A generalized structured coalescent for purifying selection without recombination.

Purifying selection is a critical factor in shaping genetic diversity. Current theoretical models mostly address scenarios of either very weak or strong selection, leaving a significant gap in our knowledge. The effects of purifying selection on patterns of genomic diversity remain poorly understood when selection against deleterious mutations is weak to moderate, particularly when recombination is limited or absent.

2024 White Paper on Recent Issues in Bioanalysis: Evolution of Immunogenicity Assessment beyond ADA/NAb; Regulated Genomic/NGS Assays; Hypersensitivity Reactions; Minimum Noise Reduction; False Positive Range; Modernized Vaccine Approaches; NAb/TAb Correlation - Recommendations on Advanced Strategies for Molecular Assays and Immunogenicity of Gene Therapy, Cell Therapy, Vaccine; Biotherapeutics Immunogenicity Assessment & Clinical Relevance - Regulatory Agencies' Input on Immunogenicity/Technologies of Biotherapeutics, Gene, Cell & Vaccine Therapies).

The 18 Workshop on Recent Issues in Bioanalysis (18 WRIB) took place in San Antonio, TX, USA on May 6-10, 2024. Over 1100 professionals representing pharma/biotech companies, CROs, and multiple regulatory agencies convened to actively discuss the most current topics of interest in bioanalysis. The 18 WRIB included 3 Main Workshops and 7 Specialized Workshops that together spanned 1 week to allow an exhaustive and thorough coverage of all major issues in bioanalysis of biomarkers, immunogenicity, gene therapy, cell therapy and vaccines.

Eight Years of Norovirus Surveillance in Urban Wastewater: Insights from Next-Generation.

Human noroviruses (HNoVs) are a leading cause of acute gastroenteritis worldwide, with significant public health implications. In this study, wastewater-based epidemiology (WBE) was used to monitor the circulation and genetic diversity of HNoVs in Rome over an eight-year period (2017-2024). A total of 337 wastewater samples were analyzed using RT-nested PCR and next-generation sequencing (NGS) to identify genogroups GI and GII and their respective genotypes.

Genomic, Evolutionary, and Pathogenic Characterization of a New in Traditional Chinese Medicine .

, a medicinal herbaceous plant documented in the Chinese Pharmacopoeia, is a promising candidate for research into plant-derived pharmaceuticals. However, the study of newly emerging viruses that threaten the cultivation of remains limited. In this study, plants exhibiting symptoms such as leaf yellowing, mottled leaves, and vein chlorosis were collected and subjected to RNA sequencing to identify potential viral pathogens.

Expanding the Diversity of : A Novel Genus from .

Six novel phages belonging to the family were isolated using as a host. Phages MuffinTheCat, Badulia, DesireeRose, Bee17, SCoupsA, and LuzDeMundo were purified from environmental samples by students participating in the Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) program at Alliance University, New York. The phages have linear dsDNA genomes 15,438-15,636 bp with 112-120 bp inverted terminal repeats.

RNA Virus Discovery Sheds Light on the Virome of a Major Vineyard Pest, the European Grapevine Moth ().

The European grapevine moth () poses a significant threat to vineyards worldwide, causing extensive economic losses. While its ecological interactions and control strategies have been well studied, its associated viral diversity remains unexplored. Here, we employ high-throughput sequencing data mining to comprehensively characterize the virome, revealing novel and diverse RNA viruses.

Serological and Molecular Characterization of the Hepatitis B Virus in Blood Donors in Maputo City, Mozambique.

Hepatitis B virus (HBV) is a major public health concern responsible for hepatitis and hepatocellular carcinoma (HCC) worldwide. In Mozambique, HBsAg prevalence is high and endemic, and despite the strategies to mitigate the spread of the disease, the HCC incidence is still high and one of the highest in the world. There is still limited data on the serological profile and molecular epidemiology of HBV in Mozambique given the burden of this disease.

Molecular Epidemiology and Genetic Evolution of Porcine Reproductive and Respiratory Syndrome Virus in Northern China During 2021-2023.

Porcine reproductive and respiratory syndrome virus (PRRSV), an important pathogen affecting the pig industry, is an RNA virus with high genetic diversity. In this study, 12,299 clinical samples were collected from northern China during 2021-2023 to investigate the molecular epidemiological characteristics and genetic evolution of PRRSV. All samples were screened using qRT-PCR and further analyzed through gene and whole-genome sequencing.

Current Situation of Goose Astrovirus in China: A Review.

