{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T09:57:17Z","timestamp":1753869437860,"version":"3.41.2"},"reference-count":35,"publisher":"Wiley","issue":"6","license":[{"start":{"date-parts":[[2023,6,21]],"date-time":"2023-06-21T00:00:00Z","timestamp":1687305600000},"content-version":"vor","delay-in-days":20,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Journal of Medical Virology"],"published-print":{"date-parts":[[2023,6]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Many evidence suggests that long\u2010lasting infection can develop with severe acute respiratory syndrome coronavirus 2 (SARS\u2010CoV\u20102). This occurrence has been widely described in immunocompromised individuals. In these patients, ineffective clearance of virus infection provides an opportunity for developing immune escape mutants. This study aimed to characterize SARS\u2010CoV\u20102 intrahost evolution in five immunocompromised in comparison with five immunocompetent COVID\u201019 patients during treatment. We performed next\u2010generation sequencing (NGS) on collected two oropharyngeal samples from immunocompromised and immunocompetent COVID\u201019 patients before and after treatment. In this study, we detected alpha and delta variants of SARS\u2010CoV\u20102. The most common substitutions in structural proteins in patients with alpha variant were S\u2010\u0394Y143\u2010144, A570D, D614G and D1118H, and N\u2010R203K and G204R, and in delta variant S\u2010T19R, G142D, E156G, 157\u2010158del, L452R, T478K, D614G, D950N and N\u2010D63G, R203M and D377Y were dominant. The common variations in nonstructural and accessory proteins including nsp3\u2010A488S, P1228L, nsp6\u2010T77A, nsp12\u2010P323L, G671S, nsp13\u2010P77L, NS3\u2010S26L, and NS7a\u2010T120I were detected. Also some infrequent substitutions were seen in immunocompromised and immunocompetent patients. After treatment, nsp12\u2010V166A was emerged as a remdesivir resistance and S\u2010L452M in a patient with common variable immunodeficiency. S\u2010E484Q was detected in a patient with acute lymphoma leukemia. This study showed the possibility of the genetic diversity and development of some new mutations in immunocompromised patients. Therefore, surveillance of these patients to characterize any new variants is necessary.<\/jats:p>","DOI":"10.1002\/jmv.28877","type":"journal-article","created":{"date-parts":[[2023,6,21]],"date-time":"2023-06-21T13:34:44Z","timestamp":1687354484000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["SARS\u2010CoV\u20102 intrahost evolution in immunocompromised patients in comparison with immunocompetent populations after treatment"],"prefix":"10.1002","volume":"95","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2219-4259","authenticated-orcid":false,"given":"Akram Sadat","family":"Ahmadi","sequence":"first","affiliation":[{"name":"Department of Virology, School of Public Health Tehran University of Medical Sciences Tehran Iran"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4326-4722","authenticated-orcid":false,"given":"Sevrin","family":"Zadheidar","sequence":"additional","affiliation":[{"name":"Department of Virology, School of Public Health Tehran University of Medical Sciences Tehran Iran"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4527-9167","authenticated-orcid":false,"given":"Kaveh","family":"Sadeghi","sequence":"additional","affiliation":[{"name":"Department of Virology, School of Public Health Tehran University of Medical Sciences Tehran Iran"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2435-3065","authenticated-orcid":false,"given":"Ahmad","family":"Nejati","sequence":"additional","affiliation":[{"name":"Department of Virology, School of Public Health Tehran University of Medical Sciences Tehran Iran"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8541-7846","authenticated-orcid":false,"given":"Vahid","family":"Salimi","sequence":"additional","affiliation":[{"name":"Department of Virology, School of Public Health Tehran University of Medical Sciences Tehran Iran"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4200-386X","authenticated-orcid":false,"given":"Mahboobeh","family":"Hajiabdolbaghi","sequence":"additional","affiliation":[{"name":"Iranian Research Center for HIV\/AIDS, Iranian Institute for Reduction of High\u2010Risk Behaviors Tehran University of Medical Sciences Tehran Iran"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6556-4072","authenticated-orcid":false,"given":"Talat","family":"Mokhtari\u2010Azad","sequence":"additional","affiliation":[{"name":"Department of Virology, School of Public Health Tehran University of Medical Sciences Tehran Iran"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3239-9397","authenticated-orcid":false,"given":"Jila","family":"Yavarian","sequence":"additional","affiliation":[{"name":"Department of Virology, School of Public Health Tehran University of Medical Sciences Tehran Iran"},{"name":"Research Center for Antibiotic Stewardship and Antimicrobial Resistance Tehran University of Medical Sciences Tehran Iran"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2023,6,21]]},"reference":[{"key":"e_1_2_11_2_1","doi-asserted-by":"publisher","DOI":"10.1016\/S2666-5247(22)00061-1"},{"key":"e_1_2_11_3_1","doi-asserted-by":"publisher","DOI":"10.1007\/s10875-021-01065-9"},{"key":"e_1_2_11_4_1","doi-asserted-by":"publisher","DOI":"10.3390\/v14040752"},{"key":"e_1_2_11_5_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jiph.2021.04.005"},{"key":"e_1_2_11_6_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jiac.2022.04.004"},{"key":"e_1_2_11_7_1","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2022.946549"},{"key":"e_1_2_11_8_1","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMsb2104756"},{"key":"e_1_2_11_9_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2020.10.049"},{"key":"e_1_2_11_10_1","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.00791-22"},{"key":"e_1_2_11_11_1","doi-asserted-by":"publisher","DOI":"10.3390\/jcm10153276"},{"key":"e_1_2_11_12_1","unstructured":"CormanV BleickerT Br\u00fcninkS DrostenC.Diagnostic detection of 2019\u2010nCoV by real\u2010time RT\u2010PCR.World Health Organization.2020;17:1\u201013"},{"key":"e_1_2_11_13_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0267847"},{"key":"e_1_2_11_14_1","doi-asserted-by":"publisher","DOI":"10.1111\/irv.13135"},{"key":"e_1_2_11_15_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.meegid.2021.104897"},{"key":"e_1_2_11_16_1","doi-asserted-by":"publisher","DOI":"10.1128\/jvi.01162-22"},{"key":"e_1_2_11_17_1","doi-asserted-by":"publisher","DOI":"10.1002\/jmv.28407"},{"key":"e_1_2_11_18_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-021-02874-z"},{"key":"e_1_2_11_19_1","doi-asserted-by":"publisher","DOI":"10.1002\/jmv.27445"},{"key":"e_1_2_11_20_1","doi-asserted-by":"publisher","DOI":"10.3201\/eid2710.211509"},{"key":"e_1_2_11_21_1","doi-asserted-by":"publisher","DOI":"10.3390\/ijms23010029"},{"key":"e_1_2_11_22_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.virol.2021.06.009"},{"key":"e_1_2_11_23_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12985-022-01951-7"},{"key":"e_1_2_11_24_1","article-title":"Analysis of Whole\u2010Genome sequencing of SARS\u2010CoV\u20102 reveals recurrent mutations among Iranian patients","author":"Abbasian MH","year":"2023","journal-title":"medRxiv (Preprint)"},{"key":"e_1_2_11_25_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-29104-y"},{"key":"e_1_2_11_26_1","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/ciac769"},{"key":"e_1_2_11_27_1","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/ciaa1474"},{"key":"e_1_2_11_28_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.xcrm.2022.100735"},{"key":"e_1_2_11_29_1","doi-asserted-by":"publisher","DOI":"10.1128\/aac.00198-22"},{"key":"e_1_2_11_30_1","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.abo0718"},{"key":"e_1_2_11_31_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0263563"},{"key":"e_1_2_11_32_1","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.00711-20"},{"key":"e_1_2_11_33_1","doi-asserted-by":"publisher","DOI":"10.3390\/v14071408"},{"key":"e_1_2_11_34_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.trre.2020.100588"},{"key":"e_1_2_11_35_1","unstructured":"Control CDC Prevention Control CDC Prevention.People of any age with underlying medical conditions.Coronavirus Disease.2019."},{"key":"e_1_2_11_36_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijid.2021.01.023"}],"container-title":["Journal of Medical Virology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/jmv.28877","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,8,17]],"date-time":"2023-08-17T15:45:01Z","timestamp":1692287101000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/jmv.28877"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,6]]},"references-count":35,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2023,6]]}},"alternative-id":["10.1002\/jmv.28877"],"URL":"https:\/\/doi.org\/10.1002\/jmv.28877","archive":["Portico"],"relation":{},"ISSN":["0146-6615","1096-9071"],"issn-type":[{"type":"print","value":"0146-6615"},{"type":"electronic","value":"1096-9071"}],"subject":[],"published":{"date-parts":[[2023,6]]},"assertion":[{"value":"2023-01-18","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2023-06-02","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2023-06-21","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e28877"}}