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For: Nakamura S, Yang CS, Sakon N, Ueda M, Tougan T, Yamashita A, Goto N, Takahashi K, Yasunaga T, Ikuta K, Mizutani T, Okamoto Y, Tagami M, Morita R, Maeda N, Kawai J, Hayashizaki Y, Nagai Y, Horii T, Iida T, Nakaya T. Direct metagenomic detection of viral pathogens in nasal and fecal specimens using an unbiased high-throughput sequencing approach. PLoS One 2009;4:e4219. [PMID: 19156205 PMCID: PMC2625441 DOI: 10.1371/journal.pone.0004219] [Citation(s) in RCA: 174] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2008] [Accepted: 12/01/2008] [Indexed: 12/27/2022]  Open
Number Cited by Other Article(s)
1
Thapliyal P, Sah V, Rautela I, Joshi M, Tyagi S, Verma R, Sharma MD. Next Generation Sequencing: Latent applications in clinical diagnostics with the advent of bioinformatic frameworks. Pathol Res Pract 2024;263:155606. [PMID: 39357183 DOI: 10.1016/j.prp.2024.155606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Revised: 09/03/2024] [Accepted: 09/24/2024] [Indexed: 10/04/2024]
2
Downie DL, Rao P, David-Ferdon C, Courtney S, Lee JS, Quiner C, MacDonald PDM, Barnes K, Fisher S, Andreadis JL, Chaitram J, Mauldin MR, Salerno RM, Schiffer J, Gundlapalli AV. Surveillance for Emerging and Reemerging Pathogens Using Pathogen Agnostic Metagenomic Sequencing in the United States: A Critical Role for Federal Government Agencies. Health Secur 2024;22:85-92. [PMID: 38574329 PMCID: PMC11044857 DOI: 10.1089/hs.2023.0099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 08/04/2023] [Accepted: 08/04/2023] [Indexed: 04/06/2024]  Open
3
Arts PJ, Kelly JD, Midgley CM, Anglin K, Lu S, Abedi GR, Andino R, Bakker KM, Banman B, Boehm AB, Briggs-Hagen M, Brouwer AF, Davidson MC, Eisenberg MC, Garcia-Knight M, Knight S, Peluso MJ, Pineda-Ramirez J, Diaz Sanchez R, Saydah S, Tassetto M, Martin JN, Wigginton KR. Longitudinal and quantitative fecal shedding dynamics of SARS-CoV-2, pepper mild mottle virus, and crAssphage. mSphere 2023;8:e0013223. [PMID: 37338211 PMCID: PMC10506459 DOI: 10.1128/msphere.00132-23] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/03/2023] [Indexed: 06/21/2023]  Open
4
Liu S, Li Q, Jiang R, Liu P, Zhang XX. Shift of human pathogen community composition and their potential human health risk after supply suspension in tap water. Sci Rep 2023;13:12419. [PMID: 37528119 PMCID: PMC10393962 DOI: 10.1038/s41598-023-39225-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 07/21/2023] [Indexed: 08/03/2023]  Open
5
Claro IM, Ramundo MS, Coletti TM, da Silva CAM, Valenca IN, Candido DS, Sales FCS, Manuli ER, de Jesus JG, de Paula A, Felix AC, Andrade PDS, Pinho MC, Souza WM, Amorim MR, Proenca-Modena JL, Kallas EG, Levi JE, Faria NR, Sabino EC, Loman NJ, Quick J. Rapid viral metagenomics using SMART-9N amplification and nanopore sequencing. Wellcome Open Res 2023;6:241. [PMID: 37224315 PMCID: PMC10189296 DOI: 10.12688/wellcomeopenres.17170.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/05/2023] [Indexed: 12/08/2023]  Open
6
Claro IM, Ramundo MS, Coletti TM, da Silva CAM, Valenca IN, Candido DS, Sales FCS, Manuli ER, de Jesus JG, de Paula A, Felix AC, Andrade PDS, Pinho MC, Souza WM, Amorim MR, Proenca-Modena JL, Kallas EG, Levi JE, Faria NR, Sabino EC, Loman NJ, Quick J. Rapid viral metagenomics using SMART-9N amplification and nanopore sequencing. Wellcome Open Res 2023;6:241. [PMID: 37224315 PMCID: PMC10189296 DOI: 10.12688/wellcomeopenres.17170.2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/05/2023] [Indexed: 05/26/2023]  Open
