Browsing by Subject "Dengue"
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Item Open Access A Comprehensive Needs Assessment to Identify Priority Program Targets for Mosquito Vector Control and related Diseases in Belmopan, Belize(2017) Schooler, Mary ElizabethThis was a mixed-methods study aimed to comprehensively assess factors associated with mosquito control in Belmopan, Belize, in order to better inform stakeholders on the effectiveness of their efforts. A knowledge, attitudes, and perceptions (KAP) survey was employed within the four target communities of San Martin, Salvapan, Maya Mopan, and Las Flores. Additional epidemiological and entomological data was provided by relevant stakeholders. A total of 228 households were surveyed among the four target communities. Only 1/3 of respondents were able to demonstrate proficient knowledge. Knowledge was attained mostly through TV, Ministry of Health, hospital, and radio sources. Over 90% of respondents believed that mosquitos and the diseases they carry were a real issue for the community. Respondents living in Salvapan and Las Flores were more likely to have contracted Dengue Fever, Malaria, Chikungunya, or Zika than in other areas. Fan usage and regularly cleaning the yard were the two most employed practices for preventing mosquito bites and breeding. Approximately 85% of those surveyed viewed insecticide spraying to be effective. This assessment provides valuable insight into the needs of at- risk communities in regards to vector control. An increased focus on community outreach, education, and behavioral change can greatly impact the effectiveness of current vector control efforts. Stakeholders must work together and pool resources in order to effectively employ control interventions. Continued evaluation and community involvement is necessary to control mosquitos and prevent disease outbreaks.
Item Open Access Characterization of Host Factors and Anti-viral Compounds for Diverse Mosquito-borne Flaviviruses(2016) Barrows, Nicholas J.Our ability to convert basic knowledge into robust anti-viral therapeutics requires discovery of novel host-virus interactions as well as an informed anti-viral discovery pipeline. We used a genome-scale RNAi-based screen followed by a chemical screen of FDA-approved therapeutics to identify scores of novel dengue virus (DENV) human host dependency factors (HDF) and identified more than 20 potential anti-Zika virus (ZIKV) therapeutics.
Two genes in particular, TTC35 and TMEM111, strongly inhibited DENV infection and, based on comparisons with published literature, implicated a larger protein, the ER Membrane Protein Complex (EMC), as a pan-flavivirus HDF. The EMC is a poorly characterized multiprotein complex that may function in ER-associated protein biogenesis and/or lipid metabolism. Based on our screen data, we hypothesized that the EMC is an uncharacterized HDF that functions through a common mechanism to promote replication of flaviviruses. We report that DENV, ZIKV, and yellow fever virus (YFV) infections were impressively inhibited, while West Nile Virus (WNV) infection was unchanged, in cell lines engineered to lack EMC subunit 4 (EMC4). Furthermore, targeted depletion of EMC subunits in live mosquitos significantly reduced DENV-2 propagation in vivo. In addition, the accumulation of DENV proteins shortly after infection in EMC4 knockout cells was significantly reduced, suggesting that the EMC promotes viral protein biogenesis.
We interrogated a library of FDA-approved drugs for their ability to block infection of human HuH-7 cells by a newly isolated ZIKV strain. Selected compounds were further validated for inhibition of ZIKV infection in human cervical, placental, and neural stem cell lines, as well as primary human amnion cells. Established anti-flaviviral drugs (e.g., bortezomib and mycophenolic acid) and others that had no previously known antiviral activity (e.g., daptomycin) were identified as inhibitors of ZIKV infection. Several drugs reduced ZIKV infection across multiple cell types.
We propose that the EMC may be exploited as a novel therapeutic target for multiple flaviviruses in the future. Also we identified drugs that could be tested in clinical studies of ZIKV infection and provides a resource of small molecules to study ZIKV pathogenesis.
