{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T19:56:31Z","timestamp":1772222191489,"version":"3.50.1"},"reference-count":18,"publisher":"Public Library of Science (PLoS)","issue":"5","license":[{"start":{"date-parts":[[2025,5,30]],"date-time":"2025-05-30T00:00:00Z","timestamp":1748563200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000265","name":"Medical Research Council","doi-asserted-by":"publisher","award":["MC_ST_00034"],"award-info":[{"award-number":["MC_ST_00034"]}],"id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000265","name":"Medical Research Council","doi-asserted-by":"publisher","award":["MC_UU_12014\/3 and MC_UU_12014\/12"],"award-info":[{"award-number":["MC_UU_12014\/3 and MC_UU_12014\/12"]}],"id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["204870\/Z\/16\/Z"],"award-info":[{"award-number":["204870\/Z\/16\/Z"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS One"],"abstract":"<jats:sec id=\"sec007\">\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>Congenital cytomegalovirus disease (cCMV) is uncommon but can be severe. Investigations of the role of genome sequence variation in the causative virus (human cytomegalovirus, HCMV) in clinical outcome have to date depended on small sample numbers derived from fresh tissues. Extensive formalin-fixed, paraffin-embedded (FFPE) cCMV biorepositories established worldwide potentially provide much larger sample numbers for future investigations. However, there are no published reports of sequencing whole HCMV genomes from such material.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"sec008\">\n                    <jats:title>Objective<\/jats:title>\n                    <jats:p>To sequence whole HCMV genomes from cCMV FFPE material<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"sec009\">\n                    <jats:title>Study design<\/jats:title>\n                    <jats:p>Sixteen FFPE samples of foetal kidney or placental tissue were processed from ten cCMV cases in foetuses or neonates. Two commercial kits for extracting DNA from FFPE material were evaluated, HCMV DNA was enriched in the extracts, and the samples were sequenced on the Illumina platform. The sequence read datasets were analysed by genotyping, genome assembly and variant calling using a published software pipeline.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"sec010\">\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Whole HCMV genomes were sequenced for five cases using either DNA extraction kit.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"sec011\">\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>Sequencing whole HCMV genomes from cCMV FFPE material is feasible. This potentially facilitates future studies of the effects of HCMV variation on the clinical outcome of cCMV.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1371\/journal.pone.0318897","type":"journal-article","created":{"date-parts":[[2025,5,30]],"date-time":"2025-05-30T16:03:40Z","timestamp":1748621020000},"page":"e0318897","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["DNA sequencing of whole human cytomegalovirus genomes from formalin-fixed, paraffin-embedded tissues from congenital cytomegalovirus disease cases"],"prefix":"10.1371","volume":"20","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5843-1653","authenticated-orcid":true,"given":"Kathy K.","family":"Li","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nicol\u00e1s M.","family":"Su\u00e1rez","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Salvatore","family":"Camiolo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4991-9128","authenticated-orcid":true,"given":"Andrew J.","family":"Davison","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Richard J.","family":"Orton","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2025,5,30]]},"reference":[{"issue":"1","key":"pone.0318897.ref001","doi-asserted-by":"crossref","first-page":"86","DOI":"10.1128\/CMR.00062-12","article-title":"The \u201csilent\u201d global burden of congenital cytomegalovirus","volume":"26","author":"S Manicklal","year":"2013","journal-title":"Clin Microbiol Rev"},{"issue":"3","key":"pone.0318897.ref002","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1016\/j.idc.2015.05.009","article-title":"Strain variation and disease severity in congenital cytomegalovirus infection: in search of a viral marker","volume":"29","author":"R Arav-Boger","year":"2015","journal-title":"Infect Dis Clin North Am"},{"issue":"5","key":"pone.0318897.ref003","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1002\/rmv.544","article-title":"New estimates of the prevalence of neurological and sensory sequelae and mortality associated with congenital cytomegalovirus infection","volume":"17","author":"SC Dollard","year":"2007","journal-title":"Rev Med Virol"},{"issue":"9","key":"pone.0318897.ref004","doi-asserted-by":"crossref","first-page":"1413","DOI":"10.1097\/PAS.0b013e318290f171","article-title":"Diagnosis of congenital CMV using PCR performed on formalin-fixed, paraffin-embedded placental tissue","volume":"37","author":"AK Folkins","year":"2013","journal-title":"Am J Surg Pathol"},{"issue":"4","key":"pone.0318897.ref005","doi-asserted-by":"crossref","first-page":"115075","DOI":"10.1016\/j.diagmicrobio.2020.115075","article-title":"Utility of two DNA extraction methods using formalin-fixed paraffin-embedded tissues in identifying congenital cytomegalovirus infection by polymerase chain reaction","volume":"97","author":"A de la Cruz-de la Cruz","year":"2020","journal-title":"Diagn Microbiol Infect Dis"},{"issue":"6","key":"pone.0318897.ref006","article-title":"The isolation of nucleic acids from fixed, paraffin-embedded tissues-which methods are useful when?","volume":"2","author":"MTP Gilbert","year":"2007","journal-title":"PLoS One"},{"issue":"9","key":"pone.0318897.ref007","doi-asserted-by":"crossref","first-page":"1604","DOI":"10.1002\/jmv.24499","article-title":"Development and optimization of a sensitive TaqMan\u00ae real-time PCR with synthetic homologous extrinsic control for quantitation of Human 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Camiolo","year":"2020","journal-title":"Virus Evol"},{"issue":"1","key":"pone.0318897.ref011","doi-asserted-by":"crossref","first-page":"689","DOI":"10.1186\/s12864-019-6056-8","article-title":"Bioinformatics and DNA-extraction strategies to reliably detect genetic variants from FFPE breast tissue samples","volume":"20","author":"AV Bhagwate","year":"2019","journal-title":"BMC Genomics"},{"issue":"5","key":"pone.0318897.ref012","doi-asserted-by":"crossref","first-page":"781","DOI":"10.1093\/infdis\/jiz208","article-title":"Human cytomegalovirus genomes sequenced directly from clinical material: variation, multiple-strain infection, recombination, and gene loss","volume":"220","author":"NM Su\u00e1rez","year":"2019","journal-title":"J Infect Dis"},{"issue":"5","key":"pone.0318897.ref013","doi-asserted-by":"crossref","first-page":"792","DOI":"10.1093\/infdis\/jiz209","article-title":"Multiple-strain infections of human cytomegalovirus with high genomic diversity are common in breast milk from human immunodeficiency virus-infected women in Zambia","volume":"220","author":"NM Su\u00e1rez","year":"2019","journal-title":"J Infect Dis"},{"issue":"4","key":"pone.0318897.ref014","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"B Langmead","year":"2012","journal-title":"Nat Methods"},{"issue":"2","key":"pone.0318897.ref015","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1093\/bib\/bbs012","article-title":"Using tablet for visual exploration of second-generation sequencing data","volume":"14","author":"I Milne","year":"2013","journal-title":"Brief Bioinform"},{"issue":"8","key":"pone.0318897.ref016","doi-asserted-by":"crossref","first-page":"543","DOI":"10.1369\/0022155420945050","article-title":"Why formalin-fixed, paraffin-embedded biospecimens must be used in genomic medicine: an evidence-based review and conclusion","volume":"68","author":"W Mathieson","year":"2020","journal-title":"J Histochem Cytochem"},{"issue":"5","key":"pone.0318897.ref017","doi-asserted-by":"crossref","first-page":"809","DOI":"10.1086\/367900","article-title":"Inter- and intragenic variations complicate the molecular epidemiology of human cytomegalovirus","volume":"187","author":"L Rasmussen","year":"2003","journal-title":"J Infect Dis"},{"issue":"1","key":"pone.0318897.ref018","doi-asserted-by":"crossref","DOI":"10.1093\/ve\/vew017","article-title":"Islands of linkage in an ocean of pervasive recombination reveals two-speed evolution of human cytomegalovirus genomes","volume":"2","author":"F Lassalle","year":"2016","journal-title":"Virus Evol"}],"container-title":["PLOS 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