Gosling gout disease is an infectious disease caused by goose astrovirus (GAstV), which can result in urate deposition in the internal organs and joints of goslings. Since 2015, outbreaks of gosling gout disease have occurred in several goose-producing areas in China. Subsequently, the disease spread to the vast majority of eastern China, becoming a major threat to goose farms and causing huge economic losses to the goose industry.

Genetic and Molecular Characterization of Avian Influenza A(H9N2) Viruses from Live Bird Markets (LBM) in Senegal.

Despite extensive experience with influenza surveillance in humans in Senegal, there is limited knowledge about the actual situation and genetic diversity of avian influenza viruses (AIVs) circulating in the country, hindering control measures and pandemic risk assessment. Therefore, as part of the "One Health" approach to influenza surveillance, we conducted active AIV surveillance in two live bird markets (LBMs) in Dakar to better understand the dynamics and diversity of influenza viruses in Senegal, obtain genetic profiles of circulating AIVs, and assess the risk of emergence of novel strains and their transmission to humans. Cloacal swabs from poultry and environmental samples collected weekly from the two LBMs were screened by RT-qPCR for H5, H7, and H9 AIVs.

Two Years of SARS-CoV-2 Omicron Genomic Evolution in Brazil (2022-2024): Subvariant Tracking and Assessment of Regional Sequencing Efforts.

SARS-CoV-2, the virus responsible for COVID-19, has undergone significant genetic evolution since its emergence in 2019. This study examines the genomic diversity of SARS-CoV-2 in Brazil after the worst phase of the pandemic, the wider adoption of routine vaccination, and the abolishment of other non-pharmacological preventive measures from July 2022 to July 2024 using 55,951 sequences retrieved from the GISAID database. The analysis focuses on the correlation between confirmed COVID-19 cases, sequencing efforts across Brazilian states, and the distribution and evolution of viral lineages.

Development of Primer Panels for Whole-Genome Amplification and Sequencing of Human Seasonal Coronaviruses: hCoV-OC43, hCoV-HKU1, hCoV-229E, and hCoV-NL63.

Human seasonal coronaviruses (hCoVs) are a group of viruses that affect the upper respiratory tract. While seasonal patterns and the annual variability of predominant hCoV species are well-documented, their genetic and species diversity in St. Petersburg and across Russia remains largely unexplored.

The Presence of Two Distinct Lineages of the Foot-And-Mouth Disease Virus Type A in Russia in 2013-2014 Has Significant Implications for the Epidemiology of the Virus in the Region.

Molecular surveillance of FMD epidemiology is a fundamental tool for advancing our understanding of virus biology, monitoring virus evolution, and guiding vaccine design. The accessibility of genetic data will facilitate a more comprehensive delineation of FMDV phylogeny on a global scale. In this study, we investigated the FMDV strains circulating in Russia during the 2013-2014 period in geographically distant regions utilizing whole genome sequencing followed by maximum-likelihood phylogenetic reconstruction of whole genome and VP1 gene sequences.

Evolutionary Trajectories of Shoots vs. Roots: Plant Volatile Metabolomes Are Richer but Less Structurally Diverse Belowground in the Tropical Tree Genus .

The breadth and depth of plant leaf metabolomes have been implicated in key interactions with plant enemies aboveground. In particular, divergence in plant species chemical composition-amongst neighbors, relatives, or both-is often suggested as a means of escape from insect herbivore enemies. Plants also experience strong pressure from enemies such as belowground pathogens; however, little work has been carried out to examine the evolutionary trajectories of species' specialized chemistries in both roots and leaves.

Dressed Up to the Nines: The Interplay of Phytohormones Signaling and Redox Metabolism During Plant Response to Drought.

Plants must effectively respond to various environmental stimuli to achieve optimal growth. This is especially relevant in the context of climate change, where drought emerges as a major factor globally impacting crops and limiting overall yield potential. Throughout evolution, plants have developed adaptative strategies for environmental stimuli, with plant hormones and reactive oxygen species (ROS) playing essential roles in their development.

Spatial Distribution of Genetic, Ploidy, and Morphological Variation of the Edaphic Steno-Endemic (Brassicaceae) from the Western Balkans.

Polyploidy is a powerful mechanism driving genetic, physiological, and phenotypic changes among cytotypes of the same species across both large and small geographic scales. These changes can significantly shape population structure and increase the evolutionary and adaptation potential of cytotypes. , an edaphic steno-endemic species with a narrow distribution in the Balkan Peninsula, serves as an intriguing case study.

