The Microbial Detection Array for Detection of Emerging Viruses in Clinical Samples - A Useful Panmicrobial Diagnostic Tool

Rosenstierne, Maiken W.; McLoughlin, Kevin S.; Olesen, Majken Lindholm; Papa, Anna; Gardner, Shea N.; Engler, Olivier; Plumet, Sebastien; Mirazimi, Ali; Weidmann, Manfred; Niedrig, Matthias; Fomsgaard, Anders; Erlandsson, Lena

doi:10.1371/journal.pone.0100813

The Microbial Detection Array for Detection of Emerging Viruses in Clinical Samples - A Useful Panmicrobial Diagnostic Tool

Journal Article · Wed Jun 25 00:00:00 EDT 2014 · PLoS ONE

DOI:https://doi.org/10.1371/journal.pone.0100813· OSTI ID:1627710

Rosenstierne, Maiken W. ^[1]; McLoughlin, Kevin S. ^[2]; Olesen, Majken Lindholm ^[3]; Papa, Anna ^[4]; Gardner, Shea N. ^[3]; Engler, Olivier ^[5]; Plumet, Sebastien ^[6]; Mirazimi, Ali ^[7]; Weidmann, Manfred ^[8]; Niedrig, Matthias ^[9]; Fomsgaard, Anders ^[10]; Erlandsson, Lena ^[3]

Statens Serum Inst., Copenhagen (Denmark). Dept. of Microbiological Diagnostics and Virology; DOE/OSTI
Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Global Security
Statens Serum Inst., Copenhagen (Denmark). Dept. of Microbiological Diagnostics and Virology
Aristotle Univ. of Thessaloniki (Greece). Dept. of Microbiology
Federal Office for Civil Protection, Spiez (Switzerland). Spiez Lab.
French Army Forces Biomedical Institute (IRBA), Marseille (France). Virology Dept.
Swedish Inst. for Communicable Disease Control, Solna (Sweden); National Veterinary Institute (SVA), Uppsala (Sweden); Linkoping Univ. (Sweden). Dept. of Clinical and Experimental Medicine
University of Stirling (United Kingdom). Inst. of Aquaculture
Robert Koch-Inst., Berlin (Germany). Centre for biosafety
Statens Serum Inst., Copenhagen (Denmark). Dept. of Microbiological Diagnostics and Virology; Univ. of Southern Denmark, Odense (Denmark). Inst. of Clinical Research

Emerging viruses are usually endemic to tropical and sub-tropical regions of the world, but increased global travel, climate change and changes in lifestyle are believed to contribute to the spread of these viruses into new regions. Many of these viruses cause similar disease symptoms as other emerging viruses or common infections, making these unexpected pathogens difficult to diagnose. Broad-spectrum pathogen detection microarrays containing probes for all sequenced viruses and bacteria can provide rapid identification of viruses, guiding decisions about treatment and appropriate case management. We report a modified Whole Transcriptome Amplification (WTA) method that increases unbiased amplification, particular of RNA viruses. Using this modified WTA method, we tested the specificity and sensitivity of the Lawrence Livermore Microbial Detection Array (LLMDA) against a wide range of emerging viruses present in both nonclinical and clinical samples using two different microarray data analysis methods.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: AC52-07NA27344

OSTI ID:: 1627710

Journal Information:: PLoS ONE, Journal Name: PLoS ONE Journal Issue: 6 Vol. 9; ISSN 1932-6203

Publisher:: Public Library of ScienceCopyright Statement

Country of Publication:: United States

Language:: English

References (54)