Item Open Access Chikungunya and dengue fever among hospitalized febrile patients in northern Tanzania.(Am J Trop Med Hyg, 2012-01) Hertz, Julian T; Munishi, O Michael; Ooi, Eng Eong; Howe, Shiqin; Lim, Wen Yan; Chow, Angelia; Morrissey, Anne B; Bartlett, John A; Onyango, Jecinta J; Maro, Venance P; Kinabo, Grace D; Saganda, Wilbrod; Gubler, Duane J; Crump, John AConsecutive febrile admissions were enrolled at two hospitals in Moshi, Tanzania. Confirmed acute Chikungunya virus (CHIKV), Dengue virus (DENV), and flavivirus infection were defined as a positive polymerase chain reaction (PCR) result. Presumptive acute DENV infection was defined as a positive anti-DENV immunoglobulin M (IgM) enzyme-linked immunsorbent assay (ELISA) result, and prior flavivirus exposure was defined as a positive anti-DENV IgG ELISA result. Among 870 participants, PCR testing was performed on 700 (80.5%). Of these, 55 (7.9%) had confirmed acute CHIKV infection, whereas no participants had confirmed acute DENV or flavivirus infection. Anti-DENV IgM serologic testing was performed for 747 (85.9%) participants, and of these 71 (9.5%) had presumptive acute DENV infection. Anti-DENV IgG serologic testing was performed for 751 (86.3%) participants, and of these 80 (10.7%) had prior flavivirus exposure. CHIKV infection was more common among infants and children than adults and adolescents (odds ratio [OR] 1.9, P = 0.026) and among HIV-infected patients with severe immunosuppression (OR 10.5, P = 0.007). CHIKV infection is an important but unrecognized cause of febrile illness in northern Tanzania. DENV or other closely related flaviviruses are likely also circulating.Item Open Access Cross-Reactive Dengue Virus Antibodies Augment Zika Virus Infection of Human Placental Macrophages.(Cell host & microbe, 2018-11) Zimmerman, Matthew G; Quicke, Kendra M; O'Neal, Justin T; Arora, Nitin; Machiah, Deepa; Priyamvada, Lalita; Kauffman, Robert C; Register, Emery; Adekunle, Oluwaseyi; Swieboda, Dominika; Johnson, Erica L; Cordes, Sarah; Haddad, Lisa; Chakraborty, Rana; Coyne, Carolyn B; Wrammert, Jens; Suthar, Mehul SZika virus (ZIKV), which emerged in regions endemic to dengue virus (DENV), is vertically transmitted and results in adverse pregnancy outcomes. Antibodies to DENV can cross-react with ZIKV, but whether these antibodies influence ZIKV vertical transmission remains unclear. Here, we find that DENV antibodies increase ZIKV infection of placental macrophages (Hofbauer cells [HCs]) from 10% to over 80% and enhance infection of human placental explants. ZIKV-anti-DENV antibody complexes increase viral binding and entry into HCs but also result in blunted type I interferon, pro-inflammatory cytokine, and antiviral responses. Additionally, ZIKV infection of HCs and human placental explants is enhanced in an immunoglobulin G subclass-dependent manner, and targeting FcRn reduces ZIKV replication in human placental explants. Collectively, these findings support a role for pre-existing DENV antibodies in enhancement of ZIKV infection of select placental cell types and indicate that pre-existing immunity to DENV should be considered when addressing ZIKV vertical transmission.Item Open Access Dengue Myocarditis: A Case Report and Major Review.(Global heart, 2023-01) Cristodulo, Roberto; Luoma-Overstreet, Gracia; Leite, Fernando; Vaca, Manuel; Navia, Michelle; Durán, Gustavo; Molina, Fernando; Zonneveld, Bozorg; Perrone, Sergio Víctor; Barbagelata, Alejandro; Kaplinsky, EdgardoDengue is a viral disease transmitted by the bite of a female arthropod, prevalent primarily in tropical and subtropical regions. Its manifestations include asymptomatic infections, dengue fever, and a severe form called hemorrhagic dengue or dengue shock syndrome. Atypical manifestations can also occur, called expanded dengue syndrome. We describe the case of a 43-year-old man with an unusual presentation of dengue, demonstrating a workup suggestive of myocardial and pericardial damage. Symptoms and markers indicative of cardiac compromise improved after five days on anti-inflammatory treatment. Dengue myocarditis is considered an uncommon complication of dengue, although its reported incidence is likely an underestimation. In general, most cases of dengue myocarditis are self-limited, with only a minority at risk of progressing to heart failure. In order to improve recognition and prevent progression, healthcare providers should maintain a high degree of suspicion regarding potential cardiac complications in patients with dengue.Item Open Access Dengue Virus Host Factors(2009) Sessions, October MichaelDengue fever and dengue hemorrhagic fever are estimated to afflict 50-100 million people annually and are caused by one of the four serotypes of dengue virus. Dengue virus is carried and transmitted to humans by mosquitoes of the Aedes genus. Given the broad geographic distribution of Aedes mosquitoes, it has been estimated that nearly half the world's population is at risk of contracting the disease. Currently, no vaccine or specific antiviral treatment is available to combat this emerging menace.
