ArticleNature communications2023
Rapid transmission and tight bottlenecks constrain the evolution of highly transmissible SARS-CoV-2 variants.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers, 2 of them syntheses that pooled it.
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Who cites it
42 citing papers in PubMed, 2 syntheses or guidelines pooled it, 62 citations in OpenAlex.
- The Asymptomatic Proportion of SARS-CoV-2 Omicron Variant Infections in Households: A Systematic Review.Influenza and other respiratory viruses · 2024Pooled it
- Rapid review and meta-analysis of serial intervals for SARS-CoV-2 Delta and Omicron variants.BMC infectious diseases · 2023Pooled it
- SARS-CoV-2 intra-host variation shows evidence of transmission and convergent evolution in a university surveillance cohort.Microbial genomics · 2026Article
- Identification and masking of artifactual and misleading within-host variants in deep-sequencing SARS-CoV-2 data.Molecular biology and evolution · 2026Article
- Within-host SARS-CoV-2 diversity in immunocompromised patients during acute infection.Journal of virology · 2026Article
- Large-scale genomic surveillance reveals immunosuppression drives mutation dynamics in persistent SARS-CoV-2 infections.Nature communications · 2026Article
- The impact of viral and host factors on the influenza A virus transmission bottleneck.PLoS pathogens · 2026Article
- Antibody escape drives emergence of diverse spike haplotypes resembling variants of concern in persistent SARS-CoV-2 infections.Cell reports. Medicine · 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
- Tissue tropism and functional adaptation of the SARS-CoV-2 spike protein in a fatal case of COVID-19.Journal of virology · 2025Article
- Genomic and epidemiologic characteristics of SARS-CoV-2 persistent infections in California, January 2021 - July 2023.PLoS pathogens · 2025Article
- Strong Bottlenecks Constrain Adaptive Coevolution in a Host-Parasite Metapopulation.Molecular ecology · 2025Article
- SARS-CoV-2 keeps evolving, so must our research efforts.National science review · 2025Article
- The consequences of SARS-CoV-2 within-host persistence.Nature reviews. Microbiology · 2025Review
- SARS-CoV-2 cellular coinfection is limited by superinfection exclusion.Journal of virology · 2025Article
- Geospatial and demographic patterns of SARS-CoV-2 spread in Massachusetts from over 130,000 genomes.medRxiv : the preprint server for health sciences · 2025Article
- In depth sequencing of a serially sampled household cohort reveals the within-host dynamics of Omicron SARS-CoV-2 and rare selection of novel spike variants.PLoS pathogens · 2025Article
- Barcoded SARS-CoV-2 viruses define the impact of duration and route of exposure on the transmission bottleneck in a hamster model.Science advances · 2025Article
- ViralBottleneck: an R package for estimating viral transmission bottlenecks from deep sequencing data using multiple methods.Virus evolution · 2025Article
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Authors and funding
8 authors at 1 institution in 1 country.
Funding
Abstract
Transmission bottlenecks limit the spread of novel mutations and reduce the efficiency of selection along a transmission chain. While increased force of infection, receptor binding, or immune evasion may influence bottleneck size, the relationship between transmissibility and the transmission bottleneck is unclear. Here we compare the transmission bottleneck of non-VOC SARS-CoV-2 lineages to those of Alpha, Delta, and Omicron. We sequenced viruses from 168 individuals in 65 households. Most virus populations had 0-1 single nucleotide variants (iSNV). From 64 transmission pairs with detectable iSNV, we identify a per clade bottleneck of 1 (95% CI 1-1) for Alpha, Delta, and Omicron and 2 (95% CI 2-2) for non-VOC. These tight bottlenecks reflect the low diversity at the time of transmission, which may be more pronounced in rapidly transmissible variants. Tight bottlenecks will limit the development of highly mutated VOC in transmission chains, adding to the evidence that selection over prolonged infections may drive their evolution.
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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.