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Part 1: Document Description
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Citation |
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Title: |
Replication Data for: Genomic Epidemiology of SARS-CoV-2 in Seychelles, 2020-2021 |
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Identification Number: |
doi:10.7910/DVN/AYT2UA |
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Distributor: |
Harvard Dataverse |
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Date of Distribution: |
2022-03-17 |
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Version: |
2 |
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Bibliographic Citation: |
Morobe, John M., 2022, "Replication Data for: Genomic Epidemiology of SARS-CoV-2 in Seychelles, 2020-2021", https://doi.org/10.7910/DVN/AYT2UA, Harvard Dataverse, V2 |
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Citation |
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Title: |
Replication Data for: Genomic Epidemiology of SARS-CoV-2 in Seychelles, 2020-2021 |
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Identification Number: |
doi:10.7910/DVN/AYT2UA |
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Authoring Entity: |
Morobe, John M. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Distributor: |
Harvard Dataverse |
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Access Authority: |
Agoti, Charles N. |
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Access Authority: |
The Data Governance Committee |
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Depositor: |
Morobe, John Mwita |
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Date of Deposit: |
2022-03-17 |
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Holdings Information: |
https://doi.org/10.7910/DVN/AYT2UA |
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Study Scope |
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Keywords: |
Medicine, Health and Life Sciences, Medicine, Health and Life Sciences |
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Abstract: |
<p>This is a replication dataset for the submitted manuscript: "<a href="">Genomic Epidemiology of SARS-CoV-2 in Seychelles, 2020-2021</a>." The data package contains data and analysis scripts for generating figures included in the manuscript. Whole genome sequences are available from <a href="https://www.gisaid.org/">GISAID</a> database accession number EPI_ISL_4880527 - EPI_ISL_4880796, EPI_ISL_4880796 - EPI_ISL_5943661 and EPI_ISL_6705004 - EPI_ISL_6705093. </p> <p>The related study is part of a regional collaborative COVID-19 public health rapid response initiative overseen by WHO-AFRO and Africa-CDC do decribe the SARS-CoV-2 genomic epidemiology in Africa.</p> <p>Data analysis R code and python script is as provided below; <ol> <li>Figure_1&2_17Feb2022.R - This r code plots the Seychelles government intervention levels, number of daily COVID-19 cases, the temporal patterns of SARS CoV-2 Lineages in Seychelles. </li> <li> Figure3_12March2022.R - This r code plots the lineages-specific phylogenetic tree of Omicron, Alpha, Beta, Delta VOC, and Non-VOC.</li> <li>Figure4_12March2022.R - This r code plots the global time resolved tree and the number of transition events between discrete locations.</li> <li>Supplimentary Figure1_12March2022 - This r code plots the monthly COVID-19 cases and number of samples received at KWTRP for whole genome sequencing.</li> <li>SupplemenataryFigure3a_b_12March2022.R -This r code plots the frequency of amino acid and deletion mutation in Seychelles sequences.</li> <li> AncestralChanges.py</li> </ol> </p> |
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Notes: |
<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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Label: |
AncestralChanges.py |
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Notes: |
text/plain |
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Figure1_2.zip |
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Notes: |
application/zip |
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Figure3-1.zip |
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Notes: |
application/zip |
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Figure4-2.zip |
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Notes: |
application/zip |
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Jmwita_Covid19_Genomics_Seychelles_Codebook.pdf |
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Notes: |
application/pdf |
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JMwita_Covid19_Genomics_Seychelles_Readme.txt |
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Notes: |
text/plain |
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SupplementaryFigure1.zip |
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Notes: |
application/zip |
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Label: |
SupplementaryFigure3.zip |
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Notes: |
application/zip |