Natalie Exner Dean

Natalie Exner Dean
Emory University | EU · Department of Biostatistics and Bioinformatics

PhD, Biostatistics

About

84
Publications
19,712
Reads
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4,720
Citations
Introduction
Natalie Exner Dean currently works at the Department of Biostatistics, University of Florida. Natalie does research in Biostatistics, Infectious Diseases and Vaccine Trial Design.
Additional affiliations
July 2017 - July 2017
University of Florida
Position
  • Professor
January 2015 - present
University of Florida
Position
  • PostDoc Position
Education
August 2009 - May 2014
Harvard University
Field of study
  • Biostatistics
August 2005 - May 2009
Boston University
Field of study
  • Mathematics/Statistics, Biology

Publications

Publications (84)
Article
Full-text available
Detailed characterization of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission across different settings can help design less disruptive interventions. We used real-time, privacy-enhanced mobility data in the New York City, NY and Seattle, WA metropolitan areas to build a detailed agent-based model of SARS-CoV-2 infection to...
Article
Full-text available
Objective To estimate the change in odds of covid-19 over time following primary series completion of the inactivated whole virus vaccine CoronaVac (Sinovac Biotech) in São Paulo State, Brazil. Design Test negative case-control study. Setting Community testing for covid-19 in São Paulo State, Brazil. Participants Adults aged ≥18 years who were r...
Preprint
Importance The benefit of primary and booster vaccination in people who experienced prior SARS-CoV-2 infection remains unclear. Objective To estimate the effectiveness of a primary (two-dose) and booster (third dose) vaccination against Omicron infection among previously infection people. Design Test-negative case-control study. Setting Yale New...
Article
Background COVID-19 vaccines have proven highly effective among individuals without a previous SARS-CoV-2 infection, but their effectiveness in preventing symptomatic infection and severe outcomes among individuals with previous infection is less clear. We aimed to estimate the effectiveness of four COVID-19 vaccines against symptomatic infection,...
Preprint
Background Large outbreaks of the SARS-CoV-2 Omicron (B.1.1.529) variant have occurred in countries with high coverage of inactivated Covid-19 vaccines, raising urgent questions about effectiveness of these vaccines against disease and hospitalization with Omicron. Methods We conducted a nationwide, test-negative, case-control study of adults who...
Article
Post-authorization observational studies play a key role in understanding COVID-19 vaccine effectiveness following the demonstration of efficacy in clinical trials. While bias due to confounding, selection bias, and misclassification can be mitigated through careful study design, unmeasured confounding is likely to remain in these observational stu...
Article
Importance: An overall household secondary attack rate (SAR) of 18.9% (95% CI, 16.2%-22.0%) through June 17, 2021 was previously reported for SARS-CoV-2. Emerging variants of concern and increased vaccination have affected transmission rates. Objective: To evaluate how reported household SARs changed over time and whether SARs varied by viral va...
Article
How much do COVID-19 vaccines reduce transmission? The answer is a moving target.
Article
Full-text available
We have come a long way since the start of the COVID-19 pandemic-from hoarding toilet paper and wiping down groceries to sending our children back to school and vaccinating billions. Over this period, the global community of epidemiologists and evolutionary biologists has also come a long way in understanding the complex and changing dynamics of se...
Article
The ring vaccination trial is a recently developed approach for evaluating the efficacy and effectiveness of vaccines, modeled after the surveillance and containment strategy of ring vaccination. Contacts and contacts of contacts of a newly identified disease case form a ring, and these rings are randomized as part of a cluster-randomized trial or...
Preprint
Full-text available
We previously reported a household secondary attack rate (SAR) for SARS-CoV-2 of 18.9% through June 17, 2021. To examine how emerging variants and increased vaccination have affected transmission rates, we searched PubMed from June 18, 2021, through January 7, 2022. Meta-analyses used generalized linear mixed models to obtain SAR estimates and 95%C...
Preprint
Full-text available
Background. COVID-19 vaccines have proven highly effective among SARS-CoV-2 naive individuals, but their effectiveness in preventing symptomatic infection and severe outcomes among individuals with prior infection is less clear. Methods. Utilizing national COVID-19 notification, hospitalization, and vaccination datasets from Brazil, we performed a...
Article
Full-text available
Considerable uncertainty surrounds the timeline of introductions and onsets of local transmission of SARS-CoV-2 globally1–7. Although a limited number of SARS-CoV-2 introductions were reported in January and February 20208,9, the narrowness of the initial testing criteria, combined with a slow growth in testing capacity and porous travel screening1...
