bluuebunny/crossref_metadata_2025_split huggingface dataset:
A-250 Rapid molecular Identification of Herpes Simplex, Varicella-zoster, and Enteroviruses from Cerebrospinal Fluid
Authors: Bialas J , Joki L , Hermanowski M , Brea-Sellheim K , Leibhan H , Jacobs M , Lång M , Vainio J , Martelin J 
Published: September 2023

Abstract

Background
Accurate and efficient molecular testing of viral meningitis/encephalitis is crucial for proper patient care. Here we describe the clinical evaluation of the GenomEra® HSV-1/2, VZV + EV Assay Kit (Uniogen, Finland) allowing simultaneous detection of four key viruses responsible for causing meningitis/encephalitis, namely HSV-1 and HSV-2, VZV, and enteroviruses.

Methods
The study was carried out at three European institutions in 2022, with a total of 193 frozen, anonymized leftover cerebrospinal fluid (CSF) specimens analyzed retrospectively. For the GenomEra HSV-1/2, VZV + EV Assay Kit, 50 µL of CSF was mixed with lysis buffer in a 1:1 ratio, allowed to incubate for 1 min at room temperature, and then filtered by a 1-min centrifugation through an Extraction Column utilizing size-exclusion chromatography. A 35-µL sample of the flow-through was applied into the Test Chip and analyzed using the GenomEra CDX System. The cotemporally performed comparison tests included the FilmArray Meningitis/Encephalitis (ME) panel (bioMérieux), Xpert® EV Assay (Cepheid), artus VZV assay (Qiagen), and a well-established, validated non-commercial real-time RT-PCR assay for the detection of HSV-1/2, VZV, and EV.

Results
The GenomEra HSV-1/2, VZV + EV Assay Kit produced results in 70 min with a sensitivity and specificity of 92.2% (95% CI: 82.7–97.4%) and 99.9% (95% CI: 99.2–100%), respectively, as compared to the reference tests. Of the discordant results, five tested negative with the GenomEra assay, whereas the reference tests produced low positive results (Ct values ≥ 35). In addition, one specimen yielded a positive signal for VZV while remaining negative with the reference tests.

Conclusion
The GenomEra HSV-1/2, VZV + EV Assay Kit showed a high overall specificity and a high level of sensitivity particularly for herpes simplex and varicella-zoster viruses. For enteroviruses, while the specificity reached 100%, the sensitivity was not as high as with the reference methods. The high clinical performance, together with the simple sample preparation protocol and short turnaround time make the GenomEra assay a competitive molecular test especially for small and medium-sized laboratories that may not have a specialist in molecular biology. In addition, the GenomEra assay only requires a small amount of sample, conserving the valuable specimens for additional testing.
A-252 Differentiation of SARS-CoV-2, Influenza A and B, and Respiratory Syncytial Virus Using a Single Swab: A Clinical Performance Evaluation of the BD MAX System Multiplex PCR Assay
Authors: Faron M , Ledeboer N , Van Der Pol B , Davis T , Lockamy E , Paradis S , Andrews J 
Published: September 2023

Abstract

Background
Some shared clinical features of SARS-CoV-2, influenza (flu), and respiratory syncytial virus (RSV) infection often pose a diagnostic challenge for clinicians. In that context, the use of molecular diagnostic systems multiplex assays, using a nasopharyngeal or nasal swab, facilitates the detection of the causing virus by differentiating between the RNA of each disease. Our study evaluated the clinical accuracy of one such multiplex PCR assay, the BD Respiratory Viral Panel for BD MAX™ System (BD MAX RVP).

Methods
Symptomatic patients that had a nasopharyngeal and nasal specimen prospectively collected from 6 geographical locations in the US were enrolled in the study between January and April 2022 along with nasopharyngeal swabs retrospectively collected between December 2019 and January 2022. All specimen testing was performed using the BD MAX System. Hologic® Flu A/B/RSV assay on Panther Fusion™ System was the comparator for flu A, flu B, and RSV while a composite of two out of three assays authorized under FDA Emergency Use Authorization (Roche cobas® SARS-CoV-2 on cobas® 6800 System, Hologic® Aptima® SARS-CoV-2 on Panther® System, and Quidel Lyra® SARS-CoV-2 on Applied Biosystems® 7500 Fast Dx) was used as comparator for SARS-CoV-2. Positive and negative percentage agreements (PPA and NPA, respectively) were calculated to determine performance. Reproducibility and precision assessments were also performed as part of the study.

