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At least 55 records · Page 3

Peru Health & Air Quality: Land Use Change in the Rapidly Developing Peruvian Amazon and Implications on Zoonotic Disease Incidence

In the Madre de Dios region of the Peruvian Amazon, forests are being cleared for mining, timber harvesting, road construction, and hydroelectric dam development. These rapid land use changes are increasing human presence in previously sparsely populated areas, disrupting ecosystems and increasing the proximity of human settlement to zoonotic disease vectors. Dengue fever and leishmaniasis are two neglected tropical diseases which are prevalent in Madre de Dios and have been associated with urbanization and road construction. In partnership with the Peruvian Ministries of Health (MINSA) and the Environment (MINAM) and other in-country collaborators, our team examined Land Use Land Cover (LULC) correlations with reported dengue and leishmaniasis incidence in the Madre de Dios region to help partners understand the spatial relationship between land use change and zoonotic disease incidence. We created a LULC classification script using Google Earth Engine with Landsat 5 Thematic Mapper and Landsat 8 Operational Land Imager imagery to classify land cover in 2010, 2015, and 2020 and evaluate changes over this time period. We then used the quantified results of the LULC assessment in conjunction with reported disease cases to evaluate correlations between disease incidence and key land cover changes across Madre de Dios’s 11 districts. In the second term, the team will use these products to develop more detailed disease incidence risk maps and models. High risk areas will then be classified, using PeruSat-1 that allow for even higher resolution mapping at less than 3 meters. These products will allow the partners to understand hotspots of land cover change in Peru and the relationship with outbreaks to inform public health decision making and environmental policy.

Elizabeth Stapleton↗

Assessing Land Cover Change Dynamics in the Peruvian Amazon to Map Outbreak Risk and Inform Public Health Interventions for Zoonotic Disease Prevention

Dengue fever and leishmaniasis are two tropical diseases prevalent in Madre de Dios Region of Peru and have been associated with urbanization and road construction. Rapid land use changes such as mining, timber harvesting, and hydroelectric dam development lead to denser human presence in previously sparsely-populated areas which increases the proximity of human settlements to zoonotic disease vectors. In partnership with the Peruvian Ministries of Health (MINSA), the Environment (MINAM), and other in-country collaborators, a NASA DEVELOP team examined Land Use Land Cover (LULC) changes and reported dengue and leishmaniasis incidence in the Madre de Dios region. This sought to help MINSA and MINAM understand the spatial relationship between land use change and zoonotic disease incidence. We created a LULC classification script using Google Earth Engine (GEE) with Landsat 5 Thematic Mapper (TM) and Landsat 8 Operational Land Imager (OLI) imagery to classify land cover in 2010, 2015, and 2020 and evaluate changes over this time period. The team then compared the quantified results of the LULC assessment in conjunction with reported disease cases to evaluate disease incidence and key land cover changes across Madre de Dios’s 11 districts. Follow on work will use these products to develop more detailed outbreak risk maps. These products will allow MINSA, MINAM, and other partners to understand hotspots of land cover change in Peru and the relationship with outbreaks to inform public health decision makers and environmental policy.

Nataly Chacon-Buitrago↗

Scraping Unstructured Data to Explore the Relationship between Rainfall Anomalies and Vector-Borne Disease Outbreaks

