Article
Virology
Andre Felipe Streck, Claudio Wageck Canal, Uwe Truyen
Summary: This study found that mutant strains of the 27a-like porcine parvovirus have a clear advantage in replication efficiency and antibody binding activity. These mutant viruses modify viral fitness and antigenicity, possibly as a result of viral adaptation to immune response against commercial vaccines.
JOURNAL OF VIROLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Suparat Taengchaiyaphum, Prapatsorn Wongkhaluang, Kanchana Sittikankaew, Nitsara Karoonuthaisiri, Timothy W. Flegel, Kallaya Sritunyalucksana
Summary: Shrimp have the ability to accommodate viruses in long term, persistent infections without signs of disease. EVE in shrimp genome may play a role in this process to dampen viral replication. Specificity of EVE clusters could be advantageous for genetic improvement in shrimp breeding.
Article
Virology
Robert A. Lopez-Astacio, Oluwafemi F. Adu, Daniel J. Goetschius, Hyunwook Lee, Wendy S. Weichert, Brian R. Wasik, Simon P. Frueh, Brynn K. Alford, Ian E. H. Voorhees, Joseph F. Flint, Sarah Saddoris, Laura B. Goodman, Edward C. Holmes, Susan L. Hafenstein, Colin R. Parrish
Summary: Canine parvovirus (CPV) is a small DNA virus that causes serious diseases in dogs worldwide. In this study, in vitro selection and deep sequencing were used to investigate the escape mutations in CPV induced by two antibodies. The results provide insights into the selection of viral variants and the interactions between antibodies and receptors.
JOURNAL OF VIROLOGY
(2023)
Article
Computer Science, Interdisciplinary Applications
Jorge Lopez-Ruiz, Salvador Botello-Rionda, Rafael Herrera-Guzman, Mauricio Carrillo-Tripp
Summary: Viruses affect all forms of life and their relevance cannot be overstated. This work describes a methodology to generate mesh representations of viral capsids and evaluates their response through simulations using high performance computing techniques.
MATHEMATICS AND COMPUTERS IN SIMULATION
(2023)
Article
Immunology
Suparat Taengchaiyaphum, Phasini Buathongkam, Suchitraporn Sukthaworn, Prapatsorn Wongkhaluang, Kallaya Sritunyalucksana, Timothy William Flegel
Summary: This study reveals the existence of endogenous reverse transcriptase mechanisms in shrimp similar to those found in insects to inhibit viral replication. Extracted circular viral copy DNA from giant tiger shrimp significantly reduced the replication of infectious hypodermal and hematopoietic necrosis virus. The discovery that endogenous viral elements can give rise to cvcDNA provides a new pathway for using cvcDNA to enhance shrimp tolerance to viruses.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Yiqiao Li, Magda Bletsa, Zafeiro Zisi, Ine Boonen, Sophie Gryseels, Liana Kafetzopoulou, Joanne P. Webster, Stefano Catalano, Oliver G. Pybus, Frederik Van de Perre, Haotian Li, Yaoyao Li, Yuchun Li, Alexei Abramov, Petros Lymberakis, Philippe Lemey, Sebastian Lequime
Summary: A study discovered endogenous viral elements (EVEs) derived from the Flaviviridae family in mammalian genomes, particularly in the Indochinese shrew. These newly identified EVEs were also found in 27 shrew species, suggesting an ancient origin of pestiviruses and Flaviviridae as well as the possible role of shrews as natural reservoirs for pestiviruses.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Virology
Thomas Labadie, Deborah Garcia, Doriane Mutuel, Mylene Ogliastro, Guillaume Cambray
Summary: The study attempted to engineer insect parvovirus and found that the translocation of nonstructural genes led to replication defects, suggesting intricate replication mechanisms in viral genomes.
JOURNAL OF VIROLOGY
(2021)
Article
Biochemistry & Molecular Biology
Ieva Rinkunaite, Egidijus Simoliunas, Daiva Bironaite, Rasa Rutkiene, Virginija Bukelskiene, Rolandas Meskys, Julius Bogomolovas
Summary: The unique region VP1u plays a crucial role in B19V's tropism for erythroid precursor cells, but its interaction with endothelial cells leads to upregulation of cellular stress signaling pathways, potentially causing endothelial damage during acute B19V infection.
