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Plasmodium vivax being the most geographically spread Plasmodium species is considered sparsely distributed in sub-Saharan Africa (sSA) while P. falciparum is the most prevalent species in this region. Thus, control strategies in sSA have been disproportionately targeted towards falciparum malaria. Nevertheless, with the use of more sensitive malaria diagnostic platforms, there are more reports of P. vivax and other non-falciparum malaria in sSA. In addition, P. vivax is presumed benign, however there are new findings of severe cases recorded from P. vivax single or mixed infection with other Plasmodium species. Besides, the extended dormant period (lasting for weeks or months) is a challenge for achieving effective cure for vivax infections. Although, chloroquine has been proscribed for treatment P. falciparum, it still remains the drug of choice for P. vivax in most Asian countries where it is predominant. In sSA, artemisinin combination-based therapies (ACTs) are used for treatment of falciparum malaria and, it is probable that the use of ACT could be enhancing adaptive selection for P. vivax in the face of its increasing prevalence in the population. Hence, understanding epidemiological and biological factors, and data that could be contributing to the observed steady increase in P. vivax prevalence in sSA is important. In this chapter, we discuss the mechanisms for invasion of red blood cells, trends in increasing prevalence of vivax malaria, diagnostic tools, and the public health implications of P. vivax and P. falciparum co-endemicity in Africa.

Background The devastating public health impact of malaria has prompted the need for effective interventions. Malaria control gained traction after the introduction of artemisinin-based combination therapy (ACT). However, the emergence of artemisinin (ART) partial resistance in Southeast Asia and emerging reports of delayed parasite sensitivity to ACT in African parasites signal a gradual trend towards treatment failure. Monitoring the prevalence of mutations associated with artemisinin resistance in African populations is necessary to stop resistance in its tracks. Mutations in Plasmodium falciparum genes pfk13, pfcoronin and pfatpase6 have been linked with ART partial resistance. Methods Findings from published research articles on the prevalence of pfk13, pfcoronin and pfatpase6 polymorphisms in Africa were collated. PubMed, Embase and Google Scholar were searched for relevant articles reporting polymorphisms in these genes across Africa from 2014 to August 2021, for pfk13 and pfcoronin. For pfatpase6, relevant articles between 2003 and August 2021 were retrieved. Results Eighty-seven studies passed the inclusion criteria for this analysis and reported 742 single nucleotide polymorphisms in 37,864 P. falciparum isolates from 29 African countries. Five validated-pfk13 partial resistance markers were identified in Africa: R561H in Rwanda and Tanzania, M476I in Tanzania, F446I in Mali, C580Y in Ghana, and P553L in an Angolan isolate. In Tanzania, three (L263E, E431K, S769N) of the four mutations (L263E, E431K, A623E, S769N) in pfatpase6 gene associated with high in vitro IC50 were reported. pfcoronin polymorphisms were reported in Senegal, Gabon, Ghana, Kenya, and Congo, with P76S being the most prevalent mutation. Conclusions This meta-analysis provides an overview of the prevalence and widespread distribution of pfk13, pfcoronin and pfatpase6 mutations in Africa. Understanding the phenotypic consequences of these mutations can provide information on the efficacy status of artemisinin-based treatment of malaria across the continent. Graphical Abstract

MalariaGEN is a data-sharing network that enables groups around the world to work together on the genomic epidemiology of malaria. Here we describe a new release of curated genome variation data on 7,000 Plasmodium falciparum samples from MalariaGEN partner studies in 28 malaria-endemic countries. High-quality genotype calls on 3 million single nucleotide polymorphisms (SNPs) and short indels were produced using a standardised analysis pipeline. Copy number variants associated with drug resistance and structural variants that cause failure of rapid diagnostic tests were also analysed. Almost all samples showed genetic evidence of resistance to at least one antimalarial drug, and some samples from Southeast Asia carried markers of resistance to six commonly-used drugs. Genes expressed during the mosquito stage of the parasite life-cycle are prominent among loci that show strong geographic differentiation. By continuing to enlarge this open data resource we aim to facilitate research into the evolutionary processes affecting malaria control and to accelerate development of the surveillance toolkit required for malaria elimination.

