References
- Willner D , FurlanM, HaynesMet al. Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals . PLoS ONE4 ( 10 ), e7370 ( 2009 ).
- Willner D , HaynesMR, FurlanMet al. Case studies of the spatial heterogeneity of DNA viruses in the cystic fibrosis lung . Am. J. Respir. Cell Mol. Biol.46 ( 2 ), 127 – 131 ( 2012 ).
- Wylie KM , MihindukulasuriyaKA, SodergrenE, WeinstockGM, StorchGA . Sequence analysis of the human virome in febrile and afebrile children . PLoS ONE7 ( 6 ), e27735 ( 2012 ).
- Young JC , ChehoudC, BittingerKet al. Viral metagenomics reveal blooms of anelloviruses in the respiratory tract of lung transplant recipients . Am. J. Transplant.15 ( 1 ), 200 – 209 ( 2015 ).
- Lysholm F , WetterbomA, LindauCet al. Characterization of the viral microbiome in patients with severe lower respiratory tract infections, using metagenomic sequencing . PLoS ONE7 ( 2 ), e30875 ( 2012 ).
- Zoll J , Rahamat-LangendoenJ, AhoutIet al. Direct multiplexed whole genome sequencing of respiratory tract samples reveals full viral genomic information . J. Clin. Virol.66, 6 – 11 ( 2015 ).
- Prachayangprecha S , SchapendonkCME, KoopmansMPet al. Exploring the potential of next-generation sequencing in detection of respiratory viruses . J. Clin. Microbiol.52 ( 10 ), 3722 – 3730 ( 2014 ).
- Ng SHS , AziziA, EdamuraKet al. Preliminary evaluation of next-generation sequencing performance relative to qPCR and in vitro cell culture tests for human cytomegalovirus . PDA J. Pharm. Sci. Technol. PDA68 ( 6 ), 563 – 571 ( 2014 ).
- Yang J , YangF, RenLet al. Unbiased parallel detection of viral pathogens in clinical samples by use of a metagenomic approach . J. Clin. Microbiol.49 ( 10 ), 3463 – 3469 ( 2011 ).
- Popgeorgiev N , TemmamS, RaoultD, DesnuesC . Describing the silent human virome with an emphasis on giant viruses . Intervirology56 ( 6 ), 395 – 412 ( 2013 ).
- Allander T . Human bocavirus . J. Clin. Virol.41 ( 1 ), 29 – 33 ( 2008 ).
- Winther B , HaydenFG, HendleyJO . Picornavirus infections in children diagnosed by RT-PCR during longitudinal surveillance with weekly sampling: Association with symptomatic illness and effect of season . J. Med. Virol.78 ( 5 ), 644 – 650 ( 2006 ).
- Mitchell AB , OliverBGG, GlanvilleAR . Translational aspects of the human respiratory virome . Am. J. Respir. Crit. Care Med.194 ( 12 ), 1458 – 1464 ( 2016 ).
- Seemungal TA , Harper-OwenR, BhowmikA, JeffriesDJ, WedzichaJA . Detection of rhinovirus in induced sputum at exacerbation of chronic obstructive pulmonary disease . Eur. Respir. J.16 ( 4 ), 677 – 683 ( 2000 ).
- Wilkinson TMA , HurstJR, PereraWR, WilksM, DonaldsonGC, WedzichaJA . Effect of interactions between lower airway bacterial and rhinoviral infection in exacerbations of COPD . Chest129 ( 2 ), 317 – 324 ( 2006 ).
- Smith CB , GoldenCA, KannerRE, RenzettiAD . Association of viral and Mycoplasma pneumoniae infections with acute respiratory illness in patients with chronic obstructive pulmonary diseases . Am. Rev. Respir. Dis.121 ( 2 ), 225 – 232 ( 1980 ).
- Papi A , BellettatoCM, BraccioniFet al. Infections and airway inflammation in chronic obstructive pulmonary disease severe exacerbations . Am. J. Respir. Crit. Care Med.173 ( 10 ), 1114 – 1121 ( 2006 ).
