Virus taxonomy, comprising classification and nomenclature, is regulated by the International Committee on Taxonomy of Viruses (ICTV). Taxon names are standardized to facilitate recognition and communication, with defined suffixes for each rank (e.g., the names of orders, families, and genera end in -virales, -viridae, and -virus, respectively). However, until recently, a standard format for species names was lacking. In 2021, following extensive discussion and community consultation, the ICTV decided to adopt a standardized binomial (Linnaean) format for virus species names, consisting of the genus name followed by a "freeform" species epithet. Previously assigned virus species names that were non-compliant with the binomial format have been fully updated. In contrast to taxon names regulated by the ICTV, the names of viruses, or "common" names, such as yellow fever virus or human immunodeficiency virus, are not under the remit of the ICTV and have not been changed.

Taxonomic classification of cellular organisms requires the publication of descriptions and proposed names of species and the deposition of specimens. Virus taxonomy is developed through a different system of annual submission of formal taxonomy proposals (TPs) that can be submitted by anyone but are typically prepared by a study group appointed by the International Committee on Taxonomy of Viruses (ICTV) and consisting of experts on a particular group of viruses. These are initially evaluated by an expert subcommittee and by the executive committee (EC) of the ICTV. EC-approved TPs are then submitted for evaluation and a ratification vote by the wider ICTV membership. Following ratification, the new taxonomy is annually updated in the Master Species List, associated databases and bioinformatic resources. The process is consistent, creates traceability in assignments and supports a fully evaluated, hierarchical classification and nomenclature of all taxonomic ranks from species to realms. The structure also facilitates large-scale and coordinated changes to virus taxonomy, such as the recent introduction of a binomial species nomenclature.TPs are available on the ICTV website after ratification, but they are not indexed in bibliographic databases and are not easily cited. Authors of TPs do not receive citation credit for adopted proposals, and their voluntary contributions are largely invisible in the published literature. For greater visibility of TPs and their authors, the ICTV will commence the annual publication of summaries of all TPs from each ICTV subcommittee. These summaries will provide a searchable compendium of all annual taxonomy changes and additions as well as direct links to the Master Species List and other ICTV bioinformatic resources. Their publication will provide due credit and citations for their authors, form the basis for disseminating taxonomy decisions and promote greater visibility and accessibility to taxonomy changes for the virology community.

Gut microbiota modulate systemic anti-inflammatory and immune responses in the lungs, suggesting a potential to support lung health through probiotic supplementation. We hypothesized that a probiotic blend (Lactobacilli) combined with herbal extracts (resB®) could improve quality of life in patients with chronic obstructive pulmonary disease (COPD). We conducted a randomized, double-blinded, placebo-controlled study (NCT05523180) evaluating the safety and impact of resB® on quality of life in volunteers with COPD. Participants took resB® or placebo (two capsules daily) for 12 weeks. The primary endpoint was change in quality of life by Saint George’s Respiratory Questionnaire (SGRQ). Secondary outcomes included safety, serum and sputum biomarkers, and microbiome analysis. resB® was well tolerated with no related adverse events. Participants receiving resB® showed significant improvement in SGRQ symptom scores (P < 0.05), while placebo recipients did not. In the resB® group, serum and sputum levels of matrix metalloproteinase 9, C-reactive protein, and interleukin 6 decreased (P < 0.05), correlating with increased stool Lactobacilli. Additionally, Veillonella abundance increased in both stool and sputum. These findings suggest that resB® improves respiratory symptoms and reduces inflammation in patients with COPD, potentially by modulating gut and lung microbiota. ClinicalTrials.gov identifier NCT05523180. Chronic obstructive pulmonary disease (COPD) is a long-term lung condition that makes breathing difficult and greatly affects quality of life. Current treatments mostly focus on reducing symptoms, but there is a need for safe supportive approaches. The gut and the lungs communicate through what is known as the “gut–lung axis.” Changes in gut bacteria can influence inflammation and immunity in the lungs. Probiotics (beneficial bacteria) and plant-based extracts may help improve this communication and support lung health. In this study, adults with COPD were randomly assigned to receive either a probiotic and herbal blend (resB®) or a placebo for 12 weeks. Participants and researchers did not know which treatment each person received until the study ended. The main outcome was change in quality of life, measured by the Saint George’s Respiratory Questionnaire (SGRQ). We also looked at safety, inflammation in the blood and sputum, and changes in gut and lung bacteria. We found that resB® was safe and well tolerated. People who took resB® showed improvement in COPD-related symptoms compared to those who received placebo. Inflammatory markers in the blood and sputum decreased, and certain beneficial bacteria became more abundant in the gut and lungs. These results suggest that resB® may support people with COPD by improving symptoms and reducing inflammation. More research in larger studies is needed to confirm these findings and better understand how probiotics and plant extracts work through the gut–lung axis.

