Diversity and selection analyses identify transmission-blocking antigens as the optimal vaccine candidates in Plasmodium falciparum.

Background: A highly effective vaccine for malaria remains an elusive target, at least in part due to the under-appreciated natural parasite variation. This study aimed to investigate genetic and structural variation, and immune selection of leading malaria vaccine candidates across the Plasmodium falciparum 's life cycle. Methods: We analyzed 325 P. falciparum whole genome sequences from Zambia, in addition to 791 genomes from five other African countries available in the MalariaGEN Pf3k Rdatabase. Ten vaccine antigens spanning three life-history stages were examined for genetic and structural variations, using population genetics measures, haplotype network analysis, and 3D structure selection analysis. Findings: Among the ten antigens analyzed, only three in the transmission-blocking vaccine category display P . falciparum 3D7 as the dominant haplotype. The antigens AMA1, CSP, MSP1 19 and CelTOS, are much more diverse than the other antigens, and their epitope regions are under moderate to strong balancing selection. In contrast, Rh5 , a blood stage antigen, displays low diversity yet slightly stronger immune selection in the merozoite-blocking epitope region. Except for CelTOS , the transmission-blocking antigens Pfs25 , Pfs48/45 , Pfs230 , Pfs47 , and Pfs28 exhibit minimal diversity and no immune selection in epitopes that induce strain-transcending antibodies, suggesting potential effectiveness of 3D7-based vaccines in blocking transmission. Interpretations: These findings offer valuable insights into the selection of optimal vaccine candidates against P. falciparum . Based on our results, we recommend prioritizing conserved merozoite antigens and transmission-blocking antigens. Combining these antigens in multi-stage approaches may be particularly promising for malaria vaccine development initiatives. Funding: Purdue Department of Biological Sciences; Puskas Memorial Fellowship; National Institute of Allergy and Infectious Diseases (U19AI089680). Research in context: Evidence before this study: Decades of research on the most virulent malaria parasite, Plasmodium falciparum , have yielded multiple antigen candidates of pre-erythrocytic, blood-stage, and transmission-blocking vaccines in varying stages of development from preclinical development to more advanced clinical trials. The malaria vaccine, RTS,S/AS01, which was constructed using the C-terminal and NANP repeat region of the Circumsporozoite Protein ( CSP ) from the African reference strain 3D7, was approved and recommended for use in 2021. However, the vaccine's lower efficacy is likely a result of the genetic polymorphism of the target antigen shown by studies on natural variation in CSP . Similarly, another more recent pre-erythrocytic vaccine, R21/Matrix-M, showed great promise in clinical trials and was recommended in late 2023 by the WHO for use for prevention of malaria in children, but is also multi-dose and CSP -based. To maximize vaccine efficacy, it would be more strategic to first understand diversity and variation of antigens across the three types of vaccine classes, targeting various stages of the P. falciparum life cycle. Previous studies have reported analyses of vaccine candidate antigens but were mostly limited to pre-erythrocytic and blood-stage antigens, with less focus on transmission-blocking antigens. These studies revealed that most of the pre-erythrocytic and blood-stage antigens are of high diversity due to balancing selection, posing challenges for vaccine design to encompass the antigenic variation. A search conducted on PubMed on April 1, 2024, for relevant published research which used the terms "malaria vaccine", " Plasmodium falciparum " [not " vivax "], "selection" and "diversity" yielded 48 studies between 1996 and the present day, with only 14 published studies in the past 3 years. This emphasizes the need for more studies assessing genetic diversity and selection of potential P. falciparum vaccine candidates to aid in more effective vaccine development efforts. A similar search with the terms "transmission-blocking vaccine", "malaria", " Plasmodium falciparum ", not " vivax ", "selection" and "diversity" without any date or language restrictions revealed three relevant studies. This warrants future studies to explore transmission-blocking vaccines in this context. Added value of this study: By comparing the genetic and structural analyses of transmission-blocking antigens with pre-erythrocytic and blood-stage antigens, we identify promising P. falciparum vaccine antigens characterized by their conservation with low balancing selection and the presence of infection/transmission-blocking epitopes, which are essential for informing the development of new malaria vaccines. This comprehensive workflow can be adopted for studying the genetic and structural variation of other P. falciparum vaccine targets before developing the next generation of malaria vaccines for effectiveness against natural parasite populations. Implications of this study: Our suggested strategies for designing malaria vaccines include two possible approaches. We emphasize the development of a multi-stage vaccine that combines critical components such as anti-merozoite ( Rh5 ) and transmission-blocking antigens ( Pfs25 , Pfs28 , Pfs48/45 , Pfs230 ). Alternatively, we suggest the creation of transmission-blocking vaccines specifically targeting Pfs25 , Pfs28 and Pfs48/45 . These innovative approaches show great potential in advancing the development of more potent and effective malaria vaccines for the future.

