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Part 1: Document Description
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Citation |
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Title: |
Replication Data for: Rotavirus group A genotype circulation patterns across Kenya before and after nationwide vaccine introduction, 2010-2018 |
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Identification Number: |
doi:10.7910/DVN/0VQ2OK |
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Distributor: |
Harvard Dataverse |
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Date of Distribution: |
2020-06-30 |
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Version: |
1 |
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Bibliographic Citation: |
Mwanga, Mike J.; Owor, Betty E.; Ochieng, John B.; Odundo, elizabeth; Ngama, Mwanajuma; Ogwel, Billy; Onyango, clayton; Juma, Jane; Njeru, Regina; Gicheru, Elijah; Otieno, Grieven P.; Khagayi, Sammy; Agoti, Charles N.; Omore, Richard; Bigogo, Godfrey M.; Addo O. Yaw; Seheri, Mapaseka; Tate, Jacqueline E.; Parashar, Umesh D.; Hunsperger Elizabeth; Verani, Jennifer R.; Breiman, Robert F.; Nokes, D. James, 2020, "Replication Data for: Rotavirus group A genotype circulation patterns across Kenya before and after nationwide vaccine introduction, 2010-2018", https://doi.org/10.7910/DVN/0VQ2OK, Harvard Dataverse, V1, UNF:6:B6X36oRA5IhzQ/2U6PxSdg== [fileUNF] |
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Citation |
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Title: |
Replication Data for: Rotavirus group A genotype circulation patterns across Kenya before and after nationwide vaccine introduction, 2010-2018 |
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Identification Number: |
doi:10.7910/DVN/0VQ2OK |
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Authoring Entity: |
Mwanga, Mike J. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Owor, Betty E. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Ochieng, John B. (Kenya Medical Research Institute, Center for Global Health Research (KEMRI-CGHR), Kisumu) |
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Odundo, elizabeth (United States Army Medical Research Directorate-Kenya (USAMRU-K)) |
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Ngama, Mwanajuma (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Ogwel, Billy (Kenya Medical Research Institute, Center for Global Health Research (KEMRI-CGHR), Kisumu) |
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Onyango, clayton (Kenya Medical Research Institute, Center for Global Health Research (KEMRI-CGHR), Kisumu) |
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Juma, Jane (Kenya Medical Research Institute, Center for Global Health Research (KEMRI-CGHR), Kisumu) |
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Njeru, Regina (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Gicheru, Elijah (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Otieno, Grieven P. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Khagayi, Sammy (Kenya Medical Research Institute, Center for Global Health Research (KEMRI-CGHR), Kisumu) |
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Agoti, Charles N. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Omore, Richard (Kenya Medical Research Institute, Center for Global Health Research (KEMRI-CGHR), Kisumu) |
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Bigogo, Godfrey M. (Kenya Medical Research Institute, Center for Global Health Research (KEMRI-CGHR), Kisumu) |
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Addo O. Yaw (Global Health Institute – Emory University, Atlanta, GA USA) |
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Seheri, Mapaseka (Department of Virology, South African Medical Research Council/Diarrheal Pathogens Research Unit, Sefako Makgatho Health Sciences University, Pretoria, South Africa) |
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Tate, Jacqueline E. (Division of Viral Diseases, US Center for Disease Control and Prevention, Atlanta, GA USA) |
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Parashar, Umesh D. (Division of Viral Diseases, US Center for Disease Control and Prevention, Atlanta, GA USA) |
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Hunsperger Elizabeth (Division of Global Health Protection, Centers for Disease Control and Prevention, Nairobi, Kenya) |
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Verani, Jennifer R. (Division of Global Health Protection, Centers for Disease Control and Prevention, Nairobi, Kenya) |
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Breiman, Robert F. (Global Health Institute – Emory University, Atlanta, GA USA) |
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Nokes, D. James (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Distributor: |
Harvard Dataverse |
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Access Authority: |
Mwanga, Mike J. |
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Access Authority: |
Verani, Jennifer R. |
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Access Authority: |
Nokes, D. James |
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Depositor: |
Mwanga, Mike J. |
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Date of Deposit: |
2019-10-30 |
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Holdings Information: |
https://doi.org/10.7910/DVN/0VQ2OK |
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Study Scope |
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Keywords: |
Medicine, Health and Life Sciences |
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Abstract: |
<p>These data was derived from stool samples collected from children with acute gastroenteritis, who reported to Kilifi County Hospital, Siaya County Referral Hospital, Lwak Mission Hospital and Tabitha Clinic in Kibera Nairobi, with diarrhoea symptoms. The surveillance was conducted between January 2010 to December 2018. The study was aimed at describing the distribution, circulation patterns of group A rotavirus (RVA) strains circulating Kenya. This will ultimately be important in estimating the performance of a Rotavirus vaccine that was introduced in mid 2014, in Kenya.</p> <p>Sequence data was derived from Rotavirus positive samples identified by enzyme immunoassay method (ELISA) and subsequently sequenced by the di-deoxy Sanger method. After read assembly and sequence clean-up, G (derived from the VP7 glycoprotein) and P (derived from VP4 protease sensitive protein), genotypes were determined by use of NCBI BLAST and VIPR an established online RVA genotyping tool. The data was then analyzed in excel and R.</p> <p>Multiple sequence alignment was performed using MAFFT tool. Sequence visualization was undertaken using AliView. Phylogenetic trees were inferred in iqtree and visualized using Figtree. Nucleotide distances matrixes were prepared using the p-distance algorithm inferred in MEGA v10.</p> |
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Notes: |
<strong>Data Access</strong> <p>Access to these data requires submission of a formal request for consideration by our Data Governance Committee. </p> <strong>How to request</strong> <ol> <li>Download and complete the <a href="https://kemri-wellcome.org/wp-content/uploads/2016/02/Data-Sharing-guidelines-External-requests.docx"><strong>data request form</strong></a></li> <li> Email completed data request form to the Data Governance Committee at <a href="mailto:dgc@kemri-wellcome.org?cc=lmwango@kemri-wellcome.org?Subject=Data%20Access%20Request"><strong>dgc@kemri-wellcome.org</strong></a> </li> </ol> |
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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: |
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. |
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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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For access to data and more detailed information beyond the metadata and documentation provided, there is a process of managed access requiring submission of a request form for consideration by our Data Governance Committee [<a href="mailto:dgc@kemri-wellcome.org">dgc@kemri-wellcome.org</a> ]. <strong> <a href="https://kemri-wellcome.org/wp-content/uploads/2016/02/Data-Sharing-guidelines-External-requests.docx">Click to download Data Request Form</a></strong> |
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Other Study Description Materials |
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File Description--f3907851 |
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File: Genotype_Data.tab |
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Notes: |
UNF:6:B6X36oRA5IhzQ/2U6PxSdg== |
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Analysis datasets (Ms Excel) |
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Label: |
Figure_1.R |
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Notes: |
type/x-r-syntax |
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Label: |
Figure_2.R |
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Notes: |
type/x-r-syntax |
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Label: |
RIPEK_Genotype_Data_Readme.txt |
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Text: |
Data descriptor |
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Notes: |
text/plain |
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Label: |
Software_Code_Readme.txt |
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Text: |
Instructions on how to run analysis scripts |
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Notes: |
text/plain |
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Label: |
Supplementary_Figure_1.R |
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Notes: |
type/x-r-syntax |