| 1 |
Zou_X_2016 |
Simultaneous virus identification and characterization of severe unexplained pneumonia cases using a metagenomics sequencing technique |
Zou, Xiaohui; Tang, Guangpeng; Zhao, Xiang; Huang, Yan; Chen, Tao; Lei, Mingyu; Chen, Wenbing; Yang, Lei; Zhu, Wenfei; Zhuang, Li; Yang, Jing; Feng, Zhaomin; Wang, Dayan; Wang, Dingming; Shu, Yuelong |
2016 |
2016-12-02 |
COMM-USE |
N |
PMC7088591 |
27921234.0 |
10.1007/s11427-016-0244-8 |
z8thv6ar |
0.801820 |
Zhang_2020, Langelier_2017 |
|
| 2 |
Thorburn_2015 |
The use of next generation sequencing in the diagnosis and typing of respiratory infections |
Thorburn, Fiona; Bennett, Susan; Modha, Sejal; Murdoch, David; Gunson, Rory; Murcia, Pablo R. |
2015 |
2015-08-23 |
PMC |
N |
PMC4533236 |
26209388.0 |
10.1016/j.jcv.2015.06.082 |
q7jp224a |
0.784250 |
Oba_M_2018, Chen_2018, Harel_2019 |
|
| 3 |
Madi_2017 |
Metagenomic analysis of viral diversity in respiratory samples from patients with respiratory tract infections in Kuwait |
Madi, Nada; Al‐Nakib, Widad; Mustafa, Abu Salim; Habibi, Nazima |
2017 |
2017-11-11 |
PMC |
N |
PMC7167075 |
29083040.0 |
10.1002/jmv.24984 |
7w7fffqk |
0.782007 |
Zhang_2020, Langelier_2017, Taboada_2016 |
|
| 4 |
Oba_M_2018 |
A new comprehensive method for detection of livestock-related pathogenic viruses using a target enrichment system |
Oba, Mami; Tsuchiaka, Shinobu; Omatsu, Tsutomu; Katayama, Yukie; Otomaru, Konosuke; Hirata, Teppei; Aoki, Hiroshi; Murata, Yoshiteru; Makino, Shinji; Nagai, Makoto; Mizutani, Tetsuya |
2018 |
2018-01-08 |
None |
N |
PMC7124307 |
29223400.0 |
10.1016/j.bbrc.2017.12.017 |
sv6uh7hh |
0.771868 |
|
|
| 5 |
de_Vries_2012 |
Performance of VIDISCA-454 in Feces-Suspensions and Serum |
de Vries, Michel; Oude Munnink, Bas B.; Deijs, Martin; Canuti, Marta; Koekkoek, Sylvie M.; Molenkamp, Richard; Bakker, Margreet; Jurriaans, Suzanne; van Schaik, Barbera D. C.; Luyf, Angela C.; Olabarriaga, Silvia D.; van Kampen, Antoine H. C.; van der Hoek, Lia |
2012 |
2012-08-22 |
COMM-USE |
N |
PMC3446766 |
23012629.0 |
10.3390/v4081328 |
q75rus8z |
0.769772 |
Gardner_2004, Chang_2011, Francis_2016, Lee_C_2017 |
|
| 6 |
WANG_2017 |
An Improved Barcoded Oligonucleotide Primers-based Next-generation Sequencing Approach for Direct Identification of Viral Pathogens in Clinical Specimens |
WANG, Chun Hua; NIE, Kai; ZHANG, Yi; WANG, Ji; ZHOU, Shuai Feng; LI, Xin Na; ZHOU, Hang Yu; QI, Shun Xiang; MA, Xue Jun |
2017 |
2017-01-31 |
PMC |
N |
PMC7136949 |
28245896.0 |
10.3967/bes2017.003 |
p17tju4c |
0.760420 |
Chen_2018, Djikeng_2009, Deng_2015, Harel_2019 |
Lewandowska_2017, Yang_2018 |
| 7 |
Gong_2016 |
A Next-Generation Sequencing Data Analysis Pipeline for Detecting Unknown Pathogens from Mixed Clinical Samples and Revealing Their Genetic Diversity |
Gong, Yu-Nong; Chen, Guang-Wu; Yang, Shu-Li; Lee, Ching-Ju; Shih, Shin-Ru; Tsao, Kuo-Chien |
2016 |
2016-03-17 |
COMM-USE |
N |
PMC4795770 |
26986479.0 |
10.1371/journal.pone.0151495 |
f59mrabl |
0.757280 |
Langelier_2017, Zhang_2020 |
|
| 8 |
Gong_2017 |
A metagenomics study for the identification of respiratory viruses in mixed clinical specimens: an application of the iterative mapping approach |
Gong, Yu-Nong; Yang, Shu-Li; Chen, Guang-Wu; Chen, Yu-Wen; Huang, Yhu-Chering; Ning, Hsiao-Chen; Tsao, Kuo-Chien |
2017 |
2017-04-19 |
PMC |
N |
PMC7087367 |
28424887.0 |
10.1007/s00705-017-3367-4 |
rv9t40fz |
0.747798 |
Zhang_2020 |
Alquezar-Planas_2013 |
| 9 |
Lyon_2018 |
Evaluating an Upper Respiratory Disease Panel on the Portable MinION Sequencer |
Wanda J. Lyon; Zachary K. Smith; Brian Grier; James Baldwin; Clarise R. Starr |
2018 |
2018-10-05 |
BioRxiv |
N |
|
|
10.1101/436600 |
3begdfx2 |
0.742882 |
Harel_2019, Djikeng_2009, Chang_2011, Deng_2015 |
Alquezar-Planas_2013 |
| 10 |
Piantadosi_2017 |
Metagenomic Sequencing of an Echovirus 30 Genome From Cerebrospinal Fluid of a Patient With Aseptic Meningitis and Orchitis |