Malaria Transmission at The Zimbabwe-Mozambique Border: An Observational Study of Parasitemia by Travel History and Household Location.

Cross-border human population movement contributes to malaria transmission in border regions, impeding national elimination. However, its impact in low-to-moderate transmission settings is not well characterized. This community-based study in Mutasa District, Zimbabwe, estimated the association of parasite prevalence with self-reported overnight travel to Mozambique and household distance to the border from 2012-2020. A fully adjusted Poisson regression model with robust variance estimation was fit using active surveillance data. The population attributable fraction of parasite prevalence from overnight travel was also estimated. The relative risk of testing positive for malaria by rapid diagnostic test declined 14% (prevalence ratio [PR] = 0.86, 95% CI = 0.81-0.92) per kilometer from the border up to 12 km away. Travel to Mozambique was associated with a 157% increased risk (PR = 2.57, 95% CI = 1.38-4.78), although only 5.8% of cases were attributable to overnight travel (95% CI = -1.1% to 12.7%), reflecting infrequent overnight trips (1.3% of visits). This study suggests that transmission in eastern Zimbabwe is driven by increasingly conducive social or environmental conditions approaching the border and low levels of importation from overnight travel. Although day trips to Mozambique during peak biting hours were not assessed, the contribution of such trips to ongoing transmission may be significant. Future malaria control efforts should prioritize high coverage of existing interventions and continued support for community health workers and health facilities at the border, which provide free case management.

Modeling the Cost of Vaccinating a Measles Zero-Dose Child in Zambia Using Three Vaccination Strategies.

Countries with moderate to high measles-containing vaccine coverage face challenges in reaching the remaining measles zero-dose children. There is growing interest in targeted vaccination activities to reach these children. We developed a framework for prioritizing districts for targeted measles and rubella supplementary immunization activities (SIAs) for Zambia in 2020, incorporating the use of the WHO's Measles Risk Assessment Tool (MRAT) and serosurveys. This framework was used to build a model comparing the cost of vaccinating one zero-dose child under three vaccination scenarios: standard nationwide SIA, targeted subnational SIA informed by MRAT, and targeted subnational SIA informed by both MRAT and measles seroprevalence data. In the last scenario, measles seroprevalence data are acquired via either a community-based serosurvey, residual blood samples from health facilities, or community-based IgG point-of-contact rapid diagnostic testing. The deterministic model found that the standard nationwide SIA is the least cost-efficient strategy at 13.75 USD per zero-dose child vaccinated. Targeted SIA informed by MRAT was the most cost-efficient at 7.63 USD per zero-dose child, assuming that routine immunization is just as effective as subnational SIA in reaching zero-dose children. Under similar conditions, a targeted subnational SIA informed by both MRAT and seroprevalence data resulted in 8.17-8.35 USD per zero-dose child vaccinated, suggesting that use of seroprevalence to inform SIA planning may not be as cost prohibitive as previously thought. Further refinement to the decision framework incorporating additional data may yield strategies to better target the zero-dose population in a financially feasible manner.

Report from the World Health Organization's immunization and vaccines-related implementation research advisory committee (IVIR-AC) meeting, virtual gathering, 26 February-1 March 2024.

The Immunization and Vaccine-related Implementation Research Advisory Committee (IVIR-AC) is the World Health Organization's key standing advisory body to conduct an independent review of research, particularly of transmission and economic modeling analyses that estimate the impact and value of vaccines. From 26th February-1st March 2024, at its first of two semi-annual meetings, IVIR-AC provided feedback and recommendations across four sessions; this report summarizes the proceedings and recommendations from that meeting. Session topics included modeling of the impact and cost-effectiveness of the R21/Matrix-M malaria vaccine, meta-analysis of economic evaluations of vaccines, a global analysis estimating the impact of vaccination over the last 50 years, and modeling the impact of different RTS,S malaria vaccine dose schedules in seasonal settings.