- Rohde G , WiethegeA, BorgIet al. Respiratory viruses in exacerbations of chronic obstructive pulmonary disease requiring hospitalisation: a case-control study . Thorax58 ( 1 ), 37 – 42 ( 2003 ).
- Borg I , RohdeG, LösekeSet al. Evaluation of a quantitative real-time PCR for the detection of respiratory syncytial virus in pulmonary diseases . Eur. Respir. J.21 ( 6 ), 944 – 951 ( 2003 ).
- Rohde G , BorgI, ArinirUet al. Relevance of human metapneumovirus in exacerbations of COPD . Respir. Res.6, 150 ( 2005 ).
- Perotin J , DuryS, RenoisFet al. Detection of multiple viral and bacterial infections in acute exacerbation of chronic obstructive disease: a pilot prospective study . J. Med. Virol.85 ( 5 ), 866 – 873 ( 2013 ).
- Hamelin M , CôtéS, LaforgeJet al. Human metapneumovirus infection in adults with community-acquired pneumonia and exacerbation of chronic obstructive pulmonary disease . Clin. Infect. Dis.15 ( 41 ), 498 – 502 ( 2005 ).
- Clark TW , MedinaM-J, BathamS, CurranMD, ParmarS, NicholsonKG . C-reactive protein level and microbial aetiology in patients hospitalised with acute exacerbation of COPD . Eur. Respir. J.45 ( 1 ), 76 – 86 ( 2015 ).
- Anderson HR , SpixC, MedinaSet al. Air pollution and daily admissions for chronic obstructive pulmonary disease in 6 European cities: results from the APHEA project . Eur. Respir. J.10 ( 5 ), 1064 – 1071 ( 1997 ).
- Ko FWS , TamW, WongTWet al. Temporal relationship between air pollutants and hospital admissions for chronic obstructive pulmonary disease in Hong Kong . Thorax62 ( 9 ), 780 – 785 ( 2007 ).
- Sunyer J , SáezM, MurilloC, CastellsagueJ, MartínezF, AntóJM . Air pollution and emergency room admissions for chronic obstructive pulmonary disease: a 5-year study . Am. J. Epidemiol.137 ( 7 ), 701 – 705 ( 1993 ).
- Beghé B , VerduriA, RocaM, FabbriLM . Exacerbation of respiratory symptoms in COPD patients may not be exacerbations of COPD . Eur. Respir. J.41 ( 4 ), 993 – 995 ( 2013 ).
- Gallego M , PomaresX, EspasaMet al. Pseudomonas aeruginosa isolates in severe chronic obstructive pulmonary disease: characterization and risk factors . BMC Pulm. Med.14 ( 1 ), 103 ( 2014 ).
- Millares L , FerrariR, GallegoMet al. Bronchial microbiome of severe COPD patients colonised by Pseudomonas aeruginosa . Eur. J. Clin. Microbiol. Infect. Dis.33 ( 7 ), 1101 – 1111 ( 2014 ).
- GOLD: the Global initiative for chronic Obstructive Lung Disease . www.goldcopd.org/Guidelines/guidelines-resources.html .
- No authors listed . Standardization of spirometry, 1994 update. American Thoracic Society . Am. J. Respir. Crit. Care Med.152 ( 3 ), 1107 – 1136 ( 1995 ).
- Roca J , SanchisJ, Agusti-VidalAet al. Spirometric reference values from a Mediterranean population . Bull. Eur. Physiopathol. Respir.22 ( 3 ), 217 – 224 ( 1986 ).
- Murray PR , WashingtonJA . Microscopic and baceriologic analysis of expectorated sputum . Mayo Clin. Proc.50 ( 6 ), 339 – 344 ( 1975 ).
- Coiras MT , AguilarJC, GarcíaML, CasasI, Pérez-BreñaP . Simultaneous detection of fourteen respiratory viruses in clinical specimens by two multiplex reverse transcription nested-PCR assays . J. Med. Virol.72 ( 3 ), 484 – 495 ( 2004 ).
