Repeat testing of mpox specimens with late CTs improves detection of potential false positive cases

The mpox pandemic necessitated the rapid development of clinical assays for monkeypox virus detection. While the majority of mpox specimens have high viral loads with corresponding early cycle threshold (CT) values, reports have indicated some specimens with late CT values can represent false positive results. To mitigate this risk, the Centers for Disease Control and Prevention (CDC) published an advisory recommending repeat testing of all specimens with CT values ≥34. However, limited experimental data were available to support this specific cutoff. In this study, we examine whether a more conservative approach in which all specimens with CT values ≥29 are repeated would improve the detection of potential false positive results. Compared to the CDC algorithm, our approach identified an additional 20% (5/25) of potential false positive results. To assess the impact of this cutoff on laboratory workload, we modeled the expected increase in test volume and turnaround time (TAT) relative to the CDC method. Using a lower repeat threshold, test volume increased by 0.7% while mean TAT increased by less than 15 minutes. Overall, a lower threshold than recommended by the CDC for repeating late CT mpox specimens may reduce the number of false positives reported while minimally impacting testing volume and TAT.

Development and validation of a next-generation sequencing assay with open-access analysis software for detecting resistance-associated mutations in CMV

Cytomegalovirus (CMV) resistance testing by targeted next-generation sequencing (NGS) allows for the simultaneous analysis of multiple genes. We developed and validated an amplicon-based Ion Torrent NGS assay to detect CMV resistance mutations in UL27, UL54, UL56, and UL97 and compared the results to standard Sanger sequencing. NGS primers were designed to generate 83 overlapping amplicons of four CMV genes (~10 kb encompassing 138 mutation sites). An open-access software plugin was developed to perform read alignment, call variants, and interpret drug resistance. Plasmids were tested to determine NGS error rate and minor variant limit of detection. NGS limit of detection was determined using the CMV WHO International Standard and quantified clinical specimens. Reproducibility was also assessed. After establishing quality control metrics, 185 patient specimens previously tested using Sanger were reanalyzed by NGS. The NGS assay had a low error rate (<0.05%) and high accuracy (95%) for detecting CMV-associated resistance mutations present at ≥5% in contrived mixed populations. Mutation sites were reproducibly sequenced with 40× coverage when plasma viral loads were ≥2.6 log IU/mL. NGS detected the same resistance-associated mutations identified by Sanger in 68/69 (98.6%) specimens. In 16 specimens, NGS detected 18 resistance mutations that Sanger failed to detect; 14 were low-frequency variants (<20%), and six would have changed the drug resistance interpretation. The NGS assay showed excellent agreement with Sanger and generated high-quality sequence from low viral load specimens. Additionally, the higher resolution and analytic sensitivity of NGS potentially enables earlier detection of antiviral resistance.

In Search of Covariates of HIV-1 Subtype B Spread in the United States-A Cautionary Tale of Large-Scale Bayesian Phylogeography

Infections with HIV-1 group M subtype B viruses account for the majority of the HIV epidemic in the Western world. Phylogeographic studies have placed the introduction of subtype B in the United States in New York around 1970, where it grew into a major source of spread. Currently, it is estimated that over one million people are living with HIV in the US and that most are infected with subtype B variants. Here, we aim to identify the drivers of HIV-1 subtype B dispersal in the United States by analyzing a collection of 23,588 pol sequences, collected for drug resistance testing from 45 states during 2004-2011. To this end, we introduce a workflow to reduce this large collection of data to more computationally-manageable sample sizes and apply the BEAST framework to test which covariates associate with the spread of HIV-1 across state borders. Our results show that we are able to consistently identify certain predictors of spread under reasonable run times across datasets of up to 10,000 sequences. However, the general lack of phylogenetic structure and the high uncertainty associated with HIV trees make it difficult to interpret the epidemiological relevance of the drivers of spread we are able to identify. While the workflow we present here could be applied to other virus datasets of a similar scale, the characteristic star-like shape of HIV-1 phylogenies poses a serious obstacle to reconstructing a detailed evolutionary and spatial history for HIV-1 subtype B in the US.

Community-acquired pneumonia requiring hospitalization among U.S. children

BACKGROUND

Incidence estimates of hospitalizations for community-acquired pneumonia among children in the United States that are based on prospective data collection are limited. Updated estimates of pneumonia that has been confirmed radiographically and with the use of current laboratory diagnostic tests are needed.

METHODS

We conducted active population-based surveillance for community-acquired pneumonia requiring hospitalization among children younger than 18 years of age in three hospitals in Memphis, Nashville, and Salt Lake City. We excluded children with recent hospitalization or severe immunosuppression. Blood and respiratory specimens were systematically collected for pathogen detection with the use of multiple methods. Chest radiographs were reviewed independently by study radiologists.

RESULTS

From January 2010 through June 2012, we enrolled 2638 of 3803 eligible children (69%), 2358 of whom (89%) had radiographic evidence of pneumonia. The median age of the children was 2 years (interquartile range, 1 to 6); 497 of 2358 children (21%) required intensive care, and 3 (<1%) died. Among 2222 children with radiographic evidence of pneumonia and with specimens available for bacterial and viral testing, a viral or bacterial pathogen was detected in 1802 (81%), one or more viruses in 1472 (66%), bacteria in 175 (8%), and both bacterial and viral pathogens in 155 (7%). The annual incidence of pneumonia was 15.7 cases per 10,000 children (95% confidence interval [CI], 14.9 to 16.5), with the highest rate among children younger than 2 years of age (62.2 cases per 10,000 children; 95% CI, 57.6 to 67.1). Respiratory syncytial virus was more common among children younger than 5 years of age than among older children (37% vs. 8%), as were adenovirus (15% vs. 3%) and human metapneumovirus (15% vs. 8%). Mycoplasma pneumoniae was more common among children 5 years of age or older than among younger children (19% vs. 3%).

CONCLUSIONS

The burden of hospitalization for children with community-acquired pneumonia was highest among the very young, with respiratory viruses the most commonly detected causes of pneumonia. (Funded by the Influenza Division of the National Center for Immunization and Respiratory Diseases.).

Evaluation of the Abbott realtime HCV genotype II RUO (GT II) assay with reference to 5'UTR, core and NS5B sequencing

BACKGROUND

HCV genotyping is a critical tool for guiding initiation of therapy and selecting the most appropriate treatment regimen.

OBJECTIVE

To evaluate the concordance between the Abbott GT II assay and genotyping by sequencing subregions of the HCV 5'UTR, core and NS5B.

STUDY DESIGN

The Abbott assay was used to genotype 127 routine patient specimens and 35 patient specimens with unusual subtypes and mixed infection. Abbott results were compared to genotyping by 5'UTR, core and NS5B sequencing. Sequences were genotyped using the NCBI non-redundant database and the online genotyping tool COMET.

RESULTS

Among routine specimens, core/NS5B sequencing identified 93 genotype 1s, 13 genotype 2s, 15 genotype 3s, three genotype 4s, two genotype 6s and one recombinant specimen. Genotype calls by 5'UTR, core, NS5B sequencing and the Abbott assay were 97.6% concordant. Core/NS5B sequencing identified two discrepant samples as genotype 6 (subtypes 6l and 6u) while Abbott and 5'UTR sequencing identified these samples as genotype 1 with no subtype. The Abbott assay subtyped 91.4% of genotype 1 specimens. Among the 35 rare specimens, the Abbott assay inaccurately genotyped 3k, 6e, 6o, 6q and one genotype 4 variant; gave indeterminate results for 3g, 3h, 4r, 6m, 6n, and 6q specimens; and agreed with core/NS5B sequencing for mixed specimens.

CONCLUSIONS

The Abbott assay is an automated HCV genotyping method with improved accuracy over 5'UTR sequencing. Samples identified by the Abbott assay as genotype 1 with no subtype may be rare subtypes of other genotypes and thus require confirmation by another method.

