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Vatsyayan A, Arvinden VR, Scaria V. Systematic In-Silico Evaluation of the Diagnostic Impact of Mpox Genome Variants in the Current Outbreak. Mol Diagn Ther 2023; 27:275-280. [PMID: 36495397 PMCID: PMC9736716 DOI: 10.1007/s40291-022-00629-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/22/2022] [Indexed: 12/14/2022]
Abstract
BACKGROUND AND OBJECTIVE The rapid rate at which the current mpox virus outbreak has spread across the globe has led the World Health Organization to declare it a Public Health Emergency of International Concern. Polymerase chain reaction-based methods are one of the cornerstones for effective molecular detection of viruses including mpox virus. Genetic variants in primer binding sites are known to impact the efficiency of polymerase chain reaction and therefore diagnosis. Here we have analyzed the genetic variants and their impact on efficient binding of oligonucleotides used in diagnostics. METHODS In this study, we have systematically collected primers and probes used in the detection of mpox virus from published literature and public resources, and assessed the impact of primer binding region genetic variants in the detection of mpox virus by analysing the thermodynamic parameters, Gibbs free energy and melting temperature. These were calculated using the nearest neighbour method for variants in mpox virus genomes available and the deviation in parameters was computed with respect to the reference genome sequence. RESULTS We have identified 170 genetic variations that fall within the oligo binding region in 1176 mpox virus genomes out of which five oligos showed at least a 2 °C decrease in melting temperature, which could potentially affect the diagnostic efficacy. CONCLUSIONS Our analysis shows the importance of continuous monitoring of mpox virus detection primer efficacy and provides the list of oligos with potentially reduced detection efficiency in the current mpox virus outbreak.
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Affiliation(s)
- Aastha Vatsyayan
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - V R Arvinden
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Vinod Scaria
- CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India.
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Molecular detection of monkeypox and related viruses: challenges and opportunities. Virus Genes 2023; 59:343-350. [PMID: 36746846 PMCID: PMC9901828 DOI: 10.1007/s11262-023-01975-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 01/29/2023] [Indexed: 02/08/2023]
Abstract
The recent widespread emergence of monkeypox (mpox), a rare and endemic zoonotic disease by monkeypox virus (MPXV), has made global headlines. While transmissibility (R0 ≈ 0.58) and fatality rate (0-3%) are low, as it causes prolonged morbidity, the World Health Organization has declared monkeypox as a public health emergency of international concern. Thus, effective containment and disease management require quick and efficient detection of MPXV. In this bioinformatic overview, we summarize the numerous molecular tests available for MPXV, and discuss the diversity of genes and primers used in the polymerase chain reaction-based detection. Over 90 primer/probe sets are used for the detection of poxviruses. While hemagglutinin and A-type inclusion protein are the most common target genes, tumor necrosis factor receptor and complement binding protein genes are frequently used for distinguishing Clade I and Clade II of MPXV. Problems and possibilities in the detection of MPXV have been discussed.
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Nakhaie M, Arefinia N, Charostad J, Bashash D, Haji Abdolvahab M, Zarei M. Monkeypox virus diagnosis and laboratory testing. Rev Med Virol 2023; 33:e2404. [PMID: 36331049 DOI: 10.1002/rmv.2404] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 10/15/2022] [Accepted: 10/20/2022] [Indexed: 11/06/2022]
Abstract
The multi-country outbreak of monkeypox virus (MPXV) infection, while the coronavirus disease 2019 pandemic is still an ongoing issue, has caused a new challenge. The re-emergence of MPXV and the rising incidence in non-endemic countries is turning into an upcoming threat to global health. Hence, rapid identification of the virus with appropriate methodology with the lowest false results plays a critical role in estimating the global extent of the crisis and providing preventive measures. This review summarised the main applicable strategies for primary detection and confirmation of MPXV and highlighted available data in biosafety, requirements, standard operating procedures, specimen collection, transportation and storage of clinical samples, and waste disposal of the viral agent. Also, various assays including molecular techniques, immunoassays, histopathological methods, electron microscopy, genomic sequencing, and cell culture have been illustrated. Moreover, we reflected on current knowledge of the advantages and disadvantages of each approach.
