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COVID-19

This work aims to address and better understand the COVID-19 disease and corresponding pandemic via scenario modeling, forecasting and other support measures.

Amid the current pandemic, our group is using the theoretical and empirical approaches consistently implemented in our projects of focus to assist in the global combative efforts against COVID-19. Our current efforts to aid in response to COVID-19 and to better understand the transmission dynamics of the SARS-CoV-2 coronavirus strain are listed below:

Contact Tracing Evaluation and Strategic Support Application (ConTESSA)

ConTESSA is a contact tracing application developed for contact tracing program managers. It is meant to indicate the impacts of current programs, as well as emphasize areas in need of greater focus to reduce COVID-19 transmission in identified communities. The scenarios generated by the application are applicable at both the household and community level. This app is in collaboration with Johns Hopkins Bloomberg School of Public Health researchers. The application can be found here: https://iddynamics.jhsph.edu/apps/connect/contessa/ .

COVID-19 Scenario Pipeline

This scenario pipeline is a public shared code (via GitHub) used for scenario forecasting and can assist in creating reports for various government entities. The model was designed to be as versatile as possible, allowing for its use with varied parameters (i.e. different spatial scales given the shapefiles, population data and COVID-19 confirmed case data available). The pipeline has been used to support several partners including the state of California and the national US response. Access to the pipeline can be found here: https://github.com/HopkinsIDD/COVIDScenarioPipeline .

Health Intervention Tracking (HIT-COVID)

HIT-COVID is a live database focused on the collection of data related to global health COVID-19 intervention policies at the national and first-level administrative units. The intervention policies of interest are believed to have a direct impact on disease transmission. The data is anticipated to assist in the national and subnational governmental determinants of closing or reopening sectors of society. This work is in collaboration with the Boston University School of Public Health. The database can be found here: https://akuko.io/post/covid-intervention-tracking .

2019 Novel Coronavirus Research Compendium (NCRC)

The NCRC is a centralized, curated location for novel research on the SARS-CoV-2 coronavirus strain and the COVID-19 disease. The research is grouped by general topic, with new topic-related reviews continually made available. This is a collaborative effort between the Johns Hopkins School of Public Health and the School of Medicine. The compendium can be found here: https://ncrc.jhsph.edu .

Understanding SARS-COV-2 Transmission with Serologic Data

We are working with multiple collaborators, including those at Massachusetts General Hospital and Hôpitaux universitaires de Genève (Switzerland) to better characterize the human antibody response to SARS-COV-2 infections and to use these data to better understand key aspects of SARS-COV-2 transmission.

SARS-CoV-2 Genomics

We are working with groups across Johns Hopkins University to sequence the SARS-CoV-2 genome from patient samples to better understand the lineages circulating in the National Capital Region. As part of this collaboration, we have published over 100 viral genomes from the region to public databases (including GISAID and NCBI Genbank) and are working to integrate these data with epidemiological models to further characterize transmission dynamics.

COVID-19 Training Initiative

The COVID-19 Training Initiative draws on the resources at the Bloomberg School of Public Health and Johns Hopkins University to provide free online courses and tools, tailored training for public health departments in the US, and additional training for the Baltimore Health Corps. Training materials developed by the Initiative can be found here: https://www.jhsph.edu/practice/covid-19-resources/courses-and-modules/ .

Principal Investigator

Andrew Azman Assistant Scientist

M. Kate Grabowski Assistant Professor

Emily Gurley Associate Scientist

Elizabeth C. Lee Research Associate

Kyu Han Lee Research Associate

Justin Lessler Associate Professor

Shaun Truelove Assistant Scientist

Updates #covid19

1 week 2 days ago

RT @KateGrabowski: #COVID19 #transmission models are ubiquitous and critical to informing policy, but often poorly understood. This p… https://t.co/mwxUOfCKAQ
4 months 6 days ago

RT @LucyStats: 📅🎄 We are officially 14 days, or one #COVID19 quarantine, from Christmas Since folks are likely considering quara… https://t.co/0cDitzMZlL
4 months 4 weeks ago

RT @JustinLessler: 1,928 US #Covid19 deaths yesterday. Last day with over 1,900 was May 7. The cases to double the current rate are al… https://t.co/6M5o7aOjyp
5 months 13 hours ago

RT @JustinLessler: My thoughts on the need for better defining what our goals are in #COVID19 control as we enter a new phase of the p… https://t.co/vNFhlNglRb
5 months 1 week ago

RT @reichlab: Post-doc position for helping with modeling at the #COVID19 Forecast Hub still accepting applications. Come join th… https://t.co/bYSM4bKnVS
5 months 4 weeks ago

RT @JustinLessler: This is exactly the point. #COVID19 testing is a tool on the way to a solution, not the solution itself. https://t.co/yqzWBWnI07
5 months 4 weeks ago

RT @JohnsHopkinsSPH: "As we confront new stages of the #COVID19 pandemic over the coming months and years, overdispersion can help us be… https://t.co/5JAo12HcmO
6 months 1 week ago