Article
Full-text available
Outbreaks of emerging pathogens pose unique methodological and practical challenges for the design, implementation, and evaluation of vaccine efficacy trials. Lessons learned from COVID-19 highlight the need for innovative and flexible study design and application to quickly identify promising candidate vaccines. Trial design strategies should be t...
Article
Full-text available
Importance A previous systematic review and meta-analysis of household transmission of SARS-CoV-2 that summarized 54 published studies through October 19, 2020, found an overall secondary attack rate (SAR) of 16.6% (95% CI, 14.0%-19.3%). However, the understanding of household secondary attack rates for SARS-CoV-2 is still evolving, and updated ana...
Preprint
Full-text available
In this report, we provide summary estimates, from publications and reports, of vaccine efficacy (VE) for the COVID-19 vaccines that are being rolled out on a global scale. We find that, on average, the efficacy against any disease with infection is 85% (95% CI: 71 - 93%) after a full course of vaccination. The VE against severe disease, hospitaliz...
Article
Full-text available
We investigated SARS-CoV-2 transmission dynamics in Italy, one of the countries hit hardest by the pandemic, using phylodynamic analysis of viral genetic and epidemiological data. We observed the co-circulation of multiple SARS-CoV-2 lineages over time, which were linked to multiple importations and characterized by large transmission clusters conc...
Preprint
Full-text available
Given the narrowness of the initial testing criteria, the SARS-CoV-2 virus spread through cryptic transmission in January and February, setting the stage for the epidemic wave experienced in March and April, 2020. We use a global metapopulation epidemic model to provide a mechanistic understanding of the global dynamic underlying the establishment...
Article
Full-text available
Comparison of coronavirus disease (COVID-19) case numbers over time and between locations is complicated by limits to virologic testing to confirm severe acute respiratory syndrome coronavirus 2 infection. The proportion of tested individuals who have tested positive (test-positive proportion, TPP) can potentially be used to inform trends in incide...
Preprint
Full-text available
Background/Aims: Novel strategies are needed to make vaccine efficacy trials more robust given the uncertain epidemiology of outbreaks. Spatially resolved mathematical and statistical models can help investigators identify sites at highest risk of future transmission and prioritize these for inclusion in trials. Models can also characterize the unc...
Article
Background Wuhan was the first epicentre of COVID-19 in the world, accounting for 80% of cases in China during the first wave. We aimed to assess household transmissibility of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and risk factors associated with infectivity and susceptibility to infection in Wuhan. Methods This retrospectiv...
Preprint
Full-text available
We investigated SARS-CoV-2 transmission dynamics in Italy, one of the countries hit hardest by the pandemic, using phylodynamic analysis of viral genetic and epidemiological data. We observed the co-circulation of at least 13 different SARS-CoV-2 lineages over time, which were linked to multiple importations and characterized by large transmission...
Preprint
Full-text available
Detailed characterizations of SARS-CoV-2 transmission risk across different social settings can inform the design of targeted and less disruptive non-pharmaceutical interventions (NPI), yet these data have been lacking. Here we integrate real-time, anonymous and privacy-enhanced geolocalized mobility data with census and demographic data in the New...
Article
Full-text available
Importance Crowded indoor environments, such as households, are high-risk settings for the transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Objectives To examine evidence for household transmission of SARS-CoV-2, disaggregated by several covariates, and to compare it with other coronaviruses. Data Source PubMed, searc...
Article
To rapidly evaluate the safety and efficacy of COVID-19 vaccine candidates, prioritizing vaccine trial sites in areas with high expected disease incidence can speed endpoint accrual and shorten trial duration. Mathematical and statistical forecast models can inform the process of site selection, integrating available data sources and facilitating c...
Article
Full-text available
Background: Current urban vector control strategies have failed to contain dengue epidemics and to prevent the global expansion of Aedes-borne viruses (ABVs: dengue, chikungunya, Zika). Part of the challenge in sustaining effective ABV control emerges from the paucity of evidence regarding the epidemiological impact of any Aedes control method. A...
Article
Full-text available
To support optimal third-line antiretroviral therapy (ART) selection in Namibia, we investigated the prevalence of HIV drug resistance (HIVDR) at time of failure of second-line ART. A cross-sectional study was conducted between August 2016 and February 2017. HIV-infected people ≥15 years of age with confirmed virological failure while receiving rit...
