Multiple Introductions and Predominance of Rotavirus Group A Genotype G3P[8] in Kilifi, Coastal Kenya, 4 Years after Nationwide Vaccine Introduction

• Type of Material: Article
• Authors: Mike J. Mwanga, Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme; Jennifer Verani, Emory University; Richard Omore, Center for Global Health Research (KEMRI-CGHR); Jacqueline E. Tate, Centers for Disease Control and Prevention; Umesh D. Parashar, Centers for Disease Control and Prevention; Nickson Murunga, Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme; Elijah Gicheru, Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme; Robert Breiman, Emory University; D. James Nokes, Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme; Charles N. Agoti, Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme
• Language: English
• Date: 2020-12-01
• Publisher: MDPI
• Publication Version: Final Published Version
• Copyright Statement: © 2020 by the authors.
• License: Creative Commons Attribution 4.0 International
• Final Published Version (URL): http://dx.doi.org/10.3390/pathogens9120981
• Title of Journal or Parent Work: PATHOGENS
• Volume: 9
• Issue: 12
• Start Page: 1
• End Page: 16
• Grant/Funding Information: This work was funded by Gavi, The Vaccine Alliance through Emory University, to the Rotavirus Immunization Program and Evaluation in Kenya (RIPEK) and the Wellcome Trust (grant numbers 203077 and 102975). CNA is supported through the DELTAS Africa Initiative [DEL-15-003]. The DELTAS Africa Initiative is an independent funding scheme of the African Academy of Sciences (AAS)‘s Alliance for Accelerating Excellence in Science in Africa (AESA) and supported by the New Partnership for Africa’s Development Planning and Coordinating Agency (NEPAD Agency) with funding from the Wellcome Trust [107769/Z/10/Z] and the UK government. Views expressed in this publication are those of the authors and not necessarily those of Gavi, AAS, NEPAD Agency, Wellcome Trust or the UK government.
• Keywords: Life Sciences & Biomedicine; rotavirus; Science & Technology; EMERGENCE; GASTROENTERITIS; VP7; STRAINS; Microbiology; EQUINE-LIKE; equine-like; phylogenetics; G3[P8]; G3 ROTAVIRUS; gastroenteritis
• Research Categories: Biology, Virology; Biology, Microbiology; Health Sciences, Medicine and Surgery

Abstract

Globally, rotavirus group A (RVA) remains a major cause of severe childhood diarrhea, despite the use of vaccines in more than 100 countries. RVA sequencing for local outbreaks facilitates investigation into strain composition, origins, spread, and vaccine failure. In 2018, we collected 248 stool samples from children aged less than 13 years admitted with diarrheal illness to Kilifi County Hospital, coastal Kenya. Antigen screening detected RVA in 55 samples (22.2%). Of these, VP7 (G) and VP4 (P) segments were successfully sequenced in 48 (87.3%) and phylogenetic analysis based on the VP7 sequences identified seven genetic clusters with six different GP combinations: G3P[8], G1P[8], G2P[4], G2P[8], G9P[8] and G12P[8]. The G3P[8] strains predominated the season (n = 37, 67.2%) and comprised three distinct G3 genetic clusters that fell within Lineage I and IX (the latter also known as equine-like G3 Lineage). Both the two G3 lineages have been recently detected in several countries. Our study is the first to document African children infected with G3 Lineage IX. These data highlight the global nature of RVA transmission and the importance of increasing global rotavirus vaccine coverage.