Application of a new informatics tool for contamination screening in the HIV sequencing laboratory

BACKGROUND

Current HIV-1 sequencing-based methods for detecting drug resistance-associated mutations are open and susceptible to contamination. Informatic identification of clinical sequences that are nearly identical to one another may indicate specimen-to-specimen contamination or another laboratory-associated issue.

OBJECTIVES

To design an informatic tool to rapidly identify potential contamination in the clinical laboratory using sequence analysis and to establish reference ranges for sequence variation in the HIV-1 protease and reverse transcriptase regions among a U.S. patient population.

STUDY DESIGN

We developed an open-source tool named HIV Contamination Detection (HIVCD). HIVCD was utilized to make pairwise comparisons of nearly 8000 partial HIV-1 pol gene sequences from patients across the United States and to calculate percent identities (PIDs) for each pair. ROC analysis and standard deviations of PID data were used to determine reference ranges for between-patient and within-patient comparisons and to guide selection of a threshold for identifying abnormally high PID between two unrelated sequences.

RESULTS

The PID reference range for between-patient comparisons ranged from 83.8 to 95.7% while within-patient comparisons ranged from 96 to 100%. Interestingly, 48% of between-patient sequence pairs with a PID>96.5 were geographically related. The selected threshold for abnormally high PIDs was 96 (AUC=0.993, sensitivity=0.980, specificity=0.999). During routine use, HIVCD identified a specimen mix-up and the source of contamination of a negative control.

CONCLUSIONS

In our experience, HIVCD is easily incorporated into laboratory workflow, useful for identifying potential laboratory errors, and contributes to quality testing. This type of analysis should be incorporated into routine laboratory practice.

Large-scale comparison of Roche Cobas AmpliPrep/Cobas TaqMan and Abbott RealTime HIV assays

Significant underquantitation of HIV RNA has been reported with the Roche Cobas AmpliPrep/Cobas TaqMan HIV Test (Version 1) compared to other assays. However, these studies have generally involved limited numbers of samples from select patient populations or analysis of samples that were undetectable in the TaqMan assay. Random plasma samples submitted from throughout the United States for HIV RNA quantitation (n=1263) were compared in the Roche TaqMan and Abbott RealTime assays. Twenty-four samples (1.9%) were discrepant, with a maximum difference between the two assays of 1.9logcopies/mL. These data indicate that both tests may be susceptible to underquantitation, but the incidence is low in this large cohort of samples from across the United States.

Development and validation of a hepatitis B virus DNA sequencing assay for assessment of antiviral resistance, viral genotype and surface antigen mutation status

The objective of this study was to develop a DNA sequencing assay that examines sensitively and reliably all conserved domains of the reverse transcriptase-encoding region of the HBV genome for antiviral resistance-associated mutations while simultaneously producing ample information for precise genotyping and determination of HBsAg mutation. This assay was used to examine 1000 de-identified HBV DNA positive samples with known viral loads from a broad-based, unselected patient population from across the United States. Of these, 946 were assayed successfully. Antiviral resistance-associated mutations were identified in 104 samples. The escape mutation sG145R in the surface antigen was identified in 0.8% of patient samples. Infections with genotypes A, B, C, D, E, F, G and H were observed in 36.6%, 19.6%, 21.7%, 13.5%, 3.6%, 0.7%, 2.2%, and 0.5% of patient samples respectively. Fifteen samples (1.6%) appeared to harbor infections with multiple genotypes as shown by the presence of double peaks throughout sequence electropherograms. The limit of detection of this assay was approximately 150IU/mL.

A novel capillary electrophoresis-based multiplex PCR assay for detection of respiratory pathogens

The field of infectious disease testing has recently experienced rapid expansion in the number of multiplexed PCR-based assays available for detecting respiratory pathogens. This study provides a preliminary evaluation of a multiplex assay from Seegene that uses capillary electrophoresis as the detection platform for viral and bacterial respiratory pathogens. We compared this technology to a real-time PCR assay for 3 viral targets. Thirty respiratory samples were collected that had previously tested positive for either Flu A, Flu B, or RSV (ten of each). The Seegene assay detected 9/10 Flu A samples, 9/10 Flu B, and 10/10 RSV, for a total detection rate of 93%. The two samples that were undetected by the Seegene assay both generated late-crossing thresholds on the real-time platform, consistent with low viral loads. The Seeplex assay provides a promising alternative for multiplex respiratory testing.

Clinical course and spectrum of intensive care unit patients reactivating herpes simplex-1 virus: a retrospective analysis

Background:

Herpes simplex-1 virus (HSV-1) reactivation in the respiratory tract is common in intensive care unit (ICU) patients. However, susceptible ICU populations are poorly defined. Clinical recognition of HSV infection of the respiratory tract is difficult and the impact of such reactivation is not understood.

Materials and Methods:

A retrospective analysis of HSV-1 positive patients encountered over a 5-year period at a multispecialty ICU was carried out. HSV-1 was identified in respiratory secretions using a qualitative polymerase chain reaction (PCR) technique. Patient charts were reviewed for clinical features that would typify HSV-1 respiratory involvement, and the morbidity and mortality risks found with HSV-1 respiratory involvement.

Results:

A review of 48 HSV-1 positive ICU patients showed that patients reactivating HSV in the respiratory tract fell into one of the three categories: (1) septic elderly patients with and without ARDS, (2) immunosuppressed patients, especially those receiving high-dose steroids, and (3) post-thoracotomy patients. Abnormalities suggestive of HSV-1 reactivation in the respiratory tract included, haemorrhagic or excessive respiratory secretions, concomitant orofacial herpes (42%), and bronchoscopic abnormalities (hemorrhagic ulcers and mucosal friability) (83%). Twenty eight percent of the HSV-1 infected patients experienced postextubation stridor. HSV-1 reactivation was associated with extended ventilator stays, significant mortality (42%), and ventilator-associated pneumonias (52%).

Conclusions:

Identification of susceptible populations and definition of clinical features of HSV-1 related respiratory disease can enable diagnosis of HSV-1 infection in ICU patients. Although detection by a PCR technique can rapidly diagnose HSV-1 reactivation, prospective studies are required to clarify HSV disease versus mere shedding, and understand the impact of HSV-1 reactivation in hospitalized patients.

Development of a multiplex real-time RT-PCR assay for detection of influenza A, influenza B, RSV and typing of the 2009-H1N1 influenza virus

A high-throughput real-time RT-PCR assay was developed to amplify and detect a conserved region of the hemagglutinin gene of the 2009-H1N1 influenza A virus using a minor groove binder-conjugated hybridization probe. The assay was paired with a separate triplex real-time assay that detects influenza A via the matrix gene, influenza B and RSV in a multiplex format and compared with the Centers for Disease Control and Prevention (CDC) rRT-PCR assay using 143 samples. The 2009-H1N1 portion of the multiplex assay had 100% correlation with the CDC assay, while the triplex assay had a 99% agreement. An additional 105 samples collected from October to November 2009 were also tested using both the individual 2009-H1N1 and triplex assays. Of these 105 samples, eight were positive for the hemagglutinin target in the H1N1 assay and negative for the matrix target in the triplex assay. Discrepant analysis revealed single nucleotide polymorphisms within the matrix gene of 2009-H1N1 virus-positive samples. The limit of detection for the 2009-H1N1 assay was between 750 and 1,500 copies/reaction and no cross-reactivity with other respiratory pathogens was observed. Overall, this multiplexed format proved to be sensitive, robust and easy to use and serves as a useful tool for pandemic testing.

Competency-based education for the molecular genetic pathology fellow: a report of the association for molecular pathology training and education committee

The following report represents guidelines for competency-based fellowship training in Molecular Genetic Pathology (MGP) developed by the Association for Molecular Pathology Training and Education Committee and Directors of MGP Programs in the United States. The goals of the effort were to describe each of the Accreditation Council for Graduate Medical Education competencies as they apply to MGP fellowship training, provide a summary of goals and objectives, and recommend assessment tools. These guidelines are particularly pertinent to MGP training, which is a relatively new specialty that operates within a rapidly changing scientific and technological arena. It is hoped that this document will provide additional material for directors of existing MGP programs to consider for improvement of program objectives and enhancement of evaluation tools already in place. In addition, the guidelines should provide a valuable framework for the development of new MGP programs.

