{
  "abstract": "Lenacapavir, the first approved HIV-1 capsid inhibitor, is now being introduced for both treatment and pre-exposure prophylaxis, yet the capsid-coding region lies outside the pol fragment examined in routine genotypic resistance testing, and baseline data on capsid variability remain scarce, particularly in epidemics dominated by non-B lineages. We applied next-generation sequencing of the HIV-1 gag gene to 103 lenacapavir-naive individuals newly diagnosed in Bulgaria between 2023 and 2025. Nine lineages were identified. Subtype B accounted for 46.6% of the sequences, whereas non-B lineages together predominated (53.4%), led by sub-subtype F1 (13.6%) and CRF01_AE (8.7%); a further 10.7% remained unassigned and grouped predominantly with BF1 recombinant references. The distribution of these lineages differed significantly according to the probable route of transmission (p = 0.007). No major lenacapavir resistance-associated mutation was detected (0 of 103; 95% CI 0.0-3.6). Substitutions at position 107 were the only changes observed at a resistance-associated position: T107S in two individuals and a T107T/S mixture in one (2.9% combined). Notably, the two T107S sequences formed a CRF01_AE pair supported by a bootstrap value of 100, indicating that this accessory polymorphism can persist in closely related viruses. All viruses were genotypically predicted to remain susceptible to lenacapavir. These findings establish a molecular baseline for capsid surveillance in Bulgaria, a South-Eastern European country with a genetically diverse HIV-1 epidemic.",
  "abstract_shown": true,
  "affiliations": [
    "National Reference Confirmatory Laboratory of HIV, National Center of Infectious and Parasitic Diseases (NCIPD), 1504 Sofia, Bulgaria.",
    "National Reference Laboratory of Immunology, NCIPD, 1504 Sofia, Bulgaria.",
    "University Multi-Profile Hospital for Active Treatment of Infectious and Parasitic Diseases, 1606 Sofia, Bulgaria.",
    "Department of Infectious Diseases, Parasitology and Tropical Medicine, MU-Plovdiv, 4002 Plovdiv, Bulgaria.",
    "Clinic of Infectious Diseases, University Hospital \"Prof. Dr. G. Stranski\", 5800 Pleven, Bulgaria.",
    "Clinic of Infectious Diseases, University Hospital \"Prof. Dr. St. Kirkovich\", 6003 Stara Zagora, Bulgaria.",
    "University Hospital \"St. Marina\", 9010 Varna, Bulgaria."
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 15,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Ivailo Alexiev",
      "orcid": "0000-0002-3186-1124"
    },
    {
      "affs": [
        0
      ],
      "name": "Aleksandra Partsuneva"
    },
    {
      "affs": [
        0
      ],
      "name": "Reneta Dimitrova",
      "orcid": "0000-0001-7711-6798"
    },
    {
      "affs": [
        0
      ],
      "name": "Asya Kostadinova"
    },
    {
      "affs": [
        0
      ],
      "name": "Anna Gancheva"
    },
    {
      "affs": [
        0
      ],
      "name": "Lyubomira Grigorova",
      "orcid": "0000-0001-8563-5520"
    },
    {
      "affs": [
        0
      ],
      "name": "Kristina Stoyanova"
    },
    {
      "affs": [
        1
      ],
      "name": "Maria Nikolova"
    },
    {
      "affs": [
        1
      ],
      "name": "Radoslava Emilova",
      "orcid": "0000-0002-0018-1361"
    },
    {
      "affs": [
        2
      ],
      "name": "Nina Yancheva"
    },
    {
      "affs": [
        2
      ],
      "name": "Dimitar Strashimirov",
      "orcid": "0000-0001-9053-6949"
    },
    {
      "affs": [
        3
      ],
      "name": "Ivan Baltadzhiev"
    },
    {
      "affs": [
        4
      ],
      "name": "Tsetsa Doychinova"
    },
    {
      "affs": [
        5
      ],
      "name": "Pavlina Parusheva"
    },
    {
      "affs": [
        6
      ],
      "name": "Ivelina Todorova"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/dq95crp492gsg.bib",
  "cited_by": 0,
  "doi": "10.3390/pathogens15101011",
  "fulltext_url": "https://europepmc.org/articles/PMC13708529",
  "id": "dq95crp492gsg",
  "issns": [
    "2076-0817"
  ],
  "landing_url": "https://europepmc.org/article/MED/42931163",
  "language": "eng",
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "2725|HIV/AIDS drug development and treatment"
    ]
  ],
  "openalex": "W7214194693",
  "pdf_url": "https://europepmc.org/articles/PMC13708529?pdf=render",
  "pmcid": "PMC13708529",
  "pmid": "42931163",
  "published": "2026-09-24",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/dq95crp492gsg.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:22:01Z",
      "native_id": "MED:42931163",
      "source": "europepmc",
      "url": "https://europepmc.org/article/MED/42931163"
    }
  ],
  "subjects": [
    {
      "field": "medicine",
      "origin": "openalex:2725|HIV/AIDS drug development and treatment",
      "subfield": "infectious-disease"
    }
  ],
  "title": "Baseline Lenacapavir Resistance and Capsid Variability in Bulgaria: A Next-Generation Sequencing Study of Newly Diagnosed HIV-1 Infections.",
  "title_text": "Baseline Lenacapavir Resistance and Capsid Variability in Bulgaria: A Next-Generation Sequencing Study of Newly Diagnosed HIV-1 Infections.",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:22:01Z",
  "url": "https://research.draconitic.com/paper/dq95crp492gsg",
  "venue": "Pathogens (Basel, Switzerland)",
  "versions": []
}