The effect of varying analytical methods on estimates of anti-malarial clinical efficacy

<p>Abstract</p> <p>Background</p> <p>Analytical approaches for the interpretation of anti-malarial clinical trials vary considerably. The aim of this study was to quantify the magnitude of the differences between efficacy estimates derived from these approaches and identify the factors underlying these differences.</p> <p>Methods</p> <p>Data from studies conducted in Africa and Thailand were compiled and the risk estimates of treatment failure, adjusted and unadjusted by genotyping, were derived by three methods (intention to treat (ITT), modified intention to treat (mITT) and per protocol (PP)) and then compared.</p> <p>Results</p> <p>29 clinical trials (15 from Africa and 14 from Thailand) with a total of 65 treatment arms (38 from Africa and 27 from Thailand) were included in the analysis. Of the 15,409 patients enrolled, 2,637 (17.1%) had incomplete follow up for the unadjusted analysis and 4,489 (33.4%) for the adjusted analysis. Estimates of treatment failure were consistently higher when derived from the ITT or PP analyses compared to the mITT approach. In the unadjusted analyses the median difference between the ITT and mITT estimates was greater in Thai studies (11.4% [range 2.1–31.8]) compared to African Studies (1.8% [range 0–11.7]). In the adjusted analyses the median difference between PP and mITT estimates was 1.7%, but ranged from 0 to 30.9%. The discrepancy between estimates was correlated significantly with the proportion of patients with incomplete follow-up; p < 0.0001. The proportion of studies with a major difference (> 5%) between adjusted PP and mITT was 28% (16/57), with the risk difference greater in African (37% 14/38) compared to Thai studies (11% 2/19). In the African studies, a major difference in the adjusted estimates was significantly more likely in studies in high transmission sites (62% 8/13) compared to studies in moderate transmission sites (24% 6/25); p = 0.035.</p> <p>Conclusion</p> <p>Estimates of anti-malarial clinical efficacy vary significantly depending on the analytical methodology from which they are derived. In order to monitor temporal and spatial trends in anti-malarial efficacy, standardized analytical tools need to be applied in a transparent and systematic manner.</p

Evidence uptake is only part of the process: stakeholders’ insights on WHO treatment guideline recommendation processes for radical cure of P. vivax malaria

Health policy processes should be evidence-informed, transparent and timely, but these processes are often unclear to stakeholders outside the immediate policymaking environment. We spoke to 36 international malaria stakeholders to gain insights on the processes involved in the World Health Organization’s Global Malaria Programme’s recommendations for their treatment guidelines of P. vivax malaria. Four key themes which drew on the 3i policy framework and Shiffman’s four factors that influence global and national policymaking were identified to understand these processes. Triggers for policy change and change prioritisation, evidence types that inform policy, effects of funding on decision-making processes, and transparency and communication of these processes to external stakeholders. Results indicate that more clarity is needed on what triggers global malaria policy change processes, a clearer justification of evidence types used to inform policymaking, better understanding of the impact of the WHO’s funding model on policymaking and further transparency and improved communication of these processes to external stakeholders is also needed. We suggest that global malaria policymaking could be improved by using the following strategies: ensuring that identified triggers actually initiate the policy change process, expediting decision-making timelines by developing a priority framework for assessing new evidence, adopting suitable frameworks to assess contextual evidence, and increasing the transparency of the role of non-state funders in policy decision-making processes and when publishing new recommendations

A systematic review of sub-microscopic Plasmodium vivax infection.

BACKGROUND: An accurate estimate of Plasmodium vivax prevalence is essential for the successful implementation of malaria control and elimination programmes. Prevalence estimates both inform control strategies and are used in their evaluation. Light microscopy is the main method for detecting Plasmodium parasitaemia in the peripheral blood, but compared to molecular diagnostics, such as polymerase chain reaction (PCR), has limited sensitivity. METHODS: A systematic review and meta-analysis was conducted to assess the effect of detection method on the prevalence of P. vivax and to quantify the extent to which P. vivax infections are undetected by microscopy. Embase, Medline and the Cochrane Database were searched for studies reporting prevalence by PCR and by microscopy and that contained all of the following key words: vivax, PCR, and malaria. Prevalence estimates and study meta-data were extracted systematically from each publication. Combined microscopy:PCR prevalence ratios were estimated by random effects meta-analysis. Sensitivity and specificity of microscopy were calculated using PCR as the gold standard. RESULTS: Of 874 studies reviewed, 40 met the criteria for inclusion contributing 54 prevalence pairs. The prevalence of P. vivax infection measured by PCR was consistently higher than the prevalence measured by microscopy with sub-patent parasitaemia. The mean prevalence of infection detected by microscopy was 67 % (95 % CI 59-73 %) lower than the prevalence detected by PCR. The detection of sub-patent parasitaemia did not vary according to the microscopy method (thick or, thick and thin smears), the PCR prevalence (as a measure of the true P. vivax prevalence), the type of blood used or DNA extraction method. CONCLUSIONS: Quantifying P. vivax parasitaemia by PCR rather than microscopy consistently increased prevalence estimates by a factor of 2.3. Whilst the sensitivity of microscopy can be improved by better methods, molecular methods have potential to be scaled up to improve the detection of P. vivax transmission reservoirs