During the 56th annual meeting of the International Committee on Taxonomy of Viruses (ICTV), held in Bari, Italy, in August 2024, two technical proposals were presented. The first called for amended versions of accepted taxonomic proposals to be named in such a way to ensure that they are readily accessible on the ICTV website (2024.001G). The second proposed a substantial reformatting of the ICTV statutes and codes to produce a more unified text after the numerous changes made to both documents in previous years (2024.002G). Finally, the ICTV Executive Committee (EC) nominated Professor Stuart Siddell as a Life Member of the ICTV for his work over four decades on virus taxonomy, including 16 years as a member of the EC (2024.003G).

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 2024. The entire ICTV membership was invited to vote on 203 taxonomic proposals that had been approved by the ICTV Executive Committee (EC) in July 2023 at the 55th EC meeting in Jena, Germany, or in the second EC vote in November 2023. All proposals were ratified by online vote. Taxonomic additions include one new phylum (Ambiviricota), one new class, nine new orders, three new suborders, 51 new families, 18 new subfamilies, 820 new genera, and 3547 new species (excluding taxa that have been abolished). Proposals to complete the process of species name replacement to the binomial (genus + species epithet) format were ratified. Currently, a total of 14,690 virus species have been established.

Gut microbiota influence anti-tumor immunity, often by producing immune-modulating metabolites. However, microbes consume a variety of metabolites that may also impact host immune responses. We show that tumors grow unchecked in the omenta of microbe-replete mice due to immunosuppressive Tregs. By contrast, omental tumors in germ-free, neomycin-treated mice or mice colonized with altered Schaedler's flora (ASF) are spontaneously eliminated by CD8+ T cells. These mice lack Proteobacteria capable of arginine catabolism, causing increases in serum arginine that activate the mammalian target of the rapamycin (mTOR) pathway in Tregs to reduce their suppressive capacity. Transfer of the Proteobacteria, Escherichia coli (E. coli), but not a mutant unable to catabolize arginine, to ASF mice reduces arginine levels, restores Treg suppression, and prevents tumor clearance. Supplementary arginine similarly decreases Treg suppressive capacity, increases CD8+ T cell effectiveness, and reduces tumor burden. Thus, microbial consumption of arginine alters anti-tumor immunity, offering potential therapeutic strategies for tumors in visceral adipose tissue.

