bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid Method for Detection of Influenza A and B Virus Antigens by Use of a Two-Photon Excitation Assay Technique and Dry-Chemistry Reagents
Authors: Koskinen Janne O. , Vainionpää Raija , Meltola Niko J. , Soukka Jori , Hänninen Pekka E. , Soini Aleksi E. 
Published: September 2007

ABSTRACT
New separation-free assay methods for the rapid detection of influenza A and B virus antigens are presented. The methods employ dry-chemistry reagents and the recently developed two-photon excitation (TPX) fluorescence detection technology. According to the assay scheme, virus antigens are sandwiched by capture antibody onto polymer microspheres and fluorescently labeled antibody conjugate. Consequently, fluorescent immunocomplexes are formed on the surface of microspheres in proportion to the concentration of the analyte in the sample. The fluorescence signal from individual microspheres is measured, separation free, by means of two-photon excited fluorescence detection. In order to demonstrate the applicability of the new assay technique for virus antigen detection, methods for influenza A and B viruses were constructed. The assay method for influenza A virus applied a molecular fluorescent label, whereas the method for influenza B virus required a nanoparticle fluorescent reporter to reach sufficient clinical sensitivity. The new methods utilize a dry-chemistry approach, where all assay-specific reagents are dispensed into assay wells already in the manufacturing process of the test kits. The performance of the assay methods was tested with nasopharyngeal specimens using a time-resolved fluoroimmunoassay as a reference method. The results suggest that the new technique enables the rapid detection of influenza virus antigens with sensitivity and specificity comparable to that of the reference method. The dose-response curves showed linear responses with slopes equal to unity and dynamic assay ranges of 3 orders of magnitude. Applicability of the novel TPX technique for rapid multianalyte testing of respiratory infections is discussed.
Molecular Characterization of Human Immunodeficiency Virus Type 1 (HIV-1) and HIV-2 in Yaoundé, Cameroon: Evidence of Major Drug Resistance Mutations in Newly Diagnosed Patients Infected with Subtypes Other than Subtype B
Authors: Ndembi Nicaise , Abraha Awet , Pilch Heather , Ichimura Hiroshi , Mbanya Dora , Kaptue Lazare , Salata Robert , Arts Eric J. 
Published: September 2007

ABSTRACTPrior to current studies on the emergence of drug resistance with the introduction of antiretroviral therapy (ART) in Cameroon, we performed genotypic analysis on samples from drug-naïve, human immunodeficiency virus (HIV)-infected individuals in this country. Of the 79 HIV type 1 (HIV-1)polsequences analyzed from Cameroonian samples, 3 (3.8%) were identified as HIV-1 group O, 1 (1.2%) was identified as an HIV-2 intergroup B/A recombinant, and the remaining 75 (95.0%) were identified as HIV-1 group M. Group M isolates were further classified as subtypes A1 (n= 4), D (n= 4), F2 (n= 6), G (n= 12), H (n= 2), and K (n= 1) and as circulating recombinant forms CRF02_AG (n= 41), CRF11_cpx (n= 1), and CRF13_cpx (n= 2). Twopolsequences were identified as unique recombinant forms of CRF02_AG/F2 (n= 2). M46L (n= 2), a major resistance mutation associated with resistance to protease inhibitors, was observed in 2/75 (2.6%) group M samples. Single mutations associated with resistance to nucleoside reverse transcriptase inhibitors (T215Y/F [n= 3]) and nonnucleoside reverse transcriptase inhibitors (V108I [n= 1], L100I [n= 1], and Y181C [n= 2]) were observed in 7 of 75 (9.3%) group M samples. None of the patients had any history of ART exposure. Population surveillance of transmitted HIV drug resistance is required and should be included to aid in the development of appropriate guidelines.
Monitoring of Polyomavirus BK Virus Viruria and Viremia in Renal Allograft Recipients by Use of a Quantitative Real-Time PCR Assay: One-Year Prospective Study
Authors: Pang Xiaoli L. , Doucette Karen , LeBlanc Barbara , Cockfield Sandra M. , Preiksaitis Jutta K. 
Published: September 2007

