Research Articles ((SACEMA) South African Centre for Epidemiological Modelling and Analysis )

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Browsing Research Articles ((SACEMA) South African Centre for Epidemiological Modelling and Analysis ) by Author "Are, Elisha B."

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    Extinction probabilities as a function of temperature for populations of tsetse (Glossina spp.)
    (Public Library of Science, 2020) Are, Elisha B.; Hargrove, John W.
    Significant reductions in populations of tsetse (Glossina spp) in parts of Zimbabwe have been attributed to increases in temperature over recent decades. Sustained increases in temperature might lead to local extinctions of tsetse populations. Extinction probabilities for tsetse populations have not so far been estimated as a function of temperature. We develop a time-homogeneous branching process model for situations where tsetse live at different levels of fixed temperature. We derive a probability distribution pk(T) for the number of female offspring an adult female tsetse is expected to produce in her lifetime, as a function of the fixed temperature at which she is living. We show that pk(T) can be expressed as a geometric series: its generating function is therefore a fractional linear type. We obtain expressions for the extinction probability, reproduction number, time to extinction and growth rates. The results are valid for all tsetse, but detailed effects of temperature will vary between species. No G. m. morsitans population can escape extinction if subjected, for extended periods, to temperatures outside the range 16°C–32°C. Extinction probability increases more rapidly as temperatures approach and exceed the upper and lower limits. If the number of females is large enough, the population can still survive even at high temperatures (28°C–31°C). Small decreases or increases in constant temperature in the neighbourhoods of 16°C and 31°C, respectively, can drive tsetse populations to extinction. Further study is needed to estimate extinction probabilities for tsetse populations in field situations where temperatures vary continuously.
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    Improved estimates for extinction probabilities and times to extinction for populations of tsetse (Glossina spp)
    (Public Library of Science, 2019-04-09) Kajunguri, Damian; Are, Elisha B.; Hargrove, John W.
    A published study used a stochastic branching process to derive equations for the mean and variance of the probability of, and time to, extinction in population of tsetse flies (Glossina spp) as a function of adult and pupal mortality, and the probabilities that a female is inseminated by a fertile male. The original derivation was partially heuristic and provided no proofs for inductive results. We provide these proofs, together with a more compact way of reaching the same results. We also show that, while the published equations hold good for the case where tsetse produce male and female offspring in equal proportion, a different solution is required for the more general case where the probability (β) that an offspring is female lies anywhere in the interval (0, 1). We confirm previous results obtained for the special case where β = 0.5 and show that extinction probability is at a minimum for β > 0.5 by an amount that increases with increasing adult female mortality. Sensitivity analysis showed that the extinction probability was affected most by changes in adult female mortality, followed by the rate of production of pupae. Because females only produce a single offspring approximately every 10 days, imposing a death rate of greater than about 3.5% per day will ensure the eradication of any tsetse population. These mortality levels can be achieved for some species using insecticide-treated targets or cattle—providing thereby a simple, effective and cost-effective method of controlling and eradicating tsetse, and also human and animal trypanosomiasis. Our results are of further interest in the modern situation where increases in temperature are seeing the real possibility that tsetse will go extinct in some areas, without the need for intervention, but have an increased chance of surviving in other areas where they were previously unsustainable due to low temperatures.
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    Outbreak response intervention models of vaccine-preventable diseases in humans and foot-and- mouth disease in livestock : a protocol for a systematic review
    (BMJ Publishing Group, 2020) Azam, James M.; Are, Elisha B.; Pang, Xiaoxi; Ferrari, Matthew J.; Pulliam, Juliet R. C.
    Introduction Outbreaks of vaccine-preventable diseases continue to threaten public health, despite the proven effectiveness of vaccines. Interventions such as vaccination, social distancing and palliative care are usually implemented, either individually or in combination, to control these outbreaks. Mathematical models are often used to assess the impact of these interventions and for supporting outbreak response decision making. The objectives of this systematic review, which covers all human vaccine-preventable diseases, are to determine the relative impact of vaccination compared with other outbreak interventions, and to ascertain the temporal trends in the use of modelling in outbreak response decision making. We will also identify gaps and opportunities for future research through a comparison with the foot-and- mouth disease outbreak response modelling literature, which has good examples of the use of modelling to inform outbreak response intervention decision making. Methods and analysis We searched on PubMed, Scopus, Web of Science, Google Scholar and some preprint servers from the start of indexing to 15 January 2020. Inclusion: modelling studies, published in English, that use a mechanistic approach to evaluate the impact of an outbreak intervention. Exclusion: reviews, and studies that do not describe or use mechanistic models or do not describe an outbreak. We will extract data from the included studies such as their objectives, model types and composition, and conclusions on the impact of the intervention. We will ascertain the impact of models on outbreak response decision making through visualisation of time trends in the use of the models. We will also present our results in narrative style. Ethics and dissemination This systematic review will not require any ethics approval since it only involves scientific articles. The review will be disseminated in a peer-reviewed journal and at various conferences fitting its scope