Characterizing the countrywide epidemic spread of influenza A(H1N1)pdm09 virus in Kenya between 2009 and 2018
Author: David Collins Owuor
Institution: KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
Date Published: 20 March 2021
Pre-print: https://www.medrxiv.org/content/10.1101/2021.03.30.21254587v1.
This repository contains data and input files for the phylodynamic and phylogeographical analysis of human influenza A(H1N1)pdm09 virus from Kenya, 2009-2018.
The data and instructions will allow replication of the results shown in the report.
This folder contains data and input files for phylodynamic and phylogeographical analyses of Kenyan and global influenza A(H1N1)pdm09 virus sequence data:
- H1N1pdm09_Kenya_genomes_2009-2018.tsv
A list of 383 influenza A(H1N1)pdm09 virus (2009-2018) sequence data from Kenya showing: strain - virus strain identity; accession - GISAID accession number; site - location of isolation; reads - number of sequencing reads; flu - number of influenza virus reads; Ct - PCR Ct value; and date - date of virus sampling.
- H1N1pdm09_global_genomes_2009-2018.tsv
A list of 1,587 global influenza A(H1N1)pdm09 virus sequence data showing: strain - virus strain identity; accession - GISAID accession number; country - country of virus isolation; and continent - continent of virus isolation.
Analysis files for analysis of virus introductions, transmission clusters, and patterns of spread of influenza A(H1N1)pdm09 virus in Kenya.
- H1N1pdm09_metadata.tsv
A list of 383 influenza A(H1N1)pdm09 virus sequence data from Kenya collected between 2009 and 2018 showing: strain - virus strain identity; virus - virus identity; date - date of virus sampling; site - location of virus isolation in Kenya; region - region of virus isolation in Kenya; clade - genetic group membership; cluster - transmission cluster membership identified through ancestral state reconstruction.