Evaluation of the Abbott investigational use only realtime HIV-1 assay and comparison to the Roche Amplicor HIV-1 monitor test, version 1.5

Abbott Molecular's m2000 system and RealTime HIV-1 assay (RealTime) were evaluated for sensitivity, reproducibility, linearity, ability to detect diverse HIV-1 subtypes/groups, and correlation to the Roche AMPLICOR HIV-1 MONITOR Test, Version 1.5 (Amplicor). The limit of detection was determined using the second International World Health Organization Standard and Viral Quality Assurance standard material. Serial dilutions of four patient samples were used to determine inter- and intra-assay reproducibility and linearity. Samples representing HIV-1 groups M, N, and O were evaluated in the RealTime, Amplicor, and Siemens Versant HIV-1 branched chain DNA 3.0 (Versant) assays. Archived Amplicor-tested samples were tested with the 1 ml, 0.5 ml, and 0.6 ml versions of the RealTime assay. Probit analysis predicts a limit of detection of 21.94 IU/ml using the World Health Organization Standard and 26.54 copies/ml using Viral Quality Assurance material with the 1 ml assay. Linearity and reproducibility were very good between approximately 1.60 to 6.0 log(10) copies/ml. All three assays produced similar measurements for all Group M subtypes tested; the RealTime assay was the only assay that detected all three Group O samples tested. Correlation with the Amplicor assay was good, although the RealTime assay measured between 0.342 and 0.716 log(10) copies/ml lower on average, depending on the input volume. The automated RealTime assay exhibits excellent sensitivity, dynamic range, reproducibility, and group/subtype detection, albeit with consistently lower values than Amplicor.

Respiratory syncytial virus outbreak in a long-term care facility detected using reverse transcriptase polymerase chain reaction: an argument for real-time detection methods

OBJECTIVES: To report an outbreak of respiratory synctyial virus (RSV) in a long‐term care facility (LTCF) during ongoing routine respiratory illness surveillance.

DESIGN: Rapid antigen testing, viral culture, direct fluorescent antibody (DFA) testing, and reverse transcriptase polymerase chain reaction (RT‐PCR) testing for up to 15 viruses in symptomatic residents and chart review.

SETTING: A 120‐bed LTCF.

MEASUREMENTS: Comparison of rapid antigen testing, respiratory viral cultures, and DFA testing and RT‐PCR in residents with symptoms of a respiratory tract infection.

RESULTS: Twenty‐two of 52 residents developed symptoms of a respiratory tract infection between January 29, 2008, and February 26, 2008. RSV was detected using RT‐PCR in seven (32%) of the 22 cases. None of the seven cases had positive RSV rapid antigen testing, and only two had positive culture or DFA results. This outbreak occurred during a time when state wide RSV rates were rapidly declining. One patient was admitted to the hospital during the infection and subsequently died.

CONCLUSION: RSV may cause outbreaks in LTCFs that traditional diagnostic methods do not detect. RT‐PCR can provide a more timely and accurate diagnosis of outbreaks, which allows for early symptomatic treatment, rational use of antibiotics, and improved infection control.

Evaluation of Nanogen MGB Alert Detection Reagents in a multiplex real-time PCR for influenza virus types A and B and respiratory syncytial virus

A multiplex real-time RT-PCR assay that detects influenza A, influenza B and respiratory syncytial virus (RSV) using the MGB Alert Influenza A&B/RSV Detection Reagent RUO (Nanogen, San Diego, CA) was developed. The Nanogen detection reagents consist of PCR primers and minor groove binder-conjugated hybridization probes for each virus and an internal control. Virus typing was determined by post-PCR melt curve analysis. A non-competitive armored RNA internal control was co-extracted with each sample to monitor nucleic acid extraction and RT-PCR. The assay was evaluated using a collection of culture, DFA and RT-PCR (Hexaplex, Prodesse, Waukesha, WI) positive and negative samples. The real-time multiplex assay detected 236 of 237 positive specimens for a 99% correlation. Of 30 Hexaplex negative samples tested, the multiplex real-time assay detected an additional 7 positives confirmed using additional PCR assays. Melt curve analysis for each virus produced average melting peaks of 60.4 degrees C, 66.7 degrees C and 69.4 degrees C for influenza A, influenza B and RSV respectively. Sequence analysis of 7 influenza A samples producing aberrant melt curves, confirmed the presence of a single nucleotide polymorphism beneath the influenza A probe. The limit of detection of each virus in 4 different sample types was measured to be between 7 and 806 copies. Overall, the multiplexed real-time RT-PCR assay was sensitive, robust and easy to use.

Description and validation of a novel real-time RT-PCR enterovirus assay

BACKGROUND

Enteroviruses are a leading cause of aseptic meningitis in adult and pediatric populations. We describe the development of a real-time RT-PCR assay that amplifies a small target in the 5' nontranslated region upstream of the classical Rotbart enterovirus amplicon. The assay includes an RNA internal control and incorporates modified nucleotide chemistry.

METHODS

We evaluated the performance characteristics of this design and performed blinded parallel testing on clinical samples, comparing the results with a commercially available RT-PCR assay (Pan-Enterovirus OligoDetect kit) that uses an enzyme immunoassay-like plate end detection.

RESULTS

We tested 778 samples and found 14 discrepant samples between the 2 assays. Of these, the real-time assay detected 6 samples that were negative by the OligoDetect kit, 5 of which were confirmed as positive by sequence analysis using an alternative primer set. Eight discrepant samples were positive by the OligoDetect kit and real-time negative, with 6 confirmed by sequencing. Overall, detection rates of 97% and 96% were obtained for the OligoDetect kit and real-time assays, respectively. Sequence analysis revealed the presence of a number of single nucleotide polymorphisms in the targeted region. The comparative sensitivities of the 2 assays were equivalent, with the limit of detection for the real-time assay determined to be approximately 430 copies per milliliter in cerebrospinal fluid.

CONCLUSIONS

This novel real-time enterovirus assay is a sensitive and suitable assay for routine clinical testing. The presence of single nucleotide polymorphisms can affect real-time PCR assays.

Limitations of polymerase chain reaction testing for diagnosing acute Epstein-Barr virus infections

Clinicians use molecular tests to detect Herpesviridae from blood without fully appreciating limitations of testing. Studies are needed to enhance our understanding of the impact of Herpesviridae latency on molecular testing. We retrospectively performed quantitative Epstein-Barr virus (EBV) on sera from patients between the ages of 1 and 30 who demonstrated serologic evidence of acute EBV (n = 50) or remote EBV (n = 50) infection. Epstein-Barr virus DNA was detected in 70% of acutely infected and 4% of remotely infected patients. Sera from acutely infected patients had higher EBV copy number than convalescent sera. Our results suggest that serology should be performed as the initial diagnostic test for acute EBV. The role for polymerase chain reaction in immunocompromised patients with impaired antibody responses or as a 2nd-line diagnostic test when serologic results are equivocal deserves further study.