ABSTRACT

We have developed a real-time quantitative PCR (rt-QPCR) assay to detect and kinetically monitor BK virus viruria and viremia in renal transplant recipients (RTRs). A total of 607 urine and 223 plasma samples were collected from 203 individuals including those with BK virus-associated nephropathy (BKVAN) (
n
= 8), those undergoing routine posttransplant surveillance (SV) (
n
= 155), those with nontransplant chronic kidney disease (NT-CKD) (
n
= 20), and healthy living kidney donors (LD) (
n
= 20). The rt-QPCR assay was found to be highly sensitive and specific, with a wide dynamic range (2.4 to 11 log
10
copies/ml) and very good precision (coefficient of variation, ∼5.9%). There was a significant difference in the prevalences of viruria and viremia between the BKVAN (100% and 100%) and SV (23% and 3.9%) groups (
P
< 0.001). No viruria or viremia was detected in LD or in NT-CKD patients. The median (range) peak levels of BK virus viruria and viremia, in log
10
copies/ml, were 10.26 (9.04 to 10.83) and 4.83 (3.65 to 5.86) for the BKVAN group versus 0 (0 to 10.83) and 0 (0 to 5.65) for the SV group, respectively (
P
< 0.001). When the BK virus load in the urine was <7.0 log
10
copies/ml, no BK virus viremia was detected. When the BK virus load in the urine reached 7.0, 8.0, 9.0, and ≥10.0 log
10
copies/ml, the corresponding detection of BK virus viremia increased to 20, 33, 50, and 100%, respectively. We propose monitoring of BK virus viruria in RTRs, with plasma BK virus load testing reserved for those with viruria levels of ≥7.0 log
10
copies/ml.
Novel Approach for Genotyping Varicella-Zoster Virus Strains from Germany
Authors: Schmidt-Chanasit Jonas , Stürmer Martin , Hahn Anke , Schäd Susanne G. , Gross Gerd , Ulrich Rainer G. , Heckel Gerald , Doerr Hans Wilhelm 
Published: September 2007

ABSTRACT
In this study, we present a novel genotyping scheme to classify German wild-type varicella-zoster virus (VZV) strains and to differentiate them from the Oka vaccine strain (genotype B). This approach is based on analysis of four loci in open reading frames (ORFs) 51 to 58, encompassing a total length of 1,990 bp. The new genotyping scheme produced identical clusters in phylogenetic analyses compared to full-genome sequences from well-characterized VZV strains. Based on genotype A, D, B, and C reference strains, a dichotomous identification key (DIK) was developed and applied for VZV strains obtained from vesicle fluid and liquor samples originating from 42 patients suffering from varicella or zoster between 2003 and 2006. Sequencing of regions in ORFs 51, 52, 53, 56, 57, and 58 identified 18 single-nucleotide polymorphisms (SNPs), including two novel ones, SNP 89727 and SNP 92792 in ORF51 and ORF52, respectively. The DIK as well as phylogenetic analysis by Bayesian inference showed that 14 VZV strains belonged to genotype A, and 28 VZV strains were classified as genotype D. Neither Japanese (vaccine)-like B strains nor recombinant-like C strains were found within the samples from Germany. The novel genotyping scheme and the DIK were demonstrated to be practical and simple and allow the highly efficient replication of phylogenetic patterns in VZV initially derived from full-genome DNA sequence analyses. Therefore, this approach may allow us to draw a more comprehensive picture of wild-type VZV strains circulating in Germany and Central Europe by high-throughput procedures in the future.
Evaluation of MChip with Historic Subtype H1N1 Influenza A Viruses, Including the 1918 “Spanish Flu” Strain
Authors: Moore Chad L. , Smagala James A. , Smith Catherine B. , Dawson Erica D. , Cox Nancy J. , Kuchta Robert D. , Rowlen Kathy L. 
Published: September 2007

ABSTRACT
The robustness of a recently developed diagnostic microarray for influenza, the MChip, was evaluated with 16 historic subtype H1N1 influenza A viruses (A/H1N1), including A/Brevig Mission/1/1918. The matrix gene segments from all 16 viruses were successfully detected on the array. An artificial neural network trained with temporally related A/H1N1 viruses identified A/Brevig Mission/1/1918 as influenza virus A/H1N1 with 94% probability.
Antimicrobial Susceptibility and Genetic Characteristics of
Streptococcus pneumoniae
Isolates Indicating Possible Nosocomial Transmission Routes in a Community Hospital in Japan
Authors: Qin Liang , Masaki Hironori , Watanabe Kiwao , Furumoto Akitsugu , Watanabe Hiroshi 
Published: September 2007

