Replication Data for: Rotavirus group A genotype circulation patterns across Kenya before and after nationwide vaccine introduction, 2010-2018

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Mwanga, Mike J.; Owor, Betty E.; Ochieng, John B.; Odundo, elizabeth; Ngama, Mwanajuma; Ogwel, Billy; Onyango, clayton; Juma, Jane; Njeru, Regina; Gicheru, Elijah; Otieno, Grieven P.; Khagayi, Sammy; Agoti, Charles N.; Omore, Richard; Bigogo, Godfrey M.; Addo O. Yaw; Seheri, Mapaseka; Tate, Jacqueline E.; Parashar, Umesh D.; Hunsperger Elizabeth; Verani, Jennifer R.; Breiman, Robert F.; Nokes, D. James, 2020, "Replication Data for: Rotavirus group A genotype circulation patterns across Kenya before and after nationwide vaccine introduction, 2010-2018", https://doi.org/10.7910/DVN/0VQ2OK, Harvard Dataverse, V1, UNF:6:B6X36oRA5IhzQ/2U6PxSdg== [fileUNF]
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Description

These data was derived from stool samples collected from children with acute gastroenteritis, who reported to Kilifi County Hospital, Siaya County Referral Hospital, Lwak Mission Hospital and Tabitha Clinic in Kibera Nairobi, with diarrhoea symptoms. The surveillance was conducted between January 2010 to December 2018. The study was aimed at describing the distribution, circulation patterns of group A rotavirus (RVA) strains circulating Kenya. This will ultimately be important in estimating the performance of a Rotavirus vaccine that was introduced in mid 2014, in Kenya.

Sequence data was derived from Rotavirus positive samples identified by enzyme immunoassay method (ELISA) and subsequently sequenced by the di-deoxy Sanger method. After read assembly and sequence clean-up, G (derived from the VP7 glycoprotein) and P (derived from VP4 protease sensitive protein), genotypes were determined by use of NCBI BLAST and VIPR an established online RVA genotyping tool. The data was then analyzed in excel and R.

Multiple sequence alignment was performed using MAFFT tool. Sequence visualization was undertaken using AliView. Phylogenetic trees were inferred in iqtree and visualized using Figtree. Nucleotide distances matrixes were prepared using the p-distance algorithm inferred in MEGA v10.

Subject Medicine, Health and Life Sciences
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