The MalariaGEN-GSU Malaria Genomic Epidemiology Journal Clubs are a monthly forum to learn more about and discuss the latest research on malaria vector and parasite genomics from experts. The series began in 2023 as a way to bring together researchers and enthusiasts from the global malaria genomics community.
This year, we’ve had 13 speakers, welcomed 1541 attendees from 80 countries, and spent a total of 748 minutes exploring the latest research on malaria vector and parasite genomics. It has been thrilling to see a growing, globally diverse interest and participation, and we are grateful to everyone who has been a part of it – whether as a presenter or listener, sharing insights and learning together.
Recordings of all sessions are available on our YouTube channel — browse through the playlist to revisit your favourites and catch up on any you missed. And if you have a soon-to-be-published pre-print or publication on the genomic epidemiology of malaria, submit it to be considered for one of our Journal Clubs in 2025.
Thank you for journal clubbing with us this year! We will be back in January 2025, so keep an eye on our channels for announcements coming soon.
The Journal Club team at the Genomic Surveillance Unit (GSU), Wellcome Sanger Institute.
January Zach Popkin-Hall
For the first Journal Club of 2024, Dr Zach Popkin-Hall, a post-doctoral research associate at the University of North Carolina at Chapel Hill, discussed the malaria parasite species landscape in mainland Tanzania.
While Plasmodium falciparum is the most prevalent and deadliest human malaria species in sub-Saharan Africa, recent evidence shows that other non-falciparum species could be more prevalent in the region than previously thought.
Dr Popkin-Hall’s work focuses on understanding the genomics of these non-falciparum species. He discussed the malaria parasite species landscape in mainland Tanzania and why malaria elimination in the country will require increased surveillance and understanding of these parasite species.
He also shared some bonus data in addition to what’s available in the publication in the Journal of Infectious Diseases — watch the recording to learn more.
February Olivo Miotto
Could genetic adaptations of P. falciparum provide a new perspective into the evolution and transmission of malaria parasites in Africa?
Professor Olivo Miotto’s work focuses on translating the massive quantities of data produced by sequencing thousands of genomes into meaningful knowledge about the epidemiology of P. falciparum.
Based in Bangkok, he runs GenRe-Mekong, a genetic surveillance project in collaboration with the National Malaria Control Programmes in the Greater Mekong Subregion. The project provides public health bodies with actionable knowledge about drug-resistant strains, to inform decision-making and interventions.
In a now-published paper in The Lancet Microbe, Prof Miotto and colleagues identified a unique cluster of P. falciparum parasites in Africa by analysing malaria parasite genomes available on the MalariaGEN Pf7 data resource.
The results reveal interesting adaptations and shared genetic components among these parasites, which could be linked with currently unknown factors in their epidemiological environments. This reshapes our understanding of how malaria parasites evolve and spread across Africa.
March Sanjay Nagi
Dr Sanjay Nagi is a post-doctoral fellow studying genomics of the major malaria mosquito, Anopheles gambiae, at the Liverpool School of Tropical Medicine. As emerging resistance to compounds used in vector control is of major concern to malaria control programmes, a major focus of Sanjay’s research is the rapid evolution and spread of resistance in the major malaria vector, and how we can use population genomics to ultimately inform malaria control programmes.
In this vector-focused session, Dr Nagi explored a study that used a population genomic approach to identify novel mechanisms of resistance to pirimiphos-methyl, an organophosphate insecticide widely used in indoor residual spray campaigns. They discovered ongoing parallel evolution between An. gambiae s.l. and the common house mosquito, Culex pipiens, and found that a gene amplification in An. gambiae in West Africa is associated with resistance to pirimiphos-methyl.
Overall, this research demonstrates a striking example of parallel evolution which has important implications for malaria control programmes.
May Joel Odero and Brice Letcher
For the first session in May, Dr Joel Odero, a Research Scientist based at the Ifakara Health Institute, explored the first-ever discovery of knock-down resistance in An. funestus mosquitoes. This has been linked to resistance to a banned insecticide, DDT, in Tanzania, with evidence pointing to a legacy of DDT pollution in the area. The results are now published in Molecular Ecology, and you can read the fascinating story behind how the team pieced together historic environmental data with genomic insights to make this discovery.
We were lucky to have a second malaria parasite-focused Journal Club in May with Dr Brice Letcher, a post-doctoral research scientist at the École normale supérieure de Lyon. Dr Letcher explored his first-author publication which delved into how gene conversion plays a role in the evolution of two mysterious cell-surface antigens in P. falciparum.
