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Clinical and genomic signatures of SARS-CoV-2 Delta breakthrough infections in New York

BACKGROUND: In 2021, Delta became the predominant SARS-CoV-2 variant worldwide. While vaccines have effectively prevented COVID-19 hospitalization and death, vaccine breakthrough infections increasingly occurred. The precise role of clinical and genomic determinants in Delta infections is not known,...

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Autores principales: Duerr, Ralf, Dimartino, Dacia, Marier, Christian, Zappile, Paul, Levine, Samuel, Francois, Fritz, Iturrate, Eduardo, Wang, Guiqing, Dittmann, Meike, Lighter, Jennifer, Elbel, Brian, Troxel, Andrea B., Goldfeld, Keith S., Heguy, Adriana
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9323230/
https://www.ncbi.nlm.nih.gov/pubmed/35906172
http://dx.doi.org/10.1016/j.ebiom.2022.104141
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author Duerr, Ralf
Dimartino, Dacia
Marier, Christian
Zappile, Paul
Levine, Samuel
Francois, Fritz
Iturrate, Eduardo
Wang, Guiqing
Dittmann, Meike
Lighter, Jennifer
Elbel, Brian
Troxel, Andrea B.
Goldfeld, Keith S.
Heguy, Adriana
author_facet Duerr, Ralf
Dimartino, Dacia
Marier, Christian
Zappile, Paul
Levine, Samuel
Francois, Fritz
Iturrate, Eduardo
Wang, Guiqing
Dittmann, Meike
Lighter, Jennifer
Elbel, Brian
Troxel, Andrea B.
Goldfeld, Keith S.
Heguy, Adriana
author_sort Duerr, Ralf
collection PubMed
description BACKGROUND: In 2021, Delta became the predominant SARS-CoV-2 variant worldwide. While vaccines have effectively prevented COVID-19 hospitalization and death, vaccine breakthrough infections increasingly occurred. The precise role of clinical and genomic determinants in Delta infections is not known, and whether they contributed to increased rates of breakthrough infections compared to unvaccinated controls. METHODS: We studied SARS-CoV-2 variant distribution, dynamics, and adaptive selection over time in relation to vaccine status, phylogenetic relatedness of viruses, full genome mutation profiles, and associated clinical and demographic parameters. FINDINGS: We show a steep and near-complete replacement of circulating variants with Delta between May and August 2021 in metropolitan New York. We observed an increase of the Delta sublineage AY.25 (14% in vaccinated, 7% in unvaccinated), its spike mutation S112L, and AY.44 (8% in vaccinated, 2% in unvaccinated) with its nsp12 mutation F192V in breakthroughs. Delta infections were associated with younger age and lower hospitalization rates than Alpha. Delta breakthrough infections increased significantly with time since vaccination, and, after adjusting for confounders, they rose at similar rates as in unvaccinated individuals. INTERPRETATION: We observed a modest adaptation of Delta genomes in breakthrough infections in New York, suggesting an improved genomic framework to support Delta's epidemic growth in times of waning vaccine protection despite limited impact on vaccine escape. FUNDING: The study was supported by NYU institutional funds. The NYULH Genome Technology Center is partially supported by the Cancer Center Support Grant P30CA016087 at the Laura and Isaac Perlmutter Cancer Center.
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spelling pubmed-93232302022-07-27 Clinical and genomic signatures of SARS-CoV-2 Delta breakthrough infections in New York Duerr, Ralf Dimartino, Dacia Marier, Christian Zappile, Paul Levine, Samuel Francois, Fritz Iturrate, Eduardo Wang, Guiqing Dittmann, Meike Lighter, Jennifer Elbel, Brian Troxel, Andrea B. Goldfeld, Keith S. Heguy, Adriana eBioMedicine Articles BACKGROUND: In 2021, Delta became the predominant SARS-CoV-2 variant worldwide. While vaccines have effectively prevented COVID-19 hospitalization and death, vaccine breakthrough infections increasingly occurred. The precise role of clinical and genomic determinants in Delta infections is not known, and whether they contributed to increased rates of breakthrough infections compared to unvaccinated controls. METHODS: We studied SARS-CoV-2 variant distribution, dynamics, and adaptive selection over time in relation to vaccine status, phylogenetic relatedness of viruses, full genome mutation profiles, and associated clinical and demographic parameters. FINDINGS: We show a steep and near-complete replacement of circulating variants with Delta between May and August 2021 in metropolitan New York. We observed an increase of the Delta sublineage AY.25 (14% in vaccinated, 7% in unvaccinated), its spike mutation S112L, and AY.44 (8% in vaccinated, 2% in unvaccinated) with its nsp12 mutation F192V in breakthroughs. Delta infections were associated with younger age and lower hospitalization rates than Alpha. Delta breakthrough infections increased significantly with time since vaccination, and, after adjusting for confounders, they rose at similar rates as in unvaccinated individuals. INTERPRETATION: We observed a modest adaptation of Delta genomes in breakthrough infections in New York, suggesting an improved genomic framework to support Delta's epidemic growth in times of waning vaccine protection despite limited impact on vaccine escape. FUNDING: The study was supported by NYU institutional funds. The NYULH Genome Technology Center is partially supported by the Cancer Center Support Grant P30CA016087 at the Laura and Isaac Perlmutter Cancer Center. Elsevier 2022-07-26 /pmc/articles/PMC9323230/ /pubmed/35906172 http://dx.doi.org/10.1016/j.ebiom.2022.104141 Text en © 2022 The Author(s) https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Articles
Duerr, Ralf
Dimartino, Dacia
Marier, Christian
Zappile, Paul
Levine, Samuel
Francois, Fritz
Iturrate, Eduardo
Wang, Guiqing
Dittmann, Meike
Lighter, Jennifer
Elbel, Brian
Troxel, Andrea B.
Goldfeld, Keith S.
Heguy, Adriana
Clinical and genomic signatures of SARS-CoV-2 Delta breakthrough infections in New York
title Clinical and genomic signatures of SARS-CoV-2 Delta breakthrough infections in New York
title_full Clinical and genomic signatures of SARS-CoV-2 Delta breakthrough infections in New York
title_fullStr Clinical and genomic signatures of SARS-CoV-2 Delta breakthrough infections in New York
title_full_unstemmed Clinical and genomic signatures of SARS-CoV-2 Delta breakthrough infections in New York
title_short Clinical and genomic signatures of SARS-CoV-2 Delta breakthrough infections in New York
title_sort clinical and genomic signatures of sars-cov-2 delta breakthrough infections in new york
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9323230/
https://www.ncbi.nlm.nih.gov/pubmed/35906172
http://dx.doi.org/10.1016/j.ebiom.2022.104141
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