VivaxGEN: An open access platform for comparative analysis of short tandem repeat genotyping data in Plasmodium vivax populations.

BACKGROUND: The control and elimination of Plasmodium vivax will require a better understanding of its transmission dynamics, through the application of genotyping and population genetics analyses. This paper describes VivaxGEN (http://vivaxgen.menzies.edu.au), a web-based platform that has been developed to support P. vivax short tandem repeat data sharing and comparative analyses. RESULTS: The VivaxGEN platform provides a repository for raw data generated by capillary electrophoresis (FSA files), with fragment analysis and standardized allele calling tools. The query system of the platform enables users to filter, select and differentiate samples and alleles based on their specified criteria. Key population genetic analyses are supported including measures of population differentiation (FST), expected heterozygosity (HE), linkage disequilibrium (IAS), neighbor-joining analysis and Principal Coordinate Analysis. Datasets can also be formatted and exported for application in commonly used population genetic software including GENEPOP, Arlequin and STRUCTURE. To date, data from 10 countries, including 5 publicly available data sets have been shared with VivaxGEN. CONCLUSIONS: VivaxGEN is well placed to facilitate regional overviews of P. vivax transmission dynamics in different endemic settings and capable to be adapted for similar genetic studies of P. falciparum and other organisms

SARS-CoV-2 Antibody Seroprevalence in Jakarta, Indonesia

The SARS-CoV-2 transmission dynamics in low- and middle-income countries remain poorly understood. This study aimed to estimate the SARS-CoV-2 antibodies seroprevalence in Jakarta, Indonesia, and to increase knowledge of SARS-CoV-2 transmission in urban settings. A population-based serosurvey among individuals aged one year or older was conducted in Jakarta. Employing a multistage sampling design, samples were stratified by district, slum, and non-slum residency, sex, and age group. Blood samples were tested for IgG against three different SARS-CoV-2 antigens. Seroprevalence was estimated after applying sample weights and adjusting for cluster characteristics. In March 2021, this study collected 4,919 respondents. The weighted estimate of seroprevalence was 44.5% (95% CI = 42.5-46.5). Seroprevalence was highest among adults aged 30-49 years, with higher seroprevalence in women and the overweight/obese group. Respondents residing in slum areas were 1.3-fold more likely to be seropositive than non-slum residents. It was estimated that4,717,000 of Jakarta's 10.6 million residents had prior SARS-CoV-2 infection. This suggests that approximately 10 infections were undiagnosed/underreported for every reported case. About one year after the first COVID-19 case was confirmed, close to half of Jakarta's residents have been infected by SARS-CoV-2

Malaria in Wanokaka and Loli sub-districts, West Sumba District, East Nusa Tenggara Province, Indonesia.

Contains fulltext : 49453.pdf (publisher's version ) (Open Access)Malaria has long been known as one of the major public health problems in West Sumba District, East Nusa Tenggara Province, Indonesia. To obtain baseline data for establishment of a suitable malaria control program in the area, malariometric surveys were conducted in two sub-districts, Wanokaka and Loli, during the periods of January, May, and August 2005. The survey included three selected villages in each sub-district, and blood smear analyses of 701, 921, and 894 randomly selected subjects in January, May, and August revealed 30.5%, 25.3%, and 28.2% malaria positives, respectively, consisting mainly of Plasmodium falciparum and P. vivax, and in a few cases, P. malariae. Analysis of malaria prevalence at different age groups clearly reflected the common phenomenon that younger individuals are more vulnerable by infection of either P. falciparum or P. vivax. In falciparum malaria, the frequency of cases carrying gametocytes was also relatively high involving all age groups. The findings indicate that the malaria incidence and transmission in the area are relatively high and that further exploration is warranted to establish a precise malaria control program

Supervised versus unsupervised primaquine radical cure for the treatment of falciparum and vivax malaria in Papua, Indonesia: a cluster-randomised, controlled, open-label superiority trial

