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Part 1: Document Description
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Citation |
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Title: |
Replication Data for: SARS-CoV-2 Omicron Variant of Concern in Seychelles: Introduction and Spread |
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Identification Number: |
doi:10.7910/DVN/YA4LXD |
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Distributor: |
Harvard Dataverse |
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Date of Distribution: |
2023-01-16 |
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Version: |
2 |
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Bibliographic Citation: |
Morobe, John Mwita; Pool, Brigitte; Didon, Dwayne; Lambisia, Arnold W.; Makori, Timothy; Mohammed,Khadija S.; Ndwiga, Leonard; Mburu, Maureen W.; Moraa, Edidah; Murunga, Nickson; Musyoki, Jennifer; Moturi, Angela; Namulondo, Joyce; Tembo, Susan Z.; Ogendi, Edwin; Balde, Thierno; Dratibi, Fred A.; Ahmed, Yahaya A.; Gumede, Nicksy; Achilla, Rachel A.; Borus, Peter K.; Wanjohi, Dorcas; Tessema, Sofonias K.; Mwangangi, Joseph; Bejon, Philip; Nokes, D. James; Ochola-Oyier, Lynette Isabella; Githinji, George; Biscornet, Leon; Agoti, Charles N., 2023, "Replication Data for: SARS-CoV-2 Omicron Variant of Concern in Seychelles: Introduction and Spread", https://doi.org/10.7910/DVN/YA4LXD, Harvard Dataverse, V2 |
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Citation |
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Title: |
Replication Data for: SARS-CoV-2 Omicron Variant of Concern in Seychelles: Introduction and Spread |
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Identification Number: |
doi:10.7910/DVN/YA4LXD |
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Authoring Entity: |
Morobe, John Mwita (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Pool, Brigitte (Seychelles Public Health Laboratory, Public Health Authority, Ministry of Health) |
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Didon, Dwayne (Seychelles Public Health Laboratory, Public Health Authority, Ministry of Health) |
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Lambisia, Arnold W. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Makori, Timothy (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Mohammed,Khadija S. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Ndwiga, Leonard (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Mburu, Maureen W. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Moraa, Edidah (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Murunga, Nickson (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Musyoki, Jennifer (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Moturi, Angela (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Namulondo, Joyce (World Health Organization-Seychelles Country Office) |
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Tembo, Susan Z. (World Health Organization-Seychelles Country Office) |
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Ogendi, Edwin (World Health Organization-Seychelles Country Office) |
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Balde, Thierno (World Health Organization Regional Center for Africa) |
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Dratibi, Fred A. (World Health Organization Regional Center for Africa) |
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Ahmed, Yahaya A. (World Health Organization Regional Center for Africa) |
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Gumede, Nicksy (World Health Organization Regional Center for Africa) |
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Achilla, Rachel A. (World Health Organization Regional Center for Africa) |
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Borus, Peter K. (World Health Organization-Kenya Country Office) |
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Wanjohi, Dorcas (Africa Centres for Disease Control and Prevention (Africa CDC) |
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Tessema, Sofonias K. (Africa Centres for Disease Control and Prevention (Africa CDC) |
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Mwangangi, Joseph (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Bejon, Philip (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Nokes, D. James (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Ochola-Oyier, Lynette Isabella (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Githinji, George (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Biscornet, Leon (Seychelles Public Health Laboratory, Public Health Authority, Ministry of Health) |
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Agoti, Charles N. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Distributor: |
Harvard Dataverse |
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Access Authority: |
Morobe, John Mwita |
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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: |
2023-01-16 |
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Holdings Information: |
https://doi.org/10.7910/DVN/YA4LXD |
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Study Scope |
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Keywords: |
Medicine, Health and Life Sciences, Seychelles, Omicron, SARS-CoV-2, COVID-19 |
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Abstract: |
<p>This is a replication dataset for the manuscript titled: "<a href="">SARS-CoV-2 Omicron Variant of Concern in Seychelles: Introduction and Spread</a>."</p> <p>The 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 package includes R and python scripts used to analyze data: <ol> <li>Figure1.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>Figure2.R - This r code plots the Omicron lineages phylogenetic tree of BA.1-like, BA.1-like, BA.1-like, BA.1-like lineages.</li> <li>Figure3.R </li> <li>Figure4.R - This r code plots the number of transition events between Seychelles and the rest of world.</li> <li>SuppFig1.R - This r code plots the number of daily COVID-19 cases from March 2020 to September 2022 and highlights the period when Omicron VOC was circulating.</li> <li>SuppFig2.R - This r code plots the number of transition events between discrete locations i.e within Seychelles</li> <li>AncestralChanges.py</li> </ol> |
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Kind of Data: |
Open Access |
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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> For more information on these data, please get in touch with the author via John Mwita Morobe [jmwita(at)kemri-wellcome.org], Nickson Murunga [nmurunga(at)kemri-wellcome.org], Charles Nyaigoti Agoti [CNyaigoti(at)kemri-wellcome.org] or the data governance office via this email address: dgc(at)kemri-wellcome.org. |
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Other Study Description Materials |
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Label: |
data.zip |
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Text: |
Contains all data files used in the analysis: 5 csv and 4 nexus files |
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Notes: |
application/zip |
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Label: |
gisaid_supplemental_table_epi_set_230119zw.pdf |
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Notes: |
application/pdf |
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Label: |
JMwita_Omicron_Seychelles_Data_Codebook.pdf |
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Notes: |
application/pdf |
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Label: |
JMwita_Omicron_Seychelles_Data_Readme.txt |
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Notes: |
text/plain |
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Label: |
scripts-1.zip |
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Text: |
Contains R scripts used to analyze data. |
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Notes: |
application/zip |
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Label: |
SuppFig1_09012022.pdf |
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Notes: |
application/pdf |
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Label: |
SuppFig2_09012022.pdf |
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Notes: |
application/pdf |
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Label: |
Supplementary_Table1.docx |
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Notes: |
application/vnd.openxmlformats-officedocument.wordprocessingml.document |
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Label: |
Supplementary_Table2.docx |
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Notes: |
application/vnd.openxmlformats-officedocument.wordprocessingml.document |