ABSTRACT

A clinical study was designed to study
Streptococcus pneumoniae
isolates recovered from a community hospital in Japan from April 2001 to November 2002. A total of 73 isolates were defined as derived from inpatient, outpatient, and hospital staff groups. The MIC results showed that 20 strains (27.4%) were susceptible to penicillin G, 39 strains (53.4%) had intermediate resistance, and 14 strains (19.2%) had full resistance. Low susceptibility to macrolides was also detected: 32.9%, 32.9%, and 34.2% of all strains were resistant to erythromycin, clarithromycin, and azithromycin, respectively. Thirty strains (41%) were resistant to at least two different kinds of antibiotics. Nineteen disparate serotypes were detected besides two nontypeable strains, and the predominant serotypes were 19F and 23F. Pulsed-field gel electrophoresis (PFGE) pattern A was dominant in the serotype 19F group; this pattern was similar to that of the international clone Taiwan 19F. A total of 10 different patterns were detected in the 23F group and were distinguishable from those of the international clones Spain 23F and Taiwan 23F. Pattern b strains were identified in the same ward, and pattern d strains were found both in patients with nosocomial pneumococcal infections (NPI) and in outpatients. In conclusion, drug-resistant
S. pneumoniae
was spreading rapidly, especially isolates of the serotype 19F and 23F groups. PFGE data revealed interpatient transmission and suggested that there might be some association between NPI patient strains and outpatient strains.
Concordance between
Neisseria gonorrhoeae
Genotypes Recovered from Known Sexual Contacts
Authors: Bilek Nicole , Martin Iona M. , Bell Gill , Kinghorn George R. , Ison Catherine A. , Spratt Brian G. 
Published: September 2007

ABSTRACT

Neisseria gonorrhoeae
multiantigen sequence typing (NG-MAST) is a highly discriminatory molecular typing procedure that provides precise and unambiguous strain characterization. Since molecular typing can complement contact tracing for reconstructing gonorrhea sexual networks, the concordance between the NG-MAST genotypes of pairs of
N. gonorrhoeae
isolates from recent sexual contacts was examined. Among 72 pairs of gonococci from recent sexual contacts, the genotypes of each pair were concordant in 65 cases (90.3%). In two further pairs, the isolates from sexual contacts differed by only a single nonsynonymous substitution in the porin gene, and in both of these pairs, the isolates were the same by
opa
typing. The other five nonconcordant pairs of isolates were clearly different strains.
opa
typing data were available for 51 of the pairs of isolates from sexual contacts, and concordant
opa
types were obtained in 38 cases (74.5%). NG-MAST should therefore be better than
opa
typing at identifying recent sexual contacts and has the important advantage over
opa
typing of being a more precise method of strain characterization.
Multiple-Locus Variable-Number Tandem-Repeat Analysis for Rapid Typing of
Candida glabrata
Authors: Grenouillet Frédéric , Millon Laurence , Bart Jean-Mathieu , Roussel Sandrine , Biot Isabelle , Didier Emeline , Ong Anne-Sophie , Piarroux Renaud 
Published: September 2007

ABSTRACT

A multiple-locus variable-number tandem-repeat analysis (MLVA) using six microsatellite markers was assessed in 127
Candida glabrata
isolates. Thirty-seven different genotypes, stable both in vitro and in vivo, were observed. The highest discriminatory power (
D
= 0.902) was reached by using only four markers. MLVA seems to be relevant for
C. glabrata
typing.
Multiplexed Reverse Transcriptase PCR Assay for Identification of Viral Respiratory Pathogens at the Point of Care
Authors: Létant Sonia E. , Ortiz Josue I. , Bentley Tammero Lance F. , Birch James M. , Derlet Robert W. , Cohen Stuart , Manning Dannelle , McBride Mary T. 
Published: September 2007

ABSTRACT
We have developed a nucleic acid-based assay that is rapid, sensitive, and specific and can be used for the simultaneous detection of five common human respiratory pathogens, including influenza virus A, influenza virus B, parainfluenza virus types 1 and 3, respiratory syncytial virus (RSV), and adenovirus groups B, C, and E. Typically, diagnosis on an unextracted clinical sample can be provided in less than 3 h, including sample collection, preparation, and processing, as well as data analysis. Such a multiplexed panel would enable rapid broad-spectrum pathogen testing on nasal swabs and therefore allow implementation of infection control measures and the timely administration of antiviral therapies. We present here a summary of the assay performance in terms of sensitivity and specificity. The limits of detection are provided for each targeted respiratory pathogen, and result comparisons were performed on clinical samples, our goal being to compare the sensitivity and specificity of the multiplexed assay to the combination of immunofluorescence and shell vial culture currently implemented at the University of California-Davis Medical Center hospital. Overall, the use of the multiplexed reverse transcription-PCR assay reduced the rate of false-negative results by 4% and reduced the rate of false-positive results by up to 10%. The assay correctly identified 99.3% of the clinical negatives and 97% of the adenovirus, 95% of the RSV, 92% of the influenza virus B, and 77% of the influenza virus A samples without any extraction performed on the clinical samples. The data also showed that extraction will be needed for parainfluenza virus, which was only identified correctly 24% of the time on unextracted samples.
Interleukin-7 Enhances Proliferation Responses to T-Cell Receptor Stimulation in Naïve CD4
+
T Cells from Human Immunodeficiency Virus-Infected Persons
Authors: Bazdar Douglas A. , Sieg Scott F. 
Published: September 2007

