South African Centre for Epidemiological Modelling and Analysis (SACEMA)
The South African Centre for Epidemiological Modelling and Analysis (SACEMA) is a national research centre established under the Centre of Excellence programme of the Department of Science and Technology and the National Research Foundation. The Centre focuses on research in quantitative modelling of the spatial and temporal patterns of disease. The immediate aim of the research is to understand and predict the development of various diseases, and thereby to provide advice on how best to combat them. Our research focuses on issues pertaining to HIV, TB and malaria, although not to the exclusion of other epidemiological problems.
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Ranking lifestyle risk factors for cervical cancer among Black women : a case-control study from Johannesburg, South Africa
(Public Library of Science, 2021-12-08)Background: Aside from human papillomavirus (HPV), the role of other risk factors in cervical cancer such as age, education, parity, sexual partners, smoking and human immunodeficiency virus (HIV) have been described but ... -
Epidemic curves made easy using the R package incidence [version 1; peer review : 1 approved, 2 approved with reservations]
(F1000Research, 2019)The epidemiological curve (epicurve) is one of the simplest yet most useful tools used by field epidemiologists, modellers, and decision makers for assessing the dynamics of infectious disease epidemics. Here, we present ... -
SimpactCyan 1.0 : an open-source simulator for individual-based models in HIV epidemiology with R and Python interfaces
(Nature Research, 2019-12-17)SimpactCyan is an open-source simulator for individual-based models in HIV epidemiology. Its core algorithm is written in C++ for computational efficiency, while the R and Python interfaces aim to make the tool accessible ... -
Improved estimates for extinction probabilities and times to extinction for populations of tsetse (Glossina spp)
(Public Library of Science, 2019-04-09)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 ... -
Optimising targets for tsetse control : taking a fly’s-eye-view to improve the colour of synthetic fabrics
(Public Library of Science, 2019-12-12)The savannah tsetse flies, Glossina morsitans morsitans and G. pallidipes, are important vectors of Rhodesian human African trypanosomiasis and animal African trypanosomiasis in East and southern Africa. We tested in ... -
Evaluating the probability of silent circulation of polio in small populations using the silent circulation statistic
(KeAi Communications, 2019)As polio-endemic countries move towards elimination, infrequent first infections and incomplete surveillance make it difficult to determine when the virus has been eliminated from the population. Eichner and Dietz [American ... -
HIV-attributable causes of death in the medical ward at the Chris Hani Baragwanath Hospital, South Africa
(Public Library of Science, 2019-05-06)Introduction: Data on the association between HIV infection and deaths from underlying medical conditions are needed to understand and assess the impact of HIV on mortality. We present data on mortality in the Chris Hani ... -
Performance comparison of the Maxim and Sedia Limiting Antigen Avidity assays for HIV incidence surveillance
(Public Library of Science, 2019-07-26)Background: Two manufacturers, Maxim Biomedical and Sedia Biosciences Corporation, supply CDC-approved versions of the HIV-1 Limiting Antigen Avidity EIA (LAg) for detecting ‘recent’ HIV infection in cross-sectional incidence ... -
African voices and leadership is imperative for the global AIDS response
(Pan African Medical Journal, 2019-02-22)This position paper is written in reference to the recent extensive media coverage of the report of the Independent Panel describing Harassment, Including Sexual Harassment, Bullying and Abuse of Power at UNAIDS Secretariat ... -
Transmission of Nipah virus — 14 years of investigations in Bangladesh
(Massachusetts Medical Society, 2019-05-09)BACKGROUND: Nipah virus is a highly virulent zoonotic pathogen that can be transmitted between humans. Understanding the dynamics of person-to-person transmission is key to designing effective interventions. METHODS: ... -
Questionable assumptions mar modelling of Kenya home-based testing campaigns
(International AIDS Society, 2019)No abstract available. -
Cost-per-diagnosis as a metric for monitoring cost-effectiveness of HIV testing programmes in low-income settings in southern Africa : health economic and modelling analysis
(International AIDS Society, 2019)Introduction: As prevalence of undiagnosed HIV declines, it is unclear whether testing programmes will be cost-effective. To guide their HIV testing programmes, countries require appropriate metrics that can be measured. ... -
Emerging infectious diseases and biological invasions : a call for a One Health collaboration in science and management
(Royal Society, 2019)The study and management of emerging infectious diseases (EIDs) and of biological invasions both address the ecology of human-associated biological phenomena in a rapidly changing world. However, the two fields work mostly ... -
Serostatus testing and dengue vaccine cost–benefit thresholds
(Royal Society, 2019-08-21)TheWorld Health Organization (WHO) currently recommends pre-screening for past infection prior to administration of the only licensed dengue vaccine, CYD-TDV. Using a threshold modelling analysis, we identify settings ... -
Cumulative viral load as a predictor of CD4+ Tcell response to antiretroviral therapy using Bayesian statistical models
(PLoS, 2019-11-13)Introduction: There are Challenges in statistically modelling immune responses to longitudinal HIV viral load exposure as a function of covariates. We define Bayesian Markov Chain Monte Carlo mixed effects models to ... -
Engaging community health workers in maternal and infant death identification in Khayelitsha, South Africa : a pilot study
(BMC (part of Springer Nature), 2020-11-26)Background: Engaging community health workers in a formalised death review process through verbal and social autopsy has been utilised in different settings to estimate the burden and causes of mortality, where ... -
Accounting for regional transmission variability and the impact of malaria control interventions in Ghana : a population level mathematical modelling approach
(BMC (part of Springer Nature), 2020-11-23)Background: This paper investigates the impact of malaria preventive interventions in Ghana and the prospects of achieving programme goals using mathematical models based on regionally diverse climatic zones of the ... -
Extinction probabilities for tsetse (Glossina spp.) in a world of changing climate
(Stellenbosch : Stellenbosch University, 2020-12)ENGLISH ABSTRACT: Tsetse (Glossina spp) transmit trypanosomiases, as sleeping sickness to humans and nagana to livestock. These continue to have negative impacts on health and wealth in the African continent. In recent ... -
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)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 ... -
Extinction probabilities as a function of temperature for populations of tsetse (Glossina spp.)
(Public Library of Science, 2020)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 ...