Publications – Center for Communicable Disease Dynamics

Inferring bacterial transmission dynamics using deep sequencing genomic surveillance data.

Author(s): Senghore M, Read H, Oza P, Johnson S, Passarelli-Araujo H, Taylor BP, Ashley S, Grey A, Callendrello A, Lee R, Goddard MR, Lumley T, Hanage WP, Wiles SJournal: Nat CommunPMID: 37907520 October 2023

Identifying and interrupting transmission chains is important for controlling infectious diseases. One way to identify transmission pairs - two hosts…

A simple model of how heterogeneous disease transmission impacts the emergence of variants and their detection

Author(s): Taylor BP, Hanage WPJournal: medRxiv October 2023

Understanding how epidemics spread within societies is key for establishing adequate infection control responses. Dynamical models provide a means to…

Quantitatively assessing early detection strategies for mitigating COVID-19 and future pandemics

Author(s): Liu AB, Lee D, Jalihal AP, Hanage WP, Springer MJournal: medRxiv June 2023

Researchers and policymakers have proposed systems to detect novel pathogens early by monitoring samples from hospital patients, wastewater, and air…

Estimated preventable COVID-19-associated deaths due to non-vaccination in the United States.

Author(s): Jia KM, Hanage WP, Lipsitch M, Johnson AG, Amin AB, Ali AR, Scobie HM, Swerdlow DLJournal: Eur J EpidemiolPMID: 37093505 April 2023

While some studies have previously estimated lives saved by COVID-19 vaccination, we estimate how many deaths could have been averted…

Addressing spatial misalignment in population health research: a case study of US congressional district political metrics and county health data.

Author(s): Nethery RC, Testa C, Tabb LP, Hanage WP, Chen JT, Krieger NJournal: medRxivPMID: 36711902 January 2023

Areal spatial misalignment, which occurs when data on multiple variables are collected using mismatched boundary definitions, is a ubiquitous obstacle…

Association of body mass index with COVID-19-related neurologic sequelae: a retrospective cohort study

Author(s): Elsayed S, Cabrera A, Oullette D, Jones PM, Dhami R, Hanage WPJournal: Clin Exp Med December 2022

We sought to explore the relationship between body mass index (BMI) and neurologic outcomes following acute COVID-19 infection. We conducted a…

The evolving roles of US political partisanship and social vulnerability in the COVID-19 pandemic from February 2020-February 2021.

Author(s): Kaashoek J, Testa C, Chen JT, Stolerman LM, Krieger N, Hanage WP, Santillana MJournal: PLOS Glob Public HealthPMID: 36962752 December 2022

The COVID-19 pandemic has had intense, heterogeneous impacts on different communities and geographies in the United States. We explore county-level…

Relationship of political ideology of US federal and state elected officials and key COVID pandemic outcomes following vaccine rollout to adults: April 2021-March 2022.

Author(s): Krieger N, Testa C, Chen JT, Hanage WP, McGregor AJJournal: Lancet Reg Health AmPMID: 36338898 December 2022

Scant research, including in the United States, has quantified relationships between the political ideologies of elected representatives and COVID-19 outcomes…

Monkeypox Virus Infections in Humans.

Author(s): Elsayed S, Bondy L, Hanage WPJournal: Clin Microbiol RevPMID: 36374082 November 2022

Human monkeypox is a viral zoonosis endemic to West and Central Africa that has recently generated increased interest and concern…

Lineage abundance estimation for SARS-CoV-2 in wastewater using transcriptome quantification techniques.

Author(s): Baaijens JA, Zulli A, Ott IM, Nika I, van der Lugt MJ, Petrone ME, Alpert T, Fauver JR, Kalinich CC, Vogels CBF, Breban MI, Duvallet C, McElroy KA, Ghaeli N, Imakaev M, Mckenzie-Bennett MF, Robison K, Plocik A, Schilling R, Pierson M, Littlefield R, Spencer ML, Simen BB, Yale SARS-CoV-2 Genomic Surveillance Initiative., Hanage WP, Grubaugh ND, Peccia J, Baym MJournal: Genome BiolPMID: 36348471 November 2022

Effectively monitoring the spread of SARS-CoV-2 mutants is essential to efforts to counter the ongoing pandemic. Predicting lineage abundance from…