Amy Wesolowski's research while affiliated with Johns Hopkins Bloomberg School of Public Health and other places

Publications (170)

Preprint
The COVID-19 pandemic has impacted many facets of human behavior, including human mobility partially driven by the implementation of non-pharmaceutical interventions (NPIs) such as stay at home orders, travel restrictions, and workplace and school closures. Given the importance of human mobility in the transmission of SARS-CoV-2, there have been an...
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Malaria incidence has declined in southern Zambia over recent decades, leading to efforts to achieve and sustain malaria elimination. Understanding the remaining disease burden is key to providing optimal health care. A longitudinal study conducted in a rural area of Choma District, Southern Province, Zambia, assessed the prevalence of and factors...
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Background While mass COVID-19 vaccination programs are underway in high-income countries, limited availability of doses has resulted in few vaccines administered in low and middle income countries (LMICs). The COVID-19 Vaccines Global Access (COVAX) is a WHO-led initiative to promote vaccine access equity to LMICs and is providing many of the dose...
Preprint
Background Serological assays used to estimate SARS-CoV-2 seroprevalence rely on manufacturer cut-offs established based on more severe early cases who tended to be older. Methods We conducted a household-based serosurvey of 4,677 individuals from 2,619 households in Chennai, India from January to May, 2021. Samples were tested for SARS-CoV-2 IgG...
Preprint
S ummary Protein microarrays are a promising technology that measure protein levels in serum or plasma samples. Due to the high technical variability of these assays and high variation in protein levels across serum samples in any population, directly answering biological questions of interest using protein microarray measurements is challenging. U...
Preprint
Important goals of malaria surveillance efforts include accurately quantifying the burden of malaria over time, which can be useful to target and evaluate interventions. The majority of malaria surveillance methods capture active or recent infections which poses several challenges to achieving malaria surveillance goals. In high transmission settin...
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Artemisinin combination therapies (ACTs) are the WHO-recommended first-line therapies for uncomplicated Plasmodium falciparum malaria. The emergence and spread of artemisi-nin-resistant genotypes is a major global public health concern due to the increased rate of treatment failures that result. This is particularly germane for WHO designated 'high...
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Diphtheria is a potentially devastating disease whose epidemiology remains poorly described in many settings, including Madagascar. Diphtheria vaccination is delivered in combination with pertussis and tetanus antigens and coverage of this vaccine is often used as a core measure of health system functioning. However, coverage is challenging to esti...
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For emerging epidemics such as the COVID-19 pandemic, quantifying travel is a key component of developing accurate predictive models of disease spread to inform public health planning. However, in many LMICs, traditional data sets on travel such as commuting surveys as well as non-traditional sources such as mobile phone data are lacking, or, where...
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Introduction Despite gains in global coverage of childhood vaccines, many children remain undervaccinated. Although mass vaccination campaigns are commonly conducted to reach these children their effectiveness is unclear. We evaluated the effectiveness of a mass vaccination campaign in reaching zero-dose children. Methods We conducted a prospectiv...
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When a novel pathogen emerges there may be opportunities to eliminate transmission - locally or globally - whilst case numbers are low. However, the effort required to push a disease to elimination may come at a vast cost at a time when uncertainty is high. Models currently inform policy discussions on this question, but there are a number of open...
Preprint
Understanding temporal and spatial dynamics of ongoing malaria transmission will be critical to inform effective interventions and elimination strategies in low transmission regions approaching elimination. Parasite genomics are being used as a tool to monitor epidemiologic trends, including assessing residual transmission across seasons or importa...
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Technical variation, or variation from non-biological sources, is present in most laboratory assays. Correcting for this variation enables analysts to extract a biological signal that informs questions of interest. However, each assay has different sources and levels of technical variation and the choice of correction methods can impact downstream...
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The twenty-first century has witnessed a wave of severe infectious disease outbreaks, not least the COVID-19 pandemic, which has had a devastating impact on lives and livelihoods around the globe. The 2003 severe acute respiratory syndrome coronavirus outbreak, the 2009 swine flu pandemic, the 2012 Middle East respiratory syndrome coronavirus outbr...
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Technical variation, or variation from non‐biological sources, is present in most laboratory assays. Correcting for this variation enables analysts to extract a bio‐ logical signal that informs questions of interest. However, each assay has different sources and levels of technical variation and the choice of correction methods can impact downstrea...
Preprint
Introduction: Despite gains in global coverage of childhood vaccines, many children remain undervaccinated. Vaccination campaigns also known as Supplemental Immunization Activity (SIA) are commonly conducted to reach those who are undervaccinated. However, reaching these children even during an SIA is challenging. We evaluated the effectiveness of...
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Human mobility is a core component of human behavior and its quantification is critical for understanding its impact on infectious disease transmission, traffic forecasting, access to resources and care, intervention strategies, and migratory flows. When mobility data are limited, spatial interaction models have been widely used to estimate human t...
