Work on COVID-19
Members of the Prevention Policy Modeling Lab have been actively engaged in modeling and analysis for the COVID-19 response.

Real-Time Tracking of COVID-19 in US States and Counties
PPML members Nick Menzies, Ted Cohen and Josh Salomon, with Melanie Chitwood, Marcus Russi and colleagues, contribute to the Covidestim project, which conducts real-time estimates of COVID-19 outcomes and state and county levels, updated daily.

COVID-19 Contact Tracing Model
We have developed a simple interactive model to evaluate the potential impact of contact tracing programs in the context of loosened physical distancing measures.
Modeling for California Counties
PPML member Jeremy Goldhaber-Fiebert leads ongoing efforts in collaboration with the California Department of Public Health to develop models, forecasts and scenario analyses for all counties in California using the SC-COSMO simulation modeling framework.

PPML members helped to establish the COVID-19 Statistics, Policy Modeling and Epidemiology Collective (C-SPEC). C-SPEC has developed several open-source models for forecasts, scenario analysis and hospital planning.
Publications on COVID-19 Co-Authored by PPML Collaborators
2022
Asabor EN, Warren JL, Cohen T. Racial/ethnic segregation and access to COVID-19 testing: Spatial distribution of COVID-19 testing sites in the four largest highly segregated cities in the United States. Am J Public Health. 2022;112(3):518-526. doi:10.2105/AJPH.2021.306558
Assomou SA, Peterson A, Ginman E, James T, Pierre CM, Hamilton S, Chapman S, Goldie J, Koenig R, Mendez-Escobar E, Leaver H, Graham R, Crichlow R, Weaver T, Cotterell S, Valdez G, De Las Nueces D, Scott NA, Linas BP, Cherry PM. Addressing inequities in SARS-CoV-2 vaccine uptake: The Boston Medical Center Health System experience. Ann Intern Med. 2022;175(6):879-884. doi:10.7326/M22-0028
Barocas JA, Savinkina A, Lodi S, Epstein RL, Bouton TC, Sperring H, Hsu HE, Jacobson KR, Schechter-Perkins EM, Linas BP, White LF. Projected long-term impact of the COVID-19 pandemic on hepatitis C outcomes in the United States: A modelling study. Clin Infect Dis. 2022;75(1):e1112-e1119. doi:10.1093/cid/ciab779
Bilinski A, Ciaranello A, Fitzpatrick MC, Giardina J, Shah M, Salomon JA, Kendall EA. Estimated transmission outcomes and costs of SARS-CoV-2 diagnostic testing, screening, and surveillance strategies among a simulated population of primary school students. JAMA Pediatr. 2022;176(7):679-689. doi:10.1001/jamapediatrics.2022.1326
Chin ET, Leidner D, Zhang Y, Long E, Prince L, Schrag SJ, Verani JR, Wiegand RE, Alarid-Escudero F, Goldhaber-Fiebert JD, Studdert DM, Andrews JR, Salomon JA. Effectiveness of COVID-19 vaccines among incarcerated people in California state prisons: Retrospective cohort study. Clin Infect Dis. 2022;75(1):e838-e845. doi:10.1093/cid/ciab1032
Giardina J, Bilinski A, Fitzpatrick MC, Kendall EA, Linas BP, Salomon J, Ciaranello AL. Model-estimated association between simulated US elementary school-related SARS-CoV-2 transmission, mitigation interventions, and vaccine coverage across local incidence levels. JAMA Netw Open. 2022;5(2):e2147827. doi:10.1001/jamanetworkopen.2021.47827