Introduction Breast cancer survivors have an increased risk for chronic fatigue and altered gut microbiota composition, both with negative health and quality of life affects. Exercise modestly improves fatigue and is linked to gut microbial diversity and production of beneficial metabolites. Studies suggest that gut microbiota composition is a potential mechanism underlying fatigue response to exercise. Randomised controlled trials testing the effects of exercise on the gut microbiome are limited and there is a scarcity of findings specific to breast cancer survivors. The objective of this study is to determine if fitness-related modifications to gut microbiota occur and, if so, mediate the effects of aerobic exercise on fatigue response.Methods and analysis The research is a randomised controlled trial among breast cancer survivors aged 18–74 with fatigue. The primary aim is to determine the effects of aerobic exercise training compared with an attention control on gut microbiota composition. The secondary study aims are to test if exercise training (1) affects the gut microbiota composition directly and/or indirectly through inflammation (serum cytokines), autonomic nervous system (heart rate variability) or hypothalamic-pituitary-adrenal axis mediators (hair cortisol assays), and (2) effects on fatigue are direct and/or indirect through changes in the gut microbiota composition. All participants receive a standardised controlled diet. Assessments occur at baseline, 5 weeks, 10 weeks and 15 weeks (5 weeks post intervention completion). Faecal samples collect the gut microbiome and 16S gene sequencing will identify the microbiome. Fatigue is measured by a 13-item multidimensional fatigue scale.Ethics and dissemination The University of Alabama at Birmingham Institutional Review Board (IRB) approved this study on 15 May 2019, UAB IRB#30000320. A Data and Safety Monitoring Board convenes annually or more often if indicated. Findings will be disseminated in peer-reviewed journals and conference presentations.Trial registration number ClinicalTrials.gov, NCT04088708.

BACKGROUND:The gut microbiota is associated with risk for colorectal cancer (CRC), a chronic disease for which racial disparities persist with Black Americans having a higher risk of CRC incidence and mortality compared to other groups. Given documented racial differences, the gut microbiota may offer some insight into previously unexplained racial disparities in CRC incidence and mortality. A case-control analysis comparing 11 women newly diagnosed with CRC with 22 cancer-free women matched on age, BMI, and race in a 1:2 ratio was conducted. Information about participants' diet and perceived stress levels were obtained via 24-h Dietary Recall and Perceived Stress Scale-10 survey, respectively. Participants provided stool samples from which microbial genomic DNA was extracted to reveal the abundance of 26 genera chosen a priori based on their previously observed relevance to CRC, anxiety symptoms, and diet. RESULTS:Significantly lower alpha diversity was observed among cancer-free Black women compared to all other race-cancer status combinations. No group differences were observed when comparing beta diversity. Non-Hispanic White CRC cases tended to have higher relative abundance of Fusobacteria, Gemellaceae, and Peptostreptococcus compared to all other race-cancer combination groups. Perceived stress was inversely associated with alpha diversity and was associated with additional genera. CONCLUSIONS:Our findings suggest that microbiome-CRC associations may differ by racial group. Additional large, racially diverse population-based studies are needed to determine if previously identified associations between characteristics of the gut microbiome and CRC are generalizable to Black women and other racial, ethnic, and gender groups.

Accumulating evidence has revealed that alterations in the gut microbiome following spinal cord injury (SCI) exhibit similarities to those observed in metabolic syndrome. Considering the causal role of gut dysbiosis in metabolic syndrome development, SCI-induced gut dysbiosis may be a previously unidentified contributor to the increased risk of cardiometabolic diseases, which has garnered attention. With a cross-sectional design, we evaluated the correlation between gut microbiome composition and functional potential with indicators of metabolic health among 46 individuals with chronic SCI. Gut microbiome communities were profiled using next-generation sequencing techniques. Indices of metabolic health, including fasting lipid profile, glucose tolerance, insulin resistance, and inflammatory markers, were assessed through fasting blood tests and an oral glucose tolerance test. We used multivariate statistical techniques (i.e., regularized canonical correlation analysis) to identify correlations between gut bacterial communities, functional pathways, and metabolic health indicators. Our findings spotlight bacterial species and functional pathways associated with complex carbohydrate degradation and maintenance of gut barrier integrity as potential contributors to improved metabolic health. Conversely, those correlated with detrimental microbial metabolites and gut inflammatory pathways demonstrated associations with poorer metabolic health outcomes. This cross-sectional investigation represents a pivotal initial step toward comprehending the intricate interplay between the gut microbiome and metabolic health in SCI. Furthermore, our results identified potential targets for future research endeavors to elucidate the role of the gut microbiome in metabolic syndrome in this population.NEW & NOTEWORTHY Spinal cord injury (SCI) is accompanied by gut dysbiosis and the impact of this on the development of metabolic syndrome in this population remains to be investigated. Our study used next-generation sequencing and multivariate statistical analyses to explore the correlations between gut microbiome composition, function, and metabolic health indices in individuals with chronic SCI. Our results point to potential gut microbial species and functional pathways that may be implicated in the development of metabolic syndrome.