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Public health officials discouraged travel and non-household gatherings for Thanksgiving, but data suggests that travel increased over the holidays. The objective of this analysis was to assess associations between holiday gatherings and SARS-CoV-2 positivity in the weeks following Thanksgiving. Using an online survey, we sampled 7770 individuals a...
Preprint
Full-text available
Background: While mass COVID-19 vaccination programs are underway in high-income countries, limited availability of doses has resulted in few vaccines administered in low and middle income countries (LMICs). The COVID-19 Vaccines Global Access (COVAX) is a WHO-led initiative to promote vaccine access equity to LMICs and is providing many of the dos...
Preprint
Full-text available
Artemisinin combination therapies (ACTs) are the WHO-recommended first-line therapies for uncomplicated Plasmodium falciparum malaria. The emergence and spread of artemisinin-resistant genotypes is a major global public health concern. To explore how the increased adoption of ACTs may affect the high-burden high-impact malaria setting of Burkina Fa...
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Background: SARS-CoV-2 testing is critical for monitoring case counts, early detection and containment of infection, clinical management, and surveillance of variants. However, community-based data on the access, uptake, and barriers to testing have been lacking. Methods: We conducted serial cross-sectional online surveys covering demographics,...
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Human travel is one of the primary drivers of infectious disease spread. Models of travel are often used that assume the amount of travel to a specific destination decreases as cost of travel increases with higher travel volumes to more populated destinations. Trip duration, the length of time spent in a destination, can also impact travel patterns...
Preprint
Full-text available
For emerging epidemics such as the COVID-19 pandemic, quantifying travel is a key component of developing accurate predictive models of disease spread to inform public health planning. However, in many LMICs, traditional data sets on travel such as commuting surveys as well as non-traditional sources such as mobile phone data are lacking, or, where...
Article
In northwestern Kenya, Turkana County has been historically considered unsuitable for stable malaria transmission because of its unfavorable climate and predominantly semi-nomadic population; consequently, it is overlooked during malaria control planning. However, the area is changing, with substantial development, an upsurge in travel associated w...
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Many childhood vaccines require multiple doses be delivered within a narrow time window to provide adequate protection and reduce disease transmission. Accurately quantifying vaccination coverage is complicated by limited individual-level data and multiple vaccination mechanisms (routine and supplementary vaccination programs). We analyzed 12,541 v...
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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...
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Malaria control may be enhanced by targeting reservoirs of Plasmodium falciparum transmission. One putative reservoir is asymptomatic malaria infections and the scale of their contribution to transmission in natural settings is not known. We assess the contribution of asymptomatic malaria to onward transmission using a 14-month longitudinal cohort...
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Masks are effective measures to prevent the transmission of SARS-CoV-2, however, lack of a national mandate coupled with poor adherence has led to suboptimal levels of transmission reduction. Although data has suggested that mask adherence is high, few studies have captured details on how mask wearing changes with activities and how these behaviors...
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Background Current mitigation strategies for SARS-CoV-2 rely on population-wide adoption of non-pharmaceutical interventions (NPIs). Monitoring NPI adoption, mobility patterns and their association with SARS-CoV-2 infection can provide key information for public health agencies and be used to calibrate transmission models. Methods We used an onlin...
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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...
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In the US, public health officials discouraged travel and social gatherings for Thanksgiving. Data suggests that many individuals did travel over the holidays, albeit in smaller numbers than previous years. Using an online panel survey of individuals across ten US states, we found that many individuals reported spending Thanksgiving outside of thei...
Preprint
Full-text available
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...
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Full-text available
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...
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Malaria elimination strategies are designed to more effectively identify and treat infected individuals to interrupt transmission. One strategy, reactive screen-and-treat, starts with passive detection of symptomatic cases at health facilities. Individuals residing within the index case and neighboring households are screened with a malaria rapid d...
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Pertussis is a highly contagious infectious disease and remains an important cause of mortality and morbidity worldwide. Over the last decade, vaccination has greatly reduced the burden of pertussis. Yet, uncertainty in individual vaccination coverage and ineffective case surveillance systems make it difficult to estimate burden and the related qua...
Preprint
Full-text available
Human travel is one of the primary drivers of infectious disease spread. Models of travel are often used that assume the amount of travel to a specific destination decays as cost of travel increases and higher travel volumes to more populated destinations. Trip duration, the length of time spent in a destination, can also impact travel patterns. We...
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Full-text available
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...
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On March 11, 2020, the World Health Organization declared COVID-19 a pandemic1. The outbreak containment strategies in China based on non-pharmaceutical interventions (NPIs) appear to be effective2, but quantitative research is still needed to assess the efficacy of NPIs and their timings3. Using epidemiological and anonymised human movement data4,...
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Background: Current mitigation strategies for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) rely on population-wide adoption of non-pharmaceutical interventions (NPIs). Monitoring NPI adoption and their association with SARS-CoV-2 infection history can provide key information for public health. Methods: We sampled 1,030 individual...