ABSTRACT

Proliferation responses of naïve CD4
+
T cells to T-cell receptor and interleukin-7 (IL-7) stimulation were evaluated by using cells from human immunodeficiency virus-positive (HIV
+
) donors. IL-7 enhanced responses to T-cell receptor stimulation, and the magnitude of this enhancement was similar in cells from healthy controls and from HIV
+
subjects. The overall response to T-cell receptor stimulation alone or in combination with IL-7, however, was diminished among viremic HIV
+
donors and occurred independent of antigen-presenting cells. Frequencies of CD127
+
cells were related to the magnitudes of proliferation enhancement that were mediated by IL-7. Thus, IL-7 enhances but does not fully restore the function of naïve CD4
+
T cells from HIV-infected persons.
Identification of the DNA Sequence Interacting with Kaposi's Sarcoma-Associated Herpesvirus Viral Interferon Regulatory Factor 1
Authors: Park Junsoo , Lee Myung-Shin , Yoo Seung-Min , Jeong Kwi Wan , Lee Daeyoup , Choe Joonho , Seo Taegun 
Published: September 2007

ABSTRACT
Kaposi's sarcoma-associated herpesvirus (KSHV) is the etiological agent of Kaposi's sarcoma. The open reading frame (K9) of KSHV encodes viral interferon regulatory factor 1 (vIRF1), which functions as a repressor of interferon-mediated signal transduction. The amino-terminal region of vIRF1 displays significant homology to the DNA-binding domain of cellular interferon regulatory factors, supporting the theory that the protein interacts with specific DNA sequences. Here, we identify the consensus sequence of vIRF1-binding sites from a pool of random oligonucleotides. Moreover, our data show that vIRF1 interacts with the K3:viral dihydrofolate reductase:viral interleukin 6 promoter region in the KSHV genome.
Interferons and Ribavirin Effectively Inhibit Norwalk Virus Replication in Replicon-Bearing Cells
Authors: Chang Kyeong-Ok , George David W. 
Published: September 2007

ABSTRACT

The development of effective therapies for noroviral gastroenteritis has been hampered by the absence of a cell culture system. Recently, we reported the generation of Norwalk virus (NV) replicon-bearing cells in BHK21 and Huh-7 cells and demonstrated that alpha interferon (IFN-α) effectively inhibited the replication of NV in these cells. In continuing studies for screening potential antinoroviral agents, we tested IFN-γ and ribavirin for their effects on NV replication in the cells. Like IFN-α, IFN-γ inhibited the replication of NV in the replicon-bearing cells, showing the reduction of the NV genome and proteins in a dose-dependent manner. The effective dose for reducing 50% (ED
50
) of the NV genome and protein was calculated to be approximately 40 units/ml. When ribavirin was applied to the cells, it effectively reduced the NV genome and protein with the ED
50
calculated as approximately 40 μM. The combination of IFN-α and ribavirin showed additive effects on the inhibition of NV replication. With the addition of guanosine to the ribavirin treatment, moderately reversed antiviral effects were observed, suggesting that the ribavirin effect may be associated with the depletion of GTP in the cells. Sequencing analysis of the conserved polymerase regions of NV in the ribavirin-treated (100 μM) and nontreated groups showed that the mutation rates were similar and indicated that ribavirin did not induce catastrophic mutations. The NV replicon-bearing cells provide an excellent tool for screening potential antinoroviral agents, and our results indicated that IFNs and ribavirin may be good therapeutic options for noroviral gastroenteritis.
Lipid Raft Disruption by Cholesterol Depletion Enhances Influenza A Virus Budding from MDCK Cells
Authors: Barman Subrata , Nayak Debi P. 
Published: September 2007

