pratikunterwegs
commented
1 year ago I've added a new section 'Primer on heterogeneous susceptibility' in the main body of the vignette. This keeps the structure of the vignettes as > Opening paragraph > Redirection to earlier vignettes > Use case > Assumptions > Main body.
The main body text is
Susceptibility to infection may be age-dependent and vary between demographic groups, for example, between age groups due to age-related impaired or dysregulated host immunity. Susceptibility to infection in different demographic groups may be estimated from stratified attack rates or prevalence estimates from pathogens with similar immune responses (such as SARS, MERS, and Covid-19).
For between-group differences, users may prefer to gather this information from stratified prevalence estimates over observed incidence case rate due to surveillance bias towards registering more symptomatic individuals.
Patterns of heterogeneous susceptibility may also be context dependent, and different patterns may be observed for the same infectious pathogen in different countries. For example, after the first peak of Covid-19 cases in 2020, in Peru prevalence had a uniform distribution across age groups, while in the UK prevalence across age groups was heterogeneous.
Later, I've added an information box which will appear in grey.
Getting data on within-group susceptibility differences
For within-group differences in susceptibility, such as due to immunisation, users could obtain this information from age-specific vaccination uptake statistics from national governments (here, the UK). When antibody response decays are known for an immunisation course, more detailed statistics on the percentage of people vaccinated (here, in the UK) in the preceding few months only, may be more informative.
I'm a little wary of linking to Covid dashboards, as these could be taken offline in the near future (as the CMMID dashboards have been) - is the coronavirus.data.gov.uk site likely to be maintained in the long term?
avallecam
This vignette could be a good place to add references to these. They can inform users where to gather this information for their own purposes.
For example, here in the intro paragraph:
https://github.com/epiverse-trace/finalsize/blob/f0ac4127e54579754d08ee92754203f99c0f6ee9/vignettes/varying_susceptibility.Rmd#L19
We can add the following:
"(...) Such heterogeneity may be age-dependent and vary between age groups due to age-related impaired or dysregulated host immunity. The information for this can be gathered from stratified attack rates or prevalence estimates from pathogens with similar immune responses (like SARS, MERS, and COVID-19).
"For between-group differences, users may prefer to gather this information from stratified prevalence estimates over observed incidence case rate due to surveillance bias towards registering more symptomatic individuals.
"These patterns may also be context depended because different patterns were observed for the same disease in different countries. For example, after the first peak of COVID-19 cases, in Peru prevalence by age groups had a uniform distribution, while in the UK it had a heterogeneous one."
Also here:
https://github.com/epiverse-trace/finalsize/blob/f0ac4127e54579754d08ee92754203f99c0f6ee9/vignettes/varying_susceptibility.Rmd#L253
We can add the following:
"For within-group differences, users may gather this information from vaccination percentage uptake within age groups, or alternatively, the percentage of vaccinated people in last months in case of known antibody response decays."