Identification of Essential Genes in Bacteria

Essential genes are identified in duplicated regions of the bacterial chromosome. Transposition of a vector that forms operon fusions into a strain carrying a chromosomal duplication allows insertion of the transposon into essential genes because a second copy of the essential gene is present. When the duplication is allowed to segregate, only the segregant that carries the copy of the intact essential gene survives. The transposon insertion in the essential gene is maintained only in the duplication derivatives. A technique is described that uses a Tn10 derivative, Tn10dTc-araC(+), which contains a cloned copy of the Escherichia coli araC(+) gene, as a portable region of homology to generate large duplications of the Salmonella chromosome. The duplication is maintained in the population by growth in the presence of tetracycline. When the lac operon fusion vector, MudJ, is transposed into the duplicated region, removal of tetracycline from the growth media allows segregation of the duplication yielding (Ara(-)) haploid segregants which appear as red colonies or as red/white (Ara(-/+)) sectoring colonies on TTC arabinose indicator plates. However, if the insertion is in an essential gene, only segregants that lose the MudJ insertion in the essential gene survive. In this case, selection for the insertion in the essential gene yields solid white (Ara(+)) colonies in the absence of tetracycline. While the specific design presented uses Mud transposon insertions to generate lac operon (transcriptional) and lacZ gene (translational) fusions to essential genes, this technique can be used to generate transposon insertions of any kind into essential genes.

Genes expressed in a turrid venom duct: divergence and similarity to conotoxins

The toxoglossate mollusks are a large group of venomous animals (>10,000 species) conventionally divided into three groups, the cone snails, the auger snails, and the turrid snails; turrids account for >90% of the biodiversity of toxoglossans. Only the venoms of cone snails have been intensively investigated, with little work focused on turrids. We report the first broad characterization of genes expressed in venom ducts of any turrid species. Twenty-three different cDNA clones encoding putative toxins were characterized from the venom duct of the turrine species Lophiotoma olangoensis Olivera 2002 and belong to 16 different gene families. Of the 16 different Lophiotoma olangoensis gene families that encode putative toxins, for only 1 was there clear evidence of sequence similarity with any conotoxin gene family. The I-like gene family of Lophiotoma olangoensis was found to be related to the K channel-targeted I(2) conotoxin superfamily. Most putative Lophiotoma toxins are cysteine-rich polypeptides, with a significant fraction much larger (>80 amino acids) than the toxins from cone snails. A small number were not cysteine-rich but had hydrophobic amino acid clusters interspersed with arginine residues. This is only 1 of >10,000 different turrid venoms that needs to be characterized. From this study, a common origin with Conus for one family of putative turrid toxins is indicated.

Evaluation of the COBAS Hepatitis C Virus (HCV) TaqMan analyte-specific reagent assay and comparison to the COBAS Amplicor HCV Monitor V2.0 and Versant HCV bDNA 3.0 assays

Performance characteristics of the COBAS hepatitis C virus (HCV) TaqMan analyte-specific reagent (TM-ASR) assay using the QIAGEN BioRobot 9604 for RNA extraction were evaluated and compared to the COBAS Amplicor HCV Monitor V2.0 (Amplicor) and Versant HCV bDNA 3.0 (Versant) assays using clinical samples. Calibration of TM-ASR using Armored RNA allowed determination of the distribution of HCV RNA in clinical samples, using 22,399 clinical samples. Limit of detection, linearity, and inter- and intraassay assay precision were determined for the TM-ASR assay using multiple clinical specimen panels across multiple determinations. Genotype specificity for the TM-ASR assay was determined using samples with different HCV RNA genotypes evaluated and compared against predetermined results. Contamination control of the TM-ASR assay was evaluated using pools of HCV RNA-positive and -negative samples tested in a checkerboard pattern over 12 runs of 96 samples. Correlation of the TM-ASR, Amplicor, and Versant assays was determined using 100 paired clinical samples and Deming regression analysis. The TM-ASR performed well with respect to linearity, precision, and contamination control. The correlation between TM-ASR and the Amplicor and Versant assays was poor, with large differences between assay results for individual samples. Calibration of the TM-ASR assay with Armored RNA allowed for a wide dynamic range and description of the distribution of HCV RNA in clinical samples.

Evaluation of the COBAS amplicor HBV monitor assay and comparison with the ultrasensitive HBV hybrid capture 2 assay for quantification of hepatitis B virus DNA

Performance characteristics of the COBAS Amplicor HBV Monitor test (Roche Diagnostics), which measures hepatitis B virus (HBV) DNA quantitatively, were evaluated and compared with the Ultrasensitive HBV Hybrid Capture 2 (HC2; Digene Corporation) assay. Linearity and within-run precision were assessed for both methods by using eight HBV DNA-positive samples serially diluted to obtain a range of <100 to 500,000 HBV DNA copies/ml and run in triplicate. Agreement between the methods was studied with 100 clinical samples. HC2 assay performance near the limit of detection was investigated through repeat testing of 149 samples with HC2 and testing of 37 samples with HC2 results of <4,700 HBV DNA copies/ml by Amplicor assay and a qualitative PCR assay. The linearity experiment for Amplicor had regression of observed values compared to expected values (y = 1.073x - 0.247; R(2) = 0.993, n = 32; for HC2, y = 0.855x + 0.759, R(2) = 0.729, n = 18). Within-run standard deviation of log HBV DNA copies/ml ranged from 0.003 to 0.348 (Amplicor) and 0.027 to 0.253 (HC2). Agreement assessed by Deming regression was poor [Amplicor = 1.197(HC2) - 0.961; R(2) = 0.799, standard error of the estimate (SEE) = 0.710, n = 94]. Near the lower limit of detection, 32 of 149 repeat HC2 results were <4,700 HBV DNA copies/ml. Of the 37 samples with HC2 results of <4,700 HBV DNA copies/ml, HBV DNA was not detected in 15 samples, while HBV DNA was detected by at least one PCR method in 12 samples. Amplicor is linear from 200 to 200,000 HBV DNA copies/ml with undiluted samples, and this range can be expanded through dilution. Inconsistent HC2 results near the limit of detection justify use of a grey zone.

Diagnosis and outcomes of enterovirus infections in young infants

BACKGROUND

Enterovirus (EV) infections commonly cause fever in infants younger than 90 days of age. The polymerase chain reaction (PCR) has improved our ability to diagnose EV infections.

OBJECTIVE

To evaluate the utility of blood and cerebrospinal fluid (CSF) specimens for the diagnosis of EV infections by PCR and to describe a large cohort of EV-infected infants.

DESIGN/METHODS

Febrile infants younger than 90 days of age evaluated for sepsis at Primary Children's Medical Center in Salt Lake City, UT, were enrolled in a prospective study designed to identify viral infections from December 1996 to June 2002. All patients had bacterial cultures of blood, urine and CSF. Testing for EV was performed by PCR and/or viral cultures. Patients who were positive for EV were identified for this study.

RESULTS

Of 1779 febrile infants enrolled, 1061 had EV testing and 214 (20%) were EV-positive. EV infections were diagnosed by PCR of blood, CSF or both in 93% of infants. PCR testing was positive in blood in 57%, and blood was the only positive specimen for 22% of EV infected infants. PCR of CSF was positive in 74%. The mean age of infants with EV infection was 33 days, with 18% younger than 14 days and 5% younger than 7 days. Fifty percent of EV-positive infants had CSF pleocytosis. Of EV PCR-positive infants, 91% were admitted, and 2% required intensive care. Possible serious EV disease was diagnosed in <1%, and there were no deaths. Twelve infants (5.6%) had concomitant urinary tract infection, and 3 (1%) had bacteremia.

CONCLUSIONS

EV infections are common in febrile infants younger than 90 days. Blood and CSF are equally likely to yield positive results by PCR, but the combination of both specimens improved the diagnostic yield.

