SARS-CoV-2 Next Generation Sequencing (NGS) data from clinical isolates from the East Texas Region of the United States

The SARS-CoV-2 virus has evolved throughout the pandemic and is likely to continue evolving into new variants. Some of these variants may affect functional properties, including infectivity, interactions with host immunity, and disease severity. And compromised vaccine efficacy is an emerging concern with every new viral variant. Next-generation sequencing (NGS) has emerged as the tool of choice for discovering new variants and understanding the transmission dynamics of SARS-CoV-2. Deciphering the SARS-CoV-2 genome has enabled epidemiological survivance and forecast of altered etiologically. Clinical presentations of the infection are influenced by comorbidities such as age, immune status, diabetes, and the infecting variant. Thus, clinical management and vaccine efficacy may differ for new variants. For example, some monoclonal antibody treatments are variant-specific, and some vaccines are less efficacious against the omicron and delta variants of SARS-CoV-2. Consequently, determining the local outbreaks and monitoring SARS-CoV-2 Variants of Concern (VOC) is one of the primary strategies for the pandemic's containment. Although next-generation sequencing (NGS) is a gold standard for genomic surveillance and variant discovery, the assays are not approved for variant diagnosis for clinical decision-making. Advanta Genetics, Texas, USA, optimized Illumina COVID-seq protocol to reduce cost without compromising accuracy and validated the Illumina COVID-Seq assay as a Laboratory Developed Test (LDT) according to the guidelines prescribed by the College of American Pathologists (CAP) and Clinical Laboratory Improvement Amendments (CLIA). The whole genome of the virus was sequenced in (n = 161) samples from the East Texas region using the Illumina MiniSeq® instrument and analyzed by using Illumina baseSpace (https://basespace.illumina.com) bioinformatics pipeline. Briefly, the library was prepared by using Illumina COVIDSeq research use only (RUO) kit, and the individual libraries were normalized using the DNA concentration measured by Qubit Flex Fluorometer, and the pooled libraries were sequenced on Illumina MiniSeq® Instrument. Illumina baseSpace application was used for sequencing QC, FASTQ generation, genome assembly, and identification of SARS-CoV-2 variants. This whole genome shotgun project (n = 161) has been deposited at GISAID.

Advantage of precision metagenomics for urinary tract infection diagnostics

Background

Urinary tract infections (UTIs) remain a diagnostic challenge and often promote antibiotic overuse. Despite urine culture being the gold standard for UTI diagnosis, some uropathogens may lead to false-negative or inconclusive results. Although PCR testing is fast and highly sensitive, its diagnostic yield is limited to targeted microorganisms. Metagenomic next-generation sequencing (mNGS) is a hypothesis-free approach with potential of deciphering the urobiome. However, clinically relevant information is often buried in the enormous amount of sequencing data.

Methods

Precision metagenomics (PM) is a hybridization capture-based method with potential of enhanced discovery power and better diagnostic yield without diluting clinically relevant information. We collected 47 urine samples of clinically suspected UTI and in parallel tested each sample by microbial culture, PCR, and PM; then, we comparatively analyzed the results. Next, we phenotypically classified the cumulative microbial population using the Explify® data analysis platform for potential pathogenicity.

Results

Results revealed 100% positive predictive agreement (PPA) with culture results, which identified only 13 different microorganisms, compared to 19 and 62 organisms identified by PCR and PM, respectively. All identified organisms were classified into phenotypic groups (0-3) with increasing pathogenic potential and clinical relevance. This PM can simultaneously quantify and phenotypically classify the organisms readily through bioinformatic platforms like Explify®, essentially providing dissected and quantitative results for timely and accurate empiric UTI treatment.

Conclusion

PM offers potential for building effective diagnostic models beyond usual care testing in complex UTI diseases. Future studies should assess the impact of PM-guided UTI management on clinical outcomes.