Gonsalves GS, Salomon JA, Thornhill T, Paltiel AD. Adventures in COVID-19 policy modeling: Education edition. Curr HIV/AIDS Rep. 2022;19(1):94-100. doi:10.1007/s11904-021-00592-9
Haber NA, Clarke-Deelder E, Feller A, Smith ER, Salomon JA, MacCormack- Gelles B, Stone EM, Bolster-Foucault C, Daw JR, Hatfield LA, Fry CE, Boyer CB, Ben-Michael E, Joyce CM, Linas BS, Schmid I, Au EH, Wieten SE, Jarrett B, Axfors C, Nguyen VT, Griffin BA, Bilinski A, Stuart EA. Problems with evidence assessment in COVID-19 health policy impact evaluation: A systematic review of study design and evidence strength. BMJ Open. 2022;12(1):e053820. doi:10.1136/bmjopen-2021-053820
Kishore N, Taylor AR, Jacob PE, Vembar N, Cohen T, Buckee CO, Menzies NA. Evaluating the reliability of mobility metrics from aggregated mobile phone data as proxies for SARS-CoV-2 transmission in the USA: A population-based study. Lancet Digit Health. 2022;4(1):e27-e36. doi:10.1016/S2589-7500(21)00214-4
Klaassen F, Chitwood MH, Cohen T, Pitzer VE, Russi M, Swartwood NA, Salomon JA, Menzies NA. Population immunity to pre-Omicron and Omicron SARS-CoV-2 variants in US states and counties through December 1, 2021. Clin Infect Dis. 2022;ciac438. doi:10.1093/cid/ciac438
Ma KC, Hale JE, Grad YH, Alter G, Luzuriaga K, Eaton RB, Fischinger S, Kaur D, Brody R, Siddiqui SM, Leach D, Brown CM, Klevens RM, Madoff L, Comeau AM. Trends in SARS-CoV-2 seroprevalence in Massachusetts estimated from newborn screening specimens. Clin Infect Dis. 2022;75(1):e105-e113. doi:10.1093/cid/ciac158
Rao IJ, Brandeau ML. Sequential allocation of vaccine to control an infectious disease. Math Biosci. 2022;351:108879. doi:10.1016/j.mbs.2022.108879
Salomon JA, Bilinski A. Evaluating the performance of Centers for Disease Control and Prevention COVID-19 community levels as leading indicators of COVID-19 mortality. Ann Intern Med. 2022;175(9):1240-1249. doi:10.7326/M22-0803
Tai CG, Maragakis LL, Connolly S, DiFiori J, Anderson DJ, Grad YH, Mack CD. Association between COVID-19 booster vaccination and omicron infection in a highly vaccinated cohort of players and staff in the National Basketball Association. JAMA. 2022;328(2):209-211. doi:10.1001/jama.2022.9479
2021
Alarid-Escudero F, Gracia V, Luviano A, Roa J, Peralta Y, Reitsma MB, Claypool AL, Salomon JA, Studdert DM, Andrews JR, Goldhaber-Fiebert JD, Stanford-CIDE Coronavirus Simulation Model (SC-COSMO) Modeling Consortium. Dependence of COVID-19 policies on end-of-year holiday contacts in Mexico City Metropolitan Area: A modeling study. MDM Policy Pract. 2021;6(2):23814683211049249. doi: 10.1177/23814683211049249
Bilinski A, Emanuel E, Salomon JA, Venkataramani A. Better late than never: Trends in COVID-19 infection rates, risk perceptions, and behavioral responses in the USA. J Gen Intern Med. 2021;36(6):1825-1828. doi:10.1007/s11606-021-06633-8
Bilinski A, Salomon JA, Giardina J, Ciaranello A, Fitzpatrick MC. Passing the test: A model-based analysis of safe school-reopening strategies. Ann Intern Med. 2021;174(8):1090-1100. doi:10.7326/M21-0600
Bubar KM, Reinholt K, Kissler SM, Lipsitch M, Cobey S, Grad YH, Larremore DB. Model-informed COVID-19 vaccine prioritization strategies by age and serostatus. Science. 2021;371(6532):916-921. doi:10.1126/science.abe6959
