Evaluating quasi-experimental approaches for estimating epidemiological efficacy of non-randomised field trials: applications in Wolbachia interventions for dengue.

BACKGROUND: Wolbachia symbiosis in Aedes aegypti is an emerging biocontrol measure against dengue. However, assessing its real-world efficacy is challenging due to the non-randomised, field-based nature of most intervention studies. This research re-evaluates the spatial-temporal impact of Wolbachia interventions on dengue incidence using a large battery of quasi-experimental methods and assesses each method's validity. METHODS: A systematic search for Wolbachia intervention data was conducted via PUBMED. Efficacy was reassessed using commonly-used quasi-experimental approaches with extensive robustness checks, including geospatial placebo tests and a simulation study. Intervention efficacies across multiple study sites were computed using high-resolution aggregations to examine heterogeneities across sites and study periods. We further designed a stochastic simulation framework to assess the methods' ability to estimate intervention efficacies (IE). RESULTS: Wolbachia interventions in Singapore, Malaysia, and Brazil significantly decreased dengue incidence, with reductions ranging from 48.17% to 69.19%. IEs varied with location and duration. Malaysia showed increasing efficacy over time, while Brazil exhibited initial success with subsequent decline, hinting at operational challenges. Singapore's strategy was highly effective despite partial saturation. Simulations identified Synthetic Control Methods (SCM) and its variant, count Synthetic Control Method (cSCM), as superior in precision, with the smallest percentage errors in efficacy estimation. These methods also demonstrated robustness in placebo tests. CONCLUSIONS: Wolbachia interventions exhibit consistent protective effects against dengue. SCM and cSCM provided the most precise and robust estimates of IEs, validated across simulated and real-world settings.

Aedes aegypti exhibits a distinctive mode of late ovarian development.

BACKGROUND: Insects live in almost every habitat on earth. To adapt to their diverse environments, insects have developed a myriad of different strategies for reproduction reflected in diverse anatomical and behavioral features that the reproductive systems of females exhibit. Yet, ovarian development remains largely uncharacterized in most species except Drosophila melanogaster (D. melanogaster), a high Diptera model. In this study, we investigated the detailed developmental process of the ovary in Aedes aegypti (Ae. aegypti), a major vector of various disease-causing pathogens that inhabits tropical and subtropical regions. RESULTS: Compared with Drosophila melanogaster, a model of higher Diptera, the processes of pole cell formation and gonad establishment during embryonic stage are highly conserved in Ae. aegypti. However, Ae. aegypti utilizes a distinct strategy to form functional ovaries during larval/pupal development. First, during larval stage, Ae. aegypti primordial germ cells (PGCs) undergo a cyst-like proliferation with synchronized divisions and incomplete cytokinesis, leading to the formation of one tightly packed "PGC mass" containing several interconnected cysts, different from D. melanogaster PGCs that divide individually. This cyst-like proliferation is regulated by the target of rapamycin (TOR) pathway upon nutritional status. Second, ecdysone-triggered ovariole formation during metamorphosis exhibits distinct events, including "PGC mass" breakdown, terminal filament cell degeneration, and pre-ovariole migration. These unique developmental features might explain the structural and behavioral differences between Aedes and Drosophila ovaries. Importantly, both cyst-like proliferation and distinct ovariole formation are also observed in Culex quinquefasciatus and Anopheles sinensis, suggesting a conserved mode of ovarian development among mosquito species. In comparison with Drosophila, the ovarian development in Aedes and other mosquitoes might represent a primitive mode in the lower Diptera. CONCLUSIONS: Our study reveals a new mode of ovarian development in mosquitoes, providing insights into a better understanding of the reproductive system and evolutionary relationship among insects.

Degradation effects of dietary solvents on microhardness and inorganic elements of computer-aided design/computer-aided manufacturing dental composites.

