Joseph C. Lemaitre
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View article: Scenario Projections of COVID-19 Burden in the US, 2024-2025
Scenario Projections of COVID-19 Burden in the US, 2024-2025 Open
Importance COVID-19 remains a disease with high burden in the US, prompting continued debate about optimal targets for annual vaccination. Objective To project COVID-19 burden in the US for April 2024 to April 2025 under 6 scenarios of imm…
View article: A retrospective analysis of 400 publications reveals patterns of irreproducibility across an entire life sciences research field
A retrospective analysis of 400 publications reveals patterns of irreproducibility across an entire life sciences research field Open
The ReproSci project retrospectively analyzed the reproducibility of 1006 claims from 400 papers published between 1959 and 2011 in the field of Drosophila immunity. This project attempts to provide a comprehensive assessment, 14 years lat…
View article: Inferring the proportion of undetected cholera infections from serological and clinical surveillance in an immunologically naive population
Inferring the proportion of undetected cholera infections from serological and clinical surveillance in an immunologically naive population Open
Most infections with pandemic Vibrio cholerae are thought to result in subclinical disease and are not captured by surveillance. Previous estimates of the ratio of infections to clinical cases have varied widely (2 to 100 infections per ca…
View article: Evaluation of FluSight influenza forecasting in the 2021–22 and 2022–23 seasons with a new target laboratory-confirmed influenza hospitalizations
Evaluation of FluSight influenza forecasting in the 2021–22 and 2022–23 seasons with a new target laboratory-confirmed influenza hospitalizations Open
View article: Evaluation of FluSight influenza forecasting in the 2021–22 and 2022–23 seasons with a new target laboratory-confirmed influenza hospitalizations
Evaluation of FluSight influenza forecasting in the 2021–22 and 2022–23 seasons with a new target laboratory-confirmed influenza hospitalizations Open
Accurate forecasts can enable more effective public health responses during seasonal influenza epidemics. For the 2021–22 and 2022–23 influenza seasons, 26 forecasting teams provided national and jurisdiction-specific probabilistic predict…
View article: Challenges of COVID-19 Case Forecasting in the US, 2020–2021
Challenges of COVID-19 Case Forecasting in the US, 2020–2021 Open
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…
View article: Challenges of COVID-19 Case Forecasting in the US, 2020–2021
Challenges of COVID-19 Case Forecasting in the US, 2020–2021 Open
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…
View article: Potential impact of annual vaccination with reformulated COVID-19 vaccines: Lessons from the US COVID-19 scenario modeling hub
Potential impact of annual vaccination with reformulated COVID-19 vaccines: Lessons from the US COVID-19 scenario modeling hub Open
Background Coronavirus Disease 2019 (COVID-19) continues to cause significant hospitalizations and deaths in the United States. Its continued burden and the impact of annually reformulated vaccines remain unclear. Here, we present projecti…
View article: flepiMoP: The evolution of a flexible infectious disease modeling pipeline during the COVID-19 pandemic
flepiMoP: The evolution of a flexible infectious disease modeling pipeline during the COVID-19 pandemic Open
The COVID-19 pandemic led to an unprecedented demand for projections of disease burden and healthcare utilization under scenarios ranging from unmitigated spread to strict social distancing policies. In response, members of the Johns Hopki…
View article: Inferring the proportion of undetected cholera infections from serological and clinical surveillance in an immunologically naive population
Inferring the proportion of undetected cholera infections from serological and clinical surveillance in an immunologically naive population Open
Most infections with pandemic Vibrio cholerae are thought to result in subclinical disease and are not captured by surveillance. Previous estimates of the ratio of infections to clinical cases have varied widely (2 to 100 infections per ca…
View article: Evaluation of FluSight influenza forecasting in the 2021-22 and 2022-23 seasons with a new target laboratory-confirmed influenza hospitalizations
Evaluation of FluSight influenza forecasting in the 2021-22 and 2022-23 seasons with a new target laboratory-confirmed influenza hospitalizations Open
Accurate forecasts can enable more effective public health responses during seasonal influenza epidemics. Forecasting teams were asked to provide national and jurisdiction-specific probabilistic predictions of weekly confirmed influenza ho…
View article: Evaluation of the US COVID-19 Scenario Modeling Hub for informing pandemic response under uncertainty
Evaluation of the US COVID-19 Scenario Modeling Hub for informing pandemic response under uncertainty Open
Our ability to forecast epidemics far into the future is constrained by the many complexities of disease systems. Realistic longer-term projections may, however, be possible under well-defined scenarios that specify the future state of cri…
View article: Inferring the proportion of undetected cholera infections from serological and clinical surveillance in an immunologically naive population
Inferring the proportion of undetected cholera infections from serological and clinical surveillance in an immunologically naive population Open
Summary Most infections with pandemic Vibrio cholerae are thought to result in subclinical disease and are not captured by surveillance. Previous estimates of the ratio of infections to clinical cases have varied widely (2 to 100). Underst…
View article: Potential impact of annual vaccination with reformulated COVID-19 vaccines: lessons from the U.S. COVID-19 Scenario Modeling Hub
Potential impact of annual vaccination with reformulated COVID-19 vaccines: lessons from the U.S. COVID-19 Scenario Modeling Hub Open
Importance COVID-19 continues to cause significant hospitalizations and deaths in the United States. Its continued burden and the impact of annually reformulated vaccines remain unclear. Objective To project COVID-19 hospitalizations and d…
View article: Informing pandemic response in the face of uncertainty.<i>An evaluation of the U.S. COVID-19 Scenario Modeling Hub</i>
Informing pandemic response in the face of uncertainty.<i>An evaluation of the U.S. COVID-19 Scenario Modeling Hub</i> Open
Our ability to forecast epidemics more than a few weeks into the future is constrained by the complexity of disease systems, our limited ability to measure the current state of an epidemic, and uncertainties in how human action will affect…
View article: Challenges of COVID-19 Case Forecasting in the US, 2020-2021
Challenges of COVID-19 Case Forecasting in the US, 2020-2021 Open
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…
View article: 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
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 Open
Background: The COVID-19 Scenario Modeling Hub convened nine modeling teams to project the impact of expanding SARS-CoV-2 vaccination to children aged 5–11 years on COVID-19 burden and resilience against variant strains. Methods: Teams con…
View article: 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
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 Open
Various (see acknowledgments).
