Canine distemper virus (CDV) triggers a severe, often fatal disease in dogs and wildlife known as canine distemper (CD). Prior research has noted significant genetic diversity and recombination among CDV isolates from different geographical regions, potentially contributing to vaccine failures. Despite this, no genetic characterization of Mongolian CDVs has been conducted. This study, isolated CDVs from three unvaccinated dogs: two 10-month-old mixed-breeds and an 18-month-old Samoyed. All exhibited CD symptoms and subsequently died. Virus isolation was conducted using Vero/dog SLAM cells, with genome sequencing performed via nanopore technology. The mixed-breed dogs were infected with non-recombinant CDV isolates, forming a sister clade to the Asia-1 lineage prevalent in Asia. The Samoyed was infected with a non-recombinant CDV isolate, classifying as Asia-4 lineage sporadically reported in some Asian countries. This sequencing data offers foundational information on genetic diversity, aiding CD control measure development and benefiting future Eurasia and Asian studies.

BACKGROUND: Malignant phyllodes tumors (MPT) are rare fibroepithelial breast cancers with no known effective systemic therapy; metastatic progression portends a dismal prognosis. We sought to describe the genomic landscape of MPTs through genomic profiling and immunotherapeutic biomarker analysis.
METHODS: Cases of sequenced MPT were identified from a Clinical Laboratory Improvement Amendments-certified, College of American Pathologists-accredited laboratory (Foundation Medicine). All cases underwent genomic profiling using adaptor ligation-based, next-generation sequencing assay of 324 genes. Tumor agnostic immunotherapy biomarkers, microsatellite instability, tumor mutational burden (TMB), and programmed death-ligand 1 (PD-L1) expression were evaluated. Fisher\'s Exact Tests and analysis of variance were used to test for differences between groups and for continuous variables as appropriate.
RESULTS: Of 135 MPT cases identified; 94 (69.6%) were localized/locally recurrent and 41 (30.4%) were metastatic. Median age was 54 years (range 14-86). The median TMB was 2.5 mut/Mb and 3 were TMB-high (≥10 mut/Mb). 21.4% were PD-L1+ via Dako 22C3 assay (CPS ≥1). Most commonly altered genes included TERT-promoter (69.7%), CDKN2A (45.9%), TP53 (37.8%), NF1 (35.6%), CDKN2B (33.3%), MED12 (28.9%), MTAP (27.7%), KMT2D (22.2%), PIK3CA (20.0%), PTEN (18.5%), and RB1 (18.5%). Several tumors harboring genomic alterations with US Food and Drug Administration-approved indications in other tumor types were found including NF1, PIK3CA, EGFR Exon 19/20 insertions, and BRAF V600E mutations.
CONCLUSIONS: In the largest genomic evaluation of MPT to date, multiple clinically actionable mutations were found. Routine sequencing of metastatic MPT may provide additional information to guide treatment decisions and clinical trial enrollment.

BACKGROUND: As population-based screening programs to identify genetic conditions in adults using genomic sequencing (GS) are increasingly available, validated patient-centered outcome measures are needed to understand participants\' experience. We aimed to develop and validate an instrument to assess the perceived utility of GS in the context of adult screening.
METHODS: Informed by a five-domain conceptual model, we used a five-step approach to instrument development and validation: (1) item writing, (2) cognitive testing, (3) pilot testing and item reduction, (4) psychometric testing, and (5) evaluation of construct validity. Adults undergoing risk-based or population-based GS who had received GS results as part of ongoing research studies participated in structured cognitive interviews and two rounds of surveys. After item pool refinement, we conducted an exploratory factor analysis and calculated Pearson correlations with related instruments.
RESULTS: We derived the 18-item Adult Diagnostic version of the GENEtic Utility (GENE-U) scale (total sum score α = .87). Mirroring the Pediatric Diagnostic version, the instrument has a two-factor structure, including an Informational Utility subscale (14 items, α =.89) and an Emotional Utility subscale (4 items, α =.75). The Informational Utility subscale was strongly associated with empowerment and personal utility of GS. Correlations of the Emotional Utility subscale with psychosocial impact and anxiety and depression were weak to moderate.
CONCLUSIONS: Initial psychometric testing of the Adult Screening GENE-U scale demonstrates its promise, and additional validation in translational genomics research is warranted.

