Steve M. Taylor

: Children with sickle cell trait (HbAS) are protected against severe and symptomatic Plasmodium falciparum ( P. falciparum ) malaria. Although several within-host resistance mechanisms have been investigated, it is unknown whether this protection is attributable in part to reduced exposure to P. falciparum parasites via mosquito bites. In a 15-month cohort in Western Kenya, mosquito blood meals were matched to human hosts on the basis of short tandem repeat genotypes to determine individual mosquito biting rates. Using a multilevel multivariable model, mosquito biting behavior was assessed with respect to human β-globin genotypes, and no significant difference in biting rate was observed between individuals with wild-type (HbAA) and HbAS genotypes (biting rate ratio: 1.23; 95% CI: 0.86–1.77). These findings suggest that protection against malaria conferred by the sickle cell trait is unlikely to be attributable to reduced exposure to infectious mosquito bites.

Malaria in pregnancy is a major but poorly quantified contributor to maternal anaemia in sub-Saharan Africa. We combined individual-level data on haemoglobin (Hb), gravidity, gestational age and PCR-confirmed Plasmodium falciparum infection from 12,608 pregnancies in 7 African countries with a gravidity-specific model of malaria exposure and immunity linked to contemporary maps of transmission and fertility. For 2023, we estimate that 13.1 million pregnancies in malaria-endemic African regions were exposed to P. falciparum . In the absence of preventive measures, this exposure would have resulted in 2.41 million (95% credible interval 1.98–3.04 million) cases of moderate or severe anaemia (Hb < 9 g dl ⁻¹ ), including 600,000 (408,000–906,000) severe cases (Hb < 7 g dl ⁻¹ ). A counterfactual scenario using 2,000 transmission levels suggests that a 32% reduction in exposure during pregnancy translated into only a 22% decline in intrinsic anaemia burden, reflecting a shift from a concentration of risk in primigravidae to a more even distribution across gravidities as multigravid women acquire less pregnancy-specific immunity. Calibrating our model to randomized trials, we estimate that under current coverage, intermittent preventive treatment of malaria in pregnancy using sulfadoxine-pyrimethamine averted around 1.10 million (0.72–1.61 million) cases of moderate or severe anaemia and 330,000 (225,000–523,000) severe cases in 2023. These findings show that although burden has declined substantially, malaria remains a major driver of maternal anaemia risk. Meanwhile, lower immunity across multigravidae means any interruption to intermittent preventive treatment of malaria in pregnancy using sulfadoxine-pyrimethamine, or other population-based malaria control efforts, risks rapid resurgence of severe maternal anaemia, with substantial consequences for maternal and neonatal health.

: Malaria control in sub-Saharan Africa has stagnated despite widespread adoption of control measures such as long-lasting insecticidal nets (LLINs). Progress has stalled, in part, because of pyrethroid insecticide resistance, driving the need for retooling to increase the effectiveness of bed nets. Consequently, LLINs have been treated with the chemical synergist piperonyl butoxide (PBO). Piperonyl butoxide LLINs have been shown to be efficacious in controlled settings; however, their effectiveness in real - world settings warrants investigation. In Bungoma County, Western Kenya, a cohort of 768 participants was followed from June 2017 to December 2023 via active and passive surveillance. Household visits were conducted monthly, during which LLIN use for nets distributed in 2017 and 2021 was recorded, and symptomatic malaria cases were identified using rapid diagnostic tests (RDTs). The comparative effectiveness of PBO versus conventional LLINs was assessed in terms of malaria infections. A multilevel logistic regression model was fit with monthly RDT results as the dependent variable. The study results indicate that PBO LLINs provide greater protection against malaria at the individual level than conventional LLINs (odds ratio: 0.70; 95% CI: 0.47–1.03), although the findings were not statistically significant. The added protection against malaria infections provided by PBO LLINs compared with conventional LLINs observed in the current study aligns with findings from most previous studies, although this finding was not statistically significant. In areas with documented pyrethroid resistance, the use of LLINs with an added synergist, such as PBO, can provide additional protection against malaria infections (compared with pyrethroid - only LLINs) and should be considered for scaled-up scenarios despite the additional cost.

