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Measuring infectious SARS-CoV-2 in clinical samples reveals a higher viral titer:RNA ratio for Delta and Epsilon vs. Alpha variants

Novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants pose a challenge to controlling the COVID-19 pandemic. Previous studies indicate that clinical samples collected from individuals infected with the Delta variant may contain higher levels of RNA than previous variants, but t...

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Autores principales: Despres, Hannah W., Mills, Margaret G., Shirley, David J., Schmidt, Madaline M., Huang, Meei-Li, Roychoudhury, Pavitra, Jerome, Keith R., Greninger, Alexander L., Bruce, Emily A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: National Academy of Sciences 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8812544/
https://www.ncbi.nlm.nih.gov/pubmed/35058348
http://dx.doi.org/10.1073/pnas.2116518119
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author Despres, Hannah W.
Mills, Margaret G.
Shirley, David J.
Schmidt, Madaline M.
Huang, Meei-Li
Roychoudhury, Pavitra
Jerome, Keith R.
Greninger, Alexander L.
Bruce, Emily A.
author_facet Despres, Hannah W.
Mills, Margaret G.
Shirley, David J.
Schmidt, Madaline M.
Huang, Meei-Li
Roychoudhury, Pavitra
Jerome, Keith R.
Greninger, Alexander L.
Bruce, Emily A.
author_sort Despres, Hannah W.
collection PubMed
description Novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants pose a challenge to controlling the COVID-19 pandemic. Previous studies indicate that clinical samples collected from individuals infected with the Delta variant may contain higher levels of RNA than previous variants, but the relationship between levels of viral RNA and infectious virus for individual variants is unknown. We measured infectious viral titer (using a microfocus-forming assay) and total and subgenomic viral RNA levels (using RT-PCR) in a set of 162 clinical samples containing SARS-CoV-2 Alpha, Delta, and Epsilon variants that were collected in identical swab kits from outpatient test sites and processed soon after collection. We observed a high degree of variation in the relationship between viral titers and RNA levels. Despite this, the overall infectivity differed among the three variants. Both Delta and Epsilon had significantly higher infectivity than Alpha, as measured by the number of infectious units per quantity of viral E gene RNA (5.9- and 3.0-fold increase; P < 0.0001, P = 0.014, respectively) or subgenomic E RNA (14.3- and 6.9-fold increase; P < 0.0001, P = 0.004, respectively). In addition to higher viral RNA levels reported for the Delta variant, the infectivity (amount of replication competent virus per viral genome copy) may be increased compared to Alpha. Measuring the relationship between live virus and viral RNA is an important step in assessing the infectivity of novel SARS-CoV-2 variants. An increase in the infectivity for Delta may further explain increased spread, suggesting a need for increased measures to prevent viral transmission.
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spelling pubmed-88125442022-02-16 Measuring infectious SARS-CoV-2 in clinical samples reveals a higher viral titer:RNA ratio for Delta and Epsilon vs. Alpha variants Despres, Hannah W. Mills, Margaret G. Shirley, David J. Schmidt, Madaline M. Huang, Meei-Li Roychoudhury, Pavitra Jerome, Keith R. Greninger, Alexander L. Bruce, Emily A. Proc Natl Acad Sci U S A Biological Sciences Novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants pose a challenge to controlling the COVID-19 pandemic. Previous studies indicate that clinical samples collected from individuals infected with the Delta variant may contain higher levels of RNA than previous variants, but the relationship between levels of viral RNA and infectious virus for individual variants is unknown. We measured infectious viral titer (using a microfocus-forming assay) and total and subgenomic viral RNA levels (using RT-PCR) in a set of 162 clinical samples containing SARS-CoV-2 Alpha, Delta, and Epsilon variants that were collected in identical swab kits from outpatient test sites and processed soon after collection. We observed a high degree of variation in the relationship between viral titers and RNA levels. Despite this, the overall infectivity differed among the three variants. Both Delta and Epsilon had significantly higher infectivity than Alpha, as measured by the number of infectious units per quantity of viral E gene RNA (5.9- and 3.0-fold increase; P < 0.0001, P = 0.014, respectively) or subgenomic E RNA (14.3- and 6.9-fold increase; P < 0.0001, P = 0.004, respectively). In addition to higher viral RNA levels reported for the Delta variant, the infectivity (amount of replication competent virus per viral genome copy) may be increased compared to Alpha. Measuring the relationship between live virus and viral RNA is an important step in assessing the infectivity of novel SARS-CoV-2 variants. An increase in the infectivity for Delta may further explain increased spread, suggesting a need for increased measures to prevent viral transmission. National Academy of Sciences 2022-01-20 2022-02-01 /pmc/articles/PMC8812544/ /pubmed/35058348 http://dx.doi.org/10.1073/pnas.2116518119 Text en Copyright © 2022 the Author(s). Published by PNAS. https://creativecommons.org/licenses/by/4.0/This open access article is distributed under Creative Commons Attribution License 4.0 (CC BY) (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Biological Sciences
Despres, Hannah W.
Mills, Margaret G.
Shirley, David J.
Schmidt, Madaline M.
Huang, Meei-Li
Roychoudhury, Pavitra
Jerome, Keith R.
Greninger, Alexander L.
Bruce, Emily A.
Measuring infectious SARS-CoV-2 in clinical samples reveals a higher viral titer:RNA ratio for Delta and Epsilon vs. Alpha variants
title Measuring infectious SARS-CoV-2 in clinical samples reveals a higher viral titer:RNA ratio for Delta and Epsilon vs. Alpha variants
title_full Measuring infectious SARS-CoV-2 in clinical samples reveals a higher viral titer:RNA ratio for Delta and Epsilon vs. Alpha variants
title_fullStr Measuring infectious SARS-CoV-2 in clinical samples reveals a higher viral titer:RNA ratio for Delta and Epsilon vs. Alpha variants
title_full_unstemmed Measuring infectious SARS-CoV-2 in clinical samples reveals a higher viral titer:RNA ratio for Delta and Epsilon vs. Alpha variants
title_short Measuring infectious SARS-CoV-2 in clinical samples reveals a higher viral titer:RNA ratio for Delta and Epsilon vs. Alpha variants
title_sort measuring infectious sars-cov-2 in clinical samples reveals a higher viral titer:rna ratio for delta and epsilon vs. alpha variants
topic Biological Sciences
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8812544/
https://www.ncbi.nlm.nih.gov/pubmed/35058348
http://dx.doi.org/10.1073/pnas.2116518119
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