BACKGROUND: Computer-aided design/computer-aided manufacturing (CAD/CAM) dental composites were introduced with superior mechanical properties than conventional dental composites. However, little is known on effects of dietary solvents on microhardness or inorganic elemental composition of CAD/CAM composites. OBJECTIVES: The objectives of this study were to evaluate the degradation effects of each dietary solvent on the microhardness of the different CAD/CAM dental composites and to observe the degradation effects of dietary solvent on the inorganic elements of the dental composites investigated. METHODS: Fifty specimens with dimensions 12 mm x 14 mm x 1.5 mm were prepared for direct composite (Filtek Z350 XT [FZ]), indirect composite (Shofu Ceramage [CM]), and three CAD/CAM composites (Lava Ultimate [LU], Cerasmart [CS], and Vita Enamic [VE]). The specimens were randomly divided into 5 groups (n = 10) and conditioned for 1-week at 37°C in the following: air (control), distilled water, 0.02 N citric acid, 0.02 N lactic acid and 50% ethanol-water solution. Subsequently, the specimens were subjected to microhardness test (KHN) using Knoop hardness indenter. Air (control) and representative postconditioning specimens with the lowest mean KHN value for each material were analyzed using energy dispersive X-ray spectroscopy (EDX). Statistical analysis was done using one-way ANOVA and post hoc Bonferroni test at a significance level of p = 0.05. RESULTS: Mean KHN values ranged from 39.7 ± 2.7 kg/mm2 for FZ conditioned in 50% ethanol-water solution to 79.2 ± 3.4 kg/mm2 for VE conditioned in air (control). With exception to LU, significant differences were observed between materials and dietary solvents for other dental composites investigated. EDX showed stable peaks of the inorganic elements between air (control) and representative postconditioning specimens. CONCLUSIONS: The microhardness of dental composites was significantly affected by dietary solvents, except for one CAD/CAM composite [LU]. However, no changes were observed in the inorganic elemental composition of dental composites between air (control) and 1-week postconditioning.

Fine-scale estimation of effective reproduction numbers for dengue surveillance.

The effective reproduction number Rt is an epidemiological quantity that provides an instantaneous measure of transmission potential of an infectious disease. While dengue is an increasingly important vector-borne disease, few have used Rt as a measure to inform public health operations and policy for dengue. This study demonstrates the utility of Rt for real time dengue surveillance. Using nationally representative, geo-located dengue case data from Singapore over 2010-2020, we estimated Rt by modifying methods from Bayesian (EpiEstim) and filtering (EpiFilter) approaches, at both the national and local levels. We conducted model assessment of Rt from each proposed method and determined exogenous temporal and spatial drivers for Rt in relation to a wide range of environmental and anthropogenic factors. At the national level, both methods achieved satisfactory model performance (R2EpiEstim = 0.95, R2EpiFilter = 0.97), but disparities in performance were large at finer spatial scales when case counts are low (MASE EpiEstim = 1.23, MASEEpiFilter = 0.59). Impervious surfaces and vegetation with structure dominated by human management (without tree canopy) were positively associated with increased transmission intensity. Vegetation with structure dominated by human management (with tree canopy), on the other hand, was associated with lower dengue transmission intensity. We showed that dengue outbreaks were preceded by sustained periods of high transmissibility, demonstrating the potential of Rt as a dengue surveillance tool for detecting large rises in dengue cases. Real time estimation of Rt at the fine scale can assist public health agencies in identifying high transmission risk areas and facilitating localised outbreak preparedness and response.

Development of Differentiating Infected from Vaccinated Animals (DIVA) Real-Time PCR for African Horse Sickness Virus Serotype 1.

African horse sickness (AHS) is a highly infectious and often fatal disease caused by 9 serotypes of the orbivirus African horse sickness virus (AHSV). In March 2020, an AHS outbreak was reported in Thailand in which AHSV serotype 1 was identified as the causative agent. Trivalent live attenuated vaccines serotype 1, 3, and 4 were used in a targeted vaccination campaign within a 50-km radius surrounding the infected cases, which promptly controlled the spread of the disease. However, AHS-like symptoms in vaccinated horses required laboratory diagnostic methods to differentiate infected horses from vaccinated horses, especially for postvaccination surveillance. We describe a real-time reverse transcription PCR-based assay for rapid characterization of the affecting field strain. The development and validation of this assay should imbue confidence in differentiating AHS-vaccinated horses from nonvaccinated horses. This method should be applied to determining the epidemiology of AHSV in future outbreaks.