Genomics reveals heterogeneous Plasmodium falciparum transmission and selection signals in Zambia.

BACKGROUND: Genomic surveillance is crucial for monitoring malaria transmission and understanding parasite adaptation to interventions. Zambia lacks prior nationwide efforts in malaria genomic surveillance among African countries. METHODS: We conducted genomic surveillance of Plasmodium falciparum parasites from the 2018 Malaria Indicator Survey in Zambia, a nationally representative household survey of children under five years of age. We whole-genome sequenced and analyzed 241 P. falciparum genomes from regions with varying levels of malaria transmission across Zambia and estimated genetic metrics that are informative about transmission intensity, genetic relatedness between parasites, and selection. RESULTS: We provide genomic evidence of widespread within-host polygenomic infections, regardless of epidemiological characteristics, underscoring the extensive and ongoing endemic malaria transmission in Zambia. Our analysis reveals country-level clustering of parasites from Zambia and neighboring regions, with distinct separation in West Africa. Within Zambia, identity by descent (IBD) relatedness analysis uncovers local spatial clustering and rare cases of long-distance sharing of closely related parasite pairs. Genomic regions with large shared IBD segments and strong positive selection signatures implicate genes involved in sulfadoxine-pyrimethamine and artemisinin combination therapies drug resistance, but no signature related to chloroquine resistance. Furthermore, differences in selection signatures, including drug resistance loci, are observed between eastern and western Zambian parasite populations, suggesting variable transmission intensity and ongoing drug pressure. CONCLUSIONS: Our findings enhance our understanding of nationwide P. falciparum transmission in Zambia, establishing a baseline for analyzing parasite genetic metrics as they vary over time and space. These insights highlight the urgency of strengthening malaria control programs and surveillance of antimalarial drug resistance.

Malaria is caused by a parasite that is spread to humans via mosquito bites. It is a leading cause of death in children under five years old in sub-Saharan Africa. Analysis of the malaria parasite's complete set of DNA (its genome) can help us to understand transmission of the disease and how this changes in response to different strategies to control the disease. We analyzed the genomes of malaria parasites from children across Zambia. Our study revealed that 77% of children harbored multiple parasite strains, which suggests that local transmission (transmission between people within the same local area) is high. Genetic evidence for long-distance transmission was rarer. Furthermore, our findings suggest parasites are evolving in response to antimalarial drugs. Our study enhances our understanding of malaria dynamics in Zambia and may help to inform strategies for improved surveillance and control.

Who is missed in a community-based survey: Assessment and implications of biases due to incomplete sampling frame in a community-based serosurvey, Choma and Ndola Districts, Zambia, 2022.

Community-based serological studies are increasingly relied upon to measure disease burden, identify population immunity gaps, and guide control and elimination strategies; however, there is little understanding of the potential for and impact of sampling biases on outcomes of interest. As part of efforts to quantify measles immunity gaps in Zambia, a community-based serological survey using stratified multi-stage cluster sampling approach was conducted in Ndola and Choma districts in May-June 2022, enrolling 1245 individuals. We carried out a follow-up study among individuals missed from the sampling frame of the serosurvey in July-August 2022, enrolling 672 individuals. We assessed the potential for and impact of biases in the community-based serosurvey by i) estimating differences in characteristics of households and individuals included and excluded (77% vs 23% of households) from the sampling frame of the serosurvey and ii) evaluating the magnitude these differences make on healthcare-seeking behavior, vaccination coverage, and measles seroprevalence. We found that missed households were 20% smaller and 25% less likely to have children. Missed individuals resided in less wealthy households, had different distributions of sex and occupation, and were more likely to seek care at health facilities. Despite these differences, simulating a survey in which missed households were included in the sampling frame resulted in less than a 5% estimated bias in these outcomes. Although community-based studies are upheld as the gold standard study design in assessing immunity gaps and underlying community health characteristics, these findings underscore the fact that sampling biases can impact the results of even well-conducted community-based surveys. Results from these studies should be interpreted in the context of the study methodology and challenges faced during implementation, which include shortcomings in establishing accurate and up-to-date sampling frames. Failure to account for these shortcomings may result in biased estimates and detrimental effects on decision-making.