Results
Tested specimens included 252 nasopharyngeal and 254 nasal swabs, prospectively collected, and 240 retrospectively acquired nasopharyngeal specimens. For prospectively collected SARS-CoV-2 nasopharyngeal specimens, PPA of 98.8% (95% CI 93.6, 99.8) and NPA of 98.2% (95% CI 94.9, 99.4) were observed while for flu A, PPA was 100% (95% CI 61.0, 100) and NPA 99.6% (95% CI 97.7, 99.9). PPA and NPA for prospectively collected SARS-CoV-2 anterior nasal specimens were 98.8% (95% CI 93.3, 99.8) and 98.3 (95% CI 95.1, 99.4), respectively. For flu A, PPA of 100% (95% CI 61.0, 100) and NPA of 99.6% (95% CI 97.8, 99.9) were observed. Lack of enrolled positive patients with flu B or RSV precluded the PPA calculation for those viruses. However, NPA for both flu B and RSV was 100% for the two specimen types. In retrospectively obtained nasopharyngeal specimens, PPA was 100% (95% CI 93.7, 100) for flu A, 100% (95% CI 93.8, 100) for flu B, and 98.4% (95% CI 91.5, 99.7) for RSV while NPA was 98.9% (95% CI 96.1, 99.7) for flu A, 98.9% (95% CI 96.1, 99.7) for flu B, and 100% (95% CI 97.9, 100) for RSV.

Conclusion
The BD MAX RVP assay showed a strong clinical performance in detecting and differentiating between the RNA of SARS-CoV-2, flu A and B, and RSV.
A-259 Detecting Human RNase P Gene Prevents False-Negative of SARS-CoV-2
Authors: Chuang F 
Published: September 2023

Abstract

Background
Real-time Reverse transcriptase—polymerase chain reaction (RT-PCR) is a regular technique for detecting SARS-CoV-2 infection. Human RNase P sequence is using as internal control for PCR assay usually. This article discusses the correlation between SARS-CoV-2 PCR result and human RNase P gene result.

Methods
Nasopharyngeal swabs were collected from two patients within three consecutive days. We detected for SARS-CoV-2 target gene and human RNase P gene by using real-time RT-PCR assay, which SARS-CoV-2 target gene includes E gene, Rarp gene and N gene . And the threshold cycle values (Ct) were determined by cobas® z 480. Evaluate the results of SARS-CoV-2 and RNase P gene detection. All samples were also analysis for SARS-CoV-2 infection in Taiwan Centers for Disease Control.

Results
Results of SARS-CoV-2 PCR assay were consistent in both laboratories. SARS-CoV-2 target genes were detected from specimens of both patients on day1. Ct values of E gene were 29.63 and 29.50. Ct values of Rdrp gene were 32.23 and 32.50. Ct values of N gene were 33.09 and 32.68. Ct values of RNase P gene were 21.21 and 21.22. On day 2 and 3, all specimens were negative detected for SARS-CoV-2 PCR. Ct values of RNase P gene were 25.73 and 26.16 on day 2 and 29.82 and 30.28 on day 3.

Conclusion
The Ct values of human RNase P gene detection can be correlated with the numbers of collected cells. Comparing the results of two patients for three consecutive days, the Ct value of human RNase P gene related to SARS-CoV-2 PCR result. Collection technique can be a factor to affect Ct value of human RNase P gene detection. Develop acceptance range for Ct value of RNase P gene detection can be a quality standard for sample collection to prevent false-negative of SARS-CoV-2.
A-307 Spread Dynamic of SARS-CoV-2 Variants and Related Alterations in Transmission Rates: A National Scale Study
Authors: Silva J D , de Lima A B , Alvim L B , Malta F S , Mendonça C P , Fonseca P L , de Souza R P , de Aguiar R S , Zauli D A 
Published: September 2023

Abstract

Background
In late 2019, the world was surprised by the new coronavirus (SARS-CoV-2), responsible for the COVID-19 pandemic and the ability to develop and share knowledge about SARS-CoV-2 was essential in combat of the pandemic. Genomic surveillance has played a fundamental role in identifying new mutations, detecting emerging variants, and monitoring viral evolution. Although next-generation sequencing (NGS) remains the gold standard for the identification of new variants, this technology is still restricted due to the high cost. Thus, the use of accessible methods for SARS-CoV-2 monitoring is necessary. This study aimed to collect and share monitoring data of COVID-19 in Brazil and to evaluate the dynamics of SARS-CoV-2 variants during the two periods of changes in the epidemiological scenario (second and third pandemic waves) and the transmissibility rates among circulating VOCs.