Piantadosi, Anne; Mukerji, Shibani S; Chitneni, Pooja; Cho, Tracey A; Cosimi, Lisa A; Hung, Deborah T; Goldberg, Marcia B; Sabeti, Pardis C; Kuritzkes, Daniel R; Grad, Yonatan H |
2017 |
2017-07-28 |
NONCOMM |
N |
PMC5534216 |
28761901.0 |
10.1093/ofid/ofx138 |
e6rc8mvu |
0.736694 |
Langelier_2017, Zhang_2020 |
|
| 11 |
Zoll_2015 |
Direct multiplexed whole genome sequencing of respiratory tract samples reveals full viral genomic information |
Zoll, Jan; Rahamat-Langendoen, Janette; Ahout, Inge; Jonge, Marien I.de; Jans, Jop; Huijnen, Martijn A.; Ferwerda, Gerben; Warris, Adilia; Melchers, Willem J.G. |
2015 |
2015-05-31 |
PMC |
N |
|
25866327.0 |
10.1016/j.jcv.2015.02.010 |
94zykdrh |
0.731611 |
Zhang_2020 |
|
| 12 |
van_Boheemen_2020 |
Retrospective Validation of a Metagenomic Sequencing Protocol for Combined Detection of RNA and DNA Viruses Using Respiratory Samples from Pediatric Patients |
van Boheemen, Sander; van Rijn, Anneloes L.; Pappas, Nikos; Carbo, Ellen C.; Vorderman, Ruben H.P.; Sidorov, Igor; van `t Hof, Peter J.; Mei, Hailiang; Claas, Eric C.J.; Kroes, Aloys C.M.; de Vries, Jutte J.C. |
2020 |
2020-02-29 |
PMC |
N |
PMC7106021 |
31837435.0 |
10.1016/j.jmoldx.2019.10.007 |
dw1sfzqx |
0.729069 |
Oba_M_2018, Chen_2018 |
|
| 13 |
Deng_2020 |
Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance |
Deng, Xianding; Achari, Asmeeta; Federman, Scot; Yu, Guixia; Somasekar, Sneha; Bártolo, Inês; Yagi, Shigeo; Mbala-Kingebeni, Placide; Kapetshi, Jimmy; Ahuka-Mundeke, Steve; Muyembe-Tamfum, Jean-Jacques; Ahmed, Asim A.; Ganesh, Vijay; Tamhankar, Manasi; Patterson, Jean L.; Ndembi, Nicaise; Mbanya, Dora; Kaptue, Lazare; McArthur, Carole; Muñoz-Medina, José E.; Gonzalez-Bonilla, Cesar R.; López, Susana; Arias, Carlos F.; Arevalo, Shaun; Miller, Steve; Stone, Mars; Busch, Michael; Hsieh, Kristina; Messenger, Sharon; Wadford, Debra A.; Rodgers, Mary; Cloherty, Gavin; Faria, Nuno R.; Thézé, Julien; Pybus, Oliver G.; Neto, Zoraima; Morais, Joana; Taveira, Nuno; R. Hackett, John; Chiu, Charles Y. |
2020 |
2020-01-13 |
None |
N |
PMC7047537 |
31932713.0 |
10.1038/s41564-019-0637-9 |
z4j8p55m |
0.716082 |
Djikeng_2009, Chen_2018 |
Lewandowska_2017, Yang_2018 |
| 14 |
Oude_Munnink_2013 |
Autologous Antibody Capture to Enrich Immunogenic Viruses for Viral Discovery |
Oude Munnink, Bas B.; Jazaeri Farsani, Seyed Mohammad; Deijs, Martin; Jonkers, Jiri; Verhoeven, Joost T. P.; Ieven, Margareta; Goossens, Herman; de Jong, Menno D.; Berkhout, Ben; Loens, Katherine; Kellam, Paul; Bakker, Margreet; Canuti, Marta; Cotten, Matthew; van der Hoek, Lia |
2013 |
2013-11-04 |
COMM-USE |
N |
PMC3817278 |
24223808.0 |
10.1371/journal.pone.0078454 |
0mu4tkui |
0.696154 |
Smits_2014 |
|
| 15 |
Lewandowska_2015 |
Unbiased metagenomic sequencing complements specific routine diagnostic methods and increases chances to detect rare viral strains |
Lewandowska, Dagmara W.; Zagordi, Osvaldo; Zbinden, Andrea; Schuurmans, Macé M.; Schreiber, Peter; Geissberger, Fabienne-Desirée; Huder, Jon B.; Böni, Jürg; Benden, Christian; Mueller, Nicolas J.; Trkola, Alexandra; Huber, Michael |
2015 |
2015-10-31 |
PMC |
N |
|
26231254.0 |
10.1016/j.diagmicrobio.2015.06.017 |
rrq4f5ki |
0.693357 |
Djikeng_2009 |
|
| 16 |
Lewandowska_2017 |
Optimization and validation of sample preparation for metagenomic sequencing of viruses in clinical samples |
Lewandowska, Dagmara W.; Zagordi, Osvaldo; Geissberger, Fabienne-Desirée; Kufner, Verena; Schmutz, Stefan; Böni, Jürg; Metzner, Karin J.; Trkola, Alexandra; Huber, Michael |
2017 |
2017-08-08 |
COMM-USE |
N |
PMC5549297 |
28789678.0 |
10.1186/s40168-017-0317-z |
3jxyipbn |
0.690474 |
Chen_2018, Mizutani_2007, Oba_M_2018 |
Yang_2018 |
| 17 |
Erlandsson_2011 |
The Microbial Detection Array Combined with Random Phi29-Amplification Used as a Diagnostic Tool for Virus Detection in Clinical Samples |