Mentorship reconsidered: A case study of K-12 teachers' mentor-mentee relationships during the COVID-19 pandemic

This study critically examined the impact of a crisis context (COVID-19 pandemic) on K-12 teachers by placing emphasis on the mentor-mentee dyad through the perspective of the mentee in a large United States public school system. A phenomenological case study was undertaken that used semi-structured interviews to examine 14 early career teachers (mentees) participating in a formal mentoring program during the 2020-2021 school year. The study focused on mentor-mentee relationships by accounting for the single most traumatic and transformative event of the modern era of K-12 public education. The analysis yielded three findings highlighting the impact of COVID-19 on the mentor-mentee dyadic experiences of first- and second-year teachers engaged in a mentoring relationship. The findings indicate that (a) e-mentoring allowed for avoidant behaviors from mentors (b) successful mentoring involves the development of personal relationships between a mentor and mentee, and (c) peer and reverse mentoring became commonplace during the COVID-19 pandemic. Public school systems can use these findings to help develop positive mentor and mentee relationships that go beyond the traditional dyadic roles and help reduce stress in a crisis context, while developing a culture where superiority bias is improved. Research implications offer mentoring literature a view to pay more attention to temporal influences during environments of high stress, which may provide more explanatory power on mentorship roles, cultural influences, and social interactions in the course of mentor-mentee practices.

Deciphering Microbiota of Acute Upper Respiratory Infections: A Comparative Analysis of PCR and mNGS Methods for Lower Respiratory Trafficking Potential

Although it is clinically important for acute respiratory tract (co)infections to have a rapid and accurate diagnosis, it is critical that respiratory medicine understands the advantages of current laboratory methods. In this study, we tested nasopharyngeal samples (n = 29) with a commercially available PCR assay and compared the results with those of a hybridization-capture-based mNGS workflow. Detection criteria for positive PCR samples was Ct < 35 and for mNGS samples it was >40% target coverage, median depth of 1X and RPKM > 10. A high degree of concordance (98.33% PPA and 100% NPA) was recorded. However, mNGS yielded positively 29 additional microorganisms (23 bacteria, 4 viruses, and 2 fungi) beyond PCR. We then characterized the microorganisms of each method into three phenotypic categories using the IDbyDNA Explify^® Platform (Illumina^® Inc, San Diego, CA, USA) for consideration of infectivity and trafficking potential to the lower respiratory region. The findings are significant for providing a comprehensive yet clinically relevant microbiology profile of acute upper respiratory infection, especially important in immunocompromised or immunocompetent with comorbidity respiratory cases or where traditional syndromic approaches fail to identify pathogenicity. Accordingly, this technology can be used to supplement current syndrome-based tests, and data can quickly and effectively be phenotypically characterized for trafficking potential, clinical (co)infection, and comorbid consideration-with promise to reduce morbidity and mortality.

Optimization of the Illumina COVIDSeq™ protocol for decentralized, cost-effective genomic surveillance

A decentralized surveillance system to identify local outbreaks and monitor SARS-CoV-2 Variants of Concern is one of the primary strategies for the pandemic's containment. Although next-generation sequencing (NGS) is a gold standard for genomic surveillance and variant discovery, the technology is still cost-prohibitive for decentralized sequencing, particularly in small independent labs with limited resources. We have optimized the Illumina COVIDSeq™ protocol for the Illumina MiniSeq instrument to reduce cost without compromising accuracy. We slashed the library preparation cost by half by using 50% of recommended reagents at each step and normalizing the libraries before pooling to achieve uniform coverage. Reagent-only cost (∼$43.27/sample) for SARS-CoV-2 variant analysis with this normalized input protocol on MiniSeq instruments is comparable to what is achieved on high throughput instruments such as NextSeq and NovaSeq. Using this modified protocol, we tested 153 clinical samples, and 90% of genomic coverage was achieved for 142/153 samples analyzed in this study. The lineage was correctly assigned to all samples (152/153) except for one. This modified protocol can help laboratories with constrained resources to contribute in decentralized COVID-19 surveillance in the post-vaccination era.