Article
Full-text available
While severe social-distancing measures have proven effective in slowing the coronavirus disease 2019 (COVID-19) pandemic, second-wave scenarios are likely to emerge as restrictions are lifted. Here we integrate anonymized, geolocalized mobility data with census and demographic data to build a detailed agent-based model of severe acute respiratory...
Preprint
Full-text available
Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is spread by direct, indirect, or close contact with infected people via infected respiratory droplets or saliva. Crowded indoor environments with sustained close contact and conversations are a particularly high-risk setting. Methods: We performed a meta-analysis through July...
Preprint
Full-text available
We use a global metapopulation transmission model to study the establishment of sustained and undetected community transmission of the COVID-19 epidemic in the United States. The model is calibrated on international case importations from mainland China and takes into account travel restrictions to and from international destinations. We estimate w...
Preprint
Full-text available
Comparison of COVID-19 case numbers over time and between locations is complicated by limits to virologic testing confirm SARS-CoV-2 infection, leading to under-reporting of incidence, and by variations in testing capacity between locations and over time. The proportion of tested individuals who have tested positive (test positive proportion, TPP)...
Article
Background As of June 8, 2020, the global reported number of COVID-19 cases had reached more than 7 million with over 400 000 deaths. The household transmissibility of the causative pathogen, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), remains unclear. We aimed to estimate the secondary attack rate of SARS-CoV-2 among household an...
Preprint
Full-text available
The new coronavirus disease 2019 (COVID-19) has required the implementation of severe mobility restrictions and social distancing measures worldwide. While these measures have been proven effective in abating the epidemic in several countries, it is important to estimate the effectiveness of testing and tracing strategies to avoid a potential secon...
Article
In the test negative design, routine testing at healthcare facilities is leveraged to estimate the effectiveness of an intervention such as a vaccine. The odds of vaccination for individuals who test positive for a target pathogen is compared to the odds of vaccination for individuals who test negative for that pathogen, adjusting for key confounde...
Preprint
Full-text available
Background: As of April 2, 2020, the global reported number of COVID-19 cases has crossed over 1 million with more than 55,000 deaths. The household transmissibility of SARS-CoV-2, the causative pathogen, remains elusive. Methods: Based on a comprehensive contact-tracing dataset from Guangzhou, we estimated both the population-level effective repro...
Preprint
Full-text available
Background: The ongoing outbreak of the 2019 novel coronavirus (2019-nCoV) in China has led to the declaration of Public Health Emergency of International Concern by the World Health Organization. Methods: All 2019-nCoV infected patients reported to Chinese Center for Disease Control and Prevention up to 26 January 2020 were included for analysis....
Article
Public health emergencies, such as an Ebola disease outbreak, provide a complex and challenging environment for the evaluation of candidate vaccines. Here, we outline the need for flexible and responsive vaccine trial designs to be used in public health emergencies, and we summarize recommendations for their use in this setting.
Article
Full-text available
Background: Licensed vaccines are urgently needed for emerging infectious diseases, but the nature of these epidemics causes challenges for the design of phase III trials to evaluate vaccine efficacy. Designing and executing rigorous, fast, and ethical, vaccine efficacy trials is difficult, and the decisions and limitations in the design of these...
Article
We propose an adaptive enrichment approach to test an active factor, which is a factor whose effect is non-zero in at least one subpopulation. We implement a two-stage play-the-winner design where all subjects in the second stage are enrolled from the subpopulation that has the highest observed effect in the first stage. We recommend a weighted Fis...
Article
Background: Sentinel surveillance of transmitted HIV drug resistance (TDR) among recently infected populations within a country was recommended by the World Health Organization from 2004 to 2015. Methods: Serum specimens collected as part of the 2010, 2011 and 2012 National Antenatal Sentinel HIV Prevalence Surveys were used to estimate provinci...
Article
Full-text available
Background Local mosquito-borne Zika virus (ZIKV) transmission has been reported in two counties in the contiguous United States (US), prompting the issuance of travel, prevention, and testing guidance across the contiguous US. Large uncertainty, however, surrounds the quantification of the actual risk of ZIKV introduction and autochthonous transmi...
Article
We conducted a 3-year longitudinal serologic survey on an open cohort of poultry workers, swine workers, and general population controls to assess avian influenza A virus (AIV) seroprevalence and seroincidence and virologic diversity at live poultry markets (LPMs) in Wuxi City, Jiangsu Province, China. Of 964 poultry workers, 9 (0.93%) were seropos...