Torque teno virus (TTV): current status Hino, Shigeo; Miyata, Hironori Reviews in Medical Virology, Vol. 17, Issue 1 https://doi.org/10.1002/rmv.524	journal	January 2006
Laboratory detection and diagnosis of filoviruses Wang, Yun-peng; Zhang, Xian-en; Wei, Hong-ping Virologica Sinica, Vol. 26, Issue 2 https://doi.org/10.1007/s12250-011-3186-9	journal	April 2011
Crimean?Congo hemorrhagic fever Whitehouse, C. Antiviral Research, Vol. 64, Issue 3 https://doi.org/10.1016/j.antiviral.2004.08.001	journal	December 2004
Viral load among patients infected with Marburgvirus in Angola Weidmann, Manfred; Hufert, Frank T.; Sall, Amadou A. Journal of Clinical Virology, Vol. 39, Issue 1 https://doi.org/10.1016/j.jcv.2006.12.023	journal	May 2007
Challenges in designing a Taqman-based multiplex assay for the simultaneous detection of herpes simplex virus types 1 and 2 and Varicella-zoster virus Weidmann, Manfred; Armbruster, Katrin; Hufert, Frank T. Journal of Clinical Virology, Vol. 42, Issue 4 https://doi.org/10.1016/j.jcv.2008.03.005	journal	August 2008
Resequencing microarray method for molecular diagnosis of human arboviral diseases Berthet, N.; Paulous, S.; Coffey, L. L. Journal of Clinical Virology, Vol. 56, Issue 3 https://doi.org/10.1016/j.jcv.2012.10.022	journal	March 2013
Utility of DNA Microarrays for Detection of Viruses in Acute Respiratory Tract Infections in Children Chiu, Charles Y.; Urisman, Anatoly; Greenhow, Tara L. The Journal of Pediatrics, Vol. 153, Issue 1 https://doi.org/10.1016/j.jpeds.2007.12.035	journal	July 2008
Virus inactivation by nucleic acid extraction reagents Blow, Jamie A.; Dohm, David J.; Negley, Diane L. Journal of Virological Methods, Vol. 119, Issue 2 https://doi.org/10.1016/j.jviromet.2004.03.015	journal	August 2004
Development of a TaqMan® RT-PCR assay without RNA extraction step for the detection and quantification of African Chikungunya viruses Pastorino, Boris; Bessaud, Maël; Grandadam, Marc Journal of Virological Methods, Vol. 124, Issue 1-2 https://doi.org/10.1016/j.jviromet.2004.11.002	journal	March 2005
Species-specific identification of variola, monkeypox, cowpox, and vaccinia viruses by multiplex real-time PCR assay Shchelkunov, Sergei N.; Shcherbakov, Dmitrii N.; Maksyutov, Rinat A. Journal of Virological Methods, Vol. 175, Issue 2 https://doi.org/10.1016/j.jviromet.2011.05.002	journal	August 2011
Crimean–Congo hemorrhagic fever: Risk for emergence of new endemic foci in Europe? Maltezou, Helena C.; Papa, Anna Travel Medicine and Infectious Disease, Vol. 8, Issue 3 https://doi.org/10.1016/j.tmaid.2010.04.008	journal	May 2010
Development of a quantitative real-time RT-PCR assay with internal control for the laboratory detection of tick borne encephalitis virus (TBEV) RNA Schwaiger, Michaela; Cassinotti, Pascal Journal of Clinical Virology, Vol. 27, Issue 2 https://doi.org/10.1016/s1386-6532(02)00168-3	journal	July 2003
Ancient pathogen DNA in archaeological samples detected with a Microbial Detection Array Devault, Alison M.; McLoughlin, Kevin; Jaing, Crystal Scientific Reports, Vol. 4, Issue 1 https://doi.org/10.1038/srep04245	journal	March 2014
Emerging viral diseases Nichol, S. T.; Arikawa, J.; Kawaoka, Y. Proceedings of the National Academy of Sciences, Vol. 97, Issue 23 https://doi.org/10.1073/pnas.210382297	journal	October 2000
