Temporal dynamics of SARS-CoV-2 genome mutations that occurred in vivo on an aircraft

IF 3.5 Q1 PUBLIC, ENVIRONMENTAL & OCCUPATIONAL HEALTH

Biosafety and Health Pub Date : 2023-02-01 DOI:10.1016/j.bsheal.2022.10.004

Yaqing He , Shengyuan Dang , Wentai Ma , Long Chen , Renli Zhang , Shujiang Mei , Xinyi Wei , Qiuying Lv , Bo Peng , Ying Sun , Dongfeng Kong , Jiancheng Chen , Shimin Li , Xiujuan Tang , Qingju Lu , Can Zhu , Zhigao Chen , Jia Wan , Xuan Zou , Mingkun Li , Jianwei Wang

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引用次数: 1

Abstract

We analyzed variations in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome during a flight-related cluster outbreak of coronavirus disease 2019 (COVID-19) in Shenzhen, China, to explore the characteristics of SARS-CoV-2 transmission and intra-host single nucleotide variations (iSNVs) in a confined space. Thirty-three patients with COVID-19 were sampled, and 14 were resampled 3–31 days later. All 47 nasopharyngeal swabs were deep-sequenced. iSNVs and similarities in the consensus genome sequence were analyzed. Three SARS-CoV-2 variants of concern, Delta (n = 31), Beta (n = 1), and C.1.2 (n = 1), were detected among the 33 patients. The viral genome sequences from 30 Delta-positive patients had similar SNVs; 14 of these patients provided two successive samples. Overall, the 47 sequenced genomes contained 164 iSNVs. Of the 14 paired (successive) samples, the second samples (T2) contained more iSNVs (median: 3; 95% confidence interval [95% CI]: 2.77–10.22) than did the first samples (T1; median: 2; 95% CI: 1.63–3.74; Wilcoxon test, P = 0.021). 38 iSNVs were detected in T1 samples, and only seven were also detectable in T2 samples. Notably, T2 samples from two of the 14 paired samples had additional mutations than the T1 samples. The iSNVs of the SARS-CoV-2 genome exhibited rapid dynamic changes during a flight-related cluster outbreak event. Intra-host diversity increased gradually with time, and new site mutations occurred in vivo without a population transmission bottleneck. Therefore, we could not determine the generational relationship from the mutation site changes alone.

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飞机上体内发生的SARS-CoV-2基因组突变的时间动态

我们分析了中国深圳2019冠状病毒病（新冠肺炎）飞行相关集群爆发期间严重急性呼吸综合征冠状病毒2（SARS-CoV-2）基因组的变异，以探索密闭空间中SARS-CoV-2传播和宿主内单核苷酸变异（iSNVs）的特征。对33名新冠肺炎患者进行了采样，并在3–31天后对14名患者进行了重新采样。所有47个鼻咽拭子都进行了深度测序。iSNVs和一致基因组序列的相似性进行了分析。在33名患者中检测到三种严重急性呼吸系统综合征冠状病毒2变异毒株，即德尔塔（n=31）、贝塔（n=1）和C.1.2（n=1。来自30名德尔塔阳性患者的病毒基因组序列具有相似的SNV；其中14名患者提供了两个连续的样本。总的来说，47个测序的基因组包含164个iSNV。在14个配对（连续）样本中，第二个样本（T2）含有比第一个样本更多的iSNV（中位数：3；95%置信区间[95%CI]:2.77–10.22）（T1；中位数：2；95%CI:1.63–3.74；Wilcoxon检验，P=0.021）。T1样本中检测到38个iSNV，T2样本中只有7个也检测到。值得注意的是，来自14个配对样本中的两个的T2样本比T1样本具有额外的突变。严重急性呼吸系统综合征冠状病毒2型基因组的iSNV在与飞行相关的集群爆发事件中表现出快速的动态变化。宿主内多样性随着时间的推移逐渐增加，新的位点突变在体内发生，没有群体传播瓶颈。因此，我们不能仅从突变位点的变化来确定世代关系。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Biosafety and Health Medicine-Infectious Diseases

CiteScore

7.60

自引率

0.00%

发文量

116

审稿时长

66 days