Erlandsson, Lena; Rosenstierne, Maiken W.; McLoughlin, Kevin; Jaing, Crystal; Fomsgaard, Anders |
2011 |
2011-08-10 |
COMM-USE |
N |
PMC3154197 |
21853040.0 |
10.1371/journal.pone.0022631 |
ngn9x3lc |
0.683818 |
Urisman_2005 |
Lewandowska_2017 |
| 18 |
Kilianski_2016 |
Use of Unamplified RNA/cDNA–Hybrid Nanopore Sequencing for Rapid Detection and Characterization of RNA Viruses |
Kilianski, Andy; Roth, Pierce A.; Liem, Alvin T.; Hill, Jessica M.; Willis, Kristen L.; Rossmaier, Rebecca D.; Marinich, Andrew V.; Maughan, Michele N.; Karavis, Mark A.; Kuhn, Jens H.; Honko, Anna N.; Rosenzweig, C. Nicole |
2016 |
2016-08-23 |
None |
N |
PMC4982148 |
27191483.0 |
10.3201/eid2208.160270 |
icud629u |
0.627962 |
|
|
| 19 |
ZHANG_2018 |
VSITA, an Improved Approach of Target Amplification in the Identification of Viral Pathogens |
ZHANG, Yi; ZHANG, Chen; LI, Bo; LI, Yang; Zhou, HE Xiao; LI, Acher; WU, Wei; DUAN, Su Xia; QIU, Fang Zhou; WANG, Ji; SHEN, Xin Xin; YANG, Meng Jie; LI, De Xin; MA, Xue Jun |
2018 |
2018-04-30 |
PMC |
N |
PMC7135048 |
29773090.0 |
10.3967/bes2018.035 |
7dcl9txk |
0.621883 |
Endoh_2005, Whiteford_2005 |
|
| 20 |
Xu_L_2017 |
Characterization of the nasopharyngeal viral microbiome from children with community‐acquired pneumonia but negative for Luminex xTAG respiratory viral panel assay detection |
Xu, Lili; Zhu, Yun; Ren, Lili; Xu, Baoping; Liu, Chunyan; Xie, Zhengde; Shen, Kunling |
2017 |
2017-07-25 |
PMC |
N |
PMC7166964 |
28671295.0 |
10.1002/jmv.24895 |
qw7gcrqa |
0.621835 |
|
|
| 21 |
Wang_2016 |
Metagenomic analysis of viral genetic diversity in respiratory samples from children with severe acute respiratory infection in China |
Wang, Y.; Zhu, N.; Li, Y.; Lu, R.; Wang, H.; Liu, G.; Zou, X.; Xie, Z.; Tan, W. |
2016 |
2016-05-31 |
PMC |
N |
|
26802214.0 |
10.1016/j.cmi.2016.01.006 |
p0cxsrzb |
0.613876 |
Zhang_2020 |
|
| 22 |
Lewandowski_2019 |
Metagenomic Nanopore sequencing of influenza virus direct from clinical respiratory samples |
Kuiama Lewandowski; Yifei Xu; Steven T. Pullan; Sheila F. Lumley; Dona Foster; Nicholas Sanderson; Alison Vaughan; Marcus Morgan; Nicole Bright; James Kavanagh; Richard Vipond; Miles Carroll; Anthony C. Marriott; Karen E Gooch; Monique Andersson; Katie Jeffery; Timothy EA Peto; Derrick W. Crook; A Sarah Walker; Philippa C. Matthews |
2019 |
2019-06-19 |
BioRxiv |
N |
|
|
10.1101/676155 |
75j8jydo |
0.612853 |
Taboada_2016, Whiteford_2005, Gardner_2004 |
|
| 23 |
Cifaldi_2019 |
Targeted NGS Platforms for Genetic Screening and Gene Discovery in Primary Immunodeficiencies |
Cifaldi, Cristina; Brigida, Immacolata; Barzaghi, Federica; Zoccolillo, Matteo; Ferradini, Valentina; Petricone, Davide; Cicalese, Maria Pia; Lazarevic, Dejan; Cittaro, Davide; Omrani, Maryam; Attardi, Enrico; Conti, Francesca; Scarselli, Alessia; Chiriaco, Maria; Di Cesare, Silvia; Licciardi, Francesco; Davide, Montin; Ferrua, Francesca; Canessa, Clementina; Pignata, Claudio; Giliani, Silvia; Ferrari, Simona; Fousteri, Georgia; Barera, Graziano; Merli, Pietro; Palma, Paolo; Cesaro, Simone; Gattorno, Marco; Trizzino, Antonio; Moschese, Viviana; Chini, Loredana; Villa, Anna; Azzari, Chiara; Finocchi, Andrea; Locatelli, Franco; Rossi, Paolo; Sangiuolo, Federica; Aiuti, Alessandro; Cancrini, Caterina; Di Matteo, Gigliola |
2019 |
2019-04-11 |
COMM-USE |
N |
PMC6470723 |
31031743.0 |
10.3389/fimmu.2019.00316 |
ds9se405 |
0.594644 |
Deng_2015, Harel_2019, Phillippy_2009, Whiteford_2005 |
|
| 24 |
O'Flaherty_2018 |
Comprehensive viral enrichment enables sensitive respiratory virus genomic identification and analysis by next generation sequencing |
O'Flaherty, Brigid M.; Li, Yan; Tao, Ying; Paden, Clinton R.; Queen, Krista; Zhang, Jing; Dinwiddie, Darrell L.; Gross, Stephen M.; Schroth, Gary P.; Tong, Suxiang |
2018 |
2018-04-27 |
None |
N |
PMC5991510 |
29703817.0 |
