COVID-19 Findings, Simulations

From March 2020 – March 2023, we supplied inference, projections, simulations of intervention effects to the CDC, NYC DOHMH, NYCH+H, NY State DOH and others.  Posting, publications and links are provided below.

Data Links: US County-resolved projections.  NYC projections.  US Surge Capacity Projections.

Visualization Links: US Surge Capacity Line Graphs. US Surge Capacity Maps.

Multi-model Comparisons: Delphi.

2024

• Yamana, T.K., S. Rajagopal, D.C. Hall Jr, A.M. Moustafa, A. Feder, A. Ahmed, C. Bianco, R. Harris, S. Coffin, A.E. Campbell, S. Pei S, J. Chang Mell, P.J. Planet and J. Shaman, 2024: A two-variant model of SARS-COV-2 transmission: Estimating the characteristics of a newly emerging strain. BMC Infectious Diseases, 24:938, doi:10.1186/s12879-024-09823-x.
• Lopez, V.,…, S. Pei, J. Shaman, T.K. Yamana,…, M.A. Johansson, 2024: Challenges of COVID-19 case forecasting in the US, 2020-2021. PLOS Computational Biology, 20(5):e1011200, doi:10.1371/journal.pcbi.1011200.Yang, W. and J. Shaman, 2024: Reconciling the efficacy and effectiveness of masking on epidemic outcomes. Journal of the Royal Society Interface, 21(212):20230666, doi:10.1098/rsif.2023.0666.
• He, K., S. Foerster, N.M. Vora, K. Blaney, C. Keeley, L. Hendricks, J.K. Varma, T. Long, J. Shaman and S. Pei, 2024: Evaluating completion rates of COVID-19 contact tracing surveys in New York City. BMC Public Health, 24:414, doi:10.1186/s12889-024-17920-4.
• Boldea, O., A. Alipoor, S. Pei, J. Shaman and G. Rozhnova, 2024: Age-specific transmission dynamics of SARS-CoV-2 during the first two years of the pandemic. PNAS Nexus, 3:1-14, doi:10.1093/pnasnexus/pgae024. [arRxiv initial version]

2023

• Howerton, E.,…, M. Galanti, T. Yamana, S. Pei, J. Shaman,…, J. Lessler, 2023: Evaluation of the US COVID-19 Scenario Modeling Hub for informing pandemic response under uncertainty. Nature Communications, 14(1):7260, doi:10.1028/s41467-023-42680-x.
• Dai, K., S. Foerster, N.M. Vora, K. Blaney, C. Keeley, L. Hendricks, J.K. Varma, T. Long, J. Shaman and S. Pei, 2023: Community transmission of SARS-CoV-2 during the Delta wave in New York City. BMC Infectious Diseases, 23:753, doi:10.1186/s12879-023-08735-6.
• Toomre, D., S. Kandula and J. Shaman, 2023: Longitudinal association of COVID hospitalization and death with online search for loss of smell or taste. Emerging Infectious Diseases, 29(8):1711-1713, doi:10.3201/eid2908.230071.
• Yang, W. and J. Shaman, 2023: Development of accurate long-lead COVID-19 forecast. PLOS Computational Biology, 19(7):e1011278, doi:10.1371/journal.pcbi.1011278. [medRxiv initial version]
• Lopez, V.,…,S. Pei, J. Shaman, T.K. Yamana,…, M.A. Johansson, 2023: Challenges of COVID-19 case forecasting in the US, 2020-2021 -19. medRxiv, 290732, doi:10.1101/2023.05.30.23290732.
• Yang, W. and J. Shaman, 2023: Reconciling the efficacy and effectiveness of masking on epidemic outcomes. medRxiv, 289803, doi:10.1101/2023.05.10.23289803
• Yamana, T.K., M. Galanti, S. Pei, M. Di Fusco, F.J. Angulo, M.M. Moran, F. Khan, D.L. Swerdlow and J. Shaman, 2023: The impact of COVID-19 vaccination in the US: averted burden of SARS-CoV-2 related cases, hospitalizations and deaths. PLOS ONE, 18(4):e1010945, doi:10.1371/journal.pone.0275699.
• Santurtún, A. and J. Shaman, 2023: Work accidents, climate change and COVID-19. Science of the Total Environment, 871:162129, doi:10.1016/j.scitotenv.2023.162129.
• Borchering, R.K.,…, M. Galanti, T. Yamana, S. Pei, J. Shaman,…, J. Lessler, 2023: Impact of SARS-CoV-2 vaccination of children ages 5-11 years on COVID-19 disease burden and resilience to new variants in the United States, November 2021-March 2022: a multi-model study. The Lancet Regional Health – Americas, 17:100398, doi:10.1016/j.lana.2022.100398.

