Replication Data for: SARS-CoV-2 Omicron Variant of Concern in Seychelles: Introduction and Spread

Version 2.0
Replication Data for: SARS-CoV-2 Omicron Variant of Concern in Seychelles: Introduction and Spread
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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Description

This is a replication dataset for the manuscript titled: "SARS-CoV-2 Omicron Variant of Concern in Seychelles: Introduction and Spread."

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.

Data package includes R and python scripts used to analyze data:

  1. 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.
  2. 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.
  3. Figure3.R
  4. Figure4.R - This r code plots the number of transition events between Seychelles and the rest of world.
  5. 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.
  6. SuppFig2.R - This r code plots the number of transition events between discrete locations i.e within Seychelles
  7. AncestralChanges.py
Subject Medicine, Health and Life Sciences
Keyword Seychelles, Omicron, SARS-CoV-2, COVID-19
Notes

Data Access: Open

License: Creative Commons Attribution 4.0 International

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This data is licensed under the Creative Commons Attribution 4.0 International

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.

Publications based on this data collection should acknowledge this source by means of bibliographic citation.
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Our Community Norms as well as good scientific practices expect that proper credit is given via citation. Please use the data citation shown on the dataset page.

Custom Dataset Terms - the following Custom Dataset Terms have been defined for this dataset.

This data is licensed under the Creative Commons Attribution 4.0 International

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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