10.1101/gr.226316.117 |
bg1s2i6d |
0.586911 |
Deng_2015, Smits_2014, Harel_2019 |
Yang_2018, Alquezar-Planas_2013 |
| 25 |
Li_L_2015 |
Comparing viral metagenomics methods using a highly multiplexed human viral pathogens reagent |
Li, Linlin; Deng, Xutao; Mee, Edward T.; Collot-Teixeira, Sophie; Anderson, Rob; Schepelmann, Silke; Minor, Philip D.; Delwart, Eric |
2015 |
2015-03-01 |
None |
N |
PMC4344864 |
25497414.0 |
10.1016/j.jviromet.2014.12.002 |
iq6j2z9d |
0.576140 |
Chen_2018, Oba_M_2018 |
Yang_2018 |
| 26 |
Jensen_2015 |
Target-Dependent Enrichment of Virions Determines the Reduction of High-Throughput Sequencing in Virus Discovery |
Jensen, Randi Holm; Mollerup, Sarah; Mourier, Tobias; Hansen, Thomas Arn; Fridholm, Helena; Nielsen, Lars Peter; Willerslev, Eske; Hansen, Anders Johannes; Vinner, Lasse |
2015 |
2015-04-08 |
COMM-USE |
N |
PMC4390369 |
25853649.0 |
10.1371/journal.pone.0122636 |
5g2i36zz |
0.570839 |
Urayama_2016, Oba_M_2018 |
|
| 27 |
Lysholm_2012 |
Characterization of the Viral Microbiome in Patients with Severe Lower Respiratory Tract Infections, Using Metagenomic Sequencing |
Lysholm, Fredrik; Wetterbom, Anna; Lindau, Cecilia; Darban, Hamid; Bjerkner, Annelie; Fahlander, Kristina; Lindberg, A. Michael; Persson, Bengt; Allander, Tobias; Andersson, Björn |
2012 |
2012-02-15 |
COMM-USE |
N |
PMC3280267 |
22355331.0 |
10.1371/journal.pone.0030875 |
4zc8ivef |
0.567077 |
|
|
| 28 |
Lee_J_2017 |
Targeted Enrichment for Pathogen Detection and Characterization in Three Felid Species |
Lee, Justin S.; Mackie, Ryan S.; Harrison, Thomas; Shariat, Basir; Kind, Trey; Kehl, Timo; Löchelt, Martin; Boucher, Christina; VandeWoude, Sue |
2017 |
2017-05-23 |
COMM-USE |
N |
PMC5442522 |
28330894.0 |
10.1128/jcm.01463-16 |
qohrnpgq |
0.557918 |
Djikeng_2009, Priest_2012, Urisman_2005, Gardner_2004 |
|
| 29 |
Uhlenhaut_2009 |
Use of a universal virus detection assay to identify human metapneumovirus in a hematopoietic stem cell transplant recipient with pneumonia of unknown origin |
Uhlenhaut, Christine; Cohen, Jeffrey I.; Fedorko, Daniel; Nanda, Santosh; Krause, Philip R. |
2009 |
2009-04-01 |
PMC |
N |
PMC2663017 |
19250860.0 |
10.1016/j.jcv.2009.01.011 |
z5s7pmf7 |
0.548274 |
Mizutani_2007 |
|
| 30 |
Linsuwanon_2015 |
The Fecal Virome of Children with Hand, Foot, and Mouth Disease that Tested PCR Negative for Pathogenic Enteroviruses |
Linsuwanon, Piyada; Poovorawan, Yong; Li, Linlin; Deng, Xutao; Vongpunsawad, Sompong; Delwart, Eric |
2015 |
2015-08-19 |
COMM-USE |
N |
PMC4545796 |
26288145.0 |
10.1371/journal.pone.0135573 |
84hxim2n |
0.547856 |
|
|
| 31 |
Shaukat_2014 |
Identification and characterization of unrecognized viruses in stool samples of non-polio acute flaccid paralysis children by simplified VIDISCA |
Shaukat, Shahzad; Angez, Mehar; Alam, Muhammad Masroor; Jebbink, Maarten F; Deijs, Martin; Canuti, Marta; Sharif, Salmaan; de Vries, Michel; Khurshid, Adnan; Mahmood, Tariq; van der Hoek, Lia; Zaidi, Syed Sohail Zahoor |
2014 |
2014-08-12 |
COMM-USE |
N |
PMC4254409 |
25112200.0 |
10.1186/1743-422x-11-146 |
b9shffb3 |
0.534652 |
Lee_C_2017, Cheng_2013, Chang_2011, Harel_2019 |
|
| 32 |
Yang_2018 |
Targeted Sequencing of Respiratory Viruses in Clinical Specimens for Pathogen Identification and Genome-Wide Analysis |
Yang, Yu; Walls, Shannon D.; Gross, Stephen M.; Schroth, Gary P.; Jarman, Richard G.; Hang, Jun |
2018 |
2018-05-12 |
PMC |
N |
PMC7121196 |
30128994.0 |
10.1007/978-1-4939-8682-8_10 |
pbhggsh2 |
0.519077 |
Chen_2018, Cheng_2013, Deng_2015 |
Lewandowska_2017 |
| 33 |
Zhang_2018 |
Metagenomic analysis of viral nucleic acid extraction methods in respiratory clinical samples |
Zhang, Dan; Lou, Xiuyu; Yan, Hao; Pan, Junhang; Mao, Haiyan; Tang, Hongfeng; Shu, Yan; Zhao, Yun; Liu, Lei; Li, Junping; Chen, Jiang; Zhang, Yanjun; Ma, Xuejun |
2018 |
2018-10-25 |
COMM-USE |
N |
PMC6202819 |
