Replication Data for: Multi-species co-circulation of adenoviruses identified by next generation sequencing during an outbreak in coastal Kenya in 2023 (doi:10.7910/DVN/XCHBND)

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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: Multi-species co-circulation of adenoviruses identified by next generation sequencing during an outbreak in coastal Kenya in 2023

doi:10.7910/DVN/XCHBND

Harvard Dataverse

2024-03-19

1

Lambisia, Arnold W.; Mutunga, Martin; Katama, Esther N.; Agoti, Charles N.; Houldcroft, Charlotte J., 2024, "Replication Data for: Multi-species co-circulation of adenoviruses identified by next generation sequencing during an outbreak in coastal Kenya in 2023", https://doi.org/10.7910/DVN/XCHBND, Harvard Dataverse, V1, UNF:6:kMf51uUMNvnlcQnhVs8Q7g== [fileUNF]

Replication Data for: Multi-species co-circulation of adenoviruses identified by next generation sequencing during an outbreak in coastal Kenya in 2023

doi:10.7910/DVN/XCHBND

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

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

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

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

Houldcroft, Charlotte J. (University of Cambridge, Department of Genetics)

Harvard Dataverse

Lambisia, Arnold W.

Lambisia, Arnold W.

2024-03-19

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

Medicine, Health and Life Sciences, Human adenovirus, ONT, enteric, Kenya, RespiCov

<p>This is a replication dataset for the manuscript titled: "<i><strong>Multi-species co-circulation of adenoviruses identified by next-generation sequencing during an outbreak in coastal Kenya in 2023</strong></i></p> <p>The main dataset is part of long-term surveillance of enteric viruses associated with diarrhoea. These datasets are part of long-term surveillance of enteric viruses associated with diarrhea among children under 13 years admitted to the KCH study. These datasets contain the results of samples tested by real-time PCR between June 2022 and August 2023. Aside from the samples tested and results of the tests, it also contains the patients’ sociodemographic characteristics, cycle threshold, discharge outcome, and disease severity. The dataset is used to explore the circulating human adenovirus species and types in enteric samples, coinfection, and difference in sociodemographic characteristics.</p>

Open Access

• Number of cases: 19

• No. of variables per record: 4

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

UNF:6:sgtmLDMin7fmbeN2MyIL0A==

• Number of cases: 26

• No. of variables per record: 3

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

UNF:6:JyPuurKXg/mT/dHDsz/Vsw==

• Number of cases: 43

• No. of variables per record: 13

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

UNF:6:i5cE3g/xNNGfNfsMnZThMA==

• Monthly - Monthly
• Status - Status
• Freq_all - Freq_all
• prop - prop
• Monthly - Monthly
• Species - Species
• Frequency - Frequency
• barcode - barcode
• Status - Status
• HAdV - HAdV
• NV_GII - NV_GII
• RVA - RVA
• SAP - SAP
• ASV - ASV
• age_mo - age_mo
• sex - sex
• datestoolcollected - datestoolcollected
• age_strata - age_strata
• Ves_score - Ves_score
• outcome - outcome

f9648687 Location:

Variable Format: character

Notes: UNF:6:30osMS6UWpKCrs3smctO7Q==

f9648687 Location:

Variable Format: character

Notes: UNF:6:Ndvcc2ezKaZI5pnahnjGSw==

f9648687 Location:

Summary Statistics: Mean 26.94736842105263; StDev 10.987233420912384; Valid 19.0; Max. 42.0; Min. 8.0

Variable Format: numeric

Notes: UNF:6:wBIVzLDfe7YuA7bPrfRO/A==

f9648687 Location:

Summary Statistics: StDev 31.47000874585572; Valid 19.0; Max. 100.0; Min. 15.38461538; Mean 57.89473684157895;

Variable Format: numeric

Notes: UNF:6:u3mNhTClZj7JMnpfP/0JgQ==

f9648685 Location:

Variable Format: character

Notes: UNF:6:a8HCZYwcczAdx7Qy7eWYJw==

f9648685 Location:

Variable Format: character

Notes: UNF:6:Cjhv1pNPoS36aLnTxgeoYA==

f9648685 Location:

Summary Statistics: StDev 0.80860754006264; Mean 1.5769230769230769; Max. 4.0; Valid 26.0; Min. 1.0

Variable Format: numeric

Notes: UNF:6:TfzTrlshdd4yLsjrzIGMNg==

f9648686 Location:

Summary Statistics: Max. 43.0; Min. 1.0; StDev 12.556538801224908; Valid 43.0; Mean 22.0

Variable Format: numeric

Notes: UNF:6:ot9PUspZWKlqSqx357ZnFA==

f9648686 Location:

Variable Format: character

Notes: UNF:6:s5xpa7BlJbbtBBweWNdioQ==

f9648686 Location:

Summary Statistics: Mean 25.203953488372093; Min. 11.66; Valid 43.0; StDev 6.530555704326314; Max. 34.96

Variable Format: numeric

Notes: UNF:6:/gGBopr/uGUMqLT2xDK8jw==

f9648686 Location:

Summary Statistics: Max. 1.0; StDev 0.32435300622428825; Mean 0.11627906976744187; Valid 43.0; Min. 0.0;

Variable Format: numeric

Notes: UNF:6:+yrz1JRFOCE4fXZPFbXXeg==

f9648686 Location:

Summary Statistics: StDev 0.35060460356342593; Min. 0.0; Valid 43.0; Max. 1.0; Mean 0.1395348837209302;

Variable Format: numeric

Notes: UNF:6:3LBz9Vhox1hmsMxuP5Zt9Q==

f9648686 Location:

Summary Statistics: Valid 43.0; Mean 0.0697674418604651; Max. 1.0; StDev 0.25776963111323364; Min. 0.0

Variable Format: numeric

Notes: UNF:6:ja6G84mk+bL0F8qHhPiksg==

f9648686 Location:

Summary Statistics: Mean 0.023255813953488358; Max. 1.0; StDev 0.15249857033260472; Min. 0.0; Valid 43.0

Variable Format: numeric

Notes: UNF:6:qHGXOBGpYcNAU22qnrvEcA==

f9648686 Location:

Summary Statistics: Mean 17.02658536585366; Valid 41.0; Min. 4.57; StDev 10.080636043860551; Max. 50.37

Variable Format: numeric

Notes: UNF:6:A+KpHAjSbQSRiONdk4uwVA==

f9648686 Location:

Variable Format: character

Notes: UNF:6:1tTfBrCW2fS1VKMUdzjEAA==

f9648686 Location:

Variable Format: character

Notes: UNF:6:vEfW6Vf02FCBRFOEO1yq5Q==

f9648686 Location:

Variable Format: character

Notes: UNF:6:HqLPbFuvgJ/4enn0R4bWpg==

f9648686 Location:

Variable Format: character

Notes: UNF:6:5KkhSHI+1Br8TTCY/YNJ9g==

f9648686 Location:

Variable Format: character

Notes: UNF:6:IhK42/apkJpGjcEX5bVLJw==

Label:

HAdv_Figures_AWL.R

type/x-r-syntax

Label:

Lambisia_Adenovirus_Cocirculation_Codebook.pdf

application/pdf

Label:

Lambisia_Adenovirus_Cocirculation_Readme.txt

text/plain

Label:

table1_HAdV_genotypes.Rmd

text/x-r-notebook