Molecular characterization of hepatitis B virus genotype D and recombinant strains among inmates and blood donors in Northeastern Kenya

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Abstract Introduction Hepatitis B virus (HBV) persists as a major global public health burden, with hyperendemic prevalence in sub-Saharan Africa. Populations with elevated exposure to percutaneous transmission risks—including incarcerated individuals and healthcare workers—demonstrate heightened HBV susceptibility. Despite this, genomic data from Northeastern Kenya and Kenyan prison populations remain scarce. Objective To characterize HBV genotypic diversity circulating in Northeastern Kenya, among low risk (blood donors) and high-risk (prison inmates) populations. Methods A cross-sectional investigation compared HBV seroprevalence and genotypes between incarcerated individuals (n = 130) and voluntary blood donors (n = 130) in Garissa County, Northeastern Kenya. Sample size was calculated using Casagrande’s formula for binomial comparison powered at 80% (α=0.05) to detect a ≥2-fold seroprevalence difference between cohorts. Serum samples underwent Hepatitis B surface antigen (HBsAg) screening, PCR amplification of a 940-bp overlapping surface/polymerase gene, sequencing, and phylogenetic/recombination analyses of the resulting sequences. Results Seroprevalence was higher among incarcerated individuals (5.4%, 7/130) than blood donors (3.1%, 4/130). HBV DNA was detected in 22 samples. Genotype D dominated both cohorts (81.8%), while genotype A subgenotype A1 occurred exclusively in incarcerated participants (18.2%). All genotype D strains were recombinants: D/A (61%) and D/E (39%). Sequences are accessible in GenBank (accession numbers: PV816552 – PV816573 ). Conclusions This first genomic study of HBV in Kenyan prisons confirms incarcerated populations as high-risk. The predominance of genotype D—a novel finding in this region—and high recombinant frequency (100% of genotype D strains) underscore significant viral evolution. Expanded genomic surveillance is imperative to define HBV diversity, inform vaccine efficacy monitoring, and optimize control strategies in Northeastern Kenya.

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