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Background Sequencing viruses in many specimens is hindered by excessive background material from hosts, microbiota, and environmental organisms. Consequently, enrichment of target genomic material is necessary for practical high-throughput viral genome sequencing. Hybridization probes are widely used for enrichment in many fields, but their application to viral sequencing faces a major obstacle: it is difficult to design panels of probe oligo sequences that broadly target many viral taxa due to their rapid evolution, extensive diversity, and genetic hypervariability. To address this challenge, we created ProbeTools, a package of bioinformatic tools for generating effective viral capture panels, and for assessing coverage of target sequences by probe panel designs in silico . In this study, we validated ProbeTools by designing a panel of 3600 probes for subtyping the hypervariable haemagglutinin (HA) and neuraminidase (NA) genome segments of avian-origin influenza A viruses (AIVs). Using in silico assessment of AIV reference sequences and in vitro capture on egg-cultured viral isolates, we demonstrated effective performance by our custom AIV panel and ProbeTools’ suitability for challenging viral probe design applications. Results Based on ProbeTool’s in silico analysis, our panel provided broadly inclusive coverage of 14,772 HA and 11,967 NA reference sequences. For each reference sequence, we calculated the percentage of nucleotide positions covered by our panel in silico; 90% of HA and NA references sequences had at least 90.8 and 95.1% of their nucleotide positions covered respectively. We also observed effective in vitro capture on a representative collection of 23 egg-cultured AIVs that included isolates from wild birds, poultry, and humans and representatives from all HA and NA subtypes. Forty-two of forty-six HA and NA segments had over 98.3% of their nucleotide positions significantly enriched by our custom panel. These in vitro results were further used to validate ProbeTools’ in silico coverage assessment algorithm; 89.2% of in silico predictions were concordant with in vitro results. Conclusions ProbeTools generated an effective panel for subtyping AIVs that can be deployed for genomic surveillance, outbreak prevention, and pandemic preparedness. Effective probe design against hypervariable AIV targets also validated ProbeTools’ design and coverage assessment algorithms, demonstrating their suitability for other challenging viral capture applications.

We characterized highly pathogenic avian influenza A(H5N1) clade 2.3.4.4b genotype D1.1 in wild birds and a human in British Columbia, Canada, during 2024. D1.1, the predominant genotype circulating in fall 2024, is a reassortment between Eurasian A3 lineage viruses, introduced to North America in 2022, and North American lineage viruses.

Background Widespread human-to-human transmission of the severe acute respiratory syndrome coronavirus two (SARS-CoV-2) stems from a strong affinity for the cellular receptor angiotensin converting enzyme two (ACE2). We investigate the relationship between a patient’s nasopharyngeal ACE2 transcription and secondary transmission within a series of concurrent hospital associated SARS-CoV-2 outbreaks in British Columbia, Canada. Methods Epidemiological case data from the outbreak investigations was merged with public health laboratory records and viral lineage calls, from whole genome sequencing, to reconstruct the concurrent outbreaks using infection tracing transmission network analysis. ACE2 transcription and RNA viral load were measured by quantitative real-time polymerase chain reaction. The transmission network was resolved to calculate the number of potential secondary cases. Bivariate and multivariable analyses using Poisson and Negative Binomial regression models was performed to estimate the association between ACE2 transcription the number of SARS-CoV-2 secondary cases. Results The infection tracing transmission network provided n  = 76 potential transmission events across n  = 103 cases. Bivariate comparisons found that on average ACE2 transcription did not differ between patients and healthcare workers ( P  = 0.86). High ACE2 transcription was observed in 98.6% of transmission events, either the primary or secondary case had above average ACE2 . Multivariable analysis found that the association between ACE2 transcription (log 2 fold-change) and the number of secondary transmission events differs between patients and healthcare workers. In health care workers Negative Binomial regression estimated that a one-unit change in ACE2 transcription decreases the number of secondary cases (β = -0.132 (95%CI: -0.255 to -0.0181) adjusting for RNA viral load. Conversely, in patients a one-unit change in ACE2 transcription increases the number of secondary cases (β = 0.187 (95% CI: 0.0101 to 0.370) adjusting for RNA viral load. Sensitivity analysis found no significant relationship between ACE2 and secondary transmission in health care workers and confirmed the positive association among patients. Conclusion Our study suggests that ACE2 transcription has a positive association with SARS-CoV-2 secondary transmission in admitted inpatients, but not health care workers in concurrent hospital associated outbreaks, and it should be further investigated as a risk-factor for viral transmission.

Purpose The addition of ultrasound training to undergraduate medical education (UME) curricula is on the rise. Despite widespread adoption, there is little focus on the learning theories that guide implementation or how student learning is transferred from one training setting to another. Using our school's UME ultrasound curriculum, we studied how changes implemented in the pre-clerkship curriculum (grounded in specific learning theories) influenced student learning and performance during clerkship rotations. Materials and Methods This was a retrospective study of an existing educational database of student responses and ultrasound submissions obtained during clerkship rotations. Data were collected using Qualtrics, de-identified, and exported to Excel for data analysis. Results After the curriculum change students reported requiring less assistance in the process of obtaining their ultrasound images while the quality of student obtained images remained the same. When broken down by clerkship, there were noted variations in image quality and need for assistance with students on the surgery clerkship showing the greatest increase in independence during the study period. Analysis of assistance by clerkship showed substantial differences in the type of assistance provided. Conclusion Theory-based curriculum change in the pre-clerkship setting can have a measurable impact on student learning behavior in the clerkship setting. The results of this quantitative study provide evidence to guide further qualitative research to better understand how students apply pre-clerkship learning experiences in the clinical environment.

