Abstract
Nasopharyngeal swabs were taken from volunteers attending a general medical practice and a general hospital in Lancaster, UK, and at Lancaster University, in the winter of 2014–2015. 51 swabs were selected based on high RNA yield and allocated to deep sequencing pools as follows: patients with chronic obstructive pulmonary disease; asthmatics; adults with no respiratory symptoms; adults with feverish respiratory symptoms; adults with respiratory symptoms and presence of antibodies against influenza C; paediatric patients with respiratory symptoms (2 pools); adults with influenza C infection (2 pools), giving a total of 9 pools. Illumina sequencing was performed, with data yields per pool in the range of 345.6 megabases to 14 gigabases after removal of reads aligning to the human genome. The data were deposited in the Sequence Read Archive at NCBI, and constitute a resource for study of the viral, bacterial and fungal metagenome of the human nasopharynx in healthy and diseased states and comparison with other metagenomic studies on the human respiratory tract.
Highlights
Background & SummaryRespiratory infectious disease is a major cause of morbidity and mortality in the elderly, infants, the immune-compromised and those with underlying serious pulmonary conditions such as asthma or cystic fibrosis
The sheer diversity of microbes causing respiratory infections that are indistinguishable on clinical examination, means that the vast majority of patients receive only a generic diagnosis of coryza or pharyngitis
Within the Sequence Read Archive (SRA), the tag ‘human nasopharyngeal metagenome’ identifies 41 BioProject entries as of 30th August 2017, including that reported here. Within this group of datasets, there are upper respiratory tract metagenomes associated with influenza, respiratory syncytial virus, allergy, intubation, asthma, macular degeneration, oesophageal reflux, rhinosinusitis and Parkinsonism as well as samples taken from healthy volunteers
Summary
Respiratory infectious disease is a major cause of morbidity and mortality in the elderly, infants, the immune-compromised and those with underlying serious pulmonary conditions such as asthma or cystic fibrosis It is a source of considerable economic damage through working days lost to illness in adults Within the Sequence Read Archive (SRA), the tag ‘human nasopharyngeal metagenome’ identifies 41 BioProject entries as of 30th August 2017, including that reported here Within this group of datasets, there are upper respiratory tract metagenomes associated with influenza, respiratory syncytial virus, allergy, intubation, asthma, macular degeneration, oesophageal reflux, rhinosinusitis and Parkinsonism as well as samples taken from healthy volunteers. Two of our 9 sequencing pools (Data Citations 8, 9) were from individuals diagnosed with influenza C infection via quantitative RT-PCR, from one of which we could partially assemble
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