Article
Virology
Alejandra L. L. D'Antuono, Giovanna L. L. Gallo, Claudia Sepulveda, Jonas Fernandez, Julia Brignone, Graciela Gamboa, Laura Riera, Maria del Carmen Saavedra, Nora Lopez
Summary: We provide evidence demonstrating the specific involvement of the TCRV S 5' noncoding sequence adjacent to the viral promoter in replication. Our findings provide insight into the mechanism through which this 5' viral RNA noncoding region assists the L polymerase for efficient viral S RNA synthesis.
JOURNAL OF VIROLOGY
(2023)
Review
Virology
Philipp Niklas Ostermann, Anastasia Ritchie, Johannes Ptok, Heiner Schaal
Summary: The study of HIV-1 gene expression has revealed a new form of nuclear export regulation, known as intrinsic RNA code. These findings provide important insights into understanding viral replication mechanisms.
JOURNAL OF VIROLOGY
(2021)
Article
Virology
Dan Li, Hai-Tao Lu, Yu-Zhen Ding, Hong-Jiang Wang, Jing-Long Ye, Cheng-Feng Qin, Zhong-Yu Liu
Summary: The regulatory mechanisms of genome cyclization in yellow fever virus (YFV) are not fully understood. This study found that a group of cis-acting RNA elements balance genome cyclization to govern efficient viral RNA replication in YFV, highlighting the importance of RNA-based regulatory mechanisms in viral replication.
JOURNAL OF VIROLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Connor G. G. Bamford, John McLauchlan
Summary: The host IFNL4 haplotype status influences the development of chronic HCV infection. Specific amino acid variants at multiple sites on the HCV polyprotein correlate with functional SNPs in the IFNL4 locus, which may affect virus replication and infection outcome. Each individual IFNL4-associated variant has a nuanced effect on viral replication, potentially mediating resistance to IFN lambda 4 effects.
JOURNAL OF GENERAL VIROLOGY
(2021)
Article
Microbiology
Rosario Sabariegos, Laura Albentosa-Gonzalez, Blanca Palmero, Pilar Clemente-Casares, Eugenio Ramirez, Carlos Garcia-Crespo, Isabel Gallego, Ana Isabel de avila, Celia Perales, Esteban Domingo, Antonio Mas
Summary: This study identified specific amino acids of the NS5B protein phosphorylated by cellular kinases, which may affect HCV RNA polymerase activity and lead to viral inactivation. Results from RNA transfection experiments with mutant viruses showed that T53E/A and S282E/A mutations had an impact on viral titers.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Immunology
Jiangming Xiao, Yapeng Zhang, Jinghui Zhang, Bichen Liu, Hanyi Wang, Rui Yang, Yibing Yin, Xuemei Zhang
Summary: This study characterized the cis-acting elements located upstream of the regR gene using mutational analysis, gene dissection, and luciferase activity assays. The results showed that a 311 bp 3’-terminal DNA sequence of the spd0300 gene represents a central region of the upstream cis-acting element of regR. Two structurally similar enhancer-like sequences within this region were found to play a prominent role in the regulation of regR transcription. Additionally, the competence regulator ComE was identified to be involved in the regulation of regR transcription.
MICROBIAL PATHOGENESIS
(2023)
Article
Biochemistry & Molecular Biology
Seth Scott, You Li, Oya Bermek, Jack D. Griffith, Stanley M. Lemon, Kyung H. Choi
Summary: Hepatitis C virus replication relies on the interaction between cellular factors miR-122 and PCBP2. These factors compete for binding to specific sites on the RNA genome, regulating the viral replication cycle. MiR-122 disrupts genome circularization and promotes recruitment of the viral polymerase by competing with PCBP2 for binding.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Sayuri Sakuragi, Osamu Kotani, Masaru Yokoyama, Tatsuo Shioda, Hironori Sato, Jun-ichi Sakuragi
Summary: This study reveals that the dinucleotide pair at positions 226 and 227 within the psi segment of HIV-1 plays a critical role in regulating the packaging efficiency. Molecular genetic investigations and simulations suggest that nucleotide variations at these positions alter the structural dynamics of the psi element, affecting the binding interface of viral nucleocapsid protein.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Zhiyuan Luo, Jiacheng Zhang, Jingyi Fei, Shengdong Ke
Summary: The site-specificity of m(6)A mRNA modification is primarily determined by the flanking nucleotide sequences, according to a deep learning method called iM6A. The study also reveals that the cis-elements regulating the modification are predominantly located within 50 nucleotides downstream of the m(6)A sites. Experimental validations and evolutionary conservation support these findings.
NATURE COMMUNICATIONS
(2022)
Article
Virology
Susannah Stephenson-Tsoris, John L. Casey
Summary: This study identified the start site for HDV genome RNA synthesis as position 1646 and revealed some differences in the synthesis process. The findings are important for targeting virus replication.
JOURNAL OF VIROLOGY
(2022)
Article
Genetics & Heredity
Daniel Holoch, Michel Wassef, Cecilia Lovkvist, Dina Zielinski, Setareh Aflaki, Berangere Lombard, Tiphaine Hery, Damarys Loew, Martin Howard, Raphael Margueron
Summary: Epigenetic inheritance plays a role in maintaining cellular identities and transcriptional memory, particularly at Polycomb targets, depends on both histone modifications and the gene-regulatory network, varying with cellular context. Polycomb proteins are involved in regulating this type of epigenetic transcriptional memory during cell differentiation.
Article
Medicine, General & Internal
Mohammad Asrar Izhari
Summary: This study aimed to determine the increasing risk of direct-acting antiviral (DAA) resistance due to amino acid substitutions in non-structural proteins of the hepatitis C virus (HCV). Through sequence analysis, the study identified several resistance-associated amino acid substitutions in DAA target proteins. The findings highlight the importance of continuous monitoring and evaluation of DAA resistance in the treatment of HCV.
Article
Virology
Muhammad Ikram Anwar, Ni Li, Qing Zhou, Mingxiao Chen, Chengguang Hu, Tao Wu, Haihang Chen, Yi-Ping Li, Yuanping Zhou
Summary: This study identified that PPP2R5D interacts with HCV NS5B and is essential for HCV infection in cultured hepatoma cells by facilitating HCV replication.
Article
Microbiology
Hailan Meng, Xiaoli Wang, Ling Wang, Qianqian Wang, Lijie Zhu, Yuxuan Sang, Fuxiao Liu
Summary: In this study, a putative cre containing a conserved AAACA motif was predicted in the VP2-encoding sequence of SVA, and its role was tested by constructing cDNA clones with different point mutations. Some mutated cres were found to have lethal impacts on SVA replication, but the insertion of intact cre into these mutated clones successfully rescued SVAs, indicating the functional similarity of SVA's putative cre with other picornaviruses.
VETERINARY MICROBIOLOGY
(2023)
Article
Biology
Sarah Lauren Svensson, Cynthia Mira Sharma
Summary: Bacterial small RNAs (sRNAs) play important roles as post-transcriptional regulators in stress responses and virulence. RNase III is involved in processing a pair