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In particular, tropism for epithelial and endothelial cells is lost due to mutations disrupting genes <jats:italic>UL128<\/jats:italic>, <jats:italic>UL130<\/jats:italic>, or <jats:italic>UL131A,<\/jats:italic> which encode subunits of a virion-associated pentameric complex (PC) important for viral entry into these cells but not for entry into fibroblasts. The endothelial cell-adapted strain TB40\/E has a relatively intact genome and has emerged as a laboratory strain that closely resembles wild-type virus. However, several heterogeneous TB40\/E stocks and cloned variants exist that display a range of sequence and tropism properties. Here, we report the use of PacBio sequencing to elucidate the genetic changes that occurred, both at the consensus level and within subpopulations, upon passaging a TB40\/E stock on ARPE-19 epithelial cells. The long-read data also facilitated examination of the linkage between mutations. Consistent with inefficient ARPE-19 cell entry, at least 83% of viral genomes present before adaptation contained changes impacting PC subunits. In contrast, and consistent with the importance of the PC for entry into endothelial and epithelial cells, genomes after adaptation lacked these or additional mutations impacting PC subunits. The sequence data also revealed six single noncoding substitutions in the inverted repeat regions, single nonsynonymous substitutions in genes <jats:italic>UL26<\/jats:italic>, <jats:italic>UL69<\/jats:italic>, <jats:italic>US28<\/jats:italic>, and <jats:italic>UL122,<\/jats:italic> and a frameshift truncating gene <jats:italic>UL141<\/jats:italic>. Among the changes affecting protein-coding regions, only the one in <jats:italic>UL122<\/jats:italic> was strongly selected. This change, resulting in a D390H substitution in the encoded protein IE2, has been previously implicated in rendering another viral protein, UL84, essential for viral replication in fibroblasts. This finding suggests that IE2, and perhaps its interactions with UL84, have important functions unique to HCMV replication in epithelial cells.<\/jats:p>","DOI":"10.1186\/s12985-021-01583-3","type":"journal-article","created":{"date-parts":[[2021,6,3]],"date-time":"2021-06-03T11:09:23Z","timestamp":1622718563000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":18,"title":["Genome sequences of human cytomegalovirus strain TB40\/E variants propagated in fibroblasts and epithelial cells"],"prefix":"10.1186","volume":"18","author":[{"given":"Ahmed","family":"Al Qaffas","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Salvatore","family":"Camiolo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mai","family":"Vo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexis","family":"Aguiar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amine","family":"Ourahmane","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Myrna","family":"Sorono","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew J.","family":"Davison","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael A.","family":"McVoy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8057-1254","authenticated-orcid":false,"given":"Laura","family":"Hertel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2021,6,3]]},"reference":[{"key":"1583_CR1","doi-asserted-by":"publisher","first-page":"1535","DOI":"10.1099\/vir.0.018994-0","volume":"91","author":"DJ Dargan","year":"2010","unstructured":"Dargan DJ, Douglas E, Cunningham C, Jamieson F, Stanton RJ, Baluchova K, McSharry BP, Tomasec P, Emery VC, Percivalle E, et al. Sequential mutations associated with adaptation of human cytomegalovirus to growth in cell culture. J Gen Virol. 2010;91:1535\u201346.","journal-title":"J Gen Virol"},{"key":"1583_CR2","doi-asserted-by":"publisher","first-page":"3929","DOI":"10.1128\/JVI.02858-15","volume":"90","author":"I Murrell","year":"2016","unstructured":"Murrell I, Wilkie GS, Davison AJ, Statkute E, Fielding CA, Tomasec P, Wilkinson GW, Stanton RJ. Genetic stability of bacterial artificial chromosome-derived human cytomegalovirus during culture in vitro. J Virol. 2016;90:3929\u201343.","journal-title":"J Virol"},{"key":"1583_CR3","doi-asserted-by":"publisher","first-page":"10489","DOI":"10.1128\/JVI.01546-13","volume":"87","author":"I Murrell","year":"2013","unstructured":"Murrell I, Tomasec P, Wilkie GS, Dargan DJ, Davison AJ, Stanton RJ. Impact of sequence variation in the UL128 locus on production of human cytomegalovirus in fibroblast and epithelial cells. 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Monoclonal antibodies to different components of the human cytomegalovirus (HCMV) pentamer gH\/gL\/pUL128L and trimer gH\/gL\/gO as well as antibodies elicited during primary HCMV infection prevent epithelial cell syncytium formation. 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