bluuebunny/crossref_metadata_2025_split huggingface dataset:
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
Authors: Drosten Christian , Göttig Stephan , Schilling Stefan , Asper Marcel , Panning Marcus , Schmitz Herbert , Günther Stephan 
Published: July 2002

ABSTRACT

Viral hemorrhagic fevers (VHFs) are acute infections with high case fatality rates. Important VHF agents are Ebola and Marburg viruses (MBGV/EBOV), Lassa virus (LASV), Crimean-Congo hemorrhagic fever virus (CCHFV), Rift Valley fever virus (RVFV), dengue virus (DENV), and yellow fever virus (YFV). VHFs are clinically difficult to diagnose and to distinguish; a rapid and reliable laboratory diagnosis is required in suspected cases. We have established six one-step, real-time reverse transcription-PCR assays for these pathogens based on the Superscript reverse transcriptase-Platinum
Taq
polymerase enzyme mixture. Novel primers and/or 5′-nuclease detection probes were designed for RVFV, DENV, YFV, and CCHFV by using the latest DNA database entries. PCR products were detected in real time on a LightCycler instrument by using 5′-nuclease technology (RVFV, DENV, and YFV) or SybrGreen dye intercalation (MBGV/EBOV, LASV, and CCHFV). The inhibitory effect of SybrGreen on reverse transcription was overcome by initial immobilization of the dye in the reaction capillaries. Universal cycling conditions for SybrGreen and 5′-nuclease probe detection were established. Thus, up to three assays could be performed in parallel, facilitating rapid testing for several pathogens. All assays were thoroughly optimized and validated in terms of analytical sensitivity by using in vitro-transcribed RNA. The ≥95% detection limits as determined by probit regression analysis ranged from 1,545 to 2,835 viral genome equivalents/ml of serum (8.6 to 16 RNA copies per assay). The suitability of the assays was exemplified by detection and quantification of viral RNA in serum samples of VHF patients.
Horizontal Transmission of
Candida parapsilosis
Candidemia in a Neonatal Intensive Care Unit
Authors: Lupetti Antonella , Tavanti Arianna , Davini Paola , Ghelardi Emilia , Corsini Valerio , Merusi Ilaria , Boldrini Antonio , Campa Mario , Senesi Sonia 
Published: July 2002

ABSTRACT

This report describes the nosocomial acquisition of
Candida parapsilosis
candidemia by one of the six premature newborns housed in the same room of a neonatal intensive care unit at the Ospedale Santa Chiara, Pisa, Italy. The infant had progeria, a disorder characterized by retarded physical development and progressive senile degeneration. The infant, who was not found to harbor
C. parapsilosis
at the time of his admission to the intensive care unit, had exhibited symptomatic conjunctivitis before the onset of a severe bloodstream infection. In order to evaluate the source of infection and the route of transmission, two independent molecular typing methods were used to determine the genetic relatedness among the isolates recovered from the newborn, the inanimate hospital environment, hospital personnel, topically and intravenously administered medicaments, and indwelling catheters. Among the isolates collected, only those recovered from the hands of two nurses attending the newborns and from both the conjunctiva and the blood of the infected infant were genetically indistinguishable. Since
C. parapsilosis
was never recovered from indwelling catheters or from any of the drugs administered to the newborn, we concluded that (i) horizontal transmission of
C. parapsilosis
occurred through direct interaction between nurses and the newborn and (ii) the conjunctiva was the site through which
C. parapsilosis
entered the bloodstream. This finding highlights the possibility that a previous
C. parapsilosis
colonization and/or infection of other body sites may be a predisposing condition for subsequent
C. parapsilosis
hematogenous dissemination in severely ill newborns.
Occurrence of a Multidrug-Resistant
Pseudomonas aeruginosa
Clone in Different Hospitals in Rio de Janeiro, Brazil
Authors: Pellegrino Flávia Lúcia Piffano Costa , Teixeira Lúcia Martins , Carvalho Maria da Glória Siqueira , Aranha Nouér Simone , Pinto de Oliveira Márcia , Mello Sampaio Jorge Luiz , D'Ávila Freitas Andrea , Ferreira Adriana Lucia Pires , Amorim Efigenia de Lourdes Teixeira , Riley Lee W. , Moreira Beatriz Meurer 
Published: July 2002

