Intrahost evolution leading to distinct lineages in the upper and lower respiratory tracts during SARS-CoV-2 prolonged infection

IF 5.5 2区 医学 Q1 VIROLOGY Virus Evolution Pub Date : 2024-08-31 DOI:10.1093/ve/veae073
Majdouline El Moussaoui, Sebastien Bontems, Cecile Meex, Marie-Pierre Hayette, Marie Lejeune, Samuel L Hong, Simon Dellicour, Michel Moutschen, Nadine Cambisano, Nathalie Renotte, Vincent Bours, Gilles Darcis, Maria Artesi, Keith Durkin
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Abstract

Accumulating evidence points to persistent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in immunocompromised individuals as a source of novel lineages. While intrahost evolution of the virus in chronically infected patients has previously been reported, existing knowledge is primarily based on samples from the nasopharynx. In this study, we investigate the intrahost evolution and genetic diversity that accumulated during a prolonged SARS-CoV-2 infection with the Omicron sublineage BF.7, estimated to have persisted for over one year in an immunosuppressed patient. Based on the sequencing of eight samples collected at six time points, we identified 87 intrahost single-nucleotide variants (iSNVs), two indels, and a 362 bp deletion. Our analysis revealed distinct viral genotypes in the nasopharyngeal (NP), endotracheal aspirate (ETA), and bronchoalveolar (BAL) samples. This suggests that NP samples may not offer a comprehensive representation of the overall intrahost viral diversity. Our findings not only demonstrate that the Omicron sublineage BF.7 can further diverge from its already exceptionally mutated state but also highlight that patients chronically infected with SARS-CoV-2 can develop genetically specific viral populations across distinct anatomical compartments. This provides novel insights into the intricate nature of viral diversity and evolution dynamics in persistent infections.
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在 SARS-CoV-2 长期感染过程中,宿主内进化导致上呼吸道和下呼吸道出现不同的血系
越来越多的证据表明,免疫力低下的人持续感染严重急性呼吸系统综合征冠状病毒 2(SARS-CoV-2)是新病毒系的来源。虽然以前曾报道过慢性感染患者体内病毒的宿主内进化,但现有的知识主要是基于鼻咽部的样本。在本研究中,我们研究了一名免疫抑制患者在长期感染 SARS-CoV-2 期间积累的 Omicron 亚系 BF.7 的宿主内进化和遗传多样性。根据在六个时间点采集的八个样本的测序结果,我们发现了 87 个宿主内单核苷酸变异(iSNV)、两个嵌合体和一个 362 bp 的缺失。我们的分析表明,鼻咽部(NP)、气管内吸出物(ETA)和支气管肺泡(BAL)样本中的病毒基因型各不相同。这表明鼻咽样本可能无法全面代表宿主体内病毒的整体多样性。我们的研究结果不仅证明了 Omicron 亚系 BF.7 可以从其已经异常变异的状态进一步分化,而且还强调了慢性感染 SARS-CoV-2 的患者可以在不同的解剖结构中形成具有特定基因的病毒群。这为了解持续感染中病毒多样性和进化动态的复杂性提供了新的视角。
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来源期刊
Virus Evolution
Virus Evolution Immunology and Microbiology-Microbiology
CiteScore
10.50
自引率
5.70%
发文量
108
审稿时长
14 weeks
期刊介绍: Virus Evolution is a new Open Access journal focusing on the long-term evolution of viruses, viruses as a model system for studying evolutionary processes, viral molecular epidemiology and environmental virology. The aim of the journal is to provide a forum for original research papers, reviews, commentaries and a venue for in-depth discussion on the topics relevant to virus evolution.
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