30359242.0 |
10.1186/s12864-018-5152-5 |
1vo72gop |
0.511490 |
Chen_2018 |
|
| 34 |
Majchrzykiewicz-Koehorst_2015 |
Rapid and generic identification of influenza A and other respiratory viruses with mass spectrometry |
Majchrzykiewicz-Koehorst, Joanna A.; Heikens, Esther; Trip, Hein; Hulst, Albert G.; de Jong, Ad L.; Viveen, Marco C.; Sedee, Norbert J.A.; van der Plas, Jan; Coenjaerts, Frank E.J.; Paauw, Armand |
2015 |
2015-03-01 |
PMC |
N |
PMC7113647 |
25500183.0 |
10.1016/j.jviromet.2014.11.014 |
x7qtxaum |
0.499660 |
Hager_2003, Camarasa_2018 |
|
| 35 |
Bellehumeur_2015 |
Propidium monoazide (PMA) and ethidium bromide monoazide (EMA) improve DNA array and high-throughput sequencing of porcine reproductive and respiratory syndrome virus identification |
Bellehumeur, Christian; Boyle, Brian; Charette, Steve J.; Harel, Josée; L’Homme, Yvan; Masson, Luke; Gagnon, Carl A. |
2015 |
2015-09-15 |
None |
N |
PMC7119533 |
26129867.0 |
10.1016/j.jviromet.2015.06.014 |
7lrmc3qb |
0.499656 |
Oba_M_2018 |
|
| 36 |
Paskey_2019 |
Enrichment post-library preparation enhances the sensitivity of high-throughput sequencing-based detection and characterization of viruses from complex samples |
Paskey, Adrian C.; Frey, Kenneth G.; Schroth, Gary; Gross, Stephen; Hamilton, Theron; Bishop-Lilly, Kimberly A. |
2019 |
2019-02-26 |
COMM-USE |
N |
PMC6390631 |
30808306.0 |
10.1186/s12864-019-5543-2 |
cnvxlv6h |
0.492214 |
Brister_2015, Djikeng_2009, Deng_2015, Smits_2014 |
Lewandowska_2017, Yang_2018, Jensen_2015 |
| 37 |
Wylezich_2018 |
A Versatile Sample Processing Workflow for Metagenomic Pathogen Detection |
Wylezich, Claudia; Papa, Anna; Beer, Martin; Höper, Dirk |
2018 |
2018-08-30 |
None |
N |
PMC6117295 |
30166611.0 |
10.1038/s41598-018-31496-1 |
alkxz0g3 |
0.490700 |
Chang_2011, Deng_2015, Lee_C_2017 |
Tausch_2018, Baldwin_2014, Li_C_2020 |
| 38 |
Hall_2014 |
Evaluation of rapid and simple techniques for the enrichment of viruses prior to metagenomic virus discovery |
Hall, Richard J.; Wang, Jing; Todd, Angela K.; Bissielo, Ange B.; Yen, Seiha; Strydom, Hugo; Moore, Nicole E.; Ren, Xiaoyun; Huang, Q. Sue; Carter, Philip E.; Peacey, Matthew |
2014 |
2014-01-31 |
PMC |
N |
PMC7113663 |
24036074.0 |
10.1016/j.jviromet.2013.08.035 |
n6xp5mlz |
0.480843 |
Chang_2011, Siridechadilok_2013, Lee_C_2017 |
Lewandowska_2017, Dacheux_2014, Shifman_2019 |
| 39 |
Briese_2015 |
Virome Capture Sequencing Enables Sensitive Viral Diagnosis and Comprehensive Virome Analysis |
Briese, Thomas; Kapoor, Amit; Mishra, Nischay; Jain, Komal; Kumar, Arvind; Jabado, Omar J.; Lipkin, W. Ian |
2015 |
2015-09-22 |
NONCOMM |
N |
PMC4611031 |
26396248.0 |
10.1128/mbio.01491-15 |
gbguv4r2 |
0.480634 |
Oba_M_2018, Chen_2018 |
Yang_2018, Li_L_2015 |
| 40 |
Tan_S_2019 |
Rapid, Unbiased PRRSV Strain Detection Using MinION Direct RNA Sequencing and Bioinformatics Tools |
Tan, Shaoyuan; Dvorak, Cheryl M.T.; Murtaugh, Michael P. |
2019 |
2019-12-07 |
COMM-USE |
N |
PMC6950593 |
31817886.0 |
10.3390/v11121132 |
x7wy4ooh |
0.471946 |
Mizutani_2007, Smits_2014 |
Alquezar-Planas_2013 |
| 41 |
Manso_2017 |
Efficient and unbiased metagenomic recovery of RNA virus genomes from human plasma samples |
Manso, Carmen F.; Bibby, David F.; Mbisa, Jean L. |
2017 |
2017-06-23 |
COMM-USE |
N |
PMC5482852 |
28646219.0 |
10.1038/s41598-017-02239-5 |
xflhxb13 |
0.463713 |
|
Li_C_2020 |
| 42 |
Marthaler_2014 |
Complete Genome Sequence of Strain SDCV/USA/Illinois121/2014, a Porcine Deltacoronavirus from the United States |
Marthaler, Douglas; Jiang, Yin; Collins, Jim; Rossow, Kurt |
2014 |
2014-04-10 |
COMM-USE |
N |
PMC3983293 |
24723704.0 |
10.1128/genomea.00218-14 |
shizpehg |
0.463014 |
Langelier_2017, Taboada_2016, Whiteford_2005 |
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| 43 |
Friis-Nielsen_2016 |
Identification of Known and Novel Recurrent Viral Sequences in Data from Multiple Patients and Multiple Cancers |