Multiplex targeted mass spectrometry assay for one-shot flavivirus diagnosis.

Targeted proteomic mass spectrometry is emerging as a salient clinical diagnostic tool to track protein biomarkers. However, its strong analytical properties have not been exploited in the diagnosis and typing of flaviviruses. Here, we report the development of a sensitive and specific single-shot robust assay for flavivirus typing and diagnosis using targeted mass spectrometry technology. Our flavivirus parallel reaction monitoring assay (fvPRM) has the ability to track secreted flaviviral nonstructural protein 1 (NS1) over a broad diagnostic and typing window with high sensitivity, specificity, extendibility, and multiplexing capability. These features, pivotal and pertinent to efficient response toward flavivirus outbreaks, including newly emerging flavivirus strains, circumvent the limitations of current diagnostic assays. fvPRM thus carries high potential in positioning itself as a forerunner in delivering early and accurate diagnosis for disease management.

Increased Dengue Transmissions in Singapore Attributable to SARS-CoV-2 Social Distancing Measures.

Social distancing (SD) measures aimed at curbing the spread of SARS-CoV-2 remain an important public health intervention. Little is known about the collateral impact of reduced mobility on the risk of other communicable diseases. We used differences in dengue case counts pre- and post implementation of SD measures and exploited heterogeneity in SD treatment effects among different age groups in Singapore to identify the spillover effects of SD measures. SD policy caused an increase of over 37.2% in dengue cases from baseline. Additional measures to preemptively mitigate the risk of other communicable diseases must be considered before the implementation/reimplementation of SARS-CoV-2 SD measures.

Prevalence and genomic analysis of ESBL-producing Escherichia coli in retail raw meats in Singapore.

OBJECTIVES: To determine the prevalence and genetic characteristics of ESBL-producing Escherichia coli in retail raw meats from Singapore markets. METHODS: A total of 634 raw meat (chicken, pork and beef) samples were collected from markets in Singapore during June 2017-October 2018. The samples were enriched overnight and then incubated on Brilliance™ ESBL Agar. Presumptive ESBL isolates were confirmed using the double-disc synergy test. Confirmed ESBL-producing E. coli were sent for WGS and bioinformatic analysis was performed. RESULTS: The prevalence of ESBL-producing E. coli in chicken, pork and beef meats was 51.2% (109/213), 26.9% (58/216) and 7.3% (15/205), respectively. A total of 225 ESBL-producing E. coli were isolated from 184 samples. ß-Lactam resistance genes were detected in all isolates. After ß-lactam resistance genes, the most common antimicrobial resistance genes detected were aminoglycoside resistance genes (92.4%). One hundred and seventy-two (76.4%), 102 (45.3%) and 52 (23.1%) isolates carried blaCTX-M genes, blaTEM genes and blaSHV genes, respectively. blaCTX-M-55 (57/225, 25.3%) and blaCTX-M-65 (40/225, 17.8%) were the most frequent ESBL genes. Colistin resistance genes (including mcr-1, mcr-3 and mcr-5) were found in 15.6% of all isolates. CONCLUSIONS: This study indicates that ESBL-producing E. coli are widely found in retail raw meats, especially chicken, in Singapore. Occurrence of MDR (resistance to at least three classes of antimicrobial) and colistin resistance genes in retail raw meat suggests potential food safety and public health risks.

Time varying methods to infer extremes in dengue transmission dynamics.