Data
Additional methods and results, characteristics of study participant, and characteristics of molecular markers of the influenza A viruses studied.
Preprint
Background Local mosquito-borne Zika virus (ZIKV) transmission has been reported in two counties of the continental United State (US), prompting the issuance of travel, prevention, and testing guidance across the continental US. Large uncertainty, however, surrounds the quantification of the actual risk of ZIKV introduction and autochthonous transm...
Article
Conducting vaccine efficacy trials during outbreaks of emerging pathogens poses particular challenges. The “Ebola ça suffit” trial in Guinea used a novel ring vaccination cluster randomized design to target populations at highest risk of infection. Another key feature of the trial was the use of a delayed vaccination arm as a comparator, in which c...
Preprint
Full-text available
Public Health Emergencies (PHEs) provide a complex and challenging environment for vaccine evaluation. Under the R&D Blueprint Plan of Action, the World Health Organization (WHO) has convened a group of experts to agree on standard procedures to rapidly evaluate experimental vaccines during PHEs while maintaining the highest scientific and ethical...
Preprint
Full-text available
The design and execution of rigorous, fast, and ethical vaccine efficacy trials can be challenging during epidemics of emerging pathogens, such as the 2014-2016 Ebola virus and 2015-2016 Zika virus epidemics. Response to an urgent public health crisis requires accelerated research even as emerging epidemics themselves change rapidly and are inheren...
Article
Full-text available
Background Assessments of vaccine efficacy and safety capture only the minimum information needed for regulatory approval, rather than the full public health value of vaccines. Vaccine efficacy provides a measure of proportionate disease reduction, is usually limited to etiologically confirmed disease, and focuses on the direct protection of the va...
Article
Full-text available
Background: In March, 2016, a flare-up of Ebola virus disease was reported in Guinea, and in response ring vaccination with the unlicensed rVSV-ZEBOV vaccine was introduced under expanded access, the first time that an Ebola vaccine has been used in an outbreak setting outside a clinical trial. Here we describe the safety of rVSV-ZEBOV candidate v...
Article
Full-text available
We use a data-driven global stochastic epidemic model to analyze the spread of the Zika virus (ZIKV) in the Americas. The model has high spatial and temporal resolution and integrates real-world demographic, human mobility, socioeconomic, temperature, and vector density data. We estimate that the first introduction of ZIKV to Brazil likely occurred...
Article
Full-text available
Background: The World Health Organization (WHO) early warning indicators (EWIs) of HIV drug resistance (HIVDR) assess factors at individual ART sites that are known to create situations favourable to the emergence of HIVDR. Methods: In 2014, the Namibia HIV care and treatment program abstracted the following adult and pediatric EWIs from all pub...
Article
Full-text available
Background: rVSV-ZEBOV is a recombinant, replication competent vesicular stomatitis virus-based candidate vaccine expressing a surface glycoprotein of Zaire Ebolavirus. We tested the effect of rVSV-ZEBOV in preventing Ebola virus disease in contacts and contacts of contacts of recently confirmed cases in Guinea, west Africa. Methods: We did an o...
Article
Full-text available
Interim results from the Guinea Ebola ring vaccination trial suggest high efficacy of the rVSV-ZEBOV vaccine. These findings open the door to the use of ring vaccination strategies in which the contacts and contacts of contacts of each index case are promptly vaccinated to contain future Ebola virus disease outbreaks. To provide a numerical estimat...
Data
Supporting video. Pujehun district, contained outbreak. The movie shows the simulated weekly number of cases of Ebola for the period of one year considering a reproductive number R0 = 1.6. On the left we show the evolution of an outbreak where we do not consider any interventions while on the right we consider a ring vaccination intervention (C&CC,...
Data
Supporting text. Supporting text containing methodological details and additional results. (PDF)
Data
Supporting video. Pujehun district, no contained outbreak. The movie shows the simulated weekly number of cases of Ebola for the period of one year considering a reproductive number R0 = 1.6. On the left we show the evolution of an outbreak where we do not consider any interventions while on the right we consider a ring vaccination intervention (C&...
Preprint
Full-text available
Conducting vaccine efficacy trials during outbreaks of emerging pathogens poses particular challenges. The ‘Ebola ça suffit’ trial in Guinea used a novel ring vaccination cluster randomized design to target populations at highest risk of infection. Another key feature of the trial was the use of a delayed vaccination arm as a comparator, in which c...