London Calling 2023: Targeted nanopore sequencing using hybridisation probes reveals immune escape polymorphisms in malaria vaccine candidates

Pathogen populations exposed to host immunity acquire and maintain variation in surface proteins to escape immune responses and contribute to the incomplete efficacy of vaccines. The malaria parasite, Plasmodium falciparum is responsible for over 600,000 deaths and over 400 million clinical episodes of malaria each year. To investigate variation in P. falciparum antigen genes being investigated as vaccine candidates, we developed a nanopore sequencing approach using custom hybridisation probes and an automated haplotype-aware single nucleotide variant (SNV) calling pipeline. This method was applied to investigate SNVs associated with immune escape by sequencing 34 antigen genes in a cohort of children from malaria-endemic areas of Papua New Guinea. Blood-stage antigens were more likely to contain immune-escape polymorphisms than antigens expressed in other lifecycle stages. Identification of these SNVs, associated haplotypes and their prevalence allows recommendations for the formulation of the next generation of P. falciparum vaccines based on diverse antigens.