Derek A T Cummings

Johns Hopkins Bloomberg School of Public Health | JHSPH · Department of Epidemiology

Understanding the risk of infection from household- and community-exposures and the transmissibility of asymptomatic infections is critical to SARS-CoV-2 control. Limited previous evidence is based primarily on virologic testing, which disproportionately misses mild and asymptomatic infections. Serologic measures are more likely to capture all prev...

Background A two-dose regimen of ChAdOx1 coronavirus disease 19 (Covid-19) vaccine with an inter-dose interval of three months has been implemented in many countries with restricted vaccine supply. However, there is limited evidence for the effectiveness of ChAdOx1 by dose in elderly populations in countries with high prevalence of the Gamma varian...

Since it was first identified, the epidemic scale of the recently emerged novel coronavirus (2019-nCoV) in Wuhan, China, has increased rapidly, with cases arising across China and other countries and regions. Using a transmission model, we estimate a basic reproductive number of 3.11 (95% CI, 2.39–4.13), indicating that 58–76% of transmissions must...

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...

Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant, Gamma, emerged in the city of Manaus in late 2020 during a large resurgence of coronavirus disease (COVID-19), and has spread throughout Brazil. The effectiveness of vaccines in settings with widespread Gamma variant transmission has not been reported. Methods We perf...

More than half of the world’s population lives in areas at risk for dengue virus infection. A vaccine will be pivotal to controlling spread, however, the only licensed vaccine, Dengvaxia, has been shown to increase the risk of severe disease in a subset of individuals. Vaccine efforts are hampered by a poor understanding of antibody responses, incl...

Non-pharmaceutical interventions (NPIs) remain the only widely available tool for controlling the ongoing SARS-CoV-2 pandemic. We estimated weekly values of the effective basic reproductive number (Reff) using a mechanistic metapopulation model and associated these with county-level characteristics and NPIs in the United States (US). Interventions...

Background: Healthcare personnel (HCP) knowledge and attitudes toward infection control measures are important determinants of practices that can protect them from transmission of infectious diseases. Methods: Healthcare personnel were recruited from Emergency Departments and outpatient clinics at seven sites. They completed knowledge surveys at...

Background Mass vaccination is being used in response to coronavirus disease (COVID-19) epidemics, including those driven by emerging variants of concern. We evaluated the effectiveness of the inactivated whole-virus vaccine, CoronaVac, against symptomatic COVID-19 in the elderly population of Sao Paulo State, Brazil during widespread circulation o...

After the Zika virus (ZIKV) epidemic in the Americas in 2016, both Zika and dengue incidence declined to record lows in many countries in 2017–2018, but in 2019 dengue resurged in Brazil, causing ~2.1 million cases. In this study we use epidemiological, climatological and genomic data to investigate dengue dynamics in recent years in Brazil. First,...

Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant P.1 emerged in the city of Manaus in late 2020 during a large resurgence of coronavirus disease (COVID-19), and has spread throughout Brazil. The effectiveness of vaccines in settings with widespread P.1 transmission has not been reported. Methods We performed a matched...

Florida faces the challenge of repeated introduction and autochthonous transmission of arboviruses transmitted by Aedes aegypti and Aedes albopictus . Empirically-based predictive models of the spatial distribution of these species would aid surveillance and vector control efforts. To predict the occurrence and abundance of these species, we fit a...

For most pathogens, transmission is driven by interactions between the behaviours of infectious individuals, the behaviours of the wider population, the local environment, and immunity. Phylogeographic approaches are currently unable to disentangle the relative effects of these competing factors. We develop a spatiotemporally structured phylogeneti...

Background Information on the etiology and age-specific burden of respiratory viral infections among school-aged children remains limited. Though school aged children are often recognized as driving the transmission of influenza as well as other respiratory viruses, little detailed information is available on the distribution of respiratory infecti...

The spatial distribution of dengue and its vectors (spp. Aedes) may be the widest it has ever been, and projections suggest that climate change may allow the expansion to continue. However, the largest impacts of climate change on dengue might be in regions where the pathogen is already endemic. In these areas, the waxing and waning of immunity has...

Background Children are important in community-level influenza transmission. School-based monitoring may inform influenza surveillance. Methods We used reported weekly confirmed influenza in Allegheny County during the 2007, and 2010-2015 influenza seasons using Pennsylvania’s Allegheny County Health Department all-age influenza cases from health f...

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...

Estimating the size and infection severity of the SARS-CoV-2 epidemic is made challenging by inconsistencies in available data. The number of COVID-19 deaths is often used as a key indicator for the epidemic size, but observed deaths represent only a minority of all infections1,2. Additionally, the heterogeneous burden in nursing homes and variable...

Background Healthcare personnel (HCP) working in outpatient settings routinely interact with patients with acute respiratory illnesses. Absenteeism following symptom development and lack of staff trained to obtain samples limit efforts to identify pathogens among infected HCP. Methods The Respiratory Protection Effectiveness Clinical Trial assesse...

Comparisons of the utility and accuracy of methods for measuring social interactions relevant to disease transmission are rare. To increase the evidence base supporting specific methods to measure social interaction, we compared data from self-reported contact surveys and wearable proximity sensors from a cohort of schoolchildren in the Pittsburgh...

Background Stocks of yellow fever vaccine are insufficient to cover exceptional demands for outbreak response. Fractional dosing has shown efficacy, but evidence is limited to the 17DD substrain vaccine. We assessed the immunogenicity and safety of one-fifth fractional dose compared with standard dose of four WHO-prequalified yellow fever vaccines...

Objective To characterize the SARS-CoV-2 testing cascade and associated barriers in three US states. Methods We recruited participants from Florida, Illinois, and Maryland (∼1000/state) for an online survey September 16 – October 15, 2020. The survey covered demographics, COVID-19 symptoms, and experiences around SARS-CoV-2 PCR testing in the prio...

For most pathogens, transmission is driven by interactions between the behaviours of infectious individuals, the behaviours of the wider population, the local environment, and immunity. Phylogeographic approaches are currently unable to disentangle the relative effects of these competing factors. We develop a spatiotemporally structured phylogeneti...

The current COVID-19 pandemic has resulted in the unprecedented development and integration of infectious disease dynamic transmission models into policy making and public health practice. Models offer a systematic way to investigate transmission dynamics and produce short-term and long-term predictions that explicitly integrate assumptions about b...

Analysis of immunogenicity data is a critical component of vaccine development, providing a biological basis to support any observed protection from vaccination. Conventional methods for analyzing immunogenicity data use either post-vaccination titer or change in titer, often defined as a binary variable using a threshold. These methods are simple...

Non-pharmaceutical interventions (NPIs) remain the only widely available tool for controlling the ongoing SARS-CoV-2 pandemic. We estimated weekly values of the effective basic reproductive number ( R eff ) using a mechanistic metapopulation model and associated these with county-level characteristics and NPIs in the United States (US). Interventio...

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...

Background: Influenza infection is often measured by a fourfold antibody titer increase over an influenza season (ie seroconversion). However, this approach may fail when influenza seasons are less distinct as it does not account for transient effects from recent infections. Here, we present a method to determine seroconversion for non-paired sera...

Many public health responses and modeled scenarios for COVID-19 outbreaks caused by SARS-CoV-2 assume that infection results in an immune response that protects individuals from future infections or illness for some amount of time. The presence or absence of protective immunity due to infection or vaccination (when available) will affect future tra...

The ongoing coronavirus disease 2019 (COVID-19) pandemic has heightened discussion of the use of mobile phone data in outbreak response. Mobile phone data have been proposed to monitor effectiveness of non-pharmaceutical interventions, to assess potential drivers of spatiotemporal spread, and to support contact tracing efforts. While these data may...

Background: Information on the etiology and age-specific burden of respiratory viral infections among school-aged children remains limited. Methods: We conducted a cohort study to determine the etiology of ILI (influenza like illness) among 2,519 K-12 students during the 2012-13 influenza season. We obtained nasal swabs from students with ILI-relat...

Mosquitoes are important vectors for pathogens that infect humans and other vertebrate animals. Some aspects of adult mosquito behavior and mosquito ecology play an important role in determining the capacity of vector populations to transmit pathogens. Here, we re-examine factors affecting the transmission of pathogens by mosquitoes using a new app...

The duration and nature of immunity generated in response to SARS-CoV-2 infection is unknown. Many public health responses and modeled scenarios for COVID-19 outbreaks caused by SARS-CoV-2 assume that infection results in an immune response that protects individuals from future infections or illness for some amount of time. The timescale of protect...

Background: Information on the etiology and age-specific burden of respiratory viral infections among school-aged children remains limited. Though school aged children are often recognized as driving the transmission of influenza as well as other respiratory viruses, little detailed information is available on the distribution of respiratory infect...

Background The presence of pre-existing chikungunya virus (CHIKV) neutralizing antibodies (Nab) has been associated with decreased risk of symptomatic CHIKV infection in a longitudinal cohort from Cebu City, Philippines. However, the relationship between pre-existing Nab and risk of subclinical seroconversion has not been well described. Methods D...

Complex exposure histories and immune mediated interactions between influenza strains contribute to the life course of human immunity to influenza. Antibody profiles can be generated by characterizing immune responses to multiple antigenically variant strains, but how these profiles vary across individuals and determine future responses is unclear....

Human mobility is an important driver of geographic spread of infectious pathogens. Detailed information about human movements during outbreaks are, however, difficult to obtain and may not be available during future epidemics. The Ebola virus disease (EVD) outbreak in West Africa between 2014–16 demonstrated how quickly pathogens can spread to lar...

Human mobility is an important driver of geographic spread of infectious pathogens. Detailed information about human movements during outbreaks are, however, difficult to obtain and may not be available during future epidemics. The Ebola virus disease (EVD) outbreak in West Africa between 2014–16 demonstrated how quickly pathogens can spread to lar...

A growing number of infectious pathogens are spreading among geographic regions. Some pathogens that were previously not considered to pose a general threat to human health have emerged at regional and global scales, such as Zika and Ebola Virus Disease. Other pathogens, such as yellow fever virus, were previously thought to be under control but ha...

Human movement contributes to the probability that pathogens will be introduced to new geographic locations. Here we investigate the impact of human movement on the spatial spread of Chikungunya virus (CHIKV) in Southern Thailand during a recent re-emergence. We hypothesised that human movement, population density, the presence of habitat conducive...

Infectious disease transmission in animals is an inherently spatial process in which a host’s home location and their social mixing patterns are important, with the mixing of infectious individuals often different to that of susceptible individuals. Although incidence data for humans have traditionally been aggregated into low-resolution data sets,...

Human immunity influences the evolution and impact of novel influenza strains. Because individuals are infected with multiple influenza strains during their lifetime and each virus can generate a cross-reactive antibody response, it is challenging to quantify the processes that shape observed immune responses, or to reliably detect recent infection...

Athropod-borne viruses (arboviruses) pose the greatest risk of spillover into humans of any class of pathogens. Such spillover may occur as a one-step jump from a reservoir host species into humans or as a two-step jump from the reservoir to a different amplification host species and thence to humans. Despite the widespread havoc wreaked by emergin...

Numerous Zika virus vaccines are being developed. However, identifying sites to evaluate the efficacy of a Zika virus vaccine is challenging due to the general decrease in Zika virus activity. We compare results from three different modeling approaches to estimate areas that may have increased relative risk of Zika virus transmission during 2017. T...

Dengue is an important vector-borne pathogen found across much of the world. Many factors complicate our understanding of the relationship between infection with one of the four dengue virus serotypes, and the observed incidence of disease. One of the factors is a large proportion of infections appear to result in no or few symptoms, while others r...

The supplement contains the code for running the models in the paper in R with rstan. (PDF)

Zika virus (ZIKV) is causing an unprecedented epidemic linked to severe congenital abnormalities. In July 2016, mosquito-borne ZIKV transmission was reported in the continental United States; since then, hundreds of locally acquired infections have been reported in Florida. To gain insights into the timing, source, and likely route(s) of ZIKV intro...

Objective This session will provide an overview of the current systemsfor influenza surveillance; review the role of schools in influenzatransmission; discuss relationships between school closures, schoolabsenteeism, and influenza transmission; and explore the usefulnessof school absenteeism and unplanned school closure monitoring forearly detectio...

Objective To determine if all-cause and cause-specific school absencesimprove predictions of virologically confirmed influenza in thecommunity.IntroductionSchool-based influenza surveillance has been considered forreal-time monitoring of influenza, as children 5-17 years old play animportant role in community-level transmission.Methods The Alleghen...

A fundamental mystery for dengue and other infectious pathogens is how observed patterns of cases relate to actual chains of individual transmission events. These pathways are intimately tied to the mechanisms by which strains interact and compete across spatial scales. Phylogeographic methods have been used to characterize pathogen dispersal at gl...

Author Summary All four serotypes of dengue have circulated endemically throughout Southeast Asia for decades. However, despite the enormous burden of disease, there remains poor understanding of the similarity in disease patterns across the region. We analyzed data from over 100,000 cases of dengue from two of the largest cities in the region, Ban...

Monthly temperature and rainfall for the two cities. A. Comparison of mean temperature between two cities. B. Comparison of monthly rainfall between two cities (TIF)

Tau clustering statistic results when only cases geocoded with ‘ROOFTOP’ accuracy (the most accurate) are used versus when ‘RANGE INTERPOLATED’ and ‘GEOMETRIC CENTER’ are also used. (TIF)

Uncertainty in the force of infection estimates using profile likelihoods. (TIF)

Estimator for Tau statistic (DOCX)

Tau clustering statistic by individual year (2010–2013). (TIF)

Sensitivity analyses assuming that 0% (baseline scenario), 10% or 20% of hospitalized cases were as a result of primary infections with the remainder as a result of secondary infections. The panels set out the probability density function of the ages of cases under the different models. (TIF)

Sensitivity analysis using all cases, including both dengue fever and dengue hemorrhagic fever cases. The baseline model uses only dengue hemorrhagic fever cases. The panels set out the probability density function of the ages of cases under the different models. (TIF)

Distance comparison between geocoded address and real GPS (DOCX)

Sensitivity exploring impact of removing different years from the dataset (DOCX)

Background: Large Phase III trials across Asia and Latin America have recently demonstrated the efficacy of a recombinant, live-attenuated dengue vaccine (Dengvaxia) over the first 25 mo following vaccination. Subsequent data collected in the longer-term follow-up phase, however, have raised concerns about a potential increase in hospitalization r...

Social factors have been shown to create differential burden of influenza across different geographic areas. We explored the relationship between potential aggregate-level social determinants and mortality during the 1918 influenza pandemic in Chicago using a historical dataset of 7,971 influenza and pneumonia deaths. Census tract-level social fact...

Whether an individual becomes infected in an infectious disease outbreak depends on many interconnected risk factors, which may relate to characteristics of the individual (e.g., age, sex), his or her close relatives (e.g., household members), or the wider community. Studies monitoring individuals in households or schools have helped elucidate the...

The average spatial distance between transmission-linked cases is a fundamental property of infectious disease dispersal. However, the distance between a case and their infector is rarely measurable. Contact-tracing investigations are resource intensive or even impossible, particularly when only a subset of cases are detected. Here, we developed an...

The first approved dengue vaccine has now been licensed in six countries. We propose that this live attenuated vaccine acts like a silent natural infection in priming or boosting host immunity. A transmission dynamic model incorporating this hypothesis fits recent clinical trial data well and predicts that vaccine effectiveness depends strongly on...

With more than 1,700 laboratory-confirmed infections, Middle East respiratory syndrome coronavirus (MERS-CoV) remains a significant threat for public health. However, the lack of detailed data on modes of transmission from the animal reservoir and between humans means that the drivers of MERS-CoV epidemics remain poorly characterized. Here, we deve...

First discovered in 1947, Zika virus (ZIKV) infection remained a little known tropical disease until 2015, when its apparent association with a significant increase in the incidence of microcephaly in Brazil raised alarms worldwide. There is limited information on the key factors that determine the extent of the global threat from ZIKV infection an...

Background: Serum antibody to influenza can be used to identify past exposure and measure current immune status. The two most common methods for measuring this are the hemagglutination inhibition assay (HI) and the viral neutralization assay (NT), which have not been systematically compared for a large number of influenza viruses. Methods: 151 s...

Author Predicting the course of infectious disease outbreaks in real-time is a challenging task. It requires knowledge of the particular disease system as well as a pipeline that can turn raw data from a public health surveillance system into calibrated predictions of disease incidence. Dengue is a mosquito-borne infectious disease that places an...

Methodological details, supplemental figures and results. (PDF)

Background Although N95 filtering facepiece respirators and medical masks are commonly used for protection against respiratory infections in healthcare settings, more clinical evidence is needed to understand the optimal settings and exposure circumstances for healthcare personnel to use these devices. A lack of clinically germane research has led...

Global spatial clustering is the tendency of points, here cases of infectious disease, to occur closer together than expected by chance. The extent of global clustering can provide a window into the spatial scale of disease transmission, thereby providing insights into the mechanism of spread, and informing optimal surveillance and control. Here th...