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DIEPS Publications Archive
Find more information on the Division of International Epidemiology and Population Studies (DIEPS)
2024
- Differential impact of COVID-19 non-pharmaceutical interventions on the epidemiological dynamics of respiratory syncytial virus subtypes A and B , co-authored by Fogarty’s Samantha Bents, Nídia Trovão, and Cécile Viboud
Scientific Reports, June 24, 2024 - Impacts of human mobility on the citywide transmission dynamics of 18 respiratory viruses in pre- and post-COVID-19 pandemic years , co-authored by Fogarty’s Amanda C. Perofsky, Chelsea L. Hansen, and Cécile Viboud
Nature Communications, May 16, 2024 - Charting the evolutionary course of influenza: Insights into epidemic dynamics
Global Health Matters, March/April 2024 - The risk of mpox importation and subsequent outbreak potential in Chinese mainland: a retrospective statistical modelling study , co-authored by Fogarty’s Kaiyuan Sun
Infectious Diseases of Poverty, February 29, 2024 - Synchrony of Bird Migration with Global Dispersal of Avian Influenza Reveals Exposed Bird Orders , co-authored by Fogarty’s Nidia Trovão
Nature Communications, February 6, 2024 - Comparative evolution of influenza A virus H1 and H3 head and stalk domains across host species , co-authored by Fogarty’s Nidia Trovão and Joshua Cherry
mBio, January 16, 2024 - Effects of Cooking with Liquefied Petroleum Gas or Biomass on Stunting in Infants , authored by HAPIN Trial investigators, supported by Fogarty and other NIH Institutes and Centers
New England Journal of Medicine, January 4, 2024 - Liquefied Petroleum Gas or Biomass Cooking and Severe Infant Pneumonia , authored by HAPIN Trial investigators, supported by Fogarty and other NIH Institutes and Centers
New England Journal of Medicine, January 4, 2024
2023
- Evaluation of the US COVID-19 Scenario Modeling Hub for informing pandemic response under uncertainty , co-authored by Fogarty’s Cécile Viboud
Nature Communications, November 20, 2023 - A comprehensive SARS-CoV-2 and COVID-19 review, Part 2: host extracellular to systemic effects of SARS-CoV-2 infection , co-authored by Fogarty’s Nídia Trovão
European Journal of Human Genetics, November 8, 2023 - Evolutionary and spatiotemporal analyses reveal multiple introductions and cryptic transmission of SARS-CoV-2 VOC/VOI in Malta , co-authored by Fogarty's Nídia S. Trovão
Microbiology Spectrum, October 6, 2023 - Accelerating Bayesian inference of dependency between mixed-type biological traits , co-authored by Fogarty’s Nídia S. Trovão and Josh Cherry
PLOS Computational Biology, August 28, 2023 - Core mitochondrial genes are down-regulated during SARS-CoV-2 infection of rodent and human hosts , co-authored by Fogarty’s Nídia S. Trovão
Science Translational Medicine, August 9, 2023 - Sequential viral introductions and spread of BA.1 across Pakistan provinces during the Omicron wave , co-authored by Fogarty’s Nídia S. Trovão, David Spiro, and Zeba Rasmussen
BMC Genomics, August 3, 2023 - Behavioral factors and SARS-CoV-2 transmission heterogeneity within a household cohort in Costa Rica , co-authored by Fogarty’s Kaiyuan Sun
Communications Medicine, July 22, 2023 - Evaluation: Division of International Epidemiology and Population Studies , conducted November 2022, posted online June 2023
- T Residues Preceded by Runs of G Are Hotspots of T→G Mutation in Bacteria , authored by Fogarty's Joshua Cherry
Genome Biology and Evolution, June 1, 2023 - Inferring the differences in incubation-period and generation-interval distributions of the Delta and Omicron variants of SARS-CoV-2 , co-authored by Fogarty's Cécile Viboud
Proceedings of the National Academy of Sciences of the United States of America, May 30, 2023 - Application of Phylodynamic Tools to Inform the Public Health Response to COVID-19: Qualitative Analysis of Expert Opinions , co-authored by Fogarty's Nídia Trovão
JMIR Formative Research, April 21, 2023 - Direct and indirect mortality impacts of the COVID-19 pandemic in the United States, March 1, 2020 to January 1, 2022 , co-authored by Fogarty's Cécile Viboud
