Genetic Metrics Decodes Plasmodium falciparum Diversity: Complexity of Infections, Parasite Connectivity, and Transmission Intensity in Mainland Tanzania’s Diverse Regions
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Background
Recent initiatives have promoted the application of genomic data to determine the trends and patterns of malaria transmission and the impact of interventions. This study aimed to evaluate and identify the most effective genetic metrics for monitoring the genetic diversity of Plasmodium falciparum and its correlation with malaria transmission intensities in Mainland Tanzania.
Methods
A cross-sectional survey was conducted between February and July 2021 in 100 health facilities from 10 regions of Mainland Tanzania, categorized into four malaria transmission strata: high (two regions), moderate (two regions), low (three regions), and very low transmission strata (three regions). Dried blood spots (DBS) samples were collected from 12,875 symptomatic patients and all samples with positive results obtained by rapid diagnostic tests (n = 7,199) were sequenced using molecular inversion probes (MIPs). The MIPs targeted 1,832 single nucleotide polymorphisms (SNPs) distributed across the 14 P. falciparum chromosomes. Raw sequence data were analyzed using MIPTools and the filtered dataset was used to estimate different genetic metrics.
Results
After processing, 3,149 (43.0%) samples passed filtering conditions and were used for downstream analysis. The countrywide mean complexity of infection (COI) was 1.5, with 1,878 (59.6%) samples being monogenomic. The mean COI was significantly higher in high and moderate transmission strata (p < 0.001) compared to low and very low transmission strata. The odds of polyclonal infections were significantly lower in moderate (aOR = 0.67; 95% CI: 0.55-0.81; p < 0.001), low (aOR = 0.52; 95% CI: 0.43-0.63; p < 0.001), and in very low strata (aOR = 0.49; 95% CI: 0.40-0.61; p < 0.001) compared to the high transmission stratum. There was very little parasite genetic differentiation among regions with fixation index ( F ST ) values ranging from 0 to 0.006. The countrywide mean pairwise identity by descent (IBD) was 0.02. The mean pairwise IBD by transmission intensity was similar with mean IBD = 0.0155 in very low, 0.0158 in low, 0.0156 in moderate and 0.0152 in high malaria transmission strata. Using discriminant analysis of the principal component (DAPC) parasite populations from different regions clustered within regions suggesting genetic similarity among them.
Conclusion
Parasites from the sampled 10 regions had high complexity of infection and polyclonality, with a high correlation with regional malaria transmission intensities . Thus, these metrics can be potentially integrated with the current malaria surveillance and may be useful in the assessment of trends and patterns of malaria transmission. Further validation is needed to link these measures to current control strategies and evaluate how they might be used to determine the impact of different malaria transmission interventions in Mainland Tanzania.