: Seroreactivity to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antigens was commonly reported in African settings during the early stages of the coronavirus disease 2019 pandemic. Severe acute respiratory syndrome coronavirus 2 neutralizing antibodies (nAbs) are not only correlated with functional protection from disease but also are highly specific responses to the virus. These responses were used to investigate the evolution of virus exposure in a community-based, longitudinal cohort of 504 individuals in rural Western Kenya. Eluates from dried blood spots collected every 3 months from January 2020 to September 2021 were tested for nAbs using a commercial kit. Only 10 individuals developed SARS-CoV-2 nAbs, all of which were clustered in December 2020 (wildtype virus) and September 2021 (delta variant). After seroconversion, all patients seroreverted within 2 months. Despite reports of widespread viral exposure in Western Kenya from 2020 to 2021, the paucity of nAbs highlights the limited natural immunity present when vaccines became available in late 2021 in Kenya.

Plasmodium falciparum infection during pregnancy is a major contributor to maternal anemia, a leading risk factor for postpartum hemorrhage and maternal death. Yet the scale of malaria-attributable anemia is poorly quantified. We analyzed individual-level hemoglobin data from 12,608 pregnancies across seven African countries and integrated these with gravidity-specific models of malaria exposure and immunity. We estimate that in 2023, 13.1 million pregnancies in endemic African regions were exposed to P. falciparum, resulting in 2.41 million [95% credible interval: 1.98–3.04] cases of moderate or severe anemia, including 600,000 [408,000–906,000] severe cases. The burden was highest in primigravidae and declined with acquired immunity. Intermittent preventive treatment with sulfadoxine–pyrimethamine (IPTp-SP) averted 330,000 [225,000–523,000] severe anemia cases. However, falling transmission has led to a rise in multigravidae without prior exposure, heightening future vulnerability. Sustaining IPTp coverage is critical to prevent resurgence in severe maternal anemia as global malaria funding falters.

The human infectious reservoir ofPlasmodium falciparumis governed by transmission efficiency during vector-human contact and mosquito biting preferences. Understanding biting bias in a natural setting can help target interventions to interrupt transmission. In a 15-month cohort in western Kenya, we detectedP. falciparumin indoor-restingAnophelesand human blood samples by qPCR and matched mosquito bloodmeals to cohort participants using short-tandem repeat genotyping. Using risk factor analyses and discrete choice models, we assessed mosquito biting behavior with respect to parasite transmission. Biting was highly unequal; 20% of people received 86% of bites. Biting rates were higher on males (biting rate ratio (BRR): 1.68; CI: 1.28–2.19), children 5–15 years (BRR: 1.49; CI: 1.13–1.98), andP. falciparum-infected individuals (BRR: 1.25; CI: 1.01–1.55). In aggregate,P. falciparum-infected school-age (5–15 years) boys accounted for 50% of bites potentially leading to onward transmission and had an entomological inoculation rate 6.4x higher than any other group. Additionally, infectious mosquitoes were nearly 3x more likely than non-infectious mosquitoes to biteP. falciparum-infected individuals (relative risk ratio 2.76, 95% CI 1.65–4.61). Thus, persistentP. falciparumtransmission was characterized by disproportionate onward transmission from school-age boys and by the preference of infected mosquitoes to feed upon infected people.

