Genome Research Articles

MethylBERT enables read-level DNA methylation pattern identification and tumour deconvolution using a Transformer-based model

DNA methylation (DNAm) is a key epigenetic mark that shows profound alterations in cancer. Read-level methylomes enable more in-depth analyses, due to their broad genomic coverage and preservation of rare cell-type signals, compared to summarized data such as 450K/EPIC microarrays. Here, we propose MethylBERT, a Transformer-based model for read-level methylation pattern classification. MethylBERT identifies tumour-derived sequence reads based on their methylation patterns and local genomic sequence, and estimates tumour cell fractions within bulk samples. In our evaluation, MethylBERT outperforms existing deconvolution methods and demonstrates high accuracy regardless of methylation pattern complexity, read length and read coverage. Moreover, we show its applicability to cell-type deconvolution as well as non-invasive early cancer diagnostics using liquid biopsy samples. MethylBERT represents a significant advancement in read-level methylome analysis and enables accurate tumour purity estimation. The broad applicability of MethylBERT will enhance studies on both tumour and non-cancerous bulk methylomes.

Utilizing Patient-Derived Xenografts to Model Precision Oncology for Biliary Tract Cancer.

Biliary tract cancers, which are rare and aggressive malignancies, are rich in clinically actionable molecular alterations. A major challenge in the field is the paucity of clinically relevant biliary tract cancer models that recapitulate the diverse molecular profiles of these tumors. The purpose of this study was to curate a collection of patient-derived xenograft (PDX) models that reflect the spectrum of genomic alterations present in biliary tract cancers to create a resource for modeling precision oncology. PDXs were derived from biliary tract cancer samples collected from surgical resections or metastatic biopsies. Alterations present in the PDXs were identified by whole-exome sequencing and RNA sequencing. PDXs were treated with approved and investigational agents. Efficacy was assessed by change in tumor volume from baseline. Event-free survival was defined as the time to tumor doubling from baseline. Responses were categorized at day 21: >30% decrease in tumor volume = partial response, >20% increase in tumor volume = progressive disease, and any non-partial response/progressive disease was considered stable disease. Genomic sequencing demonstrated key actionable alterations across this cohort, including alterations in FGFR2, isocitrate dehydrogenase I, ERRB2, PIK3CA, PTEN, and KRAS. RNA sequencing demonstrated fusions and expression of antibody-drug conjugate targets, including TROP2, HER2, and Nectin4. Therapeutic matching revealed objective responses to approved and investigational agents that have been shown to have antitumor activity clinically. In this study, we developed a catalog of biliary tract cancer PDXs that underwent comprehensive molecular profiling and therapeutic modeling. To date, this is one of the largest collections of biliary tract cancer PDX models and will facilitate the development of personalized treatments for patients with these aggressive malignancies.

Returning genetic risk information for hereditary cancers to participants in a population-based cohort study in Japan.

Large-scale population cohort studies that collect genomic information are tasked with returning an assessment of genetic risk for hereditary cancers to participants. While several studies have applied to return identified genetic risks to participants, comprehensive surveys of participants' understanding, feelings, and behaviors toward cancer risk remain to be conducted. Here, we report our experience and surveys of returning genetic risks to 100 carriers of pathogenic variants for hereditary cancers identified through whole genome sequencing of 50 000 individuals from the Tohoku Medical Megabank project, a population cohort study. The participants werecarriers of pathogenic variants associated with either hereditary breast and ovarian cancer (n = 79, median age=41) or Lynch syndrome (n = 21, median age=62). Of these, 28% and 38% had a history of cancer, respectively. We provided information on cancer risk, heritability, and clinical actionability to the participants in person. The comprehension assessment revealed that the information was better understood by younger (under 60 years) females than by older males. Scores on the cancer worry scale were positively related to cancer experiences and general psychological distress. Seventy-one participants were followed up at Tohoku University Hospital; six females underwent risk-reducing surgery triggered by study participation and three were newly diagnosed with cancer during surveillance. Among first-degree relatives of hereditary breast and ovarian cancer carriers, participants most commonly shared the information with daughters. This study showed the benefits of returning genetic risks to the general population and will provide insights into returning genetic risks to asymptomatic pathogenic variant carriers in both clinical and research settings.

The First Complete Chloroplast Genome Sequence of Secale strictum subsp. africanum Stapf (Poaceae), the Putative Ancestor of the Genus Secale.

