Article
Cell Biology
M. Cyrus Maher, Istvan Bartha, Steven Weaver, Julia di Iulio, Elena Ferri, Leah Soriaga, Florian A. Lempp, Brian L. Hie, Bryan Bryson, Bonnie Berger, David L. Robertson, Gyorgy Snell, Davide Corti, Herbert W. Virgin, Sergei L. Kosakovsky Pond, Amalio Telenti
Summary: This study predicts future variants of SARS-CoV-2 by analyzing various factors affecting its evolution, including ACE2-mediated transmissibility and host immunity. The researchers successfully identified mutations that will emerge in different phases of the pandemic and assessed their impact on therapeutic antibodies. This modeling approach has important implications for predicting emerging variants of SARS-CoV-2 and can be applied to other rapidly evolving pathogens.
SCIENCE TRANSLATIONAL MEDICINE
(2022)
Article
Biochemical Research Methods
Rui Yin, Zihan Luo, Pei Zhuang, Zhuoyi Lin, Chee Keong Kwoh
Summary: This article proposes a new method VirPreNet for predicting the virulence of influenza A viruses, using a weighted ensemble convolutional neural network. Experimental results show that VirPreNet performs excellently on influenza dataset, outperforming baseline methods, and revealing the importance of PB2 and HA segments in virulence prediction.
Review
Endocrinology & Metabolism
Lies Langouche, Arno Teblick, Jan Gunst, Greet Van den Berghe
Summary: Based on recent insights, the classical concept of an activated hypothalamus-pituitary-adrenocortical axis in response to critical illness is in need of revision. Peripheral adaptations play a more significant role in maintaining increased systemic cortisol availability and action in response to critical illness than centrally activated cortisol production and secretion. These adaptations include suppressed cortisol metabolism, alterations in expression of certain proteins, and negative feedback inhibition at the pituitary level. Prolonged critical illness may lead to central adrenal insufficiency.
Article
Multidisciplinary Sciences
Raquel Viana, Sikhulile Moyo, Daniel G. Amoako, Houriiyah Tegally, Cathrine Scheepers, Christian L. Althaus, Ugochukwu J. Anyaneji, Phillip A. Bester, Maciej F. Boni, Mohammed Chand, Wonderful T. Choga, Rachel Colquhoun, Michaela Davids, Koen Deforche, Deelan Doolabh, Louis du Plessis, Susan Engelbrecht, Josie Everatt, Jennifer Giandhari, Marta Giovanetti, Diana Hardie, Verity Hill, Nei-Yuan Hsiao, Arash Iranzadeh, Arshad Ismail, Charity Joseph, Rageema Joseph, Legodile Koopile, Sergei L. Kosakovsky Pond, Moritz U. G. Kraemer, Lesego Kuate-Lere, Oluwakemi Laguda-Akingba, Onalethatha Lesetedi-Mafoko, Richard J. Lessells, Lockman, Alexander G. Lucaci, Arisha Maharaj, Boitshoko Mahlangu, Tongai Maponga, Kamela Mahlakwane, Zinhle Makatini, Gert Marais, Dorcas Maruapula, Kereng Masupu, Mogomotsi Matshaba, Simnikiwe Mayaphi, Nokuzola Mbhele, Mpaphi B. Mbulawa, Adriano Mendes, Koleka Mlisana, Anele Mnguni, Thabo Mohale, Monika Moir, Kgomotso Moruisi, Mosepele Mosepele, Gerald Motsatsi, Modisa S. Motswaledi, Thongbotho Mphoyakgosi, Nokukhanya Msomi, Peter N. Mwangi, Yeshnee Naidoo, Noxolo Ntuli, Martin Nyaga, Lucier Olubayo, Sureshnee Pillay, Botshelo Radibe, Yajna Ramphal, Upasana Ramphal, James E. San, Lesley Scott, Roger Shapiro, Lavanya Singh, Pamela Smith-Lawrence, Wendy Stevens, Amy Strydom, Kathleen Subramoney, Naume Tebeila, Derek Tshiabuila, Joseph Tsui, Stephanie van Wyk, Steven Weaver, Constantinos K. Wibmer, Eduan Wilkinson, Nicole Wolter, Alexander E. Zarebski, Boitumelo Zuze, Dominique Goedhals, Wolfgang Preiser, Florette Treurnicht, Marietje Venter, Carolyn Williamson, Oliver G. Pybus, Jinal Bhiman, Allison Glass, Darren P. Martin, Andrew Rambaut, Simani Gaseitsiwe, Anne von Gottberg, Tulio de Oliveira
Summary: The SARS-CoV-2 epidemic in southern Africa has experienced three distinct waves, driven by different variants. The recently identified Omicron variant has rapidly spread in South Africa and to numerous countries, raising global concern.
Article
Microbiology
Kathryn E. Kistler, John Huddleston, Trevor Bedford
Summary: This study quantifies the impact of adaptive evolution on the accumulation of mutations in the genome of SARS-CoV-2 and identifies spike S1 protein as the focus of adaptive evolution. The study also reveals positively selected mutations in other proteins that are shaping the evolutionary trajectory of SARS-CoV-2.