7
Ong'era EM, Mohammed KS, Makori TO, Bejon P, Ocholla-Oyier LI, Nokes DJ, Agoti CN, Githinji G. High-throughput sequencing approaches applied to SARS-CoV-2. Wellcome Open Res 2023. [DOI: 10.12688/wellcomeopenres.18701.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]  Open
8
Khan MA, Amin A, Farid A, Ullah A, Waris A, Shinwari K, Hussain Y, Alsharif KF, Alzahrani KJ, Khan H. Recent Advances in Genomics-Based Approaches for the Development of Intracellular Bacterial Pathogen Vaccines. Pharmaceutics 2022;15:pharmaceutics15010152. [PMID: 36678781 PMCID: PMC9863128 DOI: 10.3390/pharmaceutics15010152] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/12/2022] [Accepted: 12/19/2022] [Indexed: 01/04/2023]  Open
9
Yadana S, Cheun-Arom T, Li H, Hagan E, Mendelsohn E, Latinne A, Martinez S, Putcharoen O, Homvijitkul J, Sathaporntheera O, Rattanapreeda N, Chartpituck P, Yamsakul S, Sutham K, Komolsiri S, Pornphatthananikhom S, Petcharat S, Ampoot W, Francisco L, Hemachudha T, Daszak P, Olival KJ, Wacharapluesadee S. Behavioral-biological surveillance of emerging infectious diseases among a dynamic cohort in Thailand. BMC Infect Dis 2022;22:472. [PMID: 35578171 PMCID: PMC9109443 DOI: 10.1186/s12879-022-07439-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 04/27/2022] [Indexed: 11/10/2022]  Open
10
Jurasz H, Pawłowski T, Perlejewski K. Contamination Issue in Viral Metagenomics: Problems, Solutions, and Clinical Perspectives. Front Microbiol 2021;12:745076. [PMID: 34745046 PMCID: PMC8564396 DOI: 10.3389/fmicb.2021.745076] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/17/2021] [Indexed: 12/16/2022]  Open
11
Rajagopala SV, Bakhoum NG, Pakala SB, Shilts MH, Rosas-Salazar C, Mai A, Boone HH, McHenry R, Yooseph S, Halasa N, Das SR. Metatranscriptomics to characterize respiratory virome, microbiome, and host response directly from clinical samples. CELL REPORTS METHODS 2021;1:100091. [PMID: 34790908 PMCID: PMC8594859 DOI: 10.1016/j.crmeth.2021.100091] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 05/18/2021] [Accepted: 09/10/2021] [Indexed: 12/23/2022]
12
Xiao W, Ma Z(S. Inter-Individual Diversity Scaling Analysis of the Human Virome With Classic Diversity-Area Relationship (DAR) Modeling. Front Genet 2021;12:627128. [PMID: 33959147 PMCID: PMC8095712 DOI: 10.3389/fgene.2021.627128] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 03/30/2021] [Indexed: 11/13/2022]  Open
13
Faizuloev E, Mintaev R, Petrusha O, Marova A, Smirnova D, Ammour Y, Meskina E, Sergeev O, Zhavoronok S, Karaulov A, Svitich O, Zverev V. New approach of genetic characterization of group A rotaviruses by the nanopore sequencing method. J Virol Methods 2021;292:114114. [PMID: 33662411 DOI: 10.1016/j.jviromet.2021.114114] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 02/17/2021] [Accepted: 02/25/2021] [Indexed: 02/07/2023]
14
Kelly D, Jere KC, Darby AC, Allen DJ, Iturriza-Gómara M. Complete genome characterization of human noroviruses allows comparison of minor alleles during acute and chronic infections. Access Microbiol 2021;3:000203. [PMID: 34151158 PMCID: PMC8209700 DOI: 10.1099/acmi.0.000203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 01/24/2021] [Indexed: 11/18/2022]  Open
15
