Replication Data for: Temporal trends of SARS-CoV-2 seroprevalence in transfusion blood donors during the first wave of the COVID-19 epidemic in Kenya (doi:10.7910/DVN/FQUNVD)

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Part 2: Study Description
Part 3: Data Files Description
Part 4: Variable Description
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Replication Data for: Temporal trends of SARS-CoV-2 seroprevalence in transfusion blood donors during the first wave of the COVID-19 epidemic in Kenya

doi:10.7910/DVN/FQUNVD

Harvard Dataverse

2021-02-08

1

Adetifa, Ifedayo M.O.; Uyoga, Sophie; Gitonga, John N.; Otiende, Mark; Nyagwange, James; Karanja, Henry K.; Tuju, James; Wanjiku, Perpetual; Aman, Rashid; Mwangangi, Mercy; Amoth, Patrick; Kasera, Kadondi; Ng’ang’a, Wangari; Rombo, Charles; Yegon, Christine; Kithi, Khamisi; Odhiambo, Elizabeth; Rotich, Thomas; Orgut, Irene; Kihara, Sammy; Bottomley, Christian; Kagucia, Eunice W.; Gallagher, Katherine E.; Etyang, Anthony; Voller, Shirine; Lambe, Teresa; Wright, Daniel; Barasa, Edwine; Tsofa, Benjamin; Bejon, Philip; Ochola-Oyier, Lynette I.; Agweyu, Ambrose; Scott, J. Anthony G.; Warimwe, George M., 2021, "Replication Data for: Temporal trends of SARS-CoV-2 seroprevalence in transfusion blood donors during the first wave of the COVID-19 epidemic in Kenya", https://doi.org/10.7910/DVN/FQUNVD, Harvard Dataverse, V1, UNF:6:ItlGSwhwfrDEH/48aUySlA== [fileUNF]

Replication Data for: Temporal trends of SARS-CoV-2 seroprevalence in transfusion blood donors during the first wave of the COVID-19 epidemic in Kenya

doi:10.7910/DVN/FQUNVD

Adetifa, Ifedayo M.O. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya; Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London, United Kingdom)

Uyoga, Sophie (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Gitonga, John N. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Otiende, Mark (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Nyagwange, James (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Karanja, Henry K. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Tuju, James (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Wanjiku, Perpetual (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Aman, Rashid (Ministry of Health, Government of Kenya, Nairobi, Kenya)

Mwangangi, Mercy (Ministry of Health, Government of Kenya, Nairobi, Kenya)

Amoth, Patrick (Ministry of Health, Government of Kenya, Nairobi, Kenya)

Kasera, Kadondi (Ministry of Health, Government of Kenya, Nairobi, Kenya)

Ng’ang’a, Wangari (Presidential Policy & Strategy Unit, The Presidency, Government of Kenya)

Rombo, Charles (Kenya National Blood Transfusion Services, Ministry of Health, Nairobi, Kenya)

Yegon, Christine (Kenya National Blood Transfusion Services, Ministry of Health, Nairobi, Kenya)

Kithi, Khamisi (Kenya National Blood Transfusion Services, Ministry of Health, Nairobi, Kenya)

Odhiambo, Elizabeth (Kenya National Blood Transfusion Services, Ministry of Health, Nairobi, Kenya)

Rotich, Thomas (Kenya National Blood Transfusion Services, Ministry of Health, Nairobi, Kenya)

Orgut, Irene (Kenya National Blood Transfusion Services, Ministry of Health, Nairobi, Kenya)

Kihara, Sammy (Kenya National Blood Transfusion Services, Ministry of Health, Nairobi, Kenya)

Bottomley, Christian (Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London, United Kingdom)

Kagucia, Eunice W. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Gallagher, Katherine E. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya; Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London, United Kingdom)

Etyang, Anthony (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Voller, Shirine (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya; Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London, United Kingdom)

Lambe, Teresa (Nuffield Department of Medicine, Oxford University, United Kingdom)

Wright, Daniel (Nuffield Department of Medicine, Oxford University, United Kingdom)

Barasa, Edwine (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Tsofa, Benjamin (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Bejon, Philip (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya; Nuffield Department of Medicine, Oxford University, United Kingdom)

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

Agweyu, Ambrose (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Scott, J. Anthony G. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya; Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London, United Kingdom; Nuffield Department of Medicine, Oxford University, United Kingdom)

Warimwe, George M. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya; Nuffield Department of Medicine, Oxford University, United Kingdom)

Harvard Dataverse

Adetifa, Ifedayo M.O.