Secale strictum ssp. africanum (synonym Secale africanum), a putative ancestor of the genus Secale, has been classified within Secale strictum, although recent phylogenetic studies suggest that it represents a distinct species. This study reports the first complete chloroplast genome of S. africanum, highlighting its structure, genetic composition, and phylogenetic relationships within Secale and related Triticiceae species. Phylogeny reconstruction based on the maximum-likelihood method reveals notable genetic similarity between S. strictum and S. africanum, supporting their genetic and phylogenetic distinction. Here, we assembled the complete, annotated chloroplast genome sequence of Secale strictum ssp. africanum. The genome is 137,068 base pair (bp) long. It is the first complete chloroplast genome that can be used as a reference genome for further analysis. The genome can be accessed on GenBank with the accession number OQ700974. This work sheds light on the evolutionary history of Secale and contributes to our understanding of chloroplast genomics in cereal ancestors, with potential applications in improving cereal crop resilience, advancing breeding strategies, and informing conservation efforts for genetic diversity.

Investigating the impact of screen-sharing visual aids during genomic results disclosure via telehealth in diverse families in the TeleKidSeq pilot study.

Telehealth genetic counseling is comparable to in-person visits in terms of satisfaction, knowledge, and psychological outcomes, but using visual aids can be challenging on telehealth platforms. This pilot study assessed if the "screen-sharing" feature via Zoom to display visual aids during results disclosure session positively impacted parental experience and comprehension of their child's genomic results especially in underrepresented groups and those with limited English proficiency. In the TeleKidSeq pilot study, 409 children with suspected genetic conditions underwent genome sequencing. Families were randomized to receive genomic results via televisits with (ScrS) or without (NScrS) screen-sharing of visual aids. Spanish- or English-speaking parents/legal guardians completed surveys at three timepoints to assess perceived and objective understanding, perceived confidence, and telehealth experience. Regression models evaluated the effect of screen-sharing over time. Overall, understanding and telehealth experience ratings were high, with no significant differences between the ScrS (N = 192) and NScrS (N = 200) arms with regard to perceived (p = 0.32) or objective (0.94) understanding, confidence (p = 0.14) over time, or telehealth experience (p = 0.10). When stratifying by sociodemographic characteristics and type of device used during results disclosure, we observed subtle differences in the effect of screen-sharing within some sub-groups. While screen-sharing had no significant impact on overall outcomes, we identified modest effects of screen-sharing within population groups that highlight the need for tailored communication strategies to ensure diverse, multilingual communities derive equitable benefit from telehealth-based genomic results disclosure. Future research is needed to determine whether certain types of visual aids best enhance genomic results disclosure in larger, more robust studies designed to detect smaller effects and subgroup differences.

Phylodynamics of hepatitis B virus genotype B in East Asia: A population genomics analysis

Background: Hepatitis B virus (HBV) genotype B (HBV/B) is the predominant strain in Taiwan and several East Asian countries. Objective: The aim of this study is to use comprehensive phylogenetic analysis tools to monitor the long-term molecular evolution dynamic of HBV genotype B population in East Asia. Methods: In this study, full genome sequences of HBV with temporal information were extracted from GenBank and analyzed using the Bayesian Markov chain Monte Carlo method to identify best-fitting coalescent models. Results: Bayesian Skygrid analysis revealed a viral effective population (phylodynamic) bottleneck for HBV/B in 2003, a pattern similar to the previously described HBV genotype C (HBV/C). Despite these similarities, the viral dynamics for HBV/B and HBV/C diverged after 2005. HBV/C exhibited a marked decrease in genetic diversity across East Asia, whereas HBV/B maintained stable genetic diversity after 2005. Phylogeographic analysis using Neighbor-Joining and Bayesian maximum clade credibility trees indicated that Taiwan was likely the geographic origin of the most recent common ancestor of HBV/B in East Asia. An early clade spread to Japan and subsequently to the West Coast of the United States of America. Another clade dispersed to China, spread widely across the region, and was reintroduced to Taiwan multiple times. In contrast, HBV/C likely originated in China and spread to Japan, Korea, and Taiwan over several decades. Conclusion: This study highlights the similarities and differences between the viral dynamics and geographical evolutionary pathways between HBV/B and HBV/C.

Complete genome sequence of Bifidobacterium animalis subsp. lactis BI040, a probiotic strain with multiple health benefits from the NORDBIOTIC collection.