Imported malaria and its implication to achievement of malaria-free Bhutan

As Bhutan nears malaria elimination, imported malaria through cross-border human mobility has emerged as major source of transmission. This report highlights key epidemiological characteristics of imported infections and the need to strengthen targeted surveillance and response interventions by the national elimination program to achieve elimination and sustain it

Improving Case Definitions for Severe Malaria

The authors discuss a study by Philip Bejon et al. that adopted a new approach to balancing the sensitivity and specificity of criteria for defining severe malaria

Dealing with indeterminate outcomes in antimalarial drug efficacy trials: a comparison between complete case analysis, multiple imputation and inverse probability weighting.

BACKGROUND: Antimalarial clinical efficacy studies for uncomplicated Plasmodium falciparum malaria frequently encounter situations in which molecular genotyping is unable to discriminate between parasitic recurrence, either new infection or recrudescence. The current WHO guideline recommends excluding these individuals with indeterminate outcomes in a complete case (CC) analysis. Data from the four artemisinin-based combination (4ABC) trial was used to compare the performance of multiple imputation (MI) and inverse probability weighting (IPW) against the standard CC analysis for dealing with indeterminate recurrences. METHODS: 3369 study participants from the multicentre study (4ABC trial) with molecularly defined parasitic recurrence treated with three artemisinin-based combination therapies were used to represent a complete dataset. A set proportion of recurrent infections (10, 30 and 45%) were reclassified as missing using two mechanisms: a completely random selection (mechanism 1); missingness weakly dependent (mechanism 2a) and strongly dependent (mechanism 2b) on treatment and transmission intensity. The performance of MI, IPW and CC approaches in estimating the Kaplan-Meier (K-M) probability of parasitic recrudescence at day 28 was then compared. In addition, the maximum likelihood estimate of the cured proportion was presented for further comparison (analytical solution). Performance measures (bias, relative bias, standard error and coverage) were reported as an average from 1000 simulation runs. RESULTS: The CC analyses resulted in absolute underestimation of K-M probability of day 28 recrudescence by up to 1.7% and were associated with reduced precision and poor coverage across all the scenarios studied. Both MI and IPW method performed better (greater consistency and greater efficiency) compared to CC analysis. In the absence of censoring, the analytical solution provided the most consistent and accurate estimate of cured proportion compared to the CC analyses. CONCLUSIONS: The widely used CC approach underestimates antimalarial failure; IPW and MI procedures provided efficient and consistent estimates and should be considered when reporting the results of antimalarial clinical trials, especially in areas of high transmission, where the proportion of indeterminate outcomes could be large. The analytical solution estimating the cured proportion could provide an alternative approach, in scenarios with minimal censoring due to loss to follow-up or new infections

Comparison of three molecular methods for the detection and speciation of Plasmodium vivax and Plasmodium falciparum

<p>Abstract</p> <p>Background</p> <p>Accurate diagnosis of <it>Plasmodium </it>spp. is essential for the rational treatment of malaria. Despite its many disadvantages, microscopic examination of blood smears remains the current "gold standard" for malaria detection and speciation. PCR assays offer an alternative to microscopy which has been shown to have superior sensitivity and specificity. Unfortunately few comparative studies have been done on the various molecular based speciation methods.</p> <p>Methods</p> <p>The sensitivity, specificity and cost effectiveness of three molecular techniques were compared for the detection and speciation of <it>Plasmodium falciparum </it>and <it>Plasmodium vivax </it>from dried blood spots collected from 136 patients in western Thailand. The results from the three molecular speciation techniques (nested PCR, multiplex PCR, and real-time PCR) were used to develop a molecular consensus (two or more identical PCR results) as an alternative gold standard.</p> <p>Results</p> <p>According to the molecular consensus, 9.6% (13/136) of microscopic diagnoses yielded false negative results. Multiplex PCR failed to detect <it>P. vivax </it>in three mixed isolates, and the nested PCR gave a false positive <it>P. falciparum </it>result in one case. Although the real-time PCR melting curve analysis was the most expensive method, it was 100% sensitive and specific and least time consuming of the three molecular techniques investigated.</p> <p>Conclusion</p> <p>Although microscopy remains the most appropriate method for clinical diagnosis in a field setting, its use as a gold standard may result in apparent false positive results by superior techniques. Future studies should consider using more than one established molecular methods as a new gold standard to assess novel malaria diagnostic kits and PCR assays.</p