Background There is a high risk of Plasmodium vivax recurrence in patients treated for Plasmodium falciparum malaria in co-endemic areas. Primaquine radical cure has the potential to reduce P vivax recurrences in patients presenting with P falciparum as well as P vivax malaria but is undermined by poor adherence to the currently recommended 14-day regimen. We aimed to assess the efficacy and safety of supervised versus unsupervised primaquine radical cure in patients presenting with uncomplicated malaria. Methods We did a cluster-randomised, controlled, open-label superiority trial in Papua, Indonesia. 21 clusters of village health posts, matched by annual parasite index, were randomly assigned (1:1) to treat patients (age >12 months and body weight >5 kg) presenting with confirmed uncomplicated P falciparum or P vivax malaria with oral dihydroartemisinin–piperaquine plus either a supervised or unsupervised 14-day course of oral primaquine (0·5 mg/kg per day). Patients in the supervised group were supervised taking their primaquine dose on alternate days. Patients were followed-up for 6 months and those who presented again with malaria were retreated with the same drug regimen. Masking was not possible due to the nature of the study. The primary outcome was the incidence risk of P vivax malaria over 6 months, assessed in the modified intention-to-treat population (all patients who were assigned to a treatment group, excluding patients who were lost to follow-up after their first visit). This trial is now complete, and is registered with ClinicalTrials.gov, NCT02787070. Findings Between Sept 14, 2016, and July 31, 2018, 436 patients were screened for eligibility and 419 were enrolled; 223 (53%) patients in 11 clusters were assigned to supervised primaquine treatment and 196 (47%) in ten clusters to unsupervised primaquine treatment. 161 (72%) of 223 patients in the supervised group and 151 (77%) of 196 in the unsupervised group completed 6 months of follow-up. At 6 months, the incidence risk of P vivax recurrence in the supervised group was 29·7% (95% CI 16·4–49·9) versus 55·8% (32·3–81·8) in the unsupervised group (hazard ratio 0·23 [95% CI 0·07–0·76]; p=0·016). The incidence rate for P vivax recurrence was 539 (95% CI 390–747) infections per 1000 person-years in the supervised group versus 859 (673–1096) in the unsupervised group (incidence rate ratio 0·63 [95% CI 0·42–0·94]; p=0·025). The corresponding rates in the 224 patients who presented with P falciparum malaria were 346 (95% CI 213–563) and 660 (446–977; incidence rate ratio 0·52 [95% CI 0·28–0·98]; p=0·043). Seven serious adverse events were reported (three in the supervised group, four in the unsupervised group), none of which were deemed treatment-related, and there were no deaths. Interpretation In this area of moderate malaria transmission, supervision of primaquine radical cure treatment reduced the risk of P vivax recurrence. This finding was apparent for patients presenting with either P falciparum or P vivax malaria. Further studies are warranted to investigate the safety and efficacy of radical cure for patients presenting with uncomplicated falciparum malaria in other co-endemic areas. Funding The Bill & Melinda Gates Foundation, Wellcome Trust, and Department of Foreign Affairs and Trade of the Australian Government. Translation For the Indonesian translation of the abstract see Supplementary Materials section

Intermittent screening and treatment for malaria complementary to routine immunisation in the first year of life in Papua, Indonesia: a cluster randomised superiority trial