The complete genome of Bifidobacterium animalis subsp. lactis BI040-a human stool isolate, was sequenced using Illumina and Oxford Nanopore technologies. The BI040 genome is composed of a circular 1,944,141-bp chromosome which carries genes potentially involved in vitamin synthesis and gut health.

Epidemiology and genotypic diversity of duck hepatitis B virus identified from waterfowl in partial areas of Guangdong province, Southern China.

Duck Hepatitis B virus (DHBV) infection model is extensively utilized as an animal model for studying human hepatitis B virus infection and for comparative research. 557 liver samples from geese and ducks were collected in parts of Guangdong province, southern China. The overall prevalence of DHBV was 45.6% (254/557) in all samples. And the 27 complete genome sequences of DHBV strains in this study share 89.6%-100% genome-wide pairwise identity with previously identified DHBV genomes. Notably, DHBV-1, DHBV-2 and DHBV-3 of were found co-circulating among the waterfowl population in parts of Guangdong. More importantly, seven out of the 16 recombination events were determined involved DHBV sequences obtained in this study as major parent and minor parent, suggesting DHBV strains from Guangdong province play an important role in recombination events. Additionally, purifying selection was the dominant evolutionary pressure acting on the genomes of DHBV.

Genome Sequencing Reveals the Potential of Enterobacter sp. Strain UNJFSC003 for Hydrocarbon Bioremediation.

Bioremediation induced by bacteria offers a promising alternative for the contamination of aromatic hydrocarbons due to their metabolic processes suitable for the removal of these pollutants, as many of them are carcinogenic molecules and dangerous to human health. Our research focused on isolating a bacterium from the rhizosphere of the tara tree with the ability to degrade polycyclic aromatic hydrocarbons, using draft genomic sequencing and computational analysis. Enterobacter sp. strain UNJFSC 003 possesses 4460 protein-coding genes, two rRNA genes, 77 tRNA genes, and a GC content of 54.38%. A taxonomic analysis of our strain revealed that it has an average nucleotide identity (ANI) of 87.8%, indicating that it is a new native Enterobacteria. Additionally, a pangenomic analysis with 15 strains demonstrated that our strain has a phylogenetic relationship with strain FDAARGOS 1428 (Enterobacter cancerogenus), with a total of 381 core genes and 4778 accessory genes. Orthologous methods predicted that strain UNJFSC 003 possesses genes with potential for use in hydrocarbon bioremediation. Genes were predicted in the sub-pathways for the degradation of homoprotocatechuate and phenylacetate, primarily located in the cytoplasm. Studies conducted through molecular modeling and docking revealed the affinity of the predicted proteins in the degradation of benzo[a]pyrene in the homoprotocatechuate sub-pathway, specifically hpcB, which has enzymatic activity as a dioxygenase, and hpcC, which functions as an aldehyde dehydrogenase. This study provides information on native strains from Lomas de Lachay with capabilities for the bioremediation of aromatic hydrocarbons and other compounds.

Characterization of Streptococcus pyogenes Strains from Tonsillopharyngitis and Scarlet Fever Resurgence, 2023-FIRST Detection of M1UK in Bulgaria.

Recently a resurgence of Streptococcus pyogenes infections has arisen, with concerns around the highly virulent M1UK lineage. Our aim was to characterize S. pyogenes, the immune responses it causes, and to determine the presence of the M1UK lineage in Sofia, Bulgaria. In our study, the infections were confirmed by culture testing or rapid antigen test. Identification was performed by MALDI-TOF and was followed up by antibiotic susceptibility testing (EUCAST). Virulence factors were identified using multiplex PCR and whole genome sequencing (WGS). Immune responses were measured through detection of serum complement levels, lymphocyte subsets, and cytokine profiling. Out of 82 children, 38 had scarlet fever and the rest had streptococcal pharyngitis. Strains were susceptible to penicillin (β-lactams), macrolides, clindamycin, tetracyclines, co-trimoxazole, fluoroquinolones, and linezolid. Superantigen profiles were identified: SpeA + SpeJ (45%), SpeC, and SpeI + SpeH (27.5% each). A novel Multilocus sequence typing (MLST) haplotype in the mutS gene (d90b) was found in four strains. The M1UK lineage was detected for the first time in Bulgaria. We observed an increase in complement fractions C3 and C4 and a decrease in T lymphocytes. A significant increase in the levels of IFN-γ, IL-6, and IL-10 with corresponding reduction in IL-17A were revealed. In conclusion, the studied S. pyogenes strains were characterized by their susceptibility to antibiotics and the predominance of SpeA superantigen; for the first time in Bulgaria the presence of M1UK and a novel SNP variation in the mutS gene (d90b) were found. A mixed pattern of pro- and anti-inflammatory immune responses in patients was observed.

