ern: An [Formula: see text] package to estimate the effective reproduction number using clinical and wastewater surveillance data.

The effective reproduction number, [Formula: see text], is an important epidemiological metric used to assess the state of an epidemic, as well as the effectiveness of public health interventions undertaken in response. When [Formula: see text] is above one, it indicates that new infections are increasing, and thus the epidemic is growing, while an [Formula: see text] is below one indicates that new infections are decreasing, and so the epidemic is under control. There are several established software packages that are readily available to statistically estimate [Formula: see text] using clinical surveillance data. However, there are comparatively few accessible tools for estimating [Formula: see text] from pathogen wastewater concentration, a surveillance data stream that cemented its utility during the COVID-19 pandemic. We present the [Formula: see text] package ern that aims to perform the estimation of the effective reproduction number from real-world wastewater or aggregated clinical surveillance data in a user-friendly way.

Modeling the Interplay Between Seasonal Flu Outcomes and Individual Vaccination Decisions.

Seasonal influenza presents an ongoing challenge to public health. The rapid evolution of the flu virus necessitates annual vaccination campaigns, but the decision to get vaccinated or not in a given year is largely voluntary, at least in the USA, and many people decide against it. In some early attempts to model these yearly flu vaccine decisions, it was often assumed that individuals behave rationally, and do so with perfect information-assumptions that allowed the techniques of classical economics and game theory to be applied. However, these assumptions are not fully supported by the emerging empirical evidence about human decision-making behavior in this context. We develop a simple model of coupled disease spread and vaccination dynamics that instead incorporates experimental observations from social psychology to model annual vaccine decision-making more realistically. We investigate population-level effects of these new decision-making assumptions, with the goal of understanding whether the population can self-organize into a state of herd immunity, and if so, under what conditions. Our model agrees with the established results while also revealing more subtle population-level behavior, including biennial oscillations about the herd immunity threshold.

Age-dependence of healthcare interventions for COVID-19 in Ontario, Canada.

BACKGROUND: Patient age is one of the most salient clinical indicators of risk from COVID-19. Age-specific distributions of known SARS-CoV-2 infections and COVID-19-related deaths are available for many regions. Less attention has been given to the age distributions of serious medical interventions administered to COVID-19 patients, which could reveal sources of potential pressure on the healthcare system should SARS-CoV-2 prevalence increase, and could inform mass vaccination strategies. The aim of this study is to quantify the relationship between COVID-19 patient age and serious outcomes of the disease, beyond fatalities alone. METHODS: We analysed 277,555 known SARS-CoV-2 infection records for Ontario, Canada, from 23 January 2020 to 16 February 2021 and estimated the age distributions of hospitalizations, Intensive Care Unit admissions, intubations, and ventilations. We quantified the probability of hospitalization given known SARS-CoV-2 infection, and of survival given COVID-19-related hospitalization. RESULTS: The distribution of hospitalizations peaks with a wide plateau covering ages 60-90, whereas deaths are concentrated in ages 80+. The estimated probability of hospitalization given known infection reaches a maximum of 27.8% at age 80 (95% CI 26.0%-29.7%). The probability of survival given hospitalization is nearly 100% for adults younger than 40, but declines substantially after this age; for example, a hospitalized 54-year-old patient has a 91.7% chance of surviving COVID-19 (95% CI 88.3%-94.4%). CONCLUSIONS: Our study demonstrates a significant need for hospitalization in middle-aged individuals and young seniors. This need is not captured by the distribution of deaths, which is heavily concentrated in very old ages. The probability of survival given hospitalization for COVID-19 is lower than is generally perceived for patients over 40. If acute care capacity is exceeded due to an increase in COVID-19 prevalence, the distribution of deaths could expand toward younger ages. These results suggest that vaccine programs should aim to prevent infection not only in old seniors, but also in young seniors and middle-aged individuals, to protect them from serious illness and to limit stress on the healthcare system.

Invariant predictions of epidemic patterns from radically different forms of seasonal forcing.

Seasonal variation in environmental variables, and in rates of contact among individuals, are fundamental drivers of infectious disease dynamics. Unlike most periodically forced physical systems, for which the precise pattern of forcing is typically known, underlying patterns of seasonal variation in transmission rates can be estimated approximately at best, and only the period of forcing is accurately known. Yet solutions of epidemic models depend strongly on the forcing function, so dynamical predictions-such as changes in epidemic patterns that can be induced by demographic transitions or mass vaccination-are always subject to the objection that the underlying patterns of seasonality are poorly specified. Here, we demonstrate that the key bifurcations of the standard epidemic model are invariant to the shape of seasonal forcing if the amplitude of forcing is appropriately adjusted. Consequently, analyses applicable to real disease dynamics can be conducted with a smooth, idealized sinusoidal forcing function, and qualitative changes in epidemic patterns can be predicted without precise knowledge of the underlying forcing pattern. We find similar invariance in a seasonally forced predator-prey model, and conjecture that this phenomenon-and the associated robustness of predictions-might be a feature of many other periodically forced dynamical systems.