Bharucha T, Oeser C, Balloux F, Brown JR, Carbo EC, Charlett A, Chiu CY, Claas ECJ, de Goffau MC, de Vries JJC, Eloit M, Hopkins S, Huggett JF, MacCannell D, Morfopoulou S, Nath A, O'Sullivan DM, Reoma LB, Shaw LP, Sidorov I, Simner PJ, Van Tan L, Thomson EC, van Dorp L, Wilson MR, Breuer J, Field N. STROBE-metagenomics: a STROBE extension statement to guide the reporting of metagenomics studies. THE LANCET. INFECTIOUS DISEASES 2020;20:e251-e260. [PMID: 32768390 PMCID: PMC7406238 DOI: 10.1016/s1473-3099(20)30199-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 03/09/2020] [Accepted: 03/12/2020] [Indexed: 02/07/2023]
16
Ko S, Kim NK, Lee HJ, Ryu TH, Hong JS, Jeong RD. Detection of Plant Pathogenic Viruses in Commercial Gochujang (Fermented Red Pepper Paste) from Korea. THE PLANT PATHOLOGY JOURNAL 2020;36:503-508. [PMID: 33082735 PMCID: PMC7542032 DOI: 10.5423/ppj.nt.06.2020.0093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 01/01/2020] [Accepted: 01/01/2020] [Indexed: 06/11/2023]
17
Perlejewski K, Bukowska-Ośko I, Rydzanicz M, Pawełczyk A, Caraballo Cortѐs K, Osuch S, Paciorek M, Dzieciątkowski T, Radkowski M, Laskus T. Next-generation sequencing in the diagnosis of viral encephalitis: sensitivity and clinical limitations. Sci Rep 2020;10:16173. [PMID: 32999423 PMCID: PMC7528011 DOI: 10.1038/s41598-020-73156-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 09/07/2020] [Indexed: 12/12/2022]  Open
18
Aguado-García Y, Taboada B, Morán P, Rivera-Gutiérrez X, Serrano-Vázquez A, Iša P, Rojas-Velázquez L, Pérez-Juárez H, López S, Torres J, Ximénez C, Arias CF. Tobamoviruses can be frequently present in the oropharynx and gut of infants during their first year of life. Sci Rep 2020;10:13595. [PMID: 32788688 PMCID: PMC7423923 DOI: 10.1038/s41598-020-70684-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 07/29/2020] [Indexed: 11/09/2022]  Open
19
Sanabria A, Hjerde E, Johannessen M, Sollid JE, Simonsen GS, Hanssen AM. Shotgun-Metagenomics on Positive Blood Culture Bottles Inoculated With Prosthetic Joint Tissue: A Proof of Concept Study. Front Microbiol 2020;11:1687. [PMID: 32765476 PMCID: PMC7380264 DOI: 10.3389/fmicb.2020.01687] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 06/29/2020] [Indexed: 01/19/2023]  Open
20
Hasan MR, Sundararaju S, Tang P, Tsui KM, Lopez AP, Janahi M, Tan R, Tilley P. A metagenomics-based diagnostic approach for central nervous system infections in hospital acute care setting. Sci Rep 2020;10:11194. [PMID: 32641704 PMCID: PMC7343800 DOI: 10.1038/s41598-020-68159-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 06/16/2020] [Indexed: 01/22/2023]  Open
21
Cornejo Castro EM, Marshall V, Lack J, Lurain K, Immonen T, Labo N, Fisher NC, Ramaswami R, Polizzotto MN, Keele BF, Yarchoan R, Uldrick TS, Whitby D. Dual infection and recombination of Kaposi sarcoma herpesvirus revealed by whole-genome sequence analysis of effusion samples. Virus Evol 2020;6:veaa047. [PMID: 34211736 PMCID: PMC7474928 DOI: 10.1093/ve/veaa047] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]  Open
22
Coding-Complete Genome Sequence of a Recombinant Human Norovirus Strain Identified as Subtype GII.p12_GII.3. Microbiol Resour Announc 2020;9:9/5/e01385-19. [PMID: 32001565 PMCID: PMC6992869 DOI: 10.1128/mra.01385-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]  Open
23
