Prisons have been hotspots for COVID-19 and likely an important driver of racial disparity in disease burden. From the first COVID-19 case detected through March 25, 2022, 66,684 of 196,652 residents of California's state prison system were infected, most of them in two large winter waves of outbreaks that reached all 35 of the state prisons. We used individual-level data on disease timing and nightly room assignments in these prisons to reconstruct locations and pathways of transmission statistically, and from that estimated reproduction numbers, locations of unobserved infection events, and the subsequent magnitude and distribution of long COVID prevalence. Where earlier work has recommended smaller cells over large dormitory housing to reduce transmission, recommended use of cells with solid doors over those with bars only, and cautioned against reliance on solid doors (e.g., in cold months when HVAC systems can circulate aerosols), we found evidence of substantial transmission in both dorms and cells regardless of the door and season. Effective reproduction numbers were found to range largely between 0 and 5, in both cells and dorms of all door types. Our estimates of excess case rates suggest that as a result of disparities in incarceration, prison outbreaks contributed to disproportionate disease burden on Black and Indigenous people in California. We estimated that 9,100-11,000 people have developed long COVID as a result of infection in these prison outbreaks, 1,700-2,000 of them with disabling consequences, and that this burden is disproportionately on Black and Indigenous people in comparison to the state as a whole. We urge high-quality medical care for prison residents affected by long COVID, and decarceration to reduce the risk of future outbreaks of both COVID-19 and other diseases.

LW, HA, AK, and DS received funding from the California Prison Receivership Office.

LW and TCP were supported by NIH GM130900. SB and TCP were supported by CDC U01CK000590, as part of the Modeling Infectious Diseases in Healthcare Network. SB was also supported by NIH K12 EY031372. LW, HA, AK, and DS received funding from the California Prison Receivership Office.

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The details of the IRB/oversight body that provided approval or exemption for the research described are given below:

IRB of the University of California, San Francisco gave ethical approval for this work. The IRB (IRB no. 21-34030) waived the need for informed consent given the use of secondary deidentified datasets based on the following criteria: deemed no more than minimal risk to subjects; could not practicably be done without the waiver; will not adversely affect rights and welfare of subjects; and will provide subjects with additional pertinent information after participation.

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Our data sharing agreement with CDCR and CCHCS does not permit publication of the raw source data. Data requests may be made to the California Correctional Health Care Services and are subject to controlled access, due to requirements to enhance protection of this vulnerable incarcerated population. Source code used in the analysis is available on request from the corresponding author.