Public Health Awareness of Emerging Zoonotic Viruses of Bats: A European Perspective Poel, Wim H. M. van der; Lina, Peter H. C.; Kramps, Johannes A. Vector-Borne and Zoonotic Diseases, Vol. 6, Issue 4 https://doi.org/10.1089/vbz.2006.6.315	journal	December 2006
Microarrays for Pathogen Detection and Analysis McLoughlin, K. S. Briefings in Functional Genomics, Vol. 10, Issue 6 https://doi.org/10.1093/bfgp/elr027	journal	September 2011
Repair of DNA strand gaps and nicks containing 3'-phosphate and 5'- hydroxyl termini by purified mammalian enzymes Karimi-Busheri, F. Nucleic Acids Research, Vol. 26, Issue 19 https://doi.org/10.1093/nar/26.19.4395	journal	October 1998
Molecular diagnostic and genetic characterization of highly pathogenic viruses: application during Crimean–Congo haemorrhagic fever virus outbreaks in Eastern Europe and the Middle East Filippone, C.; Marianneau, P.; Murri, S. Clinical Microbiology and Infection, Vol. 19, Issue 2 https://doi.org/10.1111/1469-0691.12075	journal	February 2013
Detection of North American Eastern and Western Equine Encephalitis Viruses by Nucleic Acid Amplification Assays Lambert, A. J.; Martin, D. A.; Lanciotti, R. S. Journal of Clinical Microbiology, Vol. 41, Issue 1 https://doi.org/10.1128/jcm.41.1.379-385.2003	journal	January 2003
Viral Nucleic Acids in Live-Attenuated Vaccines: Detection of Minority Variants and an Adventitious Virus Victoria, J. G.; Wang, C.; Jones, M. S. Journal of Virology, Vol. 84, Issue 12 https://doi.org/10.1128/jvi.02690-09	journal	April 2010
A microbial detection array (MDA) for viral and bacterial detection Gardner, Shea N.; Jaing, Crystal J.; McLoughlin, Kevin S. BMC Genomics, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2164-11-668	journal	January 2010
Quantitative analysis of particles, genomes and infectious particles in supernatants of haemorrhagic fever virus cell cultures Weidmann, Manfred; Sall, Amadou A.; Manuguerra, Jean-Claude Virology Journal, Vol. 8, Issue 1 https://doi.org/10.1186/1743-422x-8-81	journal	February 2011
Dengue Deaths in Puerto Rico: Lessons Learned from the 2007 Epidemic Tomashek, Kay M.; Gregory, Christopher J.; Rivera Sánchez, Aidsa PLoS Neglected Tropical Diseases, Vol. 6, Issue 4 https://doi.org/10.1371/journal.pntd.0001614	journal	April 2012
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 PLoS ONE, Vol. 6, Issue 8 https://doi.org/10.1371/journal.pone.0022631	journal	August 2011
West Nile virus infections in Greece: an update Papa, Anna Expert Review of Anti-infective Therapy, Vol. 10, Issue 7 https://doi.org/10.1586/eri.12.59	journal	July 2012
A five-year perspective on the situation of haemorrhagic fever with renal syndrome and status of the hantavirus reservoirs in Europe, 2005-2010 Heyman, P.; Ceianu, C. S.; Christova, I. Eurosurveillance, Vol. 16, Issue 36 https://doi.org/10.2807/ese.16.36.19961-en	journal	September 2011
L20B cells simplify culture of polioviruses from clinical samples Wood, D. J.; Hull, B. Journal of Medical Virology, Vol. 58, Issue 2 https://doi.org/10.1002/(SICI)1096-9071(199906)58:2<188::AID-JMV15>3.0.CO;2-H	journal	June 1999
Omsk haemorrhagic fever Růžek, Daniel; Yakimenko, Valeriy V.; Karan, Lyudmila S. The Lancet, Vol. 376, Issue 9758 https://doi.org/10.1016/S0140-6736(10)61120-8	journal	December 2010