Anh NT, Hong NTT, Nhu LNT, Thanh TT, Lau CY, Limmathurotsakul D, Deng X, Rahman M, Chau NVV, van Doorn HR, Thwaites G, Delwart E, Tan LV. Viruses in Vietnamese Patients Presenting with Community-Acquired Sepsis of Unknown Cause. J Clin Microbiol 2019;57:e00386-19. [PMID: 31217274 PMCID: PMC6711913 DOI: 10.1128/jcm.00386-19] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 06/12/2019] [Indexed: 12/28/2022]  Open
24
A method to identify respiratory virus infections in clinical samples using next-generation sequencing. Sci Rep 2019;9:2606. [PMID: 30796243 PMCID: PMC6384955 DOI: 10.1038/s41598-018-37483-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 11/26/2018] [Indexed: 12/30/2022]  Open
25
Application of Support Vector Machines in Viral Biology. GLOBAL VIROLOGY III: VIROLOGY IN THE 21ST CENTURY 2019. [PMCID: PMC7114997 DOI: 10.1007/978-3-030-29022-1_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
26
Dickey AM, Schuller G, Loy JD, Clawson ML. Whole genome sequencing of Moraxella bovoculi reveals high genetic diversity and evidence for interspecies recombination at multiple loci. PLoS One 2018;13:e0209113. [PMID: 30557405 PMCID: PMC6296526 DOI: 10.1371/journal.pone.0209113] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 11/29/2018] [Indexed: 12/04/2022]  Open
27
Detection of Viral RNA Splicing in Diagnostic Virology. ADVANCED TECHNIQUES IN DIAGNOSTIC MICROBIOLOGY 2018. [PMCID: PMC7121103 DOI: 10.1007/978-3-319-95111-9_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
28
Pou C, Barrientos-Somarribas M, Marin-Juan S, Bogdanovic G, Bjerkner A, Allander T, Gustafsson B, Andersson B. Virome definition in cerebrospinal fluid of patients with neurological complications after hematopoietic stem cell transplantation. J Clin Virol 2018;108:112-120. [DOI: 10.1016/j.jcv.2018.09.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 09/06/2018] [Accepted: 09/18/2018] [Indexed: 01/16/2023]
29
Symonds EM, Nguyen KH, Harwood VJ, Breitbart M. Pepper mild mottle virus: A plant pathogen with a greater purpose in (waste)water treatment development and public health management. WATER RESEARCH 2018;144:1-12. [PMID: 30005176 PMCID: PMC6162155 DOI: 10.1016/j.watres.2018.06.066] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 06/26/2018] [Accepted: 06/28/2018] [Indexed: 05/06/2023]
30
Nasko DJ, Koren S, Phillippy AM, Treangen TJ. RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification. Genome Biol 2018;19:165. [PMID: 30373669 PMCID: PMC6206640 DOI: 10.1186/s13059-018-1554-6] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 10/01/2018] [Indexed: 12/05/2022]  Open
31
Bergner LM, Orton RJ, da Silva Filipe A, Shaw AE, Becker DJ, Tello C, Biek R, Streicker DG. Using noninvasive metagenomics to characterize viral communities from wildlife. Mol Ecol Resour 2018;19:128-143. [PMID: 30240114 PMCID: PMC6378809 DOI: 10.1111/1755-0998.12946] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 08/22/2018] [Accepted: 09/07/2018] [Indexed: 12/31/2022]
32
Xiao YL, Ren L, Zhang X, Qi L, Kash JC, Xiao Y, Wu F, Wang J, Taubenberger JK. Deep Sequencing of H7N9 Influenza A Viruses from 16 Infected Patients from 2013 to 2015 in Shanghai Reveals Genetic Diversity and Antigenic Drift. mSphere 2018;3:e00462-18. [PMID: 30232169 PMCID: PMC6147129 DOI: 10.1128/mspheredirect.00462-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 08/28/2018] [Indexed: 11/20/2022]  Open
33
