---
title: "Prolonged SARS-CoV-2 Infections and Delayed Immunity Promote Transmission of Mutated Variants"
id: "biorxiv-0-transmission-of-mutated-sars-cov-2-variants-is-favored-by-relatively-prolonged"
canonical_url: "https://medichelpline.com/clinical-feed/biorxiv-0-transmission-of-mutated-sars-cov-2-variants-is-favored-by-relatively-prolonged"
content_type: "clinical_feed_article"
specialty: "Infectious Disease"
source_name: "bioRxiv (Biomedical Preprints)"
source_url: "https://www.biorxiv.org/content/10.64898/2026.09.15.751875v1?rss=1"
published_at: "2026-09-18T12:00:00.000Z"
evidence_level: "Verified Feed"
license: "CC-BY-NC-4.0 / Informational Use"
---
# Prolonged SARS-CoV-2 Infections and Delayed Immunity Promote Transmission of Mutated Variants
## Provenance & Clinical Metadata
- **Canonical URL:** https://medichelpline.com/clinical-feed/biorxiv-0-transmission-of-mutated-sars-cov-2-variants-is-favored-by-relatively-prolonged
- **Specialty:** [Infectious Disease](https://medichelpline.com/clinical-feed/infectious-disease.md)
- **Primary Source:** bioRxiv (Biomedical Preprints)
- **Source URL:** [Original Journal Publication](https://www.biorxiv.org/content/10.64898/2026.09.15.751875v1?rss=1)
- **Published At:** 2026-09-18T12:00:00.000Z
- **Evidence Rating:** Verified Feed
## Executive GIST (TL;DR)
- The authors developed a multi-scale within-host phylodynamic model (WiPhy) that couples viral replication, innate and acquired immune responses, and viral mutation to study **SARS-CoV-2** evolution within individuals. - Model validation used quantitative viral and phylodynamic metrics reported in the source; specifics of validation metrics were not detailed in the abstract. - Typical acute infections rapidly generate genetic diversity through accumulation of minor variants, but most of these variants remain at concentrations too low to be transmitted. - A delayed **innate immune response** is associated with higher peak **viral load** and greater intrahost diversification, increasing the chance of transmitting the founder virus or a novel variant that is equally or less fit. - Transmission of a fitter variant (one with fitness-enhancing non-synonymous mutations) is most likely in the subset of infections in which viral loads remain high beyond 10–14 days; these prolonged infections constitute roughly ~10% of cases in the model. - In cases that permit fitter-variant selection, non-sustained innate responses and/or weak **acquired immune responses** allow time for selection of variants bearing beneficial non-synonymous changes. - In a simulated cohort of approximately 1,500 individuals, 5% of transmission risk arose from variants with enhanced fitness due to nonsynonymous mutations. - A small fraction of infections drove most fitter-variant transmission risk: 13% of simulated infections accounted for 90% of transmission risk involving fitter variants. - The results emphasize that within-host timing and interactions between viral replication and immune responses create strong bottlenecks that limit between-host evolutionary emergence. - Code and additional resources are available as declared in the source repository link; further methodological or validation details beyond the abstract were not reported in the source abstract provided.
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Schiffer, [ View ORCID Profile](http://orcid.org/0000-0001-5684-9538)Daniel B. Reeves doi: https://doi.org/10.64898/2026.09.15.751875 This article is a preprint and has not been certified by peer review [[what does this mean?](https://www.biorxiv.org/about/FAQ#unrefereed)]. Katherine Owens 1 Fred Hutchinson Cancer Center; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Katherine%2BOwens%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Owens%20K&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3AKatherine%2BOwens%2B) * [ORCID record for Katherine Owens](http://orcid.org/0000-0002-5695-0203 "Open in new tab") * For correspondence: kowens2@fredhutch.org Pierce Radecki 2 National Institutes of Health; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Pierce%2BRadecki%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Radecki%20P&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3APierce%2BRadecki%2B) * [ORCID record for Pierce Radecki](http://orcid.org/0000-0002-1103-5327 "Open in new tab") Stefano Tempia 3 Task Force for Global Health; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Stefano%2BTempia%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Tempia%20S&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3AStefano%2BTempia%2B) * [ORCID record for Stefano Tempia](http://orcid.org/0000-0003-4395-347X "Open in new tab") Anne von Gottberg 4 National Institute for Communicable Diseases * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Anne%2Bvon%2BGottberg%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=von%20Gottberg%20A&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3AAnne%2Bvon%2BGottberg%2B) * [ORCID record for Anne von Gottberg](http://orcid.org/0000-0002-0243-7455 "Open in new tab") Cheryl Cohen 4 National Institute for Communicable Diseases * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Cheryl%2BCohen%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Cohen%20C&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3ACheryl%2BCohen%2B) * [ORCID record for Cheryl Cohen](http://orcid.org/0000-0003-0376-2302 "Open in new tab") Eli Boritz 2 National Institutes of Health; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Eli%2BBoritz%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Boritz%20E&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3AEli%2BBoritz%2B) * [ORCID record for Eli Boritz](http://orcid.org/0000-0003-4633-4594 "Open in new tab") Joshua T. Schiffer 1 Fred Hutchinson Cancer Center; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Joshua%2BT.