Associations between genetic mutations in different SARS-CoV-2 strains and negative conversion time of viral RNA among imported cases in Hangzhou: A cross-sectional study

IF 2.5 4区医学 Q3 VIROLOGY

Virus research Pub Date : 2024-05-20 DOI:10.1016/j.virusres.2024.199400

Yi Wang , Hua Yu , Tao Zhang , Zhou Sun , Wenwu Yao , Wenhui Zhang , Qian Chen , Yao Zhong , Qian Huang , Meihua Wang , Haoqiu Wang , Beibei Wu

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Abstract

Purpose

Previous studies on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have focused on factors that influence the achievement of negative conversion of viral RNA. This study aimed to investigate the effects of the genetic mutations in different SARS-CoV-2 strains on the negative conversion time (NCT) among imported cases in Hangzhou, Zhejiang Province, China, in order to provide valuable insights for developing targeted epidemic prevention guidelines.

Methods

This retrospective study involved 146 imported SARS-CoV-2 cases in Hangzhou from 8 April 2021 to 11 June 2022. We compared the SARS-CoV-2-specific indicators, clinical indexes, and NCT among the wild-type (WT), Delta, and Omicron groups. Spearman correlation analysis was used to identify the correlations of NCT with mutation types/frequencies.

Results

The mean age of the imported cases was 35.3 (SD: 12.3) years, with 71.92 % males and 28.08 % females. The mean cycle threshold (Ct) values of open reading frame 1ab (ORF1ab) and nucleocapsid (N) RNA were 25.17 (SD: 6.44) and 23.4 (SD: 6.76), respectively. The mutations of SARS-CoV-2 strains were mainly located in N, membrane (M), spike (S), ORF1a, ORF1b, ORF3a, ORF6, and ORF9b genes among the WT, Delta, and Omicron groups. NCT was significantly prolonged in the WT and Delta groups compared to the Omicron group. T lymphocyte, white blood cell, eosinophil, and basophil counts were dramatically higher in the WT group than the Delta group. White blood cell, red blood cell, and basophil counts were significantly lower in the Delta group than the Omicron group. Spearman correlation analysis revealed a significant correlation between the NCT of viral RNA and mutation types of viral genes of WT and Omicron strains. Additionally, NCT was markedly negatively correlated with the frequencies of five mutations in Omicron strains (ORF1b:P1223L, ORF1b:R1315C, ORF1b:T2163I, ORF3a:T223I, and ORF6:D61L).

Conclusions

This study indicates that five mutations in Omicron strains (ORF1b:P1223L/R1315C/T2163I, ORF3a:T223I and ORF6:D61L) shortened NCT in imported SARS-CoV-2 cases.

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杭州市输入性病例中不同 SARS-CoV-2 株系基因突变与病毒 RNA 阴转时间之间的关系：一项横断面研究。

目的：以往关于严重急性呼吸系统综合征冠状病毒2（SARS-CoV-2）的研究主要集中在影响病毒RNA阴转时间的因素上。本研究旨在探讨浙江省杭州市输入病例中不同 SARS-CoV-2 株系的基因突变对阴转时间（NCT）的影响，从而为制定有针对性的防疫指南提供有价值的见解：这项回顾性研究涉及 2021 年 4 月 8 日至 2022 年 6 月 11 日期间杭州市的 146 例输入性 SARS-CoV-2 病例。我们比较了野生型（WT）组、Delta组和Omicron组的SARS-CoV-2特异性指标、临床指标和NCT。我们使用斯皮尔曼相关分析来确定 NCT 与突变类型/频率的相关性：输入病例的平均年龄为 35.3 岁（标准差：12.3 岁），其中男性占 71.92%，女性占 28.08%。开放阅读框1ab（ORF1ab）和核头状（N）RNA的平均周期阈值（Ct）分别为25.17（SD：6.44）和23.4（SD：6.76）。在 WT 组、Delta 组和 Omicron 组中，SARS-CoV-2 株系的突变主要位于 N、膜（M）、穗（S）、ORF1a、ORF1b、ORF3a、ORF6 和 ORF9b 基因。与 Omicron 组相比，WT 组和 Delta 组的 NCT 明显延长。WT 组的 T 淋巴细胞、白细胞、嗜酸性粒细胞和嗜碱性粒细胞计数明显高于 Delta 组。Delta 组的白细胞、红细胞和嗜碱性粒细胞计数明显低于 Omicron 组。斯皮尔曼相关分析显示，病毒 RNA 的 NCT 与 WT 株和 Omicron 株的病毒基因突变类型之间存在显著相关性。此外，NCT与Omicron毒株中5种突变（ORF1b:P1223L、ORF1b:R1315C、ORF1b:T2163I、ORF3a:T223I和ORF6:D61L）的频率呈明显负相关：这项研究表明，Omicron 株系中的五个突变（ORF1b:P1223L/R1315C/T2163I、ORF3a:T223I 和 ORF6:D61L）缩短了输入 SARS-CoV-2 病例的 NCT。

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

Virus research 医学-病毒学

CiteScore

9.50

自引率

2.00%

发文量

239

审稿时长

43 days

期刊介绍： Virus Research provides a means of fast publication for original papers on fundamental research in virology. Contributions on new developments concerning virus structure, replication, pathogenesis and evolution are encouraged. These include reports describing virus morphology, the function and antigenic analysis of virus structural components, virus genome structure and expression, analysis on virus replication processes, virus evolution in connection with antiviral interventions, effects of viruses on their host cells, particularly on the immune system, and the pathogenesis of virus infections, including oncogene activation and transduction.