Chin ET, Leidner D, Ryckman T, Liu YE, Prince L, Alarid-Escudero F, Andrews JR, Salomon JA, Goldhaber-Fiebert JD, Studdert DM. COVID-19 vaccine acceptance in California state prisons. N Engl J Med. 2021;385(4):374-376. doi:10.1056/NEJMc2105282
Chin ET, Leidner D, Zhang Y, Long E, Prince L, Li Y, Andrews JR, Studdert DM, Goldhaber-Fiebert JD, Salomon JA. Effectiveness of the mRNA-1273 vaccine during a SARS-CoV-2 Delta outbreak in a prison. N Engl J Med. 2021;385(24):2300-2301. doi:10.1056/NEJMc2114089
Chin ET, Ryckman T, Prince L, Leidner D, Alarid-Escudero F, Andrews JR, Salomon JA, Studdert DM, Goldhaber-Fiebert JD. COVID-19 in the California state prison system: An observational study of decarceration, ongoing risks, and risk factors. J Gen Intern Med. 2021;36(10):3096-3102. doi:10.1007/s11606-021-07022-x
Cobey S, Larremore DB, Grad YH, Lipsitch M. Concerns about SARS-CoV-2 evolution should not hold back efforts to expand vaccination. Nat Rev Immunol. 2021;21(5):330-335. doi:10.1038/s41577-021-00544-9
Fung HF, Martinez L, Alarid-Escudero F, Salomon JA, Studdert DM, Andrews JR, Goldhaber-Fiebert JD; SC-COSMO Modeling Group. The household secondary attack rate of SARS-CoV-2: A rapid review. Clin Infect Dis. 2021;73(Suppl 2):S138-S145. doi:10.1093/cid/ciaa1558
Gonsalves GS, Copple JT, Paltiel AD, Fenichel EP, Bayham J, Abraham M, Kline D, Malloy S, Rayo MF, Zhang N, Faulkner D, Morey DA, Wu F, Thornhill T, Iloglu S, Warren JL. Maximizing the efficiency of active case finding for SARS-CoV-2 using bandit algorithms. Med Decis Making. 2021;41(8):970-977. doi: 10.1177/0272989X211021603.
Guan G, Dery Y, Yechezkel M, Ben-Gal I, Yamin D, Brandeau ML. Early detection of COVID-19 outbreaks using human mobility data. PLoS One. 2021;16(7):e0253865. doi:10.1371/journal.pone.0253865
Greene SK, McGough SF, Culp GM, Graf LE, Lipsitch M, Menzies NA, Kahn R. Nowcasting for real-time COVID-19 tracking in New York City: An evaluation using reportable disease data from early in the pandemic. JMIR Public Health Surveill. 2021 Jan 15;7(1):e25538. doi:10.2196/25538
Haber NA, Clarke-Deelder E, Salomon JA, Feller A, Stuart EA. Impact evaluation of coronavirus disease 2019 policy: A guide to common design issues. Am J Epidemiol. 2021;190(11):2474-2486. doi:10.1093/aje/kwab185
James LP, Salomon JA, Buckee CO, Menzies NA. The use and misuse of mathematical modeling for infectious disease policymaking: Lessons for the COVID-19 pandemic. Med Decis Making. 2021;41(4):379-385. doi:10.1177/0272989X21990391
Kahn R, Kennedy-Shaffer L, Grad YH, Robins JM, Lipsitch M. Potential biases arising from epidemic dynamics in observational seroprotection studies. Am J Epidemiol. 2021;190(2):328-335. doi:10.1093/aje/kwaa188
Kissler SM, Fauver JR, Mack C, Olesen SW, Tai C, Shiue KY, Kalinich CC, Jednak S, Ott IM, Vogels CBF, Wohlgemuth J, Weisberger J, DiFiori J, Anderson DJ, Mancell J, Ho DD, Grubaugh ND, Grad YH. Viral dynamics of acute SARS-CoV-2 infection and applications to diagnostic and public health strategies. PLoS Biol. 2021;19(7):e3001333. doi:10.1371/journal.pbio.3001333
