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Absolute quantitation of individual SARS-CoV-2 RNA molecules provides a new paradigm for infection dynamics and variant differences

Despite an unprecedented global research effort on SARS-CoV-2, early replication events remain poorly understood. Given the clinical importance of emergent viral variants with increased transmission, there is an urgent need to understand the early stages of viral replication and transcription. We us...

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Autores principales: Lee, Jeffrey Y, Wing, Peter AC, Gala, Dalia S, Noerenberg, Marko, Järvelin, Aino I, Titlow, Joshua, Zhuang, Xiaodong, Palmalux, Natasha, Iselin, Louisa, Thompson, Mary Kay, Parton, Richard M, Prange-Barczynska, Maria, Wainman, Alan, Salguero, Francisco J, Bishop, Tammie, Agranoff, Daniel, James, William, Castello, Alfredo, McKeating, Jane A, Davis, Ilan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: eLife Sciences Publications, Ltd 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8776252/
https://www.ncbi.nlm.nih.gov/pubmed/35049501
http://dx.doi.org/10.7554/eLife.74153
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author Lee, Jeffrey Y
Wing, Peter AC
Gala, Dalia S
Noerenberg, Marko
Järvelin, Aino I
Titlow, Joshua
Zhuang, Xiaodong
Palmalux, Natasha
Iselin, Louisa
Thompson, Mary Kay
Parton, Richard M
Prange-Barczynska, Maria
Wainman, Alan
Salguero, Francisco J
Bishop, Tammie
Agranoff, Daniel
James, William
Castello, Alfredo
McKeating, Jane A
Davis, Ilan
author_facet Lee, Jeffrey Y
Wing, Peter AC
Gala, Dalia S
Noerenberg, Marko
Järvelin, Aino I
Titlow, Joshua
Zhuang, Xiaodong
Palmalux, Natasha
Iselin, Louisa
Thompson, Mary Kay
Parton, Richard M
Prange-Barczynska, Maria
Wainman, Alan
Salguero, Francisco J
Bishop, Tammie
Agranoff, Daniel
James, William
Castello, Alfredo
McKeating, Jane A
Davis, Ilan
author_sort Lee, Jeffrey Y
collection PubMed
description Despite an unprecedented global research effort on SARS-CoV-2, early replication events remain poorly understood. Given the clinical importance of emergent viral variants with increased transmission, there is an urgent need to understand the early stages of viral replication and transcription. We used single-molecule fluorescence in situ hybridisation (smFISH) to quantify positive sense RNA genomes with 95% detection efficiency, while simultaneously visualising negative sense genomes, subgenomic RNAs, and viral proteins. Our absolute quantification of viral RNAs and replication factories revealed that SARS-CoV-2 genomic RNA is long-lived after entry, suggesting that it avoids degradation by cellular nucleases. Moreover, we observed that SARS-CoV-2 replication is highly variable between cells, with only a small cell population displaying high burden of viral RNA. Unexpectedly, the B.1.1.7 variant, first identified in the UK, exhibits significantly slower replication kinetics than the Victoria strain, suggesting a novel mechanism contributing to its higher transmissibility with important clinical implications.
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spelling pubmed-87762522022-01-21 Absolute quantitation of individual SARS-CoV-2 RNA molecules provides a new paradigm for infection dynamics and variant differences Lee, Jeffrey Y Wing, Peter AC Gala, Dalia S Noerenberg, Marko Järvelin, Aino I Titlow, Joshua Zhuang, Xiaodong Palmalux, Natasha Iselin, Louisa Thompson, Mary Kay Parton, Richard M Prange-Barczynska, Maria Wainman, Alan Salguero, Francisco J Bishop, Tammie Agranoff, Daniel James, William Castello, Alfredo McKeating, Jane A Davis, Ilan eLife Cell Biology Despite an unprecedented global research effort on SARS-CoV-2, early replication events remain poorly understood. Given the clinical importance of emergent viral variants with increased transmission, there is an urgent need to understand the early stages of viral replication and transcription. We used single-molecule fluorescence in situ hybridisation (smFISH) to quantify positive sense RNA genomes with 95% detection efficiency, while simultaneously visualising negative sense genomes, subgenomic RNAs, and viral proteins. Our absolute quantification of viral RNAs and replication factories revealed that SARS-CoV-2 genomic RNA is long-lived after entry, suggesting that it avoids degradation by cellular nucleases. Moreover, we observed that SARS-CoV-2 replication is highly variable between cells, with only a small cell population displaying high burden of viral RNA. Unexpectedly, the B.1.1.7 variant, first identified in the UK, exhibits significantly slower replication kinetics than the Victoria strain, suggesting a novel mechanism contributing to its higher transmissibility with important clinical implications. eLife Sciences Publications, Ltd 2022-01-20 /pmc/articles/PMC8776252/ /pubmed/35049501 http://dx.doi.org/10.7554/eLife.74153 Text en © 2022, Lee, Wing et al https://creativecommons.org/licenses/by/4.0/This article is distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use and redistribution provided that the original author and source are credited.
spellingShingle Cell Biology
Lee, Jeffrey Y
Wing, Peter AC
Gala, Dalia S
Noerenberg, Marko
Järvelin, Aino I
Titlow, Joshua
Zhuang, Xiaodong
Palmalux, Natasha
Iselin, Louisa
Thompson, Mary Kay
Parton, Richard M
Prange-Barczynska, Maria
Wainman, Alan
Salguero, Francisco J
Bishop, Tammie
Agranoff, Daniel
James, William
Castello, Alfredo
McKeating, Jane A
Davis, Ilan
Absolute quantitation of individual SARS-CoV-2 RNA molecules provides a new paradigm for infection dynamics and variant differences
title Absolute quantitation of individual SARS-CoV-2 RNA molecules provides a new paradigm for infection dynamics and variant differences
title_full Absolute quantitation of individual SARS-CoV-2 RNA molecules provides a new paradigm for infection dynamics and variant differences
title_fullStr Absolute quantitation of individual SARS-CoV-2 RNA molecules provides a new paradigm for infection dynamics and variant differences
title_full_unstemmed Absolute quantitation of individual SARS-CoV-2 RNA molecules provides a new paradigm for infection dynamics and variant differences
title_short Absolute quantitation of individual SARS-CoV-2 RNA molecules provides a new paradigm for infection dynamics and variant differences
title_sort absolute quantitation of individual sars-cov-2 rna molecules provides a new paradigm for infection dynamics and variant differences
topic Cell Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8776252/
https://www.ncbi.nlm.nih.gov/pubmed/35049501
http://dx.doi.org/10.7554/eLife.74153
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