Post-campaign coverage evaluation of a measles and rubella supplementary immunization activity in five districts in India, 2019-2020.

BACKGROUND: In alignment with the Measles and Rubella (MR) Strategic Elimination plan, India conducted a mass measles and rubella vaccination campaign across the country between 2017 and 2020 to provide a dose of MR containing vaccine to all children aged 9 months to 15 years. We estimated campaign vaccination coverage in five districts in India and assessed campaign awareness and factors associated with vaccination during the campaign to better understand reasons for not receiving the dose. METHODS AND FINDINGS: Community-based cross-sectional serosurveys were conducted in five districts of India among children aged 9 months to 15 years after the vaccination campaign. Campaign coverage was estimated based on home-based immunization record or caregiver recall. Campaign coverage was stratified by child- and household-level risk factors and descriptive analyses were performed to assess reasons for not receiving the campaign dose. Three thousand three hundred and fifty-seven children aged 9 months to 15 years at the time of the campaign were enrolled. Campaign coverage among children aged 9 months to 5 years documented or by recall ranged from 74.2% in Kanpur Nagar District to 90.4% in Dibrugarh District, Assam. Similar coverage was observed for older children. Caregiver awareness of the campaign varied from 88.3% in Hoshiarpur District, Punjab to 97.6% in Dibrugarh District, Assam, although 8% of children whose caregivers were aware of the campaign were not vaccinated during the campaign. Failure to receive the campaign dose was associated with urban settings, low maternal education, and lack of school attendance although the associations varied by district. CONCLUSION: Awareness of the MR vaccination campaign was high; however, campaign coverage varied by district and did not reach the elimination target of 95% coverage in any of the districts studied. Areas with lower coverage among younger children must be prioritized by strengthening the routine immunization programme and implementing strategies to identify and reach under-vaccinated children.

Report from the World Health Organization's immunization and vaccines related implementation research advisory committee (IVIR-AC) meeting, Geneva, 11-13 September 2023.

Evaluating vaccine-related research is critical to maximize the potential of vaccination programmes. The WHO Immunization and Vaccine-related Implementation Research Advisory Committee (IVIR-AC) provides an independent review of research that estimates the performance, impact and value of vaccines, with a particular focus on transmission and economic modelling. On 11-13 September 2023, IVIR-AC was convened for a bi-annual meeting where the committee reviewed research and presentations across eight different sessions. This report summarizes the background information, proceedings and recommendations from that meeting. Sessions ranged in topic from timing of measles supplementary immunization activities, analyses of conditions necessary to meet measles elimination in the South-East Asia region, translating modelled evidence into policy, a risk-benefit analysis of dengue vaccine, COVID-19 scenario modelling in the African region, therapeutic vaccination against human papilloma virus, the Vaccine Impact Modelling Consortium, and the Immunization Agenda 2030 vaccine impact estimates.

Genomics reveals heterogeneous Plasmodium falciparum transmission and population differentiation in Zambia and bordering countries.

Genomic surveillance plays a critical role in monitoring malaria transmission and understanding how the parasite adapts in response to interventions. We conducted genomic surveillance of malaria by sequencing 241 Plasmodium falciparum genomes from regions with varying levels of malaria transmission across Zambia. We found genomic evidence of high levels of within-host polygenomic infections, regardless of epidemiological characteristics, underscoring the extensive and ongoing endemic malaria transmission in the country. We identified country-level clustering of parasites from Zambia and neighboring countries, and distinct clustering of parasites from West Africa. Within Zambia, our identity by descent (IBD) relatedness analysis uncovered spatial clustering of closely related parasite pairs at the local level and rare cases of long-distance sharing. Genomic regions with large shared IBD segments and strong positive selection signatures identified genes involved in sulfadoxine-pyrimethamine and artemisinin combination therapies drug resistance, but no signature related to chloroquine resistance. Together, our findings enhance our understanding of P. falciparum transmission nationwide in Zambia and highlight the urgency of strengthening malaria control programs and surveillance of antimalarial drug resistance.

Assessing the relationship between existing childhood, adolescent and adult immunization programmes and national COVID-19 vaccination capacities in 2021.