Bacterial strains coded 21LM367, 21LM07, and 21LM1136 were isolated from the urine of patients with urinary tract infections (UTIs) at the Centre Hospitalier Régional de Daloa in Côte d\'Ivoire. Based on average nucleotide identity (ANI) analysis, DNA-DNA digital hybridisation (dDDH), and other comparative genomic methods, strains 21LM07, 21LM367, and 21LM1136 were determined to be Priestia flexa. The size of the assembled complete genomes ranged from 8,624,538 to 4,007,501 bp. The average GC content was 37.76%, 46.33%, and 43.03% for strains 21LM07, 21LM367, and 21LM1136, respectively. The total number of coding regions (CDS) in each genome was 4172, 8497, and 6795, respectively, for strains 21LM07, 21LM367, and 21LM1136. Genomic prediction analysis revealed that a total of 4241, 8583, and 6881 genes were annotated in the 21LM07, 21LM367, and 21LM1136 genomes, respectively. No virulence or resistance genes were predicted in the genomes of strains 21LM07 and 21LM1136. On the other hand, two genes conferring resistance to beta-lactam and tetracyclines as well as nine virulence genes were predicted in the genome of 21LM367. In addition, 438, 350, and 153 mobile genetic elements (MGEs) were predicted in the genomes of strains 21LM367, 21LM1136, and 21LM07, respectively. Strain 21LM07 was characterised by the absence of plasmids in its genome. Two plasmids were predicted in the genomes of isolates 21LM367 and 21LM1136; however, rep7a and IncI2 were predicted to contain the tet(K) resistance gene. No typical multilocus sequences could be characterised in the genomes of the different strains.

This study presents the comprehensive analysis of the genomic sequence of Klebsiella pneumoniae strain FAHZZU7042hy, having a 5,690,191 bp chromosome size. This strain was obtained from a blood sample of a patient suffering from severe neurological problems in Zhengzhou, China, 2023.

The Hardy-Weinberg Equilibrium (HWE) is a fundamental principle employed in the analysis of genetic data, encompassing studies of meta-analysis and genomic sequencing. It has been demonstrated that HWE possesses the property of transitivity, wherein a multi-allelic polymorphism in equilibrium will persist in its equilibrium state even when alleles are deleted or combined. Nonetheless, the practice of filtering loci that do not adhere to HWE has been observed to impact the inference of population genetics within RADseq datasets. In response to this concern, the Robust Unified Test for HWE (RUTH) has been devised to consider population structure and genotype uncertainty, thereby offering a more precise evaluation of the quality of genotype data. Furthermore, deviations from HWE, such as extreme heterozygote excess, can be effectively utilized to identify genotyping errors or to pinpoint the presence of rare recessive disease-causing variants. In summary, it is evident that HWE holds immense significance in the field of genetic analysis, and its application in meta-analysis studies and genomic sequencing can yield invaluable insights into the intricacies of population structure and the genetics of diseases.

Respiratory syncytial virus (RSV) is a significant cause of morbidity, particularly in infants. This study describes RSV genomic diversity and disease outcomes during the 2023-2024 season in the Johns Hopkins Hospital System (JHHS). Between August and December 2023, 406 patient samples were sequenced, showing that RSV-B GB5.0.5a was the dominant genotype detected. RSV-A genotype GA2.3.5 was detected less frequently. Metadata analysis of patient data revealed that, although RSV-B was more commonly detected, patients with RSV-A infections were more frequently hospitalized. Analysis of both the G- and F-genes revealed multiple amino acid substitutions in both RSV-A and RSV-B, with some positions within the F-protein that could be associated with evasion of antibody responses. Phylogenetic analysis revealed the genetic diversity of circulating GB5.0.5a and GA2.3.5 genotypes. This study serves as an important baseline for genomic surveillance of RSV within the JHHS and will assist in characterizing the impact of the newly approved RSV vaccines on RSV genomic evolution and the emergence of escape mutations.

