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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.

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 members


Bilinski A, Emanuel EJ. COVID-19 and excess all-cause mortality in the US and 18 comparison countries. JAMA. 2020;324(20):2100-2102.

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; doi: 10.1007/s11606-021-06633-8. Online ahead of print.

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.

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 Aug;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 Feb 26;371(6532):916-921. doi: 10.1126/science.abe6959.

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 Apr 10;368(6487):145-146. doi: 10.1126/science.abb8021. 

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 May 12. doi: 10.1056/NEJMc2105282. Epub ahead of print.

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 Dec 9;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 Oct;36(10):3096-3102. doi: 10.1007/s11606-021-07022-x. 

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. 2020 Oct 12: doi: 10.1093/cid/ciaa1558.

Gonsalves GS, Salomon JA, Thornhill T, Paltiel AD. Adventures in COVID-19 Policy Modeling: Education Edition. Curr HIV/AIDS Rep. 2021 Nov 26:1–7. doi: 10.1007/s11904-021-00592-9. Epub ahead of print.

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 Nov;41(8):970-977. doi: 10.1177/0272989X211021603. Epub 2021 Jun 14. PMID: 34120510; PMCID: PMC8484027.

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. PMID: 33406053; PMCID: PMC7812916.

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. doi: 10.1177/0272989X21990391. Online ahead of print.

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 Feb 1;190(2):328-335. doi: 10.1093/aje/kwaa188. PMID: 32870977; PMCID: PMC7499481.

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.

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. 2021 Nov 2:S2589-7500(21)00214-4. doi: 10.1016/S2589-7500(21)00214-4. 

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 Jul 12;19(7):e3001333. doi: 10.1371/journal.pbio.3001333. 

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 Sep 16;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. 

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.

Larremore DB, Bubar KM, Grad YH. Implications of test characteristics and population seroprevalence on 'immune passport' strategies. Clin Infect Dis. 2020;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 Mar 5;10:e64206. doi: 10.7554/eLife.64206. 

Lipsitch M, Grad YH, Sette A, Crotty S. Cross-reactive memory T cells and herd immunity to SARS-CoV-2. Nat Rev Immunol. 2020 Nov;20(11):709-713. doi: 10.1038/s41577-020-00460-4.

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 May 18;10:e66601. doi: 10.7554/eLife.66601. 

Paltiel AD, Schwartz JL, Zheng A, Walensky RP. Clinical Outcomes Of A COVID-19 Vaccine: Implementation Over Efficacy. Health Aff (Millwood). 2021 Jan;40(1):42-52. 

Paltiel AD, Schwartz JL. Assessing COVID-19 Prevention Strategies to Permit the Safe Opening of Residential Colleges in Fall 2021. Ann Intern Med. 2021 Nov;174(11):1563-1571. doi: 10.7326/M21-2965.

Paltiel AD, Zheng A, Sax PE. Clinical and economic effects of widespread rapid testing to decrease SARS-CoV-2 Transmission. Ann Intern Med. 2021. doi: 10.7326/M21-0510. Online ahead of print.

Paltiel AD, Zheng A, Schwartz JL. Speed Versus Efficacy: Quantifying Potential Tradeoffs in COVID-19 Vaccine Deployment. Ann Intern Med. 2021 Jan 5:M20-7866. doi: 10.7326/M20-7866.

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.

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 Infectious Disease 2020; S1473-3099(20)30361-3.

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 Sep 1;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. 2020;S1047-2797(20)30347-1.

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 May 12:101377hlthaff202100098. doi: 10.1377/hlthaff.2021.00098. Epub ahead of print.

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. doi: 10.1007/s11606-021-06603-0. Online ahead of print.

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.

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 Oct;6(10):e760-e770. doi: 10.1016/S2468-2667(21)00162-6.

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

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 Jul 1:e203391.

Weinstein MC, Freedberg KA, Hyle EP, Paltiel AD. Waiting for Certainty on Covid-19 Antibody Tests - At What Cost? N Engl J Med. 2020 Jun 5. doi:10.1056/NEJMp2017739. 

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. doi: 10.1177/0272989X21990371. Online ahead of print.