ABSTRACT

Multidrug-resistant
Pseudomonas aeruginosa
nosocomial infections are increasingly recognized worldwide. The existence of metallo-β-lactamase- and extended-spectrum β-lactamase-producing isolates exhibiting resistance to most β-lactam antimicrobial agents greatly complicates the clinical management of patients infected with such isolates. Since 1998,
P. aeruginosa
isolates resistant to all commercially available antimicrobial agents have been detected at a university-affiliated public hospital in Rio de Janeiro, Brazil. The present study was designed to characterize the antimicrobial resistance profiles and the genetic diversity of the
P. aeruginosa
strains isolated at this hospital and four private hospitals in Rio de Janeiro. Between April 1999 and March 2000, 200 consecutive isolates were obtained and analyzed for antimicrobial resistance. The genetic diversity of a selected number of them was evaluated by pulsed-field gel electrophoresis and PCR with the ERIC-2 primer. A predominant genotype, designated genotype A, was identified among isolates from four of the five hospitals evaluated. Eighty-four ceftazidime-resistant isolates were evaluated for metallo-β-lactamase production, which was detected in 20 (91%) of 22 genotype A isolates and 11 (18%) of 62 isolates belonging to other genotypes (
P
< 0.05). Two metallo-β-lactamase-producing genotype A isolates also produced an extended-spectrum β-lactamase. The occurrence of multidrug-resistant
P. aeruginosa
strains belonging to a unique genotype in different hospitals in Rio de Janeiro underscores the importance of the contribution of a single clone to the increase in the incidence of multidrug-resistant
P. aeruginosa
nosocomial infections.
VIDAS Test for Avidity of
Toxoplasma
-Specific Immunoglobulin G for Confirmatory Testing of Pregnant Women
Authors: Montoya Jose G. , Liesenfeld Oliver , Kinney Sandra , Press Cynthia , Remington Jack S. 
Published: July 2002

ABSTRACT
Because congenital toxoplasmosis is almost solely the result of maternal infection acquired during gestation, it is critical to determine whether infection during pregnancy has occurred. In the United States, definitive diagnosis of the acute infection and the time of its occurrence have been compromised by a lack of systematic screening and the fact that only a single serum sample is submitted for testing. In studies in Europe, and depending on the method used, the demonstration of high-avidity immunoglobulin G (IgG) toxoplasma antibodies has been shown to exclude infection having occurred in the first 3 to 5 months of pregnancy. We investigated the usefulness of determining the avidity of IgG toxoplasma antibodies with a VIDAS kit (herein referred to as the VIDAS Toxo-IgG avidity kit, the VIDAS kit essentially rules out acute infection having occurred within the 4 prior months) in the setting of a reference serology laboratory in the United States. Sera (132 samples) from 132 women in the first 16 weeks of pregnancy were chosen because at least one test in the toxoplasma serological profile (TSP) suggested or was equivocal for a recently acquired infection. High-avidity antibodies were demonstrated in 75% of 99 sera positive with the IgM enzyme-linked immunosorbent assay (ELISA) and 31.3% of 16 sera with acute TSP results. A significant percentage of sera with equivocal results wtih the IgM ELISA or TSP also had high-avidity test results. Of 39 women for whom treatment with spiramycin had been suggested to attempt to prevent congenital transmission, 19 (48.7%) had high-avidity antibodies. These findings highlight the value of the VIDAS IgG avidity kit when used in combination with the TSP to exclude recent infection, especially when only a single serum sample is available.
Detection of Isoniazid-Resistant
Mycobacterium tuberculosis
Strains by a Multiplex Allele-Specific PCR Assay Targeting
katG
Codon 315 Variation
Authors: Mokrousov Igor , Otten Tatiana , Filipenko Maxim , Vyazovaya Anna , Chrapov Eugeny , Limeschenko Elena , Steklova Lidia , Vyshnevskiy Boris , Narvskaya Olga 
Published: July 2002

ABSTRACT

We describe a simple multiplex allele-specific (MAS)-PCR assay to detect mutations in the second base of the
katG
gene codon 315, including AGC→ACC and ACA (Ser→Thr) substitutions that confer resistance to isoniazid (INH) in
Mycobacterium tuberculosis
clinical isolates. The 315 ACC allele is found in the majority of Inh
r
strains worldwide, especially in areas with a high incidence of tuberculosis. The 315 ACA allele is characteristic of the New York City multidrug-resistant (MDR) strain W and its progenies in the United States. The mutations in
katG315
are revealed depending on the presence or absence of an indicative fragment amplified from the wild-type allele of this codon. Initially optimized on the purified DNA samples, the assay was then tested on crude cell lysates and auramine-stained sputum slide preparations with the same reproducibility and interpretability of profiles generated by agarose gel electrophoresis. The MAS-PCR assay can be used for the detection of resistance to INH in clinical laboratories in regions with a high prevalence of MDR
M. tuberculosis
strains.
Detection of Duck Hepatitis B Virus DNA on Filter Paper by PCR and SYBR Green Dye-Based Quantitative PCR
Authors: Wang Chi-Young J. , Giambrone Joseph J. , Smith Bruce F. 
Published: July 2002