Uyoga, Sophie

Adetifa, Ifedayo M.O.

2021-02-08

Medicine, Health and Life Sciences, COVID-19, SARS-CoV-2, Sero-epidemiology

<p>This is a replication dataset for the manuscriot titled: "<a href="">Temporal trends of SARS-CoV-2 seroprevalence in transfusion blood donors during the first wave of the COVID-19 epidemic in Kenya</a>". </p> <p>These data contain anonymised residual donor serum samples used for screening of transfusion transmissible infections were collected at the KNBTS regional centres in 4 sites (Mombasa, Nairobi, Eldoret and Kisumu) which has been used to compute standardised prevalence by age, sex and region using KNBS population as the standard population.</p>

<strong>Data Availability</strong> <p>Access to these data requires submission of a formal request for consideration by our Data Governance Committee. </p> <strong>How to request</strong> <ol> <li>Download and complete the <a href="https://kemri-wellcome.org/wp-content/uploads/2016/02/Data-Sharing-guidelines-External-requests.docx"><strong>data request form</strong></a></li> <li> Email completed data request form to the Data Governance Committee at <a href="mailto:dgc@kemri-wellcome.org?cc=lmwango@kemri-wellcome.org?Subject=Data%20Access%20Request"><strong>dgc@kemri-wellcome.org</strong></a> </li> </ol>

<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>

Access to the dataset is restricted. Accompanying documentation is available under open access. For more detailed information beyond the metadata and documentation provided, there is a process of managed access requiring submission of a request form for consideration by our Data Governance Committee [dgc@kemri-wellcome.org].<strong> <a href="https://kemri-wellcome.org/wp-content/uploads/2016/02/Data-Sharing-guidelines-External-requests.docx">Click to download Data Request Form</a></strong>

• Number of cases: 9922

• No. of variables per record: 9

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

UNF:6:nr4PLdhgftlPltZpxDf8KQ==

• Number of cases: 9922

• No. of variables per record: 16

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

UNF:6:sfAAO4kZH9epmxXuxhB3GA==

• Number of cases: 9922

• No. of variables per record: 16

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

UNF:6:1+imDPSsuDANocYLjxqlsQ==

• Number of cases: 4747

• No. of variables per record: 5

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

UNF:6:r2+wX5d88nSlP1/nWjJVtA==

• Number of cases: 4747

• No. of variables per record: 5

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

UNF:6:C1NSKEVBEfBTxhbn/9SsYg==

• region - region
• agecat - agecat
• sex - sex
• pop - pop
• pw - pw
• period3 - period3
• period10 - period10
• collect_date - collect_date
• spikepos - spikepos
• sample_id - sample_id
• collect_date - collect_date
• age_yr - age_yr
• spikeod - spikeod
• spike_negod - spike_negod
• spikeratio - spikeratio
• spikepos - spikepos
• rbtc - rbtc
• county - county
• vnrd - vnrd
• batch - batch
• sex - sex
• province - province
• age_category - age_category
• period3 - period3
• period10 - period10
• sample_id - unique identifier of the sample
• collect_date - date of sample collection
• age_yr - age in years
• spikeod - spikeod
• spike_negod - spike_negod
• spikeratio - spikeratio
• spikepos - SARS-CoV-2 antibody status: 1=positive; 0=negative
• rbtc - Regional Blood Transfusion Center
• county - county - 31 out of all the 47
• vnrd - voluntary non-remunerated blood donors
• batch - data batch - first batch was 3156 and second one is 7042
• sex - sex
• province - former administrative units in Kenya
• age_category - RECODE of age_yr (age in years)
• period3
• period10
• age_yr - age_yr
• male - male
• female - female
• total - total
• county - county
• age_yr
• male
• female
• total
• county

f4372958 Location:

Summary Statistics: Valid 9922.0; StDev 2.0711849957144026; Min. 1.0; Mean 4.44033460995773; Max. 8.0;

Variable Format: numeric

Notes: UNF:6:GLtafhcG6cOlfe4tqckvCA==

f4372958 Location:

Summary Statistics: Valid 9922.0; Mean 2.1705301350534083; Min. 1.0; Max. 5.0; StDev 0.990299844505186

Variable Format: numeric

Notes: UNF:6:cQ0c/+1sppW3aXEPoC/MOQ==

f4372958 Location:

Summary Statistics: Mean 1.8082039911308194; Valid 9922.0; Min. 1.0; Max. 2.0; StDev 0.3937333162361006;

Variable Format: numeric

Notes: UNF:6:A+k4KleJgAaGU91rHHqFJA==

f4372958 Location:

Summary Statistics: Max. 1300000.0; StDev 341910.0732092176; Min. 17586.0; Mean 473949.08637373295; Valid 9922.0

Variable Format: numeric

Notes: UNF:6:+TfGjII6X2+TlRXt/Kl3jw==

f4372958 Location:

Summary Statistics: StDev 0.012814562492774184; Mean 0.017547928189880973; Min. 6.477E-4; Max. 0.0493087; Valid 9922.0;

Variable Format: numeric

Notes: UNF:6:EcpHwq4w081lXGKYv+SkKQ==

f4372958 Location:

Summary Statistics: Max. 3.0; Min. 1.0; Valid 9922.0; StDev 0.8442853816788196; Mean 2.0363837935899993;

Variable Format: numeric

Notes: UNF:6:UVlvq5NWzAQgphdYtSsd0Q==

f4372958 Location:

Summary Statistics: Max. 10.0; StDev 2.7425295587641507; Min. 1.0; Mean 5.773835920177393; Valid 9922.0

Variable Format: numeric

Notes: UNF:6:25vsr+EWj0DM+bhHK+LZDQ==

f4372958 Location:

Variable Format: character

Notes: UNF:6:8cnZtgfE9U7BG06yMiDZGA==

f4372958 Location:

Summary Statistics: Max. 1.0; StDev 0.2911877452405886; Mean 0.09352953033662646; Valid 9922.0; Min. 0.0

Variable Format: numeric

Notes: UNF:6:qsdU7SyWivmY1cwgrPdSzA==

f4372962 Location:

Variable Format: character

Notes: UNF:6:/bqPYbtcehEuJoALI192rQ==

f4372962 Location:

Variable Format: character

Notes: UNF:6:AM2RywnNzAtVuJ6tFzfkUg==

f4372962 Location:

Summary Statistics: Max. 64.0; Valid 9922.0; StDev 9.36411650017372; Mean 31.222334206813088; Min. 15.0

Variable Format: numeric

Notes: UNF:6:+9TnL5hpIJMw0pWVwZXaSg==

f4372962 Location:

Summary Statistics: StDev 0.273078821988565; Mean 0.19325176372404743; Max. 3.8299999; Min. 0.048; Valid 9922.0;

Variable Format: numeric

Notes: UNF:6:Hs/ty9X0r1wYWHGFiugqWA==

f4372962 Location:

Summary Statistics: Mean 0.14038913525498906; Max. 0.189; StDev 0.019564764680732656; Min. 0.108; Valid 9922.0

Variable Format: numeric

Notes: UNF:6:Zdt5k1mYp8WxrSIE8Ak0/g==

f4372962 Location:

Summary Statistics: Max. 30.8871; Valid 9922.0; Min. 0.283; Mean 1.3745853785325541; StDev 1.9021173348553915

Variable Format: numeric

Notes: UNF:6:OYFcY8dFkLKD7fzbA9hW6A==

f4372962 Location:

Summary Statistics: Mean 0.09352953033662323; StDev 0.291187745240587; Min. 0.0; Max. 1.0; Valid 9922.0;

Variable Format: numeric

Notes: UNF:6:5EQGYSF5k7hSNVOOad2ELA==

f4372962 Location:

Variable Format: character

Notes: UNF:6:DzE44gysrDKncryg5b+HnQ==

f4372962 Location:

Variable Format: character

Notes: UNF:6:VwFYd5W8koKjrXb0r5YGkA==

f4372962 Location:

Variable Format: character

Notes: UNF:6:XOjfj4W24Uwn24j/aRSNpw==

f4372962 Location:

Summary Statistics: Mean 1.6877645635960121; StDev 0.4634286504991575; Min. 1.0; Max. 2.0; Valid 9922.0

Variable Format: numeric

Notes: UNF:6:MCfwn7h1JEDUU9T3B5YBqQ==

f4372962 Location:

Variable Format: character

Notes: UNF:6:Zrm3oK9osDn3kKpDIinSew==

f4372962 Location:

Variable Format: character

Notes: UNF:6:I4QWG4d2Vb5rFICBaGP6PQ==

f4372962 Location:

Variable Format: character

Notes: UNF:6:hs4Tm5wEBf1SAH38Md3JJA==

f4372962 Location:

Summary Statistics: Min. 1.0; StDev 0.8442853816789069; Valid 9922.0; Max. 3.0; Mean 2.036383793589941

Variable Format: numeric

Notes: UNF:6:i28OeDEkaH59KxYMMWIu4w==

f4372962 Location:

Summary Statistics: Max. 10.0; Mean 5.773835920177221; StDev 2.742529558764224; Min. 1.0; Valid 9922.0

Variable Format: numeric

Notes: UNF:6:aNytJBEUpxhN44vme8CEQQ==

f4372961 Location:

Variable Format: character

Notes: UNF:6:/bqPYbtcehEuJoALI192rQ==

f4372961 Location:

Variable Format: character

Notes: UNF:6:NP79t90lMVdeIExzQ1Fm0w==

f4372961 Location:

Summary Statistics: Min. 15.0; Max. 64.0; StDev 9.36411650017372; Valid 9922.0; Mean 31.222334206813088;

Variable Format: numeric

Notes: UNF:6:+9TnL5hpIJMw0pWVwZXaSg==

f4372961 Location:

Summary Statistics: Valid 9922.0; Min. 0.04800000041723251; Max. 3.8299999237060547; Mean 0.1932517638568366; StDev 0.27307882223132524

Variable Format: numeric

Notes: UNF:6:Hs/ty9X0r1wYWHGFiugqWA==

f4372961 Location:

Summary Statistics: Valid 9922.0; Max. 0.1889999955892563; Min. 0.1080000028014183; Mean 0.1403891347995562; StDev 0.019564764722199462

Variable Format: numeric

Notes: UNF:6:Zdt5k1mYp8WxrSIE8Ak0/g==

f4372961 Location:

Summary Statistics: Min. 0.28299999237060547; Valid 9922.0; StDev 1.902117329328536; Max. 30.887096405029297; Mean 1.3745853753147221

Variable Format: numeric

Notes: UNF:6:uWWdunG+hBOaeaknAtNMaw==

f4372961 Location:

Summary Statistics: Mean 0.09352953033662323; StDev 0.291187745240587; Min. 0.0; Max. 1.0; Valid 9922.0

Variable Format: numeric

Notes: UNF:6:5EQGYSF5k7hSNVOOad2ELA==

f4372961 Location:

Variable Format: character

Notes: UNF:6:DzE44gysrDKncryg5b+HnQ==

f4372961 Location:

Variable Format: character

Notes: UNF:6:VwFYd5W8koKjrXb0r5YGkA==

f4372961 Location:

Summary Statistics: Valid 9922.0; Min. 0.0; Max. 1.0; Mean 0.029227978230197342; StDev 0.1684534460402456

Variable Format: numeric

Notes: UNF:6:LI+ix8IpuuZlHpc0US9/Jg==

f4372961 Location:

Summary Statistics: StDev 0.4634286504991575; Max. 2.0; Min. 1.0; Valid 9922.0; Mean 1.6877645635960121

Variable Format: numeric

Notes: UNF:6:MCfwn7h1JEDUU9T3B5YBqQ==

f4372961 Location:

Summary Statistics: Max. 2.0; StDev 0.3937333162360972; Min. 1.0; Mean 1.808203991130821; Valid 9922.0;

