Infection and transmission dynamics of plasmodium vivax in Papua New Guinea

Background Plasmodium vivax mainly affects Asia, Central and South America and is responsible for 350-450 millions cases per year, hence 25-40% of annual infections of malaria worldwide. In Papua New Guinea (PNG) P. vivax prevalence is among the highest worldwide. The biggest challenge for the control of P. vivax infections is the formation of dormant liver stages, which have the ability to relapse and cause disease even after successful clearance of asexual stages in the blood circulation. P. vivax strains in PNG relapse frequently and fast, and one of the highest doses of Primaquine is necessary to reduce the relapse rate in this region. Aims and objectives The overall aim of this thesis was to deepen our understanding of P. vivax molecular epidemiology, infections, transmission and its contribution to the infectious reservoir of P. vivax malaria in PNG. The specific objectives pursued can be summarized as follows. First, to assess P. vivax infection dynamics and transmission dynamics in semi-immune children and to contribute to the understanding of the biology of relapses by comparing two treatment arms. Second, to identify the best RNA sampling strategy for field surveys and improve molecular detection and quantification of P. falciparum and P. vivax gametocytes in field samples. Third, to develop genotyping tools to better study the dynamics of gametocyte production in multi-clone infections in consecutive samples. Methods For the above objectives, the laboratory work of this thesis was split into three parts. (i) P. vivax PCR-positive blood samples from a treatment-to-reinfection survey were genotyped by the marker msp1F3 and analyzed for gametocyte carriage by pvs25 qRT-PCR. These samples were collected from 524 children aged 5-10 years and actively and passively followed-up over 8 months in PNG. The children were randomly attributed to two treatment arms consisting of blood-stage clearing drugs and either PQ or placebo. Genotyping data and gametocyte positivity were used to investigate the contribution of relapses to the infectious reservoir of P. vivax malaria. The molecular epidemiology of relapses was assessed by comparing the investment in gametocytogenesis, the molecular force of blood-stage infections (molFOB, number of distinct blood-stage infections per child and year) and the duration of infections in both trial arms using a Bayesian approach that allows for imperfect detection of blood-stage infections. (ii) In a cross-sectional survey in 315 5-10 years old children from Papua New Guinea, the optimal strategy for gametocyte detection in field studies was assessed. Gametocytes need to be detected by amplification of stage-specific transcripts, which requires RNA-preserving blood sampling. The efficiency of sampling and storage on filter paper versus in solution were compared. (iii) 111 archived DNA samples from PNG were genotyped by capillary electrophoresis for 6 length-polymorphic and gametocyte-specific markers and their diversity was determined. Serial dilution of gametocyte enriched culture of P. falciparum 3D7 strain permitted to establish the detection limit of each marker in vitro. The two most promising markers, pfg377 and pfs230, were then tested to simultaneously genotype paired RNA and DNA samples from 46 individuals from Burkina Faso. Results (i) In the randomized treatment-to-reinfection trial, children who received PQ showed 82% lower risk of experiencing at least one P. vivax infection. The estimated duration of infection, the parasite density and the probability of detection of individual infecting clone (detectability) was similar in both arms of the trial. Gametocyte densities and carriage in positive samples also did not differ between trial arms. Durations increased by age, whereas parasite density and detectability decreased by age. Over the 8 months follow-up, molFOB in placebo arm was 9.9 infections per child and year and almost three times as high as molFOB in PQ arm with 3.5. About 2 relapses were observed per each new infection at all villages. The increasing individual exposure of participants, as measured by molFOB, translated proportionally into an increased relapse burden. (ii) In the cross-sectional survey in PNG, RNAprotect resulted in the highest proportion of gametocyte positive samples and gametocyte-specific transcript yields. The RNA-based detection resulted in a P. falciparum positivity of 24.1%; of these 40.8% carried gametocytes. P. vivax positivity was 38.4% with 38.0% carrying gametocytes. Most of the gametocyte carriers were also positive by DNA-based detection. (iii) Analysis of genotyping markers of P. falciparum gametocytes revealed highest discrimination power for pfs230 with 18 alleles, followed by pfg377 with 15 alleles. When assays were performed in parallel on RNA and DNA, only 85% pfs230 samples and 60% pfg377 samples contained at least one matching genotype in DNA and RNA. Conclusion This thesis was the first attempt to fill the gaps in the knowledge of infection dynamics of relapses and new infections in semi-immune children. By comparing two trial arms results demonstrated how relapses and new infections have similar duration, parasite density, detectability and investment in gametocytogenesis. The mathematical model applied to genotyping data from the two treatment arms proved very useful to evaluate the infection dynamics of P. vivax. This was achieved despite a major complication of P. vivax molecular epidemiology, namely the unknown history of infections in our participants giving rise to relapses. Data generated during the course of this thesis was used to highlight that relapses are the major contributors to P. vivax infections and transmission in PNG. The molecular genotyping tools developed to study P. falciparum gametocyte transmission dynamics will open up new investigations of clone interaction, within-host competition, and clonal fitness. So far, very little is known on gametocyte dynamics in natural infections, where concurrent clonal infections might contribute to transmission equally or in competition with each other. This determines parasite recombination in mosquitoes, which in turn has major consequences for development of multi-locus drug resistance phenotypes or antigenic diversity