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Affiliation(s)
- Mohsen Nakhaie
- Gastroenterology and Hepatology Research Center, Institute of Basic and Clinical Physiology Sciences, Kerman University of Medical Sciences, Kerman, Iran
| | - Nasir Arefinia
- Department of Medical Microbiology, Kerman University of Medical Sciences, Kerman, Iran
| | - Javad Charostad
- Department of Microbiology, Shahid Sadoghi University of Medical Science, Yazd, Iran
| | - Davood Bashash
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohadeseh Haji Abdolvahab
- Recombinant Proteins Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Mohammad Zarei
- Renal Division, Brigham & Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,John B. Little Center for Radiation Sciences, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
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4
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Milewska A, Ner‐Kluza J, Dabrowska A, Bodzon‐Kulakowska A, Pyrc K, Suder P. MASS SPECTROMETRY IN VIROLOGICAL SCIENCES. MASS SPECTROMETRY REVIEWS 2020; 39:499-522. [PMID: 31876329 PMCID: PMC7228374 DOI: 10.1002/mas.21617] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 12/15/2019] [Indexed: 05/24/2023]
Abstract
Virology, as a branch of the life sciences, discovered mass spectrometry (MS) to be the pivotal tool around two decades ago. The technique unveiled the complex network of interactions between the living world of pro- and eukaryotes and viruses, which delivered "a piece of bad news wrapped in protein" as defined by Peter Medawar, Nobel Prize Laureate, in 1960. However, MS is constantly evolving, and novel approaches allow for a better understanding of interactions in this micro- and nanoworld. Currently, we can investigate the interplay between the virus and the cell by analyzing proteomes, interactomes, virus-cell interactions, and search for the compounds that build viral structures. In addition, by using MS, it is possible to look at the cell from the broader perspective and determine the role of viral infection on the scale of the organism, for example, monitoring the crosstalk between infected tissues and the immune system. In such a way, MS became one of the major tools for the modern virology, allowing us to see the infection in the context of the whole cell or the organism. © 2019 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Aleksandra Milewska
- Malopolska Centre of BiotechnologyJagiellonian UniversityGronostajowa 7A30‐387KrakowPoland
| | - Joanna Ner‐Kluza
- Department of Biochemistry and Neurobiology, Faculty of Materials Sciences and CeramicsAGH University of Science and TechnologyMickiewicza 30 Ave.30‐059KrakowPoland
| | - Agnieszka Dabrowska
- Malopolska Centre of BiotechnologyJagiellonian UniversityGronostajowa 7A30‐387KrakowPoland
- Faculty of Biochemistry, Biophysics and BiotechnologyJagiellonian UniversityGronostajowa 730‐387KrakowPoland
| | - Anna Bodzon‐Kulakowska
- Department of Biochemistry and Neurobiology, Faculty of Materials Sciences and CeramicsAGH University of Science and TechnologyMickiewicza 30 Ave.30‐059KrakowPoland
| | - Krzysztof Pyrc
- Malopolska Centre of BiotechnologyJagiellonian UniversityGronostajowa 7A30‐387KrakowPoland
| | - Piotr Suder
- Department of Biochemistry and Neurobiology, Faculty of Materials Sciences and CeramicsAGH University of Science and TechnologyMickiewicza 30 Ave.30‐059KrakowPoland
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5
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Smithson C, Meyer H, Gigante CM, Gao J, Zhao H, Batra D, Damon I, Upton C, Li Y. Two novel poxviruses with unusual genome rearrangements: NY_014 and Murmansk. Virus Genes 2017; 53:883-897. [PMID: 28762208 DOI: 10.1007/s11262-017-1501-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 07/27/2017] [Indexed: 10/19/2022]
Abstract
The genome sequence and annotation of two novel poxviruses, NY_014 and Murmansk, are presented. Despite being isolated on different continents and from different hosts, the viruses are relatively similar, albeit distinct species. The closest known relative of the novel viruses is Yoka poxvirus. Five novel genes were found in these genomes, two of which were MHC class I homologs. Although the core of these genomes was well conserved, the terminal regions showed significant variability with large deletions and surprising evidence of recombination with orthopoxviruses.
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Affiliation(s)
- Chad Smithson
- Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 3P6, Canada
| | - Hermann Meyer
- Bundeswehr Institute of Microbiology, Munich, Germany
| | - Crystal M Gigante
- The National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jinxin Gao
- The National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Hui Zhao
- The National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Dhwani Batra
- The National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Inger Damon
- The National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Chris Upton
- Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 3P6, Canada.
| | - Yu Li
- The National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
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6
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Dumont C, Irenge LM, Magazani EK, Garin D, Muyembe JJT, Bentahir M, Gala JL. Simple technique for in field samples collection in the cases of skin rash illness and subsequent PCR detection of orthopoxviruses and varicella zoster virus. PLoS One 2014; 9:e96930. [PMID: 24841633 PMCID: PMC4026132 DOI: 10.1371/journal.pone.0096930] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 04/13/2014] [Indexed: 11/18/2022] Open
Abstract
Background In case of outbreak of rash illness in remote areas, clinically discriminating monkeypox (MPX) from severe form of chickenpox and from smallpox remains a concern for first responders. Objective The goal of the study was therefore to use MPX and chickenpox outbreaks in Democratic Republic of Congo (DRC) as a test case for establishing a rapid and specific diagnosis in affected remote areas. Methods In 2008 and 2009, successive outbreaks of presumed MPX skin rash were reported in Bena Tshiadi, Yangala and Ndesha healthcare districts of the West Kasai province (DRC). Specimens consisting of liquid vesicle dried on filter papers or crusted scabs from healing patients were sampled by first responders. A field analytical facility was deployed nearby in order to carry out a real-time PCR (qPCR) assay using genus consensus primers, consensus orthopoxvirus (OPV) and smallpox-specific probes spanning over the 14 kD fusion protein encoding gene. A PCR-restriction fragment length polymorphism was used on-site as backup method to confirm the presence of monkeypox virus (MPXV) in samples. To complete the differential diagnosis of skin rash, chickenpox was tested in parallel using a commercial qPCR assay. In a post-deployment step, a MPXV-specific pyrosequencing was carried out on all biotinylated amplicons generated on-site in order to confirm the on-site results. Results Whereas MPXV proved to be the agent causing the rash illness outbreak in the Bena Tshiadi, VZV was the causative agent of the disease in Yangala and Ndesha districts. In addition, each on-site result was later confirmed by MPXV-specific pyrosequencing analysis without any discrepancy. Conclusion This experience of rapid on-site dual use DNA-based differential diagnosis of rash illnesses demonstrates the potential of combining tests specifically identifying bioterrorism agents and agents causing natural outbreaks. This opens the way to rapid on-site DNA-based identification of a broad spectrum of causative agents in remote areas.