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2016 |
2016-02-19 |
COMM-USE |
N |
PMC4776208 |
26907326.0 |
10.3390/v8020053 |
wjf3c7a7 |
0.461204 |
Chang_2011, Deng_2015, Lee_C_2017, Harel_2019, Gardner_2004 |
Alquezar-Planas_2013, Zou_X_2016, Wang_2003, Yang_2018 |
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Chen_2018 |
Next-generation sequencing library preparation method for identification of RNA viruses on the Ion Torrent Sequencing Platform |
Chen, Guiqian; Qiu, Yuan; Zhuang, Qingye; Wang, Suchun; Wang, Tong; Chen, Jiming; Wang, Kaicheng |
2018 |
2018-05-09 |
PMC |
N |
PMC7088580 |
29744712.0 |
10.1007/s11262-018-1568-x |
utvf8yh6 |
0.461094 |
Deng_2015, Harel_2019, Xu_L_2019 |
Yang_2018, Qiu_Y_2017 |
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Ayginin_2018 |
The Study of Viral RNA Diversity in Bird Samples Using De Novo Designed Multiplex Genus-Specific Primer Panels |
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2018 |
2018-08-12 |
COMM-USE |
N |
PMC6109506 |
30158979.0 |
10.1155/2018/3248285 |
6w8qcv1c |
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Chang_2011 |
Dacheux_2014, Lee_J_2017 |
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Li_C_2020 |
High resolution metagenomic characterization of complex infectomes in paediatric acute respiratory infection |
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2020 |
2020-03-03 |
COMM-USE |
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PMC7054269 |
32127629.0 |
10.1038/s41598-020-60992-6 |
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0.448079 |
Gardner_2004 |
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A complete protocol for whole-genome sequencing of virus from clinical samples: Application to coronavirus OC43 |
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2019 |
2019-05-31 |
None |
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PMC7112119 |
30878524.0 |
10.1016/j.virol.2019.03.006 |
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0.446513 |
Mizutani_2007, Chang_2011 |
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Pulmonary Metagenomic Sequencing Suggests Missed Infections in Immunocompromised Children |
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2018 |
2018-09-15 |
PMC |
N |
PMC6784263 |
30239621.0 |
10.1093/cid/ciy802 |
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0.441355 |
Gardner_2004, Smits_2014, Francis_2016 |
Zinter_2018 |
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McGowan_2014 |
Ribosomal RNA depletion or exclusion has negligible effect on the detection of viruses in a pan viral microarray |
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2014 |
2014-10-31 |
PMC |
N |
PMC7119560 |
25034125.0 |
10.1016/j.jviromet.2014.07.012 |
ddge24x7 |
0.434979 |
Chang_2011, Chen_2018 |
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Protocol for Metagenomic Virus Detection in Clinical Specimens |
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2015 |
2015-01-23 |
None |
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PMC4285256 |
25532973.0 |
10.3201/eid2101.140766 |
gx9oexv8 |
0.433095 |
Djikeng_2009, Mizutani_2007 |
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A Universal Next-Generation Sequencing Protocol To Generate Noninfectious Barcoded cDNA Libraries from High-Containment RNA Viruses |
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2016 |
2016-06-07 |
COMM-USE |
N |
PMC5069770 |
27822536.0 |
10.1128/msystems.00039-15 |
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Chen_2018, Mizutani_2007 |
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Dumarest_2015 |
Viral diversity in swine intestinal mucus used for the manufacture of heparin as analyzed by high-throughput sequencing |
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2015 |