Genomic characterization of pathotype diversity and drug resistance among generic Escherichia coli isolated from broiler chickens in Canada.

Escherichia coli is a Gram-negative bacterium that is ubiquitous in animals and humans, with some strains capable of causing disease. The aim of this study was to perform a comparative genomic analysis of 2,732 generic E. coli isolates that were recovered from poultry samples collected from six regions in Canada as part of the National Microbiological Baseline study in Broiler Chicken. Isolates were subjected to whole genome sequencing and a subset (1,122/2,732) were tested for phenotypic resistance to fifteen antimicrobials. These E. coli isolates were highly diverse, representing 376 serotypes, 236 Sequence Types and twenty-one pathotypes, of which 19 were hybrid pathotypes. A high concordance (>85%) between resistance phenotype and the presence of antimicrobial resistance genes and point mutations (resistance determinants) was observed for 13/15 antimicrobials. Over 95% of the β-lactam, fluoroquinolone, and phenicol resistance genes were predicted to be plasmid-borne. The number of resistance determinants per genome was highest in Quebec, while resistance genes associated with β-lactam resistance were more frequently detected in isolates from British Columbia. Generic E. coli in Canadian poultry are highly diverse, can carry pathotype-associated virulence factors and resistance determinants of clinical significance with a risk of emerging into pathogenic strains.

Sherlock-Genome: an R Shiny application for genomic analysis and visualization

MotivationNext-generation sequencing technologies, such as whole genome sequencing (WGS), have become prominent in cancer genomics. However, managing, visualizing, and integratively analyzing WGS results across various bioinformatic pipelines remains challenging, particularly for non-bioinformaticians, hindering the usability of WGS data for biological discovery.ResultsWe developed Sherlock-Genome, an R Shiny app for data harmonization, visualization, and integrative analysis of WGS-based cancer genomics studies. Following FAIR principles, Sherlock-Genome provides a platform and guidelines for managing and sharing finalized sample-level WGS analysis results, enabling users to upload results, inspect analyses locally, and perform integrative analyses. It includes modules for major cancer genomic analyses, allowing interactive data visualizations and integrative analyses with other data types. Sherlock-Genome supports both local and cloud deployment, facilitating the sharing of results for related publications. This tool has the potential to be widely adopted in cancer genomics, significantly enhancing the accessibility and usability of sample-level WGS analysis results for comprehensive biological discovery and research advancements.Availability and implementationThe source code and installation instructions for Sherlock-Genome can be accessed via Github https://github.com/xtmgah/Sherlock-Genome. Documentation and data requirements for user project data can also be found on the same GitHub page.

A Review of the Molecular Understanding of the Mpox Virus (MPXV): Genomics, Immune Evasion, and Therapeutic Targets

The Mpox virus (MPXV), a zoonotic pathogen from the Orthopoxvirus genus, has emerged as a significant global public health concern, especially after the unprecedented outbreak in 2022. This review synthesizes the MPXV’s molecular features, focusing on its genomic structure, replication mechanisms, immune evasion strategies, and implications for diagnostics and therapeutics. The study examines the virus’s genomic organization utilizing recent peer-reviewed literature, highlighting essential genes like OPG027 and D1L, which contribute to host adaptation, increased transmissibility, and immune evasion. Advances in molecular diagnostics, including real-time PCR and genome sequencing, are reviewed, emphasizing their critical role in outbreak monitoring and control. However, challenges persist, such as diagnostic limitations in resource-constrained settings and the lack of targeted vaccines and antivirals. This review discusses new antiviral candidates, confirmed through computational and in vitro techniques, identifying thymidine kinase and VP39 as key therapeutic targets. Emphasizing the need for genomic surveillance to track adaptive evolution, results show that particular mutations, such as in the OPG027 and D1L genes, increase the transmissibility and immune evasion of the MPXV. These molecular revelations highlight the urgent necessity for better diagnostics catered towards addressing present constraints and developing focused treatments that reduce the effect of the virus. This study emphasizes how these results underscore the need for combined public health plans to handle the changing MPXV epidemiology properly.