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Affiliation(s)
- Catherine Dumont
- Royal Military Academy, Bruxelles, Belgium
- Center for Applied Molecular Technologies, Institut de Recherche Expérimentale et Clinique, Université catholique de Louvain, Brussels, Belgium
| | - Leonid M. Irenge
- Defense Laboratories Department, ACOS Ops&Trg, Belgian Armed Forces, Peutie, Belgium
- Center for Applied Molecular Technologies, Institut de Recherche Expérimentale et Clinique, Université catholique de Louvain, Brussels, Belgium
| | | | - Daniel Garin
- IRBA, Institut de Recherches Biomédicales des Armées, Service de Santé des Armées, Bretigny-sur-Orge, Cedex, France
| | - Jean-Jacques T. Muyembe
- Laboratoire National de Santé Publique, Institut National de Recherche Biomedicale, Kinshasa, Democratic Republic of Congo
| | - Mostafa Bentahir
- Defense Laboratories Department, ACOS Ops&Trg, Belgian Armed Forces, Peutie, Belgium
- Center for Applied Molecular Technologies, Institut de Recherche Expérimentale et Clinique, Université catholique de Louvain, Brussels, Belgium
| | - Jean-Luc Gala
- Defense Laboratories Department, ACOS Ops&Trg, Belgian Armed Forces, Peutie, Belgium
- Center for Applied Molecular Technologies, Institut de Recherche Expérimentale et Clinique, Université catholique de Louvain, Brussels, Belgium
- * E-mail:
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7
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Improving the diagnosis of bloodstream infections: PCR coupled with mass spectrometry. BIOMED RESEARCH INTERNATIONAL 2014; 2014:501214. [PMID: 24818144 PMCID: PMC4000954 DOI: 10.1155/2014/501214] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Accepted: 02/27/2014] [Indexed: 12/22/2022]
Abstract
The reference method for the diagnosis of bloodstream infections is blood culture followed by biochemical identification and antibiotic susceptibility testing of the isolated pathogen. This process requires 48 to 72 hours. The rapid administration of the most appropriate antimicrobial treatment is crucial for the survival of septic patients; therefore, a rapid method that enables diagnosis directly from analysis of a blood sample without culture is needed. A recently developed platform that couples broad-range PCR amplification of pathogen DNA with electrospray ionization mass spectrometry (PCR/ESI-MS) has the ability to identify virtually any microorganism from direct clinical specimens. To date, two clinical evaluations of the PCR/ESI-MS technology for the diagnosis of bloodstream infections from whole blood have been published. Here we discuss them and describe recent improvements that result in an enhanced sensitivity. Other commercially available assays for the molecular diagnosis of bloodstream infections from whole blood are also reviewed. The use of highly sensitive molecular diagnostic methods in combination with conventional procedures could substantially improve the management of septic patients.
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8
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Chen J, Fu Y, Ju L, Miao X, Shen Y, He L, Wang W, Jin J, Shao L, Sampath R, Ecker DJ, Zhang Y, Li M, Cheng X, Zhang W. Detection and identification of viral pathogens in patients with hand, foot, and mouth disease by multilocus PCR, reverse-transcription PCR and electrospray ionization mass spectrometry. J Clin Virol 2014; 59:115-9. [DOI: 10.1016/j.jcv.2013.11.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 11/11/2013] [Accepted: 11/18/2013] [Indexed: 11/25/2022]
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9
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Deyde VM, Sampath R, Gubareva LV. RT-PCR/electrospray ionization mass spectrometry approach in detection and characterization of influenza viruses. Expert Rev Mol Diagn 2014; 11:41-52. [DOI: 10.1586/erm.10.107] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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10
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Jordana-Lluch E, Martró Català E, Ausina Ruiz V. [Mass spectrometry in the clinical microbiology laboratory]. Enferm Infecc Microbiol Clin 2012; 30:635-44. [PMID: 22381225 PMCID: PMC7103318 DOI: 10.1016/j.eimc.2012.01.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Revised: 12/23/2011] [Accepted: 01/04/2012] [Indexed: 11/30/2022]
Abstract
Infectious diseases are still a cause of high mortality and morbidity rates. Current microbiological diagnostic methods are based on culture and phenotypic identification of isolated microorganisms, which can be obtained in about 24-48 h. Given that the microbiological identification is of major importance for patient management, new diagnostic methods are needed in order to detect and identify microorganisms in a timely and accurate manner. Over the last few years, several molecular techniques based on the amplification of microbial nucleic acids have been developed with the aim of reducing the time needed for the identification of the microorganisms involved in different infectious processes. On the other hand, mass spectrometry has emerged as a rapid and consistent alternative to conventional methods for microorganism identification. This review describes the most widely used mass spectrometry technologies -matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) and electrospray ionization time-of-flight (ESI-TOF)-, both for protein and nucleic acid analysis, as well as the commercial platforms available. Related publications of most interest in clinical microbiology are also reviewed.
