Article
Biochemical Research Methods
Arifa S. Khan, Sebastiaan Theuns, Laurent Mallet, Gwenael Cirefice, Ravneet Bhuller, Ana Goios, Rajinder Suri, Pieter Neels
Summary: Next Generation Sequencing (NGS) is a new technology that can overcome limitations of current viral testing methods in biologics. A webinar organized by IABS and DCVMN introduced the technical and bioinformatics concepts of NGS, as well as its strengths and limitations in vaccine production. The 3rd Conference on NGS for Adventitious Virus Detection further discussed the scientific knowledge and readiness of NGS to replace or supplement current viral tests, and efforts are ongoing to validate and establish NGS as a new method for virus detection.
Article
Immunology
William S. Probert, Rosie Glenn-Finer, Alex Espinosa, Cynthia Yen, Lauren Stockman, Kathleen Harriman, Jill K. Hacker
Summary: In 2019, the United States saw the highest number of measles importations and cases in the post-elimination era, with more than a quarter of the cases entering through California. Measles surveillance efforts in California discovered 26 importations, 6 outbreaks, and 72 cases, highlighting the importance of maintaining appropriate vaccination status and a strong surveillance system to prevent outbreaks and preserve measles elimination status.
JOURNAL OF INFECTIOUS DISEASES
(2021)
Article
Virology
Izabela Fabianska, Stefan Borutzki, Benjamin Richter, Hon Q. Tran, Andreas Neubert, Dietmar Mayer
Summary: High-throughput sequencing (HTS) is effective in detecting both known and unknown viruses in samples, providing support for determining the safety of biological products such as vaccines. Due to the complexity of bioinformatics, standardized and reliable methods are necessary for managing HTS data. The LABRADOR analysis pipeline demonstrates reliable detection of viruses in mixtures of model viruses, vaccines, and clinical samples.
Article
Chemistry, Analytical
Ana Carolina Ferreira Balleste Ajorio, Vinicius Pessanha Rhodes, Anderson Peclat Rodrigues, Vanessa Alvaro Diniz, Greice Maria Silva da Conceicao, Stephen James Forsythe, Igor Barbosa da Silva, Marcelo Luiz Lima Brandao
Summary: The aim of this study was to establish a certified reference material (RM) for use as an internal control in the potency assay for the production chain of yellow fever vaccine. It was concluded that the new certified RM is sufficiently homogeneous and stable and can be used in routine analysis.
JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS
(2023)
Article
Immunology
Pascale Beurdeley-Fehlbaum, Matthew Pennington, Nicolas Hegerle, Melanie Albert, Amy Bennett, Justine Cheval, Allison Clark, Stephane Cruveiller, Celine Desbrousses, Janalyn Frederick, Edwige Gros, Kathryn Hunter, Tareq Jaber, Madison Gaiser, Ophelie Jouffroy, Arnaud Lamamy, Mickael Melkowski, Jennifer Moro, Paula Niksa, Shenba Pillai, Marc Eloit, Horst Ruppach
Summary: The viral safety of biological products is ensured by tests throughout the production chain. Traditional in vivo tests have limitations, and transcriptomic assay based on NGS can provide a broader detection range for viral contaminants. This supports the replacement of conventional in vivo tests for virus safety testing.
Article
Multidisciplinary Sciences
Yukie Sano, Ai Hori
Summary: Despite the availability of a rubella vaccine, there have been periodic outbreaks of the disease in Japan, primarily affecting adult males. Lack of interest in vaccination among this target population is a contributing factor. In order to gain insight into the discussion surrounding rubella and provide resources for awareness campaigns, Twitter posts related to rubella from January 2010 to May 2022 in Japanese were collected and analyzed. The study revealed a correlation between the number of rubella reports and the volume of Twitter posts, with an increase during the 2018 rubella epidemic due to vaccination campaigns and awareness-raising efforts.
Article
Microbiology
Madolyn L. MacDonald, Shawn W. Polson, Kelvin H. Lee
Summary: The detection of adventitious agents during vaccine and biotechnology-based medicine production is crucial for ensuring product safety. Rapid viral metagenomics approaches were tested for their sensitivity and specificity, with a method involving KrakenUniq showing promise for efficient viral detection. Further research is needed for establishing next-generation sequencing as a main viral detection technology.
