Background With a sustained national malaria incidence of fewer than one case per 1000 population at risk, in 2012 South Africa officially transitioned from controlling malaria to the ambitious goal of eliminating malaria within its borders by 2018. This review assesses the progress made in the 3 years since programme re-orientation while highlighting challenges and suggesting priorities for moving the malaria programme towards elimination.Methods National malaria case data and annual spray coverage data from 2010 until 2014 were assessed for trends. Information on surveillance, monitoring and evaluation systems, human and infrastructure needs and community malaria knowledge was sourced from the national programme mid-term review.ResultsMalaria cases increased markedly from 6811 in 2013 to 11,711 in 2014, with Mpumalanga and Limpopo provinces most affected. Enhanced local transmission appeared to drive malaria transmission in Limpopo Province, while imported malaria cases accounted for the majority of cases reported in Mpumalanga Province. Despite these increases only Vhembe and Mopani districts in Limpopo Province reported malaria incidences more than one case per 1000 population at risk by 2014. Over the review period annual spray coverage did not reach the recommended target of 90 % coverage, with information gaps identified in parasite prevalence, artemether-lumefantrine therapeutic utilization, asymptomatic/sub-patent carriage, drug efficacy, vector distribution and insecticide resistance.ConclusionsAlthough South Africa has made steady progress since adopting an elimination agenda, a number of challenges have been identified. The heterogeneity of malaria transmission suggests interventions in Vhembe and Mopani districts should focus on control, while in KwaZulu-Natal Province eliminating transmission foci should be prioritized. Cross-border initiatives with neighbouring countries should be established/strengthened as a matter of urgency since malaria importation poses a real threat to the country’s elimination efforts. It is also critical that provincial programmes are adequately resourced to effectively conduct the necessary targeted elimination activities, informed by current vector/parasite distribution and resistance data. More sensitive methods to detect sub-patent infections, primaquine as a transmission-blocking drug, and alternative vector control methods need to be investigated. Knowledge gaps among malaria health workers and affected communities should be identified and addressed.

Locally specific epidemiological understanding is pivotal to the success of malaria elimination in South Africa. Here, we focus on how the host, vector, parasite and environment and their interactions have influenced malaria incidence in South Africa between 1995 and 2012. Broad environmental considerations are necessary, including the physical (temperature and humidity), social (migration patterns), economic (quality of housing stock) and political (regional collaboration).

Laboratory diagnosis of malaria in South Africa has traditionally relied on microscopic examination of stained blood films. More recently, rapid diagnostic tests (RDTs) have been introduced into routine use, and molecular methods like polymerase chain reaction are useful in certain situations. As with all laboratory tests, each technique has its advantages and disadvantages. Microscopy and RDTs, if appropriately quality assured, are adequate for clinical case management. For elimination, active surveillance will need to be expanded substantially, with wider use of more sensitive diagnostic nucleic acid amplification techniques, and/or serology. To facilitate surveillance activities, techniques suitable for field or near-field use would be ideal. A long-running external quality assessment programme in South Africa has shown some deficiencies in the quality of malaria diagnosis in routine laboratories. Quality systems across the spectrum of diagnostic facilities in South Africa need strengthening, to ensure progress towards elimination.