Methods
The study evaluated 27 003 samples from all federative units in Brazil between April/2021 and January/2022. Specific primers and probes were used for the mutations K417T/N, L452R, E484K/Q, N501Y, P681R (TaqMan SARS-CoV-2 Mutation Panel), and the SGTF (S-gene target failure) by the TaqPath COVID-19 CE-IVD RT-PCR Kit according to the frequencies of the Gamma, Delta, and Omicron VOCs in the evaluated time. Samples showing an unexpected mutation profile in RT-qPCR genotyping were submitted to NGS. Data for viral targets of about 227 661 positive samples were collected to assess the period of predominance of each VOC as an inference of transmissibility potential.

Results
Samples were collected in all 27 Brazilian federative units. The replacement of the Gamma by Delta variant occurred in about 5 months, between June and September 2021, when the Delta variant reached 100% of infections. The transition of predominance among the Delta to Omicron variant was only 2 months, demonstrated by the progressive increase of Omicron in November (3.4%), December (67.5%), and January (97%), accompanied by the consequent growth of COVID-19 positive cases in the country. These results reinforce the higher transmissibility of Omicron compared to other variants identified in Brazil. The adopted strategy was able to identify the Gamma, Delta, and Omicron VOCs as well as the presence of other variants in 99.2% of the samples. Only 0.8% of the samples were not characterized and it was submitted to NGS.

Conclusion
We described a methodology that was able to effectively follow the fast establishment of Omicron VOC related to its higher transmission rates and genomic mutations that explain the highest peak of COVID-19 in our country. This study comprises the largest national-scale of genomic surveillance of SARS-CoV-2, providing information about the virus spread in Brazil.
A-338 TSH Reference Range in the First Trimester in a Iodine Sufficient Population of Pregnant Women Attended by the Public Health System in Curitiba South of Brazil
Authors: Paula R F , Felchner P C , Telles T M , Júnior C O , Valdati K D , Panizza T M , Moraes T P , Carlos G B 
Published: September 2023

Abstract

Background
Thyroid diseases are common among women of reproductive age, and the serum concentration of thyroid-stimulating hormone (TSH) is the most used index to assess thyroid function during pregnancy. Changes in thyroid function during pregnancy can have a clinical impact on a woman's health and pregnancy outcome, as well as interfere with fetal health and child development. An adequate thyroid function is essential for normal intrauterine development. When comparing the levels of TSH between pregnant and non-pregnant women, TSH levels are lower in pregnancy, mainly in the first trimester, with gradual increase during pregnancy. Although some guidelines propose fixed TSH reference values in pregnancy according to the gestational trimester, the main recommendation is to carry out a study of their local population due to the significant variation in TSH reference range levels in different populations and different assays. Therefore, it is necessary to determine values of a reference interval for TSH for the local population of pregnant women. This study aims to determine the normal reference range of TSH in the first trimester of gestation in the public health system pregnant women from Curitiba.

Methods
This is an ongoing prospective cohort study, with the population sample from the pregnant women using the public health system, with age &gt;18 years old in Curitiba, South of Brazil. 383 pregnant women were invited to participate. After evaluate the exclusion criteria (gestational age more than 13 weeks, twin pregnancy, thyroid disease, iodine ingestion, identification of the samples in the laboratory), 225 pregnant women had the TSH measured by chemiluminescent immunoassay on Atellica IM Analyzer (Siemens Healthineers), as well as the TPO-ab presence, FreeT4 and Total T4. The 2.5, 50 end 97,5 TSH percentiles were estimated for the normal pregnant population.

Results
The mean gestational age was 8,6 weeks (standard deviation 2.33). From 225 pregnant women, 22 (9.8%) had TPO-ab positive. The 2.5 and 97.5 percentiles of TSH were 0.12 and 5.28 μIU/mL after using de exclusion criteria. The populational iodine status was sufficient. In the TPO-ab positive population was found a higher level of TSH. The proportion of TPO-ab positive was significantly higher in the population with TSH &gt;2.5 μIU/mL.

