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Work on COVID-19

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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 


Asabor EN, Warren JL, Cohen TRacial/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 JRSalomon JAEffectiveness 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 ADAdventures 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 NAEvaluating 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 JAMenzies NAPopulation 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 MLSequential allocation of vaccine to control an infectious disease. Math Biosci. 2022;351:108879. doi:10.1016/j.mbs.2022.108879

Salomon JABilinski AEvaluating 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


Alarid-Escudero F, Gracia V, Luviano A, Roa J, Peralta Y, Reitsma MB, Claypool AL, Salomon JA, Studdert DM, Andrews JRGoldhaber-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 ASalomon 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 JRSalomon JAGoldhaber-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 JDSalomon JAEffectiveness 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 JRSalomon JA, Studdert DM, Goldhaber-Fiebert JDCOVID-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 JRGoldhaber-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 MLEarly 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 NAThe 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 YHViral 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 YHViral 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 YHImplications 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 YHEstimating 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 ADResponding 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 TThe 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 MLOptimal 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 MLOptimal 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 JAGoldhaber-Fiebert JDRacial/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 MBGoldhaber-Fiebert JDSalomon JAQuantifying 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 MBSalomon JAGoldhaber-Fiebert JDMapping 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 JRGoldhaber-Fiebert JDOutbreaks 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 BPCombination 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 JAAlternative 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 JAPaltiel ADCohen TAdaptive 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


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 JAModeling 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 YHReductions 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 THousehold 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 ADWaiting for certainty on COVID-19 antibody tests - At what cost? N Engl J Med. 2020;383(6):e37. doi:10.1056/NEJMp2017739