Background In Papua (Indonesia), infants with P. falciparum and/or P. vivax malaria are at risk of severe anaemia and death. We hypothesized that in an area of high malaria transmission, intermittent screening and treatment of infants with malaria (ISTi) will reduce morbidity compared to passive case detection (PCDi). Methods We conducted a cluster randomised, open label, superiority trial. A total of 21 clusters of village health posts (VHP) were randomised 1:1 to either IST for infants coinciding with 4 routine immunisation visits or PCDi. Healthy term infants born to consenting mothers enrolled into a maternal malaria cluster randomised trial were included in the study and followed for 12 months. Point of care malaria rapid diagnostic tests were used to detect peripheral parasitaemia at 2, 3, 4 and 9 months old in all infants in ISTi clusters and when symptomatic in PCDi clusters. Infants with detected peripheral parasitaemia were treated with dihydroartemisinin-piperaquine. The co-primary outcomes were the incidence rate of clinical malaria in the first year of life and the prevalence of parasitaemia at age 12 months. The incidence rate ratio and prevalence ratio between ISTi and PCDi were estimated using mixed-effects Poisson and log-binomial regression modelling (accounting for clustering at VHP level). Results Between May 2014 and February 2017, 757 infants were enrolled into the study, 313 into 10 ISTi clusters, and 444 into 11 PCDi clusters. Overall, 132 episodes of parasitaemia were detected, of whom 17 (12.9%) were in symptomatic infants. Over 12 months, the incidence rate (IR) of clinical malaria was 24 [95% CI, 10–50] per 1000 children-years at risk in the ISTi arm and 19 [95% CI, 8,38] per 1000 children-years in the PCDi arm (adjusted incidence rate ratio [aIRR] 1.77 [95% CI, 0.62–5.01]; p = 0.280). The prevalence of parasitaemia at 12 months was 13% (33/254) in the IST clusters and 15% (57/379) in the PCD clusters (adjusted prevalence ratio (aPR) = 0.92 (95% CI, 0.70–1.21), p = 0.55). There was no difference in the risk of anaemia between treatment arms. Conclusions In high malaria transmission area outside of Africa, our study suggests that compared to PCDi, ISTi offers no significant benefit in reducing the risk of clinical malaria in infants born to women receiving effective protection from malaria during pregnancy. Trial registration ClinicalTrials.gov NCT 02001428, registered on 20 Nov 2013

Plasmodium falciparum and P. vivax demonstrate contrasting chloroquine resistance reversal phenotypes

High-grade chloroquine (CQ) resistance has emerged in both P. falciparum and P. vivax The aim of the present study was to investigate phenotypic differences of CQ resistance in both of these species and the ability of known CQ resistance reversal agents (CQRRAs) to alter CQ susceptibility.Between April 2015 and April 2016, the potential of verapamil (VP), mibefradil (MF), L703,606 (L7), and primaquine (PQ) to reverse CQ resistance was assessed in 46 P. falciparum and 34 P. vivax clinical isolates in Papua, Indonesia, where CQ resistance is present in both species, using a modified schizont maturation assay.In P. falciparum, CQ IC50s were reduced when CQ was combined with VP (1.4-fold), MF (1.2-fold), L7 (4.2 fold), or PQ (1.8 fold). The degree of CQ resistance reversal in P. falciparum was highly correlated with CQ susceptibility for all CQRRAs: VP (R(2)=0.951), (R(2)=0.852), L7 (R(2)=0.962), and PQ (R(2)=0.901), in line with observations in P. falciparum laboratory strains. In contrast, no reduction in CQ IC50s was observed with any of the CQRRAs in P. vivax, even in those isolates with high chloroquine IC50s.The differential effect of CQRRAs in P. falciparum and P. vivax suggests significant differences in CQ kinetics and potentially the likely mechanism of CQ resistance between these two species

Potent ex vivo activity of naphthoquine and methylene blue against drug-resistant clinical isolates of Plasmodium falciparum and Plasmodium vivax

The 4-aminoquinoline naphthoquine (NQ) and the thiazine dye methylene blue (MB) have potent in vitro efficacies against Plasmodium falciparum, but susceptibility data for P. vivax are limited. The species- and stage-specific ex vivo activities of NQ and MB were assessed using a modified schizont maturation assay on clinical field isolates from Papua, Indonesia, where multidrug-resistant P. falciparum and P. vivax are prevalent. Both compounds were highly active against P. falciparum (median [range] 50% inhibitory concentration [IC50]: NQ, 8.0 nM [2.6 to 71.8 nM]; and MB, 1.6 nM [0.2 to 7.0 nM]) and P. vivax (NQ, 7.8 nM [1.5 to 34.2 nM]; and MB, 1.2 nM [0.4 to 4.3 nM]). Stage-specific drug susceptibility assays revealed significantly greater IC50s in parasites exposed at the trophozoite stage than at the ring stage for NQ in P. falciparum (26.5 versus 5.1 nM, P = 0.021) and P. vivax (341.6 versus 6.5 nM, P = 0.021) and for MB in P. vivax (10.1 versus 1.6 nM, P = 0.010). The excellent ex vivo activities of NQ and MB against both P. falciparum and P. vivax highlight their potential utility for the treatment of multidrug-resistant malaria in areas where both species are endemic

Asymptomatic Vivax and Falciparum Parasitaemia with Helminth Co-Infection: Major Risk Factors for Anaemia in Early Life.