- Cabello H , TorresA, CelisRet al. Bacterial colonization of distal airways in healthy subjects and chronic lung disease: a bronchoscopic study . Eur. Respir. J.10 ( 5 ), 1137 – 1144 ( 1997 ).
- Sethi S , SethiR, EschbergerKet al. Airway bacterial concentrations and exacerbations of chronic obstructive pulmonary disease . Am. J. Respir. Crit. Care Med.176 ( 4 ), 356 – 361 ( 2007 ).
- Schmieder R , EdwardsR . Quality control and preprocessing of metagenomic datasets . Bioinformatics27 ( 6 ), 863 – 864 ( 2011 ).
- Langmead B , SalzbergSL . Fast gapped-read alignment with Bowtie 2 . Nat. Methods9 ( 4 ), 357 – 359 ( 2012 ).
- The National Center for Biotechnology Information . Assembly accession bioproject biosample . ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/viral/assembly_summary.txt .
- The National Center for Biotechnology Information . ftp://ftp.ncbi.nlm.nih.gov/genomes/Viruses/ .
- European Nucleotide Archive . Genomes Pages – Virus . www.ebi.ac.uk/genomes/virus.html .
- The National Center for Biotechnology Information . ftp://ftp.ebi.ac.uk/pub/databases/fastafiles/embl_genomes/genomes/Phage/ .
- The National Center for Biotechnology Information . ftp://ftp.ebi.ac.uk/pub/databases/fastafiles/emblrelease/ .
- The National Center for Biotechnology Information . ftp://ftp.ebi.ac.uk/pub/databases/fastafiles/emblnew/ .
- Pérez-Brocal V , García-LópezR, Vázquez-CastellanosJFet al. Study of the viral and microbial communities associated with Crohn’s disease: a metagenomic approach . Clin. Transl. Gastroenterol.4, e36 ( 2013 ).
- Caporaso JG , KuczynskiJ, StombaughJet al. QIIME allows analysis of high-throughput community sequencing data . Nat. Methods7 ( 5 ), 335 – 336 ( 2010 ).
- Wylie KM , MihindukulasuriyaKA, ZhouY, SodergrenE, StorchGA, WeinstockGM . Metagenomic analysis of double-stranded DNA viruses in healthy adults . BMC Biol.12 ( 1 ), 71 ( 2014 ).
- Hofer U . Microbiome: anelloviridae go viral . Nat. Rev. Microbiol.12 ( 1 ), 4 – 5 ( 2014 ).
- Wootton SC , KimDS, KondohYet al. Viral Infecion in acute exacerbation of idiopathic pulmonary fibrosis . Am. J. Respir. Crit. Care Med.183, 1698 – 1702 ( 2011 ).
- Feyzioğlu B , TekeT, OzdemirM, KaraibrahimoğluA, DoğanM, YavşanM . The presence of Torque teno virus in chronic obstructive pulmonary disease . Int. J. Clin. Exp. Med.7 ( 10 ), 3461 – 3466 ( 2014 ).
- Pifferi M , MaggiF, CaramellaDet al. High TTV loads are correlated with bronchiectasis and peripheral airflow limitation in children . Pediatr. Infect. Dis. J.25 ( 9 ), 804 – 808 ( 2006 ).
- Utokaparch S , SzeMA, GosselinkJVet al. Respiratory viral detection and small airway inflammation in lung tissue of patients with stable, mild COPD . COPD11 ( 2 ), 197 – 203 ( 2014 ).
- Wilkinson TMA , DonaldsonGC, JohnstonSL, OpenshawPJM, WedzichaJA . Respiratory syncytial virus, airway inflammation, and FEV1 decline in patients with chronic obstructive pulmonary disease . Am. J. Respir. Crit. Care Med.173 ( 8 ), 871 – 876 ( 2006 ).