elife, February 22, 2023 - A Retrospective Modeling Study of the Targeted Non-Pharmaceutical Interventions During the Xinfadi Outbreak in the Early Stage of the COVID-19 Pandemic - Beijing, China, 2020 , co-authored by Fogarty's Kaiyuan Sun
China CDC Weekly, February 3, 2023 - Restriction Endonuclease-Based Modification-Dependent Enrichment (REMoDE) of DNA for Metagenomic Sequencing , co- authored by Fogarty's Joshua Cherry
Applied and Environmental Microbiology, January 31, 2023 - Rapidly shifting immunologic landscape and severity of SARS-CoV-2 in the Omicron era in South Africa , co-authored by Fogarty’s Kaiyuan Sun & Cécile Viboud
Nature Communications, January 16, 2023 - Global dissemination of influenza A virus is driven by wild bird migration through arctic and subarctic zones , co-authored by Fogarty's Nídia Trovão
Molecular Ecology, January 2023
2022
- Estimation of disease burden and clinical severity of COVID-19 caused by Omicron BA.2 in Shanghai, February-June 2022 , co-authored by Fogarty’s Kaiyuan Sun
Emerging Microbes & Infections, November 21, 2022 - Assessing the feasibility of sustaining SARS-CoV-2 local containment in China in the era of highly transmissible variants , co-authored by Fogarty’s Kaiyuan Sun & Cécile Viboud
BMC Medicine, November 15, 2022 - Global dissemination of influenza A virus is driven by wild bird migration through arctic and subarctic zones , co-authored by Fogarty's Nídia S Trovão
Molecular Ecology, October 14, 2022 - Liquefied Petroleum Gas or Biomass for Cooking and Effects on Birth Weight authored by HAPIN Trial investigators, supported by Fogarty and other NIH Institutes and Centers
New England Journal of Medicine, October 10, 2022 - COVID-19 Exposure Assessment Tool (CEAT): Exposure quantification based on ventilation, infection prevalence, group characteristics, and behavior , co-authored by Fogarty's Nídia S Trovão
Science Advances, September 30, 2022 - Origins and Evolution of Seasonal Human Coronaviruses co-authored by Fogarty’s James Otieno, Joshua Cherry, David Spiro, and, Nídia Trovão
Viruses, July 15, 2022 - A systematic review of household energy transition in low and middle income countries , co-authored by Fogarty's Joshua Rosenthal
Energy Research and Social Science, April 2022 - Evolutionary history and introduction of SARS-CoV-2 Alpha VOC/B.1.1.7 in Pakistan through international travelers , co-authored by Fogarty's Nídia Trovão, Zeba Rasmussen, and David Spiro
Virus Evolution, March 17, 2022 - Mortality Associated With Influenza and Respiratory Syncytial Virus in the US, 1999-2018 , co-authored by Fogarty's Chelsea Hansen and Dr. Cecile Viboud
JAMA Network Open, February 28, 2022 - Assessing the Effects of Cooking Fuels on Anopheles Mosquito Behavior: An Experimental Study in Rural Rwanda , co-authored by Fogarty's Joshua Rosenthal
The American Journal of Tropical Medicine and Hygiene, February 21, 2022 - Determinants of vaccine coverage and timeliness in a northern Pakistani village , co-authored by Fogarty's Chelsea Hansen and Zeba Rasmussen
PLOS One, February 17, 2022 - Epidemiology and genetic diversity of SARS-CoV-2 lineages circulating in Africa , featuring Fogarty's David J Spiro and Nídia S Trovão as co-authors
iScience, February 5, 2022 - SARS-CoV-2 introductions and early dynamics of the epidemic in Portugal , co-authored by Fogarty's Dr. Nídia Trovão
Communications Medicine, January 28, 2022 - The direct and indirect effects of the COVID-19 pandemic on private healthcare utilization in South Africa, March 2020 – September 2021 , co-authored by Fogarty's Amanda Perofsky and Dr. Cecile Viboud
Clinical Infectious Diseases, January 27, 2022 - Association between personal exposure to household air pollution and gestational blood pressure among women using solid cooking fuels in rural Tamil Nadu, India , authored by HAPIN trial investigators
Environmental Research, January 2022
2021
- LPG stove and fuel intervention among pregnant women reduce fine particle air pollution exposures in three countries: Pilot results from the HAPIN trial
Environmental Pollution, December 15, 2021 - SARS-CoV-2 incidence, transmission and reinfection in a rural and an urban setting: results of the PHIRST-C cohort study, South Africa, 2020-2021 , co-authored by Fogarty's Dr. Kaiyuan Sun and Dr. Cecile Viboud