BACKGROUND: During the COVID-19 pandemic, nearly all countries introduced COVID-19 vaccination programmes. Yet, countries had a wide range of programmatic experiences. This analysis aims to identify national characteristics associated with COVID-19 vaccination programmatic success. METHODS: We used the following outcome measures: the presence of national COVID-19 vaccination capacities and COVID-19 coverage as of December 2021, June 2022, and December 2022. We developed a standardized metric for assessing national COVID-19 vaccination capacities as a proxy for speed of introduction. We developed this metric through adaptation of the WHO Guide for Conducting an Expanded Programme on Immunization Review and consultations with technical experts specializing in vaccine introduction and emergency deployment; monitoring and data; childhood, adolescent and adult programmes; and COVID-19 vaccination roll-out. Through multivariable linear regressions, we evaluated whether having a mature immunization programme for children, adolescents and adults; recent use of emergency vaccination; World Bank income classification; past early adoption of new vaccines; density of the health workforce; and/or trust in science and government were associated with higher COVID-19 vaccination capacities and coverage. RESULTS: The COVID-19 vaccination capacities scores ranged from 0 to 5 points with a global median score of 2 and an interquartile range of 1;4. After adjusting for World Bank income classifications, the presence of a mature influenza vaccination programme was independently correlated with statistically significant higher scores of national COVID-19 vaccination capacities and higher COVID-19 vaccination coverage in December 2021, June 2022, and December 2022. Trust in government was also associated with higher coverage for all three time stamps. CONCLUSIONS: As countries consider how to prepare for and respond to future pandemics, having an adult seasonal influenza vaccination programme, building trust in government, and ensuring equitable access to vaccines supply emerged as key aspects that can benefit from additional national and global focus.

The 2020 immunization programme landscape: Piloting an assessment metric to evaluate the maturity of national immunization programmes across the life course.

BACKGROUND: The World Health Organization (WHO) encourages countries to provide appropriate vaccinations for children, adolescents, and relevant adult populations. Childhood programme have been the focus of global investments, but recent pandemics have increasingly demonstrated the value of life course vaccination. Our objective is to compare national life course immunization programmatic maturity prior to mass COVID-19 vaccine introduction, the largest adult vaccination programme, globally. As coverage estimates (typically used to assess childhood programmes) are not available for adult vaccinations, this analysis pilots a standardized quantitative metric of programmatic maturity. METHODS: Through consultation with vaccination experts, we developed a standardized approach to assess national immunization programme maturity across the life course. In accordance with expert input, five vaccines were selected to represent delivery across the life course: diphtheria tetanus toxoid and pertussis (DTP); measles (MCV) second dose; human papillomavirus (HPV) final dose; pneumococcal conjugate (PCV) final dose; and seasonal influenza annual dose. Experts recommended inclusion of the following indicators for each vaccine: a legal mandate (national policy), experience delivering the vaccine (programme duration), and vaccine use (uptake for relevant populations). We developed a metric accordingly that provides up to 5 points per vaccine ("vaccine specific maturity score") which when summed forms the "life course maturity score", with a maximum score of 25. We analysed the prevalence of national policies, experience, and use by region and World Bank income group. RESULTS: More than 55% of the 194 WHO Member States had childhood vaccine policies for all three of the vaccines considered (DTP, MCV, and PCV) compared to 60% for HPV (proxy for adolescent vaccination programme) and 52% for seasonal influenza (proxy for adult vaccination programme). Childhood vaccination programmes (e.g., MCV and DTP) had the highest vaccine specific maturity scores, while seasonal influenza and HPV vaccination programmes had much lower scores. The national life course maturity scores ranged from 1 to 23, with a global median of 12 (IQR: 8; 16). DISCUSSION: The piloted metric provides an overview of the maturity of life course immunization programmes. The metric is structured to be a flexible, rapid resource that can be used to assess other combinations of vaccines across the life course. The findings from this paper provide a baseline of immunization programme maturity for childhood, adolescent, and adult vaccination programmes immediately prior to the COVID-19 vaccine introduction. This maturity score, or adaptations of this approach, could be used to monitor the trajectory of national immunization programme maturity across the life course in the years ahead.

Apicomplexan phosphodiesterases in cyclic nucleotide turnover: conservation, function, and therapeutic potential.

