Molecular Profile and Antiviral Resistance of Hepatitis B and Human Immunodeficiency Viruses in Patients from an Army Conflict-Affected Region, South Kivu Province, Democratic Republic of Congo

Background: This study characterized HBV and HIV molecular profiles and drug resistance mutations in South Kivu, DRC. Methods: A cross-sectional study included 3,421 participants aged 18–70 years. Serological testing was performed using ELISA, and viral loads (VL) were quantified by GeneXpert. Molecular analyses involved 132 HBV-positive and 383 HIV-positive samples. Nucleic acids were extracted using QIAamp® MiniElute®. HBV genotyping was performed by PCR, and HIV-1 sequencing using the Viroseq® system. Results: HBV prevalence was 7.4% and >8% in high-risk groups (PLHIV, sex workers, survivors of sexual violence). HBV VL was low in 76.3% and high in 23.7%. Genotype A predominated (87.1%), mainly subgenotype A1 (93.4%), followed by genotype E (12.9%). HIV prevalence was 3.5%, highest among women aged 26–45 years. Among ART patients, 60.7% had undetectable VL. HIV subtypes A1 (38.1%) and C (27.4%) were most frequent, with CRFs (CRF11_cpx: 6.5%; CRF26_A5U: 3.1%). Drug resistance was detected in 23.3% of ART-naïve and 70.0% of treated patients, with predominant NNRTI resistance followed by NRTI (52.5%) and PI (15.6%). Integrase-associated polymorphisms were found in 4.2%. key mutations were M184I/V (96.8%) and K103N (74.1%). Conclusion: HBV and HIV show substantial prevalence, marked genetic diversity, and significant drug resistance in South Kivu.