Laos malaria outbreak in 2020–21 likely caused by multidrug-resistant strains of P. falciparum

A recent study published in The Lancet Infectious Diseases journal describes the genetic epidemiology and dynamics of the parasite Plasmodium falciparum responsible for malaria outbreaks in Attapeu Province, Laos, during the 2020-2021 malaria season.

Study: Malaria outbreak in Laos driven by a selective sweep for Plasmodium falciparum kelch13 R539T mutants: a genetic epidemiology analysis. Image Credit: PPK_studio / Shutterstock.com

Background

Plasmodium falciparum is a lethal parasite responsible for the deadliest form of malaria, particularly in sub-Saharan Africa. Nevertheless, the implementation of highly effective artemisinin-based combination therapies, together with strict public health measures, have significantly reduced malaria-related mortality rate over the past several decades.     

In recent years, some novel variants of Plasmodium falciparum have emerged and spread in the Greater Mekong Subregion, where pathogen transmission and related mortality is low. These variants have developed resistance to multiple drugs including artemisinin, mefloquine, and piperaquine and, as a result, can easily escape currently available therapeutic interventions.

In the current study, scientists analyze the genetic characteristics of multidrug-resistant variants responsible for malaria outbreaks in Attapeu Province, Laos.

Laos is a country in the Greater Mekong Subregion that is aiming to eliminate transmission of Plasmodium falciparum by 2023. Despite strict implementation of public health measures, a sudden outbreak of Plasmodium falciparum occurred in the Attapeu province during the 2020-2021 malaria season.

As a part of routine genetic surveillance, southern Laos public health authorities collected 249 samples from Attapeu province during the outbreak. In an attempt to understand the epidemiological characteristics of the outbreak parasite, these samples were genotyped and their genetic signatures were compared with those of parasites circulating in previous seasons and other geographical regions.   

Important observations

About 130% induction in malaria cases was observed in Attapeu province during the 2020-2021 malaria season. The genetic analyses conducted in the current study revealed a stable diversity of genetic barcodes during the 2017-2019 period that was similar to that observed between 2011-2012.

A significant loss of genetic diversity was observed in samples collected from Attapeu province during recent outbreaks in 2020. The scientists hypothesized that the reduction in diversity could be due to expanding populations.

In an attempt to identify populations of highly related individuals, pairwise genetic distances were estimated and used to cluster genetically similar parasites. A total of 30 clusters were identified.

The cluster analysis revealed that rapid clonal expansion of a multidrug-resistant parasite strain carrying the R539T mutation is responsible for recent outbreaks in Attapeu. Three variants of the dominant strain were identified and termed as LAA1, LAA2, and LAA7.

Some of these variants were circulating at a low frequency before 2019. However, in 2021, they became the dominantly (94%) circulating variants because of aggressive clonal expansion.

The most rapidly expanding variant was LAA1 (84%), which was primarily responsible for the reduction in genetic diversity. The second largest variant was LAA2, which expanded more gradually to reach a frequency of 8% in 2021. The third largest variant was LAA7, whose expansion reduced over time with the induction in LAA1 expansion.

Overall, these observations indicate that the outbreaks are driven by beneficial mutations that increased in frequency and became fixed in a given population, which is otherwise known as a selective sweep.

Mutational analysis of outbreak variants

The genotyping of outbreak isolates revealed that all parasite variants carry alleles associated with resistance to chloroquine, sulfadoxine, pyrimethamine, and artemisinin. While the LAA2 variant carried the C580Y mutation, both LAA1 and LAA7 carried the R539T mutation.

A strong correlation was observed between the emergence of the R539T mutation and the onset of the outbreak in Attapeu. This mutation was not found in other provinces of Laos; however, it was present in Attapeu at a low frequency before the outbreak.

Further analysis revealed that LAA1 inherited about 58% of its genome from a previously circulating strain in Cambodia in 2008. In fact, the genome of LAA2 was identical to a Cambodian strain from 2009. The genome of LAA7 represented a recombination of a previously dominant dihydroartemisinin-piperaquine resistant strain with a R539T mutation.   

Study significance

The study findings indicate the recent Plasmodium falciparum outbreaks in Attapeu, Laos are driven by beneficial mutations associated with multidrug-resistant phenotypes of outbreak variants.

These variants may circulate at low frequency for years. The establishment of favorable conditions for selection, such as changes in front-line therapies, can lead to the emergence of beneficial mutations and rapid clonal expansion of variants.