Article
Biochemical Research Methods
Chunyan Niu, Lianhua Dong, Jiejie Zhang, Di Wang, Yunhua Gao
Summary: Nucleic acid testing is an effective method for detecting pathogens, and reference materials for respiratory syncytial virus (RSV) have been developed to improve the reliability of RSV testing. These reference materials contain RNA with specific genes of RSV and a duplex reverse transcription digital PCR method was established with specific detection limits for RSV-A and RSV-B. The certified values and uncertainties of the reference materials were determined, and they can be used to evaluate the performance of RSV detection assays.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2023)
Article
Virology
Hang Yin, Zheng Dong, Xulong Wang, Shuhao Lu, Fei Xia, Annihaer Abuduwaili, Yang Bi, Yongqiang Li
Summary: Various viruses infecting marigold plants were identified, including marigold mosaic virus and marigold cryptic virus, through deep sequencing. Genetic and phylogenetic analysis revealed the relationships between these viruses and other known viruses, enriching our understanding of viral infections in marigolds.
Article
Chemistry, Analytical
Goncalo J. Gouveia, Amanda O. Shaver, Brianna M. Garcia, Alison M. Morse, Erik C. Andersen, Arthur S. Edison, Lauren M. McIntyre
Summary: The study developed stable and sustainable reference materials (RM) using the iterative batch averaging method (IBAT), which was then applied in a metabolomics experiment to estimate the proportion of sample variation.
ANALYTICAL CHEMISTRY
(2021)
Article
Biochemical Research Methods
Jiayi Yang, Ruohui Guo, Huijie Li, Guifang Chen, Yanmin Lin, Xia Wang, Chunyan Niu, Lianhua Dong
Summary: A high order reference method based on digital PCR (dPCR) is developed for the detection of monkeypox virus (MPXV), with limits of quantification (LoQ) and detection (LoD) of 38 and 6 copies/reaction, respectively. A pseudovirus reference material (RM) containing the conserved F3L gene is developed and found to be homogeneous. Using this method, the reference value for MPXV is determined to be (2.74 +/- 0.46) x 10(3) copies/μL. Four out of six MPXV test kits tested with this RM fail to reach their claimed LoDs, which can lead to false-negative results and incorrect diagnosis and treatment. The establishment of a high order reference method using dPCR and pseudovirus RM is crucial for improving the accuracy and reliability of MPXV detection.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Delphine Yeghicheyan, Patricia Grinberg, Laurent Y. Alleman, Moustafa Belhadj, Lea Causse, Jerome Chmeleff, Laure Cordier, Irina Djouraev, David Dumoulin, Jean Dumont, Remi Freydier, Helene Mariot, Christophe Cloquet, Paramee Kumkrong, Bruno Malet, Catherine Jeandel, Aurelie Marquet, Jean Riotte, Mickael Tharaud, Gabriel Billon, Guillaume Trommetter, Fabienne Seby, Abel Guihou, Pierre Deschamps, Zoltan Mester
Summary: The Isotrace CNRS workgroup, in collaboration with the National Research Council of Canada, characterized trace element mass fractions and isotope ratios in the AQUA-1 natural drinking water reference material. The study expands the material's use as a tool for environmental quality control and method validation. Additionally, analysis of SLRS-6 river water was conducted for quality control and comparison with treated water from the same area.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2021)
Article
Oncology
Rongxue Peng, Guigao Lin, Lin Li, Jinming Li
Summary: In this study, novel formalin-fixed and paraffin-embedded (FFPE) samples were developed as reference materials for tumor mutational burden (TMB) estimation. These samples demonstrated sufficient quantity, high reproducibility, and provided matched wild type samples as the genetic background. They can be used for validation, verification, internal quality control, and proficiency testing of TMB assessment.
FRONTIERS IN ONCOLOGY
(2022)
Article
Virology
Lizheng Guan, Gongxun Zhong, Shufang Fan, Erin M. Plisch, Robert Presler, Chunyang Gu, Lavanya Babujee, David Pattinson, Hang Le Khanh Nguyen, Vu Mai Phuong Hoang, Mai Quynh Le, Harm van Bakel, Gabriele Neumann, Yoshihiro Kawaoka
Summary: Surveillance in Vietnam's northern live poultry markets identified 27 highly pathogenic avian influenza H5N1 and H5N6 viruses from 2016 to 2017, belonging to 3 different clades. Sequencing and phylogenetic analysis revealed reassortment with low pathogenic avian influenza viruses and identified minor viral subpopulations encoding variants that may affect pathogenicity and antiviral drug sensitivity. Mice infected with clade 2.3.2.1c viruses rapidly lost weight and died, while those infected with clade 2.3.4.4f or 2.3.4.4g experienced non-lethal infections.
Article
Biotechnology & Applied Microbiology
Chenge Yan, Hang Yin, Yongjiang Zhang, Zhengguang Ren, Jinzhong Wang, Yongqiang Li
Summary: Two new viruses infecting jujube plants were identified, and mixed infections of JYMaV and JaBV were common in jujube in Beijing.
