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Challenges of COVID-19 Case Forecasting in the US, 2020-2021

ContributorsLopez, Velma Korcid; Cramer, Estee Yorcid; Pagano, Robert; Drake, John M; O'Dea, Eamon B; Adee, Madeline; Ayer, Turgay; Chhatwal, Jagpreet; Dalgic, Ozden O; Ladd, Mary A; Linas, Benjamin P; Mueller, Peter P; Xiao, Jadeorcid; Bracher, Johannes; Castro Rivadeneira, Alvaro J; Gerding, Aaron; Gneiting, Tilmannorcid; Huang, Yuxin; Jayawardena, Dasuni; Kanji, Abdul H; Le, Khoa; Mühlemann, Anja; Niemi, Jaradorcid; Ray, Evan L; Stark, Ariane; Wang, Yijinorcid; Wattanachit, Nutcha; Zorn, Martha W; Pei, Sen; Shaman, Jeffrey; Yamana, Teresa Korcid; Tarasewicz, Samuel R; Wilson, Daniel J; Baccam, Sid; Gurung, Heidi; Stage, Steve; Suchoski, Brad; Gao, Leiorcid; Gu, Zhiling; Kim, Myungjinorcid; Li, Xinyiorcid; Wang, Guannan; Wang, Lily; Wang, Yueying; Yu, Shan; Gardner, Lauren; Jindal, Sonia; Marshall, Maximilian; Nixon, Kristen; Dent, Juanorcid; Hill, Alison L; Kaminsky, Joshua; Lee, Elizabethorcid; Lemaitre, Joseph Corcid; Lessler, Justin; Smith, Claire P; Truelove, Shaun; Kinsey, Matt; Mullany, Luke C; Rainwater-Lovett, Kaitlinorcid; Shin, Lauren; Tallaksen, Katharine; Wilson, Shelby; Karlen, Dean; Castro, Lauren; Fairchild, Geoffrey; Michaud, Isaac; Osthus, Dave; Bian, Jiang; Cao, Wei; Gao, Zhifeng; Lavista Ferres, Juan; Li, Chaozhuo; Liu, Tie-Yan; Xie, Xing; Zhang, Shun; Zheng, Shun; Chinazzi, Matteoorcid; Davis, Jessica T; Mu, Kunpeng; Pastore Y Piontti, Ana; Vespignani, Alessandro; Xiong, Xinyue; Walraven, Robert; Chen, Jinghui; Gu, Quanquan; Wang, Lingxiao; Xu, Panorcid; Zhang, Weitong; Zou, Difan; Gibson, Graham Casey; Sheldon, Daniel; Srivastava, Ajitesh; Adiga, Aniruddha; Hurt, Benjamin; Kaur, Gursharn; Lewis, Bryan; Marathe, Madhav; Peddireddy, Akhil Sai; Porebski, Przemyslaw; Venkatramanan, Srinivasan; Wang, Lijing; Prasad, Pragati V; Walker, Jo W; Webber, Alexander E; Slayton, Rachel B; Biggerstaff, Matthew; Reich, Nicholas G; Johansson, Michael A
Published inPLOS computational biology, vol. 20, no. 5, e1011200
Publication date2024-05
First online date2024-05-06
Abstract

During the COVID-19 pandemic, forecasting COVID-19 trends to support planning and response was a priority for scientists and decision makers alike. In the United States, COVID-19 forecasting was coordinated by a large group of universities, companies, and government entities led by the Centers for Disease Control and Prevention and the US COVID-19 Forecast Hub (https://covid19forecasthub.org). We evaluated approximately 9.7 million forecasts of weekly state-level COVID-19 cases for predictions 1-4 weeks into the future submitted by 24 teams from August 2020 to December 2021. We assessed coverage of central prediction intervals and weighted interval scores (WIS), adjusting for missing forecasts relative to a baseline forecast, and used a Gaussian generalized estimating equation (GEE) model to evaluate differences in skill across epidemic phases that were defined by the effective reproduction number. Overall, we found high variation in skill across individual models, with ensemble-based forecasts outperforming other approaches. Forecast skill relative to the baseline was generally higher for larger jurisdictions (e.g., states compared to counties). Over time, forecasts generally performed worst in periods of rapid changes in reported cases (either in increasing or decreasing epidemic phases) with 95% prediction interval coverage dropping below 50% during the growth phases of the winter 2020, Delta, and Omicron waves. Ideally, case forecasts could serve as a leading indicator of changes in transmission dynamics. However, while most COVID-19 case forecasts outperformed a naïve baseline model, even the most accurate case forecasts were unreliable in key phases. Further research could improve forecasts of leading indicators, like COVID-19 cases, by leveraging additional real-time data, addressing performance across phases, improving the characterization of forecast confidence, and ensuring that forecasts were coherent across spatial scales. In the meantime, it is critical for forecast users to appreciate current limitations and use a broad set of indicators to inform pandemic-related decision making.

Keywords
  • COVID-19 / epidemiology
  • COVID-19 / transmission
  • Humans
  • Forecasting / methods
  • United States / epidemiology
  • SARS-CoV-2
  • Pandemics / statistics & numerical data
  • Computational Biology
  • Models, Statistical
UNIGE affiliation entities Not a UNIGE publication
Funding
  • NIAID NIH HHS [T32 AI165369]
  • NCIRD CDC HHS [U01 IP001137]
  • ACL HHS [U01IP001122]
  • NCIRD CDC HHS [U01 IP001122]
  • ACL HHS [U01IP001137]
  • NIGMS NIH HHS [R35 GM119582]
  • NIGMS NIH HHS [R01 GM109718]
  • NIAID NIH HHS [R01 AI163023]
  • Swiss National Science Foundation [200021172578]
  • National Science Foundation [DMS-2203207]
  • Laboratory Directed Research and Development [20200700ER]
  • Centers for Disease Control and Prevention [6U01IP001137]
  • National Institute of General Medical Sciences [1R01GM109718]
  • University of Virginia Strategic Investment Fund [SIF160]
  • Fondo Integrativo Speciale Ricerca [EPIDOC, FISR-2020IP-04249]
  • Defense Threat Reduction Agency [HDTRA1-19-D-0007]
  • Virginia Department of Health [VDH-21-501-0141]
  • Council of State and Territorial Epidemiologists [5 NU38OT000297]
  • Division of Intramural Research, National Institute of Allergy and Infectious Diseases [AI163023]
Citation (ISO format)
LOPEZ, Velma K et al. Challenges of COVID-19 Case Forecasting in the US, 2020-2021. In: PLOS computational biology, 2024, vol. 20, n° 5, p. e1011200. doi: 10.1371/journal.pcbi.1011200
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Identifiers
Journal ISSN1553-734X
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