Apicomplexa encompasses a large number of intracellular parasites infecting a wide range of animals. Cyclic nucleotide signaling is crucial for a variety of apicomplexan life stages and cellular processes. The cyclases and kinases that synthesize and respond to cyclic nucleotides (i.e., 3',5'-cyclic guanosine monophosphate and 3',5'-cyclic adenosine monophosphate) are highly conserved and essential throughout the parasite phylum. Growing evidence indicates that phosphodiesterases (PDEs) are also critical for regulating cyclic nucleotide signaling via cyclic nucleotide hydrolysis. Here, we discuss recent advances in apicomplexan PDE biology and opportunities for therapeutic interventions, with special emphasis on the major human apicomplexan parasite genera Plasmodium, Toxoplasma, Cryptosporidium, and Babesia. In particular, we show a highly flexible repertoire of apicomplexan PDEs associated with a wide range of cellular requirements across parasites and lifecycle stages. Despite this phylogenetic diversity, cellular requirements of apicomplexan PDEs for motility, host cell egress, or invasion are conserved. However, the molecular wiring of associated PDEs is extremely malleable suggesting that PDE diversity and redundancy are key for the optimization of cyclic nucleotide turnover to respond to the various environments encountered by each parasite and life stage. Understanding how apicomplexan PDEs are regulated and integrating multiple signaling systems into a unified response represent an untapped avenue for future exploration.

An Estimate Of The Return On Investment Of A Malaria Vaccine In 20 Sub-Saharan African Countries, 2021-30.

Malaria is a leading global health problem that was responsible for an estimated 619,000 deaths worldwide in 2021. We modeled the return on investment (ROI) for the introduction and continuation of a four-dose malaria vaccine, RTS,S/AS01, from 2021 to 2030 in twenty sub-Saharan African countries supported by Gavi, the Vaccine Alliance. We used the Decade of Vaccine Economics benefits and costing outputs to calculate an ROI using health impact data modeled by the Swiss Tropical and Public Health Institute (hereafter "Swiss") and Imperial College London (hereafter "Imperial"). The Swiss estimates with a base vaccine price of US$7.00 resulted in an ROI of 0.42, and the Imperial impact estimates with the same base vaccine price resulted in an ROI of 2.30. Inclusion of the fifth seasonal dose for ten countries exhibiting high seasonal disease burden increased the Swiss ROI by 143 percent, to 1.02, and the Imperial ROI by 23.5 percent, to 2.84. To improve ROI, decision makers should continue to improve delivery platforms, decrease vaccine delivery costs, deliver the malaria vaccine in fewer doses, and provide access to vaccine resources.

Novel bioinformatic methods and machine learning approaches reveal candidate biomarkers of the intensity and timing of past exposure to Plasmodium falciparum.

Accurately quantifying the burden of malaria over time is an important goal of malaria surveillance efforts and can enable effective targeting and evaluation of interventions. Malaria surveillance methods capture active or recent infections which poses several challenges to achieving malaria surveillance goals. In high transmission settings, asymptomatic infections are common and therefore accurate measurement of malaria burden demands active surveillance; in low transmission regions where infections are rare accurate surveillance requires sampling large subsets of the population; and in any context monitoring malaria burden over time necessitates serial sampling. Antibody responses to Plasmodium falciparum parasites persist after infection and therefore measuring antibodies has the potential to overcome several of the current obstacles to accurate malaria surveillance. Identifying which antibody responses are markers of the timing and intensity of past exposure to P. falciparum remains challenging, particularly among adults who tend to be re-exposed multiple times over the course of their lifetime and therefore have similarly high antibody responses to many Plasmodium antigens. A previous analysis of 479 serum samples from individuals in three regions in southern Africa with different historical levels of P. falciparum malaria transmission (high, intermediate, and low) revealed regional differences in antibody responses to P. falciparum antigens among children under 5 years of age. Using a novel bioinformatic pipeline optimized for protein microarrays that minimizes between-sample technical variation, we used antibody responses to Plasmodium antigens as predictors in random forest models to classify samples from adults into these three regions of differing historical malaria transmission with high accuracy (AUC = 0.99). Many of the most important antigens for classification in these models do not overlap with previously published results and are therefore novel candidate markers for the timing and intensity of past exposure to P. falciparum. Measuring antibody responses to these antigens could lead to improved malaria surveillance.

Temporal and spatial analysis of Plasmodium falciparum genomics reveals patterns of parasite connectivity in a low-transmission district in Southern Province, Zambia.