ABSTRACT

Duck hepatitis B virus
(DHBV) belongs to the
Hepadnaviridae
family, which includes human
Hepatitis B virus
(HBV) and
Woodchuck hepatitis virus
. It is widely distributed in wild and domestic ducks due to congenital transmission. HBV is a worldwide health problem, with carriers at risk of developing cirrhosis and liver cancer. Medical staff and scientists working with HBV must be vaccinated because of its contagious nature. DHBV is a safe surrogate for HBV because of their similarities. Collection of serum and blood samples on filter paper has been used to screen for metabolic disorders, genetic diseases, and viral infection and for evolutionary studies of the genome. In this study, DHBV from serum and blood dried on filters was detected by PCR. A 0.1-μl sample was sufficient for detection. The immobilization potential of filter papers for DHBV was examined, and the highest yield of PCR products was observed with Whatman paper. Dried serum was stable under different storage temperatures for 4 weeks, but the yields of PCR products decreased when the temperature was ⩾4°C. The optimal condition for storage was −70°C. A newly developed quantitative PCR based on monitoring the amplification by measuring the increase in fluorescence caused by the binding of SYBR green dye to double-stranded products was applied herein. DHBV genomic DNA cloned in a plasmid was used for the generation of standard DHBV DNA for quantitative PCR. It validated results from PCR in terms of the copy number of DHBV particles. The specificity of PCR was demonstrated by melting curve analysis, and the differentiation of two DHBV isolates amplified from dried serum was demonstrated based on their melting temperatures determined by GC contents and sequence. It was easier and simpler than other PCR-based DNA techniques. The use of serum dried on filters allows samples from distant field for which cold storage and transportation are a problem to be mailed to the diagnostic laboratory. Samples can be archived for comparison and used as a source of DNA for cloning and sequencing.
Use of the Sensititre Colorimetric Microdilution Panel for Antifungal Susceptibility Testing of Dermatophytes
Authors: Pujol I. , Capilla J. , Fernández-Torres B. , Ortoneda M. , Guarro J. 
Published: July 2002

ABSTRACT

The Sensititre YeastOne antifungal panel was used to test 49 dermatophytes belonging to the species
Epidermophyton floccosum
,
Microsporum gypseum
,
Microsporum canis
,
Trichophyton tonsurans
,
Trichophyton rubrum
, and
Trichophyton mentagrophytes
. The MICs of four antifungals obtained with the Sensititre YeastOne antifungal panel were compared with those obtained by the reference NCCLS microdilution method. The levels of agreement between the two methods (≤2 dilutions) were 81.6% with amphotericin B, 87.7% with itraconazole, 67.3% with fluconazole, and 69.4% with ketoconazole.
Prevalence of
Helicobacter pylori
in Sri Lanka as Determined by PCR
Authors: Fernando N. , Holton J. , Vaira D. , DeSilva M. , Fernando D. 
Published: July 2002

ABSTRACT

Fifty-seven Sinhalese patients were investigated for the presence of
Helicobacter pylori
by PCR. A prevalence of 70.1%, with 47.5% positive for
cagA
, was demonstrated. The most common
vacA
allele was s1am1. There was no significant association between either the s1 allele or the
cagA
allele and severe gastroduodenal disease. There was an association between the s1 allele and the
cagA
locus.
Spoligotyping of
Mycobacterium tuberculosis
Isolates from Multiple-Drug-Resistant Tuberculosis Patients from Bombay, India
Authors: Mistry Nerges F. , Iyer Anand M. , D'souza Desirée T. B. , Taylor G. Michael , Young Douglas B. , Antia Noshir H. 
Published: July 2002

ABSTRACT

Spoligotyping was undertaken in 65 multiple-drug-resistant
Mycobacterium tuberculosis
isolates from Bombay, India. The spoligotype patterns showed seven closely related clusters, a cluster with 2 Beijing-like isolates, and unique spoligotypes (43%). Of the clusters, one with 29% of all the isolates suggested transmission of a dominant resistant clone.
Catheter-Related
Microbacterium
Bacteremia Identified by 16S rRNA Gene Sequencing
Authors: Lau Susanna K. P. , Woo Patrick C. Y. , Woo Gibson K. S. , Yuen Kwok-Yung 
Published: July 2002