Plasmids are extrachromosomal DNA found in microorganisms. They often carry beneficial genes that help bacteria adapt to harsh conditions. Plasmids are also important tools in genetic engineering, gene therapy, and drug production. However, it can be difficult to identify plasmid sequences from chromosomal sequences in genomic and metagenomic data. Here, we have developed a new tool called PlasmidHunter, which uses machine learning to predict plasmid sequences based on gene content profile. PlasmidHunter can achieve high accuracies (up to 97.6%) and high speeds in benchmark tests including both simulated contigs and real metagenomic plasmidome data, outperforming other existing tools.

We aimed to characterize SARS-CoV-2 infection in companion animals living in households with COVID-19-positive people and understand the dynamics surrounding how these animals become infected. Public health investigators contacted households with at least one confirmed, symptomatic person with COVID-19 for study recruitment. Blood, nasal, and rectal swab specimens were collected from pet dogs and cats and a questionnaire was completed. Specimens were tested for SARS-CoV-2 by RT-PCR, and for neutralizing antibodies; genomic sequencing was performed on viral-positive samples. A total of 36.4% of 110 pets enrolled had evidence of infection with SARS-CoV-2. Pets were more likely to test positive if the pet was immunocompromised, and if more than one person in the home was positive for COVID-19. Among 12 multi-pet households where at least one pet was positive, 10 had at least one other pet test positive. Whole-genome sequencing revealed the genomes of viral lineages circulating in the community during the time of sample collection. Our findings suggest a high likelihood of viral transmission in households with multiple pets and when pets had very close interactions with symptomatic humans. Further surveillance studies are needed to characterize how new variants impact animals and to understand opportunities for infection and spillover in susceptible species.

UNASSIGNED: In October 2020, rapid prenatal exome sequencing (pES) was introduced into routine National Health Service (NHS) care in England, requiring the coordination of care from specialist genetics, fetal medicine (FM) and laboratory services. This mixed methods study explored the experiences of professionals involved in delivering the pES service during the first 2 years of its delivery in the NHS.
UNASSIGNED: A survey (n = 159) and semi-structured interviews (n = 63) with healthcare professionals, including clinical geneticists, FM specialists, and clinical scientists (interviews only) were used to address: 1) Views on the pES service; 2) Capacity and resources involved in offering pES; 3) Awareness, knowledge, and educational needs; and 4) Ambitions and goals for the future.
UNASSIGNED: Overall, professionals were positive about the pES service with 77% rating it as Good or Excellent. A number of benefits were reported, including the increased opportunity for receiving actionable results for parental decision-making, improving equity of access to genomic tests and fostering close relationships between FM and genetics departments. Nonetheless, there was evidence that the shift to offering pES in a clinical setting had brought some challenges, such as additional clinic time, administrative processes, perceived lack of autonomy in decision-making regarding pES eligibility and difficulty engaging with peripheral maternity units. Concerns were also raised about the lack of confidence and gaps in genomics knowledge amongst non-genetics professionals - especially midwives. However, the findings also highlighted value in both FM, obstetric and genetics professionals benefiting from further training with a focus on recognising and managing prenatally diagnosed genetic conditions.
UNASSIGNED: Healthcare professionals are enthusiastic about the benefits of pES, and through multi-collaborative working, have developed relationships that have contributed to effective communication across specialisms. Although limitations on resources and variation in knowledge about pES have impacted service delivery, professionals were hopeful that improvements to infrastructure and the upskilling of all professionals involved in the pathway would optimise the benefits of pES for both parents and professionals.