Estimating spatiotemporally varying malaria reproduction numbers in a near elimination setting

June 26, 2018


In 2016 the World Health Organization identified 21 countries that could eliminate malaria by 2020. Monitoring progress towards this goal requires tracking ongoing transmission. Here we develop methods that estimate individual reproduction numbers and their variation through time and space.


Great strides have been made since 2000 in reducing the burden and mortality of malaria. The World Health Organisation (WHO) estimates that 57 out of the 106 countries with endemic malaria transmission in 2000 reduced their incidence of malaria by >75% between 2000 and 20151. As a result, malaria elimination at the national level, defined as the absence of local transmission within a country2, is now one of the targets in the WHO Global Strategy for Malaria 2016–20303. In 2016 the WHO identified 21 countries for which it would be realistic to eliminate malaria within the next five years.

Figure 3.

a Distribution of Rc values by location of residential address. Red points represent an Rc (individual reproduction number) below one, blue points represent an Rc value above 1. b Distribution of imported and locally acquired cases by location of residential address. Yellow points represent locally acquired cases, green points represent imported cases. c Map of risk of Rc exceeding 1 if a case were to occur in an area. Note this estimate does not consider risk of importation, but estimates receptivity to transmission if importation were to occur. d Standard deviation in risk estimates from c

Impact of imported cases on transmission

The mean marginal gain to the likelihood of including infections from imported cases into the constructed transmission networks was much higher than including locally acquired cases (0.081 compared to 3.44e−7), suggesting that imported cases are a major driver of transmission. Visual inspection of the most likely chains of transmission (Fig. 1c) also are suggestive of this, where the index case in a cluster of linked cases was almost always an imported case.