Genomic epidemiology of the rotavirus G2P[4] strains in coastal Kenya pre- and post-rotavirus vaccine introduction, 2012 – 2018

The introduction of rotavirus vaccines into the national immunization programme in many countries has led to a decline of childhood diarrhoea disease burden. Coincidentally, the incidence of some rotavirus group A (RVA) genotypes, has increased, which may result from non-vaccine-type replacement. Here we investigate the evolutionary genomics of rotavirus G2P[4] which has shown an increase in countries that introduced the monovalent Rotarix® vaccine. We examined the 63 RVA G2P[4] strains sampled from children (aged below 13 years) admitted to Kilifi County Hospital, Coastal Kenya, pre- (2012 to June 2014) and post- (July 2014-2018) rotavirus vaccine introduction. All the 63 genome sequences showed a typical DS-1 like genome constellation G2-P[4]-I2-R2-C2-M2-A2-N2-T2-E2-H2. G2 sub-lineage IVa-3 strains predominated in the pre-vaccine era co-circulating with low numbers of G2 sub-lineage IVa-1 strains, whereas sub-lineage IVa-3 strains dominated the post-vaccine period. In addition, in the pre-vaccine period, P[4] sub-lineage IVa strains co-circulated with low numbers of P[4] lineage II strains, but P[4] sub-lineage IVa strains predominated in the post-vaccine period. On the global phylogeny, the Kenyan pre- and post-vaccine G2P[4] strains clustered separately, suggesting that different virus populations circulated in the two periods. However, the strains from both periods exhibited conserved amino acid changes in the known antigenic epitopes, suggesting that replacement of the predominant G2P[4] cluster was unlikely a result of immune escape. Our findings demonstrate that the pre- and post-vaccine G2P[4] strains circulating in Kilifi, coastal Kenya, differed genetically, but likely were antigenically similar. This information informs the discussion on the consequences of rotavirus vaccination on rotavirus diversity. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This study was funded by the Wellcome Trust (102975 and 203077). The authors Timothy Makori and Charles Agoti were supported by the Initiative to Develop African Research Leaders (IDeAL) through the DELTAS Africa Initiative (DEL-15-003). The DELTAS Africa Initiative is an independent funding scheme of the African Academy of Sciences (AAS) Alliance for Accelerating Excellence in Science in Africa (AESA) and supported by the New Partnership for Africa Development Planning and Coordinating Agency (NEPAD Agency) with funding from the Wellcome Trust (107769/Z/10/Z) and the UK government. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The scientific ethics review unit of Kenya Medical Research Institution (KEMRI) gave ethical approval for this work (REF: 3049 and 2861). I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes All the sequence data produced in the present work are available online under accessions under [MZ093788][1] to [MZ097268][2] and [OP677569][3] to [OP677754][4]. All the epidemiological produced in the present work are available online at Virus Epidemiology and Control Dataverse [1]: /lookup/external-ref?link_type=GEN&access_num=MZ093788&atom=%2Fmedrxiv%2Fearly%2F2022%2F10%2F24%2F2022.10.21.22281210.atom [2]: /lookup/external-ref?link_type=GEN&access_num=MZ097268&atom=%2Fmedrxiv%2Fearly%2F2022%2F10%2F24%2F2022.10.21.22281210.atom [3]: /lookup/external-ref?link_type=GEN&access_num=OP677569&atom=%2Fmedrxiv%2Fearly%2F2022%2F10%2F24%2F2022.10.21.22281210.atom [4]: /lookup/external-ref?link_type=GEN&access_num=OP677754&atom=%2Fmedrxiv%2Fearly%2F2022%2F10%2F24%2F2022.10.21.22281210.atom