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Part 1: Document Description
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Citation |
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Title: |
Replication Data for: Whole genome sequencing of two human rhinovirus A types (A101 and A15) detected in Kenya, 2016-2018 |
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Identification Number: |
doi:10.7910/DVN/QGXZLI |
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Distributor: |
Harvard Dataverse |
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Date of Distribution: |
2021-05-20 |
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Version: |
1 |
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Bibliographic Citation: |
Luka, Martha M.; Kamau, Everlyn; de Laurent, Zaydah R.; Morobe, John M.; Alii, Leonard K.; Nokes, David James; Agoti, Charles N., 2021, "Replication Data for: Whole genome sequencing of two human rhinovirus A types (A101 and A15) detected in Kenya, 2016-2018", https://doi.org/10.7910/DVN/QGXZLI, Harvard Dataverse, V1, UNF:6:sHiQY2P6RU/NhRKOoAUfXw== [fileUNF] |
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Citation |
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Title: |
Replication Data for: Whole genome sequencing of two human rhinovirus A types (A101 and A15) detected in Kenya, 2016-2018 |
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Identification Number: |
doi:10.7910/DVN/QGXZLI |
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Authoring Entity: |
Luka, Martha M. (Kemri-Wellcome Trust Research Programme, Kilifi, Kenya; Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya) |
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Kamau, Everlyn (Kemri-Wellcome Trust Research Programme, Kilifi, Kenya; Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya) |
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de Laurent, Zaydah R. (Kemri-Wellcome Trust Research Programme, Kilifi, Kenya; Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya) |
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Morobe, John M. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Alii, Leonard K. (Department of Mathematics and Computer Science, Pwani University, Kilifi, Kenya.) |
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Nokes, David James (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya; School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK.) |
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Agoti, Charles N. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya; Department of Public Health, Pwani University, Kilifi, Kenya) |
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Grant Number: |
102975 |
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Grant Number: |
U2RTW010677 |
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Grant Number: |
DEL-15-003 |
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Distributor: |
Harvard Dataverse |
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Access Authority: |
Luka, Martha M. |
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Access Authority: |
Agoti, Charles N. |
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Access Authority: |
The Data Governance Committee |
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Depositor: |
Luka, Martha M. |
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Date of Deposit: |
2021-05-19 |
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Holdings Information: |
https://doi.org/10.7910/DVN/QGXZLI |
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Study Scope |
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Keywords: |
Medicine, Health and Life Sciences, human rhinovirus, whole-genome, sequencing, phylogenetics |
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Abstract: |
<p>This is a replication dataset for the manuscript titled: "<a href="">Whole genome sequencing of two human rhinovirus A types (A101 and A15) detected in Kenya, 2016-2018</a>." The dataset contains contains Cycle threshold (Ct) values, and read/sequencing depth. </p> <p>The related study utilized nasopharyngeal swabs collected during two previous studies in Kilifi County, coastal Kenya: outpatient surveillance of nine health dispensaries within the Kilifi Health and Demographic Surveillance System (KHDSS) between January and December 2016 and primary school surveillance between May 2017 and April 2018. All samples were collected from symptomatic individuals (mild symptoms of acute respiratory tract infection) of varied age (1 month - 49 years) and archived at -80°C. Samples were screened for HRV and typed as previously described8. A cycle threshold (Ct) value < 35.0 was used to define positives. HRV positives underwent VP4/2 sequencing to characterize the diversity, spatial and temporal occurrence of HRV in the two settings. Comparison of the HRV diversity within the school in Junju and the health dispensary located in Junju revealed 12 common types, and the most frequent common type was HRV-A101 (n=5 in each setting). </p> |
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Notes: |
<p>The assembled sequences are available in the GenBank database under accession numbers MW713746-MW713793. The raw data are available in the <a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA701406/">NCBI SRA archive under</a> BioProject accession number <a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA701406/">PRJNA701406</a>. </p> <p><strong>Data Access:</strong> Open </p> <p><strong>License:</strong> <a href="https://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</a> <a href="https://creativecommons.org/licenses/by/4.0/legalcode"><img src="https://i.creativecommons.org/l/by/3.0/88x31.png"> </a></p> |
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Methodology and Processing |
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Sources Statement |
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Data Access |
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Citation Requirement: |
<p>Publications based on this data collection should acknowledge this source by means of bibliographic citation.</p> |
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Notes: |
<p>This data is licensed under the <a href="https://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</a> <a href="https://creativecommons.org/licenses/by/4.0/legalcode"><img src="https://i.creativecommons.org/l/by/3.0/88x31.png"> </a> </p> |
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Other Study Description Materials |
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Related Publications |
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Citation |
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Title: |
Morobe, J.M., Nyiro, J.U., Brand, S., Kamau, E., Gicheru, E., Eyase, F., Otieno, G.P., Munywoki, P.K., Agoti, C.N. and Nokes, D.J., 2018. Human rhinovirus spatial-temporal epidemiology in rural coastal Kenya, 2015-2016, observed through outpatient surveillance. Wellcome open research, 3. |
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Identification Number: |
10.12688%2Fwellcomeopenres.14836.2 |
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Bibliographic Citation: |
Morobe, J.M., Nyiro, J.U., Brand, S., Kamau, E., Gicheru, E., Eyase, F., Otieno, G.P., Munywoki, P.K., Agoti, C.N. and Nokes, D.J., 2018. Human rhinovirus spatial-temporal epidemiology in rural coastal Kenya, 2015-2016, observed through outpatient surveillance. Wellcome open research, 3. |
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Citation |
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Title: |
Luka, M.M., Kamau, E., Adema, I., Munywoki, P.K., Otieno, G.P., Gicheru, E., Gichuki, A., Kibinge, N., Agoti, C.N. and Nokes, D.J., 2020, October. Molecular Epidemiology of Human Rhinovirus From 1-Year Surveillance Within a School Setting in Rural Coastal Kenya. In Open forum infectious diseases (Vol. 7, No. 10, p. ofaa385). US: Oxford University Press. |
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Identification Number: |
10.1093/ofid/ofaa385 |
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Bibliographic Citation: |
Luka, M.M., Kamau, E., Adema, I., Munywoki, P.K., Otieno, G.P., Gicheru, E., Gichuki, A., Kibinge, N., Agoti, C.N. and Nokes, D.J., 2020, October. Molecular Epidemiology of Human Rhinovirus From 1-Year Surveillance Within a School Setting in Rural Coastal Kenya. In Open forum infectious diseases (Vol. 7, No. 10, p. ofaa385). US: Oxford University Press. |
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File Description--f4724092 |
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File: spred.tab |
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Notes: |
UNF:6:sHiQY2P6RU/NhRKOoAUfXw== |
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Label: |
HiLiter.py |
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Notes: |
text/plain |
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Label: |
LukaMM_spred_script.R |
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Notes: |
type/x-r-syntax |
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Label: |
MLuka_SPRED_Codebook.pdf |
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Notes: |
application/pdf |
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Label: |
MLuka_SPRED_data_Readme.txt |
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Notes: |
text/plain |