Malaria parasites can evade rapid tests, threatening eradication goals

Mutations that render Plasmodium falciparum invisible to these tests are spreading globally

A nurse's hand drops human blood on a small, white plastic malaria rapid test.

A health care worker at a hospital in Sierra Leone tests a blood sample for malaria. Genetic mutations that render malaria parasites invisible to such tests are spreading across Africa, Asia and South America.

Karen Kasmauski/Getty Images

Over the last couple of decades, rapid diagnostic tests have emerged as a vital tool in the fight to control malaria. The relatively inexpensive test strips, which work in just minutes, have diagnosed millions of cases, hastening access to lifesaving treatment. They’ve also drastically improved surveillance in harder-to-reach rural areas, sharpening public health experts’ view of the toll of this mosquito-borne disease that kills around half a million people globally each year.

But this progress could be undermined by the malaria-causing parasite itself. 

Mutations that render Plasmodium falciparum invisible to the current gold-standard rapid test are spreading across many countries, contributing to false-negative test rates as high as 80 percent at some hospitals. While prevalence of the mutations is rarely that high, scientists worry they could be spreading unnoticed, causing potentially hundreds of thousands of cases of this deadly disease to go undetected, delaying treatment. Without the development of new tests, the mutations could pose a major obstacle to global eradication efforts.

“This is a huge concern, right up there with drug and insecticide resistance,” says Jane Carlton, a biologist and director of Johns Hopkins Malaria Research Institute. “That’s because it looks like it’s spreading.”

Scientists first reported these mutations in 2010, after reviewing blood samples from patients in Peru. Though malaria parasites showed up in the samples under the microscope, the patients’ rapid test results were negative. Most malaria rapid tests work by detecting P. falciparum histidine-rich protein 2 and 3, which are usually reliable indicators of infection. But in malaria parasites isolated from these Peruvian samples, portions of the genes pfhrp2 and pfhrp3, which code for the proteins, had been deleted, the team found. The mutations effectively cloaked the parasites from widely used rapid tests.

“That has a clear impact on our ability to diagnose and treat individuals,” says Oliver Watson, an infectious disease modeler at Imperial College London. While there are alternative rapid tests that rely on other proteins, these tests aren’t widely used because they are “not quite as sensitive and a little more expensive,” Watson says. As a result, the global supply of alternative tests is quite limited.

A microscope image of human red blood cells infected by malaria parasites. The parasites look like dark purple rings on the pink-stained blood cells.
When rapid tests fail due to genetic mutations in malaria parasites, more precise methods such as microscopy are required to confirm that a false-negative result is actually positive. In this microscope image of human red blood cells, the parasites show up as purple rings.Ed Reschke/Getty Images

The test-evading mutations have popped up in at least 40 countries across South America, Africa and Asia. While many of the countries have reported barely a trace of the deletions, there’s evidence of rapid spread in certain regions, especially the Horn of Africa (SN: 11/2/22).

In Eritrea, researchers began finding startling numbers of false-negative rapid tests in 2014. Subsequent studies found the test-evading parasites were to blame. For instance, at one Eritrean hospital, these parasites infected 21 out of 26 malaria patients — nearly 81 percent. At another, the parasites infected 10 out of 24 patients, or about 42 percent. The high prevalence prompted Eritrea to switch its testing regime to alternative rapid tests. Ethiopia and Djibouti, which also have high test-evading mutation rates, have also started using alternative tests.

According to some experts, these efforts have largely worked. “There are no indications that [the spread of mutations had] a major impact in malaria control efforts, especially because of the prompt detection and subsequent test policy changes,” says microbiologist Michael Aidoo, associate director for laboratory science in the Division of Parasitic Diseases and Malaria at the U.S. Centers for Disease Control and Prevention.

In 2019, The World Health Organization released a response plan, advising countries to switch testing strategies when the prevalence of cloaking mutations rises above 5 percent. Figuring out whether that threshold has been met in enough time to switch up testing strategies can be a challenge.

“It’s not an automatic thing to detect these mutant parasites,” says Carlton. It requires extensive testing of samples via more precise methods, like microscopy or detecting the parasite by DNA, to confirm that a negative rapid test is actually positive and that the parasite contains test-evading deletions. “It can be quite expensive to do that,” she says, so the quality of existing studies assessing the prevalence of these mutations, known as surveys, is highly variable.

Consequently, the global picture is still fuzzy in some areas.

“There’s a vital need for more surveys,” Watson says. “Both to ensure that we have data from all malaria-endemic countries, but also to get more surveys in locations where we’re already seeing the deletions, to see how quickly they’re increasing.”

Within 20 years, 29 of 49 malaria-endemic countries in Africa could have some areas that surpass the 5 percent threshold, Watson and colleagues estimated in a paper posted at in January. East Africa, Senegal and Mali are among the areas at highest risk, while Central Africa — which has the highest malaria burden — is at lower risk. The work hasn’t yet been peer-reviewed.

Existing alternative tests won’t be enough to meet this need, Watson says. More research is needed to develop tests that have higher sensitivity, “and we need a change from the manufacturing side, to ensure we have the [testing] capacity when countries need to switch,” he says.

If inexpensive and accurate alternative tests are widely available, this problem can be effectively controlled, Watson says. But if they aren’t, it’s going to become much harder to control malaria in many countries. “It’s just an incredibly worrying problem.”

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