Kissler SM, Fauver JR, Mack C, Tai CG, Breban MI, Watkins AE, Samant RM, Anderson DJ, Metti J, Khullar G, Baits R, MacKay M, Salgado D, Baker T, Dudley JT, Mason CE, Ho DD, Grubaugh ND, Grad YH. Viral dynamics of SARS-CoV-2 variants in vaccinated and unvaccinated persons. N Engl J Med. 2021;385(26):2489-2491. doi:10.1056/NEJMc2102507
Larremore DB, Bubar KM, Grad YH. Implications of test characteristics and population seroprevalence on 'immune passport' strategies. Clin Infect Dis. 2021;72(9):e412-e414. doi:10.1093/cid/ciaa1019
Larremore DB, Fosdick BK, Bubar KM, Zhang S, Kissler SM, Metcalf CJE, Buckee CO, Grad YH. Estimating SARS-CoV-2 seroprevalence and epidemiological parameters with uncertainty from serological surveys. Elife. 2021;10:e64206. doi:10.7554/eLife.64206
Linas BP, Savinkina A, Barbosa C, Mueller PP, Cerdá M, Keyes K, Chhatwal J. A clash of epidemics: Impact of the COVID-19 pandemic response on opioid overdose. J Subst Abuse Treat. 2021;120:108158. doi:10.1016/j.jsat.2020.108158
Ma KC, Menkir TF, Kissler S, Grad YH, Lipsitch M. Modeling the impact of racial and ethnic disparities on COVID-19 epidemic dynamics. Elife. 2021;10:e66601. doi:10.7554/eLife.66601
Malloy GSP, Puglisi L, Brandeau ML, Harvey TD, Wang EA. Effectiveness of interventions to reduce COVID-19 transmission in a large urban jail: A model- based analysis. BMJ Open. 2021;11(2):e042898. doi:10.1136/bmjopen-2020-042898
McQuaid CF, Vassall A, Cohen T, Fiekert K, White RG. The impact of COVID-19 on TB: A review of the data. Int J Tuberc Lung Dis. 2021;25(6):436-446. doi:10.5588/ijtld.21.0148
Ng TC, Cheng HY, Chang HH, Liu CC, Yang CC, Jian SW, Liu DP, Cohen T, Lin HH. Comparison of estimated effectiveness of case-based and population-based interventions on COVID-19 containment in Taiwan. JAMA Intern Med. 2021 Jul 1;181(7):913-921. doi:10.1001/jamainternmed.2021.1644
Paltiel AD. Responding to SARS-CoV-2 on college campuses-Only beginning to understand what works and why. JAMA Netw Open. 2021;4(12):e2138904. doi:10.1001/jamanetworkopen.2021.38904
Paltiel AD, Schwartz JL. Assessing COVID-19 prevention strategies to permit the safe opening of residential colleges in fall 2021. Ann Intern Med. 2021;174(11):1563-1571. doi:10.7326/M21-2965
Paltiel AD, Schwartz JL, Zheng A, Walensky RP. Clinical outcomes of a COVID-19 vaccine: Implementation over efficacy. Health Aff (Millwood). 2021;40(1):42-52. doi:10.1377/hlthaff.2020.02054
Paltiel AD, Zheng A, Sax PE. Clinical and economic effects of widespread rapid testing to decrease SARS-CoV-2 Transmission. Ann Intern Med. 2021;174(6):803-810. doi:10.7326/M21-0510
Paltiel AD, Zheng A, Schwartz JL. Speed versus efficacy: Quantifying potential tradeoffs in COVID-19 vaccine deployment. Ann Intern Med. 2021;174(4):568-570. doi:10.7326/M20-7866
Pitzer VE, Chitwood M, Havumaki J, Menzies NA, Perniciaro S, Warren JL, Weinberger DM, Cohen T. The impact of changes in diagnostic testing practices on estimates of COVID-19 transmission in the United States. Am J Epidemiol. 2021;190(9):1908-1917. doi:10.1093/aje/kwab089
Puglisi LB, Malloy GSP, Harvey TD, Brandeau ML, Wang EA. Estimation of COVID-19 basic reproduction ratio in a large urban jail in the United States. Ann Epidemiol. 2021;53:103-105. doi:10.1016/j.annepidem.2020.09.002
