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By May 2021, South Africa (SA) had experienced two 'waves' of COVID-19 infections, with an initial peak of infections reached in July 2020, followed by a larger peak of infections in January 2021. Public health decisions rely on accurate and timely disease surveillance and epidemiological analyses, and accessibility of data at all levels of government is critical to inform stakeholders to respond effectively. In this paper, we describe the adaptation, development and operation of epidemiological surveillance and modelling systems in SA in response to the COVID-19 epidemic, including data systems for monitoring laboratory-confirmed COVID-19 cases, hospitalisations, mortality and recoveries at a national and provincial level, and how these systems were used to inform modelling projections and public health decisions. Detailed descriptions on the characteristics and completeness of individual datasets are not provided in this paper. Rapid development of robust data systems was necessary to support the response to the SA COVID-19 epidemic. These systems produced data streams that were used in decision-making at all levels of government. While much progress was made in producing epidemiological data, challenges remain to be overcome to address gaps to better prepare for future waves of COVID-19 and other health emergencies.

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The COVID-19 pandemic has strained healthcare delivery systems in a number of southern African countries. Despite this, it is imperative that malaria control and elimination activities continue, especially to reduce as far as possible the number and rate of hospitalisations caused by malaria. The implementation of enhanced malaria control/elimination activities in the context of COVID-19 requires measures to protect healthcare workers and the communities they serve. The aim of this review is therefore to present innovative ideas for the timely implementation of malaria control without increasing the risk of COVID-19 to healthcare workers and communities. Specific recommendations for parasite and vector surveillance, diagnosis, case management, mosquito vector control and community outreach and sensitisation are given.

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The COVID-19 global pandemic reached South Africa (SA), Mozambique and Eswatini in March 2020.[1] Since then an exponential increase in SARS-CoV-2 infections has severely stretched SA's healthcare system, especially in terms of in-hospital treatment of severe cases. The impact of COVID-19 in Mozambique and Eswatini at the time of writing has been comparatively mild, but is increasing. It is therefore imperative to reduce as far as possible the number and rate of hospitalisations caused by trauma and other diseases, including malaria. Malaria incidence in SA is seasonal and peaks in the wetter summer months, especially during January to April.[2] Although malaria incidence in SA is currently low, the risk of outbreaks is always present, with the most recent having occurred in 2017 and, at a more localised level in Limpopo Province, in 2019. The reasons for these latest outbreaks are varied and include unusually high rainfall and cross-border movement of migrant populations, fuelling local transmission. These issues are particularly pertinent to COVID-19 in SA's malaria-affected districts. They highlight the importance of mitigating factors contributing to high malaria incidence and consequent hospitalisations, which may be further exacerbated by COVID-19/malaria coinfections and the re-opening of SA's borders with those neighbouring countries with higher malaria transmission intensities.

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Following major successes in malaria control over the past 75 years, South Africa is now embarking on a malaria elimination campaign with the goal of zero local transmission by the year 2018. The key control elements have been intensive vector control, primarily through indoor residual spraying, case management based on parasitological diagnosis using evidence-based drug policies with artemisinin-based combination therapy since 2001, active health promotion in partnership with communities living in the malaria transmission areas, and cross-border collaborations. Political commitment and long-term funding for the malaria control programme have been a critical component of the programme's success. Breaking the cycle of transmission through strengthening of active surveillance using sensitive molecular tests and field treatment of asymptomatic persons, monitoring for antimalarial drug resistance and insecticide resistance, strengthening cross-border initiatives, and ongoing programme advocacy in the face of a significant decrease in disease burden are key priorities for achieving the elimination goal.

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BACKGROUND: Malaria case numbers reported in South Africa have reduced considerably over the last decade, necessitating a revision of the national risk map to guide malaria prevention, including the use of chemoprophylaxis. OBJECTIVES: To update the national malaria risk map based on recent case data and to consider the implications of the new transmission profile for guiding prophylaxis. METHODS: The geographical distribution of confirmed malaria cases detected both passively and actively over the last six malaria seasons was used to redefine the geographic distribution and intensity of malaria transmission in the country. RESULTS: The national risk map was revised to reflect zones of transmission reduced both in their extent and their intensity. Most notably, the area of risk has been reduced in the north-western parts of Limpopo Province and is limited to the extreme northern reaches of KwaZulu-Natal Province. Areas previously considered to be of high risk are now regarded to be of moderate risk. CONCLUSION: Chemoprophylaxis is now only recommended from September to May in the north-eastern areas of Limpopo and Mpumalanga Provinces. The recommended options for chemoprophylaxis have not changed from mefloquine, doxycycline or atovaquone-proguanil.

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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). 

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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. 

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Malaria case management is a vital component of programmatic strategies for malaria control and elimination. Malaria case management encompasses prompt and effective treatment to minimise morbidity and mortality, reduce transmission and prevent the emergence and spread of antimalarial drug resistance. Malaria is an acute illness that may progress rapidly to severe disease and death, especially in non-immune populations, if not diagnosed early and promptly treated with effective drugs. In this article, the focus is on malaria case management, addressing treatment, monitoring for parasite drug resistance, and the impact of drug resistance on treatment policies; it concludes with chemoprophylaxis and treatment strategies for malaria elimination in South Africa. 

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In this supplement, several authors have shared lessons from the past and identified factors that led to the significant reductions in malaria morbidity and mortality during the past half-century in South Africa. In addition, strategies for achieving malaria elimination have been proposed. Here, we highlight the gaps that have been identified and make proposals for taking South Africa from malaria control to elimination.

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