Surveillance data from wildlife and poultry was used to describe the spread of highly pathogenic avian influenza (HPAI) H5N1 clade 2.3.4.4b in British Columbia (B.C.) and the Yukon, Canada from September 2022 - June 2023 compared to the first \"wave\" of the outbreak in this region, which occurred April - August 2022, after the initial viral introduction. Although the number of HPAI-positive poultry farms and wildlife samples was greater in \"Wave 2\", cases were more tightly clustered in southwestern B.C. and the most commonly affected species differed, likely due to an influx of overwintering waterfowl in the area. Eight HPAI genetic clusters, representing seven genotypes and two inter-continental viral incursions, were detected, with significant variation in the relative abundance of each cluster between the waves. Phylogenetic data suggests multiple spillover events from wild birds to poultry and mammals but could not rule out transmission among farms and among mammals.

The aim of this study was to assess the performance of the Pediatric Canadian Triage and Acuity Scale (PaedCTAS) in adolescent patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. A time-series study was conducted in the Emergency Departments (EDs) of 17 public hospitals during the Delta (B.1.617.2) variant spread in Israel. Data were collected prospectively from June 11, 2021 to August 15, 2021. Multivariate regression analyses were performed to identify independent variables associated with hospital admission and with admission to an Intensive Care Unit (ICU). During the study period, 305 SARS-CoV-2 patients ages 12–18 years presenting to the ED were included, and 267 (87.5%) were unvaccinated. Sixty-seven (22.0%) and 12 (3.9%) patients were admitted to pediatric wards and ICUs, respectively. PaedCTAS level 1–2 and the presence of chronic disease increased the odds of hospital admission (adjusted odds ratio (aOR) 5.74, 95% CI, 2.30–14.35, p < 0.0001), and (aOR 2.9, 95% CI, 1.48–5.67, p < 0.02), respectively. PaedCTAS level 1–2 and respiratory symptoms on presentation to ED increased the odds of ICU admission (aOR 27.79; 95% CI, 3.85–176.91, p < 0.001), and (aOR 26.10; 95% CI, 4.47–172.63, p < 0.0001), respectively. PaedCTAS level 3–5 was found in 217/226 (96%) of the patients who were discharged home from the ED. The findings suggest that PaedCTAS level 1–2 was the strongest factor associated with hospital and ICU admission. Almost all the patients who were discharged home had PaedCTAS level 3–5. Study findings suggest good performance of the PaedCTAS in this cohort.

Highly pathogenic avian influenza (HPAI) is a viral disease that causes significant rates of morbidity and mortality in domestic poultry and wild birds, with occasional spillover into mammals, including humans. Beginning in November 2021, Canada experienced its longest and largest outbreak of HPAI in history. A portion of this outbreak (H5N1, clade 2.3.4.4b) occurred in western Canada, specifically in British Columbia (B.C.) and the Yukon, between April 12 and September 11, 2022, which was classified as the “first wave” in this region. Wild birds and mammals identified through passive surveillance and suspect domestic poultry flocks were screened for avian influenza virus (AIV), typed H5 by qPCR, and positive cases were whole genome sequenced. Descriptive epidemiological and phylodynamic analyses were performed to: (1) understand the taxonomic and geographic extent of wild species involved; and (2) examine the origins and probable transmission networks of HPAI viruses introduced into B.C./Yukon by comparing local viruses with those circulating elsewhere in North America. This outbreak included 21 species of wild birds, 2 species of wild mammals, 4 commercial, and 12 domestic small flock infected premises. Canada geese (Branta canadensis) and bald eagles (Haliaeetus leucocephalus) were the most common wild species detected. We demonstrate that north-south avian migration via the Pacific Flyway is the probable route of multiple incursions into this region. Phylogenetic analysis of the hemagglutinin (HA) segment revealed that the B.C./Yukon viruses detected formed five distinct genetic clusters which were maintained across the whole genome. Although, the genome segments were predominantly Eurasian in origin, NP and PB2 segments from all samples, as well as NS and PB1 segments from Cluster 3, had North American origins. Overall, we demonstrate the utility of genomic epidemiology to inform HPAI transmission dynamics across Western Canada and discuss potential knowledge gaps that exist in passive surveillance strategies for HPAI.

Academic mentoring relationships are frequently identified in the literature as important components of the learning experience; however, little research investigates how mentor-mentee relationships form and the effects of the relationships on learning. This study builds upon traditional mentoring theory, Cognitive Apprenticeship Theory, and other accepted academic mentoring frameworks to explore graduate students' perceptions of the influences of their mentor-mentee relationships on learning. In addition, the study includes a review of the literature on mentoring, mentoring in academic settings, and mentoring military students.This study used a qualitative, multi-case design to explore three mentor-mentee dyads at the beginning, middle, and end of the U.S. Army's Master of Military Arts (MMAS) graduate degree program. The mentors were all faculty members who served as MMAS committee chairs for their students. The study used reflective journals, semi-structured interviews, document reviews, field notes, and a conceptual framework based on Cognitive Apprenticeship Theory to explore student perceptions. Research guidance and feedback emerged as the primary themes aligned with how graduate students perceived they we challenged and supported by their mentors. Similarly, new perspectives, improved communication skills, and greater self-efficacy emerged as themes aligned with how graduate students perceived their relationships with their mentors influenced the acquisition or modification of existing knowledge, skills, and behaviors.The results of this study provide insights other researchers can use to understand better the importance of mentoring in academic settings, advance mentoring theory and its application in faculty development, and better prepare faculty and students to navigate their graduate-degree journeys.