Coronavirus disease 2019 (COVID-19), a severe acute respiratory syndrome caused by SARS-CoV-2 was declared a global pandemic by the World Health Organization (WHO) in March 2020. As of 21stApril 2021, the disease had affected more than 143 million people with more than 3 million deaths worldwide. Urgent effective strategies are required to control the scourge of the pandemic. Rapid sample collection and effective testing of appropriate specimens from patients meeting the suspect case definition for COVID-19 is a priority for clinical management and outbreak control. The WHO recommends that suspected cases be screened for SARS-CoV-2 virus with nucleic acid amplification tests such as real-time Reverse Transcription-Polymerase Chain Reaction (rRT-PCR). Other COVID-19 screening techniques such as serological and antigen tests have been developed and are currently being used for testing at ports of entry and for general surveillance of population exposure in some countries. However, there are limited testing options, equipment, and trained personnel in many African countries. Previously, positive patients have been screened more than twice to determine viral clearance prior to discharge after treatment. In a new policy directive, the WHO now recommends direct discharge after treatment of all positive cases without repeated testing. In this review, we discuss COVID-19 testing capacity, various diagnostic methods, test accuracy, as well as logistical challenges in Africa with respect to the WHO early discharge policy.

Additional file 1: Table S1. Mutations in PfRH5 sequences from Lagos, Nigeria.

Plasmodium vivax and P. falciparum are the most important human malaria species. P. falciparum is considered the most virulent and widespread species in sub-Saharan Africa. Hence, control efforts have focused on reducing the morbidity and mortality associated with falciparum malaria. However, with improved malaria diagnostics, there is more evidence of high vivax burden in Africa. As P. vivax is capable of dormancy in the liver, it is suspected that artemisinin-based combination treatment widely use across Africa to combat falciparum malaria may be favouring adaptive selection for P. vivax. Additionally, a better understanding of the mechanism of erythrocytes invasion in Duffy-negative individuals who were previously believed to be protected against P. vivax is needed. Therefore, this review discusses the epidemiological implications of P. vivax and P. falciparum co-endemicity in Africa. We also examine available tools for diagnosis of vivax malaria. We conclude by recommending specific interventions against P. vivax that can impact current malaria elimination strategies.

Background: COVID-19 continues to wreak havoc in different countries across the world, claiming thousands of lives, increasing morbidity and disrupting lifestyles. The global scientific community is in urgent need of relevant evidence, to understand the challenges and knowledge gaps, as well as the opportunities to contain the spread of the virus. Considering the unique socio-economic, demographic, political, ecological and climatic contexts in Africa, the responses which may prove to be successful in other regions may not be appropriate on the continent. This paper aims to provide insight for scientists, policy makers and international agencies to contain the virus and to mitigate its impact at all levels. Methods: The Affiliates of the African Academy of Sciences (AAS), came together to synthesize the current evidence, identify the challenges and opportunities to enhance the understanding of the disease. We assess the potential impact of this pandemic and the unique challenges of the disease on African nations. We examine the state of Africa’s preparedness and make recommendations for steps needed to win the war against this pandemic and combat potential resurgence. Results: We identified gaps and opportunities among cross-cutting issues which is recommended to be addressed or harnessed in this pandemic. Factors such as the nature of the virus and the opportunities for drug targeting, point of care diagnostics, health surveillance systems, food security, mental health, xenophobia and gender-based violence, shelter for the homeless, water and sanitation, telecommunications challenges, domestic regional coordination and financing. Conclusion: Based on our synthesis of the current evidence, while there are plans for preparedness in several African countries, there are significant limitations. Multi-sectoral efforts from the science, education, medical, technological, communication, business and industry sectors as well as local communities is required in order to win this fight.