A greater understanding of how dengue virus interacts with its insect and human hosts will facilitate the intelligent design of specific antivirals to combat the disease and enable the selective breeding of mosquitoes resistant to the virus. Although the genomes of the two primary mosquito vectors have been sequenced, the molecular tools necessary for conducting a systematic genetic analysis of host factors required for DEN infection are not yet available. These tools do however exist in the closely related fruit fly, Drosophila melanogaster. By using a strain of dengue virus that was adapted to propagate in fruit fly cells, we completed a full genetic screen for host factors required for efficient dengue virus propagation. When homologues of these host factors were assayed in a human cell line, over half were also shown to be required for efficient viral propagation. This indicates that while the virus is utilizing many of the same pathways in both of its hosts, the interaction with the insect vector has unique features that may contribute to the observed lack of pathogenesis in mosquitoes.
Item Open Access Detection of Dengue, Chikungunya, and Zika Viruses Among Patients in Sarawak, Malaysia by a Novel Multiplexing Platform(2019) Zemke, Juliana NashIntroduction: According to the World Health Organization (WHO), 500 million arbovirus cases are diagnosed around the world annually, with 2.7 million associated deaths [1]. The burden of disease caused by dengue, chikungunya, and Zika viruses is likely to be underestimated due to a lack of accurate diagnostic tools and knowledge gaps regarding their epidemiology [2, 3]. This thesis uses a subset of data from an on-going 24-month study to evaluate the potential etiology of dengue-like symptoms of patients recruited from medical facilities in Sarawak, Malaysia. A secondary aim is to assess the diagnostic clinical effectiveness of a new detection method, the novel T-Cor 8 Multiplexing Platform (Tetracore, Inc., USA), using qRT-PCR assays as the gold standard method for comparison. The prevalence of arboviral infections as determined by gold-standard qRT-PCR assays and potential risk factors in the study population were also analysed.
Methods: In this cross-sectional study, patients more than seven years of age with dengue-like symptoms were enrolled at medical facilities in the towns of Sibu and Kapit in Sarawak, Malaysia. Blood, urine, and gingival crevicular fluid samples, as well as risk factor data, were collected from participants at the time of enrolment. These samples were studied by qRT-PCR assays and the novel T-Cor 8 Multiplexing Platform.
Results: Seven (14%) of 51 participants’ serum RNA samples tested positive for arbovirus infection by gold-standard qRT-PCR assays. Two participants (4%) were positive for dengue subtype-1, four participants (8%) were positive for dengue subtype-2, and one participant (2%) was positive for dengue subtype-4. No patient samples had molecular evidence of chikungunya or Zika viruses. The T-Cor 8 multiplexing platform demonstrated a 71% sensitivity (95% confidence interval 29-96%), 93% specificity (95% confidence interval 81-99%), and 90% accuracy (95% confidence interval 78-97%) compared to the gold-standard assays on serum RNA samples. From this subset of data, we failed to identify important risk factors for arboviral infection.
Conclusion: From this limited subset of data, we conclude that the T-Cor 8 platform’s simplicity and accuracy in detecting at least dengue virus infections has considerable potential for clinical usefulness in low-resource settings.