INTERNATIONAL MICROBIOLOGY
(2023)
Article
Infectious Diseases
H. A. Shaw, M. D. Preston, K. E. W. Vendrik, M. D. Cairns, H. P. Browne, R. A. Stabler, M. J. T. Crobach, J. Corver, H. Pituch, A. Ingebretsen, M. Pirmohamed, A. Faulds-Pain, E. Valiente, T. D. Lawley, N. F. Fairweather, E. J. Kuijper, B. W. Wren
CLINICAL MICROBIOLOGY AND INFECTION
(2020)
Review
Biotechnology & Applied Microbiology
Paul Kellam, Wendy Barclay
JOURNAL OF GENERAL VIROLOGY
(2020)
Article
Virology
D. C. Busse, D. Habgood-Coote, S. Clare, C. Brandt, I. Bassano, M. Kaforou, J. Herberg, M. Levin, J. -F. Eleouet, P. Kellam, J. S. Tregoning
JOURNAL OF VIROLOGY
(2020)
Correction
Biology
Camilla T. O. Benfield, Farrell MacKenzie, Markus Ritzefeld, Michela Mazzon, Stuart Weston, Edward W. Tate, Boon Han Teo, Sarah E. Smith, Paul Kellam, Edward C. Holmes, Mark Marsh
LIFE SCIENCE ALLIANCE
(2020)
Letter
Medicine, General & Internal
Nisreen A. Alwan, Rochelle Ann Burgess, Simon Ashworth, Rupert Beale, Nahid Bhadelia, Debby Bogaert, Jennifer Dowd, Isabella Eckerle, Lynn R. Goldman, Trisha Greenhalgh, Deepti Gurdasani, Adam Hamdy, William P. Hanage, Emma B. Hodcroft, Zoe Hyde, Paul Kellam, Michelle Kelly-Irving, Florian Krammer, Marc Lipsitch, Alan McNally, Martin McKee, Ali Nouri, Dominic Pimenta, Viola Priesemann, Harry Rutter, Joshua Silver, Devi Sridhar, Charles Swanton, Rochelle P. Walensky, Gavin Yamey, Hisham Ziauddeen
Article
Developmental Biology
Alice Neal, Svanhild Nornes, Pakavarin Louphrasitthiphol, Natalia Sacilotto, Mark D. Preston, Lucija Fleisinger, Sophie Payne, Sarah De Val
Summary: These results suggest that ETS factors are essential for vein, arterial and angiogenic-specific enhancer activities, but the specificity of VEGFA-induced arterial and angiogenic enhancer activity is regulated by non-ETS transcription factors.
DEVELOPMENTAL BIOLOGY
(2021)
Article
Medicine, Research & Experimental
Eve Richardson, Jacob D. Galson, Paul Kellam, Dominic F. Kelly, Sarah E. Smith, Anne Palser, Simon Watson, Charlotte M. Deane
Summary: This study introduces a method for clustering antibodies with common antigen reactivity from different clonotypes using the antibody binding site. Experimental validation on a pertussis toxoid dataset confirmed that even the simplest abstraction of the antibody binding site is sufficient to group antigen-specific antibodies and provide additional information for conventional clonotype analysis.
Correction
Multidisciplinary Sciences
Mailis Maes, Zoe A. Dyson, Sarah E. Smith, David A. Goulding, Catherine Ludden, Stephen Baker, Paul Kellam, Stephen T. Reece, Gordon Dougan, Josefin Bartholdson Scott
SCIENTIFIC REPORTS
(2021)
Article
Microbiology
Alexander G. Shaw, Kathleen Sim, Graham Rose, David J. Wooldridge, Ming-Shi Li, Raju Misra, Saheer Gharbia, J. Simon Kroll
Summary: The study identified two distinct microbial community patterns in infants with necrotising enterocolitis (NEC): one with low levels of CpG DNA and another with high abundances of LPS-expressing organisms. These patterns may represent extremes of TLR4 pathway stimulation.
Article
Multidisciplinary Sciences
Kathryn M. Hastie, Haoyang Li, Daniel Bedinger, Sharon L. Schendel, S. Moses Dennison, Kan Li, Vamseedhar Rayaprolu, Xiaoying Yu, Colin Mann, Michelle Zandonatti, Ruben Diaz Avalos, Dawid Zyla, Tierra Buck, Sean Hui, Kelly Shaffer, Chitra Hariharan, Jieyun Yin, Eduardo Olmedillas, Adrian Enriquez, Diptiben Parekh, Milite Abraha, Elizabeth Feeney, Gillian Q. Horn, Yoann Aldon, Hanif Ali, Sanja Aracic, Ronald R. Cobb, Ross S. Federman, Joseph M. Fernandez, Jacob Glanville, Robin Green, Gevorg Grigoryan, Ana G. Lujan Hernandez, David D. Ho, Kuan-Ying A. Huang, John Ingraham, Weidong Jiang, Paul Kellam, Cheolmin Kim, Minsoo Kim, Hyeong Mi Kim, Chao Kong, Shelly J. Krebs, Fei Lan, Guojun Lang, Sooyoung Lee, Cheuk Lun Leung, Junli Liu, Yanan Lu, Anna MacCamy, Andrew T. McGuire, Anne L. Palser, Terence H. Rabbitts, Zahra Rikhtegaran Tehrani, Mohammad M. Sajadi, Rogier W. Sanders, Aaron K. Sato, Liang Schweizer, Jimin Seo, Bingqing Shen, Jonne L. Snitselaar, Leonidas Stamatatos, Yongcong Tan, Milan T. Tomic, Marit J. van Gils, Sawsan Youssef, Jian Yu, Tom Z. Yuan, Qian Zhang, Bjoern Peters, Georgia D. Tomaras, Timothy Germann, Erica Ollmann Saphire
Summary: Antibody-based therapeutics and vaccines are crucial in combating COVID-19, especially with mutations and transmission of SARS-CoV-2. An international consortium identified multiple RBD-directed antibody communities, providing a framework for selecting treatment cocktails.