Introduction: Extensive genetic diversity of malaria parasites is a major draw back to ongoing control efforts. Population-specific investigation of genetic structure of the parasite is important for effective malaria intervention in endemic populations such as Nigeria where about one-third of the global burden of the disease is borne. This study describes the genetic diversity of Plasmodium falciparum isolates in the Niger River basins, North-Central Nigeria. Methodology: Parasite DNA w as extracted fr om finger -prick blood samples collected from eighty P. falciparum positive individuals. Polymerase Chain Reaction (PCR) genotyping was carried out to target K1, MAD20 and R033 allelic families of Merozoite Surface Protein (MSP) -1 gene and FC27 and 3D7 allelic families of MSP-2 gene. Results: Proportion of isolates with K1 family w as 28(70%) with two alleles in Idah and 16(40%) with two alleles in Ibaji. Proportion of isolates with MAD20 family was 8 (20%) and a total of two alleles were observed in Idah and 4(10%) with two alleles in Ibaji. RO33 proportion was 16 (40%) in Idah one allele and 8(20%) in Ibaji where the allelic family was also observed to be monomorphic. K1 was the most predominant MSP1 allele in the two parasite populations and the frequency of FC27 genotype was higher than 3D7 in both populations. Multiplicity of infection (Mol) with MSP-1 loci was higher in Ibaji (1.30) than Idah (1.05) while MoI with MSP-2 loci was lower in Ibaji (2.00) than Idah (2.13). However, there is no significant difference in the mean Mol between Idah and Ibaji (P > 0.05). The expected heterozygosity (HE) value was 0.56 for MSP-1 and 0.84 for MSP-2. Conclusion: Our findings revealed high levels of monoclonal infections with P. falciparum, suggesting low parasite diversity. This may be a pointer to a reduction in malaria transmission in the river basins.

Map of the study area in South Western Nigeria. Shaded areas indicate regions of study and lines linking regions show the spatial distance (km) between sites. (PDF 89Â kb)

Map of the study area in South Western Nigeria. Shaded areas indicate regions of study and lines linking regions show the spatial distance (km) between sites. (PDF 89Â kb)

Background: There are emerging reports of poor efficacy of artemisinin-based combination treatment (ACT). However, mutations on the Kelch-13 gene marking delayed parasite clearance have no clinically defined relationship with ACT resistance across Africa. With increasing malaria control efforts, declining acquired immunity could be responsible for varying drug response profiles that may be dependent on levels of exposure to infections. To examine antibody responses against malaria and the influence on the efficacy of artemether-lumefantrine (AL), plasma samples were collected, prior to treatment, from individuals presenting with uncomplicated malaria. Methods: Participants were stratified into two groups: early (within 24 hours, N = 20) and late (between 48 – 72 hours, N = 30) parasite clearance after treatment, as determined by var gene acidic terminal sequence (varATS) polymerase chain reaction. Magnetic bead-based luminex assay was used to profile antibody responses specific to a panel of 21 Plasmodium falciparum sporozoite, merozoite and An. gambiae salivary antigens. Results: Median fluorescence intensity (MFI) of the antibodies was highest against glutamate-rich protein (GLURP-R0) and lowest against merozoite surface protein (MSP2) antigen. Analysis showed a positive correlation between expression of immunity and age of individuals (P = 0.023). However, there was no association between parasite density and antibody responses, except a significant positive relationship with reticulocyte binding protein-like homologue 5 (Rh5), P = 0.047; Plasmodium exported protein (Hyp2), P = 0.037 and merozoite surface protein 11 (H103), P = 0.038. Though higher levels of antibodies against erythrocyte binding antigens (EBA 140 and 175), MSP1.19, GLURP, circumsporozoite protein (CSP) and Rh4.2 were observed in individuals who recorded early parasite clearance, there was no significant difference in antibody responses in the early and late parasitological response groups. Conclusions: Characterization of additional markers in larger populations is required to reveal potential immunological correlates of drug efficacy.

Additional file 2. Additional tables.

Additional file 2. Additional tables.

Table S1. Primer sequences and qPCR conditions for varATS assay. Table S2. High Resolution Melting Drug Resistance Assay. Table 3 Relationship between day 0 parasite density and percentage of individuals with day 3 parasitaemia. Table S4. Linkage disequilibrium analysis for pre- and post-treatment parasite populations. (DOCX 26 kb)

Table S1. Primer sequences and qPCR conditions for varATS assay. Table S2. High Resolution Melting Drug Resistance Assay. Table 3 Relationship between day 0 parasite density and percentage of individuals with day 3 parasitaemia. Table S4. Linkage disequilibrium analysis for pre- and post-treatment parasite populations. (DOCX 26 kb)