Definition of the M-Conotoxin Superfamily: Characterization of Novel Peptides from Molluscivorous Conus Venoms

Most of the >50,000 different pharmacologically active peptides in Conus venoms belong to a small number of gene superfamilies. In this work, the M-conotoxin superfamily is defined using both biochemical and molecular criteria. Novel excitatory peptides purified from the venoms of the molluscivorous species Conus textile and Conus marmoreus all have a characteristic pattern of Cys residues previously found in the mu-, kappaM-, and psi-conotoxins (CC-C-C-CC). The new peptides are smaller (12-19 amino acids) than the mu-, kappaM-, and psi-conotoxins (22-24 amino acids). One peptide, mr3a, was chemically synthesized in a biologically active form. Analysis of the disulfide bridges of a natural peptide tx3c from C. textile and synthetic peptide mr3a from C. marmoreus showed a novel pattern of disulfide connectivity, different from that previously established for the mu- and psi-conotoxins. Thus, these peptides belong to a new group of structurally and pharmacologically distinct conotoxins that are particularly prominent in the venoms of mollusc-hunting Conus species. Analysis of cDNA clones encoding the novel peptides as well as those encoding mu-, kappaM-, and psi-conotoxins revealed highly conserved amino acid residues in the precursor sequences; this conservation in both amino acid sequence and in the Cys pattern defines a gene superfamily, designated the M-conotoxin superfamily. The peptides characterized can be provisionally assigned to four distinct groups within the M-superfamily based on sequence similarity within and divergence between each group. A notable feature of the superfamily is that two distinct structural frameworks have been generated by changing the disulfide connectivity on an otherwise conserved Cys pattern.

Evaluation of the ELVIS plate method for the detection and typing of herpes simplex virus in clinical specimens

This study was conducted to assess the reliability of a commercial enzyme-linked viral inducible system (ELVIS) (Diagnostic Hybrids, Inc., Athens, OH) for rapid detection and typing of herpes simplex virus (HSV). Results using ELVIS were compared to those of shell vial culture (SVC) and HSV detection with monoclonal antibodies and an immunoperoxidase stain plus typing with MicroTrak direct fluorescent antibodies (Trinity Biotech PLC, Wicklow, Ireland). Specimens yielding discrepant HSV results were tested by polymerase chain reaction (PCR); those with discrepant typing results were stained with Simulfluor (Chemicon, Temecula, CA). Of the 206 samples tested, 144 were negative and 54 were HSV-positive by both methods (agreement, 96.1%). Five specimens were positive by ELVIS but negative by SVC; 3 of these were positive and 2 were negative by HSV PCR. Both of the latter were the result of mechanical problems early in the study. Three specimens were positive by SVC but negative by ELVIS; all 3 were positive by HSV PCR. After resolution of discrepancies, the sensitivity and specificity for detection of HSV were 95.0% and 100% for SVC, respectively, and 95.0% and 98.6% for ELVIS. Of the 46 HSV-positive samples that were typed, 26 were called type 2 and 18 were type 1 by both methods (agreement, 95.7%). The 2 specimens with discrepant results were called HSV-2 by SVC, staining with MicroTrak, and HSV-1 with ELVIS; both of these were type 2 when stained with the Simulfluor reagent. ELVIS is a reliable alternative to SVC for rapid detection and typing of HSV.

Serious bacterial infections in febrile infants 1 to 90 days old with and without viral infections

OBJECTIVE

The risk of serious bacterial infection (SBI) in febrile infants who are classified as low risk (LR) or high risk (HR) by the Rochester criteria has been established. LR infants average a 1.4% occurrence of SBI, whereas HR infants have an occurrence of 21%. The occurrence of SBI in Rochester LR or HR infants with confirmed viral infections is unknown. The objective of this study was to determine the occurrence of SBI in Rochester LR and HR infants with and without viral infections.

METHODS

All febrile infants who were 90 days or younger and evaluated at Primary Children's Medical Center between December 1996 and June 2002 were eligible. Infants were classified as Rochester LR or HR, and discharge diagnoses were collected. Viral testing for enteroviruses, respiratory viruses, rotavirus, and herpesvirus was performed as indicated by study protocol, clinical presentation, and season of the year. Results of all bacterial cultures were reviewed.

RESULTS

Of 1779 infants enrolled, 1385 (78%) had some form of viral diagnostic testing and 491 (35%) had 1 or more viruses identified. By the Rochester criteria, 456 (33%) infants were classified as LR and 922 (67%) infants as HR. For infants with viral infections, the occurrence of SBI was significantly lower than in infants without a viral infection (4.2% vs 12.3%). Rochester HR virus-positive (HR+) infants had significantly fewer bacterial infections than HR virus-negative (HR-) infants (5.5% vs 16.7%). When compared with HR- infants, HR+ infants were less likely to have bacteremia, urinary tract infection, or soft tissue infections, and HR+ infants had a similar occurrence of bacteremia as LR infants (0.92% vs 1.97%).

CONCLUSIONS

Febrile infants with confirmed viral infections are at lower risk for SBI than those in whom a viral infection is not identified. Viral diagnostic data can positively contribute to the management of febrile infants, especially those who are classified as HR.

The A-superfamily of Conotoxins

The generation of functional novelty in proteins encoded by a gene superfamily is seldom well documented. In this report, we define the A-conotoxin superfamily, which is widely expressed in venoms of the predatory cone snails (Conus), and show how gene products that diverge considerably in structure and function have arisen within the same superfamily. A cDNA clone encoding alpha-conotoxin GI, the first conotoxin characterized, provided initial data that identified the A-superfamily. Conotoxin precursors in the A-superfamily were identified from six Conus species: most (11/16) encoded alpha-conotoxins, but some (5/16) belong to a family of excitatory peptides, the kappaA-conotoxins that target voltage-gated ion channels. alpha-Conotoxins are two-disulfide-bridged nicotinic antagonists, 13-19 amino acids in length; kappaA-conotoxins are larger (31-36 amino acids) with three disulfide bridges. Purification and biochemical characterization of one peptide, kappaA-conotoxin MIVA is reported; five of the other predicted conotoxins were previously venom-purified. A comparative analysis of conotoxins purified from venom, and their precursors reveal novel post-translational processing, as well as mutational events leading to polymorphism. Patterns of sequence divergence and Cys codon usage define the major superfamily branches and suggest how these separate branches arose.

The augertoxins: biochemical characterization of venom components from the toxoglossate gastropod Terebra subulata

We describe the purification and biochemical characterization of three components from the venom of the toxoglossate gastropod Terebra subulata. The three polypeptide venom components, augertoxins s6a, s7a and s11a, are 40-41AA in length with 3-4 disulfide linkages. The arrangement of Cys residues is reminiscent of certain conopeptide superfamilies, but molecular cloning failed to show the highly conserved sequence features diagnostic of the conopeptide gene superfamily with a similar arrangement of Cys residues. One of the purified peptides, s7a, elicited an uncoordinated twisting syndrome when injected into the nematode Caenorhabditis elegans, but had no effect on mice. T. subulata belongs to the family Terebridae, one of four major groups of toxoglossate gastropods in the superfamily Conacea. The results reveal that some features of the augertoxins and conotoxins are generally similar, such as the organization of prepropeptide precursors and their proteolytic processing into mature toxins; however, Terebra may have evolved generally larger venom components that are less highly post-translationally modified. The results suggest that Conus peptide gene superfamilies probably do not extend to the Terebridae, suggesting that distinctive venom gene superfamilies may be expressed in each major division of Conacean gastropods.

Human herpesvirus 6 infection in febrile infants ninety days of age and younger

BACKGROUND

The importance of human herpesvirus 6 (HHV-6) as a pathogen in febrile infants </=90 days of age is unknown.

OBJECTIVE

To determine whether febrile infants 90 days of age and younger evaluated for sepsis have evidence of HHV-6 DNA in plasma or cerebrospinal fluid (CSF).

METHODS

Febrile infants </=90 days of age were tested for HHV-6 DNA using a real time quantitative fluorescent probe polymerase chain reaction assay.

RESULTS

Eighty samples from 47 infants were tested for HHV-6 DNA; 5 of 47 infants (10.6%) had HHV-6 DNA in plasma. In 2 of the 5 infants with HHV-6 DNA in plasma, HHV-6 DNA was also detected in the CSF. Both infants with evidence of HHV-6 DNA in plasma and CSF had HHV-6 Variant A infection. The quantity of HHV-6 DNA detected ranged from 70 to 169,000 DNA copies/ml. One infant with HHV-6 variant B infection had concomitant Escherichia coli bacteremia and urinary tract infection.