Dengue is an arbovirus affecting global populations. Frequent outbreaks occur, especially in equatorial cities such as Singapore, where year-round tropical climate, large daily influx of travelers and population density provide the ideal conditions for dengue to transmit. Little work has, however, quantified the peaks of dengue outbreaks, when health systems are likely to be most stretched. Nor have methods been developed to infer differences in exogenous factors which lead to the rise and fall of dengue case counts across extreme and non-extreme periods. In this paper, we developed time varying extreme mixture (tvEM) methods to account for the temporal dependence of dengue case counts across extreme and non-extreme periods. This approach permits inference of differences in climatic forcing across non-extreme and extreme periods of dengue case counts, quantification of their temporal dependence as well as estimation of thresholds with associated uncertainties to determine dengue case count extremities. Using tvEM, we found no evidence that weather affects dengue case counts in the near term for non-extreme periods, but that it has non-linear and mixed signals in influencing dengue through tvEM parameters in the extreme periods. Using the most appropriate tvEM specification, we found that a threshold at the 70th (95% credible interval 41.1, 83.8) quantile is optimal, with extreme events of 526.6, 1052.2 and 1183.6 weekly case counts expected at return periods of 5, 50 and 75 years. Weather parameters at a 1% scaled increase was found to decrease the long-run expected case counts, but larger increases would lead to a drastic expected rise from the baseline correspondingly. The tvEM approach can provide valuable inference on the extremes of time series, which in the case of infectious disease notifications, allows public health officials to understand the likely scale of outbreaks in the long run.

Public sentiments towards the use of Wolbachia-Aedes technology in Singapore.

BACKGROUND: Wolbachia technology is a novel vector control approach that can reduce mosquito populations and the risk of mosquito-borne diseases, which has recently gained popularity amongst countries. In 2016, Singapore embarked on a multi-phased field study named Project Wolbachia - Singapore, to evaluate the use of Wolbachia technology as an Aedes aegypti mosquito population suppression tool to fight dengue. Due to the novelty of this technology in Singapore, this study aims to understand the public's acceptance and sentiments towards the use of Wolbachia technology. METHODS: Several public sentiment survey approaches - including online, face-to-face in the streets, as well as door-to-door household surveys - were conducted. RESULTS: The surveys conducted prior to the first field releases and implementation of the project revealed high support for the use of Wolbachia technology in Singapore. A household perception survey conducted in the interim of the first project phase was encouraging, with the majority of the respondents being aware of the project and having no concerns with the release of male Wolbachia-carrying Aedes aegypti (Wolbachia-Aedes) mosquitoes in their neighbourhood. CONCLUSIONS: The study reveal high support for the use of Wolbachia technology in Singapore and also provided invaluable insights that were used in the development of a public communications and engagement framework model, which thus helped to guide these elements in the subsequent phases and expansion of the project.

Effect of meteorological factors on Culex mosquitoes in Singapore: a time series analysis.

Culex mosquitoes transmit West Nile virus (WNV). We examined the weather dependence of adult Culex activity. Maximum temperature and absolute humidity were positively associated with adult Culex activity. Our findings support the use of weather data in timing WNV vector control measures.

Utility of Spatial Point-Pattern Analysis Using Residential and Workplace Geospatial Information to Localize Potential Outbreak Sources.

Identifying the source of an outbreak facilitates its control. Spatial methods are not optimally used in outbreak investigation, due to a mix of the complexities involved (e.g., methods requiring additional parameter selection), imperfect performance, and lack of confidence in existing options. We simulated 30 mock outbreaks and compared 5 simple methods that do not require parameter selection but could select between mock cases' residential and workplace addresses to localize the source. Each category of site had a unique spatial distribution; residential and workplace address were visually and statistically clustered around the residential neighborhood and city center sites respectively, suggesting that the value of workplace addresses is tied to the location where an outbreak might originate. A modification to centrographic statistics that we propose-the center of minimum geometric distance with address selection-was able to localize the mock outbreak source to within a 500 m radius in almost all instances when using workplace in combination with residential addresses. In the sensitivity analysis, when given sufficient workplace data, the method performed well in various scenarios with only 10 cases. It was also successful when applied to past outbreaks, except for a multisite outbreak from a common food supplier.

Force of Infection and True Infection Rate of Dengue in Singapore: Implications for Dengue Control and Management.

