{
  "abstract": "Orsay virus (OrV), a positive-sense RNA virus infecting Caenorhabditis elegans, establishes latent infections with minimal impact on host fitness. Using strand-specific RNA-seq across twelve time points spanning larval development, we characterized OrV replication dynamics and short-term evolutionary patterns. Viral accumulation followed four distinct phases and exhibited strong strand asymmetry, consistent with a predominance of the stamping-machine replication mechanism. Diversity analyses revealed that negative-strand genomes harbor more mutations than positive strands, with hotspots concentrated in the replicase C-terminal tail and structural protein regions. Many negative-strand variants failed to propagate to positive strands, suggesting within-cell constraints or purifying selection at the RNA level. We also report the first evidence of non-standard viral genomes in OrV, dominated by deletions in RNA2, including a recurrent large deletion that may function as a subgenomic RNA encoding a shorter version of the {delta} protein. These findings highlight replication asymmetry, strand-specific mutational filtering, and pervasive non-standard genomes as key features shaping OrV evolution during a primary infection.",
  "abstract_shown": true,
  "affiliations": [
    "I2SysBio-CSIC"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 4,
  "authors": [
    {
      "name": "M. J. Olmo-Uceda"
    },
    {
      "name": "D. Herek"
    },
    {
      "name": "V. G. Castiglioni"
    },
    {
      "affs": [
        0
      ],
      "name": "S. F. Elena"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/6ze6bww1j94cz.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.09.04.749430",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.09.04.749430v1.full",
  "id": "6ze6bww1j94cz",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.09.04.749430v1",
  "language": null,
  "licence": "CC-BY-NC-ND",
  "licence_label": "CC BY-NC-ND",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc-nd/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "evolutionary biology"
    ],
    [
      "openalex",
      "1311|Evolution and Genetic Dynamics"
    ]
  ],
  "openalex": "W7212018248",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.09.04.749430v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-09-04",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/6ze6bww1j94cz.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:20:38Z",
      "native_id": "10.64898/2026.09.04.749430",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.09.04.749430v2"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:evolutionary biology",
      "subfield": "evolutionary-biology"
    }
  ],
  "title": "The hidden diversity: Replication-strand asymmetry shapes short-term nucleotide and structural variation in an RNA virus",
  "title_text": "The hidden diversity: Replication-strand asymmetry shapes short-term nucleotide and structural variation in an RNA virus",
  "type": "preprint",
  "updated_at": "2026-10-30T12:21:32Z",
  "url": "https://research.draconitic.com/paper/6ze6bww1j94cz",
  "venue": "bioRxiv",
  "versions": []
}