20.500.12556/DiRROS-29154 Respiratory microbiome alterations, coinfections and virus intra-host evolution in a persistently active SARS-CoV-2 infection Background: Respiratory microbiome alterations, coinfections, and virus intrahost evolution are of great interest in persistently viable SARS-CoV-2 infections in the context of antiviral treatment and immune response. However, samples before, during, and after infection are seldom available to researchers. Therefore, there has been a significant lack of opportunities to comprehensively study microbiota homeostasis, coinfections, and virus intra-host evolution on the consensus and minor variants scale in response to antiviral treatments and patient immune response. Case presentation: A 63-year-old female patient with diffuse large B-cell lymphoma received multiple treatments for SARS-CoV-2 that remained active 169 days. Together, 32 respiratory and 19 serum samples were collected before, during, and after (- 398 to 233 days) COVID-19. Subsets were selected for virus viability testing by culture (20) and subgenomic (sg) RNA (20) measurement, intra-host evolution assessment (18), microbiome composition analysis (28), and coinfection identification (11). IgA/IgG and neutralizing anti-SARS-CoV-2 antibodies were measured 19 times throughout the infection. SARSCoV-2 lineage XBB.1.16.11 persisted and remained viable until 116 days post infection (PI) regardless of treatments. No sgRNA marker tested was suitable for virus viability prediction. IgG/IgA antibodies first appeared after 38 days, but the virus persisted regardless of multiple plasma treatments before neutralizing antibodies appeared (100 days PI) and finally cleared the virus 116 days PI. Consensus-level mutations fluctuated around 102.7 ± 4.0, and minor variants increased from six to 61 with a mutation rate of 4.9 × 10-3 per site per year, with the highest average number of mutations per gene length in S and E (0.013) with surges after every antiviral treatment. The transversion/transition ratio increased from 0.50 (day 0) to 0.57 (day 24) with a steady decrease to 0.48 (day 147). Mutational signature analysis showed dominance of C > T substitutions consistent with APOBEC antiviral enzyme activity. Upper respiratory microbiota showed three distinct profiles with varying α-/β-diversity and an association of Staphylococcus spp. with COVID-19. Conclusions: These findings further elucidate the dynamics of intra-host viral evolution and complexities of virus clearance in individuals with hematological malignancies and highlight the impact of antiviral treatments on the potential of virus variants emergence in longitudinally infectious patients due to delayed immune response. B-cell lymphoma hematological malignancies microbiome prolonged SARS-CoV_2 infection virus evolution virus shedding B-celični limfom hematološke malignosti mikrobiom dolgotrajna okužba s SARS-CoV-2 razvoj virusa izločanje virusa true false true Angleški jezik Slovenski jezik Neznano 2026-04-22 12:34:52 2026-04-22 12:34:53 2026-04-23 04:02:13 0000-00-00 00:00:00 2025 0 0 Nasl. z nasl. zaslona; Opis vira z dne 7. 8. 2025; 1-11 str. iss. 1, [article no.] 932 Vol. 25 2025 0000-00-00 Zaloznikova Objavljeno NiDoloceno 0000-00-00 0000-00-00 0000-00-00 616.9 1471-2334 10.1186/s12879-025-11355-x 245172995 RAZ_Boltezar_Lucka_2025.pdf RAZ_Boltezar_Lucka_2025.pdf 1 98575D8D5858133BC99271E535B897B4 746fca04464834806c5f2447b0100e80f622b27fa491f483140c79b44b87c60a 2ae56766-3e37-11f1-a343-001a4af901a5 https://dirros.openscience.si/Dokument.php?lang=slv&id=43571 https://bmcinfectdis.biomedcentral.com/articles/10.1186/s12879-025-11355-x 1 e8f3c78c-3e36-11f1-a343-001a4af901a5 https://dirros.openscience.si/Dokument.php?lang=slv&id=43570 Univerzitetni klinični center Ljubljana 0 0 0