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Drivers of adaptive evolution during chronic SARS-CoV-2 infections

In some immunocompromised patients with chronic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, considerable adaptive evolution occurs. Some substitutions found in chronic infections are lineage-defining mutations in variants of concern (VOCs), which has led to the hypothesis...

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Autores principales: Harari, Sheri, Tahor, Maayan, Rutsinsky, Natalie, Meijer, Suzy, Miller, Danielle, Henig, Oryan, Halutz, Ora, Levytskyi, Katia, Ben-Ami, Ronen, Adler, Amos, Paran, Yael, Stern, Adi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group US 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9307477/
https://www.ncbi.nlm.nih.gov/pubmed/35725921
http://dx.doi.org/10.1038/s41591-022-01882-4
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author Harari, Sheri
Tahor, Maayan
Rutsinsky, Natalie
Meijer, Suzy
Miller, Danielle
Henig, Oryan
Halutz, Ora
Levytskyi, Katia
Ben-Ami, Ronen
Adler, Amos
Paran, Yael
Stern, Adi
author_facet Harari, Sheri
Tahor, Maayan
Rutsinsky, Natalie
Meijer, Suzy
Miller, Danielle
Henig, Oryan
Halutz, Ora
Levytskyi, Katia
Ben-Ami, Ronen
Adler, Amos
Paran, Yael
Stern, Adi
author_sort Harari, Sheri
collection PubMed
description In some immunocompromised patients with chronic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, considerable adaptive evolution occurs. Some substitutions found in chronic infections are lineage-defining mutations in variants of concern (VOCs), which has led to the hypothesis that VOCs emerged from chronic infections. In this study, we searched for drivers of VOC-like emergence by consolidating sequencing results from a set of 27 chronic infections. Most substitutions in this set reflected lineage-defining VOC mutations; however, a subset of mutations associated with successful global transmission was absent from chronic infections. We further tested the ability to associate antibody evasion mutations with patient-specific and virus-specific features and found that viral rebound is strongly correlated with the emergence of antibody evasion. We found evidence for dynamic polymorphic viral populations in most patients, suggesting that a compromised immune system selects for antibody evasion in particular niches in a patient’s body. We suggest that a tradeoff exists between antibody evasion and transmissibility and that extensive monitoring of chronic infections is necessary to further understanding of VOC emergence.
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spelling pubmed-93074772022-07-24 Drivers of adaptive evolution during chronic SARS-CoV-2 infections Harari, Sheri Tahor, Maayan Rutsinsky, Natalie Meijer, Suzy Miller, Danielle Henig, Oryan Halutz, Ora Levytskyi, Katia Ben-Ami, Ronen Adler, Amos Paran, Yael Stern, Adi Nat Med Article In some immunocompromised patients with chronic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, considerable adaptive evolution occurs. Some substitutions found in chronic infections are lineage-defining mutations in variants of concern (VOCs), which has led to the hypothesis that VOCs emerged from chronic infections. In this study, we searched for drivers of VOC-like emergence by consolidating sequencing results from a set of 27 chronic infections. Most substitutions in this set reflected lineage-defining VOC mutations; however, a subset of mutations associated with successful global transmission was absent from chronic infections. We further tested the ability to associate antibody evasion mutations with patient-specific and virus-specific features and found that viral rebound is strongly correlated with the emergence of antibody evasion. We found evidence for dynamic polymorphic viral populations in most patients, suggesting that a compromised immune system selects for antibody evasion in particular niches in a patient’s body. We suggest that a tradeoff exists between antibody evasion and transmissibility and that extensive monitoring of chronic infections is necessary to further understanding of VOC emergence. Nature Publishing Group US 2022-06-20 2022 /pmc/articles/PMC9307477/ /pubmed/35725921 http://dx.doi.org/10.1038/s41591-022-01882-4 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Harari, Sheri
Tahor, Maayan
Rutsinsky, Natalie
Meijer, Suzy
Miller, Danielle
Henig, Oryan
Halutz, Ora
Levytskyi, Katia
Ben-Ami, Ronen
Adler, Amos
Paran, Yael
Stern, Adi
Drivers of adaptive evolution during chronic SARS-CoV-2 infections
title Drivers of adaptive evolution during chronic SARS-CoV-2 infections
title_full Drivers of adaptive evolution during chronic SARS-CoV-2 infections
title_fullStr Drivers of adaptive evolution during chronic SARS-CoV-2 infections
title_full_unstemmed Drivers of adaptive evolution during chronic SARS-CoV-2 infections
title_short Drivers of adaptive evolution during chronic SARS-CoV-2 infections
title_sort drivers of adaptive evolution during chronic sars-cov-2 infections
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9307477/
https://www.ncbi.nlm.nih.gov/pubmed/35725921
http://dx.doi.org/10.1038/s41591-022-01882-4
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