Comparison of real-time PCR and the Kato-Katz method for the diagnosis of soil-transmitted helminthiasis and assessment of cure in a randomized controlled trial

Diagnosis of soil-transmitted helminths (STHs) in developing countries is commonly based on microscopic detection of eggs in stool samples, using the Kato-Katz (KK) method, which has a poor sensitivity for detecting light intensity infections. We compared the performance of the KK method and real-time PCR in the framework of a randomized trial, which evaluated four novel treatments against Trichuris trichiura and concomitant STH infections.; Two stool samples obtained from 320 participants were examined at baseline and follow-up with quadruplicate KK and PCR analyses of one of the two samples using "bead-beating" for DNA extraction. At follow-up, 80 samples were negative according to both PCR and KK and 173 were positive with both methods for any of the STHs. Relative to PCR, the calculated sensitivity of KK at follow-up was 83.6%, 43.0% and 53.8% for T. trichiura, for hookworm and for Ascaris lumbricoides, respectively. The sensitivity of PCR compared with KK at this time point was 89.1% for T. trichiura, 72.7% for hookworm and 87.5% for A. lumbricoides. Cure rates (CRs) for T. trichiura and A. lumbricoides were slightly lower with the PCR method. For hookworm CRs with KK were mostly significantly lower, namely 36.7%, 91.1%, 72.2% and 77.8% for moxidectin, moxidectin in combination with tribendimidine, moxidectin in combination with albendazole and albendazole in combination with oxantel pamoate, respectively, whereas with PCR the CRs were 8.3%, 82.6%, 37.1% and 57.1%, respectively.; In conclusion, a single real-time PCR is as sensitive as quadruplicate KK for T. trichiura and A. lumbricoides detection but more sensitive for hookworm, which has an influence on the estimated treatment efficacy. PCR method with DNA extraction using the "bead-beating protocol" should be further promoted in endemic areas and laboratories that can afford the needed equipment. The study is registered at ISRCTN (no. 20398469)

Novel Genotyping Tools for Investigating Transmission Dynamics of Plasmodium falciparum

Background. Differentiation between gametocyte-producing Plasmodium falciparum clones depends on both high levels of stage-specific transcripts and high genetic diversity of the selected genotyping marker obtained by a high-resolution typing method. By analyzing consecutive samples of one host, the contribution of each infecting clone to transmission and the dynamics of gametocyte production in multiclone infections can be studied. Methods. We have evaluated capillary electrophoresis based differentiation of 6 length-polymorphic gametocyte genes. RNA and DNA of 25 µL whole blood from 46 individuals from Burkina Faso were simultaneously genotyped. Results. Highest discrimination power was achieved by pfs230 with 18 alleles, followed by pfg377 with 15 alleles. When assays were performed in parallel on RNA and DNA, 85.7% of all pfs230 samples and 59.5% of all pfg377 samples contained at least one matching genotype in DNA and RNA. Conclusions. The imperfect detection in both, DNA and RNA, was identified as major limitation for investigating transmission dynamics, owing primarily to the volume of blood processed and the incomplete representation of all clones in the sample tested. Abundant low-density gametocyte carriers impede clone detectability, which may be improved by analyzing larger volumes and detecting initially sequestered gametocyte clones in follow-up sample