BACKGROUND: Anaemia in children under five years old is associated with poor health, growth and developmental outcomes. In Papua, Indonesia, where the burden of anaemia in infants is high, we conducted a community survey to assess the association between Plasmodium infection, helminth carriage and the risk of anaemia. METHODS: A cross sectional household survey was carried out between April and July 2013 in 16 villages in the District of Mimika using a multistage sampling procedure. A total of 629 children aged 1-59 months from 800 households were included in the study. Demographic, symptom and anthropometry data were recorded using a standardized questionnaire. Blood and stool samples were collected for examination. RESULTS: Of the 533 children with blood film examination, 8.8% (47) had P. vivax parasitaemia and 3.9% (21) had P. falciparum; the majority of children with malaria were asymptomatic (94.4%, 68/72). Soil transmitted helminth (STH) infection was present in 43% (105/269) of children assessed; those with STH were at significantly greater risk of P. vivax parasitaemia compared to those without STH (OR = 3.7 [95%CI 1.5-9.2], p = 0.004). Anaemia (Hb<10 g/dl) was present in 24.5% (122/497) of children and associated with P. vivax parasitaemia (OR = 2.9 [95%CI, 1.7-4.9], p = 0.001), P. falciparum parasitaemia (OR = 4.3 [95%CI, 2.0-9.4], p<0.001), hookworm carriage (OR = 2.6 [95%CI, 1.2-5.8], p = 0.026), Plasmodium-helminth coinfection (OR 4.0 [95%CI, 1.4-11.3], p = 0.008) and severe stunting (OR = 1.9 ([95%CI, 1.1-3.3], p = 0.012). CONCLUSIONS: Asymptomatic P. vivax and P. falciparum infections and hookworm all contribute to risk of paediatric anaemia in coendemic areas and should be targeted with prevention and treatment programs. The relationship between helminth infections and the increased risk of P. vivax parasitaemia should be explored prospectively

Asymptomatic Vivax and Falciparum Parasitaemia with Helminth Co-Infection: Major Risk Factors for Anaemia in Early Life.

BACKGROUND: Anaemia in children under five years old is associated with poor health, growth and developmental outcomes. In Papua, Indonesia, where the burden of anaemia in infants is high, we conducted a community survey to assess the association between Plasmodium infection, helminth carriage and the risk of anaemia. METHODS: A cross sectional household survey was carried out between April and July 2013 in 16 villages in the District of Mimika using a multistage sampling procedure. A total of 629 children aged 1-59 months from 800 households were included in the study. Demographic, symptom and anthropometry data were recorded using a standardized questionnaire. Blood and stool samples were collected for examination. RESULTS: Of the 533 children with blood film examination, 8.8% (47) had P. vivax parasitaemia and 3.9% (21) had P. falciparum; the majority of children with malaria were asymptomatic (94.4%, 68/72). Soil transmitted helminth (STH) infection was present in 43% (105/269) of children assessed; those with STH were at significantly greater risk of P. vivax parasitaemia compared to those without STH (OR = 3.7 [95%CI 1.5-9.2], p = 0.004). Anaemia (Hb<10 g/dl) was present in 24.5% (122/497) of children and associated with P. vivax parasitaemia (OR = 2.9 [95%CI, 1.7-4.9], p = 0.001), P. falciparum parasitaemia (OR = 4.3 [95%CI, 2.0-9.4], p<0.001), hookworm carriage (OR = 2.6 [95%CI, 1.2-5.8], p = 0.026), Plasmodium-helminth coinfection (OR 4.0 [95%CI, 1.4-11.3], p = 0.008) and severe stunting (OR = 1.9 ([95%CI, 1.1-3.3], p = 0.012). CONCLUSIONS: Asymptomatic P. vivax and P. falciparum infections and hookworm all contribute to risk of paediatric anaemia in coendemic areas and should be targeted with prevention and treatment programs. The relationship between helminth infections and the increased risk of P. vivax parasitaemia should be explored prospectively