Comparing the dynamics of COVID-19 infection and mortality in the United States, India, and Brazil (preprint)

This paper compares and contrasts the spread and impact of COVID-19 in the three countries most heavily impacted by the pandemic: the United States (US), India and Brazil. All three of these countries have a federal structure, in which the individual states have largely determined the response to the pandemic. Thus, we perform an extensive analysis of the individual states of these three countries to determine patterns of similarity within each. First, we analyse structural similarity and anomalies in the trajectories of cases and deaths as multivariate time series. Next, we study the lengths of the different waves of the virus outbreaks across the three countries and their states. Finally, we investigate suitable time offsets between cases and deaths as a function of the distinct outbreak waves. In all these analyses, we consistently reveal more characteristically distinct behaviour between US and Indian states, while Brazilian states exhibit less structure in their wave behaviour and changing progression between cases and deaths.

Understanding spatial propagation using metric geometry with application to the spread of COVID-19 in the United States (preprint)

This paper introduces a novel approach to spatio-temporal data analysis using metric geometry to study the propagation of COVID-19 across the United States. Using a geodesic Wasserstein metric, we analyse discrepancies between the density functions of new case counts on any given day, incorporating the geographic spread of cases. First, we apply this to identify the periods during which the changes in the geographic distribution of COVID-19 were most profound. The greatest shift occurred between May and June of 2020, when COVID-19 shifted from mostly dominating the Northeastern states to a wider distribution across the country. We support our findings with a new measure of the extent of geodesic variance of a distribution, demonstrating that the geographic imprint of COVID-19 was most concentrated in May 2020. Next, we investigate whether the epidemic exhibited meaningful patterns of spatial reversion, where similar geographic distributions return later. We identify broad similarity between the spread of COVID-19 across the US between the second and third waves, and to a lesser extent, the reemergence of the first wave's Northeastern dominance closer to the present day. This methodology could provide new insights for analysts to monitor the dynamical spread of epidemics and enable regional policymakers to protect their localities. More broadly, the framework we introduce could be applied to a variety of problems evolving over space and time.

Optimal allocation of PCR tests to minimise disease transmission through contact tracing and quarantine (preprint)

PCR testing is a crucial capability for managing disease outbreaks, but it is also a limited resource and must be used carefully to ensure the information gain from testing is valuable. Testing has two broad uses, namely to track epidemic dynamics and to reduce transmission by identifying and managing cases. In this work we develop a modelling framework to examine the effects of test allocation in an epidemic, with a focus on using testing to minimise transmission. Using the COVID-19 pandemic as an example, we examine how the number of tests conducted per day relates to reduction in disease transmission, in the context of logistical constraints on the testing system. We show that if daily testing is above the routine capacity of a testing system, which can cause delays, then those delays can undermine efforts to reduce transmission through contact tracing and quarantine. This work highlights that the two goals of aiming to reduce transmission and aiming to identify all cases are different, and it is possible that focusing on one may undermine achieving the other. To develop an effective strategy, the goals must be clear and performance metrics must match the goals of the testing strategy. If metrics do not match the objectives of the strategy, then those metrics may incentivise actions that undermine achieving the objectives.