Kilifi Malaria Longitudinal Cohort cross-sectional survey and weekly-follow-up surveillance data for the estimation of parasite prevalence and factors associated with gametocyte carriage. (doi:10.7910/DVN/18QB3V)

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Part 1: Document Description
Part 2: Study Description
Part 3: Data Files Description
Part 5: Other Study-Related Materials
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Kilifi Malaria Longitudinal Cohort cross-sectional survey and weekly-follow-up surveillance data for the estimation of parasite prevalence and factors associated with gametocyte carriage.

doi:10.7910/DVN/18QB3V

Harvard Dataverse

2019-03-18

2

Muthui, Michelle K.; Mogeni, Polycarp; Mwai, Kennedy; Nyundo, Christopher; Macharia, Alex; Williams, Thomas N.; Nyangweso, George; Wambua, Juliana; Mwanga, Daniel; Marsh, Kevin; Bejon, Philip; Kapulu, Melissa C., 2019, "Kilifi Malaria Longitudinal Cohort cross-sectional survey and weekly-follow-up surveillance data for the estimation of parasite prevalence and factors associated with gametocyte carriage.", https://doi.org/10.7910/DVN/18QB3V, Harvard Dataverse, V2, UNF:6:VSyf/XWsFzLJUkYIBzxl4A== [fileUNF]

Kilifi Malaria Longitudinal Cohort cross-sectional survey and weekly-follow-up surveillance data for the estimation of parasite prevalence and factors associated with gametocyte carriage.

doi:10.7910/DVN/18QB3V

Muthui, Michelle K. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Mogeni, Polycarp (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Mwai, Kennedy (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Nyundo, Christopher (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Macharia, Alex (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Williams, Thomas N. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Nyangweso, George (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Wambua, Juliana (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Mwanga, Daniel (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Marsh, Kevin (Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine)

Bejon, Philip (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Kapulu, Melissa C. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Harvard Dataverse

Muthui, Michelle K

Kapulu, Melissa C.

Muthui, Michelle K.

2019-03-12

https://doi.org/10.7910/DVN/18QB3V

Medicine, Health and Life Sciences

<p>Data from a longitudinally monitored cohort of children from Kilifi county located along the Kenyan coast collected between 1998-2016 were analysed to describe the distribution and prevalence of gametocytaemia in relation to transmission intensity, time and age. The datasets comprise data from cross-sectional surveys and weekly follow-up visits carried out within the Kilifi Malaria Longitudinal Cohort based in Kilifi County, Kenya on children aged between 0 – 15 years. The datasets were used to carry out analyses aimed at describing the prevalence of gametocyte carriage in this cohort as well as factors that predispose gametocyte carriage. The overall aim of the analyses was to identify prognostic indicators of populations contributing disproportionately to the infectious reservoir of malaria. </p>

Publications based on this data collection should acknowledge this source by means of bibliographic citation. To ensure that such source attributions are captured for bibliographic utilities, citations must appear in footnotes or in the reference section of publications. The bibliographic citation for this data collection is: "Muthui, Michelle K.; Mogeni, Polycarp; Mwai, Kennedy; Nyundo, Christopher; Macharia, Alex; Williams, Thomas N.; Nyangweso, George; Wambua, Juliana; Mwanga, Daniel; Marsh, Kevin; Bejon, Philip; Kapulu, Melissa C., 2019, "Kilifi Malaria Longitudinal Cohort cross-sectional survey and weekly-follow-up surveillance data for the estimation of parasite prevalence and factors associated with gametocyte carriage.", https://doi.org/10.7910/DVN/18QB3V, Harvard Dataverse, V1"

This data is made available under the Creative Commons Attribution 4.0 International (CC BY 4.0) - https://creativecommons.org/licenses/by/4.0/legalcode. Publications based on these data should acknowledge this source by means of bibliographic citations. For more information on these data, please contact the author(s) OR the data governance office via this email address: dgc@kemri-wellcome.org

<p>The data are under restricted access, however, are available through the KEMRI-Wellcome Trust Research Programme Data Governance Committee if the use of the data is complaint with the consent provided by the participants. Details of the criteria can be found in the KEMRI-Wellcome data sharing guidelines (https://kemri-wellcome.org/about-us/#ChildVerticalTab_15). Requests for the data can be made to the Data Governance Committee through the corresponding author.</p> <p>Supporting documentation files - analysis code, codebook, readme file, and supplementary figures - are openly available for all users</p>