June Cynthia Awuor
Cynthia Awuor is a researcher and MSc student in Molecular Biology and Bioinformatics at the Kenya Medical Research Institute (KEMRI). She is part of the G-AVENIR project, which uses whole genome data to identify insecticide resistance markers in malaria vectors to aid public health decision-making within National Malaria Control Programmes in Benin and Kenya.
In this Journal Club, Cynthia presented findings in a pre-print which uses a systems biology approach to identify insecticide resistance markers in two mosquito species.
Using a weighted gene co-expression network analysis (WGCNA) method, the team identified insecticide-resistant markers in An. gambiae and An. arabiensis, revealing new insights into the molecular mechanisms of underlying resistance.
July Beatus Lyimo
The two WHO-approved malaria vaccines, RTS,S and R21, are made with the P. falciparum circumsporozoite protein (Pfcsp). Dr Beatus Lyimo, a post-doctoral research fellow at the Nelson Mandela African Institution of Science and Technology, presented a study which explores the genetic diversity and population structures of Pfcsp in mainland Tanzania.
As genetic variations in the Pfcsp gene in different parasite populations could affect vaccine effectiveness, the study analysed P. falciparum genomic data from Tanzania, which is available through MalariaGEN, to explore the genetic diversity and population structure of this gene in mainland Tanzania. Elaborating on the evidence published in Malaria Journal, Dr Lyimo discussed important genetic insights to support the introduction of malaria vaccines in the country.
August Nina White, Chiyun Lee, and Kelly Bennett
In August, Dr Nina White and Chiyun Lee, senior data scientists at the Wellcome Sanger Institute, teamed up for a double act on Pf-HaploAtlas, a free online application that enables researchers and public health officials to study patterns of mutations across time and space in unprecedented detail.
During this interactive session, they provided context on how the app was developed by drawing on the vast Pf7 data resource, followed by a live demo on analysing haplotypes of interest.
Dr Kelly Bennett, a senior data scientist at the Wellcome Sanger Institute, presented a second Journal Club in August focusing on malaria vectors. For the first time, researchers and public health authorities identified Anopheles coluzzii mosquitoes in Kenya. A study published in Malaria Journal describes this discovery, which was achieved by analysing mosquito whole genome sequencing data from the Malaria Vector Genome Observatory.
Dr Bennett and colleagues used genomics to confirm the identity of the Anopheles coluzzii mosquitoes among samples collected from five counties in Kenya. They also explored the genetic structures and insecticide resistance profiles of these mosquitoes, providing key information to support vector control in the country.
Read our article about how this elusive malaria vector was uncovered using genomics.
September Clara Rehmann
Could there be a genetic link between how malaria parasites and mosquitoes spread across regions? Clara Rehamnn, a PhD researcher at the University of Oregon, explored this fascinating vector-host relationship at our September Journal Club.
Findings published in her first-author paper in G3 Genes|Genomes|Genetics revealed how the shared evolutionary history between parasites and vectors provides clues about their similar geographic patterns. By analysing the location and whole genome data of An. gambiae mosquitoes and P. falciparum parasites, Clara and colleagues investigated a possible genetic link between the distribution of the malaria parasites and its mosquito host in sub-Saharan Africa.
October Andrew Balmer
What can genomic data from malaria parasites tell us about the spread of artemisinin resistance globally and what can we expect in the future? These are the questions that Dr Andrew Balmer and colleagues aimed to understand in their recent deep-dive on kelch13 mutations from 112,000+ P. falciparum genome sequences worldwide.
By analysing all publicly available genome sequence data on P. falciparum parasites worldwide, Dr Balmer delved into the findings from the review, which follows the emergence of artemisinin partial resistance in Southeast Asia and the concerning parallels now being seen in East and Northeast Africa. By mapping data from over 112,000 P. falciparum genome sequences worldwide, he explained how they tracked kelch13 mutations, which are key markers of artemisinin partial resistance.
Read an explainer article that highlights key findings from the pre-print.
November Alessandra della Torre
What if another mosquito species may be confounding malaria vector control efforts in West Africa? A recent study analysing the genomes of Anopheles mosquito populations from seven West African countries uncovered compelling evidence of a potential cryptic taxon.
During the final Journal Club of the year, Professor Alessandra della Torre from the Sapienza Università di Roma explored genomic evidence for this cryptic taxon, provisionally named the ‘Bissau molecular form.’
Since members of the An. gambiae complex look identical, they can only be distinguished through genomics. By analysing data available through the Malaria Vector Genome Observatory, Prof della Torre and colleagues discovered clues suggesting that the Bissau molecular form has a distinct evolutionary lineage with unique genetic traits. Notably, it lacks common insecticide resistance mechanisms found in An. gambiae and An. coluzzii. She also touched on what this means for malaria vector control in far-west Africa.
