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Scholarly Works (9 results)

  • Thesis
  • Peer Reviewed
UC Berkeley Electronic Theses and Dissertations (2020)

Background

Zika and chikungunya are arboviral diseases of growing concern in regard to human health. Chikungunya virus (CHIKV) and Zika virus (ZIKV) recently expanded their traditional niches from Africa and Asia into the Americas. Starting in late 2013 and extending through 2016, Latin American countries experienced massive chikungunya epidemics followed by even larger Zika epidemics. Established epidemiological knowledge about Zika and chikungunya mostly derive from a few studies, usually of small or modest sample sizes. The clinical aspects of Zika in children are not well understood, as the existing literature on the topic is based on small studies using strict criteria for laboratory testing and suboptimal statistical methods. In addition, because the two arboviral diseases share a similar set of signs and symptoms, making an accurate diagnosis can be difficult in the absence of laboratory methods. Spatial studies of chikungunya and Zika to date are based on a sample of cases (i.e., instances of symptomatic infection), which creates two problems. First, spatially analyzing only cases conflates the separate processes of infection and disease; second, spatial case-only analyses ignore inapparent infections, which constitute the majority of CHIKV and ZIKV infections. Together, the existing limitations in the Zika and chikungunya literature preclude a full understanding of the viruses’ epidemiological, clinical, and spatial impacts at the population level.

Methods

The Pediatric Dengue Cohort Study (PDCS) is an ongoing, prospective cohort. At the time of the present studies, it enrolled approximately 3,700 children aged 2-14 years in Managua, Nicaragua. It was established in 2004 to study dengue virus infections but expanded to cover CHIKV and ZIKV in 2014 and 2015, respectively. We analyzed demographic, clinical, serological, and geospatial data from participants of the PDCS during the 2004-2019 timeframe. The main parameters of interest were: the percentage of CHIKV infections that are inapparent; the prevalence of anti-ZIKV antibodies (ZIKV seroprevalence), the sensitivity of the Zika case definitions from the World Health Organization and the Pan American Health Organization, the prevalence of signs and symptoms caused by symptomatic ZIKV infections, and the spatiotemporal patterns of CHIKV and ZIKV infections and cases. We used generalized additive models, Monte Carlo resampling, Bayesian statistics, hierarchical agglomerative clustering, generalized estimating equations, geostatistics, and non-parametric approaches in the analysis of PDCS data. Systematic searches of the CHIKV and ZIKV literature were used to augment and verify analyses conducted on PDCS data.

Results

The percentage of CHIKV infections that were inapparent varied by CHIKV lineage. Epidemics of the Asian CHIKV lineage exhibited a median proportion of inapparent infection of 48% (95% credible interval: 20%, 77%) and the CHIKV East/Central/South African lineage exhibited a median proportion of inapparent infection of 18% (95% credible interval: 0%, 47%). An inverse association between CHIKV seroprevalence and the percentage of CHIKV infections that were inapparent was observed in the PDCS and for most studies in the CHIKV literature, verifying a decade-old hypothesis in the field. After a three-month Zika epidemic in Managua, Nicaragua, ZIKV seroprevalence was 36% among children (aged 2-14 years), 46% among the overall population (aged 2-80 years), and 56% among adults (aged 15-80 years), as measured by the biotinylated Zika NS1 blockade-of-binding assay. The clinical spectrum of Zika was observed to vary across age; older children exhibited a higher number and wider range of signs, symptoms, and complete blood count findings than younger children. Official case definitions for Zika exhibited low sensitivity (20-32%) in children because the case definitions were derived from clinical data in adults, and adults tend to exhibit different clinical manifestations of Zika than children. The 2014-2015 chikungunya epidemics and the 2016 Zika epidemic had different spatiotemporal patterns and exhibited distinct spatial clusters of infections. Overall, distance from participants’ households to a cemetery abutting the study area was a robust indicator of infection risk in both the large 2015 chikungunya epidemic and the large 2016 Zika epidemic.