Conclusions
This preliminary data shows the TSH reference range with levels higher than other regions, reinforcing to do not use fixed values of TSH from other populations to evaluate the thyroid function in pregnancy. Comparing to the laboratory reference for non-pregnant adult (0.48 to 5.60 μIU/mL), the recommended reduction of 0.5 μIU/mL on upper limit and 0.4 μIU/mL on the lower limit found similar values to our findings.
A-363 Evaluating the Performance of Emerging STI Point of Care Assays Using Novel, Room Temperature Stable CT/NG/TV/MG Positive Swab Quality Control Materials
Authors: Rivers S , Zhelev P , Thakur M , Alagic A , Li J , Randall C , Luscher M , Hughes K 
Published: September 2023

Abstract

Background
The emergence of Point of Care tests that detect Sexually Transmitted Infections (STIs) is critical for screening and diagnostic programs in low-resource settings. Point of Care tests that are designed to simultaneously detect Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG), Trichomonas vaginalis (TV), and Mycoplasma genitalium (MG) promote rapid diagnosis and early treatment of the most common etiological agents causing STIs. Along with the roll-out and use of these tests, there is a growing need for complex multi-analyte quality control materials that are stable at room temperature and challenge test performance by identifying result deviations, lot-to-lot variability, and routine laboratory workflow errors. Microbix developed a whole-workflow multiplex quality control desiccated on a Copan FLOQSwab® that is stable at 2–30°C and contains inactivated whole-genome target pathogens. The objective of this study is to evaluate sample performance with multiple Point of Care diagnostic platforms that are currently in development and commercial IVD tests that are routinely used in the laboratory.

Methods
Microbix designed an inactivated STI whole-workflow control that contains whole-genome CT, NG, TV, MG, and human cells to satisfy sample adequacy control requirements. The formulation is desiccated on a Copan FLOQSwab® to mimic patient specimen formats and ensure sample compatibility with all assay workflows and elution buffers. Sample performance was evaluated with Cepheid Xpert® CT/NG assay, Cepheid Xpert® TV assay, Abbott Alinity m STI assay, BD MAX™ CT/GC/TV assay, Seegene Novaplex™ CT/NG/TV/MG assay, EliTechGroup STI PLUS ELITe MGB®Kit, and commercial Point of Care assays currently in development.

Results
The STI positive swab formulation demonstrated acceptable performance when tested with various nucleic acid amplification tests that detect CT, NG, TV, and MG targets. The formulations also behaved as useful quality management tools by highlighting design limitations for commercial Point of Care assays that are currently in development.

Conclusion
CT/NG/TV/MG whole-genome multiplex formulation desiccated on a Copan FLOQSwab® is an advantageous prospective quality control material that is stable at room temperature and supports the clinical use and accuracy of emerging STI assays, including the most challenging Point of Care test formats. The formulations showed acceptable performance on multiple platforms, demonstrating excellent commutability. Additionally, the dry swab format offers great practicality for monitoring assay performance in low-resource settings.
A-379 Frequency of Reassignment of Blood Gas Sample Source at a Large Tertiary Care Hospital
Authors: Kim R , Altura M , Gantt K , Hashim I A 
Published: September 2023

Abstract

Introduction
Arterial blood gases analysis are central to the assessment and management of the critical patient acid-base status and its collection requires expertise and is often collected by trained respiratory therapists, nursing, and medical staff. Venous blood gases, arterialized venous blood gases, and capillary samples are however easier to collect. In this retrospective, study we examined the frequency of reassignment of blood gases results to a different sample type.

Method
Retrospective review of blood gases results requiring sample type reassignment collected during the last three years from January 2020 to December 2022 were obtained. Results were analyzed for concordance with sampling site and workflow analysis.

Results
Over the three years study period (2020 to 2022), a total of 196 samples for blood gases analysis required reassignment to a different collection site representing 0.12% of all blood gases testing. Among the 123 initial arterial collections, 72 were reassigned as venous, 40 reassigned to mixed venous sample, and one to capillary collection. Whereas, among the initial 24 venous samples collections 16 were reassigned as arterial and 8 to mixed venous collections. Additionally, among the 25 initial mixed venous collections, 16 were reassigned as arterial, 9 reassigned as venous and 3 were reassigned as capillary collections. The frequency of reassignment from arterial to venous was significantly higher compared to venous to arterial (P &lt; 0.05) or for the reassignment in the mixed venous collections. Although a smaller number of samples were amended to capillary, capillary blood gases reflect arterial samples.There was no significant difference in the frequency of sample type reassignment between the three years of collection with the exception of a slight drop in year 2020 where the majorly of patients were of COVID-19 infection and that collections were likely performed by the same assigned medical personnel.