• Number of cases: 76

• No. of variables per record: 3

• Type of File: text/tab-separated-values

UNF:6:HCdQf837gliHQwM8Zlrayg==

List of the number of cross-sectional surveys carried out each year for each of the KMLC cohorts

• Number of cases: 16760

• No. of variables per record: 10

• Type of File: text/tab-separated-values

UNF:6:Cx1KBVSGnRZgI+QODOEr0A==

Data from all the cross-sectional surveys carried out between 1998 and 2016 for all participants sampled from the Kilifi Malaria Longitudinal Cohort (KMLC) aged between 0-15 years. This dataset includes information on the cohort the participant is from, their age, sex, blood group, study number and participant identification number. It also includes each participant’s axillary body temperature on day of sampling, the date of the survey and their asexual and sexual parasite density on the day of sampling.

• Number of cases: 557237

• No. of variables per record: 10

• Type of File: text/tab-separated-values

UNF:6:ybdRf6hqPH3IMFXPpHvcUg==

Data from weekly follow-up visits carried out between 1998 and 2016 for all participants sampled from the Kilifi Malaria Longitudinal Cohort (KMLC) aged between 0-15 years. This dataset includes information on the cohort the participant is from, their age, sex, blood group, study number and participant identification number. It also includes the date of the visit and each participant’s axillary body temperature, asexual and sexual parasite density if they reported having a fever or possible symptoms of malaria

• Number of cases: 2213

• No. of variables per record: 3

• Type of File: text/tab-separated-values

UNF:6:SNqLc6iip9AbSp3pMmIokQ==

Data on the sickle cell and α-thalassaemia genotype of each participant included in the analysis for whom this data was available

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Age and parasite prevalence.R

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R code used to plot out the variation in parasite prevalence with age.

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Chi-square analysis.R

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R code used to draw 2 X 2 tables based on asexual and sexual parasite positiviy and carry out chi-square analysis

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Cross-sectional_survey_summary.R

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R code used to plot out the frequency of the different number of cross-sectional surveys attended by the study participants

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Gametocyte Poitivity Model - Recent episodes malaria pre- and post-ACT.R

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R code used to assess malaria episodes occurring before a cross-sectional survey and generate a models to predict gametocyte positivity

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Gametocyte Positivity Models.R

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R code used to generate models to predict gametocyte positivity from select covariates

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Kilifi_Malaria_Longitudinal_Cohort_Codebook KMLC.pdf

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Contains variable descriptions, value labels and formats

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Kilifi_Malaria_Longitudinal_Cohort_Data Readme.txt

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Contains project and dataset(s) description and data access/use statements

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Parasitaemia over time.R

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R code used to plot out the variation in parasite prevalence over time

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Parasite density over time.R

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R code used to plot out the variation in parasite densities over time

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Parasite prevalence by ACT period.R

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R code used to plot the prevalence of parasite densities before and after the introduction of artemisinin combination therapies

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Summary of Parasite Positive Events.R

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R code used to plot the distribution of asexual parasites and gametocytes for each of the cohorts

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Summary of the csbleeds per year per cohort.R

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R code used to plot the number of cross-sectional surveys carried out per year for each of the cohorts

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Summary Statistics - csbleed.R

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R code used to generate summary statistics for participants attending the cross-sectional survey

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Summary statistics - malaria episodes.R

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R code used to identify the total number of malaria episodes for the study participants

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Summary Statistics - wfu.R

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R code used to generate summary statistics for participants surveyed during the weekly follow-up visits

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Supplementary Figure Legends.docx

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Extended data - Supplementary information

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Supplementary tables.docx

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Extended data - Supplementary information

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Supp_figure_1_No. of Cross-sectional surveys attended.eps

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Extended data - Supplementary information

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Supp_fig_1_No. of cross-sectional surveys attended.tif

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Figure 1. Image (eps file format)

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R code.zip

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Zipped package contains all R code files

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Datasets.zip

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Zipped package containing all data files: csbleed_summary.csv imm_csbleed_data.csv imm_weekly_fu_overall.csv sickle.thal data.xlsx

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