Mathematical modelling of COVID-19 transmission dynamics in a partially comorbid community.

A deterministic S,Em,Ec,Im,Ic,H,R epidemic model that describes the spreading of SARS-COV-2 within a community with comorbidities is formulated. Size dependent area is incorporated into the model to quantify the effect of social distancing and the results indicate that the risk of community transmission is optimally minimised when the occupancy area is increased. The reproduction number is shown to have a positive relationship with the infection rate, the proportion of individuals with comorbidities and the proportion of susceptible individuals adhering to standard operating procedures. The model exhibits a unique endemic equilibrium whose stability largely depends on the rate of hospitalisation of individuals with underlying health conditions (ωm) as compared to those without these conditions (ωc), such that stability is guaranteed if ωm<ωc. Furthermore, if individuals with comorbidities effectively report for treatment and hospitalisation at a rate of 0.5 per day, the epidemic curve peaks 3-fold higher among people with comorbidities. The infection peaks are delayed if the area occupied by community is increased. In conclusion, we observed that community infections increase significantly with decreasing detection rates for both individuals with or without comorbidities.

Mathematical model for COVID-19 management in crowded settlements and high-activity areas.

This paper develops and analyses a habitat area size dependent mathematical model to study the transmission dynamics of COVID-19 in crowded settlements such as refugee camps, schools, markets and churches. The model quantifies the potential impact of physical/social distancing and population density on the disease burden. Results reveal that with no fatalities and no infected entrants, the reproduction numbers associated with asymptomatic and symptomatic cases are inversely proportional to; the habitat area size, and the efforts employed in tracing and hospitalising these cases. The critical habitat area below which the disease dies out is directly proportion to the time taken to identify and hospitalise infected individuals. Results also show that disease persistence in the community is guaranteed even with minimal admission of infected individuals. Our results further show that as the level of compliance to standard operating procedures (SOPs) increases, then the disease prevalence peaks are greatly reduced and delayed. Therefore, proper adherence to SOPs such as use of masks, physical distancing measures and effective contact tracing should be highly enforced in crowded settings if COVID-19 is to be mitigated.

Estimation of the HIV-1 backward mutation rate from transmitted drug-resistant strains.

One of the serious threats facing the administration of antiretroviral therapy to human immunodeficiency virus (HIV-1) infected patients is the reported increasing prevalence of transmitted drug resistance. However, given that HIV-1 drug-resistant strains are often less fit than the wild-type strains, it is expected that drug-resistant strains that are present during the primary phase of the HIV-1 infection are replaced by the fitter wild-type strains. This replacement of HIV-1 resistant mutations involves the emergence of wild-type strains by a process of backward mutation. How quickly the replacement happens is dependent on the class of HIV-1 mutation group. We estimate the backward mutation rates and relative fitness of various mutational groups known to confer HIV-1 drug resistance. We do this by fitting a stochastic model to data for individuals who were originally infected by an HIV-1 strain carrying any one of the known drug resistance-conferring mutations and observed over a period of time to see whether the resistant strain is replaced. To do this, we seek a distribution, generated from simulations of the stochastic model, that best describes the observed (clinical data) replacement times of a given mutation. We found that Lamivudine/Emtricitabine-associated mutations have a distinctly higher, backward mutation rate and low relative fitness compared to the other classes (as has been reported before) while protease inhibitors-associated mutations have a slower backward mutation rate and high relative fitness. For the other mutation classes, we found more uncertainty in their estimates.

A mathematical model for Crimean-Congo haemorrhagic fever: tick-borne dynamics with conferred host immunity.

Crimean-Congo haemorrhagic fever (CCHF) is a highly contagious tick-borne disease that impacts many countries in parts of Africa, Europe, Asia, and the Middle East. Outbreaks are episodic, but deadly. Due to the highly contagious nature of this disease, suspected cases are taken extremely serious, with very strong control measures implemented almost immediately. It is primarily those living on farms, livestock workers, and medical workers who are at risk. The virus responsible for CCHF is transmitted asymptomatically and transiently to livestock, and symptomatically to humans. The fatality rate in human cases can be very high. The number of methods and directions of viral transmission is large, including tick-to-tick, tick-to-livestock, tick-to-human, livestock-to-tick, livestock-to-human, and human-to-human. We model CCHF using a deterministic system of nonlinear differential equations. This compartment model allows us to analyse threshold parameters and equilibria describing the magnitude and progression of cases of the disease in a hypothetical outbreak.

Modelling the use of insecticide-treated cattle to control tsetse and Trypanosoma brucei rhodesiense in a multi-host population.

We present a mathematical model for the transmission of Trypanosoma brucei rhodesiense by tsetse vectors to a multi-host population. To control tsetse and T. b. rhodesiense, a proportion, ψ, of cattle (one of the hosts considered in the model) is taken to be kept on treatment with insecticides. Analytical expressions are obtained for the basic reproduction number, R0n in the absence, and R(0n)(T) in the presence of insecticide-treated cattle (ITC). Stability analysis of the disease-free equilibrium was carried out for the case when there is one vertebrate host untreated with insecticide. By considering three vertebrate hosts (cattle, humans and wildlife) the sensitivity analysis was carried out on the basic reproduction number (R(0n)(T)) in the absence and presence of ITC. The results show that R(03)(T) is more sensitive to changes in the tsetse mortality. The model is then used to study the control of tsetse and T. b. rhodesiense in humans through application insecticides to cattle either over the whole-body or to restricted areas of the body known to be favoured tsetse feeding sites. Numerical results show that while both ITC strategies result in decreases in tsetse density and in the incidence of T. b. rhodesiense in humans, the restricted application technique results in improved cost-effectiveness, providing a cheap, safe, environmentally friendly and farmer based strategy for the control of vectors and T. b. rhodesiense in humans.

A mathematical model for the dynamics of HIV/AIDS with gradual behaviour change.

An HIV/AIDS model that incorporates gradual behaviour change is formulated with a variable force of infection for the adult population. The variability is modelled using a general function of time since introduction of the initial infective and exemplified for three specific functions. Expressions for the time taken for the reproductive number to reduce to unity and expressions for the time taken to attain a stationary steady state are deduced and discussed. Model projections for urban, peri-urban and rural Uganda are compared with corresponding antenatal clinic sites prevalence trends. The analysis shows that the dramatic decline in HIV prevalence in Uganda in the early 1990s was only possible through drastic declines in the force of infection. Since prevalence was high and reductions in frequency of sexual acts was minimal, the huge reduction could be attributed to reductions in probability of transmission per sexual act probably due to increased selective condom use among high risk sexual partnerships since overall condom use was low.

Mathematical model for HIV/AIDS with complacency in a population with declining prevalence.

An HIV/AIDS model incorporating complacency for the adult population is formulated. Complacency is assumed a function of number of AIDS cases in a community with an inverse relation. A method to find the equilibrium state of the model is given by proving a stated theorem. An example to illustrate use of the theorem is also given. Model analysis and simulations show that complacency resulting from dependence of HIV transmission on number of AIDS cases in a community leads to damped periodic oscillations in the number of infectives with oscillations more marked at lower rates of progression to AIDS. The implications of these results to public health with respect to monitoring the HIV/AIDS epidemic and widespread use of antiretroviral (ARV) drugs is discussed.