2022

• Casey, J.A., M.A. Kioumourtzoglou, E. Ogburn, A. Melamed, J. Shaman, S. Kandula, A. Neophytou, K. Darwin, J. Sheffield and C. Gyamfi-Bannerman: 2022. Long-term fine particulate matter concentrations and prevalence of severe acute respiratory syndrome coronavirus 2: differential relationships by socioeconomic status among pregnant individuals in New York City. American Journal of Epidemiology, 191(11):1897-1905, doi:10.1093/aje/kwac139.
• Pei, S., S. Kandula, J.C. Vega, W. Yang, S. Foerster, C. Thompson, J. Baumgartner, S.D. Ahuja, K. Blakey, J.K. Varma, T. Long and J. Shaman: 2022. Contact tracing reveals community transmission of COVID-19 in New York City. Nature Communications, 13:6307, doi:10.1038/s41467-022-34130-x.
• Yang, W. and J. Shaman, 2022: COVID-19 pandemic dynamics in South Africa and epidemiological characteristics of three variants of concern (Beta, Delta, and Omicron). eLife, 11:e78933, doi:10.7554/eLife.78933. [medRxiv initial version]
• Schneider, T., O.R.A. Dunbar, J. Wu, L. Boettcher, D. Burov, A. Garbuno-Inigo, G.L. Wagner, S. Pei, C. Daraio, R. Ferrari and J. Shaman, 2022: Epidemic management and control through risk-dependent individual contact interventions. PLOS Computational Biology, 18(6):e1010171, doi:10.1371/journal.pcbi.1010171. [arXiv initial version]
• Yang, W. and J. Shaman, 2022: COVID-19 pandemic dynamics in India, the SARS-CoV-2 Delta variant, and implications for vaccination. Journal of the Royal Society Interface, 19(191):20210900, doi:10.1098/rsif.2021.0900. [medRxiv initial version]
• Cramer, E.Y.,…,T.K. Yamana, S. Pei, J. Shaman,…, N.G. Reich, 2022: Evaluation of individual and ensemble probabilistic forecasts of COVID-19 mortality in the US. Proceedings of the National Academy of Sciences, 119(15):e2113561119, doi:10.1073/pnas.2113561119.
• Yang, W. and J. Shaman, 2022: Viral replication dynamics could critically modulate vaccine effectiveness and should be accounted for when assessing new SARS-CoV-2 variants. Influenza and Other Respiratory Viruses, 16(2):366-367, doi:10.1111/irv.12961. [arXiv initial version]
• Kannoth, S., S. Kandula and J. Shaman, 2022: The association between early country-level COVID-19 testing capacity and later COVID-19 mortality outcomes. Influenza and  Other Respiratory Viruses, 16(1):56-62, doi:10.1111/irv.12906 [medRxiv, initial version.]

