Title: Spread of yellow fever virus outbreak in Angola and the Democratic Republic of the Congo 2015-16: a modelling study
Authors: Kraemer MUG, Faria NR, Reiner Jr RC, Golding N, Nikolay B, Stasse S, Johansson MA, Salje H, Faye O, Wint GRW, Niedrig M, Shearer FM, Hill SC, Thompson RN, Bisanzio D, Taveira N, Nax HH, Pradelski BSR, Nsoesie EO, Murphy NR, Bogoch II, Khan K, Brownstein JS, Tatem AJ, de Oliveira T, Smith DL, Sall AA, Pybus OG, Hay SI, Cauchemez S.
Journal: Lancet Infectious Diseases,http://dx.doi.org/10.1016/S1473-3099(16)30513-8: (2017)
Background Since late 2015, an epidemic of yellow fever has caused more than 7334 suspected cases in Angola and the Democratic Republic of the Congo, including 393 deaths. We sought to understand the spatial spread of this outbreak to optimise the use of the limited available vaccine stock.
Methods We jointly analysed datasets describing the epidemic of yellow fever, vector suitability, human demography, and mobility in central Africa to understand and predict the spread of yellow fever virus. We used a standard logistic model to infer the district-specific yellow fever virus infection risk during the course of the epidemic in the region.
Findings The early spread of yellow fever virus was characterised by fast exponential growth (doubling time of 5-7 days) and fast spatial expansion (49 districts reported cases after only 3 months) from Luanda, the capital of Angola. Early invasion was positively correlated with high population density (Pearson's r 0.52, 95% CI 0.34-0.66). The further away locations were from Luanda, the later the date of invasion (Pearson's r 0.60, 95% CI 0.52-0.66). In a Cox model, we noted that districts with higher population densities also had higher risks of sustained transmission (the hazard ratio for cases ceasing was 0.74, 95% CI 0.13-0.92 per log-unit increase in the population size of a district). A model that captured human mobility and vector suitability successfully discriminated districts with high risk of invasion from others with a lower risk (area under the curve 0.94, 95% CI 0.92-0.97). If at the start of the epidemic, sufficient vaccines had been available to target 50 out of 313 districts in the area, our model would have correctly identified 27 (84%) of the 32 districts that were eventually affected.
Interpretation Our findings show the contributions of ecological and demographic factors to the ongoing spread of the yellow fever outbreak and provide estimates of the areas that could be prioritised for vaccination, although other constraints such as vaccine supply and delivery need to be accounted for before such insights can be translated into policy.
Citation: Kraemer MUG, Faria NR, Reiner Jr RC, Golding N, Nikolay B, Stasse S, Johansson MA, Salje H, Faye O, Wint GRW, Niedrig M, Shearer FM, Hill SC, Thompson RN, Bisanzio D, Taveira N, Nax HH, Pradelski BSR, Nsoesie EO, Murphy NR, Bogoch II, Khan K, Brownstein JS, Tatem AJ, de Oliveira T, Smith DL, Sall AA, Pybus OG, Hay SI, Cauchemez S. Spread of yellow fever virus outbreak in Angola and the Democratic Republic of the Congo 2015-16: a modelling study Lancet Infectious Diseases,http://dx.doi.org/10.1016/S1473-3099(16)30513-8: (2017).
Newsletter, Dec 2016: Ethics & phylogenetics, HIV transmission cycle, UNAIDS Report, Drug resistance increases in Africa - BioAfrica & SATuRN - 2016-12-15
The concept behind this newsletter is that anyone with 15 minutes to spare can learn about our research work. In this December 2016 issue of our newsletter, we have included interesting news, blogs, reports, tweets, publications and training information produced by our group.
By Professor Ayesha Kharsany, December 1, 2016, Durban - Globally, over 1.6 billion people are in the age group 12-24 years, the largest generation of adolescents and young people. However, almost 42% of new HIV infections occur in this age group, nearly 80% of these live in sub-Saharan Africa and more than 70% of these infections occur in adolescent girls and young women. Not only do these adolescent girls and young women have higher rates of HIV, they also acquire infection 5-7 years earlier than their male peers.
Two manuscripts featured in the Lancet website front webpage on AIDS day. - The Lancet - 2016-12-01
Two of our recently published manuscripts (de Oliveira et al. Lancet HIV 2016 & Gregson et al Lancet Infectious Diseases 2016) are highlighed in the Lancet website front webpage...
UNAIDS Report 2016 - Get on the Fast-Track - The life-cycle approach to HIV - UNAIDS - 2016-11-22
In this report, UNAIDS is announcing that 18.2 million people now have access to HIV treatment. The Fast-Track response is working. Increasing treatment coverage is reducing AIDS-related deaths among adults and children. But the life-cycle approach, which highlight our phylogenetics manuscript (de Oliveira et al. Lancet HIV 2016), has to include more than just treatment.
More than 18 million people now have access to life-saving AIDS treatment, 1.2 million more than at the end of last year, the United Nations said on Monday. With detailed data showing some of the many complexities of the HIV epidemic, the report found that people are particularly vulnerable to HIV at certain points in their lives (de Oliveira et al. Lancet HIV 2016). It called for 'life-cycle; approach to offer help and prevention measures for everyone at every stage of life.
Social cycle aids HIV spread - Nature - 2016-07-21
Nature (Vol. 535, pp. 335, 2016) report our recent results on the use of genetic sequences to uncover HIV-1 transmission patterns in young woman in South Africa (de Oliveira et al. Lancet HIV 2016). The paper was presented as a Keynote at AIDS 2016 conference.
Studies Offer Fresh Hope in Fight Against HIV/AIDS in South Africa. - Wall Street Journal - 2016-07-18
Researchers with the Centre for the AIDS Programme of Research in South Africa, or CAPRISA, a consortium of South African and North American scientists, analyzed genetic codes (de Oliveira et al. Lancet HIV 2016) from study subjects in South Africa to try to pinpoint biological factors that may contribute, along with behavioral factors, to the large number of infections.
South Africa's bid to end AIDS - Science - 2016-06-29
Science magazine (Vol. 353, Issue 6294, pp. 18-21, 2016). This issue was published before the AIDS conference in Durban 2016 and highlights some of our research, including our treatment as prevention trial (TasP) as well our phylogenetic analysis (de Oliveira et al. Lancet HIV 2016).
KRISP has been created by the coordinated effort of the University of KwaZulu-Natal (UKZN), the Technology Innovation Agency (TIA) and the South African Medical Research Countil (SAMRC).