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Affiliation(s)
- Elena Jordana-Lluch
- Servicio de Microbiología, Fundación Instituto de Investigación en Ciencias de la Salud Germans Trias y Pujol, Hospital Universitario Germans Trias y Pujol, Universidad Autónoma de Barcelona, Badalona, Barcelona, España
| | - Elisa Martró Català
- Servicio de Microbiología, Fundación Instituto de Investigación en Ciencias de la Salud Germans Trias y Pujol, Hospital Universitario Germans Trias y Pujol, Universidad Autónoma de Barcelona, Badalona, Barcelona, España
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, España
| | - Vicente Ausina Ruiz
- Servicio de Microbiología, Fundación Instituto de Investigación en Ciencias de la Salud Germans Trias y Pujol, Hospital Universitario Germans Trias y Pujol, Universidad Autónoma de Barcelona, Badalona, Barcelona, España
- CIBER Enfermedades Respiratorias (CIBERES), Bunyola, Mallorca, España
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11
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Duncan D, Vogler A, Wolcott M, Li F, Sarovich D, Birdsell D, Watson L, Hall T, Sampath R, Housley R, Blyn L, Hofstadler S, Ecker D, Keim P, Wagner D, Eshoo M. Identification and typing of Francisella tularensis
with a highly automated genotyping assay. Lett Appl Microbiol 2012; 56:128-34. [DOI: 10.1111/lam.12022] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 10/24/2012] [Accepted: 10/29/2012] [Indexed: 01/21/2023]
Affiliation(s)
- D.D. Duncan
- Ibis Biosciences, an Abbott company; Carlsbad CA USA
| | - A.J. Vogler
- Center for Microbial Genetics and Genomics; Northern Arizona University; Flagstaff AZ USA
| | - M.J. Wolcott
- United States Army Medical Research Institute of Infectious Diseases; Fort Detrick MD USA
| | - F. Li
- Ibis Biosciences, an Abbott company; Carlsbad CA USA
| | - D.S. Sarovich
- Center for Microbial Genetics and Genomics; Northern Arizona University; Flagstaff AZ USA
| | - D.N. Birdsell
- Center for Microbial Genetics and Genomics; Northern Arizona University; Flagstaff AZ USA
| | - L.M. Watson
- Center for Microbial Genetics and Genomics; Northern Arizona University; Flagstaff AZ USA
| | - T.A. Hall
- Ibis Biosciences, an Abbott company; Carlsbad CA USA
| | - R. Sampath
- Ibis Biosciences, an Abbott company; Carlsbad CA USA
| | - R. Housley
- Ibis Biosciences, an Abbott company; Carlsbad CA USA
| | - L.B. Blyn
- Ibis Biosciences, an Abbott company; Carlsbad CA USA
| | | | - D.J. Ecker
- Ibis Biosciences, an Abbott company; Carlsbad CA USA
| | - P. Keim
- Center for Microbial Genetics and Genomics; Northern Arizona University; Flagstaff AZ USA
| | - D.M. Wagner
- Center for Microbial Genetics and Genomics; Northern Arizona University; Flagstaff AZ USA
| | - M.W. Eshoo
- Ibis Biosciences, an Abbott company; Carlsbad CA USA
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12
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Detection, identification, and distribution of fungi in bronchoalveolar lavage specimens by use of multilocus PCR coupled with electrospray ionization/mass spectrometry. J Clin Microbiol 2012; 51:136-41. [PMID: 23100337 DOI: 10.1128/jcm.01907-12] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
As pulmonary fungal infections continue to increase due to an increasing number of immunocompromised patients, rapid detection and accurate identification of these fungal pathogens are critical. A broad fungal assay was developed by incorporating broad-range multilocus PCR amplification and electrospray ionization/mass spectrometry (PCR/ESI-MS) to detect and identify fungal organisms directly from clinical specimens. The aims of this study were to evaluate the performance of PCR/ESI-MS for detection, identification, and determination of the distribution of fungal organisms in bronchoalveolar lavage (BAL) fluid specimens. The BAL fluid specimens submitted for fungal culture at Vanderbilt University Medical Center between May 2005 and October 2011 were included. Cultures and identification were done using standard procedures. In addition, DNA was extracted from BAL fluid specimens, and fungal DNA amplification/identification were performed by PCR/ESI-MS. The results were compared with those of the standard cultures. A total of 691 nonduplicated BAL fluid specimens with sufficient leftover volume for molecular testing were evaluated using PCR/ESI-MS. Among them, 134 specimens (19.4%) were positive for fungi by both culture and PCR/ESI-MS testing. Of the dual-positive specimens, 125 (93.3%) were positive for Candida and Aspergillus species, with concordances between culture and PCR/ESI-MS results being 84 (67.2%) at the species level and 109 (87.2%) at the genus level. In addition, 243 (35.2%) and 30 (4.3%) specimens were positive only by PCR/ESI-MS or by culture, respectively (odds ratio [OR] = 11.95, 95% confidence interval [CI] = 7.90 to 18.17, P = 0.0000). Codetection of fungal organisms was noted in 23 (3.3%) specimens by PCR/ESI-MS, which was significantly higher than the 4 (0.6%) in which they were noted by culture (OR = 5.91, 95% CI = 1.93 to 20.27, P = 0.0002). Among 53 specimens in which cultures failed because of bacterial overgrowth, at least one fungus was identified in 26 specimens (47.3%) by PCR/ESI-MS. PCR/ESI-MS provides an advanced tool for rapid and sensitive detection, identification, and determination of the distribution of fungal organisms directly from BAL fluid specimens. Moreover, it detected fungal organisms in specimens in which cultures failed because of bacterial overgrowth. The clinical relevance of the significantly higher detection rate of fungal organisms by PCR/ESI-MS merits further investigation.
