Yellow fever is a vector-borne acute viral hemorrhagic disease. It is endemic in tropical areas of Africa and Latin America but demonstrated the potential for international spread during the 2016 outbreak in Luanda, Angola. Yellow fever can be prevented by vaccination, vector control, and avoiding mosquito bites. To account for human behavior in disease dynamics, we add a game-theoretic component to a recent compartmental model of yellow fever transmission. The self-interested individuals evaluate the risks of contracting yellow fever and choose to vaccinate or avoid the bites to minimize the overall costs. We find the Nash equilibria, the optimal levels of vaccination and bite protections if the individuals can decide on the use of only one of the prevention methods as well as when they can decide on the use of both of them. In the later case, we show that vaccination is the preferred method of protection from the individual standpoint and, in the Nash equilibrium, individuals use vaccination only. Our model predicts the vaccination coverage in Angola to be around 65%, which is in reasonable agreement with the empirical value of 68%. We also study whether voluntary prevention can lead to the elimination of the disease in endemic areas. We show that voluntary vaccination alone is not enough to mitigate the risks of outbreaks, suggesting that a mandatory vaccination policy is necessary.
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Primary case inference in viral outbreaks through analysis of intra-host variant population
Abstract Background Investigation of outbreaks to identify the primary case is crucial for the interruption and prevention of transmission of infectious diseases. These individuals may have a higher risk of participating in near future transmission events when compared to the other patients in the outbreak, so directing more transmission prevention resources towards these individuals is a priority. Although the genetic characterization of intra-host viral populations can aid the identification of transmission clusters, it is not trivial to determine the directionality of transmissions during outbreaks, owing to complexity of viral evolution. Here, we present a new computational framework, PYCIVO: primary case inference in viral outbreaks. This framework expands upon our earlier work in development of QUENTIN, which builds a probabilistic disease transmission tree based on simulation of evolution of intra-host hepatitis C virus (HCV) variants between cases involved in direct transmission during an outbreak. PYCIVO improves upon QUENTIN by also adding a custom heterogeneity index and identifying the scenario when the primary case may have not been sampled. Results These approaches were validated using a set of 105 sequence samples from 11 distinct HCV transmission clusters identified during outbreak investigations, in which the primary case was epidemiologically verified. Both models can detect the correct primary case in 9 out of 11 transmission clusters (81.8%). However, while QUENTIN issues erroneous predictions on the remaining 2 transmission clusters, PYCIVO issues a null output for these clusters, giving it an effective prediction accuracy of 100%. To further evaluate accuracy of the inference, we created 10 modified transmission clusters in which the primary case had been removed. In this scenario, PYCIVO was able to correctly identify that there was no primary case in 8/10 (80%) of these modified clusters. This model was validated with HCV; however, this approach may be applicable to other microbial pathogens. Conclusions PYCIVO improves upon QUENTIN by also implementing a custom heterogeneity index which empowers PYCIVO to make the important ‘No primary case’ prediction. One or more samples, possibly including the primary case, may have not been sampled, and this designation is meant to account for these scenarios.
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- Award ID(s):
- 2047828
- NSF-PAR ID:
- 10395446
- Date Published:
- Journal Name:
- BMC Bioinformatics
- Volume:
- 23
- Issue:
- 1
- ISSN:
- 1471-2105
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract Real‐time trends from surveillance data are important to assess and develop preparedness for influenza outbreaks. The overwhelming testing demand and limited capacity of testing laboratories for viral positivity render daily confirmed case data inaccurate and delay its availability in preparedness. Using Bayesian dynamic downscaling models, we obtained posterior estimates for daily influenza incidences from weekly estimates of the Centers for Disease Control and Prevention and daily reported constitutional and respiratory complaints during emergency department (ED) visits obtained from the state health departments. Our model provides one‐day and seven‐day lead forecasts along with 95 prediction intervals. Our hybrid Markov Chain Monte Carlo and Kalman filter algorithms facilitate faster computation and enable us to update our estimates as new data become available. Our method is tested and validated using the State of Michigan data over the years 2009‐2013. Reported constitutional and respiratory complaints at the EDs showed strong correlations of 0.81 and 0.68 respectively, with influenza rates. In general, our forecast model can be adapted to track an outbreak with only one respiratory virus as a causative agent.
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Abstract Background The
Aedes aegypti mosquito is a vector of several viruses including dengue, chikungunya, zika, and yellow fever. Vector surveillance and control are the primary methods used for the control and prevention of disease transmission; however, public health institutions largely rely on measures of population abundance as a trigger for initiating control activities. Previous research found evidence that at the northern edge ofAe. aegypti ’s geographic range, survival, rather than abundance, is likely to be the factor limiting disease transmission. In this study, we sought to test the utility of using body size as an entomological index to surveil changes in the age structure of field-collected femaleAedes aegypti .Methods We collected female
Ae. aegypti mosquitoes using BG sentinel traps in three cities at the northern edge of their geographic range. Collections took place during their active season over the course of 3 years. Female wing size was measured as an estimate of body size, and reproductive status was characterized by examining ovary tracheation. Chronological age was determined by measuring transcript abundance of an age-dependent gene. These data were then tested with female abundance at each site and weather data from the estimated larval development period and adulthood (1 week prior to capture). Two sources of weather data were tested to determine which was more appropriate for evaluating impacts on mosquito physiology. All variables were then used to parameterize structural equation models to predict age.Results In comparing city-specific NOAA weather data and site-specific data from HOBO remote temperature and humidity loggers, we found that HOBO data were more tightly associated with body size. This information is useful for justifying the cost of more precise weather monitoring when studying intra-population heterogeneity of eco-physiological factors. We found that body size itself was not significantly associated with age. Of all the variables measured, we found that best fitting model for age included temperature during development, body size, female abundance, and relative humidity in the 1 week prior to capture . The strength of models improved drastically when testing one city at a time, with Hermosillo (the only study city with seasonal dengue transmission) having the best fitting model for age. Despite our finding that there was a bias in the body size of mosquitoes collected alive from the BG sentinel traps that favored large females, there was still sufficient variation in the size of females collected alive to show that inclusion of this entomological indicator improved the predictive capacity of our models.
Conclusions Inclusion of body size data increased the strength of weather-based models for age. Importantly, we found that variation in age was greater within cities than between cities, suggesting that modeling of age must be made on a city-by-city basis. These results contribute to efforts to use weather forecasts to predict changes in the probability of disease transmission by mosquito vectors.
Graphical abstract
- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1186/s12859-022-04585-2
