Multiplicity and molecular epidemiology of Plasmodium vivax and Plasmodium falciparum infections in East Africa

Abstract

BackgroundParasite genetic diversity and multiplicity of infection (MOI) affect clinical outcomes, response to drug treatment and naturally-acquired or vaccine-induced immunity. Traditional methods often underestimate the frequency and diversity of multiclonal infections due to technical sensitivity and specificity. Next-generation sequencing techniques provide a novel opportunity to study complexity of parasite populations and molecular epidemiology.MethodsSymptomatic and asymptomatic Plasmodium vivax samples were collected from health centres/hospitals and schools, respectively, from 2011 to 2015 in Ethiopia. Similarly, both symptomatic and asymptomatic Plasmodium falciparum samples were collected, respectively, from hospitals and schools in 2005 and 2015 in Kenya. Finger-pricked blood samples were collected and dried on filter paper. Long amplicon (> 400 bp) deep sequencing of merozoite surface protein 1 (msp1) gene was conducted to determine multiplicity and molecular epidemiology of P. vivax and P. falciparum infections. The results were compared with those based on short amplicon (117 bp) deep sequencing.ResultsA total of 139 P. vivax and 222 P. falciparum samples were pyro-sequenced for pvmsp1 and pfmsp1, yielding a total of 21 P. vivax and 99 P. falciparum predominant haplotypes. The average MOI for P. vivax and P. falciparum were 2.16 and 2.68, respectively, which were significantly higher than that of microsatellite markers and short amplicon (117 bp) deep sequencing. Multiclonal infections were detected in 62.2% of the samples for P. vivax and 74.8% of the samples for P. falciparum. Four out of the five subjects with recurrent P. vivax malaria were found to be a relapse 44–65 days after clearance of parasites. No difference was observed in MOI among P. vivax patients of different symptoms, ages and genders. Similar patterns were also observed in P. falciparum except for one study site in Kenyan lowland areas with significantly higher MOI.ConclusionsThe study used a novel method to evaluate Plasmodium MOI and molecular epidemiological patterns by long amplicon ultra-deep sequencing. The complexity of infections were similar among age groups, symptoms, genders, transmission settings (spatial heterogeneity), as well as over years (pre- vs. post-scale-up interventions). This study demonstrated that long amplicon deep sequencing is a useful tool to investigate multiplicity and molecular epidemiology of Plasmodium parasite infections.Electronic supplementary materialThe online version of this article (10.1186/s12936-018-2337-y) contains supplementary material, which is available to authorized users.

Genetic diversity and population structure of Plasmodium falciparum in Kenyan–Ugandan border areas

“…In 2018, Zhong et al . reported the prevalence of polyclonal infections to be 75% in western Kenya . This was a slight reduction from the ≥ 80% prevalence reported by previous studies .…”

“…Unexpectedly, we observed a lower proportion of polyclonal infections (51%) than previously reported in western Kenya. In 2018, Zhong et al reported the prevalence of polyclonal infections to be 75% in western Kenya [37]. This was a slight reduction from the ≥ 80% prevalence reported by previous studies [13,14,19,38].…”

Dynamics of Plasmodium vivax populations in border areas of the Greater Mekong sub-region during malaria elimination

“…In most of its geographic range, P. vivax showed high levels of genetic diversity as revealed by population genetic studies using various genotyping markers [12][13][14][15][16][17][18][19][20][21]. Paradoxically, even in many low transmission settings, P. vivax still maintains high levels of diversity [22][23][24][25][26]. As a result, in areas of P. vivax and P. falciparum co-endemicity, these two parasites tend to exhibit markedly different genetic diversity and population structures, with P. vivax showing more stable transmission patterns [14,15,[27][28][29].…”

Prevalence of Plasmodium falciparum field isolates with deletions in histidine-rich protein 2 and 3 genes in context with sub-Saharan Africa and India: a systematic review and meta-analysis

“…It should be noted that the prevalence of deletions in pfhrp2 gene found in each individual study could be higher and generally the malaria infections are polyclonal in SSA and Indian endemic regions [64][65][66]. It is likely that individuals are infected with both malaria parasites with deletions in pfhrp2 gene and without deletions wherein, the presence of malaria parasites with no pfhrp2 deletions can overshadow that of their counterparts with deletions in pfhrp2 gene.…”