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13
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Muharemagic D, Labib M, Ghobadloo SM, Zamay AS, Bell JC, Berezovski MV. Anti-Fab aptamers for shielding virus from neutralizing antibodies. J Am Chem Soc 2012; 134:17168-77. [PMID: 23016897 DOI: 10.1021/ja306856y] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Oncolytic viruses are promising therapeutics that can selectively replicate in and kill tumor cells. However, repetitive administration of viruses provokes the generation of neutralizing antibodies (nAbs) that can diminish their anticancer effect. In this work, we selected DNA aptamers against the antigen binding fragment (Fab) of antivesicular stomatitis virus polyclonal antibodies to shield the virus from nAbs and enhance its in vivo survival. For the first time, we used flow cytometry and electrochemical immunosensing to identify aptamers targeting the Fab region of antibodies. We evaluated the aptamers in a cell-based infection assay and found that several aptamer clones provide more than 50% shielding of VSV from nAbs and thus have the potential to enhance the delivery of VSV without compromising the patient's immune system. In addition, we developed a bifunctional label-free electrochemical immunosensor for the quantitation of aptamer-mediated degree of shielding and the amount of vesicular stomatitis virus (VSV) particles. Electrochemical impedance spectroscopy was employed to interrogate the level of VSV in a linear range from 5 × 10(4) to 5 × 10(6) PFU mL(-1) with a detection limit of 10(4) PFU mL(-1).
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Affiliation(s)
- Darija Muharemagic
- Department of Chemistry, University of Ottawa, 10 Marie Curie, Ottawa, Ontario K1N 6N5, Canada
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14
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Sampath R, Mulholland N, Blyn LB, Massire C, Whitehouse CA, Waybright N, Harter C, Bogan J, Miranda MS, Smith D, Baldwin C, Wolcott M, Norwood D, Kreft R, Frinder M, Lovari R, Yasuda I, Matthews H, Toleno D, Housley R, Duncan D, Li F, Warren R, Eshoo MW, Hall TA, Hofstadler SA, Ecker DJ. Comprehensive biothreat cluster identification by PCR/electrospray-ionization mass spectrometry. PLoS One 2012; 7:e36528. [PMID: 22768032 PMCID: PMC3387173 DOI: 10.1371/journal.pone.0036528] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Accepted: 04/02/2012] [Indexed: 11/18/2022] Open
Abstract
Technology for comprehensive identification of biothreats in environmental and clinical specimens is needed to protect citizens in the case of a biological attack. This is a challenge because there are dozens of bacterial and viral species that might be used in a biological attack and many have closely related near-neighbor organisms that are harmless. The biothreat agent, along with its near neighbors, can be thought of as a biothreat cluster or a biocluster for short. The ability to comprehensively detect the important biothreat clusters with resolution sufficient to distinguish the near neighbors with an extremely low false positive rate is required. A technological solution to this problem can be achieved by coupling biothreat group-specific PCR with electrospray ionization mass spectrometry (PCR/ESI-MS). The biothreat assay described here detects ten bacterial and four viral biothreat clusters on the NIAID priority pathogen and HHS/USDA select agent lists. Detection of each of the biothreat clusters was validated by analysis of a broad collection of biothreat organisms and near neighbors prepared by spiking biothreat nucleic acids into nucleic acids extracted from filtered environmental air. Analytical experiments were carried out to determine breadth of coverage, limits of detection, linearity, sensitivity, and specificity. Further, the assay breadth was demonstrated by testing a diverse collection of organisms from each biothreat cluster. The biothreat assay as configured was able to detect all the target organism clusters and did not misidentify any of the near-neighbor organisms as threats. Coupling biothreat cluster-specific PCR to electrospray ionization mass spectrometry simultaneously provides the breadth of coverage, discrimination of near neighbors, and an extremely low false positive rate due to the requirement that an amplicon with a precise base composition of a biothreat agent be detected by mass spectrometry.
