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Malaria, one of the world’s oldest and deadliest diseases, continues to threaten global health despite significant advancements in treatment and prevention that have been achieved in the 21st century.  

As a disease caused by the parasite, the parasite’s remarkable genetic diversity creates gaps in diagnosis and treatment, particularly in regions where healthcare resources are limited.

With the support of high-throughput sequencing (HTS) technology, regions with high burden and high-impact (HBHI) can now determine the infectious origin and the types of parasite and improve malaria prevention and management.

Global Malaria Burden and Challenge

Malaria is a life-threatening disease caused by Plasmodium parasites, transmitted to humans through the bites of infected Anopheles mosquitoes. The infection leads to symptoms like fever, chills, and flu-like illness.

If left untreated, it can progress to severe illness and often death. Malaria is most prevalent in tropical and subtropical regions, including sub-Saharan Africa, Southeast Asia, and parts of Latin America.

According to the World Health Organization (WHO)’s World Malaria Report 2024, malaria continues to impact millions worldwide. In 2023, an estimated 263 million cases were reported, with 597,000 deaths. This marks an increase of 11 million cases (a 4% rise) compared to 2022. The majority of malaria cases and deaths occur in HBHI regions, where healthcare infrastructure is limited.

Young children remain the most vulnerable group. In 2023, 73.7% of all malaria deaths—around 440,000—occurred in children under the age of five. Pregnant women are also at heightened risk, with 4 million (34%) of pregnancies in sub-Saharan Africa exposed to malaria in 2023.

Despite decades of progress in controlling malaria through tools like insecticide-treated bed nets, antimalarial drugs, vaccination, and improved diagnostics, the disease remains a leading cause of death and disease in HBHI areas.

Malaria’s persistence is fueled by factors such as mosquito resistance to insecticides, parasite resistance to treatments, and the challenges of diagnosing and treating cases in remote areas with limited healthcare access.

Genetic Diversity of the Malaria Parasite

Blood films for Malaria parasite.

The primary cause of malaria, Plasmodium falciparum, is a master of adaptation. Its genetic makeup is constantly shifting, leading to the emergence of new strains. Some of these strains carry mutations that allow them to evade detection by rapid diagnostic tests (RDTs), a vital tool in resource-poor regions.

For instance, certain strains of P. falciparum lack the protein PfHRP2, which many RDTs target. These “stealth” strains evade detection, leaving individuals undiagnosed and untreated.

Moreover, the parasite's ability to develop resistance to treatment compounds the problem. Mutations in the Kelch13 gene, for example, are linked to resistance to artemisinin, the main drug used to treat malaria. In areas where treatment is already limited, these mutations make it even harder to combat the disease effectively.

Genomic Surveillance’s Global Application

To combat the challenges posed by the parasite's genetic diversity, scientists are turning to HTS technologies as a powerful tool to combat malaria’s evolving threat.

Metagenomic next-generation sequencing (mNGS) and other HTS technologies provide real-time data that can guide public health decisions. For example, if genomic surveillance detects strains lacking PfHRP2, health authorities can quickly switch to RDTs that target alternative proteins like PfLDH. This ensures that diagnostic tools remain accurate, even as the parasite evolves.

Genomic surveillance is already showing its potential in the field. In Uganda, early detection of PfHRP2 deletions through genomic surveillance prompted a regional shift to more accurate RDTs, preventing missed diagnoses.

Similarly, in Southeast Asia, genomic tools have been crucial in tracking the spread of artemisinin resistance, and a high-sensitivity ddPCR assay for Pfkelch13 mutation detection, to enable timely changes to treatment protocols.

These examples demonstrate how combining genomic surveillance with traditional diagnostic methods can improve malaria control efforts, ensuring that interventions are responsive to the latest developments in parasite evolution.

Precision Public Health

The fight against malaria requires more than just bed nets and medications. It demands a deep understanding of the parasite’s genetic makeup and the tools to monitor its evolution.

The HTS technology, like mNGS, can help doctors and health departments provide timely diagnosis and treatment methods by quickly and accurately detecting pathogens. This effectively prevents and treats malaria and deals with emerging strains and drug resistance. In addition, HTS can also support the understanding of transmission dynamics of malaria parasites and provide a basis for formulating prevention and control strategies.

While the road to eradication is challenging, the integration of genomic technologies into malaria control strategies offers a hopeful future. Through precision public health and adaptive strategy, fewer cases will be missed, treatments will be more effective, and, ultimately, fewer lives will be lost.

About BGI Genomics PMseq™

PMseq™ uses mNGS to extract nucleic acids from clinical infection samples after performing pre-processing, followed by sequencing on a high-throughput platform. By comparing the results against the specialized clinical database PMDB and utilizing advanced bioinformatic algorithms, PMseq™ can efficiently identify potential pathogens. This method enables unbiased detection of bacteria, fungi, viruses, parasites, and other pathogens, as well as the assessment of drug resistance and virulence genes. As a result, it significantly enhances the accuracy of pathogen diagnosis and helps guide the targeted use of antibiotics, making infection diagnosis and treatment more precise.

About BGI Genomics

BGI Genomics, headquartered in Shenzhen, China, is the world's leading integrated solutions provider of precision medicine. Our services cover more than 100 countries and regions, involving more than 2,300 medical institutions. In July 2017, as a subsidiary of BGI Group, BGI Genomics (300676.SZ) was officially listed on the Shenzhen Stock Exchange.