Item Open Access Distribution of Aedes mosquitoes in the Kilimanjaro Region of northern Tanzania.(Pathog Glob Health, 2016-05) Hertz, Julian T; Lyaruu, Lucille J; Ooi, Eng Eong; Mosha, Franklin W; Crump, John ALittle is known about the presence and distribution of Aedes mosquitoes in northern Tanzania despite the occurence of viruses transmitted by these mosquitoes such as Chikungunya virus (CHIKV) and Dengue virus (DENV) in the region. Adult and larval mosquitoes were collected from rural and urban settings across a wide range of altitudes in the Kilimanjaro Region using the Mosquito Magnet CO2 Trap for collection of adults and old tires for breeding of larvae. Polymerase chain reaction assays were performed on captured adult mosquitoes to detect the presence of CHIKV and DENV. A total of 2609 Aedes aegypti adult mosquitoes were collected; no other Aedes species larvae were found. Mosquito yields were significantly higher in urban settings than rural settings (26.5 vs. 1.9 mosquitoes per day, p = 0.037). A total of 6570 Ae. aegypti larvae were collected from old tires; no other Aedes species larvae were found. Of the 2609 adult mosquitoes collected, none tested positive for CHIKV or DENV. As far as we are aware, this paper reports for the first time the presence of Ae. aegypti in the Kilimanjaro Region of northern Tanzania. Although CHIKV and DENV were not isolated from any of the collected mosquitoes in this study, the apparent absence of other Aedes species in the area suggests that Ae. aegypti is the primary local vector of these infections.Item Open Access Drivers of Dengue Within-Host Dynamics and Virulence Evolution(2016) BenShachar, RotemDengue is an important vector-borne virus that infects on the order of 400 million individuals per year. Infection with one of the virus's four serotypes (denoted DENV-1 to 4) may be silent, result in symptomatic dengue 'breakbone' fever, or develop into the more severe dengue hemorrhagic fever/dengue shock syndrome (DHF/DSS). Extensive research has therefore focused on identifying factors that influence dengue infection outcomes. It has been well-documented through epidemiological studies that DHF is most likely to result from a secondary heterologous infection, and that individuals experiencing a DENV-2 or DENV-3 infection typically are more likely to present with more severe dengue disease than those individuals experiencing a DENV-1 or DENV-4 infection. However, a mechanistic understanding of how these risk factors affect disease outcomes, and further, how the virus's ability to evolve these mechanisms will affect disease severity patterns over time, is lacking. In the second chapter of my dissertation, I formulate mechanistic mathematical models of primary and secondary dengue infections that describe how the dengue virus interacts with the immune response and the results of this interaction on the risk of developing severe dengue disease. I show that only the innate immune response is needed to reproduce characteristic features of a primary infection whereas the adaptive immune response is needed to reproduce characteristic features of a secondary dengue infection. I then add to these models a quantitative measure of disease severity that assumes immunopathology, and analyze the effectiveness of virological indicators of disease severity. In the third chapter of my dissertation, I then statistically fit these mathematical models to viral load data of dengue patients to understand the mechanisms that drive variation in viral load. I specifically consider the roles that immune status, clinical disease manifestation, and serotype may play in explaining viral load variation observed across the patients. With this analysis, I show that there is statistical support for the theory of antibody dependent enhancement in the development of severe disease in secondary dengue infections and that there is statistical support for serotype-specific differences in viral infectivity rates, with infectivity rates of DENV-2 and DENV-3 exceeding those of DENV-1. In the fourth chapter of my dissertation, I integrate these within-host models with a vector-borne epidemiological model to understand the potential for virulence evolution in dengue. Critically, I show that dengue is expected to evolve towards intermediate virulence, and that the optimal virulence of the virus depends strongly on the number of serotypes that co-circulate. Together, these dissertation chapters show that dengue viral load dynamics provide insight into the within-host mechanisms driving differences in dengue disease patterns and that these mechanisms have important implications for dengue virulence evolution.
Item Open Access Drug Development in Dengue Virus and Molecular Epidemiology of Malaria in Western Kenya(2017) Levitt, Brandt E.Dengue viruses (DENV) and other mosquito-borne flaviviruses are rapidly emerging human pathogens that threaten nearly half of the world’s population. There is currently no effective vaccine or antiviral therapeutics for the prophylaxis or treatment of DENV. While traditional drug development efforts have focused on inhibitors of viral enzymes, an alternative approach is to target host proteins that support virus replication. In an effort to identify novel human enzymes important for the DENV-2 life-cycle, we conducted a genome-wide RNAi screen and identified ERI3, a putative 3′-5′ exonuclease, as a novel DENV-2 host factor. Cell-free assays confirmed that purified ERI3 is capable of degrading single-stranded RNA in a 3′ to 5′ direction. We conducted a screen for compounds that inhibit ERI3 in vitro and identified small molecules that antagonized both exonuclease activity. In summary, we identified a host exonuclease that is important for DENV-2 replication and is a potential therapeutic target. Our approach illustrates the utility of identifying host enzymatic functions for development of anti-viral drugs.