A Human Oral Fluid Assay for D- and L- Isomer Detection of Amphetamine and Methamphetamine Using Liquid-Liquid Extraction

Medical providers are increasingly confronted with clinical decision-making that involves (meth)amphetamines. And clinical laboratories need a sensitive, efficient assay for routine assessment of D- and L-isomers to determine the probable source of these potentially illicit analytes. This paper presents a validated method of D- and L-isomer detection in human oral fluid from an extract used for determination of a large oral fluid assay (63 analytes) on an older AB SCIEX 4000 instrument. Taken from the positive extract, D- and L-analytes were added. The method for extraction included addition of internal standard and a 2-step liquid-liquid extraction and dry-down step to concentrate and clean the samples. The samples were suspended in 50% MeOH in water, diluted with mobile phase, with separation and detection accomplished using LC-MS/MS to determine analyte concentration. Once samples were confirmed positive for (meth)amphetamine from the large oral fluid assay, they were further examined for the enantiomeric forms with 50 μl aliquots of the standards and samples of interest combined with 450 μl of D- and L-assay mobile phase, then analyzed using chiral column separation, and LC-MS/MS detection with standard curve spanning the range from 2.5 to 1000 ng/mL. The result is a sensitive and accurate detection of D- and L-isomers of amphetamine and methamphetamine in human oral fluid performed on an older model mass spectrometer (AB SCIEX 4000). The novelty of this assay is twofold (a) the 2-step liquid-liquid extraction and dry-down step to concentrate and clean the samples, and (b) its adoption characteristics as a reflex test from a large ODT panel without the need to invest in newer or expensive LC-MS/MS instruments. Finally, this assay also has potential to add a valuable option to high-throughput laboratories seeking a D- and L-testing alternative to urine drug testing methods.

The Student Engagement Effect of Team-Based Learning on Student Pharmacists

Objective. To expand our understanding of student engagement by qualitatively examining how student pharmacists experienced the psychological state of engagement when applying team-based learning (TBL) pedagogy.Methods. A qualitative case study was conducted. Data were obtained through semi-structured interviews with a purposeful and convenience sample of student pharmacists (n=14). Our initial data analysis identified common themes for student engagement in TBL. We then characterized each common theme by deductively coding the themes into predetermined focal concepts of engagement based upon Kearsley and Shneiderman's 1 previous characterization of student engagement as either relate, create, or donate components.Results. Seven common themes arose from this research: accountability, communication, conflict, learning, preparation, purpose, and teamwork. Results indicated that student pharmacists engaged in TBL pedagogy mostly experience the psychological state of student engagement through a relate (41%) component by drawing on team support and trust, followed by the donate (32%) and create (27%) components.Conclusion. Findings in this study are consistent with other research on TBL pedagogy which concluded that, at least in part, this type of learning was a conduit for building student pharmacists' engagement skills. The novelty of this research is that it deductively characterized how student pharmacists perceive, comprehend, and interpret the psychological state of engagement in TBL. Specifically, our findings concluded student pharmacists mostly identify with a relate component of engagement by drawing on team support and trust developed from TBL tenets that encourage communication, conflict resolution, and teamwork.

COVIDSeq as Laboratory Developed Test (LDT) for Diagnosis of SARS-CoV-2 Variants of Concern (VOC)