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Madagascar has experienced significant environmental change since 1960, particularly through forest clearing for agricultural expansion. Climatic patterns are undergoing change in Madagascar as well, with increasing temperatures, droughts, and cyclonic activity. The impact of these environmental and climatic changes will pose threats to food availa...
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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...
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Humans can impact the spatial transmission dynamics of infectious diseases by introducing pathogens into susceptible environments. The rate at which this occurs depends in part on human-mobility patterns. Increasingly, mobile-phone usage data are used to quantify human mobility and investigate the impact on disease dynamics. Although the number of...
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Background: Current mitigation strategies for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) rely on population-wide adoption of non-pharmaceutical interventions (NPIs). Collecting demographically and geographically resolved data on NPIs and their association with SARS-CoV-2 infection history can provide critical information related...
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Patterns of measles infection in large urban populations have long been considered the paradigm of synchronized nonlinear dynamics. Indeed, recurrent epidemics appear approximately mass-action despite underlying heterogeneity. However, using a subset of rich, newly digitized mortality data (1897-1906), we challenge that proposition. We find that su...
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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...
Article
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the cause of coronavirus disease (COVID-19), has spurred a global health crisis. To date, there are no proven options for prophylaxis for those who have been exposed to SARS-CoV-2, nor therapy for those who develop COVID-19. Immune (i.e. "convalescent") plasma refers to plasma that is co...
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Measles vaccination is a public health ‘best buy’, with the highest cost of illness averted of any vaccine-preventable disease [1]. In the last decades, substantial reductions have been made in the number of measles cases, with an estimated 20 million deaths averted from 2000 to 2017 [2]. Yet, an important feature of epidemic dynamics is that large...
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Background The COVID-19 outbreak containment strategies in China based on non-pharmaceutical interventions (NPIs) appear to be effective. Quantitative research is still needed however to assess the efficacy of different candidate NPIs and their timings to guide ongoing and future responses to epidemics of this emerging disease across the World. Met...
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Background: Spread of malaria and antimalarial resistance through human movement present major threats to current goals to eliminate the disease. Bordering the Greater Mekong Subregion, southeast Bangladesh is a potentially important route of spread to India and beyond, but information on travel patterns in this area are lacking. Methods: Using...
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Background: While the utility of parasite genotyping for malaria elimination has been extensively documented in low to moderate transmission settings, it has been less well-characterized in holoendemic regions. High malaria burden settings have received renewed attention acknowledging their critical role in malaria elimination. Defining the role f...
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After many decades of vaccination, measles epidemiology varies greatly between and within countries. National immunization programs are therefore encouraged to conduct regular situation analyses and to leverage models to adapt interventions to local needs. Here, we review applications of models to develop locally tailored interventions to support c...
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A key question in ecology is the relative impact of internal nonlinear dynamics and external perturbations on the long-term trajectories of natural systems. Measles has been analyzed extensively as a paradigm for consumer-resource dynamics due to the oscillatory nature of the host-pathogen life cycle, the abundance of rich data to test theory, and...
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For countries aiming for malaria elimination, travel of infected individuals between endemic areas undermines local interventions. Quantifying parasite importation has therefore become a priority for national control programs. We analyzed epidemiological surveillance data, travel surveys, parasite genetic data, and anonymized mobile phone data to m...
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Local and cross-border importation remain major challenges to malaria elimination and are difficult to measure using traditional surveillance data. To address this challenge, we systematically collected parasite genetic data and travel history from thousands of malaria cases across northeastern Namibia and estimated human mobility from mobile phone...
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Introduction: Measles elimination depends on the successful deployment of measles containing vaccine. Vaccination programs often depend on a combination of routine and non-routine services, including supplementary immunization activities (SIAs) and vaccination weeks (VWs), that both aim to vaccinate all eligible children regardless of vaccination...
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The original article [1] contained an error in the presentation of Figure 1; this error has now been rectified and Figure 1 is now presented correctly.
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Background Recent global progress in scaling up malaria control interventions has revived the goal of complete elimination in many countries. Decreasing transmission intensity generally leads to increasingly patchy spatial patterns of malaria transmission in elimination settings, with control programs having to accurately identify remaining foci in...
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Background: Southern Province, Zambia, has experienced a dramatic decline in Plasmodium falciparum malaria transmission in the past decade and is targeted for elimination. Zambia's National Malaria Elimination Program recommends reactive case detection (RCD) within 140m of index households to enhance surveillance and eliminate remaining transmissi...
Data
The appendix includes the materials and methods of data collation and analysis, tables A and B, and figs A–U. (PDF)
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Author summary Given the global expanding distribution of Aedes mosquitoes, dengue has established itself throughout the world’s tropical and subtropical regions in both endemic and epidemic transmission cycles, causing significant morbidity and mortality. Moreover, the rise of air travel over the past century has resulted in a highly inter-connect...