 variants B.1.351 and B.1.1.7. Nature 593, 130–135 (2021).
doi: 10.1038/s41586-021-03398-2
Kuzmina, A. et al. SARS-CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera. Cell Host Microbe 29, 522–528 (2021).
doi: 10.1016/j.chom.2021.03.008
Korber, B. et al. Tracking changes in SARS-CoV-2 spike: evidence that D614G increases infectivity of the COVID-19 virus. Cell 182, 812–827 (2020).
doi: 10.1016/j.cell.2020.06.043
Liu, Y. et al. Neutralizing activity of BNT162b2-elicited serum—preliminary report. N. Engl. J. Med. 384, 1466–1468 (2021).
doi: 10.1056/NEJMc2102017
Tarke, A. et al. Negligible impact of SARS-CoV-2 variants on CD4
South African variant found in about 1% of all positive tests. MOH https://www.gov.il/en/departments/news/22022021-01 (2021).
Planas, D. et al. Sensitivity of infectious SARS-CoV-2 B.1.1.7 and B.1.351 variants to neutralizing antibodies. Nat. Med. 27, 917–924 (2021).
doi: 10.1038/s41591-021-01318-5
Khoury, D. S. et al. Neutralizing antibody levels are highly predictive of immune protection from symptomatic SARS-CoV-2 infection. Nat. Med. https://doi.org/10.1038/s41591-021-01377-8 (2021).
Marks, M. et al. Transmission of COVID-19 in 282 clusters in Catalonia, Spain: a cohort study. Lancet Infect. Dis. 21, 629–636 (2021).
doi: 10.1016/S1473-3099(20)30985-3
Walsh, E. E. et al. Safety and immunogenicity of two RNA-based Covid-19 vaccine candidates. N. Engl. J. Med. 383, 2439–2450 (2020).
doi: 10.1056/NEJMoa2027906
Optimising the COVID-19 vaccination programme for maximum short-term impact. GOV.UK https://www.gov.uk/government/publications/prioritising-the-first-covid-19-vaccine-dose-jcvi-statement/optimising-the-covid-19-vaccination-programme-for-maximum-short-term-impact (2021).
Abu-Raddad, L. J. et al. Effectiveness of the BNT162b2 Covid-19 vaccine against the B.1.1.7 and B.1.351 variants. N. Engl. J. Med. https://doi.org/10.1056/NEJMc2104974 (2021).
Greaney, A. J. et al. Comprehensive mapping of mutations to the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human serum antibodies. Preprint at bioRxiv https://doi.org/10.1101/2020.12.31.425021 (2021).
Weisblum, Y. et al. Escape from neutralizing antibodies by SARS-CoV-2 spike protein variants. Elife 9, e61312 (2020).
doi: 10.7554/eLife.61312
Greaney, A. J. et al. Complete mapping of mutations to the SARS-CoV-2 spike receptor-binding domain that escape antibody recognition. Cell Host Microbe 29, 44–57 (2021).
doi: 10.1016/j.chom.2020.11.007
Starr, T. N. et al. Prospective mapping of viral mutations that escape antibodies used to treat COVID-19. Science 371, 850–854 (2021).
doi: 10.1126/science.abf9302
Garcia-Beltran, W. F. et al. Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. Cell 184, 2372–2383.e9 (2021).
doi: 10.1016/j.cell.2021.03.013
Walker, A. S. et al. Increased infections, but not viral burden, with a new SARS-CoV-2 variant. Preprint at medRxiv https://doi.org/10.1101/2021.01.13.21249721 (2021).
Levine-Tiefenbrun, M. et al. Initial report of decreased SARS-CoV-2 viral load after inoculation with the BNT162b2 vaccine. Nat. Med. 27, 790–792 (2021).
doi: 10.1038/s41591-021-01316-7
Petter, E. et al. Initial real world evidence for lower viral load of individuals who have been vaccinated by BNT162b2. Preprint at medRxiv https://doi.org/10.1101/2021.02.08.21251329 (2021).
COVID-19 Dashboard (Israeli Ministry of Health); https://datadashboard.health.gov.il/COVID-19/general (accessed 26 May 2021)
Itokawa, K. et al. Disentangling primer interactions improves SARS-CoV-2 genome sequencing by multiplex tiling PCR. PLoS ONE 15, e0239403 (2020).
doi: 10.1371/journal.pone.0239403
Zhang, X. et al. pTrimmer: an efficient tool to trim primers of multiplex deep sequencing data. BMC Bioinformatics 20, 236 (2019).
doi: 10.1186/s12859-019-2854-x
Gelbart, M. et al. Drivers of within-host genetic diversity in acute infections of viruses. PLoS Pathog. 16, e1009029 (2020).
doi: 10.1371/journal.ppat.1009029
Altschul, S. F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402 (1997).
doi: 10.1093/nar/25.17.3389
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
Dudas, G. et al. Travel-driven emergence and spread of SARS-CoV-2 lineage B.1.620 with multiple VOC-like mutations and deletions in Europe. Preprint at medRxiv https://doi.org/10.1101/2021.05.04.21256637 (2021).
McKinney, W. Data structures for statistical computing in Python. In Proc. 9th Python in Science Conference (2010).
Hunter, J. D. Matplotlib: a 2D graphics environment. Comput. Sci. Eng. 9, 90–95 (2007).
doi: 10.1109/MCSE.2007.55
Villanueva, R. A. M. & Chen, Z. J. ggplot2: Elegant Graphics for Data Analysis (Taylor & Francis, 2019).
Katoh, K. et al. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30, 3059–3066 (2002).
doi: 10.1093/nar/gkf436
Guindon, S. et al. in Bioinformatics for DNA Sequence Analysis (ed Posada, D.) 113–137 (Springer, 2009).

