Replication Data for: A new Omicron lineage with Spike Y451H mutation dominating a new COVID-19 wave in Kilifi, Coastal Kenya: March-May 2023 (doi:10.7910/DVN/ZMGR5P)

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Part 1: Document Description
Part 2: Study Description
Part 3: Data Files Description
Part 4: Variable Description
Part 5: Other Study-Related Materials
Entire Codebook

Document Description

Citation

Title:

Replication Data for: A new Omicron lineage with Spike Y451H mutation dominating a new COVID-19 wave in Kilifi, Coastal Kenya: March-May 2023

Identification Number:

doi:10.7910/DVN/ZMGR5P

Distributor:

Harvard Dataverse

Date of Distribution:

2023-06-30

Version:

2

Bibliographic Citation:

Mwanga, Mike J.; Lambisia, Anorld W.; Morobe, John M.; Murunga, Nickson; Cheruiyot, Robinson; Moraa, Edidah O.; Ndwiga, Leonard; Mutunga, Martin; Laura,Guzman-Rincon; Musyoki, Jennifer; Sande, Charles; Mwangangi, Joseph; Bejon, Philip; Oyier, Isabella Lynette-Ochola; Nokes, D. James; Agoti, Charles N.; Nyiro, Joyce; Githinji, George, 2023, "Replication Data for: A new Omicron lineage with Spike Y451H mutation dominating a new COVID-19 wave in Kilifi, Coastal Kenya: March-May 2023", https://doi.org/10.7910/DVN/ZMGR5P, Harvard Dataverse, V2, UNF:6:q6pTyD3YKStTyrKYHjqbfg== [fileUNF]

Study Description

Citation

Title:

Replication Data for: A new Omicron lineage with Spike Y451H mutation dominating a new COVID-19 wave in Kilifi, Coastal Kenya: March-May 2023

Identification Number:

doi:10.7910/DVN/ZMGR5P

Authoring Entity:

Mwanga, Mike J. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Lambisia, Anorld W. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Morobe, John M. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Murunga, Nickson (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Cheruiyot, Robinson (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Moraa, Edidah O. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Ndwiga, Leonard (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Mutunga, Martin (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Laura,Guzman-Rincon (Mathematics Institute, University of Warwick)

Musyoki, Jennifer (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Sande, Charles (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Mwangangi, Joseph (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Bejon, Philip (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Oyier, Isabella Lynette-Ochola (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Nokes, D. James (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Agoti, Charles N. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Nyiro, Joyce (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Githinji, George (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Distributor:

Harvard Dataverse

Access Authority:

Mwanga, Mike J.

Access Authority:

The Data Governance Committee

Depositor:

Mwanga, Mike J.

Date of Deposit:

2023-06-30

Holdings Information:

https://doi.org/10.7910/DVN/ZMGR5P

Study Scope

Keywords:

Medicine, Health and Life Sciences, FY.4, Kenya

Abstract:

<p>This dataset is part of a study that investigated the genomic epidemiology of SARS-CoV-2 in Kenya. This dataset contains results of samples positive for SARS-COV-2 by real-time PCR for the period 1st January to 27th May 2023 from Kilifi. Aside from the samples tested and results of the tests, it also contains the patients’ sociodemographic characteristic and and symptoms. The dataset is used to generate new SARS-CoV-2 genome sequences from RT-PCR positive samples collected in Kilifi. Furthermore, sequenced data from SARS-CoV-2 positive samples gathered in Nairobi, Lamu, Kwale, Mombasa, and Kwale have also been incorporated in the analysis. </p>

Methodology and Processing

Sources Statement

Data Access

Other Study Description Materials

File Description--f7225022

File: country_FY4.tab

  • Number of cases: 21

  • No. of variables per record: 4

  • Type of File: text/tab-separated-values

Notes:

UNF:6:PBBiVNAZ+VZ83QqkZLEtoQ==

File Description--f7225021

File: gisaid_map.tab

  • Number of cases: 1

  • No. of variables per record: 2

  • Type of File: text/tab-separated-values

Notes:

UNF:6:5J5RopfK5fYi4lG96pa4Fg==

Variable Description

List of Variables:

Variables

area

f7225022 Location:

Variable Format: character

Notes: UNF:6:l/4MEO2tGFKjrVX5SkJ7xg==

Week.prior.to

f7225022 Location:

Variable Format: character

Notes: UNF:6:70QXDCvmyFk0My/ZK3KEqQ==

lineage

f7225022 Location:

Variable Format: character

Notes: UNF:6:szdGGpfoJ2GjBdr4wcf7Dg==

total

f7225022 Location:

Summary Statistics: Max. 29.0; Mean 5.7142857142857135; Valid 21.0; StDev 7.669047249449289; Min. 1.0

Variable Format: numeric

Notes: UNF:6:3AUrkuDdXnrnWMkx0ulaWw==

lineage

f7225021 Location:

Variable Format: character

Notes: UNF:6:uNnCRH9Vf4vmI+zli5zuQQ==

lineage_group

f7225021 Location:

Variable Format: character

Notes: UNF:6:PzkWaqUWPTxo1+xYdLoQEw==

Other Study-Related Materials

Label:

FY4_Dataset_Codebook_MM_V1.pdf

Notes:

application/pdf

Other Study-Related Materials

Label:

FY4_Dataset_Readme_MM_V1.txt

Notes:

text/plain

Other Study-Related Materials

Label:

kenya_summary.txt

Notes:

text/plain

Other Study-Related Materials

Label:

kilifi_variants.txt

Notes:

text/plain

Other Study-Related Materials

Label:

Metadata_FY.xlsx

Notes:

application/vnd.openxmlformats-officedocument.spreadsheetml.sheet

Other Study-Related Materials

Label:

sarscov_2_positives.xls

Notes:

application/vnd.ms-excel

Other Study-Related Materials

Label:

scripts.zip

Notes:

application/zip

Other Study-Related Materials

Label:

sequence_accession_numbers.pdf

Notes:

application/pdf