In a recent paper in Molecular Ecology, Argyropoulos and Ruybal-Pesántez et al. (2021) investigated the effects of indoor spraying on Plasmodium falciparum, the human malaria-causing protist. They find that 3 consecutive years of indoor spraying reduced transmission and prevalence of malaria by 90% and 35%, respectively, in the high malaria transmission site they surveyed. Despite these large reductions, a change in genetic diversity in P. falciparum that would indicate a large reduction in population size was not detected, illustrating the incredible resiliency of this parasite. Based on these data, the authors suggest that limiting malaria transmission in high transmission areas will require continued indoor spraying or other interventions such as mass drug administration. See the full article and interview with first authors Argyropoulos and Ruybal-Pesántez below for more details of this exciting work.

• 

What led to your interest in this topic / what was the motivation for this study? Global efforts over the past 20 years have significantly reduced malaria mortality and morbidity around the world, but malaria transmission remains high in many countries in sub-Saharan Africa. A major challenge is the fact that most Plasmodium falciparum infections are asymptomatic creating a persistent parasite reservoir that continually fuels transmission to mosquitos. Our group has a long-standing collaboration with colleagues at the Navrongo Health Research Centre and Noguchi Memorial Institute of Medical Research in Ghana, and the University of Chicago in the US, to conduct longitudinal field-based epidemiological studies of the P. falciparumreservoir in Bongo District, Ghana (Tiedje et al., 2017). Our motivation for this study was to understand P. falciparum transmission dynamics in the context of the roll-out of a malaria control intervention by combining population genetics with more traditional epidemiological and entomological parameters. Our previous research in Bongo District established there was high levels of P. falciparum genetic diversity with no population structure (Ruybal‐Pesántez et al., 2017). We were therefore interested in exploring whether the addition of a short-term indoor residual spraying (IRS) programme against a background of widespread long-lasting insecticidal nets (LLINs) would bottleneck this P. falciparum population in Bongo and lead to reductions in diversity and changes in population structure. 

What difficulties did you run into along the way? One of the major technical limitations in P. falciparum genotyping is phasing multi-genome infections to assign multilocus haplotypes. Eighty per cent of the population of all ages where we work in Ghana have multiple diverse parasite genomes. This is  also a problem for whole genome sequencing of isolates. To get around this problem, we focus on genotyping monoclonal infections using panels of multi-allelic microsatellite markers or biallelic SNPs. In high-transmission settings like our study site in Ghana microsatellite genotyping of P. falciparum provides increased power of inference and higher resolution than biallelic SNPs (Anderson et al., 2000; Ellegren, 2004; Selkoe and Toonen, 2006).

What is the biggest or most surprising innovation highlighted in this study? In our paper, we find that despite the addition of three-rounds of IRS against a background of LLINs between 2013 – 2015, it did not lead to a population bottleneck or dramatic change in parasite genetic diversity. This was striking because IRS did achieve a >90% reduction in local malaria transmission intensity and 37.5% fewer malaria infections in the community. The potential for rebound of P. falciparum transmission is therefore highly likely if these control programmes are not implemented long-term. 

Moving forward, what are the next steps in this area of research? Population genomic approaches are increasingly being applied to enhance our understanding of epidemiology, transmission dynamics, and public health strategies for a variety of pathogens. In the malaria field, the potential of genomic data to guide control and elimination strategies has been recognized but is still in early stages with respect to its translation into general practice. In our paper, we highlight that genomic surveillance is pivotal to assess progress towards achieving the World Health Organisation Global Technical Strategy for Malaria 2016-2030 targets. Along with our collaborators in Ghana, we have conducted follow-up surveys in our study site to track the long-term implications of this IRS intervention, as well as other interventions that have been rolled out across Bongo District since 2015. We are also applying phylodynamic approaches to characterize variant antigen genes to further explore the impact of interventions on P. falciparum adaptation and fitness, as alternate but complementary surveillance metrics in this high-transmission setting. 

Dionne Argyropoulos, co-first author on this paper, is investigating the neutral and adaptive genetic diversity of P. falciparum in these follow-up surveys and in the context of other control interventions as part of her PhD research. Shazia Ruybal-Pesántez, co-first author on this paper, is now currently applying a suite of genomic epidemiology approaches to better understand residual and resurgent malaria transmission dynamics in the Asia-Pacific and Americas regions as part of her post-doctoral research.

What have you learned about methods and resources development over the course of this project? Firstly, it is important that you understand the basic principles of the concepts that you are using. It may seem rudimentary, but these principles will ensure that you are answering the scientific question that you are interested in and are maintaining scientific integrity throughout the research process. Asking for help or support from others in your field is also useful to bounce ideas and enhance your understanding of your research findings. The most exciting part of Molecular Ecology is how we utilise the insights molecular techniques to answer big picture questions. Our study integrated population genetics and genomic surveillance to address key research questions about malaria transmission and control interventions. To do this, we used existing molecular techniques (i.e., microsatellites) in new ways (i.e., to evaluate IRS over time). We also believe that it is important to not be afraid to apply novel techniques to new research questions, such as using bioinformatic tools and various packages in R.

What would your message be for students about to start developing or using novel techniques in Molecular Ecology? This project was unique as it involved field sample collection and processing, parasite genotyping, data generation and for the analysis required combining traditional epidemiological methods with population genetics and genomics approaches. When working with large sample sets and datasets, it is critical to pay attention to detail during data generation, curation and downstream analyses. Developing and strengthening coding skills was instrumental in enabling us to execute the necessary analyses of these data. We found R to be an incredibly useful resource to document our analyses and facilitate discussion and interpretation of the data with colleagues, while ensuring reproducibility of our work. We used several well-established R packages for data management and the population genetics analyses. Overall, this multidisciplinary project would not have been possible without being part of a multi-disciplinary team with a wealth of knowledge and the strong collaborations with experienced researchers in Ghana. 

Describe the significance of this research for the general scientific community in one sentence. We show how parasite genetics can be harnessed to better understand the efficacy of malaria control interventions, particularly by identifying key factors leading to parasite resilience that may not be reflected in other commonly used evaluation metrics. 

Describe the significance of this research for your scientific community in one sentence. Short-term indoor residual spraying with insecticides did not cause a dramatic change on the genetic diversity of P. falciparum in Bongo District, Ghana, therefore long-term strategies are necessary to genetically bottleneck the parasite population. 

Argyropoulos DC*, Ruybal-Pesántez S*, Deed SL, Oduro AR, Dadzie SK, Apparu MA, Asoala V, Pascual M, Koram KA, Day KP, Tredje KE. THe impact of indoor residual spraying on Plasmodium falciparum microsatellite variation in an area of high seasonal malaria transmission in Ghana, West Africa. Molecular Ecology. https://doi.org/10.1111/mec.16029. (*joint lead authors)