BACKGROUND: Understanding temporal and spatial dynamics of malaria transmission will help to inform effective interventions and strategies in regions approaching elimination. Parasite genomics are increasingly used to monitor epidemiologic trends, including assessing residual transmission across seasons and importation of malaria into these regions. METHODS: In a low and seasonal transmission setting of southern Zambia, a total of 441 Plasmodium falciparum samples collected from 8 neighbouring health centres between 2012 and 2018 were genotyped using molecular inversion probes (MIPs n = 1793) targeting a total of 1832 neutral and geographically informative SNPs distributed across the parasite genome. After filtering for quality and missingness, 302 samples and 1410 SNPs were retained and used for downstream population genomic analyses. RESULTS: The analyses revealed most (67%, n = 202) infections harboured one clone (monogenomic) with some variation at local level suggesting low, but heterogenous malaria transmission. Relatedness identity-by-descent (IBD) analysis revealed variable distribution of IBD segments across the genome and 6% of pairs were highly-related (IBD ≥ 0.25). Some of the highly-related parasite populations persisted across multiple seasons, suggesting that persistence of malaria in this low-transmission region is fueled by parasites "seeding" across the dry season. For recent years, clusters of clonal parasites were identified that were dissimilar to the general parasite population, suggesting parasite populations were increasingly fragmented at small spatial scales due to intensified control efforts. Clustering analysis using PCA and t-SNE showed a lack of substantial parasite population structure. CONCLUSION: Leveraging both genomic and epidemiological data provided comprehensive picture of fluctuations in parasite populations in this pre-elimination setting of southern Zambia over 7 years.

The Impact of Household and Community Indoor Residual Spray Coverage with Fludora Fusion in a High Malaria Transmission Setting in Northern Zambia.

Zambia's National Malaria Elimination Program transitioned to Fludora Fusion in 2019 for annual indoor residual spraying (IRS) in Nchelenge District, an area with holoendemic malaria transmission. Previously, IRS was associated with reductions in parasite prevalence during the rainy season only, presumably because of insufficient residual insecticide longevity. This study assessed the impact of transitioning from Actellic 300CS to long-acting Fludora Fusion using active surveillance data from 2014 through 2021. A difference-in-differences analysis estimated changes in rainy season parasite prevalence associated with living in a sprayed house, comparing insecticides. The change in the 2020 to 2021 dry season parasite prevalence associated with living in a house sprayed with Fludora Fusion was also estimated. Indoor residual spraying with Fludora Fusion was not associated with decreased rainy season parasite prevalence compared with IRS with Actellic 300CS (ratio of prevalence ratios [PRs], 1.09; 95% CI, 0.89-1.33). Moreover, living in a house sprayed with either insecticide was not associated with decreased malaria risk (Actellic 300CS: PR, 0.97; 95% CI, 0.86-1.10; Fludora Fusion: rainy season PR, 1.06; 95% CI, 0.89-1.25; dry season PR, 1.21; 95% CI, 0.99-1.48). In contrast, each 10% increase in community IRS coverage was associated with a 4% to 5% reduction in parasite prevalence (rainy season: PR, 0.95; 95% CI, 0.92-0.97; dry season: PR, 0.96; 95% CI, 0.94-0.99), suggesting a community-level protective effect, and corroborating the importance of high-intervention coverage.

Declining Age-Specific Seroprevalence and Seroconversion Rates in Plasmodium falciparum from 2009 to 2018 Documents Progress toward Malaria Elimination in Southern Zambia.

Obtaining accurate malaria surveillance data is challenging in low-transmission settings because large sample sizes are required to estimate incidence and prevalence precisely. Serology is an additional tool to document progress toward malaria elimination. An enzyme immunoassay to Plasmodium falciparum lysate was used to estimate age-specific seroprevalence among residents of southern Zambia, where malaria transmission has declined to pre-elimination levels during the past two decades. Plasma was eluted from 3,362 dried blood spots collected during five cross-sectional surveys conducted between 2009 and 2012, and again in 2018. Annual seroconversion rates (SCRs), an estimate of the force of infection, were calculated using a reversible catalytic model. The SCR decreased by two thirds from a level of approximately 0.15/year in 2009 and 2010 to approximately 0.05/year in 2011 and 2012, and then decreased 5-fold to 0.01/year by 2018, demonstrating the utility of serology in documenting progress toward elimination.