Article
Multidisciplinary Sciences
Manish Gupta, Alexander J. Pak, Gregory A. Voth
Summary: Researchers use molecular dynamics simulations to reveal the molecular mechanism of HIV-1 capsid formation, including the role of IP6. This study shows that IP6 initially promotes curvature generation by trapping pentameric defects and shifts the assembly behavior towards kinetically favored outcomes. Additionally, IP6 can stabilize metastable capsid intermediates and induce structural pleomorphism in mature capsids.
Article
Virology
Angelica Bravo, Leandro Fernandez-Garcia, Rodrigo Ibarra-Karmy, Gonzalo A. Mardones, Luis Mercado, Fernando J. Bustos, Robert J. Gifford, Gloria Arriagada
Summary: Endogenous viral elements (EVEs) are genomic DNA sequences derived from viruses and some of them can express proteins with physiological roles in their host. In this study, we found that DeRep, a protein encoded in an endogenous parvoviral element (EPV), demonstrated antiviral activity against an exogenous parvovirus in degu cells. This is the first time an EPV has been shown to have such activity.
Article
Multidisciplinary Sciences
Tong Zhang, Hedvig Tamman, Kyo Coppieters 't Wallant, Tatsuaki Kurata, Michele LeRoux, Sriram Srikant, Tetiana Brodiazhenko, Albinas Cepauskas, Ariel Talavera, Chloe Martens, Gemma C. Atkinson, Vasili Hauryliuk, Abel Garcia-Pino, Michael T. Laub
Summary: In this study, a bacterial immune system called CapRel(SJ46) was identified that protects Escherichia coli from diverse phages by sensing specific proteins of the phages. The sensing and molecular mechanisms of CapRel(SJ46) were revealed, providing new insights into bacterial immune systems.
Article
Microbiology
Jucai Wang, Yunchao Liu, Yumei Chen, Teng Zhang, Aiping Wang, Qiang Wei, Dongmin Liu, Fangyu Wang, Gaiping Zhang
Summary: Porcine parvovirus (PPV) is a significant cause of reproductive failure in swine, with its viral protein 2 (VP2) playing a crucial role in capsid assembly and hemagglutination (HA) activity. Deletion and site-directed mutations within the N-terminal region of VP2 were studied, revealing the importance of residue 47 in assembly efficiency and residue 48 in stability and HA activity. Understanding these residues provides insights into PPV capsid assembly mechanisms and potential vaccine development using chimeric VLPs.
VETERINARY MICROBIOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Dominik Witzigmann, Philip Grossen, Cristina Quintavalle, Manuela Lanzafame, Susanne H. Schenk, Xue-Ting Tran, Bernhard Englinger, Patrick Hauswirth, David Gruenig, Sushilla van Schoonhoven, Stephan Krahenbuhl, Luigi M. Terracciano, Walter Berger, Salvatore Piscuoglio, Luca Quagliata, Jean Rommelaere, Juerg P. F. Nueesch, Jorg Huwyler
Summary: This study investigated a nonviral gene therapy approach targeting HCC with the NS1 protein, identifying PDK1 as a potential predictive biomarker for NS1-LPX gene therapy effectiveness. Experimental results demonstrated that the NS1-LPX therapeutic approach significantly reduced tumor growth and prolonged survival in an HCC xenograft mouse model.
JOURNAL OF CONTROLLED RELEASE
(2021)
Article
Multidisciplinary Sciences
Kenji Ohba, Yoshihide Sehara, Tatsuji Enoki, Junichi Mineno, Keiya Ozawa, Hiroaki Mizukami
Summary: In this study, a tetracycline-dependent promoter was used to regulate the expression of capsids in AAV production system, resulting in increased viral yield and decreased empty capsids in different serotypes without affecting the infectivity of AAV vectors in vitro and in vivo. The change in replicase expression pattern improved the quantity and quality of the AAV vectors, while the control of capsid expression timing reduced the presence of empty capsids. These findings provide new insights for the development of AAV vector production systems in gene therapy.
