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Part 1: Document Description
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Citation |
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Title: |
Replication Data for: Genomic analysis of respiratory syncytial virus infections in households and utility in inferring who infects the infant |
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Identification Number: |
doi:10.7910/DVN/DUCQWE |
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Distributor: |
Harvard Dataverse |
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Date of Distribution: |
2019-07-18 |
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Version: |
1 |
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Bibliographic Citation: |
Agoti, Charles N.; Phan, My V. T.; Munywoki, Patrick K.; Githinji, George; Medley, Graham F.; Cane, Patricia A.; Kellam, Paul; Cotten, Matthew; Nokes, D. James, 2019, "Replication Data for: Genomic analysis of respiratory syncytial virus infections in households and utility in inferring who infects the infant", https://doi.org/10.7910/DVN/DUCQWE, Harvard Dataverse, V1, UNF:6:pkEWKbntsO5Q/dyzI9kqew== [fileUNF] |
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Citation |
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Title: |
Replication Data for: Genomic analysis of respiratory syncytial virus infections in households and utility in inferring who infects the infant |
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Identification Number: |
doi:10.7910/DVN/DUCQWE |
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Authoring Entity: |
Agoti, Charles N. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Phan, My V. T. (Wellcome Trust Sanger Institute, Cambridge, United Kingdom) |
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Munywoki, Patrick K. (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Githinji, George (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Medley, Graham F. (London School of Hygiene and Tropical Medicine (LSHTM, Department of Global Health and Development and Centre for Mathematical Modeling of Infectious Disease, , London, United Kingdom) |
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Cane, Patricia A. (Public Health England, Porton Down, Salisbury, United Kingdom.) |
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Kellam, Paul (Imperial College London , Department of Infection, London, United Kingdom) |
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Cotten, Matthew (Wellcome Trust Sanger Institute, Cambridge, United Kingdom) |
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Nokes, D. James (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya) |
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Distributor: |
Harvard Dataverse |
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Access Authority: |
Agoti, Charles N. |
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Depositor: |
Agoti, Charles N. |
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Date of Deposit: |
2019-06-06 |
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Holdings Information: |
https://doi.org/10.7910/DVN/DUCQWE |
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Study Scope |
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Keywords: |
Medicine, Health and Life Sciences |
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Abstract: |
<p>This dataset contains whole genomic sequences (WGS) obtained from participants enrolled in a household study undertaken within Kilifi County, located in coastal Kenya. In the study, 47 households (HH) scattered across an area of approximately 21 km2 were followed up over a 6-month period beginning December 2009 and ending June 2010 coinciding with the RSV peak activity months in the area. Twice weekly throughout the study period, a nasopharyngeal-flocked swab (NPS) was obtained from each household member regardless of symptom status. The NPS samples were screened for a range of respiratory viral targets using a multiplex real-time RT-PCR method which subtyped RSV positives into RSVA and RSVB. </p> <p>The whole genome sequencing (WGS) present in this dataset targeted 20 select households that documented RSV infection of ≥2 members. </p> |
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Notes: |
The sequence data from this study have also been deposited in both GenBank and Short Read Archive databases. Accession numbers are as indicated in the dataset |
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Methodology and Processing |
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Sources Statement |
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Data Access |
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Citation Requirement: |
Publications based on this data collection should acknowledge this source by means of bibliographic citation. To ensure that such source attributions are captured for bibliographic utilities, citations must appear in footnotes or in the reference section of publications. |
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Notes: |
This data is made available under the Creative Commons Attribution 4.0 International (CC BY 4.0) - https://creativecommons.org/licenses/by/4.0/legalcode. Publications based on these data should acknowledge this source by means of bibliographic citations. For more information on these data, please contact the Principal Investigator, author(s) OR the data governance office via this email address: dgc@kemri-wellcome.org |
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Access to the dataset is restricted as it contains sensitive information on participants. 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 <a href="http://kemri-wellcome.org/about-us/#ChildVerticalTab_15">( http://kemri-wellcome.org/about-us/#ChildVerticalTab_15 )</a>. |
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Other Study Description Materials |
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File Description--f3474432 |
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File: Agoti_household_genomic_epidata.tab |
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Notes: |
UNF:6:YqJmzWlUOE9DQBgT/6vHXg== |
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Same data as 'Agoti_household_genomic_epidata.xls' in csv format |
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File Description--f3443516 |
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File: HH14.tab |
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Notes: |
UNF:6:HknNDkEofpqTWmnYYtLfUA== |
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File Description--f3443517 |
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File: snps.tab |
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Notes: |
UNF:6:wvuk0CQ9pvwHHyQrLEUeqA== |
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File Description--f3443519 |
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File: within-hh-snps.tab |
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Notes: |
UNF:6:OZepSNylmJujYvKRQQSoUw== |
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Label: |
Agoti_household_genomic_analysis_readme.TXT |
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Text: |
Readme file |
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Notes: |
text/plain |
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Label: |
Agoti_household_genomic_epidata.xls |
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Notes: |
application/vnd.ms-excel |
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Label: |
csvtofasta_ID26122012.py |
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Text: |
Python script |
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Notes: |
text/x-python-script |
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Label: |
HH14.do |
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Text: |
STATA do file used to generate figure. Uses dataset 'HH14.csv" |
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Notes: |
application/x-stata-syntax |
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Label: |
overall_snps.do |
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Text: |
STATA do file used to generate Figure 3(a). Uses dataset 'snps.csv' |
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Notes: |
application/x-stata-syntax |
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Label: |
PanelHiLiterRSVHH.py |
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Text: |
Python script |
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Notes: |
text/x-python-script |
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Label: |
within-hh-snps.do |
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Text: |
STATA do file used to generate Figure 6. Uses dataset 'within-hh-snps.csv' |
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Notes: |
application/x-stata-syntax |