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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.<\/jats:p>","DOI":"10.1371\/journal.ppat.1012338","type":"journal-article","created":{"date-parts":[[2024,7,15]],"date-time":"2024-07-15T13:45:14Z","timestamp":1721051114000},"page":"e1012338","update-policy":"https:\/\/doi.org\/10.1371\/journal.ppat.corrections_policy","source":"Crossref","is-referenced-by-count":15,"title":["Sequencing of Kaposi\u2019s 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"],"prefix":"10.1371","volume":"20","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4069-185X","authenticated-orcid":true,"given":"Vickie 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with genetic instability and genomic disorders","volume":"185","author":"D Porubsky","year":"2022","journal-title":"Cell"},{"issue":"11","key":"ppat.1012338.ref036","doi-asserted-by":"crossref","first-page":"1773","DOI":"10.1093\/hmg\/2.11.1773","article-title":"Characteristic mRNA abnormality found in half the patients with severe haemophilia A is due to large DNA inversions","volume":"2","author":"J Naylor","year":"1993","journal-title":"Hum Mol Genet"},{"key":"ppat.1012338.ref037","article-title":"Long-read sequencing resolves a complex structural variant in PRKN Parkinson\u2019s disease.","author":"K Daida","year":"2023","journal-title":"medRxiv"},{"issue":"19","key":"ppat.1012338.ref038","article-title":"Exome Sequencing and Optical Genome Mapping in Molecularly Unsolved Cases of Duchenne Muscular Dystrophy: Identification of a Causative X-Chromosomal Inversion Disrupting the DMD Gene.","volume":"24","author":"LS Erbe","year":"2023","journal-title":"Int J Mol Sci"},{"issue":"22","key":"ppat.1012338.ref039","doi-asserted-by":"crossref","DOI":"10.1128\/JVI.01132-18","article-title":"Sequence Variation of Epstein-Barr Virus: Viral Types, Geography, Codon Usage, and Diseases.","volume":"92","author":"S Correia","year":"2018","journal-title":"J Virol"},{"issue":"9","key":"ppat.1012338.ref040","doi-asserted-by":"crossref","DOI":"10.3390\/v15091935","article-title":"E3 Ubiquitin Ligases in Gammaherpesviruses and HIV: A Review of Virus Adaptation and Exploitation.","volume":"15","author":"J Oswald","year":"2023","journal-title":"Viruses"},{"issue":"24","key":"ppat.1012338.ref041","doi-asserted-by":"crossref","first-page":"3544","DOI":"10.1182\/blood-2014-07-586800","article-title":"Rituximab plus liposomal doxorubicin in HIV-infected patients with KSHV-associated multicentric Castleman disease","volume":"124","author":"TS Uldrick","year":"2014","journal-title":"Blood"},{"issue":"1","key":"ppat.1012338.ref042","doi-asserted-by":"crossref","first-page":"e1008114","DOI":"10.1371\/journal.ppat.1008114","article-title":"Signatures of oral microbiome in HIV-infected individuals with oral Kaposi\u2019s sarcoma and cell-associated KSHV DNA","volume":"16","author":"M Gruffaz","year":"2020","journal-title":"PLoS Pathog"},{"issue":"1","key":"ppat.1012338.ref043","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1002\/ijc.10190","article-title":"Prevalence of Kaposi\u2019s sarcoma-associated herpesvirus infection in sex workers and women from the general population in Spain","volume":"98","author":"S de Sanjose","year":"2002","journal-title":"Int J Cancer"},{"issue":"1","key":"ppat.1012338.ref044","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1093\/molbev\/msu300","article-title":"IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies","volume":"32","author":"LT Nguyen","year":"2015","journal-title":"Mol Biol Evol"},{"issue":"W1","key":"ppat.1012338.ref045","doi-asserted-by":"crossref","first-page":"W232","DOI":"10.1093\/nar\/gkw256","article-title":"W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis","volume":"44","author":"J Trifinopoulos","year":"2016","journal-title":"Nucleic Acids Res"},{"issue":"2","key":"ppat.1012338.ref046","doi-asserted-by":"crossref","first-page":"254","DOI":"10.1093\/molbev\/msj030","article-title":"Application of phylogenetic networks in evolutionary studies","volume":"23","author":"DH Huson","year":"2006","journal-title":"Mol Biol Evol"},{"issue":"1","key":"ppat.1012338.ref047","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1093\/bioinformatics\/14.1.68","article-title":"SplitsTree: analyzing and visualizing evolutionary data","volume":"14","author":"DH Huson","year":"1998","journal-title":"Bioinformatics"},{"issue":"3","key":"ppat.1012338.ref048","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"SF Altschul","year":"1990","journal-title":"J Mol Biol"},{"key":"ppat.1012338.ref049","author":"RC Team","year":"2023","journal-title":"R: A Language and Environment for Statistical Computing"},{"key":"ppat.1012338.ref050","author":"P. Lindenbaum","year":"2015","journal-title":"Jvarkit: java utilities for bioinformatics"},{"issue":"2","key":"ppat.1012338.ref051","doi-asserted-by":"crossref","DOI":"10.1093\/gigascience\/giab008","article-title":"Twelve years of SAMtools and BCFtools.","volume":"10","author":"P Danecek","year":"2021","journal-title":"Gigascience"},{"issue":"21","key":"ppat.1012338.ref052","doi-asserted-by":"crossref","first-page":"2987","DOI":"10.1093\/bioinformatics\/btr509","article-title":"A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data","volume":"27","author":"H. Li","year":"2011","journal-title":"Bioinformatics"},{"issue":"15","key":"ppat.1012338.ref053","doi-asserted-by":"crossref","first-page":"2156","DOI":"10.1093\/bioinformatics\/btr330","article-title":"The variant call format and VCFtools","volume":"27","author":"P Danecek","year":"2011","journal-title":"Bioinformatics"},{"issue":"1","key":"ppat.1012338.ref054","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1111\/1755-0998.12549","article-title":"vcfr: a package to manipulate and visualize variant call format data in R.","volume":"17","author":"BJ Knaus","year":"2017","journal-title":"Mol Ecol Resour"}],"updated-by":[{"DOI":"10.1371\/journal.ppat.1012338","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2024,7,25]],"date-time":"2024-07-25T00:00:00Z","timestamp":1721865600000}}],"container-title":["PLOS Pathogens"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.ppat.1012338","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,7,25]],"date-time":"2024-07-25T13:51:04Z","timestamp":1721915464000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.ppat.1012338"}},"subtitle":[],"editor":[{"given":"Wolfram","family":"Brune","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2024,7,15]]},"references-count":54,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2024,7,15]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.ppat.1012338","relation":{},"ISSN":["1553-7374"],"issn-type":[{"value":"1553-7374","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,7,15]]}}}