Molecular epidemiologic studies of malaria parasites and other pathogens commonly employ amplicon deep sequencing (AmpSeq) of marker genes derived from dried blood spots (DBS) to answer public health questions related to topics such as transmission and drug resistance. As these methods are increasingly employed to inform direct public health action, it is important to rigorously evaluate the risk of false positive and false negative haplotypes derived from clinically-relevant sample types. We performed a control experiment evaluating haplotype recovery from AmpSeq of 5 marker genes (ama1,csp,msp7,sera2, andtrap) from DBS containing mixtures of DNA from 1 to 10 knownP.falciparumreference strains across 3 parasite densities in triplicate (n = 270 samples). While false positive haplotypes were present across all parasite densities and mixtures, we optimized censoring criteria to remove 83% (148/179) of false positives while removing only 8% (67/859) of true positives. Post-censoring, the median pairwise Jaccard distance between replicates was 0.83. We failed to recover 35% (477/1365) of haplotypes expected to be present in the sample. Haplotypes were more likely to be missed in low-density samples with <1.5 genomes/μL (OR: 3.88, CI: 1.82–8.27, vs. high-density samples with ≥75 genomes/μL) and in samples with lower read depth (OR per 10,000 reads: 0.61, CI: 0.54–0.69). Furthermore, minority haplotypes within a sample were more likely to be missed than dominant haplotypes (OR per 0.01 increase in proportion: 0.96, CI: 0.96–0.97). Finally, in clinical samples the percent concordance across markers for multiplicity of infection ranged from 40%-80%. Taken together, our observations indicate that, with sufficient read depth, the majority of haplotypes can be successfully recovered from DBS while limiting the false positive rate.

People with suspected malaria may harbor Plasmodium falciparum undetected by rapid diagnostic test (RDT). The impact is not fully understood of these sub-patent infections on the risk of developing clinical malaria. We analyzed sub-patent P. falciparum infections using a longitudinal cohort in a high transmission site in Kenya. Weighted Kaplan-Meier models estimated the risk difference (RD) for clinical malaria during the 60 days following a symptomatic sub-patent infection. Stratum-specific estimates by age and transmission season assessed modification. Over 54 months, we observed 1,128 symptomatic RDT-negative suspected malaria episodes, of which 400 (35.5%) harbored sub-patent P. falciparum. Overall 60-day risk of developing clinical malaria was low following all episodes (8.6%,95% Confidence Interval: 6.7%, 10.4%). In the low transmission season, the risk of clinical malaria was slightly higher in those with sub-patent infection, whereas the opposite was true in the high transmission season (RD low season: 2.3%, CI: 0.4%, 4.2%; RD high season: -4.8%, CI: -9.5%, -0.05%). The risk of developing clinical malaria among people with undetected sub-patent infections is low. A slightly elevated risk in the low season may merit alternate management, but RDTs diagnose clinically-relevant infections in the high transmission season.

Molecular epidemiologic studies of malaria parasites commonly employ amplicon deep sequencing (AmpSeq) of marker genes derived from dried blood spots (DBS) to answer public health questions related to topics such as transmission and drug resistance. As these methods are increasingly employed to inform direct public health action, it is important to rigorously evaluate the risk of false positive and false negative haplotypes derived from clinically-relevant sample types. We performed a control experiment evaluating haplotype recovery from AmpSeq of 5 marker genes ( ama1 , csp , msp7 , sera2 , and trap ) from DBS containing mixtures of DNA from 1 to 10 known P. falciparum reference strains across 3 parasite densities in triplicate (n=270 samples). While false positive haplotypes were present across all parasite densities and mixtures, we optimized censoring criteria to remove 83% (148/179) of false positives while removing only 8% (67/859) of true positives. Post-censoring, the median pairwise Jaccard distance between replicates was 0.83. We failed to recover 35% (477/1365) of haplotypes expected to be present in the sample. Haplotypes were more likely to be missed in low-density samples with <1.5 genomes/µL (OR: 3.88, CI: 1.82-8.27, vs. high-density samples with ≥75 genomes/µL) and in samples with lower read depth (OR per 10,000 reads: 0.61, CI: 0.54-0.69). Furthermore, minority haplotypes within a sample were more likely to be missed than dominant haplotypes (OR per 0.01 increase in proportion: 0.96, CI: 0.96-0.97). Finally, in clinical samples the percent concordance across markers for multiplicity of infection ranged from 40%-80%. Taken together, our observations indicate that, with sufficient read depth, haplotypes can be successfully recovered from DBS while limiting the false positive rate.