Replication Data for: Temporal distribution of rhinovirus types in multiple regions across Kenya over one year, 2014. (doi:10.7910/DVN/CBHVTA)

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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: Temporal distribution of rhinovirus types in multiple regions across Kenya over one year, 2014.

doi:10.7910/DVN/CBHVTA

Harvard Dataverse

2024-04-02

2

Morobe, John M.; Kamau, Everlyn; Luka, Martha M.; Murunga, Nickson; Lewa, Clement; Mutunga, Martin; Bigogo, Godfrey; Nyawanda, Brian; Onyango, Clayton; Nokes, David James; Agoti, Charles N.; Munywoki, Patrick K., 2024, "Replication Data for: Temporal distribution of rhinovirus types in multiple regions across Kenya over one year, 2014.", https://doi.org/10.7910/DVN/CBHVTA, Harvard Dataverse, V2, UNF:6:sQTYC5N6hrmEF7vFz/tsTQ== [fileUNF]

Replication Data for: Temporal distribution of rhinovirus types in multiple regions across Kenya over one year, 2014.

doi:10.7910/DVN/CBHVTA

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

Kamau, Everlyn (Nuffield Department of Medicine, University of Oxford, Oxford, UK)

Luka, Martha M. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

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

Lewa, Clement (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

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

Bigogo, Godfrey (KEMRI- Centre for Global Health Research, Kisumu, Kenya)

Nyawanda, Brian (KEMRI- Centre for Global Health Research, Kisumu, Kenya)

Onyango, Clayton (U.S Centers for Disease Control and Prevention (CDC), Centers for Global Health, Division of Global Health Protection, Nairobi, Kenya)

Nokes, David James (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya; School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, United Kingdom.)

Agoti, Charles N. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya; Department of Public Health, Pwani University, Kilifi, Kenya)

Munywoki, Patrick K. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya; U.S Centers for Disease Control and Prevention (CDC), Centers for Global Health, Division of Global Health Protection, Nairobi, Kenya)

Harvard Dataverse

Morobe, John M.

Morobe, John M.

2024-04-02

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

Medicine, Health and Life Sciences, rhinovirus, phylogenetics, transmission, spatio-temporal distribution, Kenya

<p>This is a replication dataset for the manuscript titled: <i>"<strong>Temporal distribution of rhinovirus types in multiple regions across Kenya over one year, 2014</strong>"</i>.</p> <p>The dataset comprises demographic and clinical details of patients with acute respiratory illness across different age groups. Data collection spanned from January to December 2014 across three health facility-based respiratory virus surveillance programs in Kenya. It includes Nasopharyngeal (NP) and/or oropharyngeal (OP) swab test results obtained from Respiratory virus rT-RT-PCR screening and sequencing. Rhinovirus VP4/VP2 sequences are accessible on GenBank under accession numbers: MZ129390 - MZ130096. Details of methods and processing are outlined in the associated manuscript.</p>

Open Access

• Number of cases: 798

• No. of variables per record: 5

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

UNF:6:L+HN3toSdVW5rxAtxGu4Bw==

• Number of cases: 5251

• No. of variables per record: 8

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

UNF:6:Q3wP4+MPg0c9ar5pZ/DfPA==

• Number of cases: 798

• No. of variables per record: 5

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

UNF:6:4KoJ/JISVFwrrQyCrxAQSw==

• Number of cases: 798

• No. of variables per record: 3

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

UNF:6:bq/Mi3BGfLqx43zFxH55XQ==

• date_collected - date_collected
• site - site
• lineage - lineage
• lineage_1 - lineage_1
• study_no_anon - study_no_anon
• strain - strain
• date - date
• country - country
• site - site
• region1 - region1
• loc1 - loc1
• loc2 - loc2
• loc3 - loc3
• study_no_anon - study_no_anon
• date_collected - date_collected
• site_1 - site_1
• site - site
• lineage - lineage
• study_no_anon - study_no_anon
• date_collected - date_collected
• lineage - lineage

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Variable Format: character

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f10053992 Location:

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f10053992 Location:

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f10053992 Location:

Variable Format: character

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f10053992 Location:

Summary Statistics: Valid 798.0; Mean 399.5; Max. 798.0; StDev 230.5070497837322; Min. 1.0;

Variable Format: numeric

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f10053991 Location:

Variable Format: character

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f10053991 Location:

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f10053991 Location:

Variable Format: character

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f10053991 Location:

Variable Format: character

Notes: UNF:6:il+PfmbqQgcgtjMAWpuDRw==

f10053990 Location:

Summary Statistics: Min. 1.0; Mean 399.5; Max. 798.0; StDev 230.5070497837322; Valid 798.0

Variable Format: numeric

Notes: UNF:6:kwpHRpBfUFFAjNF0z8sruA==

f10053990 Location:

Variable Format: character

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f10053990 Location:

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f10053990 Location:

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f10053990 Location:

Variable Format: character

Notes: UNF:6:eVVqm/HwhpdO9TMO457CEg==

f10053988 Location:

Summary Statistics: Mean 399.5; Min. 1.0; Valid 798.0; StDev 230.5070497837322; Max. 798.0

Variable Format: numeric

Notes: UNF:6:0zDEfO0sU2ieFjjIu2Sy5w==

f10053988 Location:

Variable Format: character

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f10053988 Location:

Variable Format: character

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Appendix Table 1.csv

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Fig3_SPReD-K_temporal_plots_27032024.R

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This r code plots the temporal distribution of all the rhinovirus species in Kenya/site

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Fig4_SPPeD-K_Tree_updated.R

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This r code plots the time-resolved phylogenetic tree of the prevalent rhinovirus types in Kenya

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JMwita_ Temporal_Distribution_Rhinovirus_data_codebook_v2.pdf

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JMwita_ Temporal_Distribution_Rhinovirus_data_Readme.txt

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Suppfig1_prop_species_site.R

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This r code plots the temporal distribution of all the rhinovirus types in Kenya.

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Suppfig1_site_count.txt

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Suppfig1_species_site_count.txt

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Suppfig2_rv_types_per_site.R

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This r code plots the temporal distribution of all the rhinovirus types in Kenya

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Suppfig3_temporal_plot.R

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This r code plots the temporal distribution of all the rhinovirus types in Kenya

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