{
  "abstract": "Cryptosporidium causes diarrhea and high mortality in young children in Africa and southern Asia. Low oocyst counts in stool often limit whole-genome sequencing from clinical samples. Here, we enrich for Cryptosporidium genomic DNA directly from stool samples using 74,973 RNA baits (CryptoCap_75K; 8.2 Mb) derived from gene-rich areas (100% coding capacity) within the Cryptosporidium parvum genome. This method produces genome-wide sequence data with sufficient depth and breadth of coverage using as few as 25 oocysts, including divergent species such as Cryptosporidium ubiquitum . To minimize reference bias, we utilize a dual-mapping strategy that integrates reads aligned to both C. parvum and C. ubiquitum to capture lineage-specific variation. Phylogenetic networks, haplotypes, and admixture analyses identify three C. ubiquitum groups, A and B exclusive to humans, with B showing evidence of admixture, whereas C is zoonotic. Group-specific polymorphisms cluster within discrete genomic regions, suggesting conserved haploblocks associate with host adaptation. This capture-based genomics approach provides high-resolution insights into Cryptosporidium population genetics and lays the groundwork for studies of zoonotic transmission, anthroponosis, and GWAS directly from clinical material.",
  "abstract_shown": true,
  "affiliations": [],
  "article_type": null,
  "arxiv": null,
  "author_total": 12,
  "authors": [
    {
      "name": "E. V. C. Alves-Ferreira"
    },
    {
      "name": "A. Khan"
    },
    {
      "name": "M. D. Tettey"
    },
    {
      "name": "F. Ihara",
      "orcid": "0000-0003-2453-7710"
    },
    {
      "name": "H. Vogel"
    },
    {
      "name": "S. Botchie"
    },
    {
      "name": "I. Ayi"
    },
    {
      "name": "M. C. Pawlowic",
      "orcid": "0000-0003-2002-6681"
    },
    {
      "name": "G. Robinson",
      "orcid": "0000-0002-6594-2408"
    },
    {
      "name": "R. M. Chalmers"
    },
    {
      "name": "H. A. Lorenzi",
      "orcid": "0000-0003-0910-7894"
    },
    {
      "name": "M. E. Grigg",
      "orcid": "0000-0003-3465-3782"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/21w8whp8thzyg.bib",
  "cited_by": 0,
  "doi": "10.1038/s41467-026-78927-6",
  "fulltext_url": null,
  "id": "21w8whp8thzyg",
  "issns": [
    "2041-1723"
  ],
  "landing_url": "https://www.nature.com/articles/s41467-026-78927-6",
  "language": null,
  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "2405|Parasitic Infections and Diagnostics"
    ]
  ],
  "openalex": "W7223467021",
  "pdf_url": "https://www.nature.com/articles/s41467-026-78927-6_reference.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-24",
  "publisher": "Springer Science and Business Media LLC",
  "ris": "https://research.draconitic.com/paper/21w8whp8thzyg.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:17:39Z",
      "native_id": "10.1038/s41467-026-78927-6",
      "source": "crossref",
      "url": "https://www.nature.com/articles/s41467-026-78927-6"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "openalex:2405|Parasitic Infections and Diagnostics",
      "subfield": "microbiology"
    }
  ],
  "title": "Phylogenomics of captured Cryptosporidium sequenced directly from patient samples identifies clade-specific genomic architecture and host-adapted lineages",
  "title_text": "Phylogenomics of captured Cryptosporidium sequenced directly from patient samples identifies clade-specific genomic architecture and host-adapted lineages",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:17:39Z",
  "url": "https://research.draconitic.com/paper/21w8whp8thzyg",
  "venue": "Nature Communications",
  "versions": []
}