Replication Data for: Whole genome sequencing of two human rhinovirus A types (A101 and A15) detected in Kenya, 2016-2018

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Replication Data for: Whole genome sequencing of two human rhinovirus A types (A101 and A15) detected in Kenya, 2016-2018
Luka, Martha M.; Kamau, Everlyn; de Laurent, Zaydah R.; Morobe, John M.; Alii, Leonard K.; Nokes, David James; Agoti, Charles N., 2021, "Replication Data for: Whole genome sequencing of two human rhinovirus A types (A101 and A15) detected in Kenya, 2016-2018", https://doi.org/10.7910/DVN/QGXZLI, Harvard Dataverse, V1, UNF:6:sHiQY2P6RU/NhRKOoAUfXw== [fileUNF]
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Description

This is a replication dataset for the manuscript titled: "Whole genome sequencing of two human rhinovirus A types (A101 and A15) detected in Kenya, 2016-2018." The dataset contains contains Cycle threshold (Ct) values, and read/sequencing depth.

The related study utilized nasopharyngeal swabs collected during two previous studies in Kilifi County, coastal Kenya: outpatient surveillance of nine health dispensaries within the Kilifi Health and Demographic Surveillance System (KHDSS) between January and December 2016 and primary school surveillance between May 2017 and April 2018. All samples were collected from symptomatic individuals (mild symptoms of acute respiratory tract infection) of varied age (1 month - 49 years) and archived at -80°C. Samples were screened for HRV and typed as previously described8. A cycle threshold (Ct) value < 35.0 was used to define positives. HRV positives underwent VP4/2 sequencing to characterize the diversity, spatial and temporal occurrence of HRV in the two settings. Comparison of the HRV diversity within the school in Junju and the health dispensary located in Junju revealed 12 common types, and the most frequent common type was HRV-A101 (n=5 in each setting).

Subject Medicine, Health and Life Sciences
Keyword human rhinovirus, whole-genome, sequencing, phylogenetics
Related Publication Morobe, J.M., Nyiro, J.U., Brand, S., Kamau, E., Gicheru, E., Eyase, F., Otieno, G.P., Munywoki, P.K., Agoti, C.N. and Nokes, D.J., 2018. Human rhinovirus spatial-temporal epidemiology in rural coastal Kenya, 2015-2016, observed through outpatient surveillance. Wellcome open research, 3.doi: 10.12688%2Fwellcomeopenres.14836.2
Notes

The assembled sequences are available in the GenBank database under accession numbers MW713746-MW713793. The raw data are available in the NCBI SRA archive under BioProject accession number PRJNA701406.

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License: Creative Commons Attribution 4.0 International

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