High-resolution micro-epidemiology of parasite spatial and temporal dynamics in a high malaria transmission setting in Kenya

Abstract

1 2 3 High-resolution micro-epidemiology of parasite spatial and temporal dynamics in a high 4 malaria transmission setting in Kenya 5 6 7 Cody S. Abstract WC: 149 (150 max) 24Main Text WC: 4,830 (5,000 max) 25Methods WC: 2,450 (3,000 max) 26 ABSTRACT 27Novel interventions that leverage the heterogeneity of parasite transmission are needed to push 28 malaria further towards elimination. To better understand spatial and temporal dynamics of 29 transmission, we applied amplicon NGS of two polymorphic gene regions (csp and ama1) to a 30 cohort identified via reactive case detection in a high-transmission setting in western Kenya. From 31 4/2013-6/2014, we enrolled 442 symptomatic children with malaria, 442 matched controls, and 32 all household members of both groups. We evaluated genetic similarity between infected 33 individuals using three novel indices: sharing of parasite haplotypes on binary and proportional 34 scales and the L1 norm. Symptomatic children more commonly shared haplotypes with their own 35 household members. Furthermore, we identified robust temporal structuring of parasite genetic 36 similarity that we exploited to identify the molecular signature of an outbreak. These findings of 37 both micro-and macro-scale organization of parasite populations might be harnessed to inform 38 next-generation malaria control measures. 39 RESULTS 94Haplotype metrics and read coverage. 95Of 5,353 total study participants from across the study area (Fig. 1), 1,050 were RDT+ for 96 P. falciparum. A total of 966 RDT+ infections were submitted for amplicon NGS of csp and ama1 97 loci (Fig. 1). After haplotype assignment 17 and quality filtering of reads, we identified 120 unique 98 csp haplotypes across 655 participants and 180 ama1 haplotypes across 667 participants ( Fig. 99

Measuring changes inPlasmodium falciparumcensus population size in response to sequential malaria control interventions

“…Of interest to those working on malaria surveillance in high-transmission areas is whether measuring MOI, and in turn population size, using var repertoires or single copy antigen genes or by neutral variation with biallelic SNPs, is more relevant to the elimination agenda in high burden countries. Single copy antigen genes such as csp, msp2, and ama1 have each been used to measure MOI (e.g., (Falk et al, 2006;Lerch et al, 2017;Nelson et al, 2019)) and have become part of newer genetic panels (e.g., Paragon v1 (Tessema et al, 2020) andAMPLseq v1 (LaVerriere et al, 2022)). These genes are under balancing selection with geographically common alleles.…”

Design and implementation of multiplexed amplicon sequencing panels to serve genomic epidemiology of infectious disease: A malaria case study

“…We evaluated COI estimation based on 4CAST as opposed to the single locus AMA1 , which is commonly used for this purpose, alone or together with a single additional locus (Lerch et al, 2017; Miller et al, 2017; Nelson et al, 2019). We engineered in silico samples with COI ranging from 2 to 10 (100 engineered samples per COI level) and used the maximum number of unique microhaplotypes present at any locus as a simple data summary method to estimate COI.…”

Within-Household Clustering of Genetically Related Plasmodium Falciparum Infections In A Moderate Transmission Area of Uganda

“…(29) A recent study that employed targeted amplicon deep sequencing to genotype parasites found that symptomatic children more commonly shared haplotypes with asymptomatically infected household members; however, household members were not strati ed by age in this study. (25) Understanding more about household clustering of infections, including the dynamics of within-household transmission, would be helpful in determining whether malaria control interventions aimed at disrupting transmission within households are worth pursuing.…”

“…Other genotyping techniques that are able to resolve multiallelic loci, such as multiplex amplicon or "microhaplotype" sequencing, can provide rich data from polyclonal infections and leverage current sequencing technologies to more easily allow evaluation of larger numbers of loci, providing higher resolution to evaluate transmission particularly in moderate-high transmission settings. (25,(31)(32)(33)(34) While these methods are more expensive and require more extensive laboratory and bioinformatics structure than the methods used in this study, they may be preferred techniques in the future as sequencing costs continue to decline.…”