Large-scale molecular epidemiologic studies of Plasmodium falciparum parasites have provided insights into parasite biology and transmission, can identify the spread of drug resistance, and are useful in assessing vaccine targets. The polyclonal nature infections in high transmission settings is problematic for traditional genotyping approaches. Next-generation sequencing approaches to parasite genotyping allow sensitive detection of minority variants, disaggregation of complex parasite mixtures, and scalable processing of large samples sets. Therefore, we designed, validated, and applied to field parasites a new approach that leverages sequencing of individually barcoded samples in a multiplex manner. We utilize variant barcodes, invariant linker sequences and modular template-specific primers to allow for the simultaneous generation of high-dimensional sequencing data of multiple gene targets. This modularity permits a cost-effective and reproducible way to query many genes at once. In mixtures of reference parasite genomes, we quantitatively detected unique haplotypes comprising as little as 2% of a polyclonal infection. We applied this genotyping approach to field-collected parasites collected in Western Kenya in order to simultaneously obtain parasites genotypes at three unlinked loci. In summary, we present a rapid, scalable, and flexible method for genotyping individual parasites that enables molecular epidemiologic studies of parasite evolution, population structure and transmission.
Item Embargo Elevated Serum Chymase as a Risk Factor for Severe Dengue(2016) Farouk, Farouk ShihabDengue Virus (DENV) is one of the major viral diseases that has a high burden in Southeast Asia and the Americas. Despite advances in supportive care for mild Dengue Fever (DF) and the more severe Dengue Hemorrhagic Fever (DHF), little is known about how to identify the progression to DHF before it occurs. The purpose of our retrospective study is to assess whether there is an association between the concentration of a serum protein, chymase, with DHF (and the symptoms, pre-existing conditions, and comorbidities associated with it).
Data from 291 dengue-confirmed patients were collected from a surveillance study conducted in Sri Lanka. We selected a series of demographic, symptom, and pre-existing condition variables to see if there was an association between these, elevated chymase levels, and a DHF diagnosis. Our results confirmed that the correlation between a DHF diagnosis and increased chymase levels was statistically significant (p = <0.001). Furthermore, the negative correlation between a DF diagnosis and increased chymase levels was significant (p = <0.001). Obesity was also significantly predictive of increased chymase levels (p = <0.001). Elevated chymase levels correlated with (and predicted) a DHF diagnosis between ages 9 and 44, with those under age 9 having the strongest correlation.
Overall, an increased chymase level was associated with a DHF diagnosis. The identification of chymase as a biomarker for severe dengue may lead to improved diagnostic and surveillance systems that can identify and treat patients at risk for developing DHF.
Item Open Access Minimal within-host dengue models highlight the specific roles of the immune response in primary and secondary dengue infections.(J R Soc Interface, 2015-02-06) Ben-Shachar, Rotem; Koelle, KatiaIn recent years, the within-host viral dynamics of dengue infections have been increasingly characterized, and the relationship between aspects of these dynamics and the manifestation of severe disease has been increasingly probed. Despite this progress, there are few mathematical models of within-host dengue dynamics, and the ones that exist focus primarily on the general role of immune cells in the clearance of infected cells, while neglecting other components of the immune response in limiting viraemia. Here, by considering a suite of mathematical within-host dengue models of increasing complexity, we aim to isolate the critical components of the innate and the adaptive immune response that suffice in the reproduction of several well-characterized features of primary and secondary dengue infections. By building up from a simple target cell limited model, we show that only the innate immune response is needed to recover the characteristic features of a primary symptomatic dengue infection, while a higher rate of viral infectivity (indicative of antibody-dependent enhancement) and infected cell clearance by T cells are further needed to recover the