Rates of SARS-CoV-2 transmission between and into California state prisons (preprint)

Correctional institutions are a crucial hotspot amplifying SARS-CoV-2 spread and disease disparity in the U.S. In the California state prison system, multiple massive outbreaks have been caused by transmission between prisons. Correctional staff are a likely vector for transmission into the prison system from surrounding communities. We used publicly available data to estimate the magnitude of flows to and between California state prisons, estimating rates of transmission from communities to prison staff and residents, among and between residents and staff within facilities, and between staff and residents of distinct facilities in the state's 34 prisons through March 22, 2021. We use a mechanistic model, the Hawkes process, reflecting the dynamics of SARS-CoV-2 transmission, for joint estimation of transmission rates. Using nested models for hypothesis testing, we compared the results to simplified models (i) without transmission between prisons, and (ii) with no distinction between prison staff and residents. We estimated that transmission between different facilities' staff is a significant cause of disease spread, and that staff are a vector of transmission between resident populations and outside communities. While increased screening and vaccination of correctional staff may help reduce introductions, large-scale decarceration remains crucially needed as more limited measures are not likely to prevent large-scale disease spread.

Mitigating outbreaks in congregate settings by decreasing the size of the susceptible population (preprint)

While many transmission models have been developed for community spread of respiratory pathogens, less attention has been given to modeling the interdependence of disease introduction and spread seen in congregate settings, such as prisons or nursing homes. As demonstrated by the explosive outbreaks of COVID-19 seen in congregate settings, the need for effective outbreak prevention and mitigation strategies for these settings is critical. Here we consider how interventions that decrease the size of the susceptible populations, such as vaccination or depopulation, impact the expected number of infections due to outbreaks. Introduction of disease into the resident population from the community is modeled as a branching process, while spread between residents is modeled via a compartmental model. Control is modeled as a proportional decrease in both the number of susceptible residents and the reproduction number. We find that vaccination or depopulation can have a greater than linear effect on anticipated infections. For example, assuming a reproduction number of 3.0 for density-dependent COVID-19 transmission, we find that reducing the size of the susceptible population by 20% reduced overall disease burden by 47%. We highlight the California state prison system as an example for how these findings provide a quantitative framework for implementing infection control in congregate settings. Additional applications of our modeling framework include optimizing the distribution of residents into independent residential units, and comparison of preemptive versus reactive vaccination strategies.

Assessing the Risk of Cascading COVID-19 Outbreaks from Prison-to-Prison Transfers (preprint)

COVID-19 transmission has been widespread across the California prison system, and at least two of these outbreaks were caused by transfer of infected individuals between prisons. Risks of individual prison outbreaks due to introduction of the virus and of widespread transmission within prisons due to poor conditions have been documented. We examine the additional risk potentially posed by transfer between prisons that can lead to large-scale spread of outbreaks across the prison system if the rate of transfer is sufficiently high. We estimated the threshold number of individuals transferred per prison per month to generate supercritical transmission between prisons, a condition that could lead to large-scale spread across the prison system. We obtained numerical estimates from a range of representative quantitative assumptions, and derived the percentage of transfers that must be performed with effective quarantine measures to prevent supercritical transmission given known rates of transfers occurring between California prisons. Our mean estimate of the critical threshold rate of transfers was 14.38 individuals transferred per prison per month in the absence of quarantine measures. Available data documents transfers occurring at a rate of 60 transfers per prison per month. At that rate, estimates of the threshold rate of adherence to quarantine precautions had mean 76.03%. While the impact of vaccination and possible decarceration measures is unclear, we include estimates of the above quantities given reductions in the probability and extent of outbreaks. We conclude that the risk of supercritical transmission between California prisons has been substantial, requiring quarantine protocols to be followed rigorously to manage this risk. The rate of outbreaks occurring in California prisons suggests that supercritical transmission may have occurred. We stress that the thresholds we estimate here do not define a safe level of transfers, even if supercritical transmission between prisons is avoided, since even low rates of transfer can cause very large outbreaks. We note that risks may persist after vaccination, due for example to variant strains, and in prison systems where widespread vaccination has not occurred. Decarceration remains urgently needed as a public health measure.