Article
Microbiology
Stephanie M. Bester, Daniel Adu-Ampratwum, Arun S. Annamalai, Guochao Wei, Lorenzo Briganti, Bridget C. Murphy, Reed Haney, James R. Fuchs, Mamuka Kvaratskhelia
Summary: In this study, the researchers investigated the drug resistance of HIV-1 to Lenacapavir. They found that the Q67H and N74D mutations reduced the binding affinity of the inhibitor, and proposed a modification to increase its potency.
Article
Microbiology
Kathryn Campbell, Robert J. Gifford, Joshua Singer, Verity Hill, Aine O'Toole, Andrew Rambaut, Katie Hampson, Kirstyn Brunker
Summary: The availability of pathogen sequence data and the use of genomic surveillance are increasing rapidly. In this study, the researchers propose an updated genomic tool and classification system for better understanding the dynamics of rabies virus and improving disease control. By implementing this tool, they were able to define 96 total lineages within the globally distributed Cosmopolitan Glade of rabies virus, which is a significant increase from the previously reported 22 lineages. The integration of this tool with a new rabies virus sequence data resource enables rapid application and provides insights into the control and elimination of dog-mediated rabies.
Article
Microbiology
Christian Shema Mugisha, Tung Dinh, Abhishek Kumar, Kasyap Tenneti, Jenna E. Eschbach, Keanu Davis, Robert Gifford, Mamuka Kvaratskhelia, Sebla B. Kutluay
Summary: In addition to its catalytic function, HIV-1 integrase (IN) binds to the viral RNA genome (gRNA) through positively charged residues (i.e., R262, R263, R269, K273) within its C-terminal domain (CTD) and regulates proper virion maturation. Mutation of these residues results in the formation of morphologically aberrant viruses blocked at an early reverse transcription stage in cells.
Article
Multidisciplinary Sciences
Heather M. Callaway, Dawid Zyla, Florence Larrous, Guilherme Dias de Melo, Kathryn M. Hastie, Ruben Diaz Avalos, Alyssa Agarwal, Davide Corti, Herve Bourhy, Erica Ollmann Saphire
Summary: This study reports the cryo-electron microscopy structure of the rabies virus glycoprotein (RABV-G) and the discovery of a neutralizing antibody called RVA122. RVA122 binds to RABV-G and stabilizes the virus in its prefusion state, which may have implications for improving rabies vaccines.
Article
Multidisciplinary Sciences
Liane P. Fernandes, Rocio Enriquez-Gasca, Poppy A. Gould, James H. Holt, Lucia Conde, Gabriela Ecco, Javier Herrero, Robert Gifford, Didier Trono, George Kassiotis, Helen M. Rowe
Summary: Research has found that the regulation of cell fate can be influenced by ZFP819, which targets a satellite DNA array called ZP3AR. The depletion of ZFP819 leads to a transition from a pluripotent state to a 2-cell-like state in cells. This transition is accompanied by changes in chromatin structure and the inactivation of master transcription factor genes.
Article
Microbiology
Vamseedhar Rayaprolu, Benjamin O. Fulton, Ashique Rafique, Emilia Arturo, Dewight Williams, Chitra Hariharan, Heather Callaway, Amar Parvate, Sharon L. Schendel, Diptiben Parekh, Sean Hui, Kelly Shaffer, Kristen E. Pascal, Elzbieta Wloga, Stephanie Giordano, Nicole Negron, Min Ni, Richard Copin, Gurinder S. Atwal, Matthew Franklin, Ruth Mabel Boytz, Callie Donahue, Robert Davey, Alina Baum, Christos A. Kyratsous, Erica Ollmann Saphire
Summary: Monoclonal antibodies can provide important protection against infectious diseases for those not yet vaccinated or in individuals with a weak immune response to vaccination. Inmazeb (REGN-EB3), a three-antibody cocktail against Ebola virus, has shown effectiveness in reducing disease and improving survival. In this study, the structure of the Ebola virus glycoprotein and its complex with Inmazeb antibodies were determined using cryo-EM, revealing previously unknown details of the glycoprotein and the mechanism of action of Inmazeb.