Conclusions

Our results substantially update the epidemiological, clinical, and spatial knowledge regarding ZIKV and CHIKV. Our studies, often the largest of their kind, provide novel insights into the viruses and their respective diseases. In addition, our epidemiological results provide hypotheses that can be explored in future virological and immunological studies. Taken together, our studies provide practical knowledge that ministries of health and international health organizations can use to better prepare for future epidemics of Zika and chikungunya.

    • Article
    • Peer Reviewed
    UC Berkeley Previously Published Works (2022)
    Diarrhea remains a leading cause of death in children in developing countries, including Nicaragua, but little is known about patterns of diarrhea occurrence in Central America over long periods of time. The purpose of this study was to determine the incidence, risk factors, long-term trends, and seasonality of diarrhea in children age 2 to 14 years in Managua, Nicaragua. From 2011 to 2019, we examined episodes of diarrhea among 6,485 children who participated in a prospective cohort study and presented for care in a primary care facility. We performed a longitudinal analysis considering time-varying variables and the intra-subject correlation of outcomes. In addition, we analyzed the weekly incidence of diarrhea, applying seasonal trend decomposition to extract secular and seasonal patterns. The overall incidence rate of diarrhea was 133.4 episodes per 1,000 person-years (95% CI, 128.3-138.7). We observed a slight increase in the incidence of diarrhea from 2011 to 2019. Younger age was the strongest predictor of the risk of diarrhea, and incidence increased with every additional hour without running water in the household per day. Diarrhea incidence in Managua was seasonal, with high peaks each year between May and July. Despite reductions in childhood mortality since 1990 in Nicaragua, diarrheal morbidity remains a major problem in Managua.
      Cover page: Epidemiologic Features of Acute Pediatric Diarrhea in Managua, Nicaragua, from 2011 to 2019
      • Article
      • Peer Reviewed
      UC Berkeley Previously Published Works (2019)
      In late 2013, chikungunya virus (CHIKV) was introduced into the Americas, leading to widespread epidemics. A large epidemic caused by the Asian chikungunya virus (CHIKV) lineage occurred in Managua, Nicaragua, in 2015. Literature reviews commonly state that the proportion of inapparent CHIKV infections ranges from 3 to 28%. This study estimates the ratio of symptomatic to asymptomatic CHIKV infections and identifies risk factors of infection. In October to November 2015, 60 symptomatic CHIKV-infected children were enrolled as index cases and prospectively monitored, alongside 236 household contacts, in an index cluster study. Samples were collected upon enrollment and on day 14 or 35 and tested by real-time reverse transcription-PCR (rRT-PCR), IgM capture enzyme-linked immunosorbent assays (IgM-ELISAs), and inhibition ELISAs to detect pre- and postenrollment CHIKV infections. Of 236 household contacts, 55 (23%) had experienced previous or very recent infections, 41 (17%) had active infections at enrollment, and 21 (9%) experienced incident infections. Vehicle ownership (multivariable-adjusted risk ratio [aRR], 1.58) increased the risk of CHIKV infection, whereas ≥4 municipal trash collections/week (aRR, 0.38) and having externally piped water (aRR, 0.52) protected against CHIKV infection. Among 63 active and incident infections, 31 (49% [95% confidence interval {CI}, 36%, 62%]) were asymptomatic, yielding a ratio of symptomatic to asymptomatic infections of 1:0.97 (95% CI, 1:0.56, 1:1.60). Although our estimate is outside the 3% to 28% range reported previously, Bayesian and simulation analyses, informed by a systematic literature search, suggested that the proportion of inapparent CHIKV infections is lineage dependent and that more inapparent infections are associated with the Asian lineage than the East/Central/South African (ECSA) lineage. Overall, these data substantially improve knowledge regarding chikungunya epidemics.IMPORTANCE Chikungunya virus (CHIKV) is an understudied threat to human health. During the 2015 chikungunya epidemic in Managua, Nicaragua, we estimated the ratio of symptomatic to asymptomatic CHIKV infections, which is important for understanding transmission dynamics and