Replication Data for: Epidemiological insights from genomic analyses of the SARS-CoV-2 infection wave in coastal Kenya, 2023-24 (doi:10.7910/DVN/BMCJTI)

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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

Replication Data for: Epidemiological insights from genomic analyses of the SARS-CoV-2 infection wave in coastal Kenya, 2023-24

doi:10.7910/DVN/BMCJTI

Harvard Dataverse

2025-01-22

1

Lambisia, Arnold W.; Katama, Esther N.; Ochola-Oyier, Isabella; Agoti, Charles N., 2025, "Replication Data for: Epidemiological insights from genomic analyses of the SARS-CoV-2 infection wave in coastal Kenya, 2023-24", https://doi.org/10.7910/DVN/BMCJTI, Harvard Dataverse, V1, UNF:6:+Fycv3F2m7MyWKQZrmgbBw== [fileUNF]

Replication Data for: Epidemiological insights from genomic analyses of the SARS-CoV-2 infection wave in coastal Kenya, 2023-24

doi:10.7910/DVN/BMCJTI

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

Katama, Esther N. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

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

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

Harvard Dataverse

Lambisia, Arnold W.

The Data Governance Committee

Lambisia, Arnold W.

2025-01-22

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

Medicine, Health and Life Sciences, COVID-19, SARS-CoV-2, Omicron, XBB.2.3, JN.1, Reinfections, Coastal Kenya

<p>This is a replication dataset for the manuscript titled: "<i><strong>Epidemiological insights from genomic analyses of the SARS-CoV-2 infection wave in coastal Kenya, 2023-24</strong></i>." <p>The datasets are part of ongoing SARS-CoV-2 surveillance either in the outpatient, inpatient and community within the KHDSS in coastal Kenya. Dataset1 shows the temporal distribution of sample tested and cases positive across the three studies. Dataset2 contains individual case data with demographic characteristics (age, sex etc.), clinical characteristics (including symptoms status, fever, cough among others) and genomic characteristics (variant, nextclade lineage and genome coverage).</p>

Open Access

The Data Governance Committee, dgc@kemri-wellcome.org

• Number of cases: 70

• No. of variables per record: 6

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

UNF:6:1U6f60FeCsKSdtry5rQlyw==

• Number of cases: 247

• No. of variables per record: 25

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

UNF:6:ji0e+r04uRgUUoEKTTc2eA==

• year - year
• week - week
• tested - tested
• cases - cases
• prop - prop
• platform - platform
• serial - serial
• date_collect - date_collect
• sex - sex
• coughing - coughing
• headache - headache
• fever - fever
• vomiting - vomiting
• diarrhea - diarrhea
• sore_throat - sore_throat
• chest_pains - chest_pains
• difficulty_breathing - difficulty_breathing
• joint_pains - joint_pains
• nausea - nausea
• wheezing - wheezing
• symptom_status - symptom_status
• s_cov_2_e - s_cov_2_e
• study - study
• clade - clade
• nextclade_pango - nextclade_pango
• coverage - coverage
• lineage2 - lineage2
• age_days - age_days
• age_years - age_years
• sequenced_status - sequenced_status
• age_group - age_group

f10839784 Location:

Summary Statistics: Max. 2024.0; Valid 70.0; Mean 2023.6142857142856; StDev 0.490278156567732; Min. 2023.0

Variable Format: numeric

Notes: UNF:6:XwII+rveThJkAmMYaVQjRw==

f10839784 Location:

Summary Statistics: StDev 20.36713241513726; Min. 1.0; Valid 70.0; Max. 52.0; Mean 22.814285714285713;

Variable Format: numeric

Notes: UNF:6:34yc3ikPWbwqciqbAgHgSA==

f10839784 Location:

Summary Statistics: StDev 194.6492604033454; Max. 613.0; Mean 164.68571428571425; Valid 70.0; Min. 0.0;

Variable Format: numeric

Notes: UNF:6:9iUy9z8sGdr/vxe4Bqwf2g==

f10839784 Location:

Summary Statistics: StDev 6.816509613624067; Max. 30.0; Min. 0.0; Valid 70.0; Mean 4.357142857142854;

Variable Format: numeric

Notes: UNF:6:x1kWiwzK5B3c83biQHWbMw==

f10839784 Location:

Summary Statistics: Valid 70.0; Min. 0.0; Mean 3.7733303228571433; StDev 6.486699048852563; Max. 33.33333;

