Replication Data for: Rhinovirus transmission dynamics across different social structures

Version 1.0
Replication Data for: Rhinovirus transmission dynamics across different social structures
Luka, Martha M.; Otieno, James R.; Kamau, Everlyn; Morobe, John M.; Murunga, Nickson; Adema, Irene; Nyiro, Joyce U.; Macharia,Peter M.; Bigogo, Godfrey; Otieno, Nancy A.; Nyawanda, Bryan O.; Rabaa, Maia A.; Emukule, Gideon O.; Onyango, Clayton; Munywoki, Patrick K.; Agoti, Charles N.; Nokes, D.James, 2023, "Replication Data for: Rhinovirus transmission dynamics across different social structures", https://doi.org/10.7910/DVN/KSOPCI, Harvard Dataverse, V1, UNF:6:5Iz4Zr91WomokGKyjKfRMA== [fileUNF]
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Description

This is a replication dataset for the publication titled: "Rhinovirus transmission dynamics across different social structures ."

This dataset aims to compare rhinovirus dynamics from five previous studies conducted in Kenya in four different social structures. The studies are (i) intensive household surveillance in coastal Kenya (Dec 2009 - May 2010), (ii) surveillance of respiratory viruses within a public primary school (May 2017 – April 2018), (iii) outpatient surveillance of acute respiratory illness within the Kilifi Health and Demographic Surveillance System (KHDSS) (Dec 2015 - Nov 2016), and (iv) countrywide surveillance of severe acute respiratory syndrome illness (SARI) among inpatients and influenza-like illness (ILI) among outpatients via sentinel hospital reporting (Jan 2014 - Dec 2014). (v) We used contemporaneous data from long-term surveillance of severe pneumonia among pediatric inpatients at the Kilifi County Hospital (KCH) for comparison with the households, school, and KHDSS studies datasets. The primary dataset contains VP4/2 sequence data, alongside necessary metadata (e.g. date of sampling, site where collection, respective study). Secondary datasets generated from the primary data are also included (described in section 4 - Contents).

Subject Medicine, Health and Life Sciences
Keyword rhinovirus, transmission, social structures, phylogenetics, molecular epidemiology
License/Data Use Agreement

CC BY 4.0

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LUKA_HRV_SocialScales_Data_Dictionary.pdf
LUKA_HRV_SocialScales_Data_Dictionary.pdf
Adobe PDF - 185.6 KB
Published Jul 31, 2023
37 Downloads
MD5: c172d57944a7f8f73362992a93862879
DocumentationVariable Codebook/Data Dictionary
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LUKA_HRV_SocialScales_Readme.txt
Plain Text - 8.8 KB
Published Jul 31, 2023
18 Downloads
MD5: 30cda30fc96b375366681040b0407c50
DocumentationReadme
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anonym_metadata.tab
Tabular Data - 141.0 KB
Published Jul 31, 2023
30 Downloads
8 Variables, 2373 Observations UNF:6:fvVWoU1FnO2+TydQBF7N4A==
This dataset compiles metadata of sequence data generated across 4 social scales by five previous studies in Kenya: (i) households, (ii) school, (iii) Kilifi HDSS (KHDSS) ,(iv) Countrywide and (v) Kilifi County Hospital (KCH)
Datacsv
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anonym_sequences.fasta
Unknown - 988.3 KB
Published Jul 31, 2023
12 Downloads
MD5: b7b88414e94f678fcf4511041ddeea01
This dataset cobtains rhinovirus VP4/2 sequence data generated across 4 social scales by five previous studies in Kenya: (i) households, (ii) school, (iii) Kilifi HDSS (KHDSS) ,(iv) Countrywide and (v) Kilifi County Hospital (KCH)
Datasequences
mapShapefiles.zip
Shapefile as ZIP Archive - 225.8 KB
Published Jul 31, 2023
11 Downloads
MD5: 02bbc7c5959465b498c67a18aeec6cdf
DataShapefiles
overall_genetic_distances_per_type.tab
Tabular Data - 1.1 KB
Published Jul 31, 2023
17 Downloads
4 Variables, 40 Observations UNF:6:6po1ejojBbcxwWNfPLWfdA==
This dataset contains rhinovirus type specific overall genetic distances
Datacsv
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phylogeography_links.tab
Tabular Data - 5.2 KB
Published Jul 31, 2023
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5 Variables, 111 Observations UNF:6:dSQS89asRbBNc8q8VZ/84Q==
This dataset contains summarised transmission links of five most frequent rhinovirus types per social scale inferred under a symmetric diffusion model in BEAST v1.10.4 and summarized using SpreaD3 v0.9.7.1 software. Transmission links are not directional
Datacsv
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supp_table3_data.tab
Tabular Data - 56.4 KB
Published Jul 31, 2023
22 Downloads
3 Variables, 1781 Observations UNF:6:vE0QJVWOKWn4y+oZx0ddAA==
This dataset lists local and global sequences used in the phylogenetic analysis, location of sampling and HRV type
Datacsv
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Fig4_suppTable3.R
R Syntax - 5.6 KB
Published Jul 31, 2023
22 Downloads
MD5: 5da333f948207a1c447daa5dda22f311
CodeR script
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Fig5_suppFig2.R
R Syntax - 18.9 KB
Published Jul 31, 2023
15 Downloads
MD5: e7baf551e681f0653ec561489c004698
CodeR script
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