Robust estimation of SARS-CoV-2 epidemic in US counties

TL;DR

This paper presents a robust method to estimate COVID-19 progression at US counties, highlighting how reducing infectious periods can significantly lower deaths and emphasizing the importance of combined mitigation strategies.

Contribution

It introduces a county-level estimation approach for SARS-CoV-2 spread and quantifies the impact of shortening infectious periods on reducing COVID-19 deaths.

Findings

Shortening infectious period by 5% can reduce around 39% of deaths.

Reducing infectious period has a greater impact when R is close to 1.

Provides a dynamic map for local policy and public risk assessment.

Abstract

The COVID-19 outbreak is asynchronous in US counties. Mitigating the COVID-19 transmission requires not only the state and federal level order of protective measures such as social distancing and testing, but also public awareness of time-dependent risk and reactions at county and community levels. We propose a robust approach to estimate the heterogeneous progression of SARS-CoV-2 at all US counties having no less than 2 COVID-19 associated deaths, and we use the daily probability of contracting (PoC) SARS-CoV-2 for a susceptible individual to quantify the risk of SARS-CoV-2 transmission in a community. We found that shortening by $5\%$ of the infectious period of SARS-CoV-2 can reduce around $39\%$ (or $78$K, $95\%$ CI: $[66$K $, 89$K $]$) of the COVID-19 associated deaths in the US as of 20 September 2020. Our findings also indicate that reducing infection and deaths by a shortened infectious period is more pronounced for areas with the effective reproduction number close to 1, suggesting that testing should be used along with other mitigation measures, such as social distancing and facial mask-wearing, to reduce the transmission rate. Our deliverable includes a dynamic county-level map for local officials to determine optimal policy responses and for the public to better understand the risk of contracting SARS-CoV-2 on each day.