Auteurs

Talia Kustin (T)

The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.
Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel.

Noam Harel (N)

The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.
Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel.

Uriah Finkel (U)

Clalit Research Institute, Innovation Division, Clalit Health Services, Ramat Gan, Israel.

Shay Perchik (S)

Clalit Research Institute, Innovation Division, Clalit Health Services, Ramat Gan, Israel.

Sheri Harari (S)

The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.
Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel.

Maayan Tahor (M)

The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.

Itamar Caspi (I)

The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.

Rachel Levy (R)

The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.

Michael Leshchinsky (M)

Clalit Research Institute, Innovation Division, Clalit Health Services, Ramat Gan, Israel.

Shifra Ken Dror (S)

Clalit Health Services, Central Laboratories, Haifa and Western Galilee, Nesher, Israel.

Galit Bergerzon (G)

Clalit Health Services, Central Laboratories, Haifa and Western Galilee, Nesher, Israel.

Hala Gadban (H)

Clalit Health Services, Central Laboratories, Haifa and Western Galilee, Nesher, Israel.

Faten Gadban (F)

Clalit Health Services, Central Laboratories, Haifa and Western Galilee, Nesher, Israel.

Eti Eliassian (E)

Progenin Laboratories, Jerusalem District, Clalit Health Services, Tel Aviv, Israel.

Orit Shimron (O)

Progenin Laboratories, Jerusalem District, Clalit Health Services, Tel Aviv, Israel.

Loulou Saleh (L)

Microbiology lab, Rabin Medical Center, Beilinson Hospital, Petah Tiqva, Israel.

Haim Ben-Zvi (H)

Microbiology lab, Rabin Medical Center, Beilinson Hospital, Petah Tiqva, Israel.

Elena Keren Taraday (E)

Central Laboratory, Clalit Health Services, Tel Aviv, Israel.

Doron Amichay (D)

Central Laboratory, Clalit Health Services, Tel Aviv, Israel.
Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, Ben Gurion University of the Negev, Beersheba, Israel.

Anat Ben-Dor (A)

Central Laboratory, Clalit Health Services, Tel Aviv, Israel.

Dana Sagas (D)

Microbiology Laboratory, Emek Medical Center, Afula, Israel.

Merav Strauss (M)

Microbiology Laboratory, Emek Medical Center, Afula, Israel.

Yonat Shemer Avni (Y)

Laboratory of Clinical Virology, Soroka University Medical Center, Beersheba, Israel.
Faculty of Health Sciences, Ben Gurion University of the Negev, Beersheba, Israel.

Amit Huppert (A)

The Bio-statistical and Bio-mathematical Unit, The Gertner Institute for Epidemiology and Health Policy Research, Chaim Sheba Medical Center, Tel HaShomer, Ramat Gan, Israel.
The Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv, Israel.

Eldad Kepten (E)

Clalit Research Institute, Innovation Division, Clalit Health Services, Ramat Gan, Israel.

Ran D Balicer (RD)

Clalit Research Institute, Innovation Division, Clalit Health Services, Ramat Gan, Israel.

Doron Netzer (D)

Clalit Health Services, Tel Aviv, Israel.

Shay Ben-Shachar (S)

Clalit Research Institute, Innovation Division, Clalit Health Services, Ramat Gan, Israel. shayb@clalit.org.il.
The Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv, Israel. shayb@clalit.org.il.

Adi Stern (A)

The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel. sternadi@tauex.tau.ac.il.
Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel. sternadi@tauex.tau.ac.il.

Articles similaires

[Redispensing of expensive oral anticancer medicines: a practical application].

Lisanne N van Merendonk, Kübra Akgöl, Bastiaan Nuijen
1.00
Humans Antineoplastic Agents Administration, Oral Drug Costs Counterfeit Drugs

Smoking Cessation and Incident Cardiovascular Disease.

Jun Hwan Cho, Seung Yong Shin, Hoseob Kim et al.
1.00
Humans Male Smoking Cessation Cardiovascular Diseases Female
Humans United States Aged Cross-Sectional Studies Medicare Part C
1.00
Humans Yoga Low Back Pain Female Male

Classifications MeSH