Article
Microbiology
Joanna Houghton, Angela Rodgers, Graham Rose, Alexandre D'Halluin, Terry Kipkorir, Declan Barker, Simon J. Waddell, Kristine B. Arnvig
Summary: Studies have found that the sRNA F6 of Mycobacterium tuberculosis is up-regulated under starvation conditions, which may play a role in the long-term survival of the bacterium in human granulomas.
MICROBIOLOGY SPECTRUM
(2021)
Article
Multidisciplinary Sciences
Chris Wymant, Daniela Bezemer, Francois Blanquart, Luca Ferretti, Astrid Gall, Matthew Hall, Tanya Golubchik, Margreet Bakker, Swee Hoe Ong, Lele Zhao, David Bonsall, Mariateresa de Cesare, George MacIntyre-Cockett, Lucie Abeler-Doerner, Jan Albert, Norbert Bannert, Jacques Fellay, M. Kate Grabowski, Barbara Gunsenheimer-Bartmeyer, Huldrych F. Gunthard, Pia Kivela, Roger D. Kouyos, Oliver Laeyendecker, Laurence Meyer, Kholoud Porter, Matti Ristola, Ard van Sighem, Ben Berkhout, Paul Kellam, Marion Cornelissen, Peter Reiss, Christophe Fraser
Summary: A highly virulent variant of subtype-B HIV-1 was discovered in the Netherlands. Infected individuals with this variant had significantly higher viral loads and faster decline in CD4 cells compared to other subtype-B strains. The increased virulence is attributed to the viral strain, and the variant emerged in the 1990s with increased transmissibility and an unfamiliar molecular mechanism of virulence.
Article
Cell Biology
Elaine Thai, Rajagopal Murugan, Spela Binter, Clare Burn Aschner, Katherine Prieto, Audrey Kassardjian, Anna S. Obraztsova, Ryu Won Kang, Yevel Flores-Garcia, Shamika Mathis-Torres, Kan Li, Gillian Q. Horn, Richard H. C. Huntwork, Judith M. Bolscher, Marloes H. C. de Bruijni, Robert Sauerwein, S. Moses Dennison, Georgia D. Tomaras, Fidel Zavala, Paul Kellam, Hedda Wardemann, Jean-Philippe Julien
Summary: IGHV3-33-encoded antibodies play a crucial role in the human immune response against Plasmodium falciparum. This study investigated the molecular basis of antibody cross-reactivity and its relationship with efficacy. The findings provide insights into the development of antibody-based interventions against malaria.
Article
Virology
Lele Zhao, Chris Wymant, Francois Blanquart, Tanya Golubchik, Astrid Gall, Margreet Bakker, Daniela Bezemer, Matthew Hall, Swee Hoe Ong, Jan Albert, Norbert Bannert, Jacques Fellay, M. Kate Grabowski, Barbara Gunsenheimer-Bartmeyer, Huldrych F. Gunthard, Pia Kivela, Roger D. Kouyos, Oliver Laeyendecker, Laurence Meyer, Kholoud Porter, Ard van Sighem, Marc van der Valk, Ben Berkhout, Paul Kellam, Marion Cornelissen, Peter Reiss, Christophe Fraser, Luca Ferretti
Summary: This study investigates the relationship between viral load and transmission fitness in HIV-1. The results suggest that higher set-point viral load is associated with increased infectiousness and transmission fitness. This finding has implications for understanding the evolution and spread of HIV-1.
Article
Biology
Camilla T. O. Benfield, Farrell MacKenzie, Markus Ritzefeld, Michela Mazzon, Stuart Weston, Edward Tate, Boon Han Teo, Sarah E. Smith, Paul Kellam, Edward C. Holmes, Mark Marsh
LIFE SCIENCE ALLIANCE
(2020)