{"doi":"10.1371/journal.ppat.1012338","title":"Sequencing of Kaposi’s Sarcoma Herpesvirus (KSHV) genomes from persons of diverse ethnicities and provenances with KSHV-associated diseases demonstrate multiple infections, novel polymorphisms, and low intra-host variance","abstract":"Recently published near full-length KSHV genomes from a Cameroon Kaposi sarcoma case-control study showed strong evidence of viral recombination and mixed infections, but no sequence variations associated with disease. Using the same methodology, an additional 102 KSHV genomes from 76 individuals with KSHV-associated diseases have been sequenced. Diagnoses comprise all KSHV-associated diseases (KAD): Kaposi sarcoma (KS), primary effusion lymphoma (PEL), KSHV-associated large cell lymphoma (KSHV-LCL), a type of multicentric Castleman disease (KSHV-MCD), and KSHV inflammatory cytokine syndrome (KICS). Participants originated from 22 different countries, providing the opportunity to obtain new near full-length sequences of a wide diversity of KSHV genomes. These include near full-length sequence of genomes with KSHV K1 subtypes A, B, C, and F as well as subtype E, for which no full sequence was previously available. High levels of recombination were observed. Fourteen individuals (18%) showed evidence of infection with multiple KSHV variants (from two to four unique genomes). Twenty-six comparisons of sequences, obtained from various sampling sites including PBMC, tissue biopsies, oral fluids, and effusions in the same participants, identified near complete genome conservation between different biological compartments. Polymorphisms were identified in coding and non-coding regions, including indels in the K3 and K15 genes and sequence inversions here reported for the first time. One such polymorphism in KSHV ORF46, specific to the KSHV K1 subtype E2, encoded a mutation in the leucine loop extension of the uracil DNA glycosylase that results in alteration of biochemical functions of this protein. This confirms that KSHV sequence variations can have functional consequences warranting further investigation. This study represents the largest and most diverse analysis of KSHV genome sequences to date among individuals with KAD and provides important new information on global KSHV genomics.","journal":"PLoS Pathogens","year":2024,"id":436997,"datarank":0.44203286415678517,"base_score":2.4849066497880004,"endowment":2.4849066497880004,"self_citation_contribution":0.37273599746820013,"citation_network_contribution":0.06929686668858503,"self_endowment_contribution":0.37273599746820013,"citer_contribution":0.06929686668858503,"corpus_percentile":57.5694283283051,"corpus_rank":5486,"citation_count":11,"citer_count":8,"citers_with_citation_signal":5,"citers_with_endowment":5,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.8547,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":62.5,"fair_percentile":81.0149801284011,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":446314,"name":"Elena M. Cornejo Castro","orcid":null,"position":1,"is_corresponding":false},{"id":963132,"name":"Charles Goodman","orcid":"0000-0002-7968-9466","position":2,"is_corresponding":false},{"id":595081,"name":"Nazzarena Labo","orcid":null,"position":3,"is_corresponding":false},{"id":1245818,"name":"Isabella Liu","orcid":"0000-0003-2882-2383","position":4,"is_corresponding":false},{"id":446315,"name":"Nicholas C. Fisher","orcid":null,"position":5,"is_corresponding":false},{"id":696921,"name":"Kyle Moore","orcid":"0000-0002-1280-241X","position":6,"is_corresponding":false},{"id":743177,"name":"A. Jayakumaran Nair","orcid":"0000-0002-7005-478X","position":7,"is_corresponding":false},{"id":445261,"name":"Taina T. Immonen","orcid":"0000-0003-4521-0696","position":8,"is_corresponding":false},{"id":233486,"name":"Brandon F. Keele","orcid":"0000-0002-2381-1151","position":9,"is_corresponding":false},{"id":334816,"name":"Mark N. Polizzotto","orcid":"0000-0002-6446-183X","position":10,"is_corresponding":false},{"id":334814,"name":"Thomas S. Uldrick","orcid":"0000-0001-6959-0924","position":11,"is_corresponding":false},{"id":600044,"name":"Yunxiang Mu","orcid":"0000-0001-9754-2129","position":12,"is_corresponding":false},{"id":1246461,"name":"Tanuja Saswat","orcid":null,"position":13,"is_corresponding":false},{"id":433935,"name":"Laurie T. Krug","orcid":"0000-0002-9648-522X","position":14,"is_corresponding":false},{"id":433934,"name":"Kevin M. McBride","orcid":"0000-0001-9646-152X","position":15,"is_corresponding":false},{"id":334813,"name":"Kathryn Lurain","orcid":"0000-0002-5794-7292","position":16,"is_corresponding":false},{"id":334815,"name":"Ramya Ramaswami","orcid":"0000-0001-5709-4675","position":17,"is_corresponding":false},{"id":299038,"name":"Robert Yarchoan","orcid":"0000-0002-3057-1395","position":18,"is_corresponding":false},{"id":351604,"name":"Denise Whitby","orcid":"0000-0002-7407-2563","position":19,"is_corresponding":false},{"id":351603,"name":"Vickie Marshall","orcid":"0000-0002-4069-185X","position":0,"is_corresponding":true}],"reference_count":55,"raw_metadata":null,"created_at":"2026-07-19T02:00:29.872940Z","pmid":"39008527","pmcid":"PMC11271956","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":77.7778,"fair_a":68.75,"fair_i":60.0,"fair_r":25.0,"fair_zscore":1.1103,"fair_rationale":{"fair_score":62.5,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":77.78,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"Data Availability Data is available in GenBank referencing accession numbers OR829339-OR829404.","grounded":true,"rationale":"GenBank accession numbers are a persistent identifier scheme accepted in the rubric. 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NIH DMS Element 4 asks for both; most papers give neither.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Data is available in GenBank referencing accession numbers OR829339-OR829404.","why":"The paper states that the data are available now, but it does not mention how long they will persist; this is an availability-timing statement without a persistence commitment. [majority verdict 'partial' (3/5 passes agreed)]","gain":0.0,"priority":"useful","scored":false}],"suggestions":["Attach a standard, machine-readable open licence to the deposit — CC0 or CC BY, which is what Horizon Europe and most funders expect — and print the licence identifier in the paper. 'Free to use' is not a licence: it grants nothing a reuser's institution can rely on.","Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. Cite the genomics / sequencing repository accession (e.g. from GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA)) in the reference list.","Publish the analysis code in a public forge, archive a tagged release with a DOI (Zenodo/Software Heritage), and cite that DOI in the paper. NIH DMS Element 2 asks for the tools and code, not only the data — and 'available on request' is not a locator. Archive the analysis code in a versioned repository (GitHub + a Zenodo release DOI).","Version the deposit and cite the exact version analysed (a version-specific DOI, or an accession with its version suffix). A reader reproducing your work against 'the current release' is reproducing it against a different dataset.","Add a 'Data Records' section: itemise every file in the deposit and every variable or sample it holds, with counts and units. Describe the dataset as an object in its own right, not as a by-product of the findings — this is what makes it discoverable to someone who is not looking for your paper."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v8","fulltext_source":"epmc_xml"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v8","fair_fulltext_source":"epmc_xml","fair_has_llm":true,"fair_computed_at":"2026-07-20T12:20:27.630977Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}