2015-01-31 |
PMC |
N |
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25466699.0 |
10.1016/j.biologicals.2014.10.004 |
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A Sensitive Assay for Virus Discovery in Respiratory Clinical Samples |
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2011 |
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COMM-USE |
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PMC3025933 |
21283679.0 |
10.1371/journal.pone.0016118 |
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Endoh_2005 |
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Pulmonary Metagenomic Sequencing Suggests Missed Infections in Immunocompromised Children |
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2018 |
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BioRxiv |
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10.1101/291864 |
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Gardner_2004, Smits_2014 |
Zinter_2018 |
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Virus detection and identification using random multiplex (RT)-PCR with 3'-locked random primers |
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2007 |
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COMM-USE |
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PMC1950496 |
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10.1186/1743-422x-4-65 |
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First Identification of Human Adenovirus Subtype 21a in China With MinION and Illumina Sequencers |
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2020 |
2020-04-07 |
COMM-USE |
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PMC7155751 |
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10.3389/fgene.2020.00285 |
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Detection of viromes of RNA viruses using the next generation sequencing libraries prepared by three methods |
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2017 |
2017-06-02 |
PMC |
N |
PMC7111271 |
28501627.0 |
10.1016/j.virusres.2017.05.003 |
ecpicv5v |
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Chen_2018, Endoh_2005 |
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A Metagenomic Analysis of Pandemic Influenza A (2009 H1N1) Infection in Patients from North America |
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2010 |
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COMM-USE |
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PMC2956640 |
20976137.0 |
10.1371/journal.pone.0013381 |
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Modular approach to customise sample preparation procedures for viral metagenomics: a reproducible protocol for virome analysis |
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2015 |
2015-11-12 |
COMM-USE |
N |
PMC4642273 |
26559140.0 |
10.1038/srep16532 |
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Chang_2011, Harel_2019, Smits_2014 |
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Complete Genome Sequence of Human Coronavirus OC43 Isolated from Mexico |
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2016 |
2016-11-10 |
COMM-USE |
N |
PMC5105101 |
27834708.0 |
10.1128/genomea.01256-16 |
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Zhang_2020 |
Langelier_2017 |
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Identification of a Novel Coronavirus from Guinea Fowl Using Metagenomics |
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2014-12-18 |
PMC |
N |
PMC7120858 |
25720467.0 |
10.1007/978-1-4939-2438-7_2 |
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Djikeng_2009, Siridechadilok_2013 |
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Evolution of selective-sequencing approaches for virus discovery and virome analysis |
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2017 |