Carotid Endarterectomy Ameliorates Cognitive Impairment in Clinical and Experimental Unilateral Carotid Artery Stenosis.

Carotid endarterectomy (CEA) is widely used to treat carotid artery stenosis (CAS). However, the effects of CEA on unilateral CAS-induced cognitive impairment and the underlying mechanism remain poorly understood. Thirteen patients diagnosed with unilateral severe CAS underwent pre- and post-CEA assessments, including 18fluoro-2-deoxy-d-glucose positron emission tomography/magnetic resonance imaging, cognitive assessments, and routine blood tests before and after CEA. Unilateral carotid common artery occlusion and ligation release (reperfusion) surgeries were performed in mice to mimic CAS and CEA. Cognitive function, cerebral blood flow, and white matter damage were evaluated in mice using the Morris water maze test, Doppler flowmetry, laser-speckle imaging, diffusion tensor imaging, Luxol fast blue staining, transmission electron microscopy, and western blot assays post unilateral carotid common artery occlusion and reperfusion. Genomic sequencing of the white matter was performed to explore the potential underlying mechanism. CEA significantly enhanced the Montreal Cognitive Assessment scores in patients with CAS and preoperative cognitive impairment. Moreover, CEA led to notable improvements in cerebral blood flow, energy metabolism, and white matter integrity, while concurrently reducing blood inflammation. In the mouse model, reperfusion surgery alleviated cognitive deficits, increased cerebral blood flow, and alleviated white matter damage following unilateral carotid common artery occlusion. Furthermore, transcriptional surveys have revealed substantial alterations in the upregulation of Nrf2 signaling and metabolic pathways, coupled with the inhibition of neuroinflammation, cellular communication, and immune cell population signaling following reperfusion. CEA ameliorated CAS-induced cognitive dysfunction by improving the cerebral functional structure. These beneficial effects may be attributed to their antioxidant and anti-inflammatory properties.

Comparative analysis of the WRKY gene family between Chimonanthus praecox and C. salicifolius.

Gene duplications provide evolutionary potentials for generating novel functions. Chimonanthus praecox and C. salicifolius are closely related species from Calycantaceae, Magnoliids. In this study, we compared the WRKY gene family from C. praecox and C. salicifolius, and predicted the potential gene function through gene expression patterns to explore the evolution of orthologous and paralogous gene pairs. A total of 73 and 85 WRKY genes were identified and analyzed from the whole genome sequencing of C. praecox and C. salicifolius. Based on the phylogenetic analysis, CpWRKY and CsWRKY genes were clustered into three groups (Group I、II、III) and 5 subgroups (Group IIa、IIb、IIc、IId、IIe). In C. praecox and C. salicifolius, we identified thirty-six and fifty-four pairs of WRKY segmental duplicated genes, respectively, along with two and three pairs of tandem duplicates, indicating that segmental duplication plays a crucial role in the evolution of Chimonanthus WRKY gene family. Most WRKY duplication gene pairs originated from segmental duplications before the first whole genome duplication (WGD), highlighting this period as a significant source of genetic diversity and functionality for the WRKY family. The analysis of WRKY gene expression levels suggests that CsWRKY18 and CsWRKY68 may promote the growth of the roots in C. salicifolius. Comparisons of expression profiles between species revealed that five orthologous gene pairs presented identical expression trends, indicating functional conservation and absence of neo-functionalization or sub-functionalization. However, most orthologous gene pairs exhibit differences in expression patterns, suggesting that they have undergone functional divergence. This functional differentiation may be due to the different selective pressures faced by C. praecox and C. salicifolius during their speciation processes. This study provided detailed information on the WRKY gene family from C. praecox and C. salicifolius, and a new insight for studying gene duplication and function evolution.

Comprehensive phylogenetic analysis of newly detected rodent adenoviruses sheds light on ancient host-switches.