Rapid classification and detection of SARS-CoV-2 variants have been critical in comprehending the virus's transmission dynamics. Clinical manifestation of the infection is influenced by comorbidities such as age, immune status, diabetes, and the infecting variant. Thus, clinical management may differ for new variants. For example, some monoclonal antibody treatments are variant-specific. Yet, a U.S. Food and Drug Administration (FDA)-approved test for detecting the SARS-CoV-2 variant is unavailable. A laboratory-developed test (LDT) remains a viable option for reporting the infecting variant for clinical intervention or epidemiological purposes. Accordingly, we have validated the Illumina COVIDSeq assay as an LDT according to the guidelines prescribed by the College of American Pathologists (CAP) and Clinical Laboratory Improvement Amendments (CLIA). The limit of detection (LOD) of this test is Ct<30 (~15 viral copies) and >200X genomic coverage, and the test is 100% specific in the detection of existing variants. The test demonstrated 100% precision in inter-day, intra-day, and intra-laboratory reproducibility studies. It is also 100% accurate, defined by reference strain testing and split sample testing with other CLIA laboratories. Advanta Genetics LDT COVIDSeq has been reviewed by CAP inspectors and is under review by FDA for Emergency Use Authorization.

Transforming Prescription Opioid Practices in Primary Care With Change Theory

The opioid epidemic continues to be an ongoing public health crisis. Many primary health care providers aptly serve as the gatekeeper to opioid prescriptions. The opioid epidemic has challenged the primary care profession whilst many of these providers have opted out of opioid prescribing altogether. This unintended consequence affirms erosion to primary care that is vital to the ecosystem of opioid management. The purpose of this study was to understand strategies to deliver opioids safely and effectively. Results indicate primary care providers are uniquely positioned to make a positive opioid impact through focused change initiatives. Five common themes arose from the inductive analysis: (1) provide leadership support; (2) define standard of work; (3) conduct pre-visit reviews; (4) conduct post-visit reviews; and (5) measure progress. Then, each common theme was deductively analyzed through a view of Kotter’s change theory to support an effective proxy for implementing and sustaining chronic opioid therapy in a primary care context. These finding have potential to provide actionable implications for health care management professionals and primary care organizations such as hospitals and group practices.

Influence of physical exercise on baroreceptor sensitivity during pregnancy

BACKGROUND

Baroreceptor sensitivity (BRS) refers to the magnitude of change in the heart rate in response to change in blood pressure (e.g. upon standing). The impact of regular antenatal exercise on maternal BRS is unclear.

AIMS

To determine whether supervised weekly exercise influences BRS, and to determine if posture and calculation method are important in antenatal BRS measurement.

STUDY DESIGN AND SUBJECTS

Eighty-one healthy pregnant women were randomly assigned to an exercise or control group. The exercise group attended weekly classes from the 20th week of pregnancy onwards.

OUTCOME MEASURES

Cardiovascular assessments (beat-to-beat blood pressure, heart rate) were performed at 12-16, 26-28, 34-36 weeks and 12 weeks following birth. BRS was calculated using two methods ("sequence" and "beat-to-beat").

RESULTS

Fifty-one women (63%) completed the study. Mean BRS reduced progressively in all women (p < 0.025) and was lowest in those who exercised (0.046 < p < 0.002). Postnatal increases in BRS were independent of posture. Training-induced BRS (beat-to-beat) reduction occurred earlier than BRS (sequence), and only BRS (sequence) was affected by posture. Heart rate variability reduced with advancing gestation (p < 0.002) and was more pronounced in the exercise group (p < 0.029).

CONCLUSIONS

Weekly exercise exaggerated the reductions in BRS and HRV during pregnancy and is likely linked to diminished parasympathetic activity.

Influence of antenatal physical exercise on heart rate variability and QT variability

OBJECTIVE

We sought to characterise the influence of an antenatal exercise programme on ECG-derived cardiac variables.

METHODS

Fifity-one healthy pregnant women were recruited and randomly assigned (2 × 2×2 design) to an exercise group or a control group. Exercising groups attended weekly classes from the 20th week of pregnancy onwards. Cardiovascular assessments (heart rate variabiliy (HRV), QT, and the QT variability index (QTVI)) were performed at 12-16, 26-28, 34-36 weeks and 12 weeks following birth, during supine rest and exercise conditions.

