{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,1]],"date-time":"2026-08-01T00:43:16Z","timestamp":1785544996212,"version":"3.56.0"},"update-to":[{"DOI":"10.1371\/journal.ppat.1013967","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,2,13]],"date-time":"2026-02-13T00:00:00Z","timestamp":1770940800000}}],"reference-count":53,"publisher":"Public Library of Science (PLoS)","issue":"2","license":[{"start":{"date-parts":[[2026,2,9]],"date-time":"2026-02-09T00:00:00Z","timestamp":1770595200000},"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":["MR\/T000376\/1"],"award-info":[{"award-number":["MR\/T000376\/1"]}],"id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Wellcome Trust and Royal Society","award":["220620\/Z\/20\/Z"],"award-info":[{"award-number":["220620\/Z\/20\/Z"]}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["Isaac Newton Trust\/Wellcome Trust ISSF\/University of Cambridge Joint Research Grant"],"award-info":[{"award-number":["Isaac Newton Trust\/Wellcome Trust ISSF\/University of Cambridge Joint Research Grant"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["220814\/Z\/20\/Z"],"award-info":[{"award-number":["220814\/Z\/20\/Z"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000265","name":"Medical Research Council","doi-asserted-by":"publisher","award":["MRC DTP studentship"],"award-info":[{"award-number":["MRC DTP studentship"]}],"id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000265","name":"Medical Research Council","doi-asserted-by":"publisher","award":["MRC DTP Studentship"],"award-info":[{"award-number":["MRC DTP Studentship"]}],"id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Department of Pathology, University of Cambridge","award":["Gwynaeth Pretty PhD studentship"],"award-info":[{"award-number":["Gwynaeth Pretty PhD studentship"]}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["219447\/Z\/19\/Z"],"award-info":[{"award-number":["219447\/Z\/19\/Z"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plospathogens.org"],"crossmark-restriction":false},"short-container-title":["PLoS Pathog"],"abstract":"<jats:p>\n                    Enteroviruses comprise a large group of mammalian pathogens that often utilize two open reading frames (ORFs) to encode their proteins: the upstream protein (UP) and the main polyprotein. In some enteroviruses, in addition to the canonical upstream AUG (uAUG), there is another AUG that may represent an alternative upstream initiation site. An analysis of enterovirus sequences containing additional upstream AUGs identified several clusters, including strains of pathogenic\n                    <jats:italic>Enterovirus alphacoxsackie<\/jats:italic>\n                    and\n                    <jats:italic>E. coxsackiepol<\/jats:italic>\n                    . Using ribosome profiling on coxsackievirus CVA13 (\n                    <jats:italic>E. coxsackiepol<\/jats:italic>\n                    ), we demonstrate that both upstream AUG codons can be used for translation initiation in infected cells. Moreover, we confirm translation from both upstream AUGs using a reporter system. Mutating the additional upstream AUG in the context of CVA13 did not result in phenotypic changes in immortalized cell lines. However, the wild-type virus outcompeted this mutant in human intestinal organoids and differentiated neuronal systems, representing an advantage in physiologically relevant infection sites. Mutation of the stop codon of the shorter upstream ORF led to dysregulated translation of the other ORFs in the reporter system, suggesting a potential role for the additional uORF in modulating the expression level of the other ORFs. Additionally, we demonstrate regulation of uORF translation in response to stress. These findings reveal the remarkable plasticity of enterovirus IRES-mediated initiation and the competitive advantage of double-upstream-AUG-containing viruses in terminally differentiated intestinal organoids and neuronal systems.\n                  <\/jats:p>","DOI":"10.1371\/journal.ppat.1013967","type":"journal-article","created":{"date-parts":[[2026,2,9]],"date-time":"2026-02-09T18:40:01Z","timestamp":1770662401000},"page":"e1013967","update-policy":"https:\/\/doi.org\/10.1371\/journal.ppat.corrections_policy","source":"Crossref","is-referenced-by-count":3,"title":["Flexibility and modulation of translation initiation in enterovirus genomes"],"prefix":"10.1371","volume":"22","author":[{"given":"Rhian L.","family":"O'Connor","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Georgia M.","family":"Cook","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jacqueline","family":"Hankinson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ksenia","family":"Fominykh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samantha H.","family":"Cheng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel A.","family":"Nash","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aur\u00e9lie","family":"Cenier","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Komal M.","family":"Nayak","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephen C.","family":"Graham","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Janet E.","family":"Deane","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthias","family":"Zilbauer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew E.","family":"Firth","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6605-0727","authenticated-orcid":true,"given":"Valeria","family":"Lulla","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2026,2,9]]},"reference":[{"issue":"5","key":"ppat.1013967.ref001","doi-asserted-by":"crossref","first-page":"479","DOI":"10.1097\/QCO.0000000000000187","article-title":"The epidemiology of non-polio enteroviruses: recent advances and outstanding questions","volume":"28","author":"M Pons-Salort","year":"2015","journal-title":"Curr Opin Infect Dis"},{"issue":"6","key":"ppat.1013967.ref002","doi-asserted-by":"crossref","first-page":"368","DOI":"10.1038\/s41579-018-0005-4","article-title":"The life cycle of non-polio enteroviruses and how to target it","volume":"16","author":"J Baggen","year":"2018","journal-title":"Nat Rev Microbiol"},{"issue":"1","key":"ppat.1013967.ref003","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1002\/jmv.24933","article-title":"Non-polio enterovirus detection with acute flaccid paralysis: a systematic review","volume":"90","author":"S Suresh","year":"2018","journal-title":"J Med Virol"},{"issue":"1","key":"ppat.1013967.ref004","doi-asserted-by":"crossref","first-page":"413","DOI":"10.1007\/s00018-024-05450-6","article-title":"Understanding neurotropic enteric viruses: routes of infection and mechanisms of attenuation","volume":"81","author":"V Lulla","year":"2024","journal-title":"Cell Mol Life Sci"},{"issue":"2","key":"ppat.1013967.ref005","doi-asserted-by":"crossref","first-page":"280","DOI":"10.1038\/s41564-018-0297-1","article-title":"An upstream protein-coding region in enteroviruses modulates virus infection in gut epithelial cells","volume":"4","author":"V Lulla","year":"2019","journal-title":"Nat Microbiol"},{"issue":"1","key":"ppat.1013967.ref006","doi-asserted-by":"crossref","first-page":"4066","DOI":"10.1038\/s41467-019-12040-9","article-title":"A second open reading frame in human enterovirus determines viral replication in intestinal epithelial cells","volume":"10","author":"H Guo","year":"2019","journal-title":"Nat Commun"},{"issue":"1","key":"ppat.1013967.ref007","doi-asserted-by":"crossref","first-page":"76","DOI":"10.1002\/embj.201386124","article-title":"The mechanism of translation initiation on Type 1 picornavirus IRESs","volume":"33","author":"TR Sweeney","year":"2014","journal-title":"EMBO J"},{"issue":"10","key":"ppat.1013967.ref008","doi-asserted-by":"crossref","first-page":"6312","DOI":"10.1128\/jvi.68.10.6312-6322.1994","article-title":"Effect of mutations downstream of the internal ribosome entry site on initiation of poliovirus protein synthesis","volume":"68","author":"CU Hellen","year":"1994","journal-title":"J Virol"},{"issue":"12","key":"ppat.1013967.ref009","doi-asserted-by":"crossref","first-page":"4486","DOI":"10.1128\/jvi.62.12.4486-4492.1988","article-title":"Mutational analysis of upstream AUG codons of poliovirus RNA","volume":"62","author":"J Pelletier","year":"1988","journal-title":"J Virol"},{"key":"ppat.1013967.ref010","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkm256","article-title":"Advantages of combined transmembrane topology and signal peptide prediction--the Phobius web server","volume":"35","author":"L K\u00e4ll","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"ppat.1013967.ref011","doi-asserted-by":"crossref","first-page":"3360","DOI":"10.1099\/vir.0.83124-0","article-title":"Complete genome sequences for nine simian enteroviruses","volume":"88","author":"MS Oberste","year":"2007","journal-title":"J Gen Virol"},{"issue":"37","key":"ppat.1013967.ref012","article-title":"Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution","volume":"109","author":"S Lee","year":"2012","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"1","key":"ppat.1013967.ref013","doi-asserted-by":"crossref","first-page":"4070","DOI":"10.1038\/s41467-020-17906-x","article-title":"A hidden gene in astroviruses encodes a viroporin","volume":"11","author":"V Lulla","year":"2020","journal-title":"Nat Commun"},{"issue":"2","key":"ppat.1013967.ref014","doi-asserted-by":"crossref","first-page":"513","DOI":"10.1093\/nar\/gkw1190","article-title":"Insights into the mechanisms of eukaryotic translation gained with ribosome profiling","volume":"45","author":"DE Andreev","year":"2017","journal-title":"Nucleic Acids Res"},{"issue":"2","key":"ppat.1013967.ref015","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1005473","article-title":"High-resolution analysis of coronavirus gene expression by RNA sequencing and ribosome profiling","volume":"12","author":"N Irigoyen","year":"2016","journal-title":"PLoS Pathog"},{"issue":"7","key":"ppat.1013967.ref016","article-title":"Attenuation hotspots in neurotropic human astroviruses","volume":"21","author":"H Ali","year":"2023","journal-title":"PLoS Biol"},{"issue":"1","key":"ppat.1013967.ref017","doi-asserted-by":"crossref","DOI":"10.1002\/cpcb.51","article-title":"Transcription factor-mediated differentiation of human iPSCs into neurons","volume":"79","author":"MS Fernandopulle","year":"2018","journal-title":"Curr Protoc Cell Biol"},{"issue":"2","key":"ppat.1013967.ref018","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1016\/j.virusres.2008.07.014","article-title":"The structure-function relationship of the enterovirus 3\u2019-UTR","volume":"139","author":"J Zoll","year":"2009","journal-title":"Virus Res"},{"issue":"16","key":"ppat.1013967.ref019","doi-asserted-by":"crossref","first-page":"8396","DOI":"10.1128\/JVI.00321-07","article-title":"Genetic adaptation to untranslated region-mediated enterovirus growth deficits by mutations in the nonstructural proteins 3AB and 3CD","volume":"81","author":"P Florez de Sessions","year":"2007","journal-title":"J Virol"},{"issue":"21","key":"ppat.1013967.ref020","doi-asserted-by":"crossref","first-page":"10272","DOI":"10.1073\/pnas.89.21.10272","article-title":"Translational enhancement of the poliovirus 5\u2019 noncoding region mediated by virus-encoded polypeptide 2A","volume":"89","author":"SJ Hambidge","year":"1992","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"2","key":"ppat.1013967.ref021","doi-asserted-by":"crossref","first-page":"729","DOI":"10.1006\/viro.1994.1588","article-title":"A conserved AUG triplet in the 5\u2019 nontranslated region of poliovirus can function as an initiation codon in vitro and in vivo","volume":"204","author":"TV Pestova","year":"1994","journal-title":"Virology"},{"issue":"19","key":"ppat.1013967.ref022","doi-asserted-by":"crossref","first-page":"9557","DOI":"10.1093\/nar\/gks762","article-title":"Translation termination efficiency modulates ATF4 response by regulating ATF4 mRNA translation at 5\u2019 short ORFs","volume":"40","author":"H Ait Ghezala","year":"2012","journal-title":"Nucleic Acids Res"},{"issue":"19","key":"ppat.1013967.ref023","doi-asserted-by":"crossref","first-page":"11089","DOI":"10.1073\/pnas.95.19.11089","article-title":"Proteolysis of human eukaryotic translation initiation factor eIF4GII, but not eIF4GI, coincides with the shutoff of host protein synthesis after poliovirus infection","volume":"95","author":"A Gradi","year":"1998","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"13","key":"ppat.1013967.ref024","doi-asserted-by":"crossref","first-page":"7029","DOI":"10.1073\/pnas.111145798","article-title":"Molecular mechanisms of translation initiation in eukaryotes","volume":"98","author":"TV Pestova","year":"2001","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"23","key":"ppat.1013967.ref025","doi-asserted-by":"crossref","first-page":"9197","DOI":"10.1073\/pnas.0900153106","article-title":"Direct functional interaction of initiation factor eIF4G with type 1 internal ribosomal entry sites","volume":"106","author":"S de Breyne","year":"2009","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"1","key":"ppat.1013967.ref026","doi-asserted-by":"crossref","first-page":"1076","DOI":"10.1038\/s41467-021-21394-y","article-title":"Determinants of genome-wide distribution and evolution of uORFs in eukaryotes","volume":"12","author":"H Zhang","year":"2021","journal-title":"Nat Commun"},{"issue":"33","key":"ppat.1013967.ref027","doi-asserted-by":"crossref","first-page":"16927","DOI":"10.1074\/jbc.R116.733899","article-title":"Upstream open reading frames differentially regulate gene-specific translation in the integrated stress response","volume":"291","author":"SK Young","year":"2016","journal-title":"J Biol Chem"},{"issue":"15","key":"ppat.1013967.ref028","doi-asserted-by":"crossref","first-page":"8922","DOI":"10.1074\/jbc.273.15.8922","article-title":"Mechanism of sodium arsenite-mediated induction of heme oxygenase-1 in hepatoma cells. Role of mitogen-activated protein kinases","volume":"273","author":"KK Elbirt","year":"1998","journal-title":"J Biol Chem"},{"issue":"7","key":"ppat.1013967.ref029","doi-asserted-by":"crossref","first-page":"546","DOI":"10.1016\/j.tim.2017.01.010","article-title":"Regulation mechanisms of viral IRES-driven translation","volume":"25","author":"K-M Lee","year":"2017","journal-title":"Trends Microbiol"},{"issue":"10","key":"ppat.1013967.ref030","doi-asserted-by":"crossref","DOI":"10.1002\/pmic.201700255","article-title":"Viral short ORFs and their possible functions","volume":"18","author":"Y Finkel","year":"2018","journal-title":"Proteomics"},{"issue":"20","key":"ppat.1013967.ref031","doi-asserted-by":"crossref","first-page":"12425","DOI":"10.1093\/nar\/gku981","article-title":"Mapping overlapping functional elements embedded within the protein-coding regions of RNA viruses","volume":"42","author":"AE Firth","year":"2014","journal-title":"Nucleic Acids Res"},{"issue":"7","key":"ppat.1013967.ref032","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pbio.2003903","article-title":"Genome-wide maps of ribosomal occupancy provide insights into adaptive evolution and regulatory roles of uORFs during Drosophila development","volume":"16","author":"H Zhang","year":"2018","journal-title":"PLoS Biol"},{"key":"ppat.1013967.ref033","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.03528","article-title":"Extensive translation of small Open Reading Frames revealed by Poly-Ribo-Seq","volume":"3","author":"JL Aspden","year":"2014","journal-title":"Elife"},{"issue":"1","key":"ppat.1013967.ref034","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1016\/j.virol.2005.09.015","article-title":"One hundred years of poliovirus pathogenesis","volume":"344","author":"VR Racaniello","year":"2006","journal-title":"Virology"},{"issue":"1","key":"ppat.1013967.ref035","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1006\/viro.1996.0360","article-title":"Poliovirus neurovirulence correlates with the presence of a cryptic AUG upstream of the initiator codon","volume":"221","author":"OR Slobodskaya","year":"1996","journal-title":"Virology"},{"issue":"2","key":"ppat.1013967.ref036","doi-asserted-by":"crossref","first-page":"515","DOI":"10.1128\/jvi.57.2.515-525.1986","article-title":"Mapping of sequences required for mouse neurovirulence of poliovirus type 2 Lansing","volume":"57","author":"N La Monica","year":"1986","journal-title":"J Virol"},{"issue":"5","key":"ppat.1013967.ref037","doi-asserted-by":"crossref","first-page":"105107","DOI":"10.1016\/j.micinf.2023.105107","article-title":"The internal ribosome entry site determines the neurotropic potential of enterovirus A71","volume":"25","author":"G-H Wu","year":"2023","journal-title":"Microbes Infect"},{"key":"ppat.1013967.ref038","first-page":"112904","article-title":"Zika viruses encode multiple upstream open reading frames in the 5\u2032 viral region with a role in neurotropism","author":"C Lef\u00e8vre","year":"2023","journal-title":"bioRxiv"},{"issue":"1","key":"ppat.1013967.ref039","doi-asserted-by":"crossref","first-page":"300","DOI":"10.1038\/s41467-023-35914-5","article-title":"Kaposi\u2019s sarcoma-associated herpesvirus induces specialised ribosomes to efficiently translate viral lytic mRNAs","volume":"14","author":"JC Murphy","year":"2023","journal-title":"Nat Commun"},{"issue":"18","key":"ppat.1013967.ref040","doi-asserted-by":"crossref","first-page":"7507","DOI":"10.1073\/pnas.0810916106","article-title":"Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans","volume":"106","author":"SE Calvo","year":"2009","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"1","key":"ppat.1013967.ref041","doi-asserted-by":"crossref","first-page":"8822","DOI":"10.1038\/s41467-024-53085-9","article-title":"Zika viruses encode 5\u2019 upstream open reading frames affecting infection of human brain cells","volume":"15","author":"C Lef\u00e8vre","year":"2024","journal-title":"Nat Commun"},{"issue":"2","key":"ppat.1013967.ref042","doi-asserted-by":"crossref","first-page":"846","DOI":"10.1128\/JVI.02831-13","article-title":"Reselection of a genomic upstream open reading frame in mouse hepatitis coronavirus 5\u2019-untranslated-region mutants","volume":"88","author":"H-Y Wu","year":"2014","journal-title":"J Virol"},{"issue":"1","key":"ppat.1013967.ref043","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1003147","article-title":"An upstream open reading frame modulates ebola virus polymerase translation and virus replication","volume":"9","author":"RS Shabman","year":"2013","journal-title":"PLoS Pathog"},{"issue":"2","key":"ppat.1013967.ref044","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1016\/j.virol.2007.01.022","article-title":"A minimal uORF within the HIV-1 vpu leader allows efficient translation initiation at the downstream env AUG","volume":"363","author":"J Krummheuer","year":"2007","journal-title":"Virology"},{"issue":"17","key":"ppat.1013967.ref045","doi-asserted-by":"crossref","first-page":"2414","DOI":"10.1101\/gad.480508","article-title":"eIF3a cooperates with sequences 5\u2019 of uORF1 to promote resumption of scanning by post-termination ribosomes for reinitiation on GCN4 mRNA","volume":"22","author":"B Szamecz","year":"2008","journal-title":"Genes Dev"},{"issue":"31","key":"ppat.1013967.ref046","doi-asserted-by":"crossref","first-page":"11269","DOI":"10.1073\/pnas.0400541101","article-title":"Reinitiation involving upstream ORFs regulates ATF4 mRNA translation in mammalian cells","volume":"101","author":"KM Vattem","year":"2004","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"2","key":"ppat.1013967.ref047","first-page":"111","article-title":"A short leader sequence impairs the fidelity of initiation by eukaryotic ribosomes","volume":"1","author":"M Kozak","year":"1991","journal-title":"Gene Expr"},{"issue":"1","key":"ppat.1013967.ref048","doi-asserted-by":"crossref","first-page":"76","DOI":"10.1002\/embj.201386124","article-title":"The mechanism of translation initiation on Type 1 picornavirus IRESs","volume":"33","author":"TR Sweeney","year":"2014","journal-title":"EMBO J"},{"issue":"2","key":"ppat.1013967.ref049","doi-asserted-by":"crossref","first-page":"252","DOI":"10.1292\/jvms.22-0505","article-title":"Novel recombinant porcine enterovirus G viruses lacking structural proteins are maintained in pig farms in Japan","volume":"85","author":"R Imai","year":"2023","journal-title":"J Vet Med Sci"},{"key":"ppat.1013967.ref050","doi-asserted-by":"crossref","first-page":"103975","DOI":"10.1016\/j.meegid.2019.103975","article-title":"A novel defective recombinant porcine enterovirus G virus carrying a porcine torovirus papain-like cysteine protease gene and a putative anti-apoptosis gene in place of viral structural protein genes","volume":"75","author":"R Imai","year":"2019","journal-title":"Infect Genet Evol"},{"key":"ppat.1013967.ref051","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1186\/1471-2105-5-113","article-title":"MUSCLE: a multiple sequence alignment method with reduced time and space complexity","volume":"5","author":"RC Edgar","year":"2004","journal-title":"BMC Bioinformatics"},{"issue":"3","key":"ppat.1013967.ref052","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"},{"issue":"3","key":"ppat.1013967.ref053","doi-asserted-by":"crossref","DOI":"10.1186\/gb-2009-10-3-r25","article-title":"Ultrafast and memory-efficient alignment of short DNA sequences to the human genome","volume":"10","author":"B Langmead","year":"2009","journal-title":"Genome Biol"}],"updated-by":[{"DOI":"10.1371\/journal.ppat.1013967","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,2,13]],"date-time":"2026-02-13T00:00:00Z","timestamp":1770940800000}}],"container-title":["PLOS Pathogens"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.ppat.1013967","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,2,13]],"date-time":"2026-02-13T18:52:27Z","timestamp":1771008747000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.ppat.1013967"}},"subtitle":[],"editor":[{"given":"Peter","family":"Sarnow","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,2,9]]},"references-count":53,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2026,2,9]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.ppat.1013967","relation":{},"ISSN":["1553-7374"],"issn-type":[{"value":"1553-7374","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,2,9]]}}}