Strongyloides stercoralisprevalence and diagnostics in Vientiane, Lao People's Democratic Republic

Background: Despite the high prevalence of strongyloidiasis in the Laotian population, Laotian hospitals still lack diagnostic capacity to appropriately diagnose Strongyloides stercoralis infections. This cross-sectional hospital-based study was conducted to assess the prevalence of Strongyloides stercoralis infection among hospitalized patients treated at Mahosot Hospital, the primary reference hospital of Lao People’s Democratic Republic (Lao PDR), and to validate feasible methods for diagnosing S. stercoralis infection at hospital’s laboratory. Methods: Between September and December 2018, stool samples of 104 inpatients were investigated for S. stercoralis infection by wet smear, Baermann technique, Koga Agar plate culture (KAPC), and real-time detection polymerase chain reaction (RTD-PCR) at the Infectious Diseases Ward of the Mahosot Hospital in Vientiane. The sensitivity, the specificity, the negative predictive value (NPV) of each diagnostic test, as well as their combination(s) was calculated using a composite reference standard (CRS). The correlation of the different test methods was assessed by chi-square or Fisher’s exact test. Cohen’s kappa coefficient was used to assess the diagnostic agreement of the different test methods. Results: The overall prevalence of S. stercoralis infections among the study population was 33.4%. The cumulative infection prevalence statistically significantly increased from the lowest age group of 40 years and below (22.4%), to the medium (40.0%) and to the oldest age group of 61 year and above (72.7%)(P = 0.003). The cumulative infection prevalence of CRS was considerably higher in male (40.4%) compared to female patients (28.1%), but not statistically different (P = 0.184). The diagnostic sensitivity of Baermann technique, KAPC, RTD-PCR, and the combination of Baermann technique and KAPC were 60.0, 60.0, 74.3, and 77.1%, respectively. Only 13 patients (37.1%) of the total 35 S. stercoralis patients diagnosed with any technique had a simultaneously positive diagnostic test with Baermann, KAPC and RTD-PCR. Conclusions: We identified Baermann technique and KAPC to be currently the most feasible and implementable standard methods for diagnosing S. stercoralis at a hospital setting such as Mahosot Hospital and provincial and district hospitals in Lao PDR and other low- and middle income countries in Southeast Asia

Gambiense human african trypanosomiasis sequelae after treatment: a follow-up study 12 years after treatment

The clinical presentation of Human African Trypanosomiasis (HAT) due to; Trypanosoma brucei gambiense; is well known, but knowledge on long-term sequelae is limited. In the frame of studies conducted between 2004 and 2005 in the Democratic Republic of the Congo (DRC), the prevalence of HAT related signs and symptoms were evaluated before the start of treatment and at the end of treatment. To explore possible long-term sequelae, the same clinical parameters were assessed in 2017 in 51 first stage and 18 second stage HAT patients. Signs and symptoms 12-13 years after treatment were compared to before and immediately after treatment and to controls matched for sex and age (±5 years). In first stage HAT patients, the prevalence of all signs and symptoms decreased compared to before treatment but were still higher after 12-13 years than immediately at the end of treatment and in the control group. In second stage HAT patients, all HAT-specific findings had continuously decreased to the point where they were in the range of the healthy control group. In a selection of oligosymptomatic first stage HAT patients, no trypanosomes were detected in the blood by microscopic examination or PCR. An oligosymptomatic presentation of HAT due to the persistence of parasites in compartments, where first stage HAT medications do not penetrate, could not be ruled out

Effects of liver-stage clearance by Primaquine on gametocyte carriage of Plasmodium vivax and P. falciparum