A new Plasmodium vivax reference sequence with improved assembly of the subtelomeres reveals an abundance of pir genes

Plasmodium vivax is now the predominant cause of malaria in the Asia-Pacific, South America and Horn of Africa. Laboratory studies of this species are constrained by the inability to maintain the parasite in continuous ex vivo culture, but genomic approaches provide an alternative and complementary avenue to investigate the parasite's biology and epidemiology. To date, molecular studies of P. vivax have relied on the Salvador-I reference genome sequence, derived from a monkey-adapted strain from South America. However, the Salvador-I reference remains highly fragmented with over 2500 unassembled scaffolds.  Using high-depth Illumina sequence data, we assembled and annotated a new reference sequence, PvP01, sourced directly from a patient from Papua Indonesia. Draft assemblies of isolates from China (PvC01) and Thailand (PvT01) were also prepared for comparative purposes. The quality of the PvP01 assembly is improved greatly over Salvador-I, with fragmentation reduced to 226 scaffolds. Detailed manual curation has ensured highly comprehensive annotation, with functions attributed to 58% core genes in PvP01 versus 38% in Salvador-I. The assemblies of PvP01, PvC01 and PvT01 are larger than that of Salvador-I (28-30 versus 27 Mb), owing to improved assembly of the subtelomeres.  An extensive repertoire of over 1200 Plasmodium interspersed repeat (pir) genes were identified in PvP01 compared to 346 in Salvador-I, suggesting a vital role in parasite survival or development. The manually curated PvP01 reference and PvC01 and PvT01 draft assemblies are important new resources to study vivax malaria. PvP01 is maintained at GeneDB and ongoing curation will ensure continual improvements in assembly and annotation quality

Field evaluation of a novel semi-quantitative point-of-care diagnostic for G6PD deficiency in Indonesia

Background: The WHO recommends routine testing of G6PD activity to guide radical cure in patients with Plasmodium vivax malaria. Females may have intermediate G6PD enzyme activity and to date, only complex diagnostics are able to reliably identify them. The semi-quantitative G6PD diagnostic “One Step G6PD Test” (Humasis, RoK; “RDT”) is a lateral flow assay that can distinguish deficient, intermediate, and normal G6PD status and offers a simpler diagnostic alternative. Methods: G6PD status of participants enrolled in Malinau and Nunukan Regencies and the capital Jakarta was assessed with the RDT, and G6PD activity was measured in duplicate by reference spectrophotometry. The adjusted male median (AMM) of the spectrophotometry measurements was defined as 100% activity; 70% and 30% of the AMM were defined as thresholds for intermediate and deficient G6PD status, respectively. Results were compared to those derived from spectrophotometry at the clinically relevant G6PD activity thresholds of 30% and 70%. Results: Of the 161 participants enrolled, 10 (6.2%) were G6PD deficient and 12 (7.5%) had intermediate G6PD activity by spectrophotometry. At the 30% threshold, the sensitivity of the RDT was 10.0% (95%CI: 0.3–44.5%) with a specificity of 99.3% (95%CI: 96.4–100.0%); the positive predictive value was 50.0% (95%CI: 1.3–98.7%) and the negative predictive value 94.3% (95%CI: 89.5–97.4%). The corresponding figures at the 70% threshold were 22.7% (95%CI: 7.8–45.4%), 100.0% (95%CI: 97.4–100.0%), 100.0% (95%CI: 47.8–100.0%) and 89.1% (95%CI: 83.1–93.5%), respectively. Conclusion: While there is a dire need for an easy-to-use, economical, semi-quantitative diagnostic for the point of care, the observed performance of the “One Step G6PD Test” in its current form was insufficient to guide antimalarial treatment