Exploring the invisible genetic variations threatening malaria elimination efforts in Southeast Asia
Imagine you're a healthcare worker in a remote clinic in Myanmar. A feverish patient arrives, and you perform a rapid malaria test—the kind used worldwide to diagnose this deadly disease in minutes. The test shows a clear negative result, yet unknown to you, invisible malaria parasites are teeming in the patient's bloodstream.
HRP2/3 deletions cause diagnostic failures
This dangerous scenario is becoming increasingly common across malaria-endemic regions, and the culprit lies in genetic variations occurring within the malaria parasites themselves.
At the heart of this diagnostic challenge are two proteins: histidine-rich protein 2 (HRP2) and histidine-rich protein 3 (HRP3), produced by Plasmodium falciparum—the deadliest malaria parasite species. These proteins serve as the primary targets for most rapid diagnostic tests (RDTs), which use specialized antibodies to detect their presence in a patient's blood 3 6 .
Recent research on Myanmar's P. falciparum isolates has revealed fascinating yet concerning insights into these genetic variations. Understanding this microscopic evolutionary arms race is crucial for malaria elimination efforts, particularly in Myanmar, which carries the highest malaria burden in Southeast Asia but is steadily progressing toward elimination by 2030 1 4 .
Histidine-rich proteins 2 and 3 are unique to P. falciparum parasites and play several important roles:
Most malaria RDTs are designed as lateral flow immunoassays—similar to home pregnancy tests:
Parasites with intact HRP2/3 genes produce detectable proteins
Mutations or deletions in pfhrp2/pfhrp3 genes occur
RDTs return false-negative results despite active infection
Between 2013 and 2015, scientists embarked on a crucial study to understand the genetic landscape of pfhrp2 and pfhrp3 in Myanmar's malaria parasites. Their goal was to analyze the extent and nature of genetic variations in these genes and assess potential implications for malaria diagnosis 1 .
The research team collected 105 blood samples from malaria patients in Upper Myanmar regions, including Mandalay, Naung Cho, Tha Beik Kyin, and Pyin Oo Lwin 1 .
Blood samples were collected from confirmed P. falciparum patients and spotted onto filter paper. Genomic DNA was then extracted from these dried blood spots using specialized kits 1 .
The researchers designed specific primers to target the pfhrp2 and pfhrp3 genes. Using nested polymerase chain reaction (PCR), they successfully amplified 102 pfhrp2 and 89 pfhrp3 sequences from the 105 samples 1 .
The amplified gene fragments were cloned into specialized vectors and transformed into bacteria. Plasmids from at least two independent clones were sequenced for each sample to ensure accuracy 1 .
The resulting DNA sequences were analyzed using bioinformatics tools to identify variations, including different arrangements of amino acid repeats and novel amino acid changes 1 .
| Research Tool | Primary Function |
|---|---|
| Nested PCR | Highly specific amplification of target genes |
| Cloning Vectors | Production of multiple gene copies for accurate sequencing |
| DNA Sequencing | Determination of precise genetic sequences |
| Bioinformatics Software | Analysis of genetic variations and relationships |
The study revealed extraordinary genetic diversity in Myanmar's parasite populations:
| Gene | Sequenced | Haplotypes |
|---|---|---|
| pfhrp2 | 84 | 76 |
| pfhrp3 | 56 | 47 |
This diversity stemmed mainly from different arrangements of distinct repeat types within the genes 1 .
Perhaps most importantly, the research identified novel amino acid changes in both pfhrp2 and pfhrp3, though these occurred at low frequencies. When compared with global parasite isolates, Myanmar's genes shared similar structural organization but showed distinct differences in the frequencies of specific repeat types and their lengths 1 .
The genetic variations observed in Myanmar's parasites are part of a broader global phenomenon. Research across multiple continents has revealed that:
pfhrp2/3 deletions are spreading, with mathematical models predicting southward spread in Africa within 20 years 6
There appears to be a fitness cost for parasites with pfhrp2 deletions, potentially reducing their replicative rate by up to 10% 6
Approximately 61.7% of pfhrp2-deleted samples also show pfhrp3 deletions globally 6
| Region | Key Observation | Public Health Impact |
|---|---|---|
| Horn of Africa | High frequency of deletions causing false-negative RDTs | Several countries have switched to alternative diagnostics |
| South America | Deletions emerged in settings that never relied heavily on HRP2-RDTs | Suggests potential unknown selective advantage beyond diagnostic evasion |
| Myanmar Region | High genetic diversity but lower deletion frequency | Important to monitor as Myanmar progresses toward elimination |
The connection between pfhrp2 and pfhrp3 deletions appears to be more than random chance. Statistical analysis shows significant nonrandom association between these deletions, suggesting they may be co-selected in some populations 6 .
This relationship matters for diagnostic accuracy because HRP3 can sometimes be detected by HRP2-based tests. If both genes are deleted, this potential backup detection system fails completely 6 .
The extensive genetic diversity found in Myanmar's pfhrp2 and pfhrp3 genes could potentially affect the binding efficiency of antibodies used in RDTs, influencing test sensitivity 1 .
While the study didn't find high rates of complete gene deletions in Myanmar, the observed variations highlight the need for:
Myanmar's particular situation creates both challenges and opportunities for malaria elimination:
The silent genetic changes occurring in Myanmar's malaria parasites represent an ongoing evolutionary arms race between humans and pathogens.
The detailed study of pfhrp2 and pfhrp3 genetic variations in Myanmar provides both warning and guidance. It highlights a vulnerable point in our current malaria control strategy while also offering the knowledge needed to develop next-generation solutions.
Ongoing surveillance of these genetic variations, coupled with the development of alternative diagnostic methods, will be crucial for achieving and maintaining malaria elimination—not just in Myanmar, but worldwide.
The silent genetic revolution in Myanmar's malaria parasites reminds us that in the battle against infectious diseases, knowledge of our microscopic adversaries is our most powerful weapon.