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Affiliation(s)
- Rangarajan Sampath
- Ibis Biosciences, Abbott, Carlsbad, California, United States of America.
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Whitehouse CA, Kesterson KE, Duncan DD, Eshoo MW, Wolcott M. Identification and characterization of Francisella species from natural warm springs in Utah, USA. Lett Appl Microbiol 2012; 54:313-24. [PMID: 22283482 DOI: 10.1111/j.1472-765x.2012.03214.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIMS To characterize Francisella isolated from two natural warm springs in Utah and compare them to a strain isolated from a patient with probable exposure to one of the springs in 2001. METHODS AND RESULTS A total of 39 presumptive Francisella isolates were obtained from two springs, Wasatch Hot Spring and Hobo Warm Spring, just north of Salt Lake City, Utah. All isolates were characterized by a combination of biochemical and molecular analyses, including novel PCR/electrospray ionization-mass spectrometry (ESI-MS) typing assays. Thirty-one were identified as F. philomiragia, while the remaining eight were identified as F. tularensis ssp. novicida. Phylogenetic analysis of the 16S rRNA sequences revealed 27 isolates, which clustered with F. philomiragia, albeit into two distinct clades. The remaining isolates clustered along with other F. tularensis strains including the Utah clinical isolate. Testing with the PCR/ESI-MS assays confirmed the identities of the isolates, but both yielded DNA signatures distinct from that of the clinical isolate. CONCLUSION We were successful in isolating several Francisella strains from natural warm springs; however, none appeared to genetically match the original 2001 clinical isolate. SIGNIFICANCE AND IMPACT OF THE STUDY This work highlights the presence of viable, potentially pathogenic Franscisella species living in the unique environmental niche of natural warm springs.
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Affiliation(s)
- C A Whitehouse
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702-5011, USA.
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16
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Sibley CD, Peirano G, Church DL. Molecular methods for pathogen and microbial community detection and characterization: current and potential application in diagnostic microbiology. INFECTION GENETICS AND EVOLUTION 2012; 12:505-21. [PMID: 22342514 PMCID: PMC7106020 DOI: 10.1016/j.meegid.2012.01.011] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2011] [Revised: 01/10/2012] [Accepted: 01/12/2012] [Indexed: 12/25/2022]
Abstract
Clinical microbiology laboratories worldwide have historically relied on phenotypic methods (i.e., culture and biochemical tests) for detection, identification and characterization of virulence traits (e.g., antibiotic resistance genes, toxins) of human pathogens. However, limitations to implementation of molecular methods for human infectious diseases testing are being rapidly overcome allowing for the clinical evaluation and implementation of diverse technologies with expanding diagnostic capabilities. The advantages and limitation of molecular techniques including real-time polymerase chain reaction, partial or whole genome sequencing, molecular typing, microarrays, broad-range PCR and multiplexing will be discussed. Finally, terminal restriction fragment length polymorphism (T-RFLP) and deep sequencing are introduced as technologies at the clinical interface with the potential to dramatically enhance our ability to diagnose infectious diseases and better define the epidemiology and microbial ecology of a wide range of complex infections.
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Affiliation(s)
- Christopher D. Sibley
- Department of Microbiology, Immunology & Infectious Diseases, Faculty of Medicine, University of Calgary, Calgary, Alta, Canada
| | - Gisele Peirano
- Division of Microbiology, Calgary Laboratory Services, Calgary, Alta, Canada
| | - Deirdre L. Church
- Department of Pathology & Laboratory Medicine, Faculty of Medicine, University of Calgary, Calgary, Alta, Canada
- Department of Medicine, Faculty of Medicine, University of Calgary, Calgary, Alta, Canada
- Division of Microbiology, Calgary Laboratory Services, Calgary, Alta, Canada
- Corresponding author. Address: c/o Calgary Laboratory Services, 9-3535 Research Rd. N.W., Calgary, Alta, Canada T2L 2K8. Tel.: +1 403 770 3281; fax: +1 403 770 3347.
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Ho YP, Reddy PM. Advances in mass spectrometry for the identification of pathogens. MASS SPECTROMETRY REVIEWS 2011; 30:1203-24. [PMID: 21557290 PMCID: PMC7168406 DOI: 10.1002/mas.20320] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Revised: 08/06/2010] [Accepted: 08/06/2010] [Indexed: 05/25/2023]
Abstract
Mass spectrometry (MS) has become an important technique to identify microbial biomarkers. The rapid and accurate MS identification of microorganisms without any extensive pretreatment of samples is now possible. This review summarizes MS methods that are currently utilized in microbial analyses. Affinity methods are effective to clean, enrich, and investigate microorganisms from complex matrices. Functionalized magnetic nanoparticles might concentrate traces of target microorganisms from sample solutions. Therefore, nanoparticle-based techniques have a favorable detection limit. MS coupled with various chromatographic techniques, such as liquid chromatography and capillary electrophoresis, reduces the complexity of microbial biomarkers and yields reliable results. The direct analysis of whole pathogenic microbial cells with matrix-assisted laser desorption/ionization MS without sample separation reveals specific biomarkers for taxonomy, and has the advantages of simplicity, rapidity, and high-throughput measurements. The MS detection of polymerase chain reaction (PCR)-amplified microbial nucleic acids provides an alternative to biomarker analysis. This review will conclude with some current applications of MS in the identification of pathogens.
