Multiplex-PCR and oligonucleotide microarray for detection of eight different herpesviruses from clinical specimens

Jääskeläinen, Anne J.; Piiparinen, Heli; Lappalainen, Maija; Koskiniemi, Marjaleena; Vaheri, Antti

doi:10.1016/j.jcv.2006.05.010

Cited by 34 publications

(25 citation statements)

References 35 publications

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“…The detection limits of the MALDI-TOF MS method on all HHV controls were comparable to previous reports of multiplex herpesvirus detection using an oligonucleotide microarray and multiplex PCR techniques (8,10). Since all negative control results were negative and detection limits could be documented with positive controls, we judge the fluctuations in results of some samples to reflect a low viral load near the detection limit of the method rather than contamination, as shown by real-time PCR quantitation for CMV and HHV8 samples.…”

Section: Discussionsupporting

confidence: 84%

“…We have developed a multiplex MALDI-TOF MS method that successfully detects HHVs in a wide variety of archival (10). Multiple infections, HHV6, and HHV7 were consistently demonstrated in repeated MALDI-TOF MS analyses in a substantial proportion of the study samples.…”

Section: Discussionmentioning

confidence: 99%

“…Since most microbiological laboratories maintain large biobanks with clinical samples, large-scale evaluation of the clinical and epidemiological importance of different herpesviruses is today restricted only by cost and throughput considerations. There is therefore an increasing interest in rapid and large-scale herpesvirus detection, and methods for the multiplex detection of several herpesviruses have recently been developed using PCR and microarray techniques (8,10,23). Virus detection using the matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) system is a high-throughput technology with multiplex capacity that has been used for genotyping and detection of RNA viruses (3,7,9,11,12,16) and human papillomavirus (HPV) (28).…”

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confidence: 99%

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Multiplex Detection of Human Herpesviruses from Archival Specimens by Using Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry

Sjöholm

Dillner

Carlson³

2008

J Clin Microbiol

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The human herpesviruses are involved in a variety of diseases. Large-scale evaluation of the clinical and epidemiological importance of different herpesviruses requires high-throughput methods. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a method that has a multiplex capacity enabling simultaneous detection of several viruses in a single sample. PCR-based methods for the multiplex detection of all known human herpesviruses were developed on the MALDI-TOF MS system. A variety of 882 archival samples, including bronchoalveolar lavage, conjunctival fluid, sore secretion, blister material, plasma, serum, and urine, analyzed for herpesviruses using PCR-based reference methods, were used to evaluate the MALDI-TOF MS method. The overall concordance rate between the MALDI-TOF MS method and the reference methods was 95.6% ( ‫؍‬ 0.90). In summary, the MALDI-TOF MS method is well suited for large-scale detection of all known human herpesviruses in a wide variety of archival biological specimens.The herpesviruses infecting humans include herpes simplex virus (HSV) types 1 and 2, varicella-zoster virus (VZV), Epstein-Barr virus (EBV) types A and B, cytomegalovirus (CMV), human herpesvirus 6 (HHV6) types A and B, HHV7, and HHV8 (Kaposi's sarcoma-associated herpesvirus). Herpesvirus infections in healthy subjects are often asymptomatic but can cause oral and genital lesions (HSV), chicken pox or shingles (VZV), infectious mononucleosis (EBV and CMV) (13), or roseola (HHV6) (19). In immunologically compromised hosts, herpes infections are more severe, causing pneumonia (CMV and HHV6) (1, 19), lymphoproliferative diseases (EBV) (19), Kaposi's sarcoma (HHV8) (19), or encephalitis (HSV-1) (6). Most herpesviruses have been reported to traverse the placenta (21), and intrauterine infections may cause birth defects (CMV) (19), premature delivery (VZV) (4), and fetal mortality (HSV) (21). Herpesvirus infections during pregnancy have also been associated with childhood acute lymphoblastic leukemia (EBV) (14).Common laboratory techniques in herpesvirus detection include antibody detection such as enzyme-linked immunosorbent assay (26), PCR (15,17,18,25,27), and dot blot hybridization (27). These techniques usually require separate methods for the detection of each herpesvirus and clinical information for selection of virus assay. Since most microbiological laboratories maintain large biobanks with clinical samples, large-scale evaluation of the clinical and epidemiological importance of different herpesviruses is today restricted only by cost and throughput considerations. There is therefore an increasing interest in rapid and large-scale herpesvirus detection, and methods for the multiplex detection of several herpesviruses have recently been developed using PCR and microarray techniques (8, 10, 23). Virus detection using the matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) system is a high-throughput technology with multiplex capacity that ha...