CELL HOST & MICROBE
(2022)
Article
Biochemistry & Molecular Biology
Jiuxing Li, Zijie Zhang, Jimmy Gu, Hannah D. Stacey, Jann C. Ang, Alfredo Capretta, Carlos D. M. Filipe, Karen L. Mossman, Cynthia Balion, Bruno J. Salena, Deborah Yamamura, Leyla Soleymani, Matthew S. Miller, John D. Brennan, Yingfu Li
Summary: In vitro selection experiments identified DNA aptamers, MSA1 and MSA5, with strong binding affinity to the S1 subunit of the SARS-CoV-2 spike protein. These aptamers demonstrated comparable affinities for various forms of S1 protein and also recognized the pseudotyped lentivirus of SARS-CoV-2, highlighting their potential as diagnostic tools for COVID-19 detection. The development of a colorimetric sandwich assay using MSA1 further confirmed the utility of these aptamers in detecting the virus in saliva samples.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Meteorology & Atmospheric Sciences
Thomas von Clarmann, Steven Compernolle, Frank Hase
Summary: Contrary to GUM-2008, the error concept and the uncertainty concept are the same. The arguments in favor of the contrary have been found to be unconvincing and no evidence has been presented that errors and uncertainties define a different relation between the measured and true values of the variable of interest.
ATMOSPHERIC MEASUREMENT TECHNIQUES
(2022)
Article
Chemistry, Multidisciplinary
Wei-Tao Dou, Xiang Wang, Tingting Liu, Suwen Zhao, Jiao-Jiao Liu, Yao Yan, Jun Li, Chi-Yu Zhang, Adam C. Sedgwick, He Tian, Jonathan L. Sessler, Dong-Ming Zhou, Xiao-Peng He
Summary: In this study, a method for detecting influenza A viruses using sialyl-glycan-functionalized probes was reported. The method allows for differentiation of different IAV subtypes and determination of IAVs specific to individual species. It can also be used for preliminary assessment of adenovirus vaccines specific to a given IAV strain.
Article
Biochemical Research Methods
William T. Harvey, Vinny Davies, Rodney S. Daniels, Lynne Whittaker, Victoria Gregory, Alan J. Hay, Dirk Husmeier, John W. McCauley, Richard Reeve
Summary: The author develops a model to accurately map genotype-to-phenotype relationships in order to control seasonal influenza viruses. By incorporating protein structural data, the model improves the reliability of genotype-to-phenotype mapping and can accurately predict antigenic assay values for unknown viruses.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Mariona Torrens-Fontanals, Alejandro Peralta-Garcia, Carmine Talarico, Ramon Guixa-Gonzalez, Toni Giorgino, Jana Selent
Summary: SCoV2-MD is an online resource that organizes atomistic simulations of the SARS-CoV-2 proteome. It cross-references molecular data with pandemic evolution and allows interactive analysis through a web interface for studying the structure and function of viral proteins.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Chemistry, Medicinal
Christoph Oehlknecht, Sonja Katz, Christina Kroess, Bernhard Sprenger, Petra Engele, Rainer Schneider, Chris Oostenbrink
Summary: The article introduces an efficient method for calculating protein binding free energies by combining the one-step perturbation and the third-power fitting approach. Experimental in silico saturation mutagenesis confirms the method's high accuracy in predicting relative free energies of amino acid mutations.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Biochemistry & Molecular Biology
Kamyab Javanmardi, Chia-Wei Chou, Cynthia Terrace, Ankur Annapareddy, Tamer S. Kaoud, Qingqing Guo, Josh Lutgens, Hayley Zorkic, Andrew P. Horton, Elizabeth C. Gardner, Giaochau Nguyen, Daniel R. Boutz, Jule Goike, William N. Voss, Hung-Che Kuo, Kevin N. Dalby, Jimmy D. Gollihar, Ilya J. Finkelstein
Summary: The Spike Display platform characterized 200 variant SARS-CoV-2 spikes, revealing a public epitope in the N-terminal domain loops that is recognized by most NTD-binding nAbs. Mutations in NTDs of variants like B.1.1.7, B.1.351, B.1.1.28, B.1.427/B.1.429, and B.1.617.2 impact spike expression and escape most NTD-targeting nAbs. Certain variants like B.1.351 and B.1.1.28 completely evade binding by a potent ACE2 mimic.
Article
Multidisciplinary Sciences
Weiwei Ji, Qi Peng, Xueqiong Fang, Zehou Li, Yaxin Li, Cunfa Xu, Shuqing Zhao, Jizong Li, Rong Chen, Guoxiang Mo, Zhanyong Wei, Ying Xu, Bin Li, Shuijun Zhang
Summary: Researchers have reported the structures of porcine deltacoronavirus (PDCoV) spike protein bound to aminopeptidase receptors in pigs and humans, shedding light on the potential mechanism of cross-species transmission of the virus. The study found that PDCoV can infect various animals and humans, using aminopeptidase N from different host species as receptors to enter cells. The detailed mechanism of how PDCoV recognizes homologous receptors and insights into the cross-species transmission of the virus were provided.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Marine Biget, Tingting Wang, Cendrine Mony, Qicheng Xu, Lucie Lecoq, Veronique Chable, Kevin R. Theis, Ning Ling, Philippe Vandenkoornhuyse
Summary: The hologenome concept views the host and its microbiota as a new level of organization. A study on grafted plants reveals that the microbiota composition differs between grafted and ungrafted hosts, and the recruitment of microorganisms in chimeric plants is influenced by both the rootstock and scion. This study supports the hologenome concept and provides new insights into the understanding of plants as holobionts.
Article
Multidisciplinary Sciences
Chunyan Wang, Emma L. Hesketh, Tatiana M. Shamorkina, Wentao Li, Peter J. Franken, Dubravka Drabek, Rien van Haperen, Sarah Townend, Frank J. M. van Kuppeveld, Frank Grosveld, Neil A. Ranson, Joost Snijder, Raoul J. de Groot, Daniel L. Hurdiss, Berend-Jan Bosch
Summary: Through structural analysis, insights into the binding sites and breadth of neutralizing antibodies against human coronavirus OC43 are provided. The virus persists in the population through recurring infections and has variable antibody binding sites. These findings contribute to the understanding of protective immunity and adaptive evolution for this coronavirus.
NATURE COMMUNICATIONS
(2022)