%2BSchiffer%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Schiffer%20JT&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3AJoshua%2BT.%2BSchiffer%2B) * [ORCID record for Joshua T. Schiffer](http://orcid.org/0000-0002-2598-1621 "Open in new tab") Daniel B. Reeves 1 Fred Hutchinson Cancer Center; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Daniel%2BB.%2BReeves%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Reeves%20DB&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3ADaniel%2BB.%2BReeves%2B) * [ORCID record for Daniel B. Reeves](http://orcid.org/0000-0001-5684-9538 "Open in new tab") * [Abstract](https://www.biorxiv.org/content/10.64898/2026.09.15.751875v1)[](https://www.biorxiv.org/panels_ajax_tab/biorxiv_tab_art/node:5791229/1) * [Info/History](https://www.biorxiv.org/content/10.64898/2026.09.15.751875v1.article-info)[](https://www.biorxiv.org/panels_ajax_tab/biorxiv_tab_info/node:5791229/1) * [Metrics](https://www.biorxiv.org/content/10.64898/2026.09.15.751875v1.article-metrics)[](https://www.biorxiv.org/panels_ajax_tab/article_tab_metrics/node:5791229/1) * [Supplementary material](https://www.biorxiv.org/content/10.64898/2026.09.15.751875v1.supplementary-material)[](https://www.biorxiv.org/panels_ajax_tab/biorxiv_tab_data/node:5791229/1) * [Data/Code](https://www.biorxiv.org/content/10.64898/2026.09.15.751875v1.external-links)[](https://www.biorxiv.org/panels_ajax_tab/article_tab_data_code/node:5791229/1) * [ Preview PDF](https://www.biorxiv.org/content/10.64898/2026.09.15.751875v1.full.pdf+html)[](https://www.biorxiv.org/panels_ajax_tab/biorxiv_tab_pdf/node:5791229/1) ![Loading](https://www.biorxiv.org/sites/all/modules/contrib/panels_ajax_tab/images/loading.gif) ## Abstract SARS-CoV-2 evolution enhanced viral fitness and immune evasion, extending the COVID-19 pandemic and resulting in millions of excess deaths. Viral diversity is generated within infected individuals, yet the timing and interplay of viral and immunological forces that drive transmissible evolution are incompletely understood. We developed a multi-scale within host phylodynamic (WiPhy) model of SARS-CoV-2 infection which couples viral replication, innate and acquired immune responses, and viral mutation. We then validated the model against quantitative viral and phylodynamic metrics. Model output predicts that typical acute infections rapidly generate genetic diversity due to accumulation of minor variants which in most cases do not achieve sufficient concentrations for transmission. Delayed innate immune responses correlate with higher peak viral load and diversification, allowing higher transmission risk of the founder virus or with a novel variant that is equally or less fit. In contrast, the risk of transmitting a fitter variant is highest during the ~10% of infections in which viral loads remain sufficiently high for transmission after 10-14 days. In these cases, non-sustained innate and/or weak acquired immune responses allow sufficient time for selection of a variant with one or more fitness enhancing non-synonymous mutations. Across a simulated cohort of ~1500 individuals, 5% of transmission risk came from variants with enhanced fitness from nonsynonymous mutations, and 13% of simulated infections accounted for 90% of fitter variant transmission risk. Our results highlight how the timing and interplay of viral and immunological forces within a host create bottlenecks that severely limit between host evolution. ### Competing Interest Statement The authors have declared no competing interest. ## Footnotes * ## Funder Information Declared National Institutes of Health National Institute of Allergy and Infectious Disease, K25AI196259, R01AI186721, Intramural Research Program Copyright The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available for use under a CC0 license. bioRxiv and medRxiv thank the following for their generous financial support: > The Chan Zuckerberg Initiative, Cold Spring Harbor Laboratory, the Sergey Brin Family Foundation, California Institute of Technology, Centre National de la Recherche Scientifique, Fred Hutchinson Cancer Center, Imperial College London, Massachusetts Institute of Technology, Stanford University, The University of Edinburgh, University of Washington, and Vrije Universiteit Amsterdam. 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[ Download PDF](https://www.biorxiv.org/content/10.64898/2026.09.15.751875v1.full.pdf) Print/Save Options [Download PDF](https://www.biorxiv.org/content/biorxiv/early/2026/09/18/2026.09.15.751875.full.pdf)Full Text & In-line FiguresXML [More Info](https://www.biorxiv.org/about/FAQ#PrintOptions "More Information on Print/Save Options") [Supplementary Material ](https://www.biorxiv.org/content/10.64898/2026.09.15.751875v1.supplementary-material) [ Data/Code](https://www.biorxiv.org/content/early/2026/09/18/2026.09.15.751875.external-links) [ Email](https://www.biorxiv.org/ "Email this Article") [ Share](https://www.biorxiv.org/) Transmission of mutated SARS-CoV-2 variants is favored by relatively prolonged infections due to delayed immunity Katherine Owens, Pierce Radecki, Stefano Tempia, Anne von Gottberg, Cheryl Cohen, Eli Boritz, Joshua T. Schiffer, Daniel B. Reeves bioRxiv 2026.09.15.751875; doi: https://doi.org/10.64898/2026.09.15.751875 This article is a preprint and has not been certified by peer review [[what does this mean?](https://www.biorxiv.org/about/FAQ#unrefereed)]. Share This Article: Copy [![Twitter logo](https://www.biorxiv.org/sites/all/modules/highwire/highwire/images/twitter.png)](https://www.biorxiv.org/highwire_log/share/twitter?link=http%3A%2F%
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