CELL HOST & MICROBE
(2023)
Article
Virology
Roziah Kambol, Anna Gatseva, Robert J. Gifford
Summary: This study reports a previously unknown endogenous lentivirus lineage in the genome of the South African springhare, revealing that the host range of lentiviruses has historically extended to rodents. Through comparative and phylogenetic analysis of virus and host genomes, the long-term evolutionary history of the genus is further understood by considering biogeographic and ecological characteristics of host species.
Article
Cell Biology
Heather M. Callaway, Kathryn M. Hastie, Sharon L. Schendel, Haoyang Li, Xiaoying Yu, Jeremy Shek, Tierra Buck, Sean Hui, Dan Bedinger, Camille Troup, S. Moses Dennison, Kan Li, Michael D. Alpert, Charles C. Bailey, Sharon Benzeno, Jody L. Bonnevier, Jin-Qiu Chen, Charm Chen, Hyeseon Cho, Peter D. Crompton, Vincent Dussupt, Kevin C. Entzminger, Yassine Ezzyat, Jonathan K. Fleming, Nick Geukens, Amy E. Gilbert, Yongjun Guan, Xiaojian Han, Christopher J. Harvey, Julia M. Hatler, Bryan Howie, Chao Hu, Ailong Huang, Maya Imbrechts, Aishun Jin, Nik Kamachi, Gladys Keitany, Mark Klinger, Jay K. Kolls, Shelly J. Krebs, Tingting Li, Feiyan Luo, Toshiaki Maruyama, Michael A. Meehl, Letzibeth Mendez-Rivera, Andrea Musa, C. J. Okumura, Benjamin E. R. Rubin, Aaron K. Sato, Meiying Shen, Anirudh Singh, Shuyi Song, Joshua Tan, Jeffrey M. Trimarchi, Dhruvkumar P. Upadhyay, Yingming Wang, Lei Yu, Tom Z. Yuan, Erik Yusko, Bjoern Peters, Georgia Tomaras, Erica Ollmann Saphire
Summary: The SARS-CoV-2 Omicron variant and its sublineages are resistant to most therapeutic antibodies due to multiple mutations in the spike protein. However, 66 out of nearly 400 candidate therapeutics in the Coronavirus Immunotherapeutic Consortium (CoVIC) panel were found to neutralize Omicron and its sublineages in a neutralization assay. Most Omicron-neutralizing antibodies in natural immunoglobulin Gs (IgGs) recognize spike bivalently, while non-neutralizing IgGs either bind monovalently or have partial monovalent occupancy. Cleaving bivalent-binding IgGs to antigen-binding fragments (Fabs) abolishes neutralization and binding affinity, particularly against Omicron. These findings suggest that antibodies resistant to variant of concerns overcome mutations through avidity. Therefore, future SARS-CoV-2 vaccine strategies should consider trimeric spike epitope display with identical spacing and organization.
Article
Virology
Maria-Luisa Carrozza, Anna-Maria Niewiadomska, Maurizio Mazzei, Mounir R. Abi-Said, Stephane Hue, Joseph Hughes, Anna Gatseva, Robert J. Gifford
Summary: Small ruminant lentiviruses (SRLVs) cause chronic, persistent infections in domestic sheep and goats worldwide. Phylogenetic analysis reveals that the global diversity of SRLVs can be traced back to ancient splits into Eastern and Western lineages during the Neolithic period, and the emergence of SRLV-A is linked to the international export of Central Asian Karakul sheep in the early 20th century.
Article
Virology
Yu-An Annie Chien, Brynn K. K. Alford, Brian R. R. Wasik, Wendy S. S. Weichert, Colin R. R. Parrish, Susan Daniel
Summary: The entry of influenza A viruses into host cells is affected by the chemical forms of sialic acids, their primary receptors. A study found that host cells containing Neu5Ac are more susceptible to H3N2 influenza virus infection compared to cells with minimal Neu5Gc. This suggests that influenza viruses can adapt to host cells with different sialic acid receptors solely through changes in receptor affinity, without affecting membrane fusion.
