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

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.

To characterize HBV genotypic diversity circulating in Northeastern Kenya, among low risk (blood donors) and high-risk (prison inmates) populations.

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.

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).

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. Competing Interest Statement The authors have declared no competing interest. Funding Statement The author(s) received no specific funding for this work. 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: Kenyatta University Ethics and Review Committee (KU-ERC) 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, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes Data Availability The Sequences from the study are deposited in GenBank under Accession numbers: PV816552-PV816573