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Section: Discussionsupporting

confidence: 84%

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

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Multiplex Detection of Human Herpesviruses from Archival Specimens by Using Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry

Sjöholm

Dillner

Carlson³

2008

J Clin Microbiol

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“…In an earlier study on herpesvirus-specific B cell responses during acute CMV infection, the emergence or increment of Abs suggested the reactivation of EBV and also human herpesvirus 6, and in one patient the varicella virus also (39). More recent studies using quantitative PCR or gene arrays have provided direct evidence of the propensity of several herpesviruses to become reactivated at the same time (40,41). Also, during acute HIV infection CD8 ϩ T cells specific for EBV, CMV, and influenza start to express activation markers without detectable viral reactivation or infection (42).…”

Section: Discussionmentioning

confidence: 96%

Human CD8+ T Cell Memory Generation in Puumala Hantavirus Infection Occurs after the Acute Phase and Is Associated with Boosting of EBV-Specific CD8+ Memory T Cells

Tuuminen

Kekäläinen

Mäkelä

et al. 2007

The Journal of Immunology

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The induction and maintenance of T cell memory is incompletely understood, especially in humans. We have studied the T cell response and the generation of memory during acute infection by the Puumala virus (PUUV), a hantavirus endemic to Europe. It causes a self-limiting infection with no viral persistence, manifesting as hemorrhagic fever with renal syndrome. HLA tetramer staining of PBMC showed that the CD8+ T cell response peaked at the onset of the clinical disease and decreased within the next 3 wk. Expression of activation markers on the tetramer-positive T cells was also highest during the acute phase, suggesting that the peak population consisted largely of effector cells. Despite the presence of tetramer-positive T cells expressing cytoplasmic IFN-γ, PUUV-specific cells producing IFN-γ in vitro were rare during the acute phase. Their frequency, as well as the expression of IL-7Rα mRNA and surface protein, increased during a follow-up period of 6 wk and probably reflected the induction of memory T cells. Simultaneously with the PUUV-specific response, we also noted in seven of nine patients an increase in EBV-specific T cells and the transient presence of EBV DNA in three patients, indicative of viral reactivation. Our results show that in a natural human infection CD8+ memory T cells are rare during the peak response, gradually emerging during the first weeks of convalescence. They also suggest that the boosting of unrelated memory T cells may be a common occurrence in human viral infections, which may have significant implications for the homeostasis of the memory T cell compartment.

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“…1(b)). It has a wide variety of applications in biology and is recently spotlighted as a core tool for high throughput single nucleotide polymorphism (SNP) genotyping [1,2,3].…”

Section: Introductionmentioning

confidence: 99%

Multiplex PCR Assay Design by Hybrid Multiobjective Evolutionary Algorithm

Lee

Shin

Zhang

Lecture Notes in Computer Science

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Abstract. Multiplex Polymerase Chain Reaction (PCR) assay is to amplify multiple target DNAs simultaneously using different primer pairs for each target DNA. Recently, it is widely used for various biology applications such as genotyping. For sucessful experiments, both the primer pairs for each target DNA and grouping of targets to be actually amplified in one tube should be optimized. This involves multiple conflicting objectives such as minimizing the interaction of primers in a group and minimizing the number of groups required for the assay. Therefore, a multiobjective evolutionary approach may be an appropriate approach. In this paper, a hybrid multiobjective evolutionary algorithm which combines -multiobjective evolutionary algorithm with local search is proposed for multiplex PCR assay design. The proposed approach was compared with another multiobjective method, called MuPlex, and showed comparative performance by covering all of the given target sequences.

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Multiplex-PCR and oligonucleotide microarray for detection of eight different herpesviruses from clinical specimens

Cited by 34 publications

References 35 publications

Multiplex Detection of Human Herpesviruses from Archival Specimens by Using Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry

Multiplex Detection of Human Herpesviruses from Archival Specimens by Using Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry

Human CD8+ T Cell Memory Generation in Puumala Hantavirus Infection Occurs after the Acute Phase and Is Associated with Boosting of EBV-Specific CD8+ Memory T Cells

Multiplex PCR Assay Design by Hybrid Multiobjective Evolutionary Algorithm

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