JOURNAL OF VIROLOGY
(2023)
Article
Cell Biology
Rocio Enriquez-Gasca, Poppy A. Gould, Hale Tunbak, Lucia Conde, Javier Herrero, Alexandra Chittka, Christine R. Beck, Robert Gifford, Helen M. Rowe
Summary: Endogenous retroviruses (ERVs) have reconfigured host gene networks. Using an active murine ERV (IAPEz) and an ESC-NPC differentiation model, the origins of co-option were explored. Transcriptional silencing via TRIM28 was found to be mediated by a 190 bp sequence encoding the IAP signal peptide, which is responsible for retrotransposition. Escapee IAPs, in contrast, evade repression in both cell types, resulting in their transcriptional derepression, particularly in NPCs. It was shown that the enhancer function of a 47 bp sequence within the U3 region of the LTR is validated, and escapee IAPs have an activating effect on nearby neural genes.
Article
Fisheries
Simon P. Fruh, Oluwafemi F. Adu, Robert A. Lopez-Astacio, Wendy S. Weichert, Brian R. Wasik, Colin R. Parrish
Summary: B-cell cloning methods were used to analyze antibody responses against target antigens, reveal host antibody repertoire and protective immunity against pathogens. Improved methods for isolating canine B cells and producing monoclonal antibodies against canine parvovirus (CPV) capsids were described. The methods included fluorescence-activated cell sorting, in vitro B cell culture, screening for CPV-specific antibody production, and cloning of heavy and light chain sequences. Three different canine monoclonal antibodies were analyzed, showing broad binding to CPV variants and mapping of antigenic sites on the capsid.
DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY
(2023)
Review
Virology
Robert A. Lopez-Astacio, Oluwafemi F. Adu, Hyunwook Lee, Susan L. Hafenstein, Colin R. Parrish
Summary: Studying the structure of parvovirus capsids can enhance our understanding of their functions, although many unanswered questions still remain, including the functioning of the capsids in release, transmission, or cellular infection, as well as their interactions with host receptors, antibodies, etc. Further research is needed to provide a more comprehensive understanding of how these viruses carry out their various functions.
JOURNAL OF VIROLOGY
(2023)
Article
Virology
Angelica Bravo, Leandro Fernandez-Garcia, Rodrigo Ibarra-Karmy, Gonzalo A. Mardones, Luis Mercado, Fernando J. Bustos, Robert J. Gifford, Gloria Arriagada
Summary: Endogenous viral elements (EVEs) are genomic DNA sequences derived from viruses and some of them can express proteins with physiological roles in their host. In this study, we found that DeRep, a protein encoded in an endogenous parvoviral element (EPV), demonstrated antiviral activity against an exogenous parvovirus in degu cells. This is the first time an EPV has been shown to have such activity.
Article
Biochemistry & Molecular Biology
Michael R. Oliver, Kamilla J. Toon, Charlotte B. Lewis, Stephen Devlin, Robert J. Gifford, Joe Grove
Summary: The structures of E1E2 glycoproteins from 60 viral species in the Hepacivirus, Pegivirus, and Pestivirus genera were predicted using systematic genome annotation and AlphaFold modelling, revealing that while E2 varied widely, E1 exhibited a consistent fold across different viruses, indicating a common and novel membrane fusion mechanism. Comparison of E1E2 models from various species also provided insights into the evolution of membrane fusion in these viral genera.
Article
Biology
Samantha R. Hartmann, Andrew J. Charnesky, Simon P. Fruh, Robert A. Lopez-Astacio, Wendy S. Weichert, Nadia DiNunno, Sung Hung Cho, Carol M. Bator, Colin R. Parrish, Susan L. Hafenstein
Summary: This study investigates the immune response of dogs to vaccination using cryo-electron microscopy and computational methods. The results reveal a specific polyclonal immune response in the serum of dogs infected with canine parvovirus and provide insights into the binding of multiple antibodies or ligands to the virus.
COMMUNICATIONS BIOLOGY
(2023)