References
- Briese T, Paweska JT, McMullan LK, et al. Genetic detection and characterization of Lujo virus, a new hemorrhagic fever–associated arenavirus from Southern Africa. Plos Pathog. 2009;5:e1000455. doi: 10.1371/journal.ppat.1000455
- Negredo A, Palacios G, Vázquez-Morón S, et al. Discovery of an ebolavirus-like filovirus in Europe. PLoS Pathog. 2011;7:e1002304. doi: 10.1371/journal.ppat.1002304
- Oliveira D, Almeida FJ, Durigon EL, et al. Prolonged shedding of Zika virus associated with congenital infection. New Engl J Med. 2016;375:1202–1204. doi: 10.1056/NEJMc1607583
- Shi M, Lin X-D, Tian J-H, et al. Redefining the invertebrate RNA virosphere. Nature. 2016;540:539–543. doi: 10.1038/nature20167
- Cox-Foster DL, Conlan S, Holmes EC, et al. A metagenomic survey of microbes in honey bee colony collapse disorder. Science. 2007;318:283–287. doi: 10.1126/science.1146498
- Palacios G, Quan P-L, Jabado OJ, et al. Panmicrobial oligonucleotide array for diagnosis of infectious diseases. Emerg Infect Dis. 2007;13:73–81. doi: 10.3201/eid1301.060837
- Zhang Y-Z, Shi M, Holmes EC. Using metagenomics to characterize an expanding virosphere. Cell. 2018;172:1168–1172. doi: 10.1016/j.cell.2018.02.043
- Palacios G, Druce J, Du L, et al. A new arenavirus in a cluster of fatal transplant-associated diseases. New Engl J Med. 2008;358:991–998. doi: 10.1056/NEJMoa073785
- Whitley R. The new age of molecular diagnostics for microbial agents. New Engl J Med. 2008;358:988–989. doi: 10.1056/NEJMp0708085
- Ladner JT, Wiley MR, Beitzel B, et al. A multicomponent animal virus isolated from mosquitoes. Cell Host Microbe. 2016;20:357–367. doi: 10.1016/j.chom.2016.07.011
- Jones KE, Patel NG, Levy MA, et al. Global trends in emerging infectious diseases. Nature. 2008;451:990–993. doi: 10.1038/nature06536
- Lipkin IW. Pathogen discovery. Plos Pathog. 2008;4:e1000002. doi: 10.1371/journal.ppat.1000002
- Goodacre N, Aljanahi A, Nandakumar S, et al. A reference viral database (RVDB) to enhance bioinformatics analysis of high-throughput sequencing for novel virus detection. Msphere. 2018;3:e00069. doi: 10.1128/mSphereDirect.00069-18
- WHO G World Health Organization. Global health estimates 2016: Deaths by cause, age, sex, by country and by region, 2000–2016. 2018.
- Rudan I, O’Brien KL, Nair H, et al. Epidemiology and etiology of childhood pneumonia in 2010: estimates of incidence, severe morbidity, mortality, underlying risk factors and causative pathogens for 192 countries. J Global Heal. 2013;3:010401.
- Murdoch DR, Jennings LC, Bhat N, et al. Emerging advances in rapid diagnostics of respiratory infections. Infect Dis Clin N Am. 2010;24:791–807. doi: 10.1016/j.idc.2010.04.006
- Frenzen PD. Mortality due to gastroenteritis of unknown etiology in the United States. J Infect Dis. 2003;187:441–452. doi: 10.1086/368097
- Frenzen PD. Deaths due to unknown foodborne agents. Emerg Infect Dis. 2004;10:1536–1543. doi: 10.3201/eid1009.030403
- Kennedy PG, Quan P-L, Lipkin IW. Viral encephalitis of unknown cause: current perspective and recent advances. Viruses. 2017;9:138. doi: 10.3390/v9060138
- NIH N. National Institutes of Health Consensus Development Conference on Infantile Apnea and Home Monitoring, Sept 29 to Oct 1, 1986. Pediatrics [Internet]. 79. Available from: http://pediatrics.aappublications.org/content/79/2/292.
