Replication Data for: Trends and intensity of human rhinovirus invasions in local populations, a longitudinal analysis from Kilifi, Kenya, 2007-2018

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Replication Data for: Trends and intensity of human rhinovirus invasions in local populations, a longitudinal analysis from Kilifi, Kenya, 2007-2018
Morobe, John M.; Kamau, Everlyn; Murunga, Nickson; Gatua, Winfred; Lewa, Clement; Cheruiyot, Robinson; Mutunga, Martin; Odundo, Calleb; Agoti, Charles N.; Nokes, David James, 2021, "Replication Data for: Trends and intensity of human rhinovirus invasions in local populations, a longitudinal analysis from Kilifi, Kenya, 2007-2018", https://doi.org/10.7910/DVN/OL399P, Harvard Dataverse, V2, UNF:6:25VkNi7AihwToeZ6rwVt0g== [fileUNF]
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Description

This is a replication dataset for the manuscript titled: "Trends and intensity of human rhinovirus invasions in local populations, a longitudinal analysis from Kilifi, Kenya, 2007-2018."

This study is part of a longitudinal surveillance study established to understand the epidemiology and disease burden of HRV associated pneumonia admissions to Kilifi County Hospital (KCH).It contains month and year of sample collection, Eligibles (Under fives with severe or very severe pneumonia),sample tested, sample positives for respiratory viruses, and HRV types detected.

Subject Medicine, Health and Life Sciences
Notes Notes on running code
Data analysis R code and python script is as provided below;
  1. HRV_monthly_distribution.do- Monthly distribution of human rhinovirus cases identified from surveillance of acute respiratory infections (ARI) in patients under 5 years old admitted to the Kilifi County Hospital, Kenya, 2007–2018.
  2. Figure2.R-This r code display Annual proportion of HRV species across the 12-years period.
  3. Rplots_figure3-Quarterly proportions of HRV types detected organised at the species level.
  4. HiLiter_figure_4.py-It displays nucleotides differences between sequences of the same HRV type.
  5. Pairwise_snps_Figure4-This shows the distribution plot of pairwise nucleotide differences between sequences of the same HRV type. This code is used to run multiple datasets i.e. RV-A12, RV-A49, RV-A78, RV-A101; RV-C2, RV-C3, RV-C6, RV-C11, RV-C21, RV-C38.
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