Estimation of effects of contact tracing and mask adoption on COVID-19 transmission in San Francisco: a modeling study (preprint)

The current COVID-19 pandemic has spurred concern about what interventions may be effective at reducing transmission. The city and county of San Francisco imposed a shelter-in-place order in March 2020, followed by use of a contact tracing program and a policy requiring use of cloth face masks. We used statistical estimation and simulation to estimate the effectiveness of these interventions in San Francisco. We estimated that self-isolation and other practices beginning at the time of San Francisco's shelter-in-place order reduced the effective reproduction number of COVID-19 by 35.4% (95% CI, -20.1%--81.4%). We estimated the effect of contact tracing on the effective reproduction number to be a reduction of approximately 44% times the fraction of cases that are detected, which may be modest if the detection rate is low. We estimated the impact of cloth mask adoption on reproduction number to be approximately 8.6%, and note that the benefit of mask adoption may be substantially greater for essential workers and other vulnerable populations, residents return to circulating outside the home more often. We estimated the effect of those interventions on incidence by simulating counterfactual scenarios in which contact tracing was not adopted, cloth masks were not adopted, and neither contact tracing nor cloth masks was adopted, and found increases in case counts that were modest, but relatively larger than the effects on reproduction numbers. These estimates and model results suggest that testing coverage and timing of testing and contact tracing may be important, and that modest effects on reproduction numbers can nonetheless cause substantial effects on case counts over time.

Reparations for Black American Descendants of Persons Enslaved in the U.S. and Their Estimated Impact on SARS-CoV-2 Transmission (preprint)

BackgroundIn the United States, Black Americans are suffering from significantly disproportionate incidence and mortality rates of COVID-19. The potential for racial-justice interventions, including reparations payments, to ameliorate these disparities has not been adequately explored. MethodsWe compared the COVID-19 time-varying Rt curves of relatively disparate polities in terms of social equity (South Korea vs. Louisiana). Next, we considered a range of reproductive ratios to back-calculate the transmission rates {beta}i[->]j for 4 cells of the simplified next-generation matrix (from which R0 is calculated for structured models) for the outbreak in Louisiana. Lastly, we modeled the effect that monetary payments as reparations for Black American descendants of persons enslaved in the U.S. would have had on pre-intervention {beta}i[->]j. ResultsOnce their respective epidemics begin to propagate, Louisiana displays Rt values with an absolute difference of 1.3 to 2.5 compared to South Korea. It also takes Louisiana more than twice as long to bring Rt below 1. We estimate that increased equity in transmission consistent with the benefits of a successful reparations program (reflected in the ratio {beta}b[->]b / {beta}w[->]w) could reduce R0 by 31 to 68%. DiscussionWhile there are compelling moral and historical arguments for racial injustice interventions such as reparations, our study describes potential health benefits in the form of reduced SARS-CoV-2 transmission risk. As we demonstrate, a restitutive program targeted towards Black individuals would not only decrease COVID-19 risk for recipients of the wealth redistribution; the mitigating effects would be distributed across racial groups, benefitting the population at large. FundingETR and LW are supported by NIGMS MIDAS grant R01 GM130900. ETR is also supported by NIAID K08 AI139361. WAD is supported by NIMHD R01 MD011606, NSF SES 1851845, and IES R305A190484. MMM is supported by the Ethics and Governance of Artificial Intelligence Fund.

Estimation of COVID-19 transmission rates in California and the U.S. with reporting delays (preprint)

We estimated time-varying reproduction numbers of COVID-19 transmission in counties and regions of California and in states of the United States, using the Wallinga-Teunis method of estimations applied to publicly available data. The serial interval distribution assumed incorporates wide uncertainty in delays from symptom onset to case reporting. This assumption contributes smoothing and a small but meaningful increase in numerical estimates of reproduction numbers due to the likely existence of secondary cases not yet reported. Transmission in many areas of the U.S. may not yet be controlled, including areas in which case counts appear to be stable or slowly declining.