According to the World Health Organization (WHO), vector-borne diseases such as malaria and dengue account for 17% of all infectious disease cases and lead to more than 700,000 deaths per year. Tracking and predicting the spread of vector-borne diseases is a vital task that could save hundreds of thousands of lives annually. Oftentimes, the first reports of vector-borne disease outbreaks occur through emails and online reporting systems long before they are officially documented. Tracking and predicting the emergence and spread of vector-borne disease outbreaks requires extracting data from these unstructured sources in combination with historical weather and climate data to understand the underlying background triggers and disease dynamics. In this work, we develop a data extraction pipeline for the online outbreak reporting website ProMED-mail that utilizes a web scraper, transformer neural network summarizer, and named entity recognizer to obtain a dataset of malaria, dengue, zika, and chikungunya outbreaks over the last 30 years. This scraped dataset was further analyzed in association with global rainfall anomalies derived from NASA’s Integrated Multi-satellitE Retrievals for GPM [Global Precipitation Mission] (IMERG) dataset. This preliminary analysis was to understand the effect of global rainfall patterns on the spread of vector-borne diseases. Analysis of the ProMED-mail and GPM data shows that vector-borne disease outbreaks are clustered towards the tropics and outbreaks are often amplified during the rainy seasons. Our scraped dataset can be a valuable tool in creating comprehensive georeferenced disease records for modeling and predicting future outbreaks.

Web scraping↗

Changing Temperatures, Changing Risks

Imagine what life with dengue fever would be like in the U.S. during the year 2050. You live with your family in Houston, Texas, and enjoy frequent fishing excursions at the nearby nature reserve. On average, days are about 5° Fahrenheit warmer than in the previous decade, and a summer dengue outbreak is underway. The local public health agency recommends using insect repellent, wearing long sleeves and pants, covering strollers with mosquito netting, and installing screens on windows and doors. It also suggests eliminating mosquito habitats near homes by emptying water-holding containers like planters, toys, tires, and trash receptacles.

59 BASIC BIOLOGICAL SCIENCES↗

Zika-specific neutralizing antibodies targeting inter-dimer envelope epitopes

Zika virus (ZIKV) is an emerging pathogen that causes devastating congenital defects. The overlapping epidemiology and immunologic cross-reactivity between ZIKV and dengue virus (DENV) pose complex challenges to vaccine design, given the potential for antibody-dependent enhancement of disease. Therefore, classification of ZIKV-specific antibody targets is of notable value. From a ZIKV-infected rhesus macaque, we identify ZIKV-reactive B cells and isolate potent neutralizing monoclonal antibodies (mAbs) with no cross-reactivity to DENV. We group these mAbs into four distinct antigenic groups targeting ZIKV-specific cross-protomer epitopes on the envelope glycoprotein. Co-crystal structures of representative mAbs in complex with ZIKV envelope glycoprotein reveal envelope-dimer epitope and unique dimer-dimer epitope targeting. All four specificities are serologically identified in convalescent humans following ZIKV infection, and representative mAbs from all four groups protect against ZIKV replication in mice. These results provide key insights into ZIKV-specific antigenicity and have implications for ZIKV vaccine, diagnostic, and therapeutic development.

59 BASIC BIOLOGICAL SCIENCES↗

Structures of flavivirus RNA promoters suggest two binding modes with NS5 polymerase

Flaviviruses use a ~70 nucleotide stem-loop structure called stem-loop A (SLA) at the 5' end of the RNA genome as a promoter for RNA synthesis. Flaviviral polymerase NS5 specifically recognizes SLA to initiate RNA synthesis and methylate the 5' guanosine cap. We report the crystal structures of dengue (DENV) and Zika virus (ZIKV) SLAs. DENV and ZIKV SLAs differ in the relative orientations of their top stem-loop helices to bottom stems, but both form an intermolecular three-way junction with a neighboring SLA molecule. To understand how NS5 engages SLA, we determined the SLA-binding site on NS5 and modeled the NS5-SLA complex of DENV and ZIKV. Our results show that the gross conformational differences seen in DENV and ZIKV SLAs can be compensated by the differences in the domain arrangements in DENV and ZIKV NS5s. We describe two binding modes of SLA and NS5 and propose an SLA-mediated RNA synthesis mechanism.