2021

• Pei, S., T.K. Yamana, S. Kandula, M. Galanti and J. Shaman. Burden and characteristics of COVID-19 in the United States during 2020. Nature, 598:338-341, doi:10.1038/s41586-021-03914-4. [medRxiv initial version]
• Lieberman-Cribbin, W., M. Galanti and J. Shaman, 2021: Socioeconomic disparities in SARS-CoV-2 serological testing and positivities in New York City. Open Forum Infectious Diseases, 8(12):ofab534, doi:10.1093/ofid/ofab534.
• Schneider, T., O.R.A. Dunbar, J. Fun, L. Boettcher, D. Burov, A. Garbuno-Inigo, G.L. Wagner, S. Pei, C. Daraio, R. Ferrari and J. Shaman. Epidemic management and control through risk-dependent individual contact interventions. arXiv, 2109.10970.
• Galanti, M., S. Pei, T.K. Yamana, F.J. Angulo, A. Charos, F. Khan, K. Shea, D. Swerdlow and J. Shaman, 2021: Non-pharmaceutical interventions and inoculation rate shape SARS-CoV-2 vaccination campaign success. Epidemiology and Infection, 149:e222, doi:10.1017/S095026882100217X. [medRxiv, initial version]
• Qi, Y., J. Shaman and S. Pei, 2021: Quantifying the effects of COVID-19 non-pharmaceutical interventions on influenza transmission in the United States. The Journal of Infectious Diseases, 224(9):1500-1508, doi:10.1093/infdis/jiab485.
• Truelove, S…M. Galanti, T.K. Yamana, S. Pei, J. Shaman…C. Viboud. Projected resurgence of COVID-19 in the United States in July-December 2021 resulting from the increased transmissibility of the Delta variant and faltering vaccination. medRxiv, 262748, doi:10.1101/2021.08.28.21262748.
• Yang, W. and J. Shaman, 2021: Development of a model-inference system for estimating epidemiological characteristics of SARS-CoV-2 variants of concern. Nature Communications, 12:5573, doi:10.1038/s41467-021-25913-9. [medRxiv, initial version]
• Kandula, S. and J. Shaman, 2021: Investigating associations between COVID-19 mortality and population level health and socioeconomic indicators in the United States: A modeling study. PLOS Medicine, 18(7):e1003693, doi:10.1371/journal.pmed.1003693. [medRxiv, 250468, doi:10.1101/2021.01.25.21250468]
• Ma, Y., S. Pei, J. Shaman, R. Dubrow and K. Chen, 2021: Role of meteorological factors in the transmission of SARS-CoV-2 in the United States. Nature Communications, 12:3602, doi:10.1038/s41467-021-23866-7. [medRxiv, 231472, doi:10.1101/2020.11.13.20231472]
• Zebrowski, A., A. Rundle, S. Pei, T. Yaman, W. Yang, B.G. Carr, S. Sims, R. Doorley, N. Schluger, J. Shaman and C. Branas, 2021: A spatiotemporal tool to project hospital critical care capacity and mortality from COVID-19 in US counties. American Journal of Public Health, 111:1113-1122, doi:10.2105/AJPH.2021.306220.
• Yang, W., J. Shaff and J. Shaman, 2021: COVID-19 transmission dynamics and effectiveness of public health interventions in New York City during the 2020 spring pandemic wave. Journal of the Royal Society Interface, 18(175):20200691, doi:10.1098/rsif.2020.0822. [medRxiv, 190710, doi:10.1101/2020.09.08.20190710].
• Yang, W., S. Kandula and J. Shaman. Simulating the impact of different vaccination policies on the COVID-19 pandemic in New York City. medRxiv, 250228, doi:10.1101/2021.01.21.21250228.
• Lamb, M. R., S. Kandula and J. Shaman, 2021: Differential COVID-19 case positivity in New York City neighborhoods: socioeconomic factors and mobility. Influenza and Other Respiratory Viruses, 15(2):209-217, doi:10.1111/irv.12816. [medRxiv, 144188, doi:10.1101/2020.06.27.20144188].
• Rader, B., L.F. White, M.R. Burns, J. Chen, J. Brilliant, J. Cohen, J. Shaman, L. Brilliant, M.U.G. Kraemer, J.B. Hawkins, S.V. Scarpino, C.M. Astley and J.S. Brownstein, 2021: Mask wearing and control of SARS-CoV-2 transmission in the United States. Lancet Digital Health, 3(3):e148-e157, doi:10.1016/S2589-7500(20)30293-4. [medRxiv, 78964, doi:10.1101/2020.08.23.20078964].
• Galanti, M. and J. Shaman, 2021: Direct observations of repeated infections with endemic coronaviruses. The Journal of Infectious Diseases, 223(3):409-415, doi:10.1093/infdis/jiaa392.
• Shaman, J., 2021: An estimation of undetected COVID cases in France. Nature, 590:38-39, doi:10.1038/d41586-020-03513-9.
• Galanti, M., S. Pei, T.K. Yamana, F.J. Angulo, A. Charos, D. Swerdlow and J. Shaman, 2021: Social distancing remains key during vaccinations. Science, 371(6528): 473-474, doi:10.1126/science.abg2326.
• Yang, W., S. Kandula, M. Huynh, S. K. Greene, G. Van Wye, W. Li, H T. Chan, E. McGibbon, A. Yeung, D. Olson, A. Fine and J. Shaman. Estimating the infection fatality risk of COVID-19 in New York City during the spring 2020 pandemic wave: a model-based analysis.  Lancet Infectious Diseases, 21(2):203-212, doi:10.1016/S1473-3099(20)30769-6. [medRxiv initial version]

