Plasmodium falciparum genomic surveillance reveals spatial and temporal trends, association of genetic and physical distance, and household clustering

Abstract

Molecular epidemiology using genomic data can help identify relationships between malaria parasite population structure, malaria transmission intensity, and ultimately help generate actionable data to assess the effectiveness of malaria control strategies. Genomic data, coupled with geographic information systems data, can further identify clusters or hotspots of malaria transmission, parasite genetic and spatial connectivity, and parasite movement by human or mosquito mobility over time and space. In this study, we performed longitudinal genomic surveillance in a cohort of 70 participants over four years from different neighborhoods and households in Thiès, Senegal—a region of exceptionally low malaria transmission (entomological inoculation rate (EIR) less than 1). Genetic identity (identity by state) was established using a 24 single nucleotide polymorphism molecular barcode and a multivariable linear regression model was used to establish genetic and spatial relationships. Our results show clustering of genetically similar parasites within households and a decline in genetic similarity of parasites with increasing distance. One household showed extremely high diversity and warrants further investigation as to the source of these diverse genetic types. This study illustrates the utility of genomic data with traditional epidemiological approaches for surveillance and detection of trends and patterns in malaria transmission not only by neighborhood but also by household. This approach can be implemented regionally and countrywide to strengthen and support malaria control and elimination efforts.

Temporal and spatial analysis of Plasmodium falciparum genomics reveals patterns of connectivity in a low-transmission district in Southern Province, Zambia

“…However, relatively few studies have used genomic approaches to study malaria transmission dynamics and importation on small geographic scales, such as a single district (Searle et al, 2020). Detailed work in Senegal has shown similar findings, including persistence of clones across multiple seasons and evidence of importation into similar low transmission regions (Daniels et al, 2020(Daniels et al, , 2015Sy et al, 2020). However, the approaches used in these studies have been low density genotyping, primarily a 24 single nucleotide polymorphism (SNP) barcode.…”

High-throughput profiling of natural acquired humoral immune response to a large panel of known and novel full length ectodomain P. falciparum merozoite vaccine candidates under reduced malaria transmission

“…Study participants consisted of a total of 70 male patients with a median age of 11 (5-16) years, median parasitemia on the day of recruitment of 0.43(0.02-4.89)% and with a mean of 1 (0-5) number of past malaria infections (Table 1), described previously (Sy et al 2020).…”