CONCLUSIONS

Approximately 10% of febrile infants </=90 days of age evaluated for sepsis had evidence of HHV-6 infection. HHV-6 Variant A and B infections were seen in these young infants. HHV-6 DNA was found in infants with and without another explanation for fever. Quantification of viral DNA may be important in determining the relevance of HHV-6 DNA in clinical specimens.

Use of heat labile UNG in an RT-PCR assay for enterovirus detection

A reverse transcription-polymerase chain reaction (RT-PCR) assay was developed to replace the Roche AMPLICOR Enterovirus Test used in our laboratory from 1996 to 1999. The new assay design was optimized to match or exceed the performance of the Roche AMPLICOR Enterovirus test kit with respect to analytical sensitivity and specificity, contamination control, ease of use and availability of reagents. This new assay uses a heat labile form of the enzyme uracil DNA glycosylase (UNG) for amplicon contamination control and an RT-PCR enzyme mixture, enabling a one tube/one step amplification. RNA preparation was undertaken using a commercial extraction kit. End detection was accomplished using a probe-capture enzyme immuno assay (EIA) plate format. This EV RT-PCR assay exceeds the performance of the Roche AMPLICOR Enterovirus assay in a direct comparison. The combined enzymological approach has potential application to a wide variety of assays requiring sensitive RNA detection and stringent contamination control, including those utilizing real time detection methods.

Performance characteristics of the COBAS Amplicor Hepatitis C Virus (HCV) Monitor, Version 2.0, International Unit assay and the National Genetics Institute HCV Superquant assay

The COBAS Amplicor Hepatitis C Virus (HCV) Monitor assay, version 2.0, which reports in international units per milliliter, was compared to the assay reported in copies per milliliter by analyzing dilution series and clinical plasma samples by both methods. In addition, the Amplicor international unit assay was compared to the National Genetics Institute HCV Superquant assay. The dilution series ranged from <100 to 5,000,000 HCV RNA copies/ml and consisted of 32 points, assayed in triplicate in each assay. Thirty clinical samples ranging from 1,000 to 1,000,000 HCV RNA copies/ml were assayed in duplicate. Deming regression analysis comparing the Amplicor HCV RNA international units-per-milliliter and copies-per-milliliter assays was calculated as follows: (Amplicor international units per milliliter) = 1.030(Amplicor copies per milliliter) - 0.392; R(2) = 0.981; n = 28; S(y/x) (standard error of the estimate) = 0.129. The linearity of the Amplicor international units-per-milliliter assay was as follows: observed = 0.886(expected) + 0.437; R(2) = 0.983; n = 30. The linearity of the Superquant assay was as follows: observed= 0.918 (expected) + 0.436; R(2) = 0.986; n = 32. Deming regression analysis comparing the Amplicor and Superquant assays was calculated as follows: Superquant = 1.066(Amplicor) - 0.0197; R(2) = 0.908; S(y/x) = 0.308; n = 28. The Amplicor and Superquant assays were linear through the range of 600 to 600,000 IU of HCV RNA/ml and approximately 300 to 5,000,000 HCV RNA copies/ml, respectively. The narrow range of the Amplicor assay means that some samples will require dilution and retesting for accurate quantification above 600,000 IU of HCV RNA/ml. The Amplicor and Superquant assays agreed well within the range of 600 to 600,000 IU of HCV RNA/ml (approximately 1,000 to approximately 1,000,000 HCV RNA copies/ml). Overall, the Amplicor and Superquant assays agree well, and results obtained in one assay could be expected to compare well with results from the other when reported in copies per milliliter.

Identification of Mycobacterium spp. by using a commercial 16S ribosomal DNA sequencing kit and additional sequencing libraries

Current methods for identification of Mycobacterium spp. rely upon time-consuming phenotypic tests, mycolic acid analysis, and narrow-spectrum nucleic acid probes. Newer approaches include PCR and sequencing technologies. We evaluated the MicroSeq 500 16S ribosomal DNA (rDNA) bacterial sequencing kit (Applied Biosystems, Foster City, Calif.) for its ability to identify Mycobacterium isolates. The kit is based on PCR and sequencing of the first 500 bp of the bacterial rRNA gene. One hundred nineteen mycobacterial isolates (94 clinical isolates and 25 reference strains) were identified using traditional phenotypic methods and the MicroSeq system in conjunction with separate databases. The sequencing system gave 87% (104 of 119) concordant results when compared with traditional phenotypic methods. An independent laboratory using a separate database analyzed the sequences of the 15 discordant samples and confirmed the results. The use of 16S rDNA sequencing technology for identification of Mycobacterium spp. provides more rapid and more accurate characterization than do phenotypic methods. The MicroSeq 500 system simplifies the sequencing process but, in its present form, requires use of additional databases such as the Ribosomal Differentiation of Medical Microorganisms (RIDOM) to precisely identify subtypes of type strains and species not currently in the MicroSeq library.

Human immunodeficiency virus type 1 drug resistance testing: a comparison of three sequence-based methods

The use of genotypic assays for determining drug resistance in human immunodeficiency virus (HIV) type 1 (HIV-1)-infected patients is increasing. These tests lack standardization and validation. The aim of this study was to evaluate several tests used for the determination of HIV-1 drug resistance. Two genotypic tests, the Visible Genetics TruGene HIV-1 Genotyping Kit and the Applied Biosystems HIV Genotyping System, were compared using 22 clinical samples. Genotyping results were also obtained from an independent reference laboratory. The Visible Genetics and Applied Biosystems genotyping tests identified similar mutations when differences in the drug databases and reference strains were taken into account, and 19 of 21 samples were equivalent. The concordance between the two assays was 99% (249 of 252 mutation sites). Mutations identified by the reference laboratory varied the most among those identified by the three genotypic tests, possibly because of differences in the databases. The concordance of the reference laboratory results with the results of the other two assays was 80% (201 of 252). Samples with 500 to 750 HIV RNA copies/ml could be sequenced by the Visible Genetics and Applied Biosystems assays using 1 ml of input. The Visible Genetics and Applied Biosystems assays both generated an accurate sequence. However, the throughput of the Visible Genetics assay is more limited and may require additional instruments. The two assays differ technically but are similar in overall complexity. Data analysis in the two assays is straightforward, but only the reports provided by Visible Genetics contain information relating mutations to drug resistance. HIV drug resistance genotyping by sequencing is a complex technology which presents a challenge for analysis, interpretation, and reporting.

Evaluation of the Prodesse Hexaplex multiplex PCR assay for direct detection of seven respiratory viruses in clinical specimens

We evaluated the Hexaplex assay (Prodesse, Waukesha, WI) for the detection of 7 respiratory viruses (influenza A and B, parainfluenza 1-3, and respiratory syncytial virus [RSV] A and B). The Hexaplex assay was performed on 300 respiratory samples during the 1999-2000 respiratory virus season. Results of this assay were compared with shell vial cell culture and/or direct fluorescent antibody stain. The overall sensitivity and specificity of the assay were 96.6% and 94.1%, respectively. The respective sensitivity and specificity of the Hexaplex assay for detection of specific virus groups were as follows: influenza A, 98.6% and 97.8%; influenza B, 100% and 100%; and for parainfluenza viruses (1-3), 100% and 99.1%. The assay did not perform as well with patients infected with RSV: sensitivity and specificity were 91.0% and 98.6%, respectively. There are 2 major drawbacks to this assay: it is technically demanding (3-4 hours hands-on time), and it is expensive ($80-$90 direct cost). Nevertheless, because of the excellent sensitivity and specificity, the Hexaplex assay may be valuable in the diagnosis of respiratory viral infections in immunocompromised patients.

