Changes to virus taxonomy and the ICTV Statutes ratified by the International Committee on Taxonomy of Viruses (2023).

This article reports changes to virus taxonomy and taxon nomenclature that were approved and ratified by the International Committee on Taxonomy of Viruses (ICTV) in April 2023. The entire ICTV membership was invited to vote on 174 taxonomic proposals that had been approved by the ICTV Executive Committee in July 2022, as well as a proposed revision of the ICTV Statutes. All proposals and the revised ICTV Statutes were approved by a majority of the voting membership. Of note, the ICTV continued the process of renaming existing species in accordance with the recently mandated binomial format and included gene transfer agents (GTAs) in the classification framework by classifying them as viriforms. In total, one class, seven orders, 31 families, 214 genera, and 858 species were created.

Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR.

The National Institute of Allergy and Infectious Diseases (NIAID) established the Bioinformatics Resource Center (BRC) program to assist researchers with analyzing the growing body of genome sequence and other omics-related data. In this report, we describe the merger of the PAThosystems Resource Integration Center (PATRIC), the Influenza Research Database (IRD) and the Virus Pathogen Database and Analysis Resource (ViPR) BRCs to form the Bacterial and Viral Bioinformatics Resource Center (BV-BRC) https://www.bv-brc.org/. The combined BV-BRC leverages the functionality of the bacterial and viral resources to provide a unified data model, enhanced web-based visualization and analysis tools, bioinformatics services, and a powerful suite of command line tools that benefit the bacterial and viral research communities.

Recent changes to virus taxonomy ratified by the International Committee on Taxonomy of Viruses (2022).

This article reports the changes to virus taxonomy approved and ratified by the International Committee on Taxonomy of Viruses (ICTV) in March 2022. The entire ICTV was invited to vote on 174 taxonomic proposals approved by the ICTV Executive Committee at its annual meeting in July 2021. All proposals were ratified by an absolute majority of the ICTV members. Of note, the Study Groups have started to implement the new rule for uniform virus species naming that became effective in 2021 and mandates the binomial 'Genus_name species_epithet' format with or without Latinization. As a result of this ratification, the names of 6,481 virus species (more than 60 percent of all species names currently recognized by ICTV) now follow this format.

Leveraging Technology and Gamification to Engage Learners in a Microbiology Curriculum in Undergraduate Medical Education.

Background: Microbiology is a critical and expansive topic that many medical schools' curriculum must teach in a constrained time frame. We implemented a microbiology question bank smart phone app enhanced with game elements and clinical pearls during a microbiology course for first-year medical students. We hypothesized that these enhancements and clinical pearls would engage the students meaningfully and increase their knowledge base. Methods: Though use was optional, students' game play was recorded through the app, which was compared to test grades retrospectively. A player efficiency rating (PER) was calculated as a function of question response, accuracy, and engagement. Students were separated into tertiles of PER and median exam grades were compared using a non-parametric Kruskal-Wallis (KW) test. An anonymous satisfaction and usability feedback survey was also administered. Results: One hundred eighty-one of the 189 students (96%) answered at least one question, and 165 (87%) completed all 56 questions. The average PER was 84.75. We received feedback surveys from 61 (34%) students in the course, with positive responses regarding the perceived impact on learning microbiology. The KW test found a positive correlation for median exam scores of the player groups when divided into tertiles by PER (p = 0.0002). Conclusions: We leveraged gamification and clinical pearls to design a supplemental microbiology question bank. We found high engagement overall and higher class exam scores associated with greater use of the question bank.

Changes to virus taxonomy and to the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2021).

This article reports the changes to virus taxonomy approved and ratified by the International Committee on Taxonomy of Viruses (ICTV) in March 2021. The entire ICTV was invited to vote on 290 taxonomic proposals approved by the ICTV Executive Committee at its meeting in October 2020, as well as on the proposed revision of the International Code of Virus Classification and Nomenclature (ICVCN). All proposals and the revision were ratified by an absolute majority of the ICTV members. Of note, ICTV mandated a uniform rule for virus species naming, which will follow the binomial 'genus-species' format with or without Latinized species epithets. The Study Groups are requested to convert all previously established species names to the new format. ICTV has also abolished the notion of a type species, i.e., a species chosen to serve as a name-bearing type of a virus genus. The remit of ICTV has been clarified through an official definition of 'virus' and several other types of mobile genetic elements. The ICVCN and ICTV Statutes have been amended to reflect these changes.