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PMC |
N |
PMC5819613 |
28583442.0 |
10.1016/j.virusres.2017.06.005 |
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Djikeng_2009, Siridechadilok_2013, Yadav_2013, Deng_2015 |
Jensen_2015 |
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Complete Genome Sequences of Five Human Coronavirus NL63 Strains Causing Respiratory Illness in Hospitalized Children in China |
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2020 |
2020-02-20 |
COMM-USE |
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PMC7033275 |
32079638.0 |
10.1128/mra.01597-19 |
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Taboada_2016 |
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Challenges of the Unknown: Clinical Application of Microbial Metagenomics |
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2015-09-14 |
COMM-USE |
N |
PMC4584244 |
26451363.0 |
10.1155/2015/292950 |
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Gamermann_2014, Djikeng_2009, Brister_2015, Deng_2015, Roux_2019 |
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Viral respiratory tract infections increase platelet reactivity and activation: an explanation for the higher rates of myocardial infarction and stroke during viral illness |
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2005 |
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PMC |
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PMC7166489 |
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10.1111/j.1538-7836.2005.01474.x |
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Virus Identification in Unknown Tropical Febrile Illness Cases Using Deep Sequencing |
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COMM-USE |
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PMC3274504 |
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PathoLive - Real-time pathogen identification from metagenomic Illumina datasets |
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2018 |
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BioRxiv |
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10.1101/402370 |
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Lee_C_2017, Chang_2011, Cheng_2013, Deng_2015, Brister_2015 |
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Deconvoluting Virome-Wide Antiviral Antibody Profiling Data |
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2018 |
2018-05-30 |
BioRxiv |
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2019 |
2019-02-04 |
None |
N |
PMC6587591 |
30718881.0 |
10.1038/s41587-018-0006-x |
hyg14q69 |
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Chang_2011, Deng_2015, Cheng_2013, Smits_2014 |
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Multiple approaches for massively parallel sequencing of HCoV-19 (SARS-CoV-2) genomes directly from clinical samples |
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2020 |
2020-03-17 |
BioRxiv |
N |
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10.1101/2020.03.16.993584 |
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Chapter Two Loeffler 4.0: Diagnostic Metagenomics |
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PMC |
N |
PMC7112322 |
29029726.0 |
10.1016/bs.aivir.2017.08.001 |
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0.313956 |
Djikeng_2009 |
Alquezar-Planas_2013 |
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Virus purification and enrichment by hydroxyapatite chromatography on a chip |
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PMC |
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PMC7111472 |
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2017 |
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PMC |
N |
PMC7111618 |
28646651.0 |
10.1016/j.virol.2017.06.019 |
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