Microbiology and Infectology Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), 36312 Vigo, Spain.
Faculty of Biology, Universidade de Vigo, 36310 Vigo, Spain.
Int J Mol Sci. 2023 Nov 7;24(22):16055. doi: 10.3390/ijms242216055.
There is growing interest in the molecular surveillance of the Respiratory Syncytial Virus and the monitorization of emerging mutations that could impair the efficacy of antiviral prophylaxis and treatments. A simple, scalable protocol for viral nucleic acid enrichment could improve the surveillance of RSV. We developed a protocol for RSV-A and B amplification based on the Illumina CovidSeq workflow using an RSV primer panel. A total of 135 viral genomes were sequenced from nasopharyngeal samples through the optimization steps of this panel, while an additional 15 samples were used to test the final version. Full coverage of the G gene and over 95% of the coverage of the F gene, the target of the available RSV antivirals or monoclonal antibodies, were obtained. The F:K68N mutation, associated with decreased nirsevimab activity, was detected in our facility. Additionally, phylogenetic analysis showed several sublineages in the 2022-2023 influenza season in Europe. Our protocol allows for a simple and scalable simultaneous amplification of the RSV-A and B whole genome, increasing the yield of RSV sequencing and reducing costs. Its application would allow the world to be ready for the detection of arising mutations in relation to the widespread use of nirsevimab for RSV prevention.
人们对呼吸道合胞病毒的分子监测越来越感兴趣，也在关注可能降低抗病毒预防和治疗效果的新出现突变。一种简单、可扩展的病毒核酸富集方案可以提高 RSV 的监测能力。我们开发了一种基于 Illumina CovidSeq 工作流程的 RSV-A 和 B 扩增方案，使用 RSV 引物组。通过该小组的优化步骤，从鼻咽样本中总共测序了 135 个病毒基因组，另外还有 15 个样本用于测试最终版本。我们获得了 RSV 可用抗病毒药物或单克隆抗体的靶标 F 基因的全覆盖，以及超过 95%的 F 基因的覆盖率。我们的实验室检测到了与 nirsevimab 活性降低相关的 F:K68N 突变。此外，系统发育分析显示，2022-2023 年欧洲流感季节存在几个亚谱系。我们的方案允许简单且可扩展地同时扩增 RSV-A 和 B 的全基因组，提高 RSV 测序的产量并降低成本。它的应用将使世界能够为广泛使用 nirsevimab 预防 RSV 而出现的突变检测做好准备。