Performance characteristics of the COBAS AMPLICOR hepatitis C virus MONITOR Test, version 2.0

We evaluated the performance characteristics of the COBAS AMPLICOR Hepatitis C Virus (HCV) MONITOR Test, version 2.0. Dilution studies using patient specimens demonstrated a lower limit of detection of 1,000 copies per milliliter. The assay was linear from 1,000 to 1 million HCV RNA copies per milliliter. Within-run precision and between-run precision were acceptable (approximately 0.100 and 0.14 SD for log10 [copies per milliliter]). A comparison of this version of the test (y), with the manual AMPLICOR HCV MONITOR Test, version 1.0 (x), yielded the following Deming regression equation: y = 1.004(+/- 0.04)x + 0.654(+/- 0.22); Sy/x¿D = 0.336; n = 92; r2 = 0.846; r = 0.920. Further comparison of the COBAS version 2.0 assay (x) with the QUANTIPLEX HCV bDNA Test (y) yielded the following Deming regression equation: y = 0.943 (+/- 0.130)x + 0.473 (+/- 0.717); Sy/x¿D = 0.194; n = 26; r2 = 0.600; r = 0.774. Version 2.0 detected the spectrum of HCV genotypes better than version 1.0.

Detection of Legionella species in respiratory specimens using PCR with sequencing confirmation

Legionella spp. are a common cause of community-acquired respiratory tract infections and an occasional cause of nosocomial pneumonia. A PCR method for the detection of legionellae in respiratory samples was evaluated and was compared to culture. The procedure can be performed in 6 to 8 h with a commercially available DNA extraction kit (Qiagen, Valencia, Calif.) and by PCR with gel detection. PCR is performed with primers previously determined to amplify a 386-bp product within the 16S rRNA gene of Legionella pneumophila. We can specifically detect the clinically significant Legionella species including L. pneumophila, L. micdadei, L. longbeachae, L. bozemanii, L. feeleii, and L. dumoffii. The assay detects 10 fg (approximately two organisms) of legionella DNA in each PCR. Of 212 clinical specimens examined by culture, 100% of the culture-positive samples (31 of 31) were positive by this assay. By gel detection of amplification products, 12 of 181 culture-negative samples were positive for Legionella species by PCR, resulting in 93% specificity. Four of the 12 samples with discrepant results (culture negative, PCR positive) were confirmed to be positive for Legionella species by sequencing of the amplicons. The legionella-specific PCR assay that is described demonstrates high sensitivity and high specificity for routine detection of legionellae in respiratory samples.

Evaluation of a PCR probe capture assay for the detection of Toxoplasma gondii. Incorporation of uracil N-glycosylase for contamination control

Toxoplasma gondii is a cyst-forming parasite of clinical relevance in humans primarily because of the neurologic abnormalities it can cause. In some clinical circumstances, it is desirable to detect the pathogen directly. We modified a commercially available Toxoplasma polymerase chain reaction (PCR) probe capture assay by incorporating uracil N-glycosylase (UNG) to prevent carryover amplicon contamination. In addition, UNG inactivation and DNA denaturation were accomplished chemically to simplify the DNA hybridization to the capture probe. The incorporation of UNG effectively eliminated carryover contamination; the probe capture assay showed a log increase in detection sensitivity compared with standard agarose gel electrophoresis. To assess sensitivity and possible inhibition of amplification, different sample types were spiked with Toxoplasma organisms. After DNA extraction and PCR amplification, a sensitivity of 2 tachyzoites for the assay was determined in buffered saline, cerebrospinal fluid (CSF), serum, and amniotic fluid; 20 tachyzoites for whole blood; and 200 tachyzoites for brain tissue. An additional 20 human serum and CSF samples submitted for Toxoplasma serologic testing were run by the PCR method. Of these, only an IgM-positive CSF sample was PCR positive. The Toxoplasma PCR probe capture assay showed good sensitivity and was not substantially inhibited by several different clinically relevant samples.

Speciation of cone snails and interspecific hyperdivergence of their venom peptides. Potential evolutionary significance of introns

All 500 species of cone snails (Conus) are venomous predators. From a biochemical/genetic perspective, differences among Conus species may be based on the 50-200 different peptides in the venom of each species. Venom is used for prey capture as well as for interactions with predators and competitors. The venom of every species has its own distinct complement of peptides. Some of the interspecific divergence observed in venom peptides can be explained by differential expression of venom peptide superfamilies in different species and of peptide superfamily branching in various Conus lineages into pharmacologic groups with different targeting specificity. However, the striking interspecific divergence of peptide sequences is the dominant factor in the differences observed between venoms. The small venom peptides (typically 10-35 amino acids in length) are processed from larger prepropeptide precursors (ca. 100 amino acids). If interspecific comparisons are made between homologous prepropeptides, the three different regions of a Conus peptide precursor (signal sequence, pro-region, mature peptide) are found to have diverged at remarkably different rates. Analysis of synonymous and nonsynonymous substitution rates for the different segments of a prepropeptide suggests that mutation frequency varies by over an order of magnitude across the segments, with the mature toxin region undergoing the highest rate. The three sections of the prepropeptide which exhibit apparently different mutation rates are separated by introns. This striking segment-specific rate of divergence of Conus prepropeptides suggests a role for introns in evolution: exons separated by introns have the potential to evolve very different mutation rates. Plausible mechanisms that could underlie differing mutational frequency in the different exons of a gene are discussed.

Evaluation of the ultrasensitive Roche Amplicor HIV-1 monitor assay for quantitation of human immunodeficiency virus type 1 RNA

The ultrasensitive Amplicor HIV-1 Monitor test (Roche Diagnostic Systems) was evaluated for precision, linearity, and sensitivity and was compared to the standard Amplicor assay. The ultrasensitive assay reliably quantified samples in the range from 50 to 50,000 human immunodeficiency virus type 1 RNA copies/ml with acceptable correlation with the standard Amplicor test.

A polymerase chain reaction-based epidemiologic investigation of the incidence of nonpolio enteroviral infections in febrile and afebrile infants 90 days and younger

OBJECTIVE

Enteroviruses are important pathogens in infants, but their true contribution to febrile illness in infants </=90 days old is unknown. The purpose of this study was to use the polymerase chain reaction (PCR) for diagnosis of enteroviral (EV) infection in febrile and afebrile infants </=90 days of age to improve the understanding of the epidemiology of EV infection in this population.

METHODS

Patients included all unimmunized, febrile infants </=90 days of age admitted to Primary Children's Medical Center (Salt Lake City, UT) for sepsis evaluation from December 1996 to December 1997. Blood, urine, cerebrospinal fluid, and throat swabs were tested for enteroviruses using a PCR assay (Roche Molecular Systems, Branchburg, NJ). Alternate PCR assays separated polio and nonpolio enteroviruses. Results of bacterial cultures, outcome, and hospital charges were obtained. Blood from afebrile, control infants </=90 days old was tested for enteroviruses.

RESULTS

A total of 345 febrile infants were enrolled; 89 (25.8%) were positive for enterovirus. The incidence of EV infection ranged from 3.2% in January to 50% in August and October. Five EV-positive, febrile infants (5.6%) had concomitant urinary tract infections, and 1 (1. 1%) had concomitant bacteremia. Infants with confirmed EV infection were significantly less likely to have bacterial infection than those who were EV-negative. All infants infected with an enterovirus recovered. Average length of stay was 3 days, average charges were nearly $4500. Eighty-six afebrile, control infants were enrolled; 6 (6.9%) were positive for enterovirus; 3 had received oral polio vaccine.

CONCLUSIONS

Nonpolio EV infections commonly cause fever in infants </=90 days of age. Rates of EV positivity are low in afebrile, unimmunized infants. The use of PCR to identify febrile infants with nonpolio EV infections may decrease length of hospital stay, unnecessary antibiotic administration, and charges.