Despite over 60 years of research, the etiology of bacterial vaginosis (BV), the most common cause of vaginal discharge, remains controversial. We investigated longitudinal changes in the vaginal microbiota prior to incident BV (iBV) using shotgun metagenomic sequencing (SMS) to elucidate the role of Lactobacillus phages.

Colorectal cancer (CRC) is the third-most leading cause of cancer-related deaths in the United States. To advance the understanding of CRC tumor progression, models which mimic the tumor microenvironment (TME) and have translatable study outcomes are urgently needed. CRC patient-derived xenografts (PDXs) are promising tools for their ability to recapitulate tumor heterogeneity and key patient tumor characteristics, such as molecular characteristics. However, as in vivo models, CRC PDXs are costly and low-throughput, which leads to a need for equivalent in vitro models. To address this need, we previously established an in vitro model using a tissue engineering toolset with CRC PDX cells. However, it is unclear whether tissue engineering has the capacity to maintain patient- and/or cancer stage-specific tumor heterogeneity. To address this gap, we employed three PDX tumor lines, originated from stage II, III-B, and IV CRC tumors, in the formation of 3D engineered CRC PDX (3D-eCRC-PDX) tissues and performed an in-depth comparison between the 3D-eCRC-PDX tissues and the original CRC-PDX tumors. To form the tissues, CRC-PDX tumors were expanded in vivo and dissociated. The isolated cells were encapsulated within poly(ethylene glycol)-fibrinogen hydrogels and remained viable and proliferative post encapsulation over the course of 29 days in culture. To gain molecular insight into the maintenance of PDX line stage heterogeneity, we performed a transcriptomic analysis using RNA seq to determine the extent to which there were similarities and differences between the CRC-PDX tumors and the 3D-eCRC-PDX tissues. We observed the greatest correspondence in overlapping differentially expressed human genes, gene ontology, and Hallmark gene set enrichment between the 3D-eCRC-PDX tissues and CRC-PDX tumors in the stage II PDX line, while the least correspondence was observed in the stage IV PDX line. The Hallmark gene set enrichment from murine mapped RNA seq transcripts was PDX line-specific which suggested that the stromal component of the 3D-eCRC-PDX tissues was maintained in a PDX line-dependent manner. Consistent with our transcriptomic analysis, we observed that tumor cell subpopulations, including human proliferative (B2M+Ki67+) and CK20+ cells, remained constant for up to 15 days in culture even though the number of cells in the 3D-eCRC-PDX tissues from all three CRC stages increased over time. Yet, tumor cell subpopulation differences in the stage IV 3D-eCRC-PDX tissues were observed starting at 22 days in culture. Overall, our results demonstrate a strong correlation between our in vitro 3D-eCRC-PDX models and the originating in vivo CRC-PDX tumors, providing evidence that these engineered tissues may be capable of mimicking patient- and/or cancer stage-specific heterogeneity. Citation Format: Yuan Tian, Iman Hassani, Benjamin Anbiah, Bulbul Ahmed, William Van Der Pol, Elliot J. Lefkowitz, Peyton C. Kuhlers, Nicole L. Habbit, Martin J. Heslin, Elizabeth A. Lipke, Michael W. Greene. Transcriptomic analysis of a 3D engineered cancer model recapitulating stage-dependent heterogeneity in colorectal PDX tumors. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4567.