ABSTRACT

We describe the application of 16S rRNA gene sequencing in defining two cases of catheter-related
Microbacterium
bacteremia. In the first case, a gram-positive bacillus was isolated from both the blood culture and central catheter tip of a 39-year-old woman with chronic myeloid leukemia. The API Coryne system identified the isolate as 98.9%
Aureobacterium
or
Corynebacterium aquaticum
. In the second case, a gram-positive bacillus was recovered from five sets of blood cultures from both central catheter and percutaneous venipuncture of a 5-year-old girl with acute myeloid leukemia. The isolate was identified by the API Coryne system as 99.7%
Cellulomonas
or
Microbacterium
species. Further phenotypic tests failed to identify the two isolates. 16S rRNA gene sequencing showed 99.4% similarity between the first isolate and
Microbacterium oxydans
and 98.7% similarity between the second isolate and
Microbacterium trichotecenolyticum
, indicating that both isolates were
Microbacterium
species.
Microbacterium
infections are rarely reported in the literature. Although the central venous catheter was previously proposed to be a source of bacteremia, the first case in this report represents the first culture-documented case of catheter-related
Microbacterium
bacteremia.
Kinetic Analysis of the Role of Intersubunit Interactions in Human Immunodeficiency Virus Type 1 Capsid Protein Assembly In Vitro
Authors: Lanman Jason , Sexton Jennifer , Sakalian Michael , Prevelige, Peter E. 
Published: July 2002

ABSTRACT
The human immunodeficiency virus type 1 (HIV-1) capsid protein (CA) plays a crucial role in both assembly and maturation of the virion. Numerous recent studies have focused on either the soluble form of CA or the polymer end product of in vitro CA assembly. The CA polymer, in particular, has been used to study CA-CA interactions because it is a good model for the CA interactions within the virion core. However, analysis of the process of in vitro CA assembly can yield valuable insights into CA-CA interactions and the mechanism of core assembly. We describe here a method for the analysis of CA assembly kinetics wherein the progress of assembly is monitored by using turbidity. At pH 7.0 the addition of either of the isolated CA domains (i.e., the N or the C domain) to an assembly reaction caused a decrease in the assembly rate by competing for binding to the full-length CA protein. At pH 8.0 the addition of the isolated C domain had a similar inhibitory affect on CA assembly. However, at pH 8.0 the isolated N domain had no affect on the rate of CA assembly but, when mixed with the C domain, it alleviated the C-domain inhibition. These data provide biochemical evidence for a pH-sensitive homotypic N-domain interaction, as well as for an N- and C-domain interaction.
Novel Endogenous Retrovirus in Rabbits Previously Reported as Human Retrovirus 5
Authors: Griffiths David J. , Voisset Cécile , Venables Patrick J. W. , Weiss Robin A. 
Published: July 2002

ABSTRACT

Human retrovirus 5 (HRV-5) represented a fragment of a novel retrovirus sequence identified in human RNA and DNA preparations. In this study, the genome of HRV-5 was cloned and sequenced and integration sites were analyzed. Using PCR and Southern hybridization, we showed that HRV-5 is not integrated into human DNA. A survey of other species revealed that HRV-5 is present in the genomic DNA of the European rabbit (
Oryctolagus cuniculus
) and belongs to an endogenous retrovirus family found in rabbits. The presence of rabbit sequences flanking HRV-5 proviruses in human DNA extracts suggested that rabbit DNA was present in our human extracts, and this was confirmed by PCR analysis that revealed the presence of rabbit mitochondrial DNA sequences in four of five human DNA preparations tested. The origin of the rabbit DNA and HRV-5 in human DNA preparations remains unclear, but laboratory contamination cannot explain the preferential detection of HRV-5 in inflammatory diseases and lymphomas reported previously. This is the first description of a retrovirus genome in rabbits, and sequence analysis shows that it is related to but distinct from A-type retroelements of mice and other rodents. The species distribution of HRV-5 is restricted to rabbits; other species, including other members of the order Lagomorpha, do not contain this sequence. Analysis of HRV-5 expression by Northern hybridization and reverse transcriptase PCR indicates that the virus is transcribed at a low level in many rabbit tissues. In light of these findings we propose that the sequence previously designated HRV-5 should now be denoted RERV-H (for rabbit endogenous retrovirus H).
The Amino-Terminal Half of Sendai Virus C Protein Is Not Responsible for either Counteracting the Antiviral Action of Interferons or Down-Regulating Viral RNA Synthesis
Authors: Kato Atsushi , Ohnishi Yukano , Hishiyama Michiko , Kohase Masayoshi , Saito Sakura , Tashiro Masato , Nagai Yoshiyuki 
Published: July 2002