- Coiras MT, Pérez-Breña P, García ML, et al. Simultaneous detection of influenza A, B, and C viruses, respiratory syncytial virus, and adenoviruses in clinical samples by multiplex reverse transcription nested-PCR assay. J Med Virol. 2003;69:132–144. doi: 10.1002/jmv.10255
- Coiras MT, Aguilar JC, García ML, et al. Simultaneous detection of fourteen respiratory viruses in clinical specimens by two multiplex reverse transcription nested-PCR assays. J Med Virol. 2004;72:484–495. doi: 10.1002/jmv.20008
- Calvo C, García-García M, Pozo F, et al. Infections and coinfections by respiratory human bocavirus during eight seasons in hospitalized children. J Med Virol. 2016;88:2052–2058. doi: 10.1002/jmv.24562
- Gong Y-N, Yang S-L, Chen G-W, et al. A metagenomics study for the identification of respiratory viruses in mixed clinical specimens: an application of the iterative mapping approach. Arch Virol. 2017;162:2003–2012. doi: 10.1007/s00705-017-3367-4
- Xu L, Zhu Y, Ren L, et al. Characterization of the nasopharyngeal viral microbiome from children with community-acquired pneumonia but negative for Luminex xTAG respiratory viral panel assay detection. J Med Virol. 2017;89:2098–2107. doi: 10.1002/jmv.24895
- Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. 2011;17:10–12. doi: 10.14806/ej.17.1.200
- Schmieder R, Edwards R. Quality control and preprocessing of metagenomic datasets. Bioinformatics. 2011;27:863–864. doi: 10.1093/bioinformatics/btr026
- Langmead B, Trapnell C, Pop M, et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10:R1. doi: 10.1186/gb-2009-10-1-r1
- Boisvert S, Raymond F, Godzaridis É, et al. Ray Meta: scalable de novo metagenome assembly and profiling. Genome Biol. 2012;13:R122. doi: 10.1186/gb-2012-13-12-r122
- Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods. 2014;12. doi: 10.1038/nmeth.3176
- Advani S, Sengupta A, Forman M, et al. Detecting respiratory viruses in asymptomatic children. Pediatric Infect Dis J. 2012;31:1221–1226. doi: 10.1097/INF.0b013e318265a804
- Falsey AR, Erdman D, Anderson LJ, et al. Human metapneumovirus infections in young and Elderly Adults. J Infect Dis. 2003;187:785–790. doi: 10.1086/367901
- Falsey AR. Human metapneumovirus infection in adults. Pediatric Infect Dis J. 2008;27:S80–S83. doi: 10.1097/INF.0b013e3181684dac
- de Crom S, Rossen J, van Furth A, et al. Enterovirus and parechovirus infection in children: a brief overview. Eur J Pediatr. 2016;175:1023–1029. doi: 10.1007/s00431-016-2725-7
- Gaynor AM, Nissen MD, Whiley DM, et al. Identification of a novel polyomavirus from patients with acute respiratory tract infections. PLoS Pathog. 2007;3:e64. doi: 10.1371/journal.ppat.0030064
- Norja P, Ubillos I, Templeton K, et al. No evidence for an association between infections with WU and KI polyomaviruses and respiratory disease. J Clin Virol. 2007;40:307–311. doi: 10.1016/j.jcv.2007.09.008
- Rao S, Lucero MG, Nohynek H, et al. WU and KI polyomavirus infections in Filipino children with lower respiratory tract disease. J Clin Virol. 2016;82:112–118. doi: 10.1016/j.jcv.2016.07.013
- Wang Y, Zhu N, Li Y, et al. Metagenomic analysis of viral genetic diversity in respiratory samples from children with severe acute respiratory infection in China. Clin Microbiol Infect. 2016;22:458.e1–458.e9. doi: 10.1016/j.cmi.2016.01.006
- Gillison ML, Alemany L, Snijders P, et al. Human papillomavirus and diseases of the upper airway: head and neck cancer and respiratory papillomatosis. Vaccine. 2012;30:F34–F54. doi: 10.1016/j.vaccine.2012.05.070
- Cui L, Wu B, Zhu X, et al. Identification and genetic characterization of a novel circular single-stranded DNA virus in a human upper respiratory tract sample. Arch Virol. 2017;162:3305–3312. doi: 10.1007/s00705-017-3481-3
- Delwart E, Li L. Rapidly expanding genetic diversity and host range of the circoviridae viral family and other rep encoding small circular ssDNA genomes. Virus Res. 2012;164:114–121. doi: 10.1016/j.virusres.2011.11.021
- Rosario K, Duffy S, Breitbart M. Diverse circovirus-like genome architectures revealed by environmental metagenomics. J Gen Virol. 2009;90:2418–2424. doi: 10.1099/vir.0.012955-0
- Li L, Kapoor A, Slikas B, et al. Multiple diverse circoviruses infect farm animals and are commonly found in human and chimpanzee feces. J Virol. 2010;84:1674–1682. doi: 10.1128/JVI.02109-09
- Rosario K, Marinov M, Stainton D, et al. Dragonfly cyclovirus, a novel single-stranded DNA virus discovered in dragonflies (Odonata: Anisoptera). J Gen Virol. 2011;92:1302–1308. doi: 10.1099/vir.0.030338-0
- de Lima F. Cibulski S, dos Santos H. et al. Genomic Characterization of Novel Circular ssDNA Viruses From Insectivorous Bats in Southern Brazil. Plos One. 2015;10:e0118070. doi: 10.1371/journal.pone.0118070
- Phan T, Mori D, Deng X, et al. Small circular single stranded DNA viral genomes in unexplained cases of human encephalitis, diarrhea, and in untreated sewage. Virology. 2015;482:98–104. doi: 10.1016/j.virol.2015.03.011
- Halary S, Duraisamy R, Fancello L, et al. Novel single-stranded DNA circular viruses in pericardial fluid of patient with recurrent pericarditis. Emerg Infect. Dis. 2016;22:1839–1841. doi: 10.3201/eid2210.160052
- Tan L, van Doorn RH, Nghia H, et al. Enamel-based mark performance for marking Chinese mystery snail Bellamya chinensis. Mbio. 2013;4:231–234. doi: 10.3391/mbi.2013.4.3.05
- Phan T, Luchsinger V, Avendaño LF, et al. Cyclovirus in nasopharyngeal aspirates of Chilean children with respiratory infections. J Gen Virol. 2014;95:922–927. doi: 10.1099/vir.0.061143-0
- Taboada B, Espinoza MA, Isa P, et al. Is there still room for novel viral pathogens in pediatric respiratory tract infections? PLoS ONE. 2014;9:e113570. doi: 10.1371/journal.pone.0113570
- Zhou Y, Fernandez S, Yoon I-K, et al. Metagenomics study of viral pathogens in undiagnosed respiratory specimens and identification of human enteroviruses at a Thailand hospital. Am J Trop Med Hyg. 2016;95:663–669. doi: 10.4269/ajtmh.16-0062
- Rutvisuttinunt W, Klungthong C, Thaisomboonsuk B, et al. Retrospective use of next-generation sequencing reveals the presence of enteroviruses in acute influenza-like illness respiratory samples collected in South/South-East Asia during 2010–2013. J Clin Virol. 2017;94:91–99. doi: 10.1016/j.jcv.2017.07.004