Primaquine (PQ) is the only currently licensed antimalarial that prevents Plasmodium vivax (Pv) relapses. It also clears mature P. falciparum (Pf) gametocytes, thereby reducing post-treatment transmission. Randomized PQ treatment in a treatment-to-reinfection cohort in Papua New Guinean children permitted the study of Pv and Pf gametocyte carriage after radical cure and to investigate the contribution of Pv relapses.; Children received radical cure with Chloroquine, Artemether-Lumefantrine plus either PQ or placebo. Blood samples were subsequently collected in 2-to 4-weekly intervals over 8 months. Gametocytes were detected by quantitative reverse transcription-PCR targeting pvs25 and pfs25.; PQ treatment reduced the incidence of Pv gametocytes by 73%, which was comparable to the effect of PQ on incidence of blood-stage infections. 92% of Pv and 79% of Pf gametocyte-positive infections were asymptomatic. Pv and to a lesser extent Pf gametocyte positivity and density were associated with high blood-stage parasite densities. Multivariate analysis revealed that the odds of gametocytes were significantly reduced in mixed-species infections compared to single-species infections for both species (ORPv = 0.39 [95% CI 0.25-0.62], ORPf = 0.33 [95% CI 0.18-0.60], p<0.001). No difference between the PQ and placebo treatment arms was observed in density of Pv gametocytes or in the proportion of Pv infections that carried gametocytes. First infections after blood-stage and placebo treatment, likely caused by a relapsing hypnozoite, were equally likely to carry gametocytes than first infections after PQ treatment, likely caused by an infective mosquito bite.; Pv relapses and new infections are associated with similar levels of gametocytaemia. Relapses thus contribute considerably to the Pv reservoir highlighting the importance of effective anti-hypnozoite treatment for efficient control of Pv.; ClinicalTrials.gov NCT02143934

The complex relationship of exposure to new Plasmodium infections and incidence of clinical malaria in Papua New Guinea

The molecular force of blood-stage infection (molFOB) is a quantitative surrogate metric for malaria transmission at population level and for exposure at individual level. Relationships between molFOB, parasite prevalence and clinical incidence were assessed in a treatment-to-reinfection cohort, where P.vivax (Pv) hypnozoites were eliminated in half the children by primaquine (PQ). Discounting relapses, children acquired equal numbers of new P. falciparum (Pf) and Pv blood-stage infections/year (Pf-molFOB = 0-18, Pv-molFOB = 0-23) resulting in comparable spatial and temporal patterns in incidence and prevalence of infections. Including relapses, Pv-molFOB increased >3 fold (relative to PQ-treated children) showing greater heterogeneity at individual (Pv-molFOB = 0-36) and village levels. Pf- and Pv-molFOB were strongly associated with clinical episode risk. Yearly Pf clinical incidence rate (IR = 0.28) was higher than for Pv (IR = 0.12) despite lower Pf-molFOB. These relationships between molFOB, clinical incidence and parasite prevalence reveal a comparable decline in Pf and Pv transmission that is normally hidden by the high burden of Pv relapses. CLINICAL TRIAL REGISTRATION: ClinicalTrials.gov NCT02143934

Blood-Stage Parasitaemia and Age Determine Plasmodium falciparum and P. vivax Gametocytaemia in Papua New Guinea

A better understanding of human-to-mosquito transmission is crucial to control malaria. In order to assess factors associated with gametocyte carriage, 2083 samples were collected in a cross-sectional survey in Papua New Guinea. Plasmodium species were detected by light microscopy and qPCR and gametocytes by detection of pfs25 and pvs25 mRNA transcripts by reverse-transcriptase PCR (qRT-PCR). The parasite prevalence by PCR was 18.5% for Plasmodium falciparum and 13.0% for P. vivax. 52.5% of all infections were submicroscopic. Gametocytes were detected in 60% of P. falciparum-positive and 51% of P. vivax-positive samples. Each 10-fold increase in parasite density led to a 1.8-fold and 3.3-fold increase in the odds of carrying P. falciparum and P. vivax gametocytes. Thus the proportion of gametocyte positive and gametocyte densities was highest in young children carrying high asexual parasite densities and in symptomatic individuals. Dilution series of gametocytes allowed absolute quantification of gametocyte densities by qRT-PCR and showed that pvs25 expression is 10-20 fold lower than pfs25 expression. Between 2006 and 2010 parasite prevalence in the study site has decreased by half. 90% of the remaining infections were asymptomatic and likely constitute an important reservoir of transmission. However, mean gametocyte densities were low (approx. 1-2 gametocyte/muL) and it remains to be determined to what extent low-density gametocyte positive individuals are infective to mosquitos