ABSTRACT
Lipid rafts play critical roles in many aspects of the influenza A virus life cycle. Cholesterol is a critical structural component of lipid rafts, and depletion of cholesterol leads to disorganization of lipid raft microdomains. In this study, we have investigated the effect of cholesterol depletion by methyl-β-cyclodextrin (MβCD) treatment on influenza virus budding. When virus-infected Madin-Darby canine kidney cells were treated with MβCD at the late phase of infection for a short duration, budding of virus particles, as determined by protein analysis and electron microscopy, increased with increasing concentrations and lengths of treatment. However, infectious virus yield varied, depending on the concentration and duration of MβCD treatment. Low concentrations of MβCD increased infectious virus yield throughout the treatment period, but higher concentrations caused an initial increase of infectious virus titer followed by a decrease with a longer duration. Relative infectivity of the released virus particles, on the other hand, decreased with increasing concentrations and durations of MβCD treatment. Loss of infectivity of virus particles is due to multiple effects of MβCD-mediated cholesterol depletion causing disruption of lipid rafts, changes in structural integrity of the viral membrane, leakage of viral proteins, a nick or hole on the viral envelope, and disruption of the virus structure. Exogenous cholesterol increased lipid raft integrity, inhibited particle release, and partially restored the infectivity of the released virus particles. These data show that disruption of lipid rafts by cholesterol depletion caused an enhancement of virus particle release from infected cells and a decrease in the infectivity of virus particles.
Severe Depletion of CD4+CD25+Regulatory T Cells from the Intestinal Lamina Propria but Not Peripheral Blood or Lymph Nodes during Acute Simian Immunodeficiency Virus Infection
Authors: Chase Amanda J. , Sedaghat Ahmad R. , German Jennifer R. , Gama Lucio , Zink M. Christine , Clements Janice E. , Siliciano Robert F. 
Published: September 2007

ABSTRACTCD4+CD25+regulatory T cells (Tregs) suppress the activation and proliferation of effector lymphocytes. In human immunodeficiency virus type 1 (HIV-1) infection, Tregs play a significant role in controlling the apoptotic loss of uninfected CD4+T cells resulting from high levels of generalized immune activation. During acute HIV-1 infection, more than 50% of CD4+T cells are depleted from the gastrointestinal lamina propria. To elucidate the role of Tregs in HIV-1-induced depletion of CD4+T cells in the gut-associated lymphoid tissue (GALT), we first determine the distribution of Tregs in a setting of acute infection using the simian immunodeficiency virus (SIV)/pigtailed macaque model of HIV-1 disease. CD4+T cells from the GALT, lymph nodes, and peripheral blood were isolated from SIV-infected pigtailed macaques on days 4, 14, and 114 postinoculation. Quantitative real-time reverse transcription-PCR was used to quantitate FOXP3 copy numbers in SIV-infected and uninfected control macaques. Expression of FOXP3 in the ileal lamina propria was significantly decreased at all stages of infection compared to levels in uninfected control macaques. In addition, functional analysis of ileal CD4+T cells from SIV-infected macaques revealed a lack of suppressive activity suggestive of the absence of Tregs in that compartment. These results indicate that Tregs are rapidly depleted in the GALT of SIV-infected macaques, defining a role for the loss of Treg-mediated suppression in early events in the pathogenesis of the disease.
Phylogenetic Diversity among Low-Virulence Newcastle Disease Viruses from Waterfowl and Shorebirds and Comparison of Genotype Distributions to Those of Poultry-Origin Isolates
Authors: Kim L. Mia , King Daniel J. , Curry Phillip E. , Suarez David L. , Swayne David E. , Stallknecht David E. , Slemons Richard D. , Pedersen Janice C. , Senne Dennis A. , Winker Kevin , Afonso Claudio L. 
Published: September 2007

ABSTRACT

Low-virulence Newcastle disease viruses (loNDV) are frequently recovered from wild bird species, but little is known about their distribution, genetic diversity, or potential to cause disease in poultry. NDV isolates recovered from cloacal samples of apparently healthy waterfowl and shorebirds (WS) in the United States during 1986 to 2005 were examined for genomic diversity and their potential for virulence (
n
= 249). In addition 19 loNDV isolates from U.S. live bird markets (LBMs) were analyzed and found to be genetically distinct from NDV used in live vaccines but related to WS-origin NDV. Phylogenetic analysis of the fusion protein identified nine novel genotypes among the class I NDV, and new genomic subgroups were identified among genotypes I and II of the class II viruses. The WS-origin viruses exhibited broad genetic and antigenic diversity, and some WS genotypes displayed a closer phylogenetic relationship to LBM-origin NDV. All NDV were predicted to be lentogenic based upon sequencing of the fusion cleavage site, intracerebral pathogenicity index, or mean death time in embryo assays. The USDA real-time reverse transcription-PCR assay, which targets the matrix gene, identified nearly all of the class II NDV tested but failed to detect class I viruses from both LBM and WS. The close phylogenetic proximity of some WS and LBM loNDV suggests that viral transmission may occur among wild birds and poultry; however, these events may occur unnoticed due to the broad genetic diversity of loNDV, the lentogenic presentation in birds, and the limitations of current rapid diagnostic tools.