Variable Format: numeric

Notes: UNF:6:+YZcWvyKrUBpB6I71170OQ==

f10839784 Location:

Variable Format: character

Notes: UNF:6:tSj3XeITNaTt1MqC6x1DBQ==

f10839774 Location:

Summary Statistics: StDev 71.44695001654492; Min. 1.0; Mean 124.0; Max. 247.0; Valid 247.0;

Variable Format: numeric

Notes: UNF:6:fk1JOsScqOMlUNj0TZSR/g==

f10839774 Location:

Summary Statistics: Valid 247.0; Max. 2024.0; StDev 0.49473046910015117; Min. 2023.0; Mean 2023.421052631579;

Variable Format: numeric

Notes: UNF:6:KrnAvmxyu7zBiXqf6oUsNQ==

f10839774 Location:

Variable Format: character

Notes: UNF:6:jD7PtgdeFZ4wPmKXWvAQEQ==

f10839774 Location:

Variable Format: character

Notes: UNF:6:CSK9dOu56lkFkOQAf0OpTw==

f10839774 Location:

Variable Format: character

Notes: UNF:6:ducgMPjSTavrRB6Bipgm6g==

f10839774 Location:

Variable Format: character

Notes: UNF:6:LAeytrHQPKZS89rX54yibQ==

f10839774 Location:

Variable Format: character

Notes: UNF:6:5wxVnY8kwezV4oMvUAjPig==

f10839774 Location:

Variable Format: character

Notes: UNF:6:nu40Pf+u/Is8bt4+1CBoAg==

f10839774 Location:

Variable Format: character

Notes: UNF:6:LLBKWPRdxF4wr4Fzm0KTYQ==

f10839774 Location:

Variable Format: character

Notes: UNF:6:G5DAgedntCUYtLOHP1GkuQ==

f10839774 Location:

Variable Format: character

Notes: UNF:6:f4WSxjS8MZRlDkrbdr9ZEg==

f10839774 Location:

Variable Format: character

Notes: UNF:6:XKlcm+cxDbyUVKtPSmpdIQ==

f10839774 Location:

Variable Format: character

Notes: UNF:6:XiZIUYM37jDZ5HYWuHNwvg==

f10839774 Location:

Variable Format: character

Notes: UNF:6:94tBo8oqQ69nkzj9PjmQpw==

f10839774 Location:

Variable Format: character

Notes: UNF:6:3pW3Y+6zz35R2Y4gUfLW9w==

f10839774 Location:

Summary Statistics: Max. 34.999001; Min. 18.486; StDev 4.0873471585341035; Mean 27.697569072874494; Valid 247.0

Variable Format: numeric

Notes: UNF:6:jcUquCj/LGH0RfLhII4ukQ==

f10839774 Location:

Variable Format: character

Notes: UNF:6:oPCdvcG8sGopelSNw88jrQ==

f10839774 Location:

Variable Format: character

Notes: UNF:6:0N1Qsq5Esz8LcHJ3fh6F/g==

f10839774 Location:

Variable Format: character

Notes: UNF:6:UVX1aj+Z+rXdc8gGAu+GEg==

f10839774 Location:

Summary Statistics: Valid 185.0; Max. 0.998261044; Mean 0.9616330641135136; Min. 0.713640772; StDev 0.04892169978107212;

Variable Format: numeric

Notes: UNF:6:SOb5V+Wi2GY0OAWIVVco+Q==

f10839774 Location:

Variable Format: character

Notes: UNF:6:oviX0k/KowLvYemYGYm6RA==

f10839774 Location:

Summary Statistics: Min. 1.0; Mean 7561.6315789473665; Max. 37818.0; StDev 7831.91610345253; Valid 247.0;

Variable Format: numeric

Notes: UNF:6:bp6Ux++BZq/5axFrmjNG+A==

f10839774 Location:

Summary Statistics: Min. 0.003; StDev 21.345234961352865; Mean 20.35583400804616; Valid 247.0; Max. 100.0;

Variable Format: numeric

Notes: UNF:6:SL107Bz9fQJ5AVpWbyosOw==

f10839774 Location:

Variable Format: character

Notes: UNF:6:KW9p51CknU8LXTqAQvaRVA==

f10839774 Location:

Variable Format: character

Notes: UNF:6:50EqKxGFbZyev5emI7seYg==

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Fig1.R

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Lambisia_SARS_CoV_2_codebook.pdf

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Lambisia_SARS_CoV_2_Readme.txt

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Tables_Figures.Rmd

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