The prevalence of Plasmodium falciparum in sub-Saharan Africa since 1900

Abstract

Malaria transmission is influenced by climate, land use and deliberate interventions. Recent declines have been observed in malaria transmission. Here we show that the African continent has witnessed a long-term decline in the prevalence of Plasmodium falciparum from 40% prevalence in the period 1900-1929 to 24% prevalence in the period 2010-2015, a trend that has been interrupted by periods of rapidly increasing or decreasing transmission. The cycles and trend over the past 115 years are inconsistent with explanations in terms of climate or deliberate intervention alone. Previous global initiatives have had minor impacts on malaria transmission, and a historically unprecedented decline has been observed since 2000. However, there has been little change in the high transmission belt that covers large parts of West and Central Africa. Previous efforts to model the changing patterns of P. falciparum transmission intensity in Africa have been limited to the past 15 years or have used maps drawn from historical expert opinions. We provide quantitative data, from 50,424 surveys at 36,966 geocoded locations, that covers 115 years of malaria history in sub-Saharan Africa; inferring from these data to future trends, we would expect continued reductions in malaria transmission, punctuated with resurgences.

Extended Data 1

Survey data in time: The temporal distribution of survey data per intervals selected for analysis (number of surveys shown on top of bars)

Extended Data 2

Survey data in space: Location of 53,529 P. falciparum parasite surveys undertaken at 39,033 locations by time intervals from 1900-44 to 2010-15

Extended Data 3

The spatial range of P. falciparum Africa in between 1900-1950: light grey represents absence of natural P. falciparum transmission; pink is the natural extent of transmission; dark grey represents countries not included in the analysis

Extended Data 4

Model Convergence: Gelman-Rubin-Brooks plots demonstrating convergence during MCMC simulation for key model parameters. Black line represents ratio of within chain variability to between chain variability, the dark grey line represents the within-chain variability (pooled) and the light grey line represents the between-chain variability (average)

Extended Data 5

Model Validation: Predicted PfPR_2-10 versus observed PfPR_2-10 for 100 randomly selected data points. 99% of data points are within 95% credible interval (CI); Spearman Rank Correlation 0.46, P <0.001 (two-sided test)

Figure 1. Changing spatial patterns of P. falciparum endemicity in sub-Saharan Africa since 1900.

Predicted posterior predictions of age standardised P. falciparum prevalence (PfPR_2-10) per administrative unit on mainland SSA and Madagascar and masked (white) according to biological or control related absence of transmission (Methods and SI 2.2) and the reported changing spatial extents (Methods, SI 2.3, Source Data Figure 1).

Figure 2. Summary and plausibility framework of P. falciparum transmission cycles in sub-Saharan Africa since 1900

Panel A: The median, (central dark line) and 25-75% (medium green boundaries) and 2.5-97.5% (light green boundaries) interquartile credibility range of the posterior predictions of PfPR_2-10 (Source Data Figure 2). Panel B: Six periods of major intervention: 1) 1900-1949: restricted efforts through larval control (LC), environmental management (EM) and mass drug administration (MDA) using Quinine (QN); 2) 1950-1969; launch of Global Malaria Eradication Programme (GMEP) in 1955, introduction of DDT and drugs (e.g. chloroquine (CQ) and pyrimethamine (PYR)) and pilot elimination projects involving indoor residual house-spraying (IRS) accompanied later by MDA using CQ and PYR; 3) 1970-1999: end of most vector control efforts, presumptive treatment of fevers with CQ, use of CQ as MDA for school children; 4) 2000-2004: the Roll Back Malaria (RBM) initiative with Insecticide Treated Nets (ITN) for vulnerable children and pregnant women, expansion of Intermittent Presumptive Treatment of malaria in pregnancy (IPTp) and failing first line treatment with Sulphadoxine-Pyrimethamine (SP) and/or CQ; 5) 2005-2010; large scale Long-Lasting Insecticide Treated Nets (LLIN) distributions, IRS expanded and switch from CQ or SP to Artemisinin-based Combination Therapy (ACT); 6) 2010-2015: increased IRS in many countries, scale-up of Rapid Diagnostic Tests (RDTs); the Global Technical Strategy (GTS) was launched in 2012, re-invigorating a global ambition for eradication and seasonal malaria chemoprevention (SMC) in West African countries. Vector resistance to Organochorines detected in 1955 in Nigeria, organophosphate, carbamate and pyrethroid resistance detected in the late 1980s and have expanded rapidly since the late 1990s; CQ resistance detected in 1978, SP resistance in 1953 with significant clinical failure rates in 2000. Panel C: Climate - mean annual rainfall across the Sahara (Green line), El Niño events leading to serious climate anomalies including flooding in 1997-1998 in East Africa and drought in the horn of Africa in 2014-2015 (Red bars), monthly minimum temperature (Blue line).