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.

Transmission of SARS-CoV-2 by children to contacts in schools and households: a prospective cohort and environmental sampling study in London

“…The role of children and schools in the COVID-19 pandemic is the subject of much research and speculation. Children are recognised to be major reservoirs of viral upper respiratory tract infections that may augment spread of infection in the wider community; extrapolation of evidence from influenza studies suggest that school closures may play some role in limiting pathogen spread, at least among children (1-3). However, studies from around the world confirm that children are much less susceptible to the harmful direct effects of SARS-CoV-2 infection than adults, hence the high social cost of school closures may be unjustified (4-7).…”

Characterizing the countrywide epidemic spread of influenza A(H1N1)pdm09 virus in Kenya between 2009 and 2018

“…These clusters were then used to analyze the spread of A(H1N1)pdm09 virus in Kenya using two phylodynamic approaches. First, the effective reproduction number ( R e ), which is the average number of secondary cases generated by an infection, was estimated using a birth-death skyline (BDSKY) analysis [44], where all individual transmission clusters are assumed to be independent observations of the same process with the same parameters [45]. Second, the relative genetic diversity (effective virus population size over time) was estimated using Gaussian Markov random field (GMRF) coalescent smoothing of the effective population size [46].…”

High confidence identification of intra-host single nucleotide variants for person-to-person influenza transmission tracking in congregate settings

“…The persistence and the epidemiological success of influenza virus is mainly attributed to its rapid evolution, through which the virus continuously attains mutations resulting in escape from the immune system, vaccines, and antivirals. However, this rapid evolution has also enabled numerous genomic studies resulting in critical insights into the dynamics of influenza evolution, transmission and spread (3)(4)(5)(6)(7)(8)(9)(10).…”