59 BASIC BIOLOGICAL SCIENCES↗

Mathematical modeling of plus-strand RNA virus replication to identify broad-spectrum antiviral treatment strategies

Plus-strand RNA viruses are the largest group of viruses. Many are human pathogens that inflict a socio-economic burden. Interestingly, plus-strand RNA viruses share remarkable similarities in their replication. A hallmark of plus-strand RNA viruses is the remodeling of intracellular membranes to establish replication organelles (so-called “replication factories”), which provide a protected environment for the replicase complex, consisting of the viral genome and proteins necessary for viral RNA synthesis. In the current study, we investigate pan-viral similarities and virus-specific differences in the life cycle of this highly relevant group of viruses. We first measured the kinetics of viral RNA, viral protein, and infectious virus particle production of hepatitis C virus (HCV), dengue virus (DENV), and coxsackievirus B3 (CVB3) in the immuno-compromised Huh7 cell line and thus without perturbations by an intrinsic immune response. Based on these measurements, we developed a detailed mathematical model of the replication of HCV, DENV, and CVB3 and showed that only small virus-specific changes in the model were necessary to describe the in vitro dynamics of the different viruses. Our model correctly predicted virus-specific mechanisms such as host cell translation shut off and different kinetics of replication organelles. Further, our model suggests that the ability to suppress or shut down host cell mRNA translation may be a key factor for in vitro replication efficiency, which may determine acute self-limited or chronic infection. We further analyzed potential broad-spectrum antiviral treatment options in silico and found that targeting viral RNA translation, such as polyprotein cleavage and viral RNA synthesis, may be the most promising drug targets for all plus-strand RNA viruses. Moreover, we found that targeting only the formation of replicase complexes did not stop the in vitro viral replication early in infection, while inhibiting intracellular trafficking processes may even lead to amplified viral growth.

59 BASIC BIOLOGICAL SCIENCES↗

Cell fusing agent virus (Flavivirus) infection in Aedes aegypti in Texas: seasonality, comparison by trap type, and individual viral loads

Abstract South Texas has experienced local transmission of Zika virus and of other mosquito-borne viruses such as chikungunya virus and dengue virus in the last decades. Using a mosquito surveillance program in the Lower Rio Grande Valley (LRGV) and San Antonio, TX, from 2016 to 2018, we detected the presence of an insect-specific virus, cell fusing agent virus (CFAV), in the Aedes aegypti mosquito population. We tested 6,326 females and 1,249 males from the LRGV and 659 females from San Antonio for CFAV by RT-PCR using specific primers. Infection rates varied from 0 to 261 per 1,000 mosquitoes in the LRGV and 115 to 208 per 1,000 in San Antonio depending on the month of collection. Infection rates per 1,000 individuals appeared higher in females collected from BG Sentinel 2 traps compared to Autocidal Gravid Ovitraps, but the ratio of the percentage of infected pools did not differ by trap type. The natural viral load in individual males ranged from 1.25 x 10 2 to 5.50 x 10 6 RNA copies and in unfed females from 5.42 x 10 3 to 8.70 x 10 6 RNA copies. Gravid females were found to harbor fewer viral particles than males and unfed females.

59 BASIC BIOLOGICAL SCIENCES↗

Opportunities in multiscale modeling of mosquito-borne flaviviruses

Mosquito-borne flaviviruses, such as Zika, dengue, West Nile, and yellow fever virus, represent a growing public health concern due to their widespread distribution and the severe diseases they cause. These viruses are difficult to control as climate change and urbanization help mosquitoes expand into new areas, increasing the risk of outbreaks. Mathematical models play a key role in understanding their spread, providing insights at every level—from how the virus multiplies inside cells to how it circulates through entire populations. This review examines various approaches used in modeling arboviruses, including microscale models that focus on cellular and molecular dynamics, mesoscale models that address within-host processes, and macroscale models that capture population-level transmission. We briefly summarize the methodology used for models at each scale, which primarily consists of sets of differential equations with parameters that represent physical rates of change for different subprocesses. We particularly highlight how temperature affects virus transmission, which is key to understanding the impact of climate change. We also show how multiscale models can connect viral replication, immune response, and the spread of infection at a larger scale. This is essential for developing better vaccines and treatments, evaluating disease control measures, predicting the impact of climate change, and improving public health responses to outbreaks.