Strategies for Understanding and Reducing the Plasmodium vivax and Plasmodium ovale Hypnozoite Reservoir in Papua New Guinean Children: A Randomised Placebo-Controlled Trial and Mathematical Model

The undetectable hypnozoite reservoir for relapsing Plasmodium vivax and P. ovale malarias presents a major challenge for malaria control and elimination in endemic countries. This study aims to directly determine the contribution of relapses to the burden of P. vivax and P. ovale infection, illness, and transmission in Papua New Guinean children.; From 17 August 2009 to 20 May 2010, 524 children aged 5-10 y from East Sepik Province in Papua New Guinea (PNG) participated in a randomised double-blind placebo-controlled trial of blood- plus liver-stage drugs (chloroquine [CQ], 3 d; artemether-lumefantrine [AL], 3 d; and primaquine [PQ], 20 d, 10 mg/kg total dose) (261 children) or blood-stage drugs only (CQ, 3 d; AL, 3 d; and placebo [PL], 20 d) (263 children). Participants, study staff, and investigators were blinded to the treatment allocation. Twenty children were excluded during the treatment phase (PQ arm: 14, PL arm: 6), and 504 were followed actively for 9 mo. During the follow-up time, 18 children (PQ arm: 7, PL arm: 11) were lost to follow-up. Main primary and secondary outcome measures were time to first P. vivax infection (by qPCR), time to first clinical episode, force of infection, gametocyte positivity, and time to first P. ovale infection (by PCR). A basic stochastic transmission model was developed to estimate the potential effect of mass drug administration (MDA) for the prevention of recurrent P. vivax infections. Targeting hypnozoites through PQ treatment reduced the risk of having at least one qPCR-detectable P. vivax or P. ovale infection during 8 mo of follow-up (P. vivax: PQ arm 0.63/y versus PL arm 2.62/y, HR = 0.18 [95% CI 0.14, 0.25], p < 0.001; P. ovale: 0.06 versus 0.14, HR = 0.31 [95% CI 0.13, 0.77], p = 0.011) and the risk of having at least one clinical P. vivax episode (HR = 0.25 [95% CI 0.11, 0.61], p = 0.002). PQ also reduced the molecular force of P. vivax blood-stage infection in the first 3 mo of follow-up (PQ arm 1.90/y versus PL arm 7.75/y, incidence rate ratio [IRR] = 0.21 [95% CI 0.15, 0.28], p < 0.001). Children who received PQ were less likely to carry P. vivax gametocytes (IRR = 0.27 [95% CI 0.19, 0.38], p < 0.001). PQ had a comparable effect irrespective of the presence of P. vivax blood-stage infection at the time of treatment (p = 0.14). Modelling revealed that mass screening and treatment with highly sensitive quantitative real-time PCR, or MDA with blood-stage treatment alone, would have only a transient effect on P. vivax transmission levels, while MDA that includes liver-stage treatment is predicted to be a highly effective strategy for P. vivax elimination. The inclusion of a directly observed 20-d treatment regime maximises the efficiency of hypnozoite clearance but limits the generalisability of results to real-world MDA programmes.; These results suggest that relapses cause approximately four of every five P. vivax infections and at least three of every five P. ovale infections in PNG children and are important in sustaining transmission. MDA campaigns combining blood- and liver-stage treatment are predicted to be a highly efficacious intervention for reducing P. vivax and P. ovale transmission.; ClinicalTrials.gov NCT02143934