ArticlePLoS pathogens2021
Acute SARS-CoV-2 infections harbor limited within-host diversity and transmit via tight transmission bottlenecks.
Article in PLoS pathogens, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 95 papers.
What it found
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Who cites it
95 citing papers in PubMed, 122 citations in OpenAlex.
- Exposure route, not dose, is the primary driver of infection patterns for a respiratory virus.Science advances · 2026Article
- The other immune landscape of SARS-CoV-2 evolution.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Transmission of mutated SARS-CoV-2 variants is favored by relatively prolonged infections due to delayed immunity.bioRxiv : the preprint server for biology · 2026Article
- Identification and masking of artifactual and misleading within-host variants in deep-sequencing SARS-CoV-2 data.Molecular biology and evolution · 2026Article
- SARS-CoV-2 intra-host variation shows evidence of transmission and convergent evolution in a university surveillance cohort.Microbial genomics · 2026Article
- Evolutionary constraints limit additional mammalian adaptation of bovine-derived H5N1 influenza viruses in ferrets.bioRxiv : the preprint server for biology · 2026Article
- Within-host SARS-CoV-2 diversity in immunocompromised patients during acute infection.Journal of virology · 2026Article
- Weak selection and stochastic processes limit the emergence of antigenic variants during household transmission of influenza A viruses.PLoS pathogens · 2026Article
- Exposure route drives SARS-CoV-2 infection patterns in non-human primates.bioRxiv : the preprint server for biology · 2026Article
- Antibody escape drives emergence of diverse spike haplotypes resembling variants of concern in persistent SARS-CoV-2 infections.Cell reports. Medicine · 2026Article
- Pathology and viral evolutionary dynamics in a hamster model of persistent SARS-CoV-2 infection.Communications biology · 2026Article
- SARS-CoV-2 intra-host evolution during acute infection in COVID-19 patients.Frontiers in microbiology · 2026Article
- Chronic infections can generate SARS-CoV-2-like bursts of viral evolution without epistasis.Virus evolution · 2026Article
- SARS-CoV-2 Intra-host Variation Shows Evidence of Transmission and Convergent Evolution in a University Surveillance Cohort.bioRxiv : the preprint server for biology · 2025Article
- Review
- Tissue tropism and functional adaptation of the SARS-CoV-2 spike protein in a fatal case of COVID-19.Journal of virology · 2025Article
- Weak selection and stochastic processes limit the emergence of antigenic variants during household transmission of influenza A viruses.bioRxiv : the preprint server for biology · 2025Article
- Intra-host variation and transmission dynamics of SARS-CoV-2 Omicron outbreaks in Shandong, China.mSphere · 2025Article
- Intra-Host Evolution of SARS-CoV-2 During Persistent Infection of Pediatric COVID-19 Patients.Viruses · 2025Article
- Viral expansion after transfer is a primary driver of influenza A virus transmission bottlenecks.PLoS biology · 2025Article
35 more citing papers are in PubMed but not listed here.
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Authors and funding
11 authors at 4 institutions in 1 country.
Funding
Abstract
The emergence of divergent SARS-CoV-2 lineages has raised concern that novel variants eliciting immune escape or the ability to displace circulating lineages could emerge within individual hosts. Though growing evidence suggests that novel variants arise during prolonged infections, most infections are acute. Understanding how efficiently variants emerge and transmit among acutely-infected hosts is therefore critical for predicting the pace of long-term SARS-CoV-2 evolution. To characterize how within-host diversity is generated and propagated, we combine extensive laboratory and bioinformatic controls with metrics of within- and between-host diversity to 133 SARS-CoV-2 genomes from acutely-infected individuals. We find that within-host diversity is low and transmission bottlenecks are narrow, with very few viruses founding most infections. Within-host variants are rarely transmitted, even among individuals within the same household, and are rarely detected along phylogenetically linked infections in the broader community. These findings suggest that most variation generated within-host is lost during transmission.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.