Here we provide a comprehensive update on the diversity and genetic relatedness of adenoviruses occurring in rodents. Extensive PCR screenings revealed the presence of adenoviral DNA in samples originating from representatives of 17 rodent species from four different suborders of Rodentia. Distinct sequences of 28 different adenoviruses were obtained from the positive samples. Out of these, 20 were from hitherto unknown, putative novel adenoviruses, whereas 6 were variants of previously published murine adenoviruses. Additionally, two known viruses, guinea pig adenovirus 1 and squirrel adenovirus 1 were also detected. By PCR and primer walking, we determined the sequence of a considerable part of the genomic DNA of squirrel adenovirus 1, detected in red squirrel (Sciurus vulgaris) samples from Germany previously. We annotated the almost complete genome sequence of a novel mastadenovirus found by data mining in the bulk data of the Ord's kangaroo rat (Dipodomys ordii) genome project. We revisited the sequence of the gene of E1B 19 K protein of mouse adenovirus 3. In contrast to the prototype strain, where a truncated version of this gene has been found, in our sample of mouse adenovirus 3, it seemed to be intact. Based on phylogeny reconstructions, all rodent adenoviruses clustered in the genus Mastadenovirus. Interestingly, however, there wasn't a common monophyletic clade encompassing every adenovirus of rodent origin. Instead, three major lineages were observed. Because two lineages contained viral sequences deduced from samples of three suborders, and one consisted almost exclusively of adenoviruses from the family Muridae, we hypothesize there has been a long-term coevolution with the rodent hosts, as a result of possible ancient host-switch events. Several putative viruses appeared in distinct branches further away from the three clades. Thus, the evolutionary past of the adenoviruses of rodents remains to be studied further.

Complete genome sequence of bacteriophage Godfather isolated from Microbacterium foliorum.

Microbacteriophage Godfather was collected from a soil sample in Stephenville, Texas. The 17,452-bp double-stranded genome contains 24 protein-coding genes. The genome shares >99% nucleotide sequence identity with cluster EE microbacteriophages Scamander, Danno, Kojax4, and Burgy.

Mining Silent Biosynthetic Gene Clusters for Natural Products in Filamentous Fungi.

Filamentous fungi are of great interest due to their powerful metabolic capabilities and potentials to produce abundant various secondary metabolites as natural products (NPs), some of which have been developed into pharmaceuticals. Furthermore, high-throughput genome sequencing has revealed tremendous cryptic NPs underexplored. Based on the development of in silico genome mining, various techniques have been introduced to rationally modify filamentous fungi,awakening the silent biosynthetic gene clusters (BGCs) and visualizing the NPs originally cryptic. This review summarizes the key strategies and research advances in the activation of cryptic BGCs in filamentous fungi, including endogenous non-targeted activation, single-target activation, and heterologous expression. It also provides a critical evaluation of these strategies and offers perspectives on the current state of research.

Ongoing measles outbreak in Romania: Clinical investigation and molecular epidemiology performed on whole genome sequences.

Romania is currently facing a prolonged measles outbreak. The aim of the study was to analyse the circulating human measles virus (HMV) strains by combining whole genome sequencing (WGS) with phylogenetic analysis, with a focus on the haemagglutinin gene. We conducted an observational study in the first five months of 2024, in which 168 patients diagnosed with measles were randomly included. We have evaluated the clinical and epidemiological differences between children and adults. Screening for samples to be sequenced was performed with a commercial kit (PrimerDesign). WGS was done on Illumina MiSeq platform and phylogenetic analysis was performed with ML FastTree. No significant epidemiological and clinical differences between patients in the two age groups were identified. WGS was successfully performed for a number of 124 HMV strains. Genotype analysis indicated all the sequences as D8, except one that was B3. Phylogenetic analysis identified two well supported clusters, suggestive for at least two local transmission networks in Romania. One large transmission network (n = 108) consisted of sequences both from adults and children. Only one sequence from outside Romania (reported in Russia in 2023) clustered within this group. Another small transmission cluster was identified (14 sequences of which 11 from patients infected in the spring of 2024 and three in 2022). A few differences between the two co-circulating viral variants/clusters were observed. The median duration of hospitalisation was 2 days longer for patients in smaller cluster compared to those in the larger one (p = 0.019). Furthermore, these two clusters presented different mutation profiles in the hemagglutinin (HA) and neuraminidase (N) genes with implications for molecular surveillance. The current measles epidemic in Romania is driven mainly by two D8 genotype variants with different mutation profiles and slightly different severity of the disease, highlighting the usefulness of sustained molecular surveillance.

The genome sequence of the Hungarian meadow viper, Vipera ursinii rakosiensis (Méhely, 1893)

We present a genome assembly from an individual female Vipera ursinii rakosiensis (the Hungarian meadow viper; Chordata; Lepidosauria; Squamata; Viperidae). The genome sequence is 1,625.0 megabases in span. Most of the assembly is scaffolded into 19 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 17.38 kilobases in length.