characteristic features of a secondary dengue infection. We show that these minimal models can reproduce the increased risk of disease associated with secondary heterologous infections that arises as a result of a cytokine storm, and, further, that they are consistent with virological indicators that predict the onset of severe disease, such as the magnitude of peak viraemia, time to peak viral load, and viral clearance rate. Finally, we show that the effectiveness of these virological indicators to predict the onset of severe disease depends on the contribution of T cells in fuelling the cytokine storm.Item Open Access Molecular and Epidemiological Assessment of Dengue Fever in Southern Sri Lanka in 2012(2014) Uehara, AnnaThe mosquito-borne dengue viruses (DENV 1, 2, 3, and 4) have a rapidly expanding geographic range and have become endemic in over 100 countries with tropical and subtropical climates, including Sri Lanka. In Sri Lanka, dengue outbreaks have occurred primarily in Colombo, the capital, since the 1960s; however, recent reports suggest transmission throughout the island, with a second focus in the port city of Galle in the Southern Province. To better assess the emergence of dengue among fever-causing agents in the Southern Province of Sri Lanka, we collected epidemiological and clinical characteristics, as well as acute and convalescent sera, from febrile patients of 1 year of age or older without a defined source between June 1, 2012 and December 31, 2012 and compared with similar data collected in 2007. We performed whole genome sequencing on representative dengue isolates from Colombo and Galle to assess relatedness. Through serological testing for DENV IgM and IgG antibodies, virus isolation, and molecular testing, we confirmed acute dengue in 64.83% of the febrile population which was composed of DENV1 (93.8%) and DENV4 (6.2 %) serotypes. We did not detect DENV1 in 2007, nor did we detect DENV2 or DENV3 in 2012. Phylogenetic analysis of whole genome sequence from representative samples from 2012 demonstrated that most DENV 1 strains (25 of 26 tested) belonged to genotype 1 which was closely related to strains previously reported in Colombo during the 2009-2010 dengue season and that all DENV4 strains belong to genotype 1 These results support the spread of dengue virus strains from Colombo to southern Sri Lanka, but the timing and directionality of that movement remain unknown.
Item Open Access Phylodynamic Methods for Infectious Disease Epidemiology(2014) Rasmussen, David AlanIn this dissertation, I present a general statistical framework for phylodynamic inference that can be used to estimate epidemiological parameters and reconstruct disease dynamics from pathogen genealogies. This framework can be used to fit a broad class of epidemiological models, including nonlinear stochastic models, to genealogies by relating the population dynamics of a pathogen to its genealogy using coalescent theory. By combining Markov chain Monte Carlo and particle filtering methods, efficient Bayesian inference of all parameters and unobserved latent variables is possible even when analytical likelihood expressions are not available under the epidemiological model. Through extensive simulations, I show that this method can be used to reliably estimate epidemiological parameters of interest as well as reconstruct past disease dynamics from genealogies, or jointly from genealogies and other common sources of epidemiological data like time series. I then extend this basic framework to include different types of host population structure, including models with spatial structure, multiple-hosts or vectors, and different stages of infection. The later is demonstrated by using a multistage model of HIV infection to estimate stage-specific transmission rates and incidence from HIV sequence data collected in Detroit, Michigan. Finally, to demonstrate how the approach can be used more generally, I consider the case of dengue virus in southern Vietnam. I show how earlier phylodynamic inference methods fail to reliably reconstruct the dynamics of dengue observed in hospitalization data, but by deriving coalescent models that take into consideration ecological complexities like seasonality, vector dynamics and spatial structure, accurate dynamics can be reconstructed from genealogies. In sum, by extending phylodynamics to include more ecologically realistic and mechanistic models, this framework can provide more accurate estimates and give deeper insight into the processes driving infectious disease dynamics.
