Liu Benjamin M, Yao Qiaobin, Cruz-Cosme Ruth, Yarbrough Casey, Draper Kyah, Suslovic William, Muhammad Imaan, Contes Kaia M, Hillyard David R, Teng Shaolei, Tang Qiyi
Division of Pathology and Laboratory Medicine, Children's National Hospital, Washington, District of Columbia, USA.
Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, District of Columbia, USA.
J Med Virol. 2025 Jan;97(1):e70136. doi: 10.1002/jmv.70136.
SARS-CoV-2 Envelope (E) protein is critical in viral assembly, release, and virulence. E gene was considered highly conserved and evolving slowly. Pan-sarbecoviruses-conserved regions in the E gene have been used as targets for various RT-PCR assays to detect SARS-CoV-2. It remains elusive whether SARS-CoV-2 variants of concern (VOCs) have accumulated significant E mutations that may affect protein stability and diagnostic RT-PCR assays. Herein we aimed to perform a comprehensive genetic analysis on the conservation and diversity of the E gene of SARS-CoV-2 and its VOCs in comparison with other human coronaviruses (HCoVs). In silico analysis of 20 326 HCoV E gene sequences retrieved from GenBank and GISAID suggests that SARS-CoV-2 E gene has multiple pan-HCoVs- and pan-SARS-CoV-2-conserved positions but accumulates significant mutations in VOC B.1.351 and Omicron strains. Mutations were often found in the 5' and 3' variable regions, whereas the central region is conserved. Nucleotide changes C109U and A114G may lead to potential failure of first-line SARS-CoV-2 diagnostic/screening assays. Nucleotide change C212U and its concomitant amino acid substitution Pro71Leu (i.e., C212U/Pro71Leu) is a hallmark mutation of B.1.351 variants, while C26U/Thr9Ile is characteristic of all Omicron variants. Later Omicron subvariants, such as XBB.1.5 and EG.5, additionally acquired the A31G/Thr11Ala mutation, as was confirmed by whole genome sequencing of SARS-CoV-2 in 118 pediatric cases. Wild-type E protein exhibits cytotoxicity to cells, but the mutations Thr9Ile, Thr11Ala, Thr9Ile + Thr11Ala, or Pro71Leu reduces its cytotoxicity. The Thr9Ile + Thr11Ala mutation stabilizes the E proteins of Omicron variants, while Pro71Leu alters the cellular distribution of the E protein, reducing its colocalization with the Golgi body. Altogether, this study not only sheds light on the conservation and diversity of the E gene in SARS-CoV-2 and its VOCs but also informs the improvement and development of SARS-CoV-2 or pan-HCoVs screening and diagnostic assays.
严重急性呼吸综合征冠状病毒2（SARS-CoV-2）包膜（E）蛋白在病毒组装、释放和致病性方面至关重要。E基因被认为高度保守且进化缓慢。E基因中泛沙贝病毒保守区域已被用作各种逆转录聚合酶链反应（RT-PCR）检测方法检测SARS-CoV-2的靶标。目前尚不清楚值得关注的SARS-CoV-2变异株（VOCs）是否积累了可能影响蛋白质稳定性和诊断性RT-PCR检测的显著E基因突变。在此，我们旨在对SARS-CoV-2及其VOCs的E基因与其他人类冠状病毒（HCoVs）相比的保守性和多样性进行全面的遗传分析。对从GenBank和全球共享流感数据倡议组织（GISAID）检索到的20326条HCoV E基因序列进行的电子分析表明，SARS-CoV-2 E基因有多个泛HCoV和泛SARS-CoV-2保守位点，但在VOC B.1.351和奥密克戎毒株中积累了显著突变。突变常出现在5'和3'可变区，而中央区域是保守的。核苷酸变化C109U和A114G可能导致一线SARS-CoV-2诊断/筛查检测潜在失败。核苷酸变化C212U及其伴随的氨基酸替代脯氨酸71亮氨酸（即C212U/Pro71Leu）是B.1.351变异株的标志性突变，而C26U/苏氨酸9异亮氨酸是所有奥密克戎变异株的特征。后来的奥密克戎亚变异株，如XBB.1.5和EG.5，另外获得了A31G/苏氨酸11丙氨酸突变，这在118例儿科病例的SARS-CoV-2全基因组测序中得到证实。野生型E蛋白对细胞具有细胞毒性，但苏氨酸9异亮氨酸、苏氨酸11丙氨酸、苏氨酸9异亮氨酸+苏氨酸11丙氨酸或脯氨酸71亮氨酸突变降低了其细胞毒性。苏氨酸9异亮氨酸+苏氨酸11丙氨酸突变稳定了奥密克戎变异株的E蛋白，而脯氨酸71亮氨酸改变了E蛋白的细胞分布，减少了其与高尔基体的共定位。总之，本研究不仅揭示了SARS-CoV-2及其VOCs中E基因的保守性和多样性，还为SARS-CoV-2或泛HCoV筛查和诊断检测的改进和发展提供了信息。