In the version of this article initially published, there were mistakes in Fig. 1 (ICTV-

A universal taxonomy of viruses is essential for a comprehensive view of the virus world and for communicating the complicated evolutionary relationships among viruses. However, there are major differences in the conceptualisation and approaches to virus classification and nomenclature among virologists, clinicians, agronomists, and other interested parties. Here, we provide recommendations to guide the construction of a coherent and comprehensive virus taxonomy, based on expert scientific consensus. Firstly, assignments of viruses should be congruent with the best attainable reconstruction of their evolutionary histories, i.e., taxa should be monophyletic. This fundamental principle for classification of viruses is currently included in the International Committee on Taxonomy of Viruses (ICTV) code only for the rank of species. Secondly, phenotypic and ecological properties of viruses may inform, but not override, evolutionary relatedness in the placement of ranks. Thirdly, alternative classifications that consider phenotypic attributes, such as being vector-borne (e.g., “arboviruses”), infecting a certain type of host (e.g., “mycoviruses,” “bacteriophages”) or displaying specific pathogenicity (e.g., “human immunodeficiency viruses”), may serve important clinical and regulatory purposes but often create polyphyletic categories that do not reflect evolutionary relationships. Nevertheless, such classifications ought to be maintained if they serve the needs of specific communities or play a practical clinical or regulatory role. However, they should not be considered or called taxonomies. Finally, while an evolution-based framework enables viruses discovered by metagenomics to be incorporated into the ICTV taxonomy, there are essential requirements for quality control of the sequence data used for these assignments. Combined, these four principles will enable future development and expansion of virus taxonomy as the true evolutionary diversity of viruses becomes apparent.