the public health impact of CHIKV. This index cluster study identified and monitored persons at risk of infection, enabling capture of asymptomatic infections. We estimated that 31 (49%) of 63 at-risk participants had asymptomatic CHIKV infections, which is significantly outside the 3% to 28% range reported in literature reviews. However, recent seroprevalence studies, including two large pediatric cohort studies in the same setting, had also found percentages of inapparent infections outside the 3% to 28% range. Bayesian and simulation analyses, informed by a systematic literature search, revealed that the percentage of inapparent infections in epidemic settings varies by CHIKV phylogenetic lineage. Our study quantifies and provides the first epidemiological evidence that chikungunya epidemic characteristics are strongly influenced by CHIKV lineage.
        Cover page: Epidemiological Evidence for Lineage-Specific Differences in the Risk of Inapparent Chikungunya Virus Infection.
        • Article
        • Peer Reviewed
        UC Berkeley Previously Published Works (2018)
        Environmentally transmitted diseases are comparatively poorly understood and managed, and their ecology is particularly understudied. Here we identify challenges of studying environmental transmission and persistence with a six-sided interdisciplinary review of the biology of anthrax (Bacillus anthracis). Anthrax is a zoonotic disease capable of maintaining infectious spore banks in soil for decades (or even potentially centuries), and the mechanisms of its environmental persistence have been the topic of significant research and controversy. Where anthrax is endemic, it plays an important ecological role, shaping the dynamics of entire herbivore communities. The complex eco-epidemiology of anthrax, and the mysterious biology of Bacillus anthracis during its environmental stage, have necessitated an interdisciplinary approach to pathogen research. Here, we illustrate different disciplinary perspectives through key advances made by researchers working in Etosha National Park, a long-term ecological research site in Namibia that has exemplified the complexities of the enzootic process of anthrax over decades of surveillance. In Etosha, the role of scavengers and alternative routes (waterborne transmission and flies) has proved unimportant relative to the long-term persistence of anthrax spores in soil and their infection of herbivore hosts. Carcass deposition facilitates green-ups of vegetation to attract herbivores, potentially facilitated by the role of anthrax spores in the rhizosphere. The underlying seasonal pattern of vegetation, and herbivores' immune and behavioural responses to anthrax risk, interact to produce regular 'anthrax seasons' that appear to be a stable feature of the Etosha ecosystem. Through the lens of microbiologists, geneticists, immunologists, ecologists, epidemiologists, and clinicians, we discuss how anthrax dynamics are shaped at the smallest scale by population genetics and interactions within the bacterial communities up to the broadest scales of ecosystem structure. We illustrate the benefits and challenges of this interdisciplinary approach to disease ecology, and suggest ways anthrax might offer insights into the biology of other important pathogens. Bacillus anthracis, and the more recently emerged Bacillus cereus biovar anthracis, share key features with other environmentally transmitted pathogens, including several zoonoses and panzootics of special interest for global health and conservation efforts. Understanding the dynamics of anthrax, and developing interdisciplinary research programs that explore environmental persistence, is a critical step forward for understanding these emerging threats.
          Cover page: Spores and soil from six sides: interdisciplinarity and the environmental biology of anthrax (Bacillus anthracis)
          • Article
          • Peer Reviewed
          UC Berkeley Previously Published Works (2017)