Crimean–Congo hemorrhagic fever Whitehouse, C. Antiviral Research, Vol. 64, Issue 3 https://doi.org/10.1016/S0166-3542(04)00163-9	journal	December 2004
Development of a quantitative real-time RT-PCR assay with internal control for the laboratory detection of tick borne encephalitis virus (TBEV) RNA Schwaiger, Michaela; Cassinotti, Pascal Journal of Clinical Virology, Vol. 27, Issue 2 https://doi.org/10.1016/S1386-6532(02)00168-3	journal	July 2003
Comparison of PCR-southern hybridization and quantitative real-time PCR for the detection of JC and BK viral nucleotide sequences in urine and cerebrospinal fluid Ryschkewitsch, Caroline; Jensen, Peter; Hou, Jean Journal of Virological Methods, Vol. 121, Issue 2 https://doi.org/10.1016/j.jviromet.2004.06.021	journal	November 2004
Detection of West Nile virus and Japanese encephalitis virus using real-time PCR with a probe common to both viruses Shirato, Kazuya; Miyoshi, Hirotsugu; Kariwa, Hiroaki Journal of Virological Methods, Vol. 126, Issue 1-2 https://doi.org/10.1016/j.jviromet.2005.02.001	journal	June 2005
Analysis of sensitivity and rapid hybridization of a multiplexed Microbial Detection Microarray Thissen, James B.; McLoughlin, Kevin; Gardner, Shea Journal of Virological Methods, Vol. 201 https://doi.org/10.1016/j.jviromet.2014.01.024	journal	June 2014
Metagenomics and the molecular identification of novel viruses Bexfield, Nicholas; Kellam, Paul The Veterinary Journal, Vol. 190, Issue 2 https://doi.org/10.1016/j.tvjl.2010.10.014	journal	November 2011
Microarray-based detection and genotyping of viral pathogens Wang, D.; Coscoy, L.; Zylberberg, M. Proceedings of the National Academy of Sciences, Vol. 99, Issue 24, p. 15687-15692 https://doi.org/10.1073/pnas.242579699	journal	November 2002
Pan‐Viral Screening of Respiratory Tract Infections in Adults With and Without Asthma Reveals Unexpected Human Coronavirus and Human Rhinovirus Diversity Kistler, Amy; Avila, Pedro C.; Rouskin, Silvi The Journal of Infectious Diseases, Vol. 196, Issue 6 https://doi.org/10.1086/520816	journal	September 2007
Rapid Detection and Quantification of RNA of Ebola and Marburg Viruses, Lassa Virus, Crimean-Congo Hemorrhagic Fever Virus, Rift Valley Fever Virus, Dengue Virus, and Yellow Fever Virus by Real-Time Reverse Transcription-PCR Drosten, C.; Gottig, S.; Schilling, S. Journal of Clinical Microbiology, Vol. 40, Issue 7 https://doi.org/10.1128/JCM.40.7.2323-2330.2002	journal	July 2002
Detection of North American Eastern and Western Equine Encephalitis Viruses by Nucleic Acid Amplification Assays Lambert, A. J.; Martin, D. A.; Lanciotti, R. S. Journal of Clinical Microbiology, Vol. 41, Issue 1 https://doi.org/10.1128/JCM.41.1.379-385.2003	journal	January 2003
Identification of Genetic Evidence for Dobrava Virus Spillover in Rodents by Nested Reverse Transcription (RT)-PCR and TaqMan RT-PCR Weidmann, M.; Schmidt, P.; Vackova, M. Journal of Clinical Microbiology, Vol. 43, Issue 2 https://doi.org/10.1128/JCM.43.2.808-812.2005	journal	February 2005
Viral Nucleic Acids in Live-Attenuated Vaccines: Detection of Minority Variants and an Adventitious Virus Victoria, J. G.; Wang, C.; Jones, M. S. Journal of Virology, Vol. 84, Issue 12 https://doi.org/10.1128/JVI.02690-09	journal	April 2010
