Geo-epidemiology of malaria incidence in the Vhembe District to guide targeted elimination strategies, South-Africa, 2015-2018: a local resurgence

Abstract Background The South African population at risk of malaria represents 10% (i.e., six million inhabitants) of the population in three provinces: Limpopo, Mpumalanga and KwaZulu-Natal. In Limpopo Province, Vhembe District is most affected, showing an incidence of 3.8 cases/1000 person-years in 2018. Stratification of malaria intensity level is part of the World Health Organization (WHO) recommendations to accelerate malaria elimination. There are no studies on malaria incidence at locality level, due to difficulty of population availability at this scale. This study aimed to identify and describe malaria incidence patterns at locality level in Vhembe District. Method Using the functional data method, a smooth function (functional data or curve) was fitted from the time series of observed malaria incidence for each of the 474 localities in Vhembe District from July 2015 to June 2018, representing three malaria seasons. These 474 smooth functions were classified using hierarchical clustering (Ward's method) with testing several dissimilarity measures. Thereafter, validity indices measured from these classifications were used to determine the number of distinct temporal patterns of malaria incidence. Results The observed malaria incidence in the 474 localities in Vhembe District was 4.1 cases/1000 person-years. Four distinct patterns of malaria incidence were identified: high, intermediate, low and very low, including 9, 20, 54 and 391 localities and a cumulative observed malaria incidence of 181.2, 54.1, 16.2 and 2.4 cases/1000 person-years, respectively. Malaria incidence increased sharply in high and intermediate incidence patterns over high transmission periods, and over the last low transmission period 2017/2018. These two high incidence patterns were in the Limpopo River Valley, mostly around farms, and in localities along the Mutale River. Conclusion This study showed four malaria incidence patterns in Vhembe District with varying characteristics. Findings show unusual malaria phenomena in Vhembe District, including a high incidence level during a low transmission season and occurrence of a series of resurgences. South Africa has reached the malaria pre-elimination stage, based on development of access to diagnostics, treatment and vector control. However, the recent malaria resurgence in remote areas hinders malaria elimination, highlighting the need for assessing resurgence determinants and developing innovative targeted malaria elimination strategies.