Prospective surveillance study to detect antimalarial drug resistance, gene deletions of diagnostic relevance and genetic diversity of Plasmodium falciparum in Mozambique: protocol

Abstract

IntroductionGenomic data constitute a valuable adjunct to routine surveillance that can guide programmatic decisions to reduce the burden of infectious diseases. However, genomic capacities remain low in Africa. This study aims to operationalise a functional malaria molecular surveillance system in Mozambique for guiding malaria control and elimination.Methods and analysesThis prospective surveillance study seeks to generate Plasmodium falciparum genetic data to (1) monitor molecular markers of drug resistance and deletions in rapid diagnostic test targets; (2) characterise transmission sources in low transmission settings and (3) quantify transmission levels and the effectiveness of antimalarial interventions. The study will take place across 19 districts in nine provinces (Maputo city, Maputo, Gaza, Inhambane, Niassa, Manica, Nampula, Zambézia and Sofala) which span a range of transmission strata, geographies and malaria intervention types. Dried blood spot samples and rapid diagnostic tests will be collected across the study districts in 2022 and 2023 through a combination of dense (all malaria clinical cases) and targeted (a selection of malaria clinical cases) sampling. Pregnant women attending their first antenatal care visit will also be included to assess their value for molecular surveillance. We will use a multiplex amplicon-based next-generation sequencing approach targeting informative single nucleotide polymorphisms, gene deletions and microhaplotypes. Genetic data will be incorporated into epidemiological and transmission models to identify the most informative relationship between genetic features, sources of malaria transmission and programmatic effectiveness of new malaria interventions. Strategic genomic information will be ultimately integrated into the national malaria information and surveillance system to improve the use of the genetic information for programmatic decision-making.Ethics and disseminationThe protocol was reviewed and approved by the institutional (CISM) and national ethics committees of Mozambique (Comité Nacional de Bioética para Saúde) and Spain (Hospital Clinic of Barcelona). Project results will be presented to all stakeholders and published in open-access journals.Trial registration numberNCT05306067.

Antimalarial resistance in Mozambique: Absence of Plasmodium falciparum Kelch 13 (K13) propeller domain polymorphisms associated with resistance to artemisinins

“…Hence the need to replicate these experiences and always with the aim of better informing PNCM decision making and ultimately the genomics of malaria in Mozambique to become a programmatic activity. Further research is currently being done and will provide more information on the resistance pro le to pfKelch13 [47] Declarations Funding Figures…”

Nanopore sequencing for real-time genomic surveillance ofPlasmodium falciparum

“…Sequencing workflows that can be implemented in endemic settings are essential to drive the decentralisation of genomics, to support its integration into clinical and public health applications, and to push for a more equitable distribution of global genomics capacity. Amplicon sequencing can be a pragmatic approach to malaria molecular surveillance and generate actionable data on parasite populations, including workflows based in endemic LMICs [11,12,[94][95][96][97][98][99][100][101][102][103][104][105][106]. Moreover, by developing and investing in sequencing capacity, the technical skills, experience and technology can potentially be applied to multiple high priority pathogens and emerging infection threats, maximising the impact of genomics in public health and strengthening global pathogen surveillance and health security [107].…”

Factors Affecting the Performance of HRP2-Based Malaria Rapid Diagnostic Tests

“…Targeted deep sequencing of important genes could also be an alternative approach to identify genetic variations [ 60 ]. Advances in how genetic material is sequenced using next-generation sequencing (NGS) technology have moved genomics from the bench to the field.…”

“…The copy number variations (CNVs) such as gene deletions and duplications can be determined based on the mean depth of coverage of individual amplicons between the reference sample (3D7, without CNVs) and test sample. This approach can also be combined with other aspects of malaria elimination activities including capturing low-frequency resistant mutants [ 60 , 61 ]. Moreover, combining NGS with pooling of individual isolates can potentially provide a faster and cheaper surveillance tool at the population level [ 61 ].…”