Diversity and Distribution of Species Along an Elevation Gradient in Natural and Semi-Natural Forest Ecosystems in Portugal.

Globally, forests are constantly threatened by a plethora of disturbances of natural and anthropogenic origin, such as climate change, forest fires, urbanization, and pollution. Besides the most common stressors, during the last few years, Portuguese forests have been impacted by severe decline phenomena caused by invasive pathogens, many of which belong to the genus . The genus includes a large number of species that are invading forest ecosystems worldwide, chiefly as a consequence of global trade and human activities.

Inferring Tripartite Associations of Vector-Borne Plant Pathogens Using a Next-Generation Sequencing Approach.

Phytoplasmas are a group of plant-pathogenic, cell-wall-less bacteria vectored primarily by leafhoppers (Hemiptera Cicadellidae), one of the most diverse families of insects. Despite the importance of documenting associations between phytoplasmas, their insect vectors, and plant hosts to prevent disease outbreaks, such knowledge is currently highly incomplete and largely neglects the diversity of the system in natural areas. Here, we used anchored hybrid enrichment (AHE) to recover the DNA of five plant genes (, , , , and ) in 58 phloem-feeding leafhoppers from around the world that had previously tested positive for phytoplasma infection.

Molecular Markers for the Phylogenetic Reconstruction of : A Quantitative Review.

is the parasite responsible for Chagas disease, which has a significant amount of genetic diversification among the species complex. Many efforts are routinely made to characterize the genetic lineages of circulating in a particular geographic area. However, the genetic loci used to typify the genetic lineages of have not been consistent between studies.

Diversity of the Amoebozoa and Ciliophora Groups in Non-Human Primates Kept Ex Situ and in Their Handlers in Different Institutions in Brazil.

Parasitic infections in non-human primates (NHPs) kept ex situ can be caused by zoonotic protists like and . In Brazil, little is known about these infections in neotropical species. This study aimed to identify Amoebozoa and Ciliophora groups in fecal samples through in vitro isolation and molecular analysis, mapping their distribution in Brazil.

Genomic Insight into Isolates from Fresh Raw Mussels and Ready-to-Eat Stuffed Mussels.

Consuming raw or undercooked mussels can lead to gastroenteritis and septicemia due to contamination. This study analyzed the prevalence, density, species diversity, and molecular traits of spp. in 48 fresh raw wild mussels (FRMs) and 48 ready-to-eat stuffed mussels (RTE-SMs) through genome analysis, assessing health risks.

Cytomegalovirus Genetic Diversity and Evolution: Insights into Genotypes and Their Role in Viral Pathogenesis.

Cytomegalovirus (CMV) is a ubiquitous virus that infects most of the human population and causes significant morbidity and mortality, particularly among immunocompromised individuals. Understanding CMV's genetic diversity and evolutionary dynamics is crucial for elucidating its pathogenesis and developing effective therapeutic interventions. This review provides a comprehensive examination of CMV's genetic diversity and evolution, focussing on the role of different genotypes in viral pathogenesis.

Detection and Whole-Genome Characteristics of Isolated from Captive Snakes.

is a rare member of the genus , primarily associated with human wound infections rather than respiratory diseases. The bacterium has been isolated from various clinical specimens, including ear inflammatory discharge, diabetic ulcers, and chronic wounds. The study aimed to characterize the genomes and antimicrobial resistance (AMR) profiles of obtained from the fecal samples of asymptomatic highland eyelash pit vipers ().

Identification of Strains from Animal Cases in Ethiopia and Genetic Characterization by Whole-Genome Sequencing.

Anthrax is a zoonotic disease characterized by rapid onset with usual fatal outcomes in livestock and wildlife. In Ethiopia, anthrax is a persistent disease; however, there are limited data on the isolation and molecular characterization of strains. This study aimed to characterize isolated from animal anthrax outbreaks between 2019 and 2024, from different localities in Ethiopia.

Theoretical Study of Sphingomyelinases from and Sheds Light on the Evolution of Enzymes Needed for Survival and Colonization.

The path to survival for pathogenic organisms is not straightforward. Pathogens require a set of enzymes for tissue damage generation and to obtain nourishment, as well as a toolbox full of alternatives to bypass host defense mechanisms. Our group has shown that the parasitic protist encodes for 14 sphingomyelinases (SMases); one of them (acid sphingomyelinase 6, aSMase6) is involved in repairing membrane damage and exhibits hemolytic activity.