A B S T R A C TAccurate estimation of the parameters characterising infectious disease transmission is vital for optimising control interventions during epidemics. A valuable metric for assessing the current threat posed by an outbreak is the time-dependent reproduction number, i.e. the expected number of secondary cases caused by each infected individual. This quantity can be estimated using data on the numbers of observed new cases at successive times during an epidemic and the distribution of the serial interval (the time between symptomatic cases in a transmission chain). Some methods for estimating the reproduction number rely on pre-existing estimates of the serial interval distribution and assume that the entire outbreak is driven by local transmission. Here we show that accurate inference of current transmissibility, and the uncertainty associated with this estimate, requires: (i) upto-date observations of the serial interval to be included, and; (ii) cases arising from local transmission to be distinguished from those imported from elsewhere. We demonstrate how pathogen transmissibility can be inferred appropriately using datasets from outbreaks of H1N1 influenza, Ebola virus disease and Middle-East Respiratory Syndrome. We present a tool for estimating the reproduction number in real-time during infectious disease outbreaks accurately, which is available as an R software package (EpiEstim 2.2). It is also accessible as an interactive, user-friendly online interface (EpiEstim App), permitting its use by non-specialists. Our tool is easy to apply for assessing the transmission potential, and hence informing control, during future outbreaks of a wide range of invading pathogens.

IMPORTANCE Data about the safety of vaccines against SARS-CoV-2 during pregnancy are limited.OBJECTIVE To examine the risk of adverse pregnancy outcomes after vaccination against SARS-CoV-2 during pregnancy.

The attributable fraction (or attributable risk) is a widely used measure that quantifies the public health impact of an exposure on an outcome. Even though the theory for AF estimation is well developed, there has been a lack of up-to-date software implementations. The aim of this article is to present a new R package for AF estimation with binary exposures. The package AF allows for confounder-adjusted estimation of the AF for the three major study designs: cross-sectional, (possibly matched) case-control and cohort. The article is divided into theoretical sections and applied sections. In the theoretical sections we describe how the confounder-adjusted AF is estimated for each specific study design. These sections serve as a brief but self-consistent tutorial in AF estimation. In the applied sections we use real data examples to illustrate how the AF package is used. All datasets in these examples are publicly available and included in the AF package, so readers can easily replicate all analyses.

It is well known that the odds ratio is noncollapsible, in the sense that conditioning on a covariate that is related to the outcome typically changes the size of the odds ratio, even if this covariate is unrelated to the exposure. The risk difference and risk ratio do not have this peculiar property; we say that the risk difference and risk ratio are collapsible. However, noncollapsibility is not unique for the odds ratio; the rate difference and rate ratio are generally noncollapsible as well. This may seem paradoxical, since the rate can be viewed as a risk per unit time, and thus one would naively suspect that the rate difference/ratio should inherit collapsibility from the risk difference/ratio. Adding to the confusion, it was recently shown that the exposure coefficient in the Aalen additive hazards model is collapsible. This may seem to contradict the fact that the rate difference is generally noncollapsible, since the exposure coefficient in the Aalen additive hazards model is a rate difference. In this article, we use graphical arguments to explain why the rate difference/ratio does not inherit collapsibility from the risk difference/ratio. We also explain when and why the exposure coefficient in the Aalen additive hazards model is collapsible.