High-resolution influenza mapping of a city reveals socioeconomic determinants of transmission within and between urban quarters

Abstract

162/150) 39 40With two-thirds of the global population projected to be living in urban areas by 2050, 41 understanding the transmission patterns of viral pathogens within cities is crucial for effective 42 prevention strategies. Here, in unprecedented spatial resolution, we analysed the socioeconomic 43 determinants of influenza transmission in a European city. We combined geographical and 44 epidemiological data with whole genome sequencing of influenza viruses at the scale of urban 45 quarters and statistical blocks, the smallest geographic subdivisions within a city. We observed 46 annually re-occurring geographic clusters of influenza incidences, mainly associated with net Introduction: 54Transmission of influenza is influenced by extensive but poorly understood interactions between 55 various viral, host and environmental factors 1-3 . Influenza may serve as a model for pandemic 56 threats including the most recent COVID-19 pandemic. Whole viral genome sequencing has 57 enabled reconstruction of phylogenetic relatedness at high resolution. Using these approaches, 58the interactions and dynamics of influenza transmission events have been described across a 59 range of scales: globally 4-6 , across continents 1,7 , in university campuses 8 , or within households 9-60 12 . With two-thirds of the global population projected to be living in urban areas by 2050, 61 understanding the transmission patterns of influenza within cities is crucial for effective prevention 62 strategies and may help to prepare for pandemic threats. Previous work identified cities as 63 containing critical chains of transmission outside of peak climatic conditions (Dalziel, B. D. et al 64 Science 2019), but the resolution to look at these critical intra-city transmission chains in detail 65 has until now been lacking. Very few studies have explored transmission events and dynamics of 66 influenza viruses at the scale of a city 13-17 . Cities are heterogeneous with remarkably different 67 neighbourhoods based on the socioeconomic position of the individuals living there. 68Consequently, a high spatial resolution of the urban space and built environment is crucial to fully 69 understanding the impact of factors linked to health and disease 18,19 . 71In this study we combine epidemiologic, geographical and demographical factors at the 72 unprecedented resolution of urban quarters (i.e. neighbourhood/area) and statistical blocks (i.e. 73city block/street) levels, the smallest statistical enumeration areas within a city. Basel, 74Switzerland, serving as our model city, we explored the local patterns of influenza distribution and 75 transmission from 2013 to 2018. Basel has urban quarters that differ substantially in 76 socioeconomic indicators and housing structure. By using information at the level of statistical 77 blocks, we were able to construct a detailed picture of influenza transmission within the city. We 78 visualized kernel density estimates of influenza cases (reflecting the clustering of cases), a 79 fundamental data smoothing me...

Determinants of SARS-CoV-2 transmission to guide vaccination strategy in an urban area

“…Cluster Matcher v.1.2.4 22 was then used to combine ancillary geographic (quarter), and socioeconomic (share of 1-person households, median income, living space, seniority) information that were subdivided into tertiles (1: low, 2: intermediate, 3: high, N/A: no available data or censored for privacy reasons) on identified clusters. To test whether related genomes in Basel-City cluster according to a) quarter, b) living space per person, c) share of 1-person households, d) median income, or e) seniority a custom python-script for a random permutation test was performed 50 (github.com/appliedmicrobiologyresearch/Influenza-2016-2017). The results for clustering within and among urban quarter and tertiles in socioeconomic determinants were visualized using circos v.0.69 51 .…”

“…To test whether related genomes in Basel-City cluster according to a) quarter, b) living space per person, c) share of 1-person households, d) median income, or e) seniority a custom python-script for a random permutation test was performed 50 (github.com/appliedmicrobiologyresearch/Influenza-2016-2017). The results for clustering within and among urban quarter and tertiles in socioeconomic determinants were visualized using circos v.0.69 51 .…”

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

“…Details on the data collection are provided in [ 17 ]. The spatial and survey data were analyzed in a different study [ 18 ]. We here assess the importance of introductions of influenza into a city for seeding a seasonal epidemic, the overall dynamics of transmission throughout the season, and explore the impact of different age groups on the epidemic.…”

Determinants of SARS-CoV-2 transmission to guide vaccination strategy in an urban area

“…To test whether related genomes in Basel-City cluster according to (1) quarter, (2) living space per person, (3) share of one-person households, (4) median income or (5) seniority, with the null hypothesis of random distribution of cases and hence clusters across tertiles, a custom python-script for a random permutation test was performed ( Egli et al. 2020 ) 1 The results for clustering within and among urban quarter and tertiles in socio-economic determinants were visualised using circos v.0.69 ( Krzywinski et al.…”