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Affiliation(s)
- Yen-Peng Ho
- Department of Chemistry, National Dong Hwa University, Hualien 97401, Taiwan.
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Shchelkunov SN, Shcherbakov DN, Maksyutov RA, Gavrilova EV. Species-specific identification of variola, monkeypox, cowpox, and vaccinia viruses by multiplex real-time PCR assay. J Virol Methods 2011; 175:163-9. [DOI: 10.1016/j.jviromet.2011.05.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Revised: 04/26/2011] [Accepted: 05/03/2011] [Indexed: 01/13/2023]
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Abstract
Plague, which is most often caused by the bite of Yersinia pestis-infected fleas, is a rapidly progressing, serious disease that can be fatal without prompt antibiotic treatment. In late December 2007, an outbreak of acute gastroenteritis occurred in Nimroz Province of southern Afghanistan. Of the 83 probable cases of illness, 17 died (case fatality 20·5%). Being a case was associated with consumption or handling of camel meat (adjusted odds ratio 4·4, 95% confidence interval 2·2-8·8, P<0·001). Molecular testing of patient clinical samples and of tissue from the camel using PCR/electrospray ionization-mass spectrometry revealed DNA signatures consistent with Yersinia pestis. Confirmatory testing using real-time PCR and immunological seroconversion of one of the patients confirmed that the outbreak was caused by plague, with a rare gastrointestinal presentation. The study highlights the challenges of identifying infectious agents in low-resource settings; it is the first reported occurrence of plague in Afghanistan.
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Grant RJ, Baldwin CD, Nalca A, Zoll S, Blyn LB, Eshoo MW, Matthews H, Sampath R, Whitehouse CA. Application of the Ibis-T5000 pan-Orthopoxvirus assay to quantitatively detect monkeypox viral loads in clinical specimens from macaques experimentally infected with aerosolized monkeypox virus. Am J Trop Med Hyg 2010; 82:318-23. [PMID: 20134011 PMCID: PMC2813175 DOI: 10.4269/ajtmh.2010.09-0361] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2009] [Accepted: 09/28/2009] [Indexed: 11/07/2022] Open
Abstract
Monkeypox virus (MPXV), a member of the family Poxviridae and genus Orthopoxvirus, causes a smallpox-like disease in humans. A previously described pan-Orthopoxvirus assay, based on a broad-range polymerase chain reaction (PCR) coupled with electrospray ionization mass spectrometry (PCR/ESI-MS), was evaluated for its ability to detect MPXV from spiked human and aerosol-infected cynomolgous macaque (Macaca fascicularis) samples. Detection of MPXV DNA from macaque tissue, blood, and spiked human blood by the PCR/ESI-MS pan-Orthopoxvirus assay was comparable, albeit at slightly higher levels, to the current gold standard method of real-time PCR with the pan-Orthopoxvirus assay and had a limit of detection of 200 plaque-forming units. Furthermore, the platform was able to distinguish MPXV and vaccinia viruses that were spiked into macaque blood samples at various concentrations. This platform provides a new tool for the diagnosis and monitoring of orthopoxviral loads during vaccine or antiviral studies, but also could provide rapid identification during natural outbreaks or bioterrorism attacks.
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Affiliation(s)
- Rebecca J Grant
- U.S. Army Medical Research Institute of Infectious Diseases, 1301 Ditto Avenue, Fort Detrick, MD 21702, USA.
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Crowder CD, Rounds MA, Phillipson CA, Picuri JM, Matthews HE, Halverson J, Schutzer SE, Ecker DJ, Eshoo MW. Extraction of total nucleic acids from ticks for the detection of bacterial and viral pathogens. JOURNAL OF MEDICAL ENTOMOLOGY 2010; 47:89-94. [PMID: 20180313 DOI: 10.1093/jmedent/47.1.89] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Ticks harbor numerous bacterial, protozoal, and viral pathogens that can cause serious infections in humans and domestic animals. Active surveillance of the tick vector can provide insight into the frequency and distribution of important pathogens in the environment. Nucleic-acid based detection of tick-borne bacterial, protozoan, and viral pathogens requires the extraction of both DNA and RNA (total nucleic acids) from ticks. Traditional methods for nucleic acid extraction are limited to extraction of either DNA or the RNA from a sample. Here we present a simple bead-beating based protocol for extraction of DNA and RNA from a single tick and show detection of Borrelia burgdorferi and Powassan virus from individual, infected Ixodes scapularis ticks. We determined expected yields for total nucleic acids by this protocol for a variety of adult tick species. The method is applicable to a variety of arthropod vectors, including fleas and mosquitoes, and was partially automated on a liquid handling robot.