          Environmentally Transmitted Diseases Are Comparatively Poorly Understood And Managed, And Their Ecology Is Particularly Understudied. Here We Identify Challenges Of Studying Environmental Transmission And Persistence With A Six-Sided Interdisciplinary Review Of The Biology Of Anthrax ( Bacillus Anthracis ). Anthrax Is A Zoonotic Disease Capable Of Maintaining Infectious Spore Banks In Soil For Decades (Or Even Potentially Centuries), And The Mechanisms Of Its Environmental Persistence Have Been The Topic Of Significant Research And Controversy. Where Anthrax Is Endemic, It Plays An Important Ecological Role, Shaping The Dynamics Of Entire Herbivore Communities. The Complex Eco-Epidemiology Of Anthrax, And The Mysterious Biology Of Bacillus Anthracis During Its Environmental Stage, Have Necessitated An Interdisciplinary Approach To Pathogen Research. Here, We Illustrate Different Disciplinary Perspectives Through Key Advances Made By Researchers Working In Etosha National Park, A Long-Term Ecological Research Site In Namibia That Has Exemplified The Complexities Of Anthrax’S Enzootic Process Over Decades Of Surveillance. In Etosha, The Role Of Scavengers And Alternate Routes (Waterborne Transmission And Flies) Has Proved Unimportant, Relative To The Long-Term Persistence Of Anthrax Spores In Soil And Their Infection Of Herbivore Hosts. Carcass Deposition Facilitates Green-Ups Of Vegetation To Attract Herbivores, Potentially Facilitated By Anthrax Spores’ Role In The Rhizosphere. The Underlying Seasonal Pattern Of Vegetation, And Herbivores’ Immune And Behavioral Responses To Anthrax Risk, Interact To Produce Regular “Anthrax Seasons” That Appear To Be A Stable Feature Of The Etosha Ecosystem. Through The Lens Of Microbiologists, Geneticists, Immunologists, Ecologists, Epidemiologists, And Clinicians, We Discuss How Anthrax Dynamics Are Shaped At The Smallest Scale By Population Genetics And Interactions Within The Bacterial Communities Up To The Broadest Scales Of Ecosystem Structure. We Illustrate The Benefits And Challenges Of This Interdisciplinary Approach To Disease Ecology, And Suggest Ways Anthrax Might Offer Insights Into The Biology Of Other Important Pathogens. Bacillus Anthracis, And The More Recently Emerged Bacillus Cereus Biovar Anthracis , Share Key Features With Other Environmentally-Transmitted Pathogens, Including Several Zoonoses And Panzootics Of Special Interest For Global Health And Conservation Efforts. Understanding The Dynamics Of Anthrax, And Developing Interdisciplinary Research Programs That Explore Environmental Persistence, Is A Critical Step Forward For Understanding These Emerging Threats.
            Cover page: Spores and soil from six sides: interdisciplinarity and the environmental biology of anthrax (Bacillus anthracis)
            • Article
            • Peer Reviewed
            UC Berkeley Previously Published Works (2018)
            In 2015, a Zika epidemic in Brazil began spreading throughout the Americas. Zika virus (ZIKV) entered Managua, Nicaragua, in January 2016 and caused an epidemic that peaked in July-September 2016. ZIKV seropositivity was estimated among participants of pediatric (n = 3,740) and household (n = 2,147) cohort studies, including an adult-only subset from the household cohort (n = 1,074), in Managua. Seropositivity was based on a highly sensitive and specific assay, the Zika NS1 blockade-of-binding ELISA, which can be used in dengue-endemic populations. Overall seropositivity for the pediatric (ages 2-14), household (ages 2-80), and adult (ages 15-80) cohorts was 36, 46, and 56%, respectively. Trend, risk factor, and contour mapping analyses demonstrated that ZIKV seroprevalence increased nonlinearly with age and that body surface area was statistically associated with increasing seroprevalence in children. ZIKV seropositivity was higher in females than in males across almost all ages, with adjusted prevalence ratios in children and adults of 1.11 (95% CI: 1.02-1.21) and 1.14 (95% CI: 1.01-1.28), respectively. No household-level risk factors were statistically significant in multivariate analyses. A spatial analysis revealed a 10-15% difference in the risk of ZIKV infections across our 3-km-wide study site, suggesting that ZIKV infection risk varies at small spatial scales. To our knowledge, this is the largest ZIKV seroprevalence study reported in the Americas, and the only one in Central America and in children to date. It reveals a high level of immunity against ZIKV in Managua as a result of the 2016 epidemic, making a second large Zika epidemic unlikely in the near future.
              Cover page: Seroprevalence, risk factor, and spatial analyses of Zika virus infection after the 2016 epidemic in Managua, Nicaragua
              • Article
              • Peer Reviewed
              UC Berkeley Previously Published Works (2020)

              Background

              Paedeatric Zika remains an understudied topic. WHO and the Pan American Health Organization (PAHO) Zika case definitions have not been assessed in children. We aimed to characterise clinical profiles and evaluate the diagnostic performance of the WHO and PAHO case definitions in a large cohort of paediatric Zika cases.

              Methods

              From January, 2016 to February, 2017, encompassing the major 2016 Zika epidemic, participants in the Pediatric Dengue Cohort Study (PDCS) in Managua, Nicaragua, were encouraged to visit the study health centre at first indication of any illness. PDCS participants were aged 2-14 years, healthy at enrolment, and recruited before the initiation of the present study. Molecular and serological assays were used to test participants exhibiting any of four broad clinical profiles suspected of resulting from a symptomatic Zika virus infection. These clinical profiles were: fever and at least two of headache, retro-orbital pain, myalgia, arthralgia, rash, haemorrhagic manifestations, and leukopenia; fever and at least two of nausea or vomiting, rash, aches and pains, positive tourniquet test, leukopenia, and any dengue warning sign; undifferentiated fever without evident cause, with or without any other clinical finding; and afebrile rash with or without any other clinical finding. We characterised acute clinical findings (signs, symptoms, and complete blood counts) in both Zika cases and non-Zika cases.

              Findings

              We prospectively followed a cohort of about 3700 children, of which 1110 were deemed eligible for inclusion. Four participants with laboratory-confirmed Zika (three co-infections with dengue virus, one missing complete blood count data) and two participants who were non-Zika cases (missing complete blood count data) were excluded from analysis. We analysed 556 laboratory-confirmed Zika and 548 non-Zika cases. The WHO case definition captured 176 confirmed Zika cases, and the PAHO definition 109 confirmed Zika cases, who presented with the most clinical findings and a dengue-like clinical profile. The remaining two thirds of Zika cases, principally characterised by undifferentiated fever or afebrile rash, were missed. Among Zika cases, rash (n=440)-particularly generalised erythematous rash (n=334)-fever (n=333), leukopenia (n=217), and headache (n=203) were most common and peaked within 3 days of illness onset. The most common Zika presentation over the first week of illness was rash only (n=80). The sensitivity of Zika case definitions increased across paediatric age (from 11·3% to 56·1% for the WHO case definition and from 6·0% to 36·6% for the PAHO case definition), as the prevalence of most clinical findings (particularly arthralgia) increased with age, irrespective of previous dengue virus infection. Consequently, Zika manifested differently across paediatric age; older Zika cases presented with a dengue-like clinical profile while younger Zika cases presented with undifferentiated fever or afebrile rash.

              Interpretation

              We provide the most thorough description of paediatric Zika to date. Most paediatric Zika cases go undetected under the WHO and PAHO case definitions, suggesting that current standards for Zika case ascertainment require revision. Zika manifests with mild but differing clinical profiles across paediatric age, presenting major challenges to diagnosis, surveillance, and efforts to control future Zika epidemics.

              Funding

              US National Institutes of Health.
                Cover page: Age-dependent manifestations and case definitions of paediatric Zika: a prospective cohort study
                • Article
                • Peer Reviewed
                UC Berkeley Previously Published Works (2021)
                The only licensed dengue vaccine, Dengvaxia®, increases risk of severe dengue when given to individuals without prior dengue virus (DENV) infection but is protective against future disease in those with prior DENV immunity. The World Health Organization has recommended using rapid diagnostic tests (RDT) to determine history of prior DENV infection and suitability for vaccination. Dengue experts recommend that these assays be highly specific (≥98%) to avoid erroneously vaccinating individuals without prior DENV infection, as well as be sensitive enough (≥95%) to detect individuals with a single prior DENV infection. We evaluated one existing and two newly developed anti-flavivirus RDTs using samples collected >6 months post-infection from individuals in non-endemic and DENV and ZIKV endemic areas. We first evaluated the IgG component of the SD BIOLINE Dengue IgG/IgM RDT, which was developed to assist in confirming acute/recent DENV infections (n=93 samples). When evaluated following the manufacturers instructions, the SD BIOLINE Dengue RDT had 100% specificity for both non-endemic and endemic samples but low sensitivity for detecting DENV seropositivity (0% non-endemic, 41% endemic). Sensitivity increased (53% non-endemic, 98% endemic) when tests were allowed to run beyond manufacturer recommendations (0.5 up to 3 hours), but specificity decreased in endemic samples (36%). When tests were evaluated using a quantitative reader, optimal specificity could be achieved (≥98%) while still retaining sensitivity at earlier timepoints in non-endemic (44-88%) and endemic samples (31-55%). We next evaluated novel dengue and Zika RDTs developed by Excivion to detect prior DENV or ZIKV infections and reduce cross-flavivirus reactivity (n=207 samples). When evaluated visually, the Excivion Dengue RDT had sensitivity and specificity values of 79%, but when evaluated with a quantitative reader, optimal specificity could be achieved (≥98%) while still maintaining moderate sensitivity (48-75%). The Excivion Zika RDT had high specificity (>98%) and sensitivity (>93%) when evaluated quantitatively, suggesting it may be used alongside dengue RDTs to minimize misclassification due to cross-reactivity. Our findings demonstrate the potential of RDTs to be used for dengue pre-vaccination screening to reduce vaccine-induced priming for severe dengue and show how assay design adaptations as well quantitative evaluation can further improve RDTs for this purpose.
                  Cover page: Adapting Rapid Diagnostic Tests to Detect Historical Dengue Virus Infections.
                  • Article
                  • Peer Reviewed
                  UC Berkeley Previously Published Works (2021)
                  Dengue virus serotypes 1 to 4 (DENV1–4) and Zika virus (ZIKV) are mosquito-borne flaviviruses that induce both virus-specific and broadly reactive antibodies. A first DENV infection is thought to induce antibodies that wane over 2 years to titers that can subsequently enhance severe dengue disease. Secondary DENV infection with a different serotype is thought to induce stable, cross-serotype protective antibodies. Low dengue disease incidence after the recent Zika pandemic led to the hypothesis that ZIKV infection is also transiently cross protective. We investigated antibody kinetics in 4189 children up to 11 years after one and multiple DENV and ZIKV infections in longitudinal cohorts in Nicaragua. We used a DENV inhibition enzyme-linked immunosorbent assay (iELISA), which measures antibodies associated with protection against dengue and Zika disease and with enhancement of dengue disease severity. Unexpectedly, we found that overall DENV iELISA titers stabilized by 8 months after primary DENV infection to a half-life longer than a human life and waned, although gradually, after secondary DENV infection. Similarly, DENV iELISA titers were stable or rose after primary ZIKV infection but declined in individuals with histories of DENV and ZIKV infection. In contrast, kinetics of anti-ZIKV antibodies after ZIKV infection were similar regardless of prior DENV immunity. We observed heterogeneity in DENV iELISA titer, suggesting that individual antibody titer set point, rather than waning, is important for future dengue disease risk. Together, these findings change our understanding of anti-flavivirus antibody kinetics and have implications for measuring vaccine efficacy and for predicting future dengue and Zika outbreaks.
                    Cover page: Dengue and Zika virus infections in children elicit cross-reactive protective and enhancing antibodies that persist long term.
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