In May, 2015, WHO recommended best practices for naming new infectious diseases to avoid offense or economic effect for any ethnic, regional, or other groups.1WHOWorld Health Organization best practices for the naming of new human infectious diseases.https://www.who.int/publications/i/item/WHO-HSE-FOS-15.1Date: May 15, 2015Date accessed: January 31, 2023Google Scholar Although mpox (formerly known as monkeypox) is not new, WHO has endorsed mpox as the new name for this re-emerging disease and backed the scientific community to agree on neutral nomenclature for variants of viruses. The first report of mpox that led to the discovery of the global outbreak was made to WHO on May 13, 2022. The outbreak spread to 110 countries2WHO2022 monkeypox outbreak: global trends.https://worldhealthorg.shinyapps.io/mpx_global/Date: 2022Date accessed: January 31, 2023Google Scholar and was declared a public health emergency of international concern. The Director-General of WHO called on member states to ensure respect for human rights and to address stigma and discrimination.3WHOWHO Director-General declares the ongoing monkeypox outbreak a public health emergency of international concern.https://www.who.int/europe/news/item/23-07-2022-who-director-general-declares-the-ongoing-monkeypox-outbreak-a-public-health-event-of-international-concernDate: July 23, 2022Date accessed: January 31, 2023Google Scholar As of Jan 31, 2023, there were 85 549 confirmed cases of mpox reported by 110 countries, including 89 deaths.2WHO2022 monkeypox outbreak: global trends.https://worldhealthorg.shinyapps.io/mpx_global/Date: 2022Date accessed: January 31, 2023Google Scholar Mpox is caused by the species monkeypox virus (MPXV), genus Orthopoxvirus, discovered in 1958 in a primate research facility in Denmark, with the first human case reported in 1970.4von Magnus P Andersen EK Birkum Petersen K Birch-Andersen A A pox-like disease in cynomolgus monkeys.Acta Pathol Microbiol Scand. 1959; 46: 156-176Crossref Scopus (354) Google Scholar Two virus clades were identified: the Congo Basin (or central African) clade and the west African clade.5Likos AM Sammons SA Olson VA et al.A tale of two clades: monkeypox viruses.J Gen Virol. 2005; 86: 2661-2672Crossref PubMed Scopus (402) Google Scholar Although stigma became a concern during outbreaks in Africa,6Oyebanji O Ofonagoro U Akande O et al.Lay media reporting of monkeypox in Nigeria.BMJ Glob Health. 2019; 4e002019Crossref PubMed Scopus (7) Google Scholar the 2022 global outbreak reignited discussion with proposals to rename virus clades.7Happi C Adetifa I Mbala P et al.Urgent need for a non-discriminatory and non-stigmatizing nomenclature for monkeypox virus.PLoS Biol. 2022; 20e3001769Crossref PubMed Scopus (81) Google Scholar Although the nomenclature of virus variants is the remit of scientists, reaching consensus quickly was important. On Aug 8, 2022, WHO convened an ad-hoc expert meeting to discuss characteristics of MPXV clades and propose names for them. Participants included orthopoxvirologists, evolutionary biologists, and other scientists from (1) WHO collaborating centres on orthopoxviruses at the US Centers for Disease Control and Prevention and the Russian State Research Centre of Virology and Biotechnology; (2) the WHO Technical Advisory Group on SARS-CoV-2 Virus Evolution; (3) the WHO Advisory Committee on Variola Virus Research; (4) the Poxviridae study group of the International Committee on the Taxonomy of Viruses; (5) research and public health institutes in Africa and around the world; and (6) public virus-sequence databases. The meeting reviewed the phylogeny and characteristics of MPXVs and proposed a neutral naming convention.7Happi C Adetifa I Mbala P et al.Urgent need for a non-discriminatory and non-stigmatizing nomenclature for monkeypox virus.PLoS Biol. 2022; 20e3001769Crossref PubMed Scopus (81) Google Scholar MPXV phylogeny shows two distinct clusters corresponding to the previously recognised clades. Consensus was reached for nomenclature of a Roman numeral for each clade with lowercase Latin characters for subclades; the Congo Basin clade became Clade I and the west African clade became Clade II, encompassing two phylogenetically distinct subclades, IIa and IIb.8WHOMonkeypox: experts give virus variants new names.https://www.who.int/news/item/12-08-2022-monkeypox-experts-give-virus-variants-new-namesDate: Aug 12, 2022Date accessed: October 9, 2022Google Scholar There are appreciable genetic differences between Clades I and II, showing nearly twice the divergence as that between subclades IIa and IIb. Nonetheless, both subclades include genomes from the 1960s and 1970s and appear to have evolved separately from a most recent common ancestor dating back hundreds of years. Neither subclade is descended from the other.5Likos AM Sammons SA Olson VA et al.A tale of two clades: monkeypox viruses.J Gen Virol. 2005; 86: 2661-2672Crossref PubMed Scopus (402) Google Scholar Although the current global outbreak is related primarily to Clade IIb, new cases related to Clade IIa continue to be reported, requiring the tracking of numerous clades and lineages. To distinguish emerging lineages, nomenclature that encodes genealogical relationships between variants was proposed. Lineage labels would follow the convention used for SARS-CoV-2, with an uppercase Latin character followed by a period, and a number representing the nth descendant of the Latin character (eg, Clade IIb.A.1).9Rambaut A Holmes EC O'Toole Á et al.A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology.Nat Microbiol. 2020; 5: 1403-1407Crossref PubMed Scopus (1403) Google Scholar The assignment of virus lineage will help to identify epidemiological links within and across geographic regions and support the understanding of evolutionary dynamics. Parallel discussions considered changing the disease name in the WHO International Classification of Diseases (ICD). WHO issued a public call for new name suggestions for monkeypox in August, 2022. Over 200 proposals received on the ICD platform were reviewed with criteria such as rationale, appropriateness, current usage, scientific accuracy, pronounceability, translatability, potential for confusion, and the guidance for the naming of new diseases. Consultations involved the ICD Medical and Scientific Advisory Committee, the Classification and Statistics Advisory Committee with representation from WHO member states, and the WHO Family of International Classifications. The review recommended the use of mpox as a synonym or inclusion name for monkeypox. The new name was proposed by a men's health community organisation, endorsed by WHO after all suggestions were considered,10WHOWHO recommends new name for monkeypox disease.https://www.who.int/news/item/28-11-2022-who-recommends-new-name-for-monkeypox-diseaseDate: Nov 28, 2022Date accessed: December 1, 2022Google Scholar and is being phased in as a synonym to become the preferred term of the ICD after December, 2023. Discussions on terminology in other languages will continue throughout 2023, providing member states with a choice of preferred term in their language for national usage and statistics. Mpox is now included in ICD-10 and ICD-11, effective as of January, 2023.10WHOWHO recommends new name for monkeypox disease.https://www.who.int/news/item/28-11-2022-who-recommends-new-name-for-monkeypox-diseaseDate: Nov 28, 2022Date accessed: December 1, 2022Google Scholar WHO encourages all member states and stakeholders to follow these recommendations on mpox and its virus clades. EJL was supported by the US National Institute of Allergy and Infectious Diseases of the National Institutes of Health under award number U24AI162625. All other authors declare no competing interests. The working group thanks African scientists who advocated for new clade names for MPXV, and front-line health workers and advocates at Rézo, a Montreal community based organisation for gay, bisexual, queer, cis, and trans men who have sex with men, who led a grassroots movement to rename mpox. DU chaired the ad-hoc experts meeting on MPXV clades and variants, which involved authors AA, JB, KK, EJL, MRM, TdO, JO, AR, and RFL, and experts Ifedayo Adetifa, Oluwatoni Akinola, Olajumoke Babatunde, Sylvie Briand, Clarissa Damaso, Inger Damon, Drew Endy, Delia Enria, Mariano Esteban, Bradley Hersh, Christina Hutson, Yu Li, Abdi Mahamud, Sandy Mak, Peter Mala, Colin McInnes, Jean-Vivien Mombouli, Richard Neher, Nnaemeka Ndodo, Mark Perkins, Mike Ryan, Jilian Sacks, Soumya Swaminathan, Henda Triki. We thank Meng Zhang, Co-Chair of the ICD Classification and Statistics Advisory Committee, all participants in these discussions, and Maria Van Kerkhove for ongoing support. The findings and conclusions in this Comment are those of the authors and do not necessarily represent the views of their respective institutions.