Item Open Access Reconciling phylodynamics with epidemiology: the case of dengue virus in southern Vietnam.(Mol Biol Evol, 2014-02) Rasmussen, David A; Boni, Maciej F; Koelle, KatiaCoalescent methods are widely used to infer the demographic history of populations from gene genealogies. These approaches-often referred to as phylodynamic methods-have proven especially useful for reconstructing the dynamics of rapidly evolving viral pathogens. Yet, population dynamics inferred from viral genealogies often differ widely from those observed from other sources of epidemiological data, such as hospitalization records. We demonstrate how a modeling framework that allows for the direct fitting of mechanistic epidemiological models to genealogies can be used to test different hypotheses about what ecological factors cause phylodynamic inferences to differ from observed dynamics. We use this framework to test different hypotheses about why dengue serotype 1 (DENV-1) population dynamics in southern Vietnam inferred using existing phylodynamic methods differ from hospitalization data. Specifically, we consider how factors such as seasonality, vector dynamics, and spatial structure can affect inferences drawn from genealogies. The coalescent models we derive to take into account vector dynamics and spatial structure reveal that these ecological complexities can substantially affect coalescent rates among lineages. We show that incorporating these additional ecological complexities into coalescent models can also greatly improve estimates of historical population dynamics and lead to new insights into the factors shaping viral genealogies.Item Open Access Ribosomal Proteins RPLP1 and RPLP2 are Host Factors Critically Required for Flavivirus Infectivity by Promoting Efficient Viral Translation Elongation.(2018) Kroon Campos, RafaelThe Flavivirus genus contains several arthropod-borne viruses that pose global health threats, including dengue virus (DENV). We identified two ribosomal proteins, RPLP1 and RPLP2 (RPLP1/2), that are crucial host factors required for translation of flaviviruses and efficient flavivirus infection of human cell lines and Aedes aegypti mosquitoes, which are natural vectors for these viruses. We hypothesized that RPLP1/2 are accessory ribosomal proteins that function to promote translation of specific cellular mRNAs sharing undefined features with the DENV genome. We found that these proteins are not broadly required for cellular translation and but are necessary for efficient accumulation of DENV proteins early in infection and ectopically expressed DENV structural proteins. The ribosome profiling technique allowed us to quantitative map ribosomes across the transcriptome during early DENV infection in human cell lines depleted for RPLP1/2. We observed that local ribosome occupancy is altered in the viral open reading frame with RPLP1/2 knockdown, consistent with a role for RPLP1/2 in promoting translation elongation. The most prominent ribosome pausing site in the DENV RNA was in the 5’ end of the E protein coding sequence which is located 210 nts downstream of two adjacent TMs. We also observed that RPLP1/2 depletion resulted in altered ribosome density in mRNAs encoding two or more transmembrane domains. This work increases our knowledge on DENV translation regulation and sheds light on the function of RPLP1/2 in translation of specific cellular RNAs.
Item Open Access Study on the Weather Effects on Dengue and Dengue Surveillance System in Fiji(2017) Tong, MiaoBackground: Dengue is one of the most common vector transmitted diseases in the world and it has become a public health problem in many countries including Fiji. Efficient methods need to be taken for dengue prevention and control in Fiji. Disease surveillance is one of the most effective way for dengue prevention and idea of using weather parameters to estimate dengue cases as one part of dengue surveillance has been studied by different researchers worldwide. The study aimed to estimate the relationship between weather variables including rainfall, temperature and humidity and to identify problems existed in current surveillance system in Fiji. Methods: Both quantitative and qualitative methods were used in the study. In the quantitative study, disease data of dengue cases collected by Fiji National Notifiable Disease Surveillance System from Jan 2011 to Dec 2014 and weather data collected by meteorological station in Laucala Bay, Suva from Jan 2011 to Dec 2014 were provided by Fiji Ministry of Health. Disease data were divided into two parts, years with sporadic cases (Jan2011-Oct2013) and years with dengue outbreak (Nov2013-Dec2014), and negative binominal regression was conducted to estimate the association between weather variables including rainfall, maximum temperature, minimum temperature and relative humidity. In the qualitative study, in-depth interviews were conducted with health workers and dengue patients in Suva and evaluations of current surveillance system and problems being noticed in the surveillance system were discussed. Results: Statistically significant positive associations between weather variables including weekly cumulative rainfall and weekly average relative humidity and dengue cases were identified in years with sporadic cases. In years with dengue outbreak, weekly average maximum temperature and relative humidity were also found to be significantly positively associated with dengue cases. Average minimum temperature per week was found to be significantly negatively associated with dengue cases. Problems of timeliness, accuracy and completeness in dengue case report process were identified and inadequate public health awareness of health workers was also raised in the interviews. Conclusions: Weather variables including rainfall, temperature and humidity showed significant effects on variations of dengue cases. The significant associations between weather variables and dengue cases may establish the foundation of developing a climate-based early warning system for dengue in Fiji. Problems in the current surveillance system for dengue have been identified including lack of timeliness and compromised quality in the case reporting process. Web-based disease reporting system and standardized reporting procedures may be useful in improving the surveillance system. A more efficient disease surveillance system can be developed combining the effects of weather variations on the number of dengue cases and routine surveillance together.