Changes to virus taxonomy and the Statutes ratified by the International Committee on Taxonomy of Viruses (2020).

This article reports the changes to virus classification and taxonomy approved and ratified by the International Committee on Taxonomy of Viruses (ICTV) in March 2020. The entire ICTV was invited to vote on 206 taxonomic proposals approved by the ICTV Executive Committee at its meeting in July 2019, as well as on the proposed revision of the ICTV Statutes. All proposals and the revision of the Statutes were approved by an absolute majority of the ICTV voting membership. Of note, ICTV has approved a proposal that extends the previously established realm Riboviria to encompass nearly all RNA viruses and reverse-transcribing viruses, and approved three separate proposals to establish three realms for viruses with DNA genomes.

Changes to virus taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2019).

This article reports the changes to virus taxonomy approved and ratified by the International Committee on Taxonomy of Viruses (ICTV) in February 2019. Of note, in addition to seven new virus families, the ICTV has approved, by an absolute majority, the creation of the realm Riboviria, a likely monophyletic group encompassing all viruses with positive-strand, negative-strand and double-strand genomic RNA that use cognate RNA-directed RNA polymerases for replication.

Gamification: An Innovative Approach to Reinforce Clinical Knowledge for MD-PhD Students During Their PhD Research Years.

A longstanding challenge facing MD-PhD students and other dual-degree medical trainees is the loss of clinical knowledge that occurs during the non medical phases of training. Academic medical institutions nationwide have developed continued clinical training and exposure to maintain clinical competence; however, quantitative assessment of their usefulness remains largely unexplored. The current study therefore sought to both implement and optimize an online game platform to support MD-PhD students throughout their research training. Sixty three current MD-PhD students completing the PhD research phase of training were enrolled in an institutionally-developed online game platform for 2 preliminary and 4 competition rounds of 3-4 weeks each. During preliminary game rounds, we found that participation, though initially high, declined precipitously throughout the duration of each round, with 37 students participating to some extent. Daily reminders were implemented in subsequent rounds, which markedly improved player participation. Average participation in competition rounds exceeded 35% (23/63) active participants each round, with trending improvement in scores throughout the duration of PhD training. Both player participation and progress through the research phase of the MD-PhD program correlated positively with game performance and therefore knowledge retention and/or acquisition. Coupled with positive survey-based feedback from participants, our data therefore suggest that gamification is an effective tool for MD-PhD programs to combat loss of clinical knowledge during research training.

Educational Analytics: A New Frontier for Gamification?

To determine the effects of gamification on student education, researchers implemented "Kaizen," a software-based knowledge competition, among a first-year class of undergraduate nursing students. Multiple-choice questions were released weekly or biweekly during two rounds of play. Participation was voluntary, and students could play the game using any Web-enabled device. Analyses of data generated from the game included (1) descriptive, (2) logistic regression modeling of factors associated with user attrition, (3) generalized linear mixed model for retention of knowledge, and (4) analysis of variance of final examination performance by play styles. Researchers found a statistically significant increase in the odds of a correct response (odds ratio, 1.8; 95% confidence interval, 1.0-3.4) for a round 1 question repeated in round 2, suggesting retention of knowledge. They also found statistically significant differences in final examination performance among different play styles.To maximize the benefits of gamification, researchers must use the resulting data both to power educational analytics and to inform nurse educators how to enhance student engagement, knowledge retention, and academic performance.

Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV).