View article: Optimal control of the spatial allocation of COVID-19 vaccines: Italy as a case study
Optimal control of the spatial allocation of COVID-19 vaccines: Italy as a case study Open
While campaigns of vaccination against SARS-CoV-2 are underway across the world, communities face the challenge of a fair and effective distribution of a limited supply of doses. Current vaccine allocation strategies are based on criteria …
View article: 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
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 Open
Summary Background SARS-CoV-2 vaccination of persons aged 12 years and older has reduced disease burden in the United States. The COVID-19 Scenario Modeling Hub convened multiple modeling teams in September 2021 to project the impact of ex…
View article: Epidemicity of cholera spread and the fate of infection control measures
Epidemicity of cholera spread and the fate of infection control measures Open
The fate of ongoing infectious disease outbreaks is predicted through reproduction numbers, defining the long-term establishment of the infection, and epidemicity indices, tackling the reactivity of the infectious pool to new contagions. P…
View article: 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
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 Open
Summary What is already known about this topic? The highly transmissible SARS-CoV-2 Delta variant has begun to cause increases in cases, hospitalizations, and deaths in parts of the United States. With slowed vaccination uptake, this novel…
View article: Effect of specific non-pharmaceutical intervention policies on SARS-CoV-2 transmission in the counties of the United States
Effect of specific non-pharmaceutical intervention policies on SARS-CoV-2 transmission in the counties of the United States Open
View article: Wastewater monitoring outperforms case numbers as a tool to track COVID-19 incidence dynamics when test positivity rates are high
Wastewater monitoring outperforms case numbers as a tool to track COVID-19 incidence dynamics when test positivity rates are high Open
Wastewater-based epidemiology (WBE) has been shown to coincide with, or anticipate, confirmed COVID-19 case numbers. During periods with high test positivity rates, however, case numbers may be underreported, whereas wastewater does not su…
View article: Optimal control of the spatial allocation of COVID-19 vaccines: Italy as a case study
Optimal control of the spatial allocation of COVID-19 vaccines: Italy as a case study Open
While SARS-CoV-2 vaccine distribution campaigns are underway across the world, communities face the challenge of a fair and effective distribution of limited supplies. We wonder whether suitable spatial allocation strategies might signific…
View article: Data for Fernandez-Cassi et al., Wastewater monitoring outperforms case numbers as a tool to track COVID-19 incidence dynamics when test positivity rates are high
Data for Fernandez-Cassi et al., Wastewater monitoring outperforms case numbers as a tool to track COVID-19 incidence dynamics when test positivity rates are high Open
Measured virus concentrations (SARS-CoV-2, surrogates and pepper mild mottle virus) and flow rates for Lugano, Lausanne and Zurich wastewater treatment plants\n\nEpidemiological data (reported case numbers; test positivity rates) for Lugan…
View article: Data for Fernandez-Cassi et al., Wastewater monitoring outperforms case numbers as a tool to track COVID-19 incidence dynamics when test positivity rates are high
Data for Fernandez-Cassi et al., Wastewater monitoring outperforms case numbers as a tool to track COVID-19 incidence dynamics when test positivity rates are high Open
Measured virus concentrations (SARS-CoV-2, surrogates and pepper mild mottle virus) and flow rates for Lugano, Lausanne and Zurich wastewater treatment plants Epidemiological data (reported case numbers; test positivity rates) for Lugano, …
View article: Modeling of Future COVID-19 Cases, Hospitalizations, and Deaths, by Vaccination Rates and Nonpharmaceutical Intervention Scenarios — United States, April–September 2021
Modeling of Future COVID-19 Cases, Hospitalizations, and Deaths, by Vaccination Rates and Nonpharmaceutical Intervention Scenarios — United States, April–September 2021 Open
After a period of rapidly declining U.S. COVID-19 incidence during January-March 2021, increases occurred in several jurisdictions (1,2) despite the rapid rollout of a large-scale vaccination program. This increase coincided with the sprea…
View article: A scenario modeling pipeline for COVID-19 emergency planning
A scenario modeling pipeline for COVID-19 emergency planning Open
View article: Wastewater monitoring outperforms case numbers as a tool to track COVID-19 incidence dynamics when test positivity rates are high
Wastewater monitoring outperforms case numbers as a tool to track COVID-19 incidence dynamics when test positivity rates are high Open
Wastewater-based epidemiology (WBE) has been shown to coincide with, or anticipate, confirmed COVID-19 case numbers. During periods with high test positivity rates, however, case numbers may be underreported, whereas wastewater does not su…