RT @JustinLessler: Contrasts to @QifangB to on the successful defense of her dissertation. I assume one of the first purely #COVID19 d… https://t.co/D9bGfq0jdI
8 months 4 weeks ago

RT @NMRelleno: Excited to take over the @societyforepi Twitter account for the day! Follow along for insights into how #COVID19 is… https://t.co/SSCSSwFyim
10 months 16 hours ago

RT @JustinLessler: An important thread from @JHIDDynamics alum @NMRelleno . It both highlights the impact of #COVID19 on native commun… https://t.co/PuOjHGkH6w
10 months 1 week ago

Excellent work by @andrewazman providing insights into #COVID19 transmission from Swiss serosurveys https://t.co/JxGFrCLl2r
10 months 1 week ago

RT @JustinLessler: We are looking for an R shiny developer too help us implement an app to help guide contact tracing programs for… https://t.co/581IO1iEMy

Funders

Bloomberg Philanthropies

Federal Emergency Management Agency (FEMA)

Johns Hopkins Health System

State of California

Collaborators

Boston University School of Public Health

Hôpitaux Universitaires de Genève (HUG)

Johns Hopkins Applied Physics Laboratory

Johns Hopkins Bloomberg School of Public Health

Johns Hopkins School of Medicine

Publications

6 Apr 2021

A scenario modeling pipeline for COVID-19 emergency planning

Lemaitre JC, Grantz KH, Kaminsky J, Meredith HR, Truelove SA, Lauer SA, Keegan LT, Shah S, Wills J, Kaminsky K, Perez‐Saez J, Lessler J, Lee EC

Sci. Rep., 2021: 11: 7534, 10.1038/s41598-021-86811-0

12 Apr 2021

Coordinated Strategy for a Model-Based Decision Support Tool for Coronavirus Disease, Utah, USA

Meredith HR, Arehart E, Grantz KH, Beams A, Sheets T, Nelson R, Zhang Y, Vinik RG, Barfuss D, Pettit JC, McCaffrey K, Dunn AC, Good M, Frattaroli S, Samore MH, Lessler J, Lee EC, Keegan LT

Emerg Infect Dis, 2021: 27(5): 10.3201/eid2705.203075

2 Feb 2021

Insight into the practical performance of RT-PCR testing for SARS-CoV-2 using serological data: a cohort study

Zhang Z, Bi Q, Fang S, Wei L, Wang X, He J, Wu Y, Liu X, Gao W, Zhang R, Gong W, Su Q, Azman AS, Lessler J, Zou X

Lancet Microbe, 2021: 2(2): E79-E87, 10.1016/S2666-5247(20)30200-7

1 Aug 2020

Epidemiology and transmission of COVID-19 in 391 cases and 1286 of their close contacts in Shenzhen, China: a retrospective cohort study

Bi Q, Wu Y, Mei S, Ye C, Zou X, Zhang Z, Liu X, Wei L, Truelove SA, Tong Zhang T, Gao W, Cheng C, Tang X, Wu X, Wu Y, Sun B, Huang S, Sun Y, Zhang J, Ma T, Lessler J, Feng T

Lancet Infect Dis, 2020: 20 (8): 911-919, 10.1016/S1473-3099(20)30287-5

5 May 2020

The Incubation Period of Coronavirus Disease 2019 (COVID-19) From Publicly Reported Confirmed Cases: Estimation and Application

Lauer SA, Grantz KH, Bi Q, Jones FK, Zheng Q, Meredith HR, Azman AS, Reich NG, Lessler J

Ann Intern Med, 2020: 172 (9): 577-582, 10.7326/M20-0504

23 Sep 2020

Healthy donor T-cell responses to common cold coronaviruses and SARS-CoV-2

Woldemeskel BA, Kwaa AK, Garliss CC, Laeyendecker O, Ray SC, Blankson JN

J Clin Invest, 2020: 10.1172/JCI143120

10 Sep 2020

SARS-CoV-2 Antibody Avidity Responses in COVID-19 Patients and Convalescent Plasma Donors

Benner SE, Patel EU, Laeyendecker O, Pekosz A, Littlefield K, Eby Y, Fernandez RE, Miller J, Kirby CS, Keruly M, Klock E, Baker OR, Schmidt HA, Shrestha R, Burgess I, Bonny TS, Clarke W, Caturegli P, Sullivan D, Shoham S, Quinn TC, Bloch EM, Casadevall A, Tobian AAR, Redd AD

J Infect Dis, 2020: 10.1093/infdis/jiaa581

7 Aug 2020

Sex, age, and hospitalization drive antibody responses in a COVID-19 convalescent plasma donor population

Klein SL, Pekosz A, Park HS, Ursin RL, Shapiro JR, Benner SE, Littlefield K, Kumar S, Naik HM, Betenbaugh M, Shrestha R, Wu AA, Hughes RM, Burgess I, Caturegli P, Laeyendecker O, Quinn TC, Sullivan DJ, Shoham S, Redd AD, Bloch EM, Casadevall A, Tobian AAR

J Clin Invest, 2020: 10.1172/JCI142004

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