The International Committee on Taxonomy of Viruses (ICTV) is charged with the task of developing, refining, and maintaining a universal virus taxonomy. This task encompasses the classification of virus species and higher-level taxa according to the genetic and biological properties of their members; naming virus taxa; maintaining a database detailing the currently approved taxonomy; and providing the database, supporting proposals, and other virus-related information from an open-access, public web site. The ICTV web site (http://ictv.global) provides access to the current taxonomy database in online and downloadable formats, and maintains a complete history of virus taxa back to the first release in 1971. The ICTV has also published the ICTV Report on Virus Taxonomy starting in 1971. This Report provides a comprehensive description of all virus taxa covering virus structure, genome structure, biology and phylogenetics. The ninth ICTV report, published in 2012, is available as an open-access online publication from the ICTV web site. The current, 10th report (http://ictv.global/report/), is being published online, and is replacing the previous hard-copy edition with a completely open access, continuously updated publication. No other database or resource exists that provides such a comprehensive, fully annotated compendium of information on virus taxa and taxonomy.

Phenotype Detection Registry System (PheDRS) - Implementation of a Generalizable Single Institution Clinical Registry Architecture.

Precision medicine requires that groups of patients matching clinical or genetic characteristics be identified in a clinical care setting and treated with the appropriate intervention. In the clinical setting, this process is often facilitated by a patient registry. While the software architecture of federated patient registries for research has been well characterized, local registries focused on clinical quality and care have received less attention. Many clinical registries appear to be one-off projects that lack generalizability and the ability to scale to multiple diseases. We evaluate the applicability of existing registry guidelines for registries designed for clinical intervention, propose a software architecture more practical for single-institution clinical registries and report the implementation of a generalizable clinical patient registry architecture at the University of Alabama at Birmingham (UAB).

i3b3: Infobuttons for i2b2 as a Mechanism for Investigating the Information Needs of Clinical Researchers.

The information needs of clinicians, as they interact with the EHR, are well-studied. Clinical researchers also interact with the EHR and, while they might be expected to have some similar needs, the unique needs that arise due to nature of their work remain largely unstudied. For clinicians, infobuttons (context-aware hyperlinks) provide a mechanism of studying these information needs. Here we describe the integration of infobuttons into i2b2, a popular data warehouse commonly used by clinical researchers, using a plugin. A preliminary survey of i2b2 developers suggests a general interest in infobuttons for i2b2 and indicates good likelihood for their deployment, where they may be used as a tool for further studying these needs in greater detail.

Gamification as a tool for enhancing graduate medical education.

INTRODUCTION: The last decade has seen many changes in graduate medical education training in the USA, most notably the implementation of duty hour standards for residents by the Accreditation Council of Graduate Medical Education. As educators are left to balance more limited time available between patient care and resident education, new methods to augment traditional graduate medical education are needed. OBJECTIVES: To assess acceptance and use of a novel gamification-based medical knowledge software among internal medicine residents and to determine retention of information presented to participants by this medical knowledge software. METHODS: We designed and developed software using principles of gamification to deliver a web-based medical knowledge competition among internal medicine residents at the University of Alabama (UA) at Birmingham and UA at Huntsville in 2012-2013. Residents participated individually and in teams. Participants accessed daily questions and tracked their online leaderboard competition scores through any internet-enabled device. We completed focus groups to assess participant acceptance and analysed software use, retention of knowledge and factors associated with loss of participants (attrition). RESULTS: Acceptance: In focus groups, residents (n=17) reported leaderboards were the most important motivator of participation. Use: 16 427 questions were completed: 28.8% on Saturdays/Sundays, 53.1% between 17:00 and 08:00. Retention of knowledge: 1046 paired responses (for repeated questions) were collected. Correct responses increased by 11.9% (p<0.0001) on retest. Differences per time since question introduction, trainee level and style of play were observed. Attrition: In ordinal regression analyses, completing more questions (0.80 per 10% increase; 0.70 to 0.93) decreased, while postgraduate year 3 class (4.25; 1.44 to 12.55) and non-daily play (4.51; 1.50 to 13.58) increased odds of attrition. CONCLUSIONS: Our software-enabled, gamification-based educational intervention was well accepted among our millennial learners. Coupling software with gamification and analysis of trainee use and engagement data can be used to develop strategies to augment learning in time-constrained educational settings.