Replication Data for: Genomic epidemiology of Human Adenovirus F40 and F41 in Coastal Kenya: A retrospective hospital-based surveillance study (2013-2022) (doi:10.7910/DVN/AMP10S)

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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
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Replication Data for: Genomic epidemiology of Human Adenovirus F40 and F41 in Coastal Kenya: A retrospective hospital-based surveillance study (2013-2022)

doi:10.7910/DVN/AMP10S

Harvard Dataverse

2022-10-21

1

Lambisia, Arnold W.; Makori, Timothy N.; Murunga, Nickson; Cheruiyot, Robinson; Quick, Joshua; Githinji, George; Nokes, D.James; Houldcroft, Charlotte J.; Agoti, Charles N., 2022, "Replication Data for: Genomic epidemiology of Human Adenovirus F40 and F41 in Coastal Kenya: A retrospective hospital-based surveillance study (2013-2022)", https://doi.org/10.7910/DVN/AMP10S, Harvard Dataverse, V1, UNF:6:Lv+MfbmNzuUN9+4u1fJL3g== [fileUNF]

Replication Data for: Genomic epidemiology of Human Adenovirus F40 and F41 in Coastal Kenya: A retrospective hospital-based surveillance study (2013-2022)

doi:10.7910/DVN/AMP10S

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

Makori, Timothy N. (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)

Quick, Joshua (University of Birmingham)

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

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

Houldcroft, Charlotte J. (University of Cambridge, CB2 3EH, UK)

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

Harvard Dataverse

Lambisia, Arnold W.

Agoti, Charles N.

The Data Governance Committee

Lambisia, Arnold W.

2022-10-21

https://doi.org/10.7910/DVN/AMP10S

Medicine, Health and Life Sciences, Human adenovirus F, Kenya, recombination, F40/41

<p>This is a replication dataset for the manuscript titled:"<a href="">Genomic epidemiology of Human Adenovirus F40 and F41 in Coastal Kenya: A retrospective hospital-based surveillance study (2013-2022)</a>." <p>This dataset is part of a study investigating diarrhoeal illness among children below the age of 13 years at the Kilifi County Hospital paediatric ward. This dataset contains results of samples positive for human adenovirus F by real-time PCR for the period 17th April 2013 to 2nd May 2022 in Kilifi Kenya. Aside from the samples tested and results of the tests, it also contains the patients’ sociodemographic characteristics, cycle threshold and symptoms. The dataset generates new human adenovirus F genome sequences from RT-PCR positive samples collected in Kilifi Kenya. </p>

<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: 88

• No. of variables per record: 16

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

UNF:6:F5SMwb8mP/EEASeYohPkGg==

• Number of cases: 117

• No. of variables per record: 3

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

UNF:6:zUSX9o7ThtIsDt+SagkMtA==

• Number of cases: 117

• No. of variables per record: 3

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

UNF:6:zUSX9o7ThtIsDt+SagkMtA==

• serial - serial
• CT_Value - CT_Value
• gvov - gvov
• Genotypes - Genotypes
• date_a - date_a
• age_months - age_months
• sex - sex
• elisa - elisa
• temp - temp
• vomiting_durn - vomiting_durn
• vomiting_episode - vomiting_episode
• diarrhoea_durn - diarrhoea_durn
• diarrhoea_episode - diarrhoea_episode
• dehydration_status - dehydration_status
• treatment_type - treatment_type
• outcome - outcome
• month
• year
• diarrhoea - (sum) diarrhoea
• month - month
• year - year
• diarrhoea - diarrhoea

f6579821 Location:

Summary Statistics: Mean 42.0; Valid 83.0; Min. 1.0; Max. 83.0; StDev 24.1039415863879;

Variable Format: numeric

Notes: UNF:6:W3iM+RQTM+NtdH3mKSKW4A==

f6579821 Location:

Summary Statistics: Valid 83.0; Min. 10.77; Max. 37.86; Mean 24.502301204819275; StDev 8.161939306159875

Variable Format: numeric

Notes: UNF:6:giSLaLG4r4XXdmDzKzXaTA==

f6579821 Location:

Summary Statistics: StDev 10.071722230405937; Max. 99.98; Valid 83.0; Mean 87.29481927710843; Min. 49.87;

Variable Format: numeric

Notes: UNF:6:l82PyVuAjaWoNiAFf92k8g==

f6579821 Location:

Variable Format: character

Notes: UNF:6:jCMpv5URMcjYe3mz6l0k5w==

f6579821 Location:

Variable Format: character

Notes: UNF:6:36mHeDgmge8skRV/JJnl2g==

f6579821 Location:

Summary Statistics: Min. 2.0; Valid 83.0; StDev 19.17984204958176; Max. 118.0; Mean 19.43022191373494;

Variable Format: numeric

Notes: UNF:6:UQqBVc12eJIWx4cXKGql+A==

f6579821 Location:

Variable Format: character

Notes: UNF:6:aQHC8IFcVBSId9Ogiishdw==

f6579821 Location:

Variable Format: character

Notes: UNF:6:kLzLrA1XezhqMYJADyZQLQ==

f6579821 Location:

Summary Statistics: Valid 83.0; Min. 34.9; Max. 41.2; Mean 37.737349397590364; StDev 1.348052872540342;

Variable Format: numeric

Notes: UNF:6:rr5SwDPK1MaIUXeN+TJEqA==

f6579821 Location:

Summary Statistics: Min. 1.0; Mean 3.421875; StDev 3.250419692071037; Valid 64.0; Max. 21.0

Variable Format: numeric

Notes: UNF:6:NRcTvNBmpYl4Y0eRZv4zJw==

f6579821 Location:

Summary Statistics: Min. 0.0; Mean 3.875; Valid 64.0; Max. 10.0; StDev 2.74584823682638;

Variable Format: numeric

Notes: UNF:6:UjQtoouoU8SfVON05YKvHQ==

f6579821 Location:

Summary Statistics: StDev 11.078447597720242; Max. 99.0; Mean 4.8915662650602405; Min. 0.0; Valid 83.0

Variable Format: numeric

Notes: UNF:6:InlGVJhKbfXqddBTQl/VsA==

f6579821 Location:

Summary Statistics: Max. 15.0; StDev 3.3462186060897756; Min. 0.0; Valid 83.0; Mean 4.734939759036145

Variable Format: numeric

Notes: UNF:6:ERhvgSqj1B0qLpnaAdkqCQ==

f6579821 Location:

Variable Format: character

Notes: UNF:6:KLxTRruAiElyhUhTQhT4LQ==

f6579821 Location:

Variable Format: character

Notes: UNF:6:24uyurirKyPPSsvidoR6aA==

f6579821 Location:

Variable Format: character

Notes: UNF:6:gLoEEWdBqY2cwm+Or7+kwA==

f6579822 Location:

Summary Statistics: Min. 1.0; Valid 117.0; Mean 6.384615384615384; StDev 3.4312110907187883; Max. 12.0

Variable Format: numeric

Notes: UNF:6:/Z4Qown4up2tLzYECKNrnQ==

f6579822 Location:

Summary Statistics: Max. 2022.0; Valid 117.0; Mean 2017.3846153846155; Min. 2013.0; StDev 2.8279581821706823

Variable Format: numeric

Notes: UNF:6:sh77WZD4+ocBWqFwlbKw6A==

f6579822 Location:

Summary Statistics: Max. 88.0; Valid 117.0; StDev 15.639709109556211; Min. 1.0; Mean 31.786324786324787

Variable Format: numeric

Notes: UNF:6:Zgyglh5gWC/d44G7XlmwyQ==

f6579820 Location:

Summary Statistics: Valid 117.0; Min. 1.0; Max. 12.0; StDev 3.4312110907187883; Mean 6.384615384615384;

Variable Format: numeric

Notes: UNF:6:/Z4Qown4up2tLzYECKNrnQ==

f6579820 Location:

Summary Statistics: Valid 117.0; Max. 2022.0; StDev 2.8279581821706823; Mean 2017.3846153846155; Min. 2013.0;

Variable Format: numeric

Notes: UNF:6:sh77WZD4+ocBWqFwlbKw6A==

f6579820 Location:

Summary Statistics: Mean 31.786324786324787; Valid 117.0; Max. 88.0; Min. 1.0; StDev 15.639709109556211

Variable Format: numeric

Notes: UNF:6:Zgyglh5gWC/d44G7XlmwyQ==

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DATA1.xlsx

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Diarrhea_Trend_script.do

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Figure_HAdV_F_Lambisia.R

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Lambisia_HaDV_data_readme.txt

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Lambisia_HaDV_F_Data_Codebook.pdf

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Supplementary_figures_HAdV_F_19102022.pdf

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Supplementary tables_HAdV_F_19102022.pdf

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Table1.Rmd

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