Xiao Y, Nolting JM, Sheng ZM, Bristol T, Qi L, Bowman AS, Taubenberger JK. Design and validation of a universal influenza virus enrichment probe set and its utility in deep sequence analysis of primary cloacal swab surveillance samples of wild birds. Virology 2018;524:182-191. [PMID: 30212665 DOI: 10.1016/j.virol.2018.08.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 08/21/2018] [Accepted: 08/28/2018] [Indexed: 11/25/2022]
34
Wei HY, Huang S, Wang JY, Gao F, Jiang JZ. Comparison of methods for library construction and short read annotation of shellfish viral metagenomes. Genes Genomics 2018;40:281-288. [PMID: 29892802 DOI: 10.1007/s13258-017-0629-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 11/03/2017] [Indexed: 12/20/2022]
35
Abd El Ghany M, Alsomali M, Almasri M, Regalado EP, Naeem R, Tukestani A, Asiri A, Hill-Cawthorne GA, Pain A, Memish ZA. Enteric Infections Circulating during Hajj Seasons, 2011-2013. Emerg Infect Dis 2018;23. [PMID: 28930004 PMCID: PMC5621540 DOI: 10.3201/eid2310.161642] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]  Open
36
Haramoto E, Kitajima M, Hata A, Torrey JR, Masago Y, Sano D, Katayama H. A review on recent progress in the detection methods and prevalence of human enteric viruses in water. WATER RESEARCH 2018;135:168-186. [PMID: 29471200 DOI: 10.1016/j.watres.2018.02.004] [Citation(s) in RCA: 247] [Impact Index Per Article: 41.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 02/01/2018] [Accepted: 02/02/2018] [Indexed: 05/17/2023]
37
Sheng Q, Vickers K, Zhao S, Wang J, Samuels DC, Koues O, Shyr Y, Guo Y. Multi-perspective quality control of Illumina RNA sequencing data analysis. Brief Funct Genomics 2018;16:194-204. [PMID: 27687708 DOI: 10.1093/bfgp/elw035] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]  Open
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Forbes JD, Knox NC, Peterson CL, Reimer AR. Highlighting Clinical Metagenomics for Enhanced Diagnostic Decision-making: A Step Towards Wider Implementation. Comput Struct Biotechnol J 2018;16:108-120. [PMID: 30026887 PMCID: PMC6050174 DOI: 10.1016/j.csbj.2018.02.006] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 02/19/2018] [Accepted: 02/25/2018] [Indexed: 12/14/2022]  Open
39
Romero-Espinoza JA, Moreno-Valencia Y, Coronel-Tellez RH, Castillejos-Lopez M, Hernandez A, Dominguez A, Miliar-Garcia A, Barbachano-Guerrero A, Perez-Padilla R, Alejandre-Garcia A, Vazquez-Perez JA. Virome and bacteriome characterization of children with pneumonia and asthma in Mexico City during winter seasons 2014 and 2015. PLoS One 2018;13:e0192878. [PMID: 29447223 PMCID: PMC5813968 DOI: 10.1371/journal.pone.0192878] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 01/31/2018] [Indexed: 02/07/2023]  Open
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Madi N, Al-Nakib W, Mustafa AS, Habibi N. Metagenomic analysis of viral diversity in respiratory samples from patients with respiratory tract infections in Kuwait. J Med Virol 2017;90:412-420. [PMID: 29083040 PMCID: PMC7167075 DOI: 10.1002/jmv.24984] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 09/19/2017] [Accepted: 10/12/2017] [Indexed: 12/22/2022]
41
Carding SR, Davis N, Hoyles L. Review article: the human intestinal virome in health and disease. Aliment Pharmacol Ther 2017;46:800-815. [PMID: 28869283 PMCID: PMC5656937 DOI: 10.1111/apt.14280] [Citation(s) in RCA: 152] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Revised: 04/07/2017] [Accepted: 08/07/2017] [Indexed: 02/06/2023]
42