Conclusion
Common errors in blood gases collection are failure to obtain an arterial sample and accidental collection of venous samples instead often due to close proximity is common. In this retrospective review, the common reassignment is that of arterial to venous followed by arterial to mixed venous and venous to arterial sample types. Artifactual causes that may lead to misclassification of sample type include sample integrity as exposure to room air falsely reduces pCO2 and elevates pO2 giving a false impression of an arterial collection, similarly, dilution of arterial blood samples by heparin is common (inadequate blood fill of syringe) falsely lowers pCO2 both raising doubt as to the sample type.The impact of reassignment of change of sample type on outcomes and on interpretation requires analysis.
B-014 Impact of Centrifugation Time Reduction in Laboratory Automation System
Authors: Choosongsang P 
Published: September 2023

Abstract

Background
The centrifugation of specimens is an important preanalytical process which will be impact the most on turnaround time of the laboratory results. To verify the automation systems, we tested different combinations of tube and centrifugation settings to determine the most efficient for routine chemistry procedure. The outcomes of each combination were then compared to the benchmark to find out the best setting to reduce turnaround time for laboratory results.

Methods
In this study, we evaluated a total of 40 leftover blood samples that were collected on 4 mL plastic Vacutainer® (Becton Dickinson) lithium heparin tubes and 2 mL plastic Vacuette® (Greiner bio-one) lithium heparin tubes. All tubes were centrifuged on Abbott Automation GLP systems. The first set of samples was centrifuged according to the manufacturer’s guideline (10 min at 1300 × g, room temperature for Vacutainer® tubes and 10 min at 2200 × g, room temperature for Vacuette® tubes). The second set was centrifuged 7 min at 2700 × g, room temperature. And the third set was centrifuged 5 min at 2700 × g, room temperature. Then, analyzed all samples with 22 routine chemistry parameters on Alinity ci analyzers. The allowable total error and correlation coefficient (R) were used to determine the significance of the differences between 3 protocols of the centrifugation time.

Results
The study showed that the centrifugation times of 7 min and 5 min were not significantly different from the manufacturer’s protocol (10 min) after testing with 22 routine chemistry parameters (albumin, alkaline phosphatase, alanine aminotransferase, aspartate aminotransferase, direct bilirubin, total bilirubin, calcium, chloride, cholesterol, creatinine, low-density lipoprotein-cholesterol, iron, potassium, lactate dehydrogenase, sodium, phosphorus, total protein, triglycerides, unsaturated iron-binding capacity, high-density lipoprotein-cholesterol, urea nitrogen and uric acid) in both 4 mL plastic Vacutainer® lithium heparin tubes and 2 mL plastic Vacuette® lithium heparin tubes. Overall, the results of the study indicate that shorter centrifugation times of 7 min and 5 min at 2700 × g able to use for routine chemistry.

Conclusion
The study concluded that the centrifugation time did not affect the analytical results of 22 routine chemistry parameters. This suggests that shorter centrifugation times able to use with no impact on accuracy or reliability. The results of the study will support laboratory to have efficiency improvements by shorten the turnaround time on the results release.
B-029 Validation of an Automated Analyzer for Urine Microscopic Examination
Authors: Majoy L , Riedy H , Chappel M , Nakashima M O 
Published: September 2023

Abstract

Background
Microscopic examination of urine sediment can be time-consuming and labor intensive. Automated analyzers can help to standardize resulting and reduce manual work. Urinalysis has traditionally utilized semi-quantitative grading scales, eg. “0–3/high power field”. The Sysmex UF 5000 (Symex, Kobe, JP) uses flow cytometry to enumerate microscopic particles including white and red blood cells (WBC, RBC), bacteria, casts, and epithelial cells (EC). We sought to validate the counting of these microscopic particles against our reference manual method, and also determine if the research parameters from the analyzer could be used to accurately measure other particles in urine (eg. crystals).

Methods
Residual urine samples were analyzed for microscopic particles both by the UF 5000 and manually using KOVA tubes (KOVA International, Garden Grove, CA). Particles were enumerated using the laboratory’s current semi-quantitative grading system. Exact agreement and agreement +/- one level were calculated.

Results

Conclusion
The analyzer results were comparable to manual resulting; in discrepant cases, the UF result was typically higher than manual, which may reflect the increased sensitivity of this method. Additional studies are ongoing to determine if the UF 5000 research parameters are accurate for semi-quantitative reporting of pathologic casts, crystals, and yeast.