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MESH Headings
- Animals
- Borrelia/genetics
- Borrelia/isolation & purification
- DNA/genetics
- DNA/isolation & purification
- DNA Primers
- DNA, Bacterial/genetics
- DNA, Bacterial/isolation & purification
- DNA, Protozoan/genetics
- DNA, Protozoan/isolation & purification
- DNA, Viral/genetics
- DNA, Viral/isolation & purification
- Encephalitis Viruses, Tick-Borne/genetics
- Encephalitis Viruses, Tick-Borne/isolation & purification
- Polymerase Chain Reaction
- RNA/genetics
- RNA/isolation & purification
- RNA, Bacterial/genetics
- RNA, Bacterial/isolation & purification
- RNA, Protozoan/genetics
- RNA, Protozoan/isolation & purification
- RNA, Viral/genetics
- RNA, Viral/isolation & purification
- Reverse Transcriptase Polymerase Chain Reaction
- Tick-Borne Diseases/genetics
- Tick-Borne Diseases/prevention & control
- Ticks/genetics
- Ticks/microbiology
- Ticks/virology
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Affiliation(s)
- Chris D Crowder
- Ibis Biosciences, 1896 Rutherford Road, Carlsbad, CA 92008, USA
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Crowder CD, Rounds MA, Phillipson CA, Picuri JM, Matthews HE, Halverson J, Schutzer SE, Ecker DJ, Eshoo MW. Extraction of total nucleic acids from ticks for the detection of bacterial and viral pathogens. JOURNAL OF MEDICAL ENTOMOLOGY 2010; 47:89-94. [PMID: 20180313 PMCID: PMC2837073 DOI: 10.1603/033.047.0112] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Ticks harbor numerous bacterial, protozoal, and viral pathogens that can cause serious infections in humans and domestic animals. Active surveillance of the tick vector can provide insight into the frequency and distribution of important pathogens in the environment. Nucleic-acid based detection of tick-borne bacterial, protozoan, and viral pathogens requires the extraction of both DNA and RNA (total nucleic acids) from ticks. Traditional methods for nucleic acid extraction are limited to extraction of either DNA or the RNA from a sample. Here we present a simple bead-beating based protocol for extraction of DNA and RNA from a single tick and show detection of Borrelia burgdorferi and Powassan virus from individual, infected Ixodes scapularis ticks. We determined expected yields for total nucleic acids by this protocol for a variety of adult tick species. The method is applicable to a variety of arthropod vectors, including fleas and mosquitoes, and was partially automated on a liquid handling robot.
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MESH Headings
- Animals
- Borrelia/genetics
- Borrelia/isolation & purification
- DNA/genetics
- DNA/isolation & purification
- DNA Primers
- DNA, Bacterial/genetics
- DNA, Bacterial/isolation & purification
- DNA, Protozoan/genetics
- DNA, Protozoan/isolation & purification
- DNA, Viral/genetics
- DNA, Viral/isolation & purification
- Encephalitis Viruses, Tick-Borne/genetics
- Encephalitis Viruses, Tick-Borne/isolation & purification
- Polymerase Chain Reaction
- RNA/genetics
- RNA/isolation & purification
- RNA, Bacterial/genetics
- RNA, Bacterial/isolation & purification
- RNA, Protozoan/genetics
- RNA, Protozoan/isolation & purification
- RNA, Viral/genetics
- RNA, Viral/isolation & purification
- Reverse Transcriptase Polymerase Chain Reaction
- Tick-Borne Diseases/genetics
- Tick-Borne Diseases/prevention & control
- Ticks/genetics
- Ticks/microbiology
- Ticks/virology
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Affiliation(s)
| | | | | | - John M. Picuri
- Ibis Biosciences, 1896 Rutherford Road, Carlsbad, CA 92008
| | | | | | - Steven E. Schutzer
- University of Medicine and Dentistry of New Jersey, Dept. of Medicine, 185 South Orange Ave., Newark, NJ 07103
| | - David J. Ecker
- Ibis Biosciences, 1896 Rutherford Road, Carlsbad, CA 92008
| | - Mark W. Eshoo
- Ibis Biosciences, 1896 Rutherford Road, Carlsbad, CA 92008
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Oberacher H. Frontiers of mass spectrometry in nucleic acids analysis. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2010; 16:351-365. [PMID: 20530841 DOI: 10.1255/ejms.1045] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Nucleic acids research is a highly competitive field of research. A number of well established methods are available. The current output of high throughput ("next generation") sequencing technologies is impressive, and still technologies are continuing to make progress regarding read lengths, bp per second, accuracy and costs. Although in the 1990s MS was considered as an analytical platform for sequencing, it was soon realized that MS will never be competitive. Thus, the focus shifted from de novo sequencing towards other areas of application where MS has proven to be a powerful analytical tool. Potential niches for the application of MS in nucleic acids research include genotyping of genetic markers (single nucleotide polymorphisms, short tandem repeats, and combinations thereof), quality control of synthetic oligonucleotides, metabolic profiling of therapeutics, characterization of modified nucleobases in DNA and RNA molecules, and the study of non covalent interactions among nucleic acids as well as interactions of nucleic acids with drugs and proteins. The diversity of possible applications for MS highlights its significance for nucleic acid research.
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Affiliation(s)
- Herbert Oberacher
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria.
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