An evaluation of the early impact of the COVID-19 pandemic on Zambia's routine immunization program.

Implications of the COVID-19 pandemic for both populations and healthcare systems are vast. In addition to morbidity and mortality from COVID-19, the pandemic also disrupted local health systems, including reductions or delays in routine vaccination services and catch-up vaccination campaigns. These disruptions could lead to outbreaks of other infectious diseases that result in an additional burden of disease and strain on the healthcare system. We evaluated the impact of the COVID-19 pandemic on Zambia's routine childhood immunization program in 2020 using multiple sources of data. We relied on administrative vaccination data and Zambia's 2018 Demographic and Health Survey to project national disruptions to district-specific routine childhood vaccination coverage within the pandemic year 2020. Next, we leveraged a 2016 population-based serological survey to predict age-specific measles seroprevalence and assessed the impact of changes in vaccination coverage on measles outbreak risk in each district. We found minor disruptions to routine administration of measles-rubella and pentavalent vaccines in 2020. This was in part due to Zambia's Child Health Week held in June of 2020 which helped to reach children missed during the first six months of the year. We estimated that the two-month delay in a measles-rubella vaccination campaign, originally planned for September of 2020 but conducted in November of 2020 as a result of the pandemic, had little impact on modeled district-specific measles outbreak risks. This study estimated minimal increases in the number of children missed by vaccination services in Zambia during 2020. However, the ongoing SARS-CoV-2 transmission since our analysis concluded means efforts to maintain routine immunization services and minimize the risk of measles outbreaks will continue to be critical. The methodological framework developed in this analysis relied on routinely collected data to estimate disruptions of the COVID-19 pandemic to national routine vaccination program performance and its impact on children missed at the subnational level can be deployed in other countries or for other vaccines.

Comparison of measles IgG enzyme immunoassays (EIA) versus plaque reduction neutralization test (PRNT) for measuring measles serostatus: a systematic review of head-to-head analyses of measles IgG EIA and PRNT.

BACKGROUND: As countries move towards or achieve measles elimination status, serosurveillance is an important public health tool. However, a major challenge of serosurveillance is finding a feasible, accurate, cost-effective, and high throughput assay to measure measles antibody concentrations and estimate susceptibility in a population. We conducted a systematic review to assess, characterize, and - to the extent possible - quantify the performance of measles IgG enzyme-linked assays (EIAs) compared to the gold standard, plaque reduction neutralization tests (PRNT). METHODS: We followed the PRISMA statement for a systematic literature search and methods for conducting and reporting systematic reviews and meta-analyses recommended by the Cochrane Screening and Diagnostic Tests Methods Group. We identified studies through PubMed and Embase electronic databases and included serologic studies detecting measles virus IgG antibodies among participants of any age from the same source population that reported an index (any EIA or multiple bead-based assays, MBA) and reference test (PRNT) using sera, whole blood, or plasma. Measures of diagnostic accuracy with 95% confidence intervals (CI) were abstracted for each study result, where reported. RESULTS: We identified 550 unique publications and identified 36 eligible studies for analysis. We classified studies as high, medium, or low quality; results from high quality studies are reported. Because most high quality studies used the Siemens Enzygnost EIA kit, we generate individual and pooled diagnostic accuracy estimates for this assay separately. Median sensitivity of the Enzygnost EIA was 92.1% [IQR = 82.3, 95.7]; median specificity was 96.9 [93.0, 100.0]. Pooled sensitivity and specificity from studies using the Enzygnost kit were 91.6 (95%CI: 80.7,96.6) and 96.0 (95%CI: 90.9,98.3), respectively. The sensitivity of all other EIA kits across high quality studies ranged from 0% to 98.9% with median (IQR) = 90.6 [86.6, 95.2]; specificity ranged from 58.8% to 100.0% with median (IQR) = 100.0 [88.7, 100.0]. CONCLUSIONS: Evidence on the diagnostic accuracy of currently available measles IgG EIAs is variable, insufficient, and may not be fit for purpose for serosurveillance goals. Additional studies evaluating the diagnostic accuracy of measles EIAs, including MBAs, should be conducted among diverse populations and settings (e.g., vaccination status, elimination/endemic status, age groups).