medRxiv, December 4, 2021 - Fidelity an adherence to a liquefied petroleum gas stove and fuel intervention during gestation: the multi-country Household Air Pollution Intervention Network (HAPIN) randomized controlled trial , co-authored by Fogarty's Joshua Rosenthal
International Journal of Environmental Research and Public Health, November 29, 2021 - Synergistic interventions to control COVID-19: Mass testing and isolation mitigates reliance on distancing , co-authored by Fogarty's Dr. Cecile Viboud
PLoS Comput Biol., October 28, 2021 - Recommended reporting items for epidemic forecasting and prediction research: The EPIFORGE 2020 guidelines , co-authored by Fogarty's Dr. Cecile Viboud
PLoS Medicine, October 18, 2021 - Genetic lineage characterization and spatiotemporal dynamics of classical insect-specific flaviviruses: outcomes and limitations , co-authored by Fogarty's Nidia Trovao
Virus Research, October 2, 2021 - Examining the relationships between early childhood experiences and adolescent and young adult health status in a resource-limited population: A cohort study , co-authored by Fogarty's Zeba Rasmussen and Chelsea Hansen
PLoS Medicine, September 28, 2021 - Social groups constrain the spatiotemporal dynamics of wild sifaka gut microbiomes , co-authored by Fogarty's Amanda Perofsky
Molecular Ecology, September 24, 2021 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 , co-authored by Fogarty's Dr. Cecile Viboud
medRxiv, September 2, 2021- A comprehensive look at the COVID-19 pandemic death toll , co-authored by Dr. Cecile Viboud,
eLife, August 12, 2021 - Tracing the Source of Influenza A Virus Zoonoses in Interconnected Circuits of Swine Exhibitions , featuring Fogarty's Amanda Perofsky as co-lead author
The Journal of Infectious Diseases, August 1, 2021 Genetic and evolutionary analysis of SARS-CoV-2 circulating in the region surrounding Islamabad, Pakistan , co-authored by Fogarty's Nidia Trovao
Infection Genetics and Evolution, July 14, 2021- Proposal for Human Respiratory Syncytial Virus Nomenclature below the Species Level , co-authored by Fogarty's Nidia Trovao
Emerging Infectious Diseases, June 27, 2021 - Strategic testing approaches for targeted disease monitoring can be used to inform pandemic decision-making , co-authored by Fogarty's Dr. Cecile Viboud
PLoS Biology, June 17, 2021 - Toward the use of neural networks for influenza prediction at multiple spatial resolutions , co-authored by Fogarty's Dr. Cecile Viboud
Science Advances, June 16, 2021 - Hospital utilization rates for influenza and RSV: a novel approach and critical assessment , co-authored by Fogarty's Dr. Cecile Viboud
Population Health Metrics, June 14, 2021 - RSV genomic diversity and the development of a globally effective RSV intervention , co-authored by Fogarty's Dr. Cecile Viboud and Dr. David Spiro
Vaccine, May 18, 2021 - Modeling of Future COVID-19 Cases, Hospitalizations, and Deaths, by Vaccination Rates and Nonpharmaceutical Intervention Scenarios - United States, April-September 2021 , co-authored by Fogarty's Dr. Cecile Viboud
MMWR, May 14, 2021 - The impact of relaxing interventions on human contact patterns and SARS-CoV-2 transmission in China , co-authored by Fogarty's Dr. Cecile Viboud
Science Advances, May 7, 2021 - Modeling networks: How Fogarty made epidemiology history during the COVID-19 pandemic
May / June 2021 Global Health Matters - Model-based evaluation of alternative reactive class closure strategies against COVID-19 , co-authored by Fogarty's Dr. Cecile Viboud
medRxiv, April 23, 2021 - A risk assessment tool for resumption of research activities during the COVID-19 pandemic for field trials in low resource settings , co-authored by Fogarty's Joshua Rosenthal
BMC Medical Research Methodology, April 12, 2021 - Cryptic transmission of SARS-CoV-2 and the first COVID-19 wave in Europe and the United States , co-authored by Fogarty's Dr. Kaiyuan Sun and Dr. Cecile Viboud
medRxiv, March 26, 2021 - Genomic diversity of SARS-CoV-2 during early introduction into the Baltimore-Washington metropolitan area , co-authored by Fogarty's Nidia Trovao
JCI Insight, March 22, 2021 - Infectivity, susceptibility, and risk factors associated with SARS-CoV-2 transmission under intensive contact tracing in Hunan, China , co-authored by Fogarty's Dr. Kaiyuan Sun and Dr. Cecile Viboud
