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Unlabelled: Herpes simplex virus (HSV) is a widespread pathogen that causes epithelial lesions with recurrent disease that manifests over a lifetime. The lifelong aspect of infection results from latent viral infection of neurons, a reservoir from which the virus reactivates periodically. Recent work has demonstrated the breadth of genetic variation in globally distributed HSV strains. However, the amount of variation or capacity for mutation within one strain has not been well studied. Here we developed and applied a streamlined new approach for assembly and comparison of large DNA viral genomes such as HSV-1. This viral genome assembly (VirGA) workflow incorporates a combination of de novo assembly, alignment, and annotation strategies to automate the generation of draft genomes for large viruses. We applied this approach to quantify the amount of variation between clonal derivatives of a common parental virus stock. In addition, we examined the genetic basis for syncytial plaque phenotypes displayed by a subset of these strains. In each of the syncytial strains, we found an identical DNA change, affecting one residue in the gB (UL27) fusion protein. Since these identical mutations could have appeared after extensive in vitro passaging, we applied the VirGA sequencing and comparison approach to two clinical HSV-1 strains isolated from the same patient. One of these strains was syncytial upon first culturing; its sequence revealed the same gB mutation. These data provide insight into the extent and origin of genome-wide intrastrain HSV-1 variation and present useful methods for expansion to in vivo patient infection studies.
Importance: Herpes simplex virus (HSV) infects more than 70% of adults worldwide, causing epithelial lesions and recurrent disease that manifests over a lifetime. Prior work has demonstrated that HSV strains vary from country to country and between individuals. However, the amount of variation within one strain has not been well studied. To address this, we developed a new approach for viral genome assembly (VirGA) and analysis. We used this approach to quantify the amount of variation between sister clones of a common parental virus stock and to determine the basis of a unique fusion phenotype displayed by several variants. These data revealed that while sister clones of one HSV stock are more than 98% identical, these variants harbor enough genetic differences to change their observed characteristics. Comparative genomics approaches will allow us to explore the impacts of viral inter- and intrastrain diversity on drug and vaccine efficacy.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4453532 | PMC |
http://dx.doi.org/10.1128/mBio.02213-14 | DOI Listing |
J Chem Phys
December 2024
Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
Sequencing-based Hi-C technology has been widely used to study the three-dimensional structure of chromatin. More recently, the development of single-cell Hi-C technology has enabled the study of chromatin structural variations between individual cells. However, single-cell Hi-C data are often highly sparse, necessitating the use of imputation algorithms to address insufficient sampling.
View Article and Find Full Text PDFEur Neuropsychopharmacol
December 2024
Bipolar and Depressive Disorders Unit, Hospital Clinic de Barcelona, Barcelona, Spain; Fundació Clínic per la Recerca Biomèdica-Institut d'Investigacions Biomèdiques August Pi i Sunyer (FCRB-IDIBAPS), Barcelona, Spain; Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain.
Older Adults with Bipolar Disorder (OABD) represent a heterogeneous group, including those with early and late onset of the disorder. Recent evidence shows both groups have distinct clinical, cognitive, and medical features, tied to different neurobiological profiles. This study explored the link between polygenic risk scores (PRS) for bipolar disorder (PRS-BD), schizophrenia (PRS-SCZ), and major depressive disorder (PRS-MDD) with age of onset in OABD.
View Article and Find Full Text PDFPLoS Negl Trop Dis
December 2024
Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America.
Bacillus cereus biovar anthracis (Bcbva) causes anthrax-like disease in animals, particularly in the non-human primates and great apes of West and Central Africa. Genomic analyses revealed Bcbva as a member of the B. cereus species that carries two plasmids, pBCXO1 and pBCXO2, which have high sequence homology to the B.
View Article and Find Full Text PDFBreastfeed Med
December 2024
Pediatrics Infectious Diseases Research Center, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran.
This study aimed to investigate the influence of newborns' sex on the concentrations of minor and trace elements in the human milk of lactating mothers during early lactation. The elemental analysis focused on calcium (Ca), potassium (K), sodium (Na), and chlorine (Cl) as minor elements and iodine (I), aluminum (Al), bromine (Br), and rubidium (Rb) as trace elements. Breast milk samples were collected from 75 lactating mothers in Tehran, Iran, during the early feeding stage.
View Article and Find Full Text PDFEur J Clin Pharmacol
December 2024
Health Management and Economics Research Center, Health Management Research Institute, Iran University of Medical Sciences, Tehran, Iran.
Purpose: This study aimed to systematically review the cost-effectiveness of rivaroxaban plus aspirin (RIV + ASA) versus aspirin (ASA) alone in patients with stable coronary artery disease (CAD) or peripheral artery disease (PAD).
Methods: A systematic review was conducted using leading databases including PubMed, Scopus, and Web of Science core collection. The search was carried out up to June 25, 2024, focusing on identifying full economic evaluation studies comparing the cost-effectiveness of RIV + ASA versus ASA alone in patients with stable cardiovascular diseases (CVDs).
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