National data on dengue notifications do not capture all dengue infections and do not reflect the true intensity of disease transmission. To assess the true dengue infection rate and disease control efforts in Singapore, we conducted age-stratified serosurveys among residents after a 2013 outbreak that was the largest dengue outbreak on record. The age-weighted prevalence of dengue immunoglobulin G among residents was 49.8% (95% confidence interval: 48.4, 51.1) in 2013 and 48.6% (95% confidence interval: 47.0, 50.0) in 2017; prevalence increased with age. Combining these data with those from previous serosurveys, the year-on-year estimates of the dengue force of infection from 1930 to 2017 revealed a significant decrease from the late 1960s to the mid-1990s, after which the force of infection remained stable at approximately 10 per 1,000 persons per year. The reproduction number (R0) had also declined since the 1960s. The reduction in dengue transmission may be attributed to the sustained national vector program and partly to a change in the age structure of the population. The improved estimated ratio of notified cases to true infections, from 1:14 in 2005-2009 to 1:6 in 2014-2017, signifies that the national notification system, which relies on diagnosed cases, has improved over time. The data also suggest that the magnitudes of dengue epidemics cannot be fairly compared across calendar years and that the current disease control program remains applicable.

Detection and characterization of a novel bat-borne coronavirus in Singapore using multiple molecular approaches.

Bats are important reservoirs and vectors in the transmission of emerging infectious diseases. Many highly pathogenic viruses such as SARS-CoV and rabies-related lyssaviruses have crossed species barriers to infect humans and other animals. In this study we monitored the major roost sites of bats in Singapore, and performed surveillance for zoonotic pathogens in these bats. Screening of guano samples collected during the survey uncovered a bat coronavirus (Betacoronavirus) in Cynopterus brachyotis, commonly known as the lesser dog-faced fruit bat. Using a capture-enrichment sequencing platform, the full-length genome of the bat CoV was sequenced and found to be closely related to the bat coronavirus HKU9 species found in Leschenault's rousette discovered in the Guangdong and Yunnan provinces.

First detection of a Vssc allele V1016G conferring a high level of insecticide resistance in Aedes albopictus collected from Europe (Italy) and Asia (Vietnam), 2016: a new emerging threat to controlling arboviral diseases.

IntroductionAedes albopictus (Skuse) is an important vector of arboviral diseases, including dengue, chikungunya and Zika virus disease. Monitoring insecticide resistance and mechanisms by which the mosquito develops resistance is crucial to minimise disease transmission.AimTo determine insecticide resistance status and mechanisms in Ae. albopictus from different geographical regions.MethodsWe sampled 33 populations of Ae. albopictus from Asia, Europe and South America, and tested these for susceptibility to permethrin, a pyrethroid insecticide. In resistant populations, the target site for pyrethroids, a voltage-sensitive sodium channel (Vssc) was genotyped. Three resistant sub-strains, each harbouring a resistance allele homozygously, were established and susceptibilities to three different pyrethroids (with and without a cytochrome P450 inhibitor) were assayed.ResultsMost populations of Ae. albopictus tested were highly susceptible to permethrin but a few from Italy and Vietnam (4/33), exhibited high-level resistance. Genotyping studies detected a knockdown resistance (kdr) allele V1016G in Vssc for the first time in Ae. albopictus. Two previously reported kdr alleles, F1534C and F1534S, were also detected. The bioassays indicated that the strain homozygous for the V1016G allele showed much greater levels of pyrethroid resistance than other strains harbouring F1534C or F1534S.ConclusionThe V1016G allele was detected in bothAsian and Italian Ae. albopictus populations, thus a spread of this allele beyond Italy in Europe cannot be ruled out. This study emphasises the necessity to frequently and regularly monitor the V1016G allele in Ae. albopictus, particularly where this mosquito species is the main vector of arboviruses.

Neighbourhood level real-time forecasting of dengue cases in tropical urban Singapore.

