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Abstract Background Herpes Simplex Virus type 2 (HSV-2) has public health importance as a leading cause of genital ulcers, a co-factor in HIV-1 acquisition and transmission and as a cause of neonatal herpes infections. Little is known of its epidemiology and burden in Coastal Kenya. Methods We screened plasma samples for HSV-2 infection from 826 women aged 15-34 years who participated in an HIV-1 survey in Kilifi in 2004. The sample comprised 563 women selected randomly from a demographic surveillance system (DSS) and 263 women who presented for voluntary counseling and testing (VCT). Predictors for HSV-2 seropositivity were determined using multivariate logistic regression. The incidence of HSV-2 infection and risk of neonatal herpes were estimated by a simple catalytic model fitted to age-seroprevalence data. Results HSV-2 prevalence was 32% in the DSS recruits vs. 44% in the VCT recruits (P < 0.001), while, HIV-1 prevalence was 8% in the DSS recruits vs. 12% in the VCT recruits (P = 0.12). Independent risk factors for HSV-2 infection in all women were: older age (30-34 years; odds ratio (OR) 10.5, 95% confidence interval (CI): 5.2 - 21.0), recruitment from VCT (OR 1.5, 95% CI: 1.1 - 2.1), history of genital ulcers (OR 1.7, 95% CI: 1.2 - 2.3) and HIV infection (OR 2.7, 95% CI: 1.6-4.6). Education beyond primary (OR 0.7, 95% CI: 0.5 - 0.9) was inversely associated with HSV-2 infection. In the DSS sample, HSV-2 incidence was estimated at 4 cases (95% CI: 3.3 - 4.4) per 100 women per year, 17 cases (95% CI: 16-18) per 1,000 pregnancies per year and 33 neonatal cases (95% CI: 31-36) per 100,000 births per year. Conclusions HSV-2 transmission is rapid following the onset of sexual activity and likely to result in a significant burden of genital ulcer disease. Nevertheless, the burden of neonatal HSV-2 can be predicted to be low. Educating young women about HSV-2 infection may help in reducing its burden in this semi-urban population.

The introduction of rotavirus vaccines into the national immunization programme in many countries has led to a decline in 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 sixty-three RVA G2P[4] strains sampled from children (aged below 13 years) admitted to Kilif County Hospital, coastal Kenya, pre- (2012 to June 2014) and post-(July 2014 to 2018) rotavirus vaccine introduction. All the sixty-three genome sequences showed a typical DS-1-like genome constellation (G2-P[4]-I2-R2-C2-M2-A2-N2-T2- E2-H2). Pre-vaccine G2 sequences predominantly classifed as sub-lineage IVa-3 and co-circulated with low numbers of sub-lineage IVa-1 strains, whereas post-vaccine G2 sequences mainly classifed into sub-lineage IVa-3. 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 fndings demonstrate that the pre- and post-vaccine G2P[4] strains circulating in Kilif, coastal Kenya, differed genetically but likely were antigenically similar. This information informs the discussion on the consequences of rotavirus vaccination on rotavirus diversity. [ABSTRACT FROM AUTHOR]

Human enteric adenovirus species F (HAdV-F) is a leading cause of childhood diarrhoeal deaths. The genomic analysis would be key to understanding transmission dynamics, potential drivers of disease severity, and vaccine development. However, currently, there are limited HAdV-F genomic data globally. Here, we sequenced and analysed HAdV-F from stool samples collected in coastal Kenya between 2013 and 2022. The samples were collected at Kilif County Hospital in coastal Kenya from children <13 years of age who reported a history of three or more loose stools in the previous 24 hours. The genomes were analysed together with the data from the rest of the world by phylogenetic analysis and mutational profling. Types and lineages were assigned based on phylogenetic clustering consistent with the previously described criteria and nomenclature. Participant clinical and demographic data were linked to genotypic data. Of ninety-one cases identifed using real-time Polymerase Chain Reaction, eighty-eight near-complete genomes were assembled, and these were classifed into HAdV-F40 (n = 41) and HAdV-F41 (n = 47). These types co-circulated throughout the study period. Three and four distinct lineages were observed for HAdV-F40 (Lineages 1–3) and HAdV-F41 (Lineages 1, 2A, 3A, 3C, and 3D). Types F40 and F41 coinfections were observed in fve samples and F41 and B7 in one sample. Two children with F40 and 41 coinfections were also infected with rotavirus and had moderate and severe diseases as defned using the Vesikari Scoring System, respectively. Intratypic recombination was found in four HAdV-F40 sequences occurring between Lineages 1 and 3. None of the HAdV-F41 cases had jaundice. This study provides evidence of extensive genetic diversity, coinfections, and recombination within HAdV-F40 in a rural coastal Kenya that will inform public health policy, vaccine development that includes the locally circulating lineages, and molecular diagnostic assay development. We recommend future comprehensive studies elucidating on HAdV-F genetic diversity and immunity for rational vaccine development. [ABSTRACT FROM AUTHOR]