2020

• Galanti, M., S. Pei, T.K. Yamana, F.J. Angulo, A. Charos, D.L. Swerdlow and J. Shaman. The importance of continued non-pharmaceutical interventions during the upcoming SARS-CoV-2 vaccination campaign. medRxiv, 248784, doi:10.1101/2020.12.23.20248784.
• Shaman, J. and M. Galanti, 2020: Will SARS-CoV-2 become endemic? Science, 370(6516):527-529, doi:10.1126/science.abe5960.
• Cruz, A. T., J. Shaman and P. Dayan, 2020: The challenge of clearly counting COVID-19 in children. Pediatrics, 146(6):e2020031682, doi:10.1542/peds.2020-027425.
• Yang, W., J. Shaff and J. Shaman. COVID-19 transmission dynamics and effectiveness of public health interventions in New York City during the 2020 spring pandemic wave. Journal of the Royal Society Interface [medRxiv, 190710, doi:10.1101/2020.09.08.20190710].
• Pei, S., K. Dahl, T.K. Yamana, R. Licker and J. Shaman, 2020: Compound risks of hurricane evacuation amid the COVID-19 pandemic in the United States. GeoHealth, 4(12):e2020GH000319, doi:10.1029/2020GH000319. [medRxiv initial version]
• Emeruwa, U.N., S. Ona, J. Shaman, A. Turitz, J. D. Wright, C. Gyamfi-Bannerman and A. Melamed, 2020: Associations between built environment, neighborhood socioeconomic status and SARS-CoV-2 infection among pregnant women in New York City. JAMA, 324(4):390-392, doi:10.1001/jama.2020.11370.
• Pei, S., S. Kandula and J. Shaman, 2020: Differential Effects of Intervention Timing on COVID-19 Spread in the United States. Science Advances, 6(49):eabd6370, doi:10.1126/sciadv.abd6370. [medRxiv initial version]
• Shaman, J. Follow South Korea’s Lead.
• Yamana, T., S. Pei and J. Shaman. Projection of COVID-19 Cases and Deaths in the US as Individual States Re-open, May 4,2020. medRxiv, 90670, doi:10.1101/2020.05.04.20090670.
• Pei, S., M. Galanti, T. Yamana and J. Shaman. Reconciling diverse estimates of COVID-19 infection rates.
• Branas, C.C., A. Rundle, S. Pei, W. Yang, B.G. Carr, S. Sims, A. Zebrowski, R. Doorley, N. Schluger, J.W. Quinn, and J. Shaman. Flattening the curve before it flattens us: hospital critical care capacity limits and mortality from novel coronavirus (SARS-CoV2) cases in US counties.  The model output is here.
• Yang, W., S. Kandula and J. Shaman. Eight-week model projections of COVID-19 in New York City.  March 29, 2020.
• Pei, S. and J. Shaman. Simulation of SARS-CoV2 Spread and Intervention Effects in the Continental US with Variable Contact Rates, March 24, 2020.  The model output is posted here.
• Pei, S. and J. Shaman. Initial Simulation of SARS-CoV2 Spread and Intervention Effects in the Continental US. medRxiv, 40303, doi:10.1101/2020.03.21.20040303. Findings also published in New York Times. The model output is posted here.
• Li, R., S. Pei, B. Chen, Y. Song, T. Zhang, W. Yang and J. Shaman, 2020: Substantial undocumented infection facilitates the rapid dissemination of novel coronavirus (SARS-CoV2). Science, 368(6490):489-493, doi:10.1126/science.abb3221.
• Shaman, J. and M. Galanti, 2020: Direct measurement of rates of asymptomatic infection and clinical care-seeking for seasonal coronavirus. medRxiv, 19612, doi:10.1101/2020.01.30.20019612.