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

Abstract

The diversity of Plasmodium falciparum within human hosts requires parasite population size be defined in terms of parasite variation rather than the number of infected hosts. To calculate census population size, we rely on a definition of parasite variation known as multiplicity of infection (MOIvar), defined by the hyper-diversity of the var multigene family. We present a Bayesian approach to estimate MOIvar based on sequencing and counting the number of unique DBLα tags (or DBLα types) of var genes, taking into consideration measurement error, and derive from it census population size or the total number of distinct infections of relevance to transmission events. We track changes in parasite population size and structure, using MOIvar, from baseline and through sequential malaria interventions by indoor residual spraying (IRS) and seasonal malaria chemoprevention (SMC) in an area characterized by high-seasonal malaria transmission in northern Ghana. Var DBLα tag sequencing was completed on asymptomatic P. falciparum isolates at baseline (2012), during IRS (2014), post-IRS (2015) and during SMC (2017) from ~2,000 individuals of all ages surveyed at each time point. Following IRS, which reduced transmission intensity by > 90% and decreased parasite prevalence by ~40-50%, significant reductions in var diversity, MOIvar, and population size were observed across all ages. These changes, consistent with the loss of diverse parasite genomes, were short lived and 32-months after IRS was discontinued and SMC was introduced, var diversity and population size rebounded in all age groups except for the younger children (1-5 years) targeted by SMC. By measuring population size in this way, we show that despite major perturbations, the parasite population remained very large and retained the var population genetic characteristics of a high-transmission system (high var diversity; low var repertoire similarity) demonstrating the resilience of P. falciparum to short-term interventions in high-burden countries of sub-Saharan Africa.

Hyper-diverse antigenic variation and resilience to transmission-reducing intervention in falciparum malaria

“…This so-called “ var coding” method has been shown to provide accurate estimation in numerically simulated infections, and to perform better when transmission is high than a previous method based on a collection of neutral single nucleotide polymorphism loci (SNPs) ( 48 ). Having extended this approach to a Bayesian framework to account for measurement error in the sequencing ( 21 ), we apply the approach here to derive MOI estimates at the population level across the series of IRS interventions. We find that the MOI distribution becomes increasingly centered at low values around one and two, as the system approaches the transition regime (Fig.…”

“…We apply next the above indicators to an interrupted time-series study involving three age-stratified cross-sectional surveys undertaken at the end of the wet/high-transmission season from Bongo District in northern Ghana, respectively before, during, and immediately after the transient IRS intervention (Fig. 1E) ( 21, 35 ). Following IRS, the difference in the PTS distribution across the two age groups is reduced, almost completely overlapping at the lowest mode (Fig.…”

“…In contrast, when a strain expresses many VSAs a host has not previously encountered, long infectious periods ensue, enhancing its chance of transmission to another host ( 19, 12 ). Under high-transmission settings, local parasite populations exhibit a vast pool of var gene variants, documented to reach in the thousands to tens of thousands ( 21, 22, 23, 24 ) and generated mostly through mitotic and meiotic recombination but also mutation, as well as from migration of the human host and the mosquito vectors ( 25, 26, 27, 28 ). Previous studies have shown that negative frequency-dependent selection (NFDS) mediated by the acquisition of specific immunity by hosts contributes to the limited overlap of the var genes of both individual repertoires (individual parasite genomes) and isolates (sets of individual parasite genomes co-infecting individual hosts), in a pattern that is both non-random and non-neutral ( 23, 29 ).…”

“…A recent longitudinal field study in Bongo District, located in northern Ghana, implemented deep sampling and sequencing of var genes from individual isolates to monitor the response of the transmission system to a three-round transient intervention of indoor residual spraying (IRS) with insecticides ( 21, 35 ). Sequencing specifically concerns the DBLα tag, a small conserved ∼450bp region within var genes which encodes for the immunogenic Duffy-binding-like alpha domain of PfEMP1 ( 21, 22, 23, 24, 36, 37, 38 ). Bioinformatic analyses of a large database of exon 1 sequences of var genes showed a predominantly 1-to-1 DBLα- var relationship, such that each DBLα tag typically represents a unique var gene ( 39 ).…”

“…We use DBLα and var interchangeably hereafter. This surveillance through molecular epidemiology revealed persistent estimates of high var diversity and low parasite strain overlap (low repertoire similarity), characteristic features of high-transmission regions, despite a considerable decrease in prevalence and parasite population size ( 21, 35 ). The transmission system rebounded rapidly after the IRS was discontinued, with this transient intervention appearing to have had only a limited impact ( 21 ).…”