{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T05:16:08Z","timestamp":1787030168974,"version":"build-2736575974"},"reference-count":33,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2024,12,31]],"date-time":"2024-12-31T00:00:00Z","timestamp":1735603200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Aziza Othmana hospital (Tunis, Tunisia)"},{"name":"the National Reference Centre"},{"name":"Instituto Zooprofilattico Sperimentale dell l\u2019Abruzzo e del Moliso (Teramo, Italy)"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Coronavirus disease 2019 (COVID-19) has been associated with a significant fatality rate and persistent evolution in immunocompromised patients. In this prospective study, we aimed to determine the duration of excretion of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 37 Tunisian patients with hematological malignancies (40.5% with lymphoma and 37.8% with leukemia). In order to investigate the accumulation of viral mutations, we carried out genetic investigation on longitudinal nasopharyngeal samples using RT-PCR and whole-genome sequencing. Patients\u2019 samples were collected until the RT-PCR results became negative. SARS-CoV-2 infection was symptomatic in 48.6% of cases with fever, and cough was symptomatic in 61% of cases; the mortality rate was estimated to be 13.5%. The duration of viral RNA shedding ranged from 7 to 92 days after onset; it exceeded 18 days in 79.4% of cases. An intermittent PCR positivity was observed in two symptomatic patients. Persistent PCR positivity, defined as the presence of viral RNA for more than 30 days, was found in 51.4% of cases. No significant differences were observed for age, sex, type of hematological malignancy, or COVID-19 evolution between this group and a second one characterized by non-persistent PCR positivity. Lymphopenia was an independent predictor of prolonged SARS-CoV-2 RNA detection (p = 0.04). Three types of variants were detected; the most frequent was the Omicron. Globally, the mean intra-host variability in the SARS-CoV-2 genome was 1.31 \u00d7 10\u22123 mutations per site per year; it was 1.44 \u00d7 10\u22123 in the persistent group and 1.3 \u00d7 10\u22123 in the non-persistent group. Three types of mutations were detected; the most frequent were nucleotide substitutions in the spike (S) gene. No statistically significant difference was observed between the two groups as to the type and mean number of observed mutations in the whole genome and the S region (p = 0.650). Sequence analysis revealed the inclusion of one to eight amino acid-changing events in seventeen cases; it was characterized by genetic stability from the third to the twentieth day of evolution in six cases. For the two patients with intermittent PCR positivity, sequences obtained from samples before and after negative PCR were identical in the whole genome, confirming an intra-host evolution of the same viral strain. This study confirms the risk of persistent viral shedding in patients with hematological malignancies. However, persistence of PCR positivity seems to be correlated only with a continuous elimination of viral RNA debris. Additional studies based on cell culture analysis are needed to confirm these findings.<\/jats:p>","DOI":"10.3390\/v17010046","type":"journal-article","created":{"date-parts":[[2024,12,31]],"date-time":"2024-12-31T13:26:25Z","timestamp":1735651585000},"page":"46","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Virological Aspects of COVID-19 in Patients with Hematological Malignancies: Duration of Viral Shedding and Genetic Analysis"],"prefix":"10.3390","volume":"17","author":[{"given":"Asma","family":"Themlaoui","sequence":"first","affiliation":[{"name":"Laboratory of Microbiology and Biochemistry (LR16SP01), Aziza Othmana Hospital, University Tunis El Manar, Tunis 1068, Tunisia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7121-6373","authenticated-orcid":false,"given":"Massimo","family":"Ancora","sequence":"additional","affiliation":[{"name":"National Reference Centre for Whole Genome Sequencing of Microbial Pathogens: Database and Bioin-Formatic Analysis (GENPAT), Istituto Zooprofilattico Sperimentale dell\u2019Abruzzo e del Molise, 64100 Teramo, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kais","family":"Ghedira","sequence":"additional","affiliation":[{"name":"Laboratory of Bioinformatics, Biomathematics and Biostatistics (LR20IPT09), Pasteur Institute of Tunis, Tunis 1002, Tunisia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yosra","family":"Mhalla","sequence":"additional","affiliation":[{"name":"Laboratory of Microbiology and Biochemistry (LR16SP01), Aziza Othmana Hospital, University Tunis El Manar, Tunis 1068, Tunisia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8175-1743","authenticated-orcid":false,"given":"Manel","family":"Hamdoun","sequence":"additional","affiliation":[{"name":"Laboratory of Microbiology and Biochemistry (LR16SP01), Aziza Othmana Hospital, University Tunis El Manar, Tunis 1068, Tunisia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maroua","family":"Bahri","sequence":"additional","affiliation":[{"name":"Hematology Department, Aziza Othmana Hospital, University Tunis El Manar, Tunis 1068, Tunisia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lamia","family":"Aissaoui","sequence":"additional","affiliation":[{"name":"Hematology Department, Aziza Othmana Hospital, University Tunis El Manar, Tunis 1068, Tunisia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Raihane","family":"Ben Lakhal","sequence":"additional","affiliation":[{"name":"Hematology Department, Aziza Othmana Hospital, University Tunis El Manar, Tunis 1068, Tunisia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9328-3972","authenticated-orcid":false,"given":"Adriano","family":"Di Pasquale","sequence":"additional","affiliation":[{"name":"National Reference Centre for Whole Genome Sequencing of Microbial Pathogens: Database and Bioin-Formatic Analysis (GENPAT), Istituto Zooprofilattico Sperimentale dell\u2019Abruzzo e del Molise, 64100 Teramo, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7547-1195","authenticated-orcid":false,"given":"Cesare","family":"Camma","sequence":"additional","affiliation":[{"name":"National Reference Centre for Whole Genome Sequencing of Microbial Pathogens: Database and Bioin-Formatic Analysis (GENPAT), Istituto Zooprofilattico Sperimentale dell\u2019Abruzzo e del Molise, 64100 Teramo, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olfa","family":"Bahri","sequence":"additional","affiliation":[{"name":"Laboratory of Microbiology and Biochemistry (LR16SP01), Aziza Othmana Hospital, University Tunis El Manar, Tunis 1068, Tunisia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2024,12,31]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Mittal, A., Khattri, A., and Verma, V. (2022). Structural and antigenic variations in the spike protein of emerging SARS-CoV-2 variants. PLoS Pathog., 18.","DOI":"10.1371\/journal.ppat.1010260"},{"key":"ref_2","unstructured":"Aleem, A., Akbar Samad, A.B., and Vaqar, S. (2024). Emerging Variants of SARS-CoV-2 and Novel Therapeutics Against Coronavirus (COVID-19). StatPearls, StatPearls. Bookshelf ID: NBK570580."},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Thakur, S., Sasi, S., Pillai, S.G., Nag, A., Shukla, D., Singhal, R., Phalke, S., and Velu, G.S.K. (2022). SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. Front. Med., 9.","DOI":"10.3389\/fmed.2022.815389"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"146134","DOI":"10.1016\/j.gene.2021.146134","article-title":"From delta to Omicron: S1-RBD\/S2 mutation\/deletion equilibrium in SARS-CoV-2 defined variants","volume":"814","author":"Papanikolaou","year":"2022","journal-title":"Gene"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"108565","DOI":"10.1016\/j.intimp.2022.108565","article-title":"A review on evolution of emerging SARS-CoV-2 variants based on spike glycoprotein","volume":"105","author":"Ghosh","year":"2022","journal-title":"Int. Immunopharmacol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1038\/s41579-021-00573-0","article-title":"SARS-CoV-2 variants, spike mutations and immune escape","volume":"19","author":"Harvey","year":"2021","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"109292","DOI":"10.1016\/j.celrep.2021.109292","article-title":"Recurrent emergence of SARS-CoV-2 spike deletion H69\/V70 and its role in the Alpha variant B.1.1.7","volume":"35","author":"Meng","year":"2021","journal-title":"Cell Rep."},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Shah, M., and Woo, H.G. (2021). Omicron: A Heavily Mutated SARS-CoV-2 Variant Exhibits Stronger Binding to ACE2 and Potently Escapes Approved COVID-19 Therapeutic Antibodies. Front. Immunol., 12.","DOI":"10.3389\/fimmu.2021.830527"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"2240","DOI":"10.1093\/cid\/ciaa451","article-title":"Duration of Viral Shedding of Discharged Patients with Severe COVID-19","volume":"71","author":"Zhou","year":"2020","journal-title":"Clin. Infect. Dis."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1676","DOI":"10.1002\/jmv.25936","article-title":"SARS-CoV-2 can be detected in urine, blood, anal swabs, and oropharyngeal swabs specimens","volume":"92","author":"Peng","year":"2020","journal-title":"J. Med. Virol."},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Dudouet, P., Colson, P., Aherfi, S., Levasseur, A., Beye, M., Delerce, J., Burel, E., Lavrard, P., Bader, W., and Lagier, J.C. (2022). SARS-CoV-2 quasi-species analysis from patients with persistent nasopharyngeal shedding. Sci. Rep., 12.","DOI":"10.1038\/s41598-022-22060-z"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"e0024421","DOI":"10.1128\/mSphere.00244-21","article-title":"Long-Term Evolution of SARS-CoV-2 in an Immunocompromised Patient with Non-Hodgkin Lymphoma","volume":"6","author":"Borges","year":"2021","journal-title":"mSphere"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"e453","DOI":"10.1016\/S1473-3099(23)00815-0","article-title":"Persistent SARS-CoV-2 infection: Significance and implications","volume":"24","author":"Machkovech","year":"2024","journal-title":"Lancet Infect Dis."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"62","DOI":"10.1158\/2159-8290.CD-21-1033","article-title":"Prolonged SARS-CoV-2 Infection in Patients with Lymphoid Malignancies","volume":"12","author":"Lee","year":"2022","journal-title":"Cancer Discov."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1007\/s15010-020-01531-3","article-title":"Epidemiology of SARS-CoV-2","volume":"49","author":"Salzberger","year":"2021","journal-title":"Infection"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"312","DOI":"10.5501\/wjv.v10.i6.312","article-title":"COVID-19 (SARS-CoV-2 infection) in lymphoma patients: A review","volume":"10","author":"Bonuomo","year":"2021","journal-title":"World J. Virol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"904","DOI":"10.1016\/S1470-2045(20)30310-7","article-title":"Clinical characteristics, outcomes, and risk factors for mortality in patients with cancer and COVID-19 in Hubei, China: A multicentre, retrospective, cohort study","volume":"21","author":"Yang","year":"2020","journal-title":"Lancet Oncol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"3033","DOI":"10.1182\/blood.2020008150","article-title":"Clinical features associated with COVID-19 outcome in multiple myeloma: First results from the International Myeloma Society data set","volume":"136","author":"Chari","year":"2020","journal-title":"Blood"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"336","DOI":"10.1111\/bjh.16956","article-title":"Haematological cancers and the risk of severe COVID-19: Exploration and critical evaluation of the evidence to date","volume":"190","author":"Iyengar","year":"2020","journal-title":"Br. J. Haematol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1007\/s12561-021-09320-8","article-title":"Is 14-Days a Sensible Quarantine Length for COVID-19? Examinations of Some Associated Issues with a Case Study of COVID-19 Incubation Times","volume":"14","author":"Yi","year":"2022","journal-title":"Stat. Biosci."},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Di Pasquale, A., Radomski, N., Mangone, I., Calistri, P., Lorusso, A., and Camma, C. (2021). SARS-CoV-2 surveillance in Italy through phylogenomic inferences based on Hamming distances derived from pan-SNPs, -MNPs and -InDels. BMC Genom., 22.","DOI":"10.1186\/s12864-021-08112-0"},{"key":"ref_22","unstructured":"Instance Nationale de l\u2019Evaluation et de l\u2019Accr\u00e9diation en Sant\u00e9 (INEAS) (2022, April 20). Guide Parcours du Patient Suspect ou Atteint par le COVID-19: Consensus D\u2019experts. Available online: https:\/\/www.infectiologie.org.tn\/pdf_ppt_docs\/recommandations\/1588495687.pdf."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"3773","DOI":"10.21105\/joss.03773","article-title":"Next clade: Clade assignment, mutation calling and quality control for viral genomes","volume":"6","author":"Aksamentov","year":"2021","journal-title":"J. Open Source Softw."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"659","DOI":"10.1017\/ice.2020.1273","article-title":"Understanding viral shedding of severe acute respiratory coronavirus virus 2 (SARS-CoV-2): Review of current literature","volume":"42","author":"Fontana","year":"2021","journal-title":"Infect Control Hosp. Epidemiol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"e283","DOI":"10.1016\/S2666-5247(20)30120-8","article-title":"Humoral response and PCR positivity in patients with COVID-19 in the New York City region, USA: An observational study","volume":"1","author":"Wajnberg","year":"2020","journal-title":"Lancet Microbe"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"1919","DOI":"10.1016\/S0140-6736(20)31173-9","article-title":"COVID-19 mortality in patients with cancer on chemotherapy or other anticancer treatments: A prospective cohort study","volume":"395","author":"Lee","year":"2020","journal-title":"Lancet"},{"key":"ref_27","first-page":"258","article-title":"First case of imported and confirmed COVID-19 in Tunisia","volume":"98","author":"Chakroun","year":"2020","journal-title":"Tunis Med."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"240","DOI":"10.1016\/j.cmi.2022.08.021","article-title":"Emergence of Delta and Omicron variants carrying resistance-associated mutations in immunocompromised patients undergoing sotrovimab treatment with long-term viral excretion","volume":"29","author":"Andres","year":"2023","journal-title":"Clin. Microbiol. Infect"},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Chouikha, A., Fares, W., Laamari, A., Haddad-Boubaker, S., Belaiba, Z., Ghedira, K., Kammoun Rebai, W., Ayouni, K., Khedhiri, M., and Ben Halima, S. (2022). Molecular Epidemiology of SARS-CoV-2 in Tunisia (North Africa) through Several Successive Waves of COVID-19. Viruses, 14.","DOI":"10.3390\/v14030624"},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Haddad-Boubaker, S., Arbi, M., Souiai, O., Chouikha, A., Fares, W., Edington, K., Sims, S., Camma, C., Lorusso, A., and Diagne, M.M. (2022). The Delta variant wave in Tunisia: Genetic diversity, spatio-temporal distribution and evidence of the spread of a divergent AY.122 sub-lineage. Front. Public Health, 10.","DOI":"10.3389\/fpubh.2022.990832"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"e31","DOI":"10.3346\/jkms.2022.37.e31","article-title":"Clinical Characteristics of 40 Patients Infected with the SARS-CoV-2 Omicron Variant in Korea","volume":"37","author":"Kim","year":"2022","journal-title":"J. Korean Med. Sci."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"105300","DOI":"10.1016\/j.meegid.2022.105300","article-title":"Phylogenetic and amino acid signature analysis of the SARS-CoV-2s lineages circulating in Tunisia","volume":"102","author":"Sassi","year":"2022","journal-title":"Infect Genet. Evol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1177\/0194599820926473","article-title":"The Prevalence of Olfactory and Gustatory Dysfunction in COVID-19 Patients: A Systematic Review and Meta-analysis","volume":"163","author":"Tong","year":"2020","journal-title":"Otolaryngol. Head Neck Surg."}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/17\/1\/46\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T16:57:49Z","timestamp":1760115469000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/17\/1\/46"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,12,31]]},"references-count":33,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2025,1]]}},"alternative-id":["v17010046"],"URL":"https:\/\/doi.org\/10.3390\/v17010046","relation":{},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,12,31]]}}}