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High-Throughput Sequencing for the Detection of Viruses in Grapevine: Performance Analysis and Best Practices.
Viruses
December 2024
Foundation Plant Services, University of California-Davis, Davis, CA 95616, USA.
Among the cultivated crop species, the economically and culturally important grapevine plays host to the greatest number of distinctly characterized viruses. A critical component of the management and containment of these viral diseases in grapevine is both the identification of infected vines and the characterization of new pathogens. Next-generation high-throughput sequencing technologies, i.
View Article and Find Full Text PDFInfluenza Virus Surveillance from the 1918 Influenza Pandemic to the 2020 Coronavirus Pandemic in New York State, USA.
Viruses
December 2024
Wadsworth Center, David Axelrod Institute, New York State Department of Health, Albany, NY 12208, USA.
A historical perspective of more than one hundred years of influenza surveillance in New York State demonstrates the progression from anecdotes and case counts to next-generation sequencing and electronic database management, greatly improving pandemic preparedness and response. Here, we determined if influenza virologic surveillance at the New York State public health laboratory (NYS PHL) tests sufficient specimen numbers within preferred confidence limits to assess situational awareness and detect novel viruses that pose a pandemic risk. To this end, we analyzed retrospective electronic data on laboratory test results for the influenza seasons 1997-1998 to 2021-2022 according to sample sizes recommended in the Influenza Virologic Surveillance Right Size Roadmap issued by the Association of Public Health Laboratories and Centers for Disease Control and Prevention.
View Article and Find Full Text PDFComparative Evaluation of Open-Source Bioinformatics Pipelines for Full-Length Viral Genome Assembly.
Viruses
November 2024
Institute of Biology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary.
The increasingly widespread application of next-generation sequencing (NGS) in clinical diagnostics and epidemiological research has generated a demand for robust, fast, automated, and user-friendly bioinformatics workflows. To guide the choice of tools for the assembly of full-length viral genomes from NGS datasets, we assessed the performance and applicability of four open-source bioinformatics pipelines (shiver-for which we created a user-friendly Dockerized version, referred to as dshiver; SmaltAlign; viral-ngs; and V-pipe) using both simulated and real-world HIV-1 paired-end short-read datasets and default settings. All four pipelines produced consensus genome assemblies with high quality metrics (genome fraction recovery, mismatch and indel rates, variant calling F1 scores) when the reference sequence used for assembly had high similarity to the analyzed sample.
View Article and Find Full Text PDFA Preclinical Immunogenicity Study of the Recombinant Human Papillomavirus Nine-Valent Virus-like Particle Vaccine.
Vaccines (Basel)
November 2024
Shanghai Zerun Biotech Co., Ltd., Building 9, 1690 Zhangheng Road, Pudong, Shanghai 201203, China.
Background: Cervical cancer is associated with persistent infection of high-risk human papillomaviruses (HPVs). Prophylactic HPV vaccines have been recommended and have significant efficacy in preventing cervical cancer. Multivalent HPV vaccines have a better preventative effect on HPV-related diseases.
View Article and Find Full Text PDFNeuraminidase Antibody Response to Homologous and Drifted Influenza A Viruses After Immunization with Seasonal Influenza Vaccines.
Vaccines (Basel)
November 2024
FSBSI 'Institute of Experimental Medicine', 197022 Saint Petersburg, Russia.
Background/objectives: Humoral immunity directed against neuraminidase (NA) of the influenza virus may soften the severity of infection caused by new antigenic variants of the influenza viruses. Evaluation of NA-inhibiting (NI) antibodies in combination with antibodies to hemagglutinin (HA) may enhance research on the antibody response to influenza vaccines.
Methods: The study examined 64 pairs of serum samples from patients vaccinated with seasonal inactivated trivalent influenza vaccines (IIVs) in 2018 according to the formula recommended by the World Health Organization (WHO) for the 2018-2019 flu season.
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