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.

The International Committee on Taxonomy of Viruses (ICTV) (https://ictv.global) maintains a database of virus taxonomy, including records from 1971 up to the most recent release in 2022. Recent years have seen an increasing number of viruses, recording 11,273 distinct species in the latest report. Exploring this increasingly high number of species requires a custom data visualization approach that is both scalable and interactive. Our paper presents a structure-preserving, collapsible, node-link layout-based hierarchical visualization called the Visual Taxonomy Browser (https://ictv.global/taxonomy/visual-browser), for the virus taxonomy dataset. Developed in collaboration with microbiologists, our visualization improves over the existing Taxonomy Browser (https://ictv.global/taxonomy) which is a stacked bar-based approach that lacks scalability and does not preserve the underlying topological structure of the taxonomy. The Visual Taxonomy Browser has been deployed on the ICTV website and has been serving virologists from across the world.

The taxonomy of viruses is developed and overseen by the International Committee on Taxonomy of Viruses (ICTV), which scrutinizes, approves and ratifies taxonomic proposals, and maintains a list of virus taxa with approved names (https://ictv.global). The ICTV has approximately 180 members who vote by simple majority. Taxon-specific Study Groups established by the ICTV have a combined membership of over 600 scientists from the wider virology community; they provide comprehensive expertise across the range of known viruses and are major contributors to the creation and evaluation of taxonomic proposals. Proposals can be submitted by anyone and will be considered by the ICTV irrespective of Study Group support. Thus, virus taxonomy is developed from within the virology community and realized by a democratic decision-making process. The ICTV upholds the distinction between a virus or replicating genetic element as a physical entity and the taxon category to which it is assigned. This is reflected by the nomenclature of the virus species taxon, which is now mandated by the ICTV to be in a binomial format (genus + species epithet) and is typographically distinct from the names of viruses. Classification of viruses below the rank of species (such as, genotypes or strains) is not within the remit of the ICTV. This article, authored by the ICTV Executive Committee, explains the principles of virus taxonomy and the organization, function, processes and resources of the ICTV, with the aim of encouraging greater understanding and interaction among the wider virology community.

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.