RESULTS

Advancing gestation was associated with an increased maternal heart rate (p = 0.001), shorter QT interval (p = 0.003), diminished HRV (p = 0.002) and increased QTVI (p = 0.002). Each of these changes was reversed within 12 weeks postpartum (p < 0.004). The Exercise group displayed exaggerated changes for all variables (except QT) but only during supine rest in the third trimester (p < 0.029).

CONCLUSION

Advancing gestation is associated with a shift in HRV/QTVI towards values that have been associated with an elevated risk of arrhythmia. A 20-week exercise programme undertaken between mid and late pregnancy exaggerated these changes during rest in the third trimester of pregnancy.

Recruitment of pregnant women to an exercise-intervention study

We share here our experience of recruiting pregnant women into an exercise intervention study. Recruitment challenges were anticipated owing to the study design, which required four hospital visits for cardiovascular assessment, a long-term (nine-month) commitment, and adherence to a 20-week exercise programme. Fifty-three women were assigned to one of three groups (no-exercise, land exercise or water exercise) using a 2 × 2 × 2 flexible randomisation design. Seven hundred forty-four women were screened at an antenatal clinic, of whom 501 were eligible to participate in the study. One hundred forty-five women were subsequently approached: 46 (32%) of whom agreed to participate, 42 (29%) were interested but then declined and 57 (39%) declined outright. Our study design helped recruit pregnant women as it allowed them some choice of group membership. We also noted that the participant-researcher relationship is important in reducing attrition. Our experience provides indications of likely recruitment and attrition rates for future randomised controlled trials of this type.

Changes in heart rate variability and QT variability during the first trimester of pregnancy

The risk of new-onset arrhythmia during pregnancy is high, presumably relating to changes in both haemodynamic and cardiac autonomic function. The ability to non-invasively assess an individual's risk of developing arrhythmia during pregnancy would therefore be clinically significant. We aimed to quantify electrocardiographic temporal characteristics during the first trimester of pregnancy and to compare these with non-pregnant controls. Ninety-nine pregnant women and sixty-three non-pregnant women underwent non-invasive cardiovascular and haemodynamic assessment during a protocol consisting of various physiological states (postural manoeurvres, light exercise and metronomic breathing). Variables measured included stroke volume, cardiac output, heart rate, heart rate variability, QT and QT variability and QTVI (a measure of the variability of QT relative to that of RR). Heart rate (p < 0.0005, p < 0.0005, p < 0.0005) and cardiac output (p = 0.043, p < 0.0005, p < 0.0005) were greater in pregnant women in all physiological states (respectively for the supine position, light exercise and metronomic breathing state), whilst stroke volume was lower in pregnancy only during the supine position (p < 0.0005). QTe (Q wave onset to T wave end) and QTa (T wave apex) were significantly shortened (p < 0.05) and QTeVI and QTaVI were increased in pregnancy in all physiological states (p < 0.0005). QT variability (p < 0.002) was greater in pregnant women during the supine position, whilst heart rate variability was reduced in pregnancy in all states (p < 0.0005). Early pregnancy is associated with substantial changes in heart rate variability, reflecting a reduction in parasympathetic tone and an increase in sympathetic activity. QTVI shifted to a less favourable value, reflecting a greater than normal amount of QT variability. QTVI appears to be a useful method for quantifying changes in QT variability relative to RR (or heart rate) variability, being sensitive not only to physiological state but also to gestational age. We support the use of non-invasive markers of cardiac electrical variability to evaluate the risk of arrhythmic events in pregnancy, and we recommend the use of multiple physiological states during the assessment protocol.