An O-glycosylated neuroexcitatory conus peptide

We purified and characterized a novel peptide from the venom of the fish-hunting cone snail Conus striatus that inhibits voltage-gated K+ channels. The peptide, kappaA-conotoxin SIVA, causes characteristic spastic paralytic symptoms when injected into fish, and in frog nerve-muscle preparations exposed to the toxin, repetitive action potentials are seen in response to a single stimulus applied to the motor nerve. Other electrophysiological tests on diverse preparations provide evidence that is consistent with the peptide blocking K+ channels. The peptide has three disulfide bonds; the locations of Cys residues indicate that the spastic peptide may be the first and defining member of a new family of Conus peptides, the kappaA-conotoxins, which are structurally related to, but pharmacologically distinct from, the alphaA-conotoxins. This 30 AA tricyclic toxin has several characteristics not previously observed in Conus peptides. In addition to the distinctive biological and physiological activity, a novel biochemical feature is the unusually long linear N-terminal tail (11 residues) which contains one O-glycosylated serine at position 7. This is the first evidence for O-glycosylation as a posttranslational modification in a biologically active Conus peptide.

Enhancement of the AMPLICOR enterovirus PCR test with a coprecipitant

The incorporation of a commercially available coprecipitant into the AMPLICOR enterovirus PCR test specimen preparation enhanced the sensitivity and reproducibility of this assay. Fifty-five previously tested archived cerebrospinal fluids (CSF) specimens were tested in a blind study in duplicate with and without Pellet Paint coprecipitant (Novagen, Inc., Madison, Wis.). Of these specimens, 26 had previously been determined to be positive and 29 had previously been determined to be negative. All previously positive CSF specimens were positive when Pellet Paint was used and only 18 were positive without Pellet Paint. No previously negative specimens were positive on repeat testing with or without Pellet Paint. The background signal was not affected by the addition of Pellet Paint. These data support the utility of a coprecipitant in minimizing false-negative results.

mu-Conotoxin PIIIA, a new peptide for discriminating among tetrodotoxin-sensitive Na channel subtypes

We report the characterization of a new sodium channel blocker, mu-conotoxin PIIIA(mu-PIIIA). The peptide has been synthesized chemically and its disulfide bridging pattern determined. The structure of the new peptide is: [sequence: see text] where Z = pyroglutamate and O = 4-trans-hydroxyproline. We demonstrate that Arginine-14 (Arg14) is a key residue; substitution by alanine significantly decreases affinity and results in a toxin unable to block channel conductance completely. Thus, like all toxins that block at Site I, mu-PIIIA has a critical guanidinium group. This peptide is of exceptional interest because, unlike the previously characterized mu-conotoxin GIIIA (mu-GIIIA), it irreversibly blocks amphibian muscle Na channels, providing a useful tool for synaptic electrophysiology. Furthermore, the discovery of mu-PIIIA permits the resolution of tetrodotoxin-sensitive sodium channels into three categories: (1) sensitive to mu-PIIIA and mu-conotoxin GIIIA, (2) sensitive to mu-PIIIA but not to mu-GIIIA, and (3) resistant to mu-PIIIA and mu-GIIIA (examples in each category are skeletal muscle, rat brain Type II, and many mammalian CNS subtypes, respectively). Thus, mu-conotoxin PIIIA provides a key for further discriminating pharmacologically among different sodium channel subtypes.

Conantokin-G precursor and its role in gamma-carboxylation by a vitamin K-dependent carboxylase from a Conus snail

Conantokin-G isolated from the marine snail Conus geographus is a 17-amino acid gamma-carboxyglutamate (Gla)-containing peptide that inhibits the N-methyl-D-aspartate receptor. We describe the cloning and sequence of conantokin-G cDNA and the possible role of the propeptide sequence. The cDNA encodes a 100amino acid peptide. The N-terminal 80 amino acids constitute the prepro-sequence, and the mature peptide is derived from the remaining C-terminal residues after proteolysis, C-terminal amidation, and a unique post-translational modification, gamma-carboxylation of glutamate residues to Gla. Mature conantokin-G peptide containing Glu residues (E.Con-G) in place of Gla is a poor substrate for the vitamin K-dependent gamma-glutamyl carboxylase (apparent Km = 3.4 mM). Using peptides corresponding to different segments of the propeptide we investigated a potential role for the propeptide sequences in gamma-carboxylation. Propeptide segment -20 to -1 covalently linked to E.Con-G or the synthetic pentapeptide FLEEL increased their apparent affinities 2 orders of magnitude. These substrates are not efficiently carboxylated by the bovine microsomal gamma-glutamyl carboxylase, suggesting differences in specificities between the Conus and the mammalian enzyme. However, the role of propeptide in enhancing the efficiency of carboxylation is maintained.

kappa-Conotoxin PVIIA is a peptide inhibiting the shaker K+ channel

kappa-Conotoxin PVIIA (kappa-PVIIA), a 27-amino acid toxin from Conus purpurascens venom that inhibits the Shaker potassium channel, was chemically synthesized in a biologically active form. The disulfide connectivity of the peptide was determined. kappa-Conotoxin PVIIA has the following structure. This is the first Conus peptide known to target K+ channels. [structure: see text] Although the Shaker K+ channel is sensitive to kappa-PVIIA, the rat brain Kv1.1 subtype is resistant. Chimeras between Shaker and the Kv1.1 K+ channels were constructed and expressed in Xenopus oocytes. Only channels containing the putative pore-forming region between the fifth and sixth transmembrane domains of Shaker retained toxin sensitivity, indicating that the toxin target site is in this region of the channel. Evidence is presented that kappa-PVIIA interacts with the external tetraethyl-ammonium binding site on the Shaker channel. Although both kappa-PVIIA and charybdotoxin inhibit the Shaker channel, they must interact differently. The F425G Shaker mutation increases charybdotoxin affinity by 3 orders of magnitude but abolishes kappa-PVIIA sensitivity. The precursor sequence of kappa-PVIIA was deduced from a cDNA clone, revealing a prepropeptide comprising 72 amino acids. The N-terminal region of the kappa-PVIIA prepropeptide exhibits striking homology to the omega-, muO-, and delta-conotoxins. Thus, at least four pharmacologically distinct superfamilies of Conus peptides belong to the same "O" superfamily, with the omega- and kappa-conotoxins forming one branch, and the delta- and muO-conotoxins forming a second major branch.

A noncompetitive peptide inhibitor of the nicotinic acetylcholine receptor from Conus purpurascens venom

A paralytic peptide, psi-conotoxin Piiie has been purified and characterized from Conus purpurascens venom. Electrophysiological studies indicate that the peptide inhibits the nicotinic acetylcholine receptor (nAChR). However, the peptide does not block the binding of alpha-bungarotoxin, a competitive nAChR antagonist. Thus, psi-conotoxin Piiie appears to inhibit the receptor at a site other than the acetylcholine-binding site. As ascertained by sequence analysis, mass spectrometry, and chemical synthesis, the peptide has the following covalent structure: HOOCCLYGKCRRYOGCSSASCCQR* (O = 4-trans hydroxyproline; * indicates an amidated C-terminus). The disulfide connectivity of the toxin is unrelated to the alpha- or the alphaA-conotoxins, the Conus peptide families that are competitive inhibitors of the nAChR, but shows homology to the mu-conotoxins (which are Na+ channel blockers).

A role for C5 and C5a-ase in the acute neutrophil response to group B streptococcal infections

Congenic C5-deficient and C5-sufficient mice were infected with group B streptococci (GBS) to determine if the polymorphonuclear leukocyte (PMNL) chemoattractant C5a contributes to PMNL recruitment in GBS infection and if GBS C5a-ase reduces C5a-induced PMNL recruitment in vivo. PMNL accumulation was greater in the peritoneum and air spaces of C5-sufficient mice than in C5-deficient mice. Administration of human C5 to C5-deficient mice caused a significant increase in PMNL recruitment following infection with C5a-ase-negative GBS. GBS C5a-ase did not reduce PMNL accumulation in C5-sufficient mice but reduced PMNL recruitment in C5-deficient mice reconstituted with human C5. These data indicate that C5a is important for rapid PMNL recruitment to sites of GBS infection and that GBS C5a-ase inactivates human, but not murine, C5a in vivo. Reduction of the acute inflammatory response by C5a-ase likely contributes to GBS virulence in human neonates.