Dataset Information

Characterising the epidemic spread of influenza A/H3N2 within a city through phylogenetics.

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.

SUBMITTER: Muller NF

PROVIDER: S-EPMC7676729 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Characterising the epidemic spread of influenza A/H3N2 within a city through phylogenetics.

Müller Nicola F NF Wüthrich Daniel D Goldman Nina N Sailer Nadine N Saalfrank Claudia C Brunner Myrta M Augustin Noémi N Seth-Smith Helena Mb HM Hollenstein Yvonne Y Syedbasha Mohammedyaseen M Lang Daniela D Neher Richard A RA Dubuis Olivier O Naegele Michael M Buser Andreas A Nickel Christian H CH Ritz Nicole N Zeller Andreas A Lang Brian M BM Hadfield James J Bedford Trevor T Battegay Manuel M Schneider-Sliwa Rita R Egli Adrian A Stadler Tanja T

PLoS pathogens 20201119 11

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 isolat ...[more]

PMID: 33211775

Similar Datasets

Project description:BackgroundThe explosive epidemics of dengue that have been occurring in various countries have stimulated investigation into new approaches to improve understanding of the problem and to develop new strategies for controlling the disease. The objective of this study was to evaluate the characteristics of diffusion of the first dengue epidemic that occurred in the city of Salvador in 1995.MethodsThe epidemiological charts and records of notified cases of dengue in Salvador in 1995 constituted the source of data. The cases of the disease were georeferenced according to census areas (spatial units) and epidemiological weeks (temporal unit). Kernel density estimation was used to identify the pattern of spatial diffusion using the R-Project computer software program.ResultsOf the 2,006 census areas in the city, 1,400 (70%) registered cases of dengue in 1995 and the spatial distribution of these records revealed that by the end of 1995 practically the entire city had been affected by the virus, with the largest concentration of cases occurring in the western region, composed of census areas with a high population density and predominantly horizontal residences compared to the eastern region of the city, where there is a predominance of vertical residential buildings.ConclusionThe pattern found in this study shows the characteristics of the classic process of spreading by contagion that is common to most infectious diseases. It was possible to identify the epicenter of the epidemic from which centrifugal waves of the disease emanated. Our results suggest that, if a more agile control instrument existed that would be capable of rapidly reducing the vector population within a few days or of raising the group immunity of the population by means of a vaccine, it would theoretically be possible to adopt control actions around the epicenter of the epidemic and consequently reduce the incidence of the disease in the city. This finding emphasizes the need for further research to improve the technology available for the prevention of this disease.

Dataset Information

Characterising the epidemic spread of influenza A/H3N2 within a city through phylogenetics.

Publications

Characterising the epidemic spread of influenza A/H3N2 within a city through phylogenetics.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets