Virology Unit, Department of Microbiology, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait.
Research Core Facility and OMICS Research Unit, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait.
Microbiol Spectr. 2024 Jul 2;12(7):e0015924. doi: 10.1128/spectrum.00159-24. Epub 2024 May 29.
The human respiratory syncytial virus (RSV) is considered one of the most common viruses that infect children globally. The virus is known to have extensive gene sequence variability within and between RSV groups A and B globally; however, there is no information on the whole-genome characterization and diversity of RSV in Kuwait. Therefore, this study aimed to sequence the entire genome of RSV strains isolated from patients with acute respiratory tract infection (ARTI) in Kuwait. Therefore, this study aimed to sequence the entire genome of RSV strains isolated from patients with ARTI in Kuwait. Between January 2020 and September 2022, 7,093 respiratory samples were collected from hospitalized infants, children, and adults and were analyzed for respiratory viruses by multiplex real-time PCR. Whole-genome sequencing using the Oxford Nanopore sequencing technology was performed on 84 RSV-positive samples. The results revealed a higher prevalence of group A (76%) than group B (24%) RSV isolates. Phylogenetic analysis showed that RSV-A strains clustered with the GA2.3.5 sub-genotype and RSV-B strains clustered with the GB5.0.5a sub-genotype; however, forming new lineages of RSV-A and RSV-B circulated in Kuwait during this period. Genetic variability was higher among the group A viruses than group B viruses, and the rate of synonymous and missense mutations was high in genes other than the G protein-coding gene. We also detected several known and unique molecular markers in different protein-coding genes. This is the first study in Kuwait to characterize the whole genomes of RSV A and B to identify the circulating genotypes, comprehend the genetic diversity and the evolution of the virus, and identify important genetic markers associated with specific genotypes.IMPORTANCEWhole-genome sequencing of respiratory syncytial virus (RSV) strains in Kuwait using MinION Nanopore technology was used to characterize and analyze the genotypes and sub-genotypes of the RSV circulating among patients with acute respiratory tract infections in Kuwait. This study also identified known and unknown gene mutations and imported genetic markers associated with specific genotypes. These results will assist in establishing a framework for RSV classification and allow for a better consideration of the mechanisms leading to the generation of diversity of RSV. In addition, these data will allow a comparison of vaccine viruses with those in Kuwait, providing useful insights into future vaccine and therapy strategies for RSV in Kuwait.
人类呼吸道合胞病毒（RSV）被认为是全球范围内感染儿童最常见的病毒之一。该病毒在全球范围内的 RSV A 组和 B 组之间具有广泛的基因序列变异性；然而，关于科威特 RSV 的全基因组特征和多样性尚无信息。因此，本研究旨在对从科威特急性呼吸道感染（ARTI）患者中分离出的 RSV 株进行全基因组测序。因此，本研究旨在对从科威特 ARTI 患者中分离出的 RSV 株进行全基因组测序。在 2020 年 1 月至 2022 年 9 月期间，从住院婴儿、儿童和成人中采集了 7093 份呼吸道样本，并通过多重实时 PCR 分析了呼吸道病毒。对 84 份 RSV 阳性样本进行了 Oxford Nanopore 测序技术的全基因组测序。结果显示，组 A（76%）的 RSV 分离株比组 B（24%）更为常见。系统发育分析显示，RSV-A 株与 GA2.3.5 亚属聚类，RSV-B 株与 GB5.0.5a 亚属聚类；然而，在此期间，在科威特形成了新的 RSV-A 和 RSV-B 流行株。组 A 病毒的遗传变异性高于组 B 病毒，除 G 蛋白编码基因外，其他基因的同义突变和错义突变率较高。我们还在不同的编码基因中检测到了一些已知和独特的分子标记。这是科威特首次对 RSV A 和 B 的全基因组进行特征描述，以确定流行的基因型，了解病毒的遗传多样性和进化，并确定与特定基因型相关的重要遗传标记。
重要性：使用 MinION Nanopore 技术对科威特呼吸道合胞病毒（RSV）株进行全基因组测序，用于对科威特急性呼吸道感染患者中流行的 RSV 基因型和亚属进行特征描述和分析。本研究还鉴定了与特定基因型相关的已知和未知基因突变和导入的遗传标记。这些结果将有助于建立 RSV 的分类框架，并更好地考虑导致 RSV 多样性产生的机制。此外，这些数据将允许比较科威特的疫苗病毒与那些病毒，为科威特的 RSV 疫苗和治疗策略提供有用的见解。