Phi29 polymerase based random amplification of viral RNA as an alternative to random RT-PCR Berthet, Nicolas; Reinhardt, Anita K.; Leclercq, India BMC Molecular Biology, Vol. 9, Issue 1 https://doi.org/10.1186/1471-2199-9-77	journal	January 2008
Quantitative analysis of particles, genomes and infectious particles in supernatants of haemorrhagic fever virus cell cultures Weidmann, Manfred; Sall, Amadou A.; Manuguerra, Jean-Claude Virology Journal, Vol. 8, Issue 1 https://doi.org/10.1186/1743-422X-8-81	journal	February 2011
Virus Identification in Unknown Tropical Febrile Illness Cases Using Deep Sequencing Yozwiak, Nathan L.; Skewes-Cox, Peter; Stenglein, Mark D. PLoS Neglected Tropical Diseases, Vol. 6, Issue 2 https://doi.org/10.1371/journal.pntd.0001485	journal	February 2012
Multi-Gene Detection and Identification of Mosquito-Borne RNA Viruses Using an Oligonucleotide Microarray Grubaugh, Nathan D.; McMenamy, Scott S.; Turell, Michael J. PLoS Neglected Tropical Diseases, Vol. 7, Issue 8 https://doi.org/10.1371/journal.pntd.0002349	journal	August 2013
Mosquito, Bird and Human Surveillance of West Nile and Usutu Viruses in Emilia-Romagna Region (Italy) in 2010 Calzolari, Mattia; Gaibani, Paolo; Bellini, Romeo PLoS ONE, Vol. 7, Issue 5 https://doi.org/10.1371/journal.pone.0038058	journal	May 2012
Detection and Typing of Human Pathogenic Hantaviruses by Real-Time Reverse Transcription-PCR and Pyrosequencing Kramski, Marit; Meisel, Helga; Klempa, Boris Clinical Chemistry, Vol. 53, Issue 11 https://doi.org/10.1373/clinchem.2007.093245	journal	November 2007
Emerging viral diseases Solomon, Tom; Mallewa, Mac Medicine, Vol. 33, Issue 7 https://doi.org/10.1383/medc.2005.33.7.14	journal	July 2005
A clear and present danger: tick-borne diseases in Europe Heyman, Paul; Cochez, Christel; Hofhuis, Agnetha Expert Review of Anti-infective Therapy, Vol. 8, Issue 1 https://doi.org/10.1586/eri.09.118	journal	January 2010
Emerging Viral Diseases: The One Health Connection--Workshop Summary Choffnes, Eileen R.; Mack, Alison https://doi.org/10.17226/18975	book	March 2015
Crimean–Congo hemorrhagic fever [Крымская геморрагическая лихорадка] Ugleva, S. V.; Kuznetsov, S. D.; Shabalina, S. V. Infekcionnye bolezni, Vol. 15, Issue 4 https://doi.org/10.20953/1729-9225-2017-4-60-67	journal	January 2017
Emerging Viral Diseases Ahmed, Jamal Uddin; Rahim, Muhammad Abdur; Uddin, Khwaja Nazim BIRDEM Medical Journal, Vol. 7, Issue 3 https://doi.org/10.3329/birdem.v7i3.33785	journal	August 2017
Evaluation of a Field-Portable DNA Microarray Platform and Nucleic Acid Amplification Strategies for the Detection of Arboviruses, Arthropods, and Bloodmeals Kengluecha, Ampornpan; Lee, John S.; Pisarcik, Sarah E. The American Journal of Tropical Medicine and Hygiene, Vol. 88, Issue 2 https://doi.org/10.4269/ajtmh.2012.12-0048	journal	February 2013
Emerging viral diseases Hernández, Angel San Miguel; Rodríguez, María San Miguel; Rodriguez, Angel San Miguel Open Access Research Journal of Biology and Pharmacy, Vol. 1, Issue 2, p. 20-27 https://doi.org/10.53022/oarjbp.2021.1.2.0024	journal	June 2021
A microbial detection array (MDA) for viral and bacterial detection Gardner, Shea N.; Jaing, Crystal J.; McLoughlin, Kevin S. figshare https://doi.org/10.6084/m9.figshare.c.4872813.v1	collection	January 2021

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