Rao IJ, Brandeau ML. Optimal allocation of limited vaccine to control an infectious disease: Simple analytical conditions. Math Biosci. 2021;337:108621. doi:10.1016/j.mbs.2021.108621
Rao IJ, Brandeau ML. Optimal allocation of limited vaccine to minimize the effective reproduction number. Math Biosci. 2021;339:108654. doi:10.1016/j.mbs.2021.108654
Rao IJ, Vallon JJ, Brandeau ML. Effectiveness of face masks in reducing the spread of COVID-19: A model-based analysis. Med Decis Making. 2021;41(8):988-1003. doi:10.1177/0272989X211019029
Reitsma MB, Claypool AL, Vargo J, Shete PB, McCorvie R, Wheeler WH, Rocha DA, Myers JF, Murray EL, Bregman B, Dominguez DM, Nguyen AD, Porse C, Fritz CL, Jain S, Watt JP, Salomon JA, Goldhaber-Fiebert JD. Racial/ethnic disparities in COVID-19 exposure risk, testing, and cases at the subcounty level in California. Health Aff (Millwood). 2021;40(6):870-878. doi:10.1377/hlthaff.2021.00098
Reitsma MB, Goldhaber-Fiebert JD, Salomon JA. Quantifying and benchmarking disparities in COVID-19 vaccination rates by race and ethnicity. JAMA Netw Open. 2021;4(10):e2130343. doi:10.1001/jamanetworkopen.2021.30343
Reitsma MB, Salomon JA, Goldhaber-Fiebert JD. Mapping inequality in SARS-CoV-2 household exposure and transmission risk in the USA. J Gen Intern Med. 2021;36(5):1476-1478. doi:10.1007/s11606-021-06603-0
Ryckman T, Chin ET, Prince L, Leidner D, Long E, Studdert DM, Salomon JA, Alarid-Escudero F, Andrews JR, Goldhaber-Fiebert JD. Outbreaks of COVID-19 variants in US prisons: A mathematical modelling analysis of vaccination and reopening policies. Lancet Public Health. 2021;6(10):e760-e770. doi:10.1016/S2468-2667(21)00162-6
Salomon JA, Reinhart A, Bilinski A, Chua EJ, La Motte-Kerr W, Rönn MM, Reitsma MB, Morris KA, LaRocca S, Farag TH, Kreuter F, Rosenfeld R, Tibshirani RJ. The US COVID-19 trends and impact survey: Continuous real-time measurement of COVID-19 symptoms, risks, protective behaviors, testing, and vaccination. Proc Natl Acad Sci U S A. 2021;118(51):e2111454118. doi:10.1073/pnas.2111454118
Schultes O, Clarke V, Paltiel AD, Cartter M, Sosa L, Crawford FW. COVID-19 testing and case rates and social contact among residential college students in Connecticut during the 2020-2021 academic year. JAMA Netw Open. 2021;4(12):e2140602. doi:10.1001/jamanetworkopen.2021.40602
Sinha P, Linas BP. Combination therapy with Tocilizumab and Dexamethasone cost-effectively reduces coronavirus disease 2019 mortality. Clin Infect Dis. 2021;73(11):2116-2118. doi:10.1093/cid/ciab409
Toumi A, Zhao H, Chhatwal J, Linas BP, Ayer T. Association of limited in-person attendance in US National Football League and National Collegiate Athletic Association games with county-level COVID-19 cases. JAMA Netw Open. 2021;4(8):e2119621. doi:10.1001/jamanetworkopen.2021.19621
Tuite AR, Zhu L, Fisman DN, Salomon JA. Alternative dose allocation strategies to increase benefits from constrained COVID-19 vaccine Supply. Ann Intern Med. 2021;174(4):570-572. doi:10.7326/M20-8137
Yaesoubi R, Havumaki J, Chitwood MH, Menzies NA, Gonsalves G, Salomon JA, Paltiel AD, Cohen T. Adaptive policies to balance health benefits and economic costs of physical distancing interventions during the COVID-19 pandemic. Med Decis Making. 2021;41(4):386-392. doi:10.1177/0272989X21990371
