Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom; NIHR Oxford Biomedical Research Centre, University of Oxford, United Kingdom.
Public Health England, National Infection Service, Porton Down, Salisbury, United Kingdom.
J Infect. 2020 May;80(5):571-577. doi: 10.1016/j.jinf.2020.02.003. Epub 2020 Feb 22.
Human metapneumovirus (HMPV) infection causes a spectrum of respiratory tract disease, and may be a significant pathogen in the context of immunocompromise. Here, we report direct-from-sample metagenomic sequencing of HMPV using Oxford Nanopore Technology.
We applied this sequencing approach to 25 respiratory samples that had been submitted to a clinical diagnostic laboratory in a UK teaching hospital. These samples represented 13 patients under the care of a haematology unit over a 20-day period in Spring 2019 (two sampled twice), and ten other patients elsewhere in the hospital between 2017-2019.
We generated HMPV reads from 20/25 samples (sensitivity 80% compared to routine diagnostic testing) and retrieved complete HMPV genomes from 15/20 of these. Consensus sequences from Nanopore data were identical to those generated by Illumina, and represented HMPV genomes from two distinct sublineages, A2b and B2. Sequences from ten haematology patients formed a unique genetic group in the A2b sublineage, not previously reported in the UK. Among these, eight HMPV genomes formed a cluster (differing by ≤3 SNPs), likely to reflect nosocomial transmission, while two others were more distantly related and may represent independent introductions to the haematology unit.
Nanopore metagenomic sequencing can be used to diagnose HMPV infection, although more work is required to optimise sensitivity. Improvements in the use of metagenomic sequencing, particularly for respiratory viruses, could contribute to antimicrobial stewardship. Generation of full genome sequences can be used to support or rule out nosocomial transmission, and contribute to improving infection prevention and control practices.
人偏肺病毒（HMPV）感染可引起一系列呼吸道疾病，在免疫功能低下的情况下可能是一种重要的病原体。在此，我们报告了使用牛津纳米孔技术对 HMPV 进行的样本直接宏基因组测序。
我们将这种测序方法应用于 25 个呼吸样本，这些样本来自英国一所教学医院的临床诊断实验室。这些样本代表了 2019 年春季在血液病病房接受治疗的 13 名患者（其中 2 人在 20 天内接受了两次采样），以及 2017 年至 2019 年期间医院其他病房的 10 名患者。
我们从 25 个样本中生成了 HMPV 读段（与常规诊断检测相比，敏感性为 80%），并从其中的 15 个样本中获得了完整的 HMPV 基因组。纳米孔数据的共识序列与 Illumina 生成的序列完全一致，代表了两个不同亚谱系 A2b 和 B2 的 HMPV 基因组。10 名血液病患者的序列在 A2b 亚谱系中形成了一个独特的遗传群，在英国尚未报道过。在这些患者中，8 个 HMPV 基因组形成了一个聚类（差异≤3 个 SNP），可能反映了医院内传播，而另外两个则相关性较低，可能代表了对血液病病房的独立传入。
纳米孔宏基因组测序可用于诊断 HMPV 感染，尽管需要进一步优化以提高敏感性。改善宏基因组测序的应用，特别是针对呼吸道病毒，有助于抗菌药物管理。生成完整的基因组序列可用于支持或排除医院内传播，并有助于改进感染预防和控制措施。
