COVID-19持续和再感染的SARS-CoV-2序列特征

M. Choudhary, Charles R. Crain, Xueting Qiu, W. Hanage, Jonathan Z. Li
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引用次数: 25

摘要

背景。SARS-CoV-2再感染和持续感染都有描述,但需要对突变进行系统评估。我们评估了来自已发表的COVID-19再感染和持续感染病例的序列,表征了再感染序列的特征和持续感染中病毒进化的速度。方法。对PubMed进行了系统评价,以确定具有可用序列的SARS-CoV-2再感染和持续感染病例。再感染序列的氨基酸变化比较了初始和同时期的群落变异。进行了基于时间的系统发育重建,以比较持续性COVID-19的宿主内病毒进化与社区驱动的进化。结果。再感染14例,持续感染5例。再感染病例的报告在年龄、基线健康状况、再感染严重程度等方面分布广泛,最早发生在初次感染后1.5个月或>8个月。再感染的病毒序列中位数有9个氨基酸的变化,其中S、ORF8和N基因的变化富集。氨基酸变化的数量没有因再感染的严重程度而不同,再感染变异与社区中流行的同期序列相似。在恢复期血浆或单克隆抗体治疗期间,持续性COVID-19患者表现出比社区驱动进化更快的突变积累。结论。SARS-CoV-2再感染不需要宿主或病毒的一系列异常情况,而持续的COVID-19主要发生在免疫抑制的个体中,并且与时钟速率测量的病毒进化加速有关。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
SARS-CoV-2 Sequence Characteristics of COVID-19 Persistence and Reinfection
Background. Both SARS-CoV-2 reinfection and persistent infection have been described, but a systematic assessment of mutations is needed. We assessed sequences from published cases of COVID-19 reinfection and persistence, characterizing the hallmarks of reinfecting sequences and the rate of viral evolution in persistent infection. Methods. A systematic review of PubMed was conducted to identify cases of SARS-CoV-2 reinfection and persistent infection with available sequences. Amino acid changes in the reinfecting sequence were compared to both the initial and contemporaneous community variants. Time-measured phylogenetic reconstruction was performed to compare intra-host viral evolution in persistent COVID-19 to community-driven evolution. Results. Fourteen reinfection and five persistent infection cases were identified. Reports of reinfection cases spanned a broad distribution of ages, baseline health status, reinfection severity, and occurred as early as 1.5 months or >8 months after the initial infection. The reinfecting viral sequences had a median of 9 amino acid changes with enrichment of changes in the S, ORF8 and N genes. The number of amino acid changes did not differ by the severity of reinfection and reinfecting variants were similar to the contemporaneous sequences circulating in the community. Patients with persistent COVID-19 demonstrated more rapid accumulation of mutations than seen with community-driven evolution with continued viral changes during convalescent plasma or monoclonal antibody treatment. Conclusions. SARS-CoV-2 reinfection does not require an unusual set of circumstances in the host or virus, while persistent COVID-19 is largely described in immunosuppressed individuals and is associated with accelerated viral evolution as measured by clock rates.
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