ABSTRACT
The Sendai virus C proteins, C′, C, Y1, and Y2, are a nested set of independently initiated carboxy-coterminal proteins translated from a reading frame overlapping the P frame on the P mRNA. The C proteins are extremely versatile and have been shown to counteract the antiviral action of interferons (IFNs), to down-regulate viral RNA synthesis, and to promote virus assembly. Using the stable cell lines expressing the C, Y1, Y2, or truncated C protein, we investigated the region responsible for anti-IFN action and for down-regulating viral RNA synthesis. Truncation from the amino terminus to the middle of the C protein maintained the inhibition of the signal transduction of IFNs, the formation of IFN-stimulated gene factor 3 (ISGF3) complex, the generation of the anti-vesicular stomatitis virus state, and the synthesis of viral RNA, but further truncation resulted in the simultaneous loss of all of these inhibitory activities. A relatively small truncation from the carboxy terminus also abolished all of these inhibitory activities. These data indicated that the activities of the C protein to counteract the antiviral action of IFNs and to down-regulate viral RNA synthesis were not encoded within a region of at least 98 amino acids in its amino-terminal half.
Further Characterization of Equine Foamy Virus Reveals Unusual Features among the Foamy Viruses
Authors: Lecellier Charles-Henri , Neves Manuel , Giron Marie-Lou , Tobaly-Tapiero Joelle , Saïb Ali 
Published: July 2002

ABSTRACT

Foamy viruses (FVs) are nonpathogenic, widely spread complex retroviruses which have been isolated in nonhuman primates, cattle, cats, and more recently in horses. The equine foamy virus (EFV) was isolated from healthy horses and was characterized by molecular cloning and nucleotide sequence analysis. Here, to further characterize this new FV isolate, the location of the transcriptional cap and poly(A) addition sites as well as the main splice donor and acceptor sites were determined, demonstrating the existence of the specific subgenomic
pol
mRNA, one specific feature of FVs. Moreover, similar to what has been described for the human foamy virus (HFV), the prototype of FVs, a replication-defective EFV genome was identified during persistent infection. At the protein level, the use of specific antibodies allowed us to determine the size and the subcellular localization of EFV Gag, Env, and Tas, the viral transactivators. While EFV Gag was detected in both the cytoplasm and the nucleus, EFV Env mainly localized in the Golgi complex, in contrast to HFV Env, which is sequestered in the endoplasmic reticulum. In addition, electron microscopy analysis demonstrated that EFV budding occurs at the plasma membrane and not intracellularly, as is the case for primate FVs. Interestingly, EFV Tas was detected both in the nucleus and the cytoplasm of Tas-transfected cells, in contrast to the strict nuclear localization of other FV Tas but similar to the equine infectious anemia virus Tat gene product. Taken together, our results reveal that this new FV isolate exhibits remarkable features among FVs, bringing new insights into the biology of these unconventional retroviruses.
Efficiency of Measles Virus Entry and Dissemination through Different Receptors
Authors: Schneider Urs , von Messling Veronika , Devaux Patricia , Cattaneo Roberto 
Published: July 2002

ABSTRACTThe efficiency with which different measles virus (MV) strains enter cells through the immune cell-specific protein SLAM (CD150) or other receptors, including the ubiquitous protein CD46, may influence their pathogenicity. We compared the cell entry efficiency of recombinant MV differing only in their attachment protein hemagglutinin (H). We constructed these viruses with an additional gene expressing an autofluorescent reporter protein to allow direct detection of every infected cell. A virus with a wild-type H protein entered cells through SLAM two to three times more efficiently than a virus with the H protein of the attenuated strain Edmonston, whereas cell entry efficiency through CD46 was lower. However, these subtle differences were amplified at the cell fusion stage because the wild-type H protein failed to fuse CD46-expressing cells. We also proved formally that a mutation in H protein residue 481 (asparagine to tyrosine) results in improved CD46-specific entry. To define the selective pressure exerted on that codon, we monitored its evolution in different H protein backgrounds and found that several passages in CD46-expressing Vero cells were necessary to shift it in the majority of the MV RNA. To verify the importance of these observations for human infections, we examined MV entry into peripheral blood mononuclear cells and observed that viruses with asparagine 481 H proteins infect these cells more efficiently.