2020
Bilinski A, Emanuel EJ. COVID-19 and excess all-cause mortality in the US and 18 comparison countries. JAMA. 2020;324(20):2100-2102. doi:10.1001/jama.2020.20717
Bilinski A, Mostashari F, Salomon JA. Modeling contact tracing strategies for COVID-19 in the context of relaxed physical distancing measures. JAMA Netw Open. 2020; 3(8):e2019217. doi:10.1001/jamanetworkopen.2020.19217
Buckee CO, Balsari S, Chan J, Crosas M, Dominici F, Gasser U, Grad YH, Grenfell B, Halloran ME, Kraemer MUG, Lipsitch M, Metcalf CJE, Meyers LA, Perkins TA, Santillana M, Scarpino SV, Viboud C, Wesolowski A, Schroeder A. Aggregated mobility data could help fight COVID-19. Science. 2020;368(6487):145-146. doi:10.1126/science.abb8021
Khazanchi R, Beiter ER, Gondi S, Beckman AL, Bilinski A, Ganguli I. County-level association of social vulnerability with COVID-19 cases and deaths in the USA. J Gen Intern Med. 2020;35(9):2784-2787. doi:10.1007/s11606-020-05882-3
Kissler SM, Kishore N, Prabhu M, Goffman D, Beilin Y, Landau R, Gyamfi- Bannerman C, Bateman BT, Snyder J, Razavi AS, Katz D, Gal J, Bianco A, Stone J, Larremore D, Buckee CO, Grad YH. Reductions in commuting mobility correlate with geographic differences in SARS-CoV-2 prevalence in New York City. Nat Commun. 2020;11(1):4674. doi:10.1038/s41467-020-18271-5
Kissler SM, Tedijanto C, Goldstein E, Grad YH, Lipsitch M. Projecting the transmission dynamics of SARS-CoV-2 through the postpandemic period. Science. 2020;368(6493):860-868. doi:10.1126/science.abb5793
Kreuter F, Barkay N, Bilinski A, Bradford A, Chiu S, Eliat R, Fan J, Galili T, Haimovich D, Kim B, LaRocca S, Li Y, Morris K, Presser S, Salomon JA, Sarig T, Stewart K, Stuart EA, Tibshirani R. Partnering with Facebook on a university-based rapid turn-around global survey. Survey Research Methods. 2020;14(2): 159-62. doi:10.18148/srm/2020.v14i2.7761
Lipsitch M, Grad YH, Sette A, Crotty S. Cross-reactive memory T cells and herd immunity to SARS-CoV-2. Nat Rev Immunol. 2020;20(11):709-713. doi:10.1038/s41577-020-00460-4
Paltiel AD, Zheng A, Walensky RP. Assessment of SARS-CoV-2 screening strategies to permit the safe reopening of college campuses in the United States. JAMA Netw Open. 2020;3(7):e2016818. doi:10.1001/jamanetworkopen.2020.16818
Peak CM, Kahn R, Grad YH, Childs LM, Li R, Lipsitch M, Buckee CO. Individual quarantine versus active monitoring of contacts for the mitigation of COVID-19: a modelling study. Lancet Infect Dis. 2020;20(9):1025-1033. doi:10.1016/S1473-3099(20)30361-3
Pitzer VE, Cohen T. Household studies provide key insights on the transmission of, and susceptibility to, SARS-CoV-2. Lancet Infect Dis. 2020;20(10):1103-1104. doi:10.1016/S1473-3099(20)30514-4
Weinberger DM, Chen J, Cohen T, Crawford FW, Mostashari F, Olson D, Pitzer VE, Reich NG, Russi M, Simonsen L, Watkins A, Viboud C. Estimation of excess deaths associated with the COVID-19 pandemic in the United States, March to May 2020. JAMA Intern Med. 2020;180(10):1336-1344. doi:10.1001/jamainternmed.2020.3391
Weinstein MC, Freedberg KA, Hyle EP, Paltiel AD. Waiting for certainty on COVID-19 antibody tests - At what cost? N Engl J Med. 2020;383(6):e37. doi:10.1056/NEJMp2017739