Parasite manipulation of brain monoamines in California killifish (Fundulus parvipinnis) by the trematode Euhaplorchis californiensis

California killifish (Fundulus parvipinnis) infected with the brain-encysting trematode Euhaplorchis californiensis display conspicuous swimming behaviours rendering them more susceptible to predation by avian final hosts. Heavily infected killifish grow and reproduce normally, despite having thousands of cysts inside their braincases. This suggests that E. californiensis affects only specific locomotory behaviours. We hypothesised that changes in the serotonin and dopamine metabolism, essential for controlling locomotion and arousal may underlie this behaviour modification. We employed micropunch dissection and HPLC to analyse monoamine and monoamine metabolite concentrations in the brain regions of uninfected and experimentally infected fish. The parasites exerted density-dependent changes in monoaminergic activity distinct from those exhibited by fish subjected to stress. Specifically, E. californiensis inhibited a normally occurring, stress-induced elevation of serotonergic metabolism in the raphae nuclei. This effect was particularly evident in the experimentally infected fish, whose low-density infections were concentrated on the brainstem. Furthermore, high E. californiensis density was associated with increased dopaminergic activity in the hypothalamus and decreased serotonergic activity in the hippocampus. In conclusion, the altered monoaminergic metabolism may explain behavioural differences leading to increased predation of the infected killifish by their final host predators.

Cure of EMT-6 tumors by X rays or neutrons: effect of mixed-fractionation schemes

EMT-6 mouse tumors were treated with (a) 1 or 5 fractions of either x rays or neutrons or (b) a mixture of both in which 2 fractions of neutrons (n) plus 3 fraction of x rays (x) were given in 5 days in the sequence n-n-x-x-x or n-x-x-x-n. Using local tumor control as an end point, neutron RBEs of 1.7 for single fractions and 2.6 for 5 fractions were obtained. The two mixed schemes yielded RBEs of 1.5 and 1.4, respectively. Therapeutic gain factors, calculated as the ratio of tumor to skin RBE with neutrons or mixed radiations, were highest for the mixed fractionation schemes. These results are due to an apparent enhancement of the neutron effect in the tumor but not in the skin with these regimens. Other normal tissues must be irradiated with mixed schemes to determine whether this phenomenon is limited to the skin.

Mechanisms underlying reduced growth rate in C3HBA mammary adenocarcinomas recurring after single doses of x-rays or fast neutrons

C3HBA mammary tumors were irradiated with 3000 rads of 250-kVp X-rays or 1000 rads of 8-MeV neutrons, doses of radiation matched for producing equal growth delay. At 14 days postirradiation, tumors were regrowing at a reduced rate relative to controls. Cell kinetic parameters were examined using percentage of labeled mitoses techniques, and blood vessel spacing and tumor architecture were examined histologically to determine whether the mechanisms underlying growth rate changes were the same after neutron as after photon irradiation. The tumor volume-doubling time at 14 days posttreatment is similar in both irradiated groups (TD=117 hr for neutron-irradiated tumors, 132 hr for X-irradiated tumors) and is approximately twice as long as the doubling time of 61.4 hr in control tumors in the same size range. Control and X-irradiated tumors have median cell cycle durations of 19.3 and 18.5 hr, respectively; the more slowly growing X-irradiated tumors have a reduced growth fraction and increased cell loss factor. Regrowing neutron-irradiated tumors have a median cell cycle of 27.2 hr, with calculated growth fraction and cell loss factor values intermediate between those for control and X-irradiated tumors. Scatter in the percentage of labeled mitoses data makes it difficult to determine whether the cell cycle durations are significantly different. The average distance from tumor parenchymal interphase cells to the nearest recognizable blood vessel is nearly identical in the two irradiated groups and for both groups is significantly greater than interphase to vessel distance in controls. The average distance in irradiated tumors approaches the maximal distance for O2 diffusion in mouse adenocarcinomas of a corded structure surrounding a central blood vessel. Both neutron- and X-irradiated tumors contain more necrosis and fewer viable-appearing parenchymal cells than do control tumors of the same size. The similar growth rate and growth delay in this tumor after 3000 rads of X-rays of 1000 rads of neutrons occur in the face of possibly different cell cycle durations and seem related to similar circulatory system inadequacies which limit growth and are expressed as greater average cell-to-blood-vessel distance and increased cell loss leading to necrosis, indicating oxygen or nutrient deprivation.