BACKGROUND: Dengue, a vector-borne infectious disease caused by the dengue virus, has spread through tropical and subtropical regions of the world. All four serotypes of dengue viruses are endemic in the equatorial city state of Singapore, and frequent localised outbreaks occur, sometimes leading to national epidemics. Vector control remains the primary and most effective measure for dengue control and prevention. The objective of this study is to develop a novel framework for producing a spatio-temporal dengue forecast at a neighbourhood level spatial resolution that can be routinely used by Singapore's government agencies for planning of vector control for best efficiency. METHODS: The forecasting algorithm uses a mixture of purely spatial, purely temporal and spatio-temporal data to derive dynamic risk maps for dengue transmission. LASSO-based regression was used for the prediction models and separate sub-models were constructed for each forecast window. Data were divided into training and testing sets for out-of-sample validation. Neighbourhoods were categorised as high or low risk based on the forecast number of cases within the cell. The predictive accuracy of the categorisation was measured. RESULTS: Close concordance between the projections and the eventual incidence of dengue were observed. The average Matthew's correlation coefficient for a classification of the upper risk decile (operational capacity) is similar to the predictive performance at the optimal 30% cut-off. The quality of the spatial predictive algorithm as a classifier shows areas under the curve at all forecast windows being above 0.75 and above 0.80 within the next month. CONCLUSIONS: Spatially resolved forecasts of geographically structured diseases like dengue can be obtained at a neighbourhood level in highly urban environments at a precision that is suitable for guiding control efforts. The same method can be adapted to other urban and even rural areas, with appropriate adjustment to the grid size and shape.

Construction sites as an important driver of dengue transmission: implications for disease control.

BACKGROUND: In 2013 and 2014, Singapore experienced its worst dengue outbreak known-to-date. Mosquito breeding in construction sites stood out as a probable risk factor due to its association with major dengue clusters in both years. We, therefore, investigated the contribution of construction sites to dengue transmission in Singapore, highlighting three case studies of large construction site-associated dengue clusters recorded during 2013-16. METHODS: The study included two components; a statistical analysis of cluster records from 2013 to 2016, and case studies of three biggest construction site-associated clusters. We explored the odds of construction site-associated clusters growing into major clusters and determined whether clusters seeded in construction sites demonstrated a higher tendency to expand into major clusters. DENV strains obtained from dengue patients residing in three major clusters were genotyped to determine whether the same strains expanded into the surroundings of construction sites. RESULTS: Despite less than 5% of total recorded clusters being construction site-associated, the odds of such clusters expanding into major clusters were 17.4 (2013), 9.2 (2014), 3.3 (2015) and 4.3 (2016) times higher than non-construction site clusters. Aedes premise index and average larvae count per habitat were also higher in construction sites than residential premises during the study period. The majority of cases in clusters associated with construction sites were residents living in the surroundings. Virus genotype data from three case study sites revealed a transmission link between the construction sites and the surrounding residential areas. CONCLUSIONS: Significantly high case burden and the probability of cluster expansion due to virus spill-over into surrounding areas suggested that construction sites play an important role as a driver of sustained dengue transmission. Our results emphasise that the management of construction-site associated dengue clusters should not be limited to the implicated construction sites, but be extended to the surrounding premises to prevent further transmission.

Region-wide synchrony and traveling waves of dengue across eight countries in Southeast Asia.

Dengue is a mosquito-transmitted virus infection that causes epidemics of febrile illness and hemorrhagic fever across the tropics and subtropics worldwide. Annual epidemics are commonly observed, but there is substantial spatiotemporal heterogeneity in intensity. A better understanding of this heterogeneity in dengue transmission could lead to improved epidemic prediction and disease control. Time series decomposition methods enable the isolation and study of temporal epidemic dynamics with a specific periodicity (e.g., annual cycles related to climatic drivers and multiannual cycles caused by dynamics in population immunity). We collected and analyzed up to 18 y of monthly dengue surveillance reports on a total of 3.5 million reported dengue cases from 273 provinces in eight countries in Southeast Asia, covering ∼ 10(7) km(2). We detected strong patterns of synchronous dengue transmission across the entire region, most markedly during a period of high incidence in 1997-1998, which was followed by a period of extremely low incidence in 2001-2002. This synchrony in dengue incidence coincided with elevated temperatures throughout the region in 1997-1998 and the strongest El Niño episode of the century. Multiannual dengue cycles (2-5 y) were highly coherent with the Oceanic Niño Index, and synchrony of these cycles increased with temperature. We also detected localized traveling waves of multiannual dengue epidemic cycles in Thailand, Laos, and the Philippines that were dependent on temperature. This study reveals forcing mechanisms that drive synchronization of dengue epidemics on a continental scale across Southeast Asia.