ArticlePLoS pathogens2020
Characterising the epidemic spread of influenza A/H3N2 within a city through phylogenetics.
Article in PLoS pathogens, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Extensive cryptic circulation sustains mpox among men who have sex with men.Nature communications · 2026Article
- The Representativeness of Regional Influenza Virus Genomic Surveillance for National Trends in the United States.medRxiv : the preprint server for health sciences · 2026Article
- Multiple introductions of equine influenza virus into the United Kingdom resulted in widespread outbreaks and lineage replacement.PLoS pathogens · 2025Article
- Tracking Seasonal Influenza Trends in South Tyrol During 2022/2023 Using Genomic Surveillance Data.Influenza and other respiratory viruses · 2025Article
- Phylogenetic Study of Local Patterns Influenza A(H3N2) Virus Transmission in a Semi-Isolated Population in a Remote Island in Japan Between 2011 and 2013.Influenza and other respiratory viruses · 2025Article
- Bayesian mixture models for phylogenetic source attribution from consensus sequences and time since infection estimates.Statistical methods in medical research · 2025Article
- Local patterns of spread of influenza A H3N2 virus in coastal Kenya over a 1-year period revealed through virus sequence data.Scientific reports · 2024Article
- An Intense Out-of-Season Rebound of Influenza Activity After the Relaxation of Coronavirus Disease 2019 Restrictions in Beijing, China.Open forum infectious diseases · 2024Article
- Local-scale phylodynamics reveal differential community impact of SARS-CoV-2 in a metropolitan US county.PLoS pathogens · 2024Article
- Phylodynamics Uncovers the Transmission of Antibiotic-ResistantbioRxiv : the preprint server for biology · 2023Article
- Transmission dynamics of seasonal influenza in a remote island population.Scientific reports · 2023Article
- Reconstructing relative transmission rates in Bayesian phylodynamics: Two-fold transmission advantage of Omicron in Berlin, Germany during December 2021.Virus evolution · 2023Article
- Measurably recombining malaria parasites.Trends in parasitology · 2023Review
- Cov2clusters: genomic clustering of SARS-CoV-2 sequences.BMC genomics · 2022Article
- Characterizing the Countrywide Epidemic Spread of Influenza A(H1N1)pdm09 Virus in Kenya between 2009 and 2018.Viruses · 2021Article
- Fundamental Identifiability Limits in Molecular Epidemiology.Molecular biology and evolution · 2021Article
- Transmissibility and transmission of respiratory viruses.Nature reviews. Microbiology · 2021Review
- Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State.Science translational medicine · 2021Article
- Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State.medRxiv : the preprint server for health sciences · 2020Article
Corrections and comments
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Authors and funding
25 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Infecting large portions of the global population, seasonal influenza is a major burden on societies around the globe. While the global source sink dynamics of the different seasonal influenza viruses have been studied intensively, its local spread remains less clear. In order to improve our understanding of how influenza is transmitted on a city scale, we collected an extremely densely sampled set of influenza sequences alongside patient metadata. To do so, we sequenced influenza viruses isolated from patients of two different hospitals, as well as private practitioners in Basel, Switzerland during the 2016/2017 influenza season. The genetic sequences reveal that repeated introductions into the city drove the influenza season. We then reconstruct how the effective reproduction number changed over the course of the season. While we did not find that transmission dynamics in Basel correlate with humidity or school closures, we did find some evidence that it may positively correlated with temperature. Alongside the genetic sequence data that allows us to see how individual cases are connected, we gathered patient information, such as the age or household status. Zooming into the local transmission outbreaks suggests that the elderly were to a large extent infected within their own transmission network. In the remaining transmission network, our analyses suggest that school-aged children likely play a more central role than pre-school aged children. These patterns will be valuable to plan interventions combating the spread of respiratory diseases within cities given that similar patterns are observed for other influenza seasons and cities.
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