Variable Format: numeric

Notes: UNF:6:bUzVlUx3yBLU9JstJ4jARg==

f4372961 Location:

Variable Format: character

Notes: UNF:6:I4QWG4d2Vb5rFICBaGP6PQ==

f4372961 Location:

Summary Statistics: Valid 9922.0; Max. 5.0; Min. 1.0; Mean 2.1705301350534207; StDev 0.9902998445051721

Variable Format: numeric

Notes: UNF:6:Y3NIURtKLUBM7ooMz3DaDA==

f4372961 Location:

Summary Statistics: StDev 0.8442853816789069; Valid 9922.0; Max. 3.0; Mean 2.036383793589941; Min. 1.0

Variable Format: numeric

Notes: UNF:6:i28OeDEkaH59KxYMMWIu4w==

f4372961 Location:

Summary Statistics: Min. 1.0; Max. 10.0; Mean 5.773835920177221; Valid 9922.0; StDev 2.742529558764224

Variable Format: numeric

Notes: UNF:6:aNytJBEUpxhN44vme8CEQQ==

f4372963 Location:

Summary Statistics: Valid 4747.0; Min. 0.0; Mean 50.0; StDev 29.157830821032412; Max. 100.0;

Variable Format: numeric

Notes: UNF:6:2kdhy71MujkuZybiY7fcIQ==

f4372963 Location:

Summary Statistics: StDev 6788.8914549215815; Valid 4747.0; Min. 2.0; Mean 4960.537392037142; Max. 64070.0

Variable Format: numeric

Notes: UNF:6:RV3zzZGq7udcgN5gCXpjOw==

f4372963 Location:

Summary Statistics: Valid 4747.0; Min. 2.0; Max. 70152.0; Mean 5058.862228776113; StDev 6904.475478144375;

Variable Format: numeric

Notes: UNF:6:Fg8t7JP0OuIfHuXPqQ7X1w==

f4372963 Location:

Summary Statistics: Valid 4747.0; Mean 10019.39962081301; StDev 13664.530092712286; Min. 4.0; Max. 133373.0

Variable Format: numeric

Notes: UNF:6:VGA0MBR9KY53VBWNyIkTDg==

f4372963 Location:

Variable Format: character

Notes: UNF:6:Ah0tV++a+RMImL8vBE8zcQ==

f4372957 Location:

Variable Format: character

Notes: UNF:6:42Bz3IChAAji8YE9GNnj5A==

f4372957 Location:

Summary Statistics: Min. 2.0; Max. 64070.0; StDev 6788.8914549215815; Mean 4960.537392037142; Valid 4747.0;

Variable Format: numeric

Notes: UNF:6:RV3zzZGq7udcgN5gCXpjOw==

f4372957 Location:

Summary Statistics: Mean 5058.862228776113; Valid 4747.0; Min. 2.0; Max. 70152.0; StDev 6904.475478144375;

Variable Format: numeric

Notes: UNF:6:Fg8t7JP0OuIfHuXPqQ7X1w==

f4372957 Location:

Summary Statistics: StDev 13664.530092712286; Valid 4747.0; Min. 4.0; Max. 133373.0; Mean 10019.39962081301;

Variable Format: numeric

Notes: UNF:6:VGA0MBR9KY53VBWNyIkTDg==

f4372957 Location:

Variable Format: character

Notes: UNF:6:Ah0tV++a+RMImL8vBE8zcQ==

Label:

1.1_structuring_&_QC.do

application/x-stata-syntax

Label:

2.0_national_prevalence_age_sex_adjusted.do

Text:

for computing the age-sex adjusted national prevalence estimate

application/x-stata-syntax

Label:

4.0_province_prevalence_age_sex_adjusted.do

Text:

for computing the age-sex adjusted prevalence for each province

application/x-stata-syntax

Label:

IAdetifa_Blood_Donors_Seroprevalence_Data_Codebook.pdf

application/pdf

Label:

IAdetifa_Blood_Donors_Seroprevalence_Data_Readme.TXT

text/plain

Label:

KNBTS_dec_analysis_version 3.Rmd

Text:

for Bayesian multilevel regression and post-stratification to account for non-random sampling with respect to age, sex and province, adjusted for assay performance

application/octet-stream