Xu L, Zhu Y, Ren L, Xu B, Liu C, Xie Z, Shen K. 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. [PMID: 28671295 PMCID: PMC7166964 DOI: 10.1002/jmv.24895] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 05/17/2017] [Indexed: 12/24/2022]
43
Quick J, Grubaugh ND, Pullan ST, Claro IM, Smith AD, Gangavarapu K, Oliveira G, Robles-Sikisaka R, Rogers TF, Beutler NA, Burton DR, Lewis-Ximenez LL, de Jesus JG, Giovanetti M, Hill SC, Black A, Bedford T, Carroll MW, Nunes M, Alcantara LC, Sabino EC, Baylis SA, Faria NR, Loose M, Simpson JT, Pybus OG, Andersen KG, Loman NJ. Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples. Nat Protoc 2017;12:1261-1276. [PMID: 28538739 PMCID: PMC5902022 DOI: 10.1038/nprot.2017.066] [Citation(s) in RCA: 733] [Impact Index Per Article: 104.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
44
Lima DA, Cibulski SP, Finkler F, Teixeira TF, Varela APM, Cerva C, Loiko MR, Scheffer CM, Dos Santos HF, Mayer FQ, Roehe PM. Faecal virome of healthy chickens reveals a large diversity of the eukaryote viral community, including novel circular ssDNA viruses. J Gen Virol 2017;98:690-703. [PMID: 28100302 DOI: 10.1099/jgv.0.000711] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]  Open
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Fonager J, Stegger M, Rasmussen LD, Poulsen MW, Rønn J, Andersen PS, Fischer TK. A universal primer-independent next-generation sequencing approach for investigations of norovirus outbreaks and novel variants. Sci Rep 2017;7:813. [PMID: 28400558 PMCID: PMC5429772 DOI: 10.1038/s41598-017-00926-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 03/21/2017] [Indexed: 12/16/2022]  Open
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Brown JR, Roy S, Ruis C, Yara Romero E, Shah D, Williams R, Breuer J. Norovirus Whole-Genome Sequencing by SureSelect Target Enrichment: a Robust and Sensitive Method. J Clin Microbiol 2016;54:2530-7. [PMID: 27487952 PMCID: PMC5035417 DOI: 10.1128/jcm.01052-16] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 07/21/2016] [Indexed: 01/11/2023]  Open
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Ali R, Blackburn RM, Kozlakidis Z. Next-Generation Sequencing and Influenza Virus: A Short Review of the Published Implementation Attempts. HAYATI JOURNAL OF BIOSCIENCES 2016. [DOI: 10.1016/j.hjb.2016.12.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]  Open
48
Nikitin NA, Trifonova EA, Karpova OV, Atabekov JG. Biosafety of plant viruses for human and animals. ACTA ACUST UNITED AC 2016. [DOI: 10.3103/s0096392516030081] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Virome characterisation from Guthrie cards in children who later developed acute lymphoblastic leukaemia. Br J Cancer 2016;115:1008-1014. [PMID: 27552439 PMCID: PMC5061901 DOI: 10.1038/bjc.2016.261] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 07/22/2016] [Accepted: 07/29/2016] [Indexed: 12/17/2022]  Open
50
Bukowska-Ośko I, Perlejewski K, Nakamura S, Motooka D, Stokowy T, Kosińska J, Popiel M, Płoski R, Horban A, Lipowski D, Caraballo Cortés K, Pawełczyk A, Demkow U, Stępień A, Radkowski M, Laskus T. Sensitivity of Next-Generation Sequencing Metagenomic Analysis for Detection of RNA and DNA Viruses in Cerebrospinal Fluid: The Confounding Effect of Background Contamination. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016:53-62. [PMID: 27405447 DOI: 10.1007/5584_2016_42] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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