Nature Communications, March 9, 2021 Serological evidence of human infection with SARS-CoV-2: a systematic review and meta-analysis , co-authored by Fogarty's Dr. Cecile Viboud
Lancet Glob Health, March 8, 2021- Cryptic transmission of SARS-CoV-2 and the first COVID-19 wave , co-authored by Fogarty's Dr. Cecile Viboud
Nature, October 25, 2021
2020
- Substantial and sustained reduction in under-5 mortality, diarrhea, and pneumonia in Oshikhandass, Pakistan: evidence from two longitudinal cohort studies 15 years apart , co-authored by Fogarty scientists
BMC Public Health , May 24, 2020 - Transmission heterogeneities, kinetics, and controllability of SARS-CoV-2 , featuring Fogarty's Dr. Kaiyuan Sun as lead author, and Fogarty's Dr. Cecile Viboud as co-senior author
Science, November 24, 2020 - Preparing for the future implementation of respiratory syncytial virus vaccines , co-authored by Dr. David Spiro
The Lancet Respiratory Medicine, Jan 21, 2020
2019
- Molecular characterization of respiratory syncytial viruses circulating in a paediatric cohort in Amman, Jordan [Open access] , co-authored by Fogarty scientists
Microbial Genomics, Sep 18, 2019 - Population-level mathematical modeling of antimicrobial resistance: a systematic review [Open access] , co-authored by Fogarty scientists
BMC Medicine, Apr 24, 2019
2018
- Disease modelers mark Fogarty’s 50th anniversary
Nov / Dec 2018 Global Health Matters - Fogarty International Center collaborative networks in infectious disease modeling: Lessons learnt in research and capacity building
Epidemics via PubMed, Oct 23, 2018 (online) - Emergence and evolution of novel reassortant influenza A viruses in canines in southern China
mBio, Jun 5, 2018 - How historical disease detectives are solving mysteries of the 1918 flu
The Conversation, Mar 5, 2018 - A review of the 1918 herald pandemic wave: importance for contemporary pandemic response strategies
Annals of Epidemiology, Feb 27, 2018 - Infection forecasts powered by big data , featuring Fogarty scientist Dr. Cecile Viboud
Nature Outlook, Mar 7, 2018 - Fogarty provides training to build expertise in managing disease outbreaks
Jan / Feb 2018 Global Health Matters
2017
- Co-founder of Fogarty's RAPIDD modeling program Dr Ellis McKenzie is remembered
May / Jun 2017 Global Health Matters
2016
- Report:
DIEPSReview2016.pdf (2.08 MB) (2016) - NIH-led effort examines use of big data for infectious disease surveillance
Fogarty/NIH news, Nov 14, 2016 - Big Data for Infectious Disease Surveillance and Modeling
Supplement to the Journal of Infectious Diseases, Dec 1, 2016 - Your flu risk may be linked to the year you were born , with Fogarty's Dr Cecile Viboud
CNN, Nov 10, 2016 - First flu is forever , co-authored by Fogarty's Dr Cecile Viboud
Science, November 11, 2016 - Timing and periodicity of influenza epidemics
co-authored by Fogarty's Dr. Cecile Viboud
PNAS, Nov 3, 2016 (online) - Fogarty trains Pakistani scientists in biorisk management
Jul / Aug 2016 Global Health Matters - Fogarty's RAPIDD program has catalyzed the field of infectious disease modeling
May / Jun 2016 Global Health Matters - Ebola, Zika modelers aim to inform policy decisions
Mar / Apr 2016 Global Health Matters - Global Mortality Impact of the 1957–1959 Influenza Pandemic
The Journal of Infectious Diseases, March 1, 2016 - What dose of medication is best to prevent the evolution of drug resistance?
Penn State news, January 28, 2016
2015
- Global swine trade facilitates evolution, spread of flu
Mar / Apr 2015 Global Health Matters
2014
- Study probes link between intestinal infections, child development
Nov / Dec 2014 Global Health Matters
2013
- Fogarty study sheds light on role of climate in influenza transmission
NIH News, March 8, 2013
2011
- Solving a math puzzle to stop infectious disease
Sep / Oct 2011 Global Health Matters - Fogarty supported scientists work to slow the spread of drug-resistant disease organisms
Penn State Science News, June 22, 2011 - RAPIDD program veteran tracks viruses transmitted by bats
May / Jun 2011 Global Health Matters - Mexican flu study by Fogarty supports social distancing
May / Jun 2011 Global Health Matters
2009
- Report:
Updated March 13, 2025