Replication Data for: Temporal Distribution and Clinical Characteristics of the Alpha, Delta and Omicron SARS-CoV-2 Variants of Concern in Laikipia, Kenya: Institutional and Community-Based Genomic Surveillance (doi:10.7910/DVN/CCUVR6)

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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: Temporal Distribution and Clinical Characteristics of the Alpha, Delta and Omicron SARS-CoV-2 Variants of Concern in Laikipia, Kenya: Institutional and Community-Based Genomic Surveillance

doi:10.7910/DVN/CCUVR6

Harvard Dataverse

2022-08-22

3

Lambisia, Arnold W.; Mudhune,Godfrey H.; Morobe, John M.; Mohammed, Khadija Said; Makori, Timothy N.; Ndwiga, Leonard; Mburu, Maureen W.; Moraa, Edidah O.; Musyoki, Jennifer; Murunga, Nickson; Waliaula, Isaac N.; Mumelo, Arthur K.; Bejon,Philip; Oyier, Isabella Lynette-Ochola; Githinji, George; Nokes, D.James; Agoti, Charles N., 2022, "Replication Data for: Temporal Distribution and Clinical Characteristics of the Alpha, Delta and Omicron SARS-CoV-2 Variants of Concern in Laikipia, Kenya: Institutional and Community-Based Genomic Surveillance", https://doi.org/10.7910/DVN/CCUVR6, Harvard Dataverse, V3, UNF:6:QRSt3EilFzcJf0PplbmS+w== [fileUNF]

Replication Data for: Temporal Distribution and Clinical Characteristics of the Alpha, Delta and Omicron SARS-CoV-2 Variants of Concern in Laikipia, Kenya: Institutional and Community-Based Genomic Surveillance

doi:10.7910/DVN/CCUVR6

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

Mudhune,Godfrey H. (Laikipia Health Service (LHS))

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

Mohammed, Khadija Said (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Makori, Timothy N. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

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

Mburu, Maureen W. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

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

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

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

Waliaula, Isaac N. (Laikipia Health Service (LHS))

Mumelo, Arthur K. (Laikipia Health Service (LHS))

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

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

Githinji, George (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)

Harvard Dataverse

Lambisia, Arnold W.

The Data Governance Committee

Lambisia, Arnold W.

2022-08-22

https://doi.org/10.7910/DVN/CCUVR6

Medicine, Health and Life Sciences, SARS-CoV-2, Kenya, Laikipia, VOC, clinical characteristics

<p>This is a replication dataset for the submitted manuscript titled: "<a href="">Temporal Distribution and Clinical Characteristics of the Alpha, Delta and Omicron SARS-CoV-2 Variants of Concern in Laikipia, Kenya: Institutional and Community-Based Genomic Surveillance</a>"</p> <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 24th April to 31st December 2021 in Laikipia Kenya. Aside from the samples tested and results of the tests, it also contains the patients’ sociodemographic characteristic, cycle threshold and symptoms. The dataset is used to generate new SARS-CoV-2 genome sequences from RT-PCR positive samples collected in Laikipia Kenya. </p>

Open Access

<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>

<p>Publications based on this data collection should acknowledge this source by means of bibliographic citation.</p>

<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>

• Number of cases: 99

• No. of variables per record: 26

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

UNF:6:H2+Vgd3nE4UrnDL+F94Rqw==

• Number of cases: 140

• No. of variables per record: 3

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

UNF:6:oiyQlf2F8q6oTvePCw7F+A==

• id - id
• lineage - lineage
• VOC_lineage - VOC_lineage
• date_collected - date_collected
• IP/OP - IP/OP
• sequelae - sequelae
• vaccination_status - vaccination_status
• gender - gender
• age - age
• age_group2 - age_group2
• fever_1 - fever_1
• SOB_2 - SOB_2
• muscular_pain3 - muscular_pain3
• general_weakness4 - general_weakness4
• diarrhoea_5 - diarrhoea_5
• chest_pain6 - chest_pain6
• cough_7 - cough_7
• nausea_8 - nausea_8
• abdominal_pain9 - abdominal_pain9
• sore_throat10 - sore_throat10
• headache_11 - headache_11
• joint_pain12 - joint_pain12
• runny_nose13 - runny_nose13
• irritation_14 - irritation_14
• justification - justification
• patient_status - patient_status
• id - id
• daan_N_gene_ct - daan_N_gene_ct
• sequenced - sequenced

f6424742 Location:

Variable Format: character

Notes: UNF:6:HrAhON3DnuyB3i8UbbxMhQ==

f6424742 Location:

Variable Format: character

Notes: UNF:6:+lVOIcF9A3hO1Gz+2v+aEw==

f6424742 Location:

Variable Format: character

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f6424742 Location:

Variable Format: character

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f6424742 Location:

Variable Format: character

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f6424742 Location:

Variable Format: character

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f6424742 Location:

Variable Format: character

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f6424742 Location:

Variable Format: character

Notes: UNF:6:0A0wCDqyxc8Wuk+tq8Nd9Q==

f6424742 Location:

Summary Statistics: Valid 96.0; Max. 93.0; Min. 3.0; Mean 38.11458333333333; StDev 15.245962220702499;

Variable Format: numeric

Notes: UNF:6:8eDL4D8f5f9tSmCVzoH7ag==

f6424742 Location:

Variable Format: character

Notes: UNF:6:1C8EaN4rIE5wbUFnBu6EhQ==

f6424742 Location:

Variable Format: character

Notes: UNF:6:9qRcp3wCrqwDPPBzklnb9g==

f6424742 Location:

Variable Format: character

Notes: UNF:6:i/VxaLjGoiQMYsV1FoLKAA==

f6424742 Location:

Variable Format: character

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f6424742 Location:

Variable Format: character

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Variable Format: character

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f6424742 Location:

Variable Format: character

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f6424742 Location:

Variable Format: character

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f6424742 Location:

Variable Format: character

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f6424742 Location:

Variable Format: character

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f6424742 Location:

Variable Format: character

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f6424742 Location:

Variable Format: character

Notes: UNF:6:RvGYVb5wJTY3n012uSVTOw==

f6424742 Location:

Variable Format: character

Notes: UNF:6:U0wFSrpEcQl8bMc5Vfj4DA==

f6424742 Location:

Variable Format: character

Notes: UNF:6:slz4YBvHXYTk8zgmKQtu3A==

f6424742 Location:

Variable Format: character

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f6424742 Location:

Variable Format: character

Notes: UNF:6:tcodH7NtnAC5vwMJBQpDNA==

f6424742 Location:

Variable Format: character

Notes: UNF:6:hDZQJhy2GD0RYhL/0p63iA==

f6424745 Location:

Summary Statistics: Min. 1.0; Valid 140.0; Max. 140.0; Mean 70.5; StDev 40.55859958134649;

Variable Format: numeric

Notes: UNF:6:v3oVHFk4SrtByUM0B9+bGg==

f6424745 Location:

Summary Statistics: Max. 38.97; Min. 12.94; Valid 132.0; Mean 26.340378787878787; StDev 6.778321461848596

Variable Format: numeric

Notes: UNF:6:PGB8ap4s6E8Abom8d+8waQ==

f6424745 Location:

Variable Format: character

Notes: UNF:6:nWsLSfiCm+ksdp9sXaMhoQ==

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ALambisia_Laikipia_Data_Codebook.pdf

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ALambisia_Laikipia_Data_Readme.txt

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Figures_LKP_Manuscript.R

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supplementary Figure 1.png

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Supplementary table 1-1.csv

text/comma-separated-values

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Supplementary table 1.csv

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Tables_Rmarkdown.Rmd

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