60 APPLIED LIFE SCIENCES↗

Mechanism of glycoform specificity and in vivo protection by an anti-afucosylated IgG nanobody

Abstract Immunoglobulin G (IgG) antibodies contain a complex N -glycan embedded in the hydrophobic pocket between its heavy chain protomers. This glycan contributes to the structural organization of the Fc domain and determines its specificity for Fcγ receptors, thereby dictating distinct cellular responses. The variable construction of this glycan structure leads to highly-related, but non-equivalent glycoproteins known as glycoforms. We previously reported synthetic nanobodies that distinguish IgG glycoforms. Here, we present the structure of one such nanobody, X0, in complex with the Fc fragment of afucosylated IgG1. Upon binding, the elongated CDR3 loop of X0 undergoes a conformational shift to access the buried N -glycan and acts as a ‘glycan sensor’, forming hydrogen bonds with the afucosylated IgG N -glycan that would otherwise be sterically hindered by the presence of a core fucose residue. Based on this structure, we designed X0 fusion constructs that disrupt pathogenic afucosylated IgG1-FcγRIIIa interactions and rescue mice in a model of dengue virus infection.

59 BASIC BIOLOGICAL SCIENCES↗

Fusion and fission events regulate endosome maturation and viral escape

Endosomes are intracellular vesicles that mediate the communication of the cell with its extracellular environment. They are an essential part of the cell’s machinery regulating intracellular trafficking via the endocytic pathway. Many viruses, which in order to replicate require a host cell, attach themselves to the cellular membrane; an event which usually initiates uptake of a viral particle through the endocytic pathway. In this way viruses hijack endosomes for their journey towards intracellular sites of replication and avoid degradation without host detection by escaping the endosomal compartment. Recent experimental techniques have defined the role of endosomal maturation in the ability of enveloped viruses to release their genetic material into the cytoplasm. Endosome maturation depends on a family of small hydrolase enzymes (or GTPases) called Rab proteins, arranged on the cytoplasmic surface of its membrane. Here, we model endosomes as intracellular compartments described by two variables (its levels of active Rab5 and Rab7 proteins) and which can undergo coagulation (or fusion) and fragmentation (or fission). The key element in our approach is the “per-cell endosomal distribution” and its dynamical (Boltzmann) equation. The Boltzmann equation allows us to derive the dynamics of the total number of endosomes in a cell, as well as the mean and the standard deviation of its active Rab5 and Rab7 levels. We compare our mathematical results with experiments of Dengue viral escape from endosomes. The relationship between endosomal active Rab levels and pH suggests a mechanism that can account for the observed variability in viral escape times, which in turn regulate the viability of a viral intracellular infection.

59 BASIC BIOLOGICAL SCIENCES↗

Structural basis for Zika envelope domain III recognition by a germline version of a recurrent neutralizing antibody

Recent epidemics demonstrate the global threat of Zika virus (ZIKV), a flavivirus transmitted by mosquitoes. Although infection is usually asymptomatic or mild, newborns of infected mothers can display severe symptoms, including neurodevelopmental abnormalities and microcephaly. Given the large-scale spread, symptom severity, and lack of treatment or prophylaxis, a safe and effective ZIKV vaccine is urgently needed. However, vaccine design is complicated by concern that elicited antibodies (Abs) may cross-react with other flaviviruses that share a similar envelope protein, such as dengue virus, West Nile virus, and yellow fever virus. This cross-reactivity may worsen symptoms of a subsequent infection through Ab-dependent enhancement. To better understand the neutralizing Ab response and risk of Ab-dependent enhancement, further information on germline Ab binding to ZIKV and the maturation process that gives rise to potently neutralizing Abs is needed. In this work, we use binding and structural studies to compare mature and inferred-germline Ab binding to envelope protein domain III of ZIKV and other flaviviruses. We show that affinity maturation of the light-chain variable domain is important for strong binding of the recurrent VH3-23/VK1-5 neutralizing Abs to ZIKV envelope protein domain III, and identify interacting residues that contribute to weak, cross-reactive binding to West Nile virus. These findings provide insight into the affinity maturation process and potential cross-reactivity of VH3-23/VK1-5 neutralizing Abs, informing precautions for protein-based vaccines designed to elicit germline versions of neutralizing Abs.

59 BASIC BIOLOGICAL SCIENCES↗

Three-dimensional structure of a flavivirus dumbbell RNA reveals molecular details of an RNA regulator of replication

Abstract Mosquito-borne flaviviruses (MBFVs) including dengue, West Nile, yellow fever, and Zika viruses have an RNA genome encoding one open reading frame flanked by 5′ and 3′ untranslated regions (UTRs). The 3′ UTRs of MBFVs contain regions of high sequence conservation in structured RNA elements known as dumbbells (DBs). DBs regulate translation and replication of the viral RNA genome, functions proposed to depend on the formation of an RNA pseudoknot. To understand how DB structure provides this function, we solved the x-ray crystal structure of the Donggang virus DB to 2.1Å resolution and used structural modeling to reveal the details of its three-dimensional fold. The structure confirmed the predicted pseudoknot and molecular modeling revealed how conserved sequences form a four-way junction that appears to stabilize the pseudoknot. Single-molecule FRET suggests that the DB pseudoknot is a stable element that can regulate the switch between translation and replication during the viral lifecycle by modulating long-range RNA conformational changes.

Akiyama, Benjamin M.↗

Development of HEK-293 Cell Lines Constitutively Expressing Flaviviral Antigens for Use in Diagnostics

Flaviviruses are important human pathogens worldwide. Diagnostic testing for these viruses is difficult because many of the pathogens require specialized biocontainment. To address this issue, we generated 39 virus-like particle (VLP)- and nonstructural protein 1 (NS1)-secreting stable cell lines in HEK-293 cells of 13 different flaviviruses, including dengue, yellow fever, Japanese encephalitis, West Nile, St. Louis encephalitis, Zika, Rocio, Ilheus, Usutu, and Powassan viruses. Antigen secretion was stable for at least 10 cell passages, as measured by enzyme-linked immunosorbent assays and immunofluorescence assays. Thirty-five cell lines (90%) had stable antigen expression over 10 passages, with three of these cell lines (7%) increasing in antigen expression and one cell line (3%) decreasing in antigen expression. Antigen secretion in the HEK-293 cell lines was higher than in previously developed COS-1 cell line counterparts. These antigens can replace current antigens derived from live or inactivated virus for safer use in diagnostic testing.

59 BASIC BIOLOGICAL SCIENCES↗

High-resolution RNA tertiary structures in Zika virus stem-loop A for the development of inhibitory small molecules

Flaviviruses such as Zika (ZIKV) and dengue virus (DENV) are positive-sense RNA viruses belonging to Flaviviridae. The flavivirus genome contains a 5’ end stem-loop promoter sequence known as stem-loop A (SLA) that is recognized by the flavivirus polymerase NS5 during viral RNA synthesis and 5’ guanosine cap methylation. The crystal structures of ZIKV and DENV SLAs show a well-defined fold, consisting of a bottom stem, side loop, and top stem-loop, providing unique interaction sites for small-molecule inhibitors to disrupt the promoter function. To facilitate identification of small molecule binding sites in flavivirus SLA, we determined high-resolution structures of bottom and top stems of ZIKV SLA, which contain a single U- or G-bulge, respectively. Both bulge nucleotides exhibit multiple orientations, from folded back on the adjacent nucleotide to flipped out of the helix, and are stabilized by stacking or base triple interactions. These structures suggest that even a single unpaired nucleotide can provide flexibility to RNA structures and its conformation is mainly determined by the stabilizing chemical environment. To facilitate discovery of small molecule inhibitors that interfere with the functions of ZIKV SLA, we screened and identified compounds that bind to the bottom and top stems of ZIKV SLA.

Biochemistry & Molecular Biology↗

Addressing delayed case reporting in infectious disease forecast modeling

Infectious disease forecasting is of great interest to the public health community and policymakers, since forecasts can provide insight into disease dynamics in the near future and inform interventions. Due to delays in case reporting, however, forecasting models may often underestimate the current and future disease burden. In this paper, we propose a general framework for addressing reporting delay in disease forecasting efforts with the goal of improving forecasts. We propose strategies for leveraging either historical data on case reporting or external internet-based data to estimate the amount of reporting error. We then describe several approaches for adapting general forecasting pipelines to account for under- or over-reporting of cases. We apply these methods to address reporting delay in data on dengue fever cases in Puerto Rico from 1990 to 2009 and to reports of influenza-like illness (ILI) in the United States between 2010 and 2019. Through a simulation study, we compare method performance and evaluate robustness to assumption violations. Our results show that forecasting accuracy and prediction coverage almost always increase when correction methods are implemented to address reporting delay. Some of these methods required knowledge about the reporting error or high quality external data, which may not always be available. Provided alternatives include excluding recently-reported data and performing sensitivity analysis. This work provides intuition and guidance for handling delay in disease case reporting and may serve as a useful resource to inform practical infectious disease forecasting efforts.

59 BASIC BIOLOGICAL SCIENCES↗

Predicting Future Disease Burden in a Rapidly Changing Climate

The interplay of a rapidly changing climate and infectious disease occurrence is emerging as a critical topic, requiring investigation of possible direct, as well as indirect, connections between disease processes and climate-related variation and phenomena. First, we introduce and overview three infectious disease exemplars (dengue, influenza, valley fever) representing different transmission classes (insect-vectored, human-to-human, environmentally-transmitted) to illuminate the complex and significant interplay between climate disease processes, as well as to motivate discussion of how Sandia can transform the field, and change our understanding of climate-driven infectious disease spread. We also review state-of-the-art epidemiological and climate modeling approaches, together with data analytics and machine learning methods, potentially relevant to climate and infectious disease studies. We synthesize the modeling and disease exemplars information, suggesting initial avenues for research and development (R&D) in this area, and propose potential sponsors for this work. Whether directly or indirectly, it is certain that a rapidly changing climate will alter global disease burden. The trajectory of climate change is an important control on this burden, from local, to regional and global scales. The efforts proposed herein respond to the National Research Councils call for the creation of a multidisciplinary institute that would address critical aspects of these interlocking, cascading crises.

54 ENVIRONMENTAL SCIENCES↗

Challenges and Solutions for Leave-One-Out Biosensor Design in the Context of a Rugged Fitness Landscape

The leave-one-out (LOO) green fluorescent protein (GFP) approach to biosensor design combines computational protein design with split protein reconstitution. LOO-GFPs reversibly fold and gain fluorescence upon encountering the target peptide, which can be redefined by computational design of the LOO site. Such an approach can be used to create reusable biosensors for the early detection of emerging biological threats. Enlightening biophysical inferences for nine LOO-GFP biosensor libraries are presented, with target sequences from dengue, influenza, or HIV, replacing beta strands 7, 8, or 11. An initially low hit rate was traced to components of the energy function, manifesting in the over-rewarding of over-tight side chain packing. Also, screening by colony picking required a low library complexity, but designing a biosensor against a peptide of at least 12 residues requires a high-complexity library. This double-bind was solved using a “piecemeal” iterative design strategy. Also, designed LOO-GFPs fluoresced in the unbound state due to unwanted dimerization, but this was solved by fusing a fully functional prototype LOO-GFP to a fiber-forming protein, Drosophila ultrabithorax, creating a biosensor fiber. One influenza hemagglutinin biosensor is characterized here in detail, showing a shifted excitation/emission spectrum, a micromolar affinity for the target peptide, and an unexpected photo-switching ability.

Chemistry↗