SARS-CoV-2 epidemic after social and economic reopening in three US states reveals shifts in age structure and clinical characteristics

Wikle, Nathan B; Tran, Thu Nguyen-Anh; Gentilesco, Bethany; Leighow, Scott M; Albert, Emmy; Strong, Emily R; Brinda, Karel; Inam, Haider; Yang, Fuhan; Hossain, Sajid; Chan, Philip; Hanage, William P; Messick, Maria; Pritchard, Justin R; Hanks, Ephraim; Boni, Maciej F

In the United States, state-level re-openings in spring 2020 presented an opportunity for the resurgence of SARS-CoV-2 transmission. One important question during this time was whether human contact and mixing patterns could increase gradually without increasing viral transmission, the rationale being that new mixing patterns would likely be associated with improved distancing, masking, and hygiene practices. A second key question to follow during this time was whether clinical characteristics of the epidemic would improve after the initial surge of cases. Here, we analyze age-structured case, hospitalization, and death time series from three states – Rhode Island, Massachusetts, and Pennsylvania – that had successful reopenings in May 2020 without summer waves of infection. Using a Bayesian inference framework on eleven daily data streams and flexible daily population contact parameters, we show that population-average mixing rates dropped by >50% during the lockdown period in March/April, and that the correlation between overall population mobility and transmission-capable mixing was broken in May as these states partially re-opened. We estimate the reporting rates (fraction of symptomatic cases reporting to health system) at 96.3% (RI), 62.5% (MA), and 98.9% (PA). We show that elderly individuals were less able to reduce contacts during the lockdown period when compared to younger individuals, leading to the outbreak being concentrated in elderly congregate settings despite the lockdown. Attack rate estimates through August 31 2020 are 6.2% (95% CI: 5.7% – 6.8%) of the total population infected for Rhode Island, 6.7% (95% CI: 5.4% – 7.6%) in Massachusetts, and 2.7% (95% CI: 2.5% – 3.1%) in Pennsylvania, with some validation available through published seroprevalence studies. Infection fatality rates (IFR) estimates are higher in our analysis (>2%) than previously reported values, likely resulting from the epidemics in these three states affecting the most vulnerable sub-populations and the close matches between the states’ reported COVID-19 deaths and excess deaths. Data in Pennsylvania may have been underreported for both non-hospitalized and hospitalized patients, casting substantial uncertainty on estimates of attack rate and infection fatality rate.