Alex Perkins

Alex Perkins
University of Notre Dame | ND · Department of Biological Sciences

PhD

About

234
Publications
24,984
Reads
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4,471
Citations
Additional affiliations
September 2014 - present
University of Notre Dame
Position
  • Research Assistant
September 2011 - present
University of California, Davis
Position
  • RAPIDD Postdoctoral Fellow
Education
September 2006 - August 2011
University of California, Davis
Field of study
  • Population Biology
August 2002 - May 2006
University of Tennessee
Field of study
  • Computational Ecology

Publications

Publications (234)
Preprint
The mosquito Aedes aegypti is the vector of a number of medically-important viruses, including dengue virus, yellow virus, chikungunya virus, and Zika virus, and as such vector control is a key approach to managing the diseases they cause. Understanding the impact of vector control on these diseases is aided by first understanding its impact on Ae....
Article
Full-text available
Background Despite large outbreaks in humans seeming improbable for a number of zoonotic pathogens, several pose a concern due to their epidemiological characteristics and evolutionary potential. To enable effective responses to these pathogens in the event that they undergo future emergence, the Coalition for Epidemic Preparedness Innovations is a...
Preprint
When related segmented RNA viruses co-infect a single cell, viral reassortment can occur, potentially leading to new strains with pandemic potential. One virus capable of reassortment is bluetongue virus, which causes substantial health impacts in ruminants and is transmitted via Culicoides midges. Because midges can become co-infected by feeding o...
Preprint
In recent decades, there has been an increased interest in developing a vaccine for chikungunya. However, due to its unpredictable transmission, planning for a chikungunya vaccine trial is challenging. To inform decision making on the selection of sites for a vaccine efficacy trial, we developed a new framework for projecting the expected number of...
Preprint
Though instances of arthropod-borne (arbo)virus co-infection have been documented clinically, the overall incidence of arbovirus co-infection and its drivers are not well understood. Now that dengue, Zika, and chikungunya viruses are all in circulation across tropical and subtropical regions of the Americas, it is important to understand the enviro...
Preprint
Background Venezuela has experienced an explosive resurgence in Plasmodium falciparum and Plasmodium vivax malaria incidence over the last decade due to various social, political, and economic factors. To ensure national and regional progress towards malaria elimination, there is an urgent need to better understand the epidemiological dynamics of t...
Preprint
Full-text available
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 expanding vaccine administration to children 5-11 years old on anticipated COVID-19 burden and resilience against variant...
Article
Full-text available
Background Inference of person-to-person transmission networks using surveillance data is increasingly used to estimate spatiotemporal patterns of pathogen transmission. Several data types can be used to inform transmission network inferences, yet the sensitivity of those inferences to different data types is not routinely evaluated. Methods The i...
Article
Full-text available
Bluetongue virus (BTV) is an arthropod-borne, segmented double-stranded RNA virus that can cause severe disease in both wild and domestic ruminants. BTV evolves via several key mechanisms, including the accumulation of mutations over time and the reassortment of genome segments.Additionally, BTV must maintain fitness in two disparate hosts, the ins...
Article
Full-text available
Testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been vitally important during the COVID-19 pandemic. There are a variety of methods for testing for this virus, and it is important to understand their accuracy in choosing which one might be best suited for a given application.
Article
Full-text available
Since the start of the coronavirus disease-2019 (COVID-19) pandemic, there has been interest in using wastewater monitoring as an approach for disease surveillance. A significant uncertainty that would improve the interpretation of wastewater monitoring data is the intensity and timing with which individuals shed RNA from severe acute respiratory s...
Article
Full-text available
Background Plasmodium vivax blood-stage relapses originating from re-activating hypnozoites are a major barrier for control and elimination of this disease. Radical cure is a form of therapy capable of addressing this problem. Recent clinical trials of radical cure have yielded efficacy estimates ranging from 65 to 94%, with substantial variation a...
Preprint
Full-text available
Like other congregate living settings, military basic training has been subject to outbreaks of COVID-19. We sought to identify improved strategies for preventing outbreaks in this setting using an agent-based model of a hypothetical cohort of trainees on a U.S. Army post. Our analysis revealed unique aspects of basic training that require customiz...
Preprint
Full-text available
2.0 New vector-control technologies to fight mosquito-borne diseases are urgently needed, the adoption of which depends on efficacy estimates from large-scale cluster-randomized trials (CRTs). The release of Wolbachia -infected mosquitoes is one promising strategy to curb dengue virus (DENV) transmission, and a recent CRT reported impressive reduct...
Preprint
Full-text available
Despite large outbreaks in humans seeming improbable for a number of zoonotic pathogens, several pose a concern due to their epidemiological characteristics and evolutionary potential. To enable effective responses to these pathogens in the event that they undergo future emergence, the Coalition for Epidemic Preparedness Innovations is advancing th...
Article
Estimates of disease burden are important for setting public health priorities. These estimates involve numerous modeling assumptions, whose uncertainties are not always well described. We developed a framework for estimating the burden of yellow fever in Africa and evaluated its sensitivity to modeling assumptions that are often overlooked. We fou...
Article
Full-text available
Probabilistic forecasts play an indispensable role in answering questions about the spread of newly emerged pathogens. However, uncertainties about the epidemiology of emerging pathogens can make it difficult to choose among alternative model structures and assumptions. To assess the potential for uncertainties about emerging pathogens to affect fo...
Article
Full-text available
Background The COVID-19 pandemic has induced unprecedented reductions in human mobility and social contacts throughout the world. Because dengue virus (DENV) transmission is strongly driven by human mobility, behavioral changes associated with the pandemic have been hypothesized to impact dengue incidence. By discouraging human contact, COVID-19 co...
Preprint
Full-text available
Accurate tests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been critical in efforts to control its spread. The accuracy of molecular tests for SARS-CoV-2 has been assessed numerous times, usually in reference to a gold standard diagnosis. One major disadvantage of that approach is the possibility of error due to inaccuracy...
Article
Full-text available
In the United States, schools closed in March 2020 due to COVID-19 and began reopening in August 2020, despite continuing transmission of SARS-CoV-2. In states where in-person instruction resumed at that time, two major unknowns were the capacity at which schools would operate, which depended on the proportion of families opting for remote instruct...
Article
Full-text available
An effective and widely used vaccine could reduce the burden of dengue virus (DENV) around the world. DENV is endemic in Puerto Rico, where the dengue vaccine CYD-TDV is currently under consideration as a control measure. CYD-TDV has demonstrated efficacy in clinical trials in vaccinees who had prior dengue virus infection. However, in vaccinees wh...
Article
Full-text available
Background: Human mobility among residential locations can drive dengue virus (DENV) transmission dynamics. Recently, it was shown that individuals with symptomatic DENV infection exhibit significant changes in their mobility patterns, spending more time at home during illness. This change in mobility is predicted to increase the risk of acquiring...
Article
Full-text available
Background: Vaccination is one of the most effective public health interventions. We investigate the impact of vaccination activities for Haemophilus influenzae type b, hepatitis B, human papillomavirus, Japanese encephalitis, measles, Neisseria meningitidis serogroup A, rotavirus, rubella, Streptococcus pneumoniae, and yellow fever over the years...
Preprint
Full-text available
Since the start of the COVID-19 pandemic, there has been interest in using wastewater monitoring as an approach for disease surveillance. A significant uncertainty that would improve interpretation of wastewater monitoring data is the intensity and timing with which individuals shed RNA from severe acute respiratory syndrome coronavirus 2 (SARS-CoV...
Article
Full-text available
During the past 100 years, Rift Valley fever virus (RVFV), a mosquito-borne virus, has caused potentially lethal disease in livestock, and has been associated with significant economic losses and trade bans. Spillover to humans occurs and can be fatal. Here, we combined data on RVF disease in humans (22 countries) and animals (37 countries) from 19...
Article
Full-text available
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,...
Article
Full-text available
During the 2015-2017 Zika epidemic, dengue and chikungunya-two other viral diseases with the same vector as Zika-were also in circulation. Clinical presentation of these diseases can vary from person to person in terms of symptoms and severity, making it difficult to differentially diagnose them. Under these circumstances, it is possible that numer...
Preprint
Full-text available
When new pathogens emerge, numerous questions arise about their future spread, some of which can be addressed with probabilistic forecasts. The many uncertainties about the epidemiology of emerging pathogens can make it difficult to choose among model structures and assumptions, however. To assess the potential for uncertainties about emerging path...
Preprint
Full-text available
During the past 100 years, Rift Valley fever virus (RVFV), a mosquito-borne virus, has caused potentially lethal disease in livestock, and has been associated with significant economic losses and trade bans. Spillover to humans occurs and can be fatal. Here, we combined data on RVF disease in humans (22 countries) and animals (37 countries) from 19...
Article
Full-text available
Measles incidence in the United States has grown dramatically, as vaccination rates are declining and transmission internationally is on the rise. Because imported cases are necessary drivers of outbreaks in non-endemic settings, predicting measles outbreaks in the US depends on predicting imported cases. To assess the predictability of imported me...
Preprint
Full-text available
Background Plasmodium vivax relapses caused by reactivating hypnozoites are a major barrier for elimination and control of this form of malaria. Radical cure is a form of therapy capable of addressing this problem. Recent clinical trials of radical cure have yielded efficacy estimates ranging from 65% to 94%, with substantial variation across trial...
Article
Full-text available
Heterogeneous exposure to mosquitoes determines an individual’s contribution to vector-borne pathogen transmission. Particularly for dengue virus (DENV), there is a major difficulty in quantifying human-vector contacts due to the unknown coupled effect of key heterogeneities. To test the hypothesis that the reduction of human out-of-home mobility d...
Preprint
Full-text available
Geographically stratified estimates of disease burden play an important role in setting priorities for the management of different diseases and for targeting interventions against a single disease. Such estimates involve numerous assumptions, which uncertainty about is not always well accounted for. We developed a framework for estimating the burde...
Chapter
Prediction of spatial heterogeneity in disease incidence based on measurable spatial factors is a major goal of spatial epidemiology. There are a number of applied goals of these predictions, including appropriately targeting resources for surveillance and intervention and accurately quantifying disease burden. Although spatial heterogeneity is evi...
Preprint
Full-text available
Background The COVID-19 pandemic has induced unprecedented reductions in human mobility and social contacts throughout the world. Because dengue virus (DENV) transmission is strongly driven by human mobility, behavioral changes associated with the pandemic have been hypothesized to impact dengue incidence. By discouraging human contact, COVID-19 co...
Preprint
Full-text available
Policymakers make decisions about COVID-19 management in the face of considerable uncertainty. We convened multiple modeling teams to evaluate reopening strategies for a mid-sized county in the United States, in a novel process designed to fully express scientific uncertainty while reducing linguistic uncertainty and cognitive biases. For the scena...
Preprint
Full-text available
An effective and widely used vaccine could reduce the burden of dengue virus (DENV) around the world. DENV is endemic in Puerto Rico, where the dengue vaccine CYD-TDV is currently under consideration as a control measure. CYD-TDV has demonstrated efficacy in clinical trials in vaccinees who had prior dengue infection. However, in vaccinees who had...
Article
Full-text available
Several hundred thousand Zika cases have been reported across the Americas since 2015. Incidence of infection was likely much higher, however, due to a high frequency of asymptomatic infection and other challenges that surveillance systems faced. Using a hierarchical Bayesian model with empirically-informed priors, we leveraged multiple types of Zi...
Article
Full-text available
Spatial repellents (SRs) reduce human-mosquito contact by preventing mosquito entrance into human-occupied spaces and interfering with host-seeking and blood-feeding. A new model to synthesize experimental data on the effects of transfluthrin on Aedes aegypti explores how SR effects interact to impact the epidemiology of diseases vectored by these...
Article
The COVID-19 pandemic has forced societies across the world to resort to social distancing to slow the spread of the SARS-CoV-2 virus. Due to the economic impacts of social distancing, there is growing desire to relax these measures. To characterize a range of possible strategies for control and to understand their consequences, we performed an opt...
Preprint
Full-text available
Inference of person-to-person transmission networks using routinely collected surveillance data is being used increasingly to estimate spatiotemporal patterns of pathogen transmission. Several data types can be used to inform transmission network inferences, yet the sensitivity of those inferences to different data types is not routinely evaluated....
Preprint
Full-text available
In the United States, schools closed in March 2020 due to COVID-19 and have begun reopening as of August 2020, despite continuing transmission of SARS-CoV-2. To determine the impact of school reopening with varying levels of operating capacity and face-mask adherence, we used an agent-based model calibrated to and validated against multiple data ty...
Article
Full-text available
Significance In early 2020, delays in availability of diagnostic testing for COVID-19 prompted questions about the extent of unobserved community transmission in the United States. We quantified unobserved infections in the United States during this time using a stochastic transmission model. Although precision of our estimates is limited, we concl...
Preprint
Full-text available
After Zika virus (ZIKV) emerged and caused an epidemic in the Americas in 2016, both Zika and dengue incidence declined in the following years (2017-2018) to a record low in many countries. Following this period of low incidence, dengue resurged in 2019 in Brazil, causing ~2.1 million cases. The reasons for the recent fluctuations in dengue inciden...
Article
Full-text available
The geographic variation of human movement is largely unknown, mainly due to a lack of accurate and scalable data. Here we describe global human mobility patterns, aggregated from over 300 million smartphone users. The data cover nearly all countries and 65% of Earth’s populated surface, including cross-border movements and international migration....
Article
Full-text available
Costa Rica is a candidate to eliminate malaria by 2020. The remaining malaria transmission hotspots are located within the Huétar Norte Region (HNR), where 90% of the country's 147 malaria cases have occurred since 2016, following a 33-month period without transmission. Here, we examine changes in transmission with the implementation of a supervise...
Article
Full-text available
Human mobility, both short and long term, are important considerations in the study of numerous systems. Economic and technological advances have led to a more interconnected global community, further increasing the need for considerations of human mobility. While data on human mobility are better recorded in many developed countries, availability...
Preprint
Full-text available
The COVID-19 pandemic has forced societies across the world to resort to social distancing to slow the spread of the SARS-CoV-2 virus. Due to the economic impacts of social distancing, there is growing desire to relax these measures. To characterize a range of possible strategies for control and to understand their consequences, we performed an opt...
Article
Full-text available
Recent years have seen rising incidence of dengue and large outbreaks of Zika and chikungunya, which are all caused by viruses transmitted by Aedes aegypti mosquitoes. In most settings, the primary intervention against Aedes-transmitted viruses is vector control, such as indoor, ultra-low volume (ULV) spraying. Targeted indoor residual spraying (TI...
Preprint
Full-text available
By March 2020, COVID-19 led to thousands of deaths and disrupted economic activity worldwide. As a result of narrow case definitions and limited capacity for testing, the number of unobserved SARS-CoV-2 infections during its initial invasion of the US remains unknown. We developed an approach for estimating the number of unobserved infections based...
Article
In mathematical epidemiology, a well-known formula describes the impact of heterogeneity on the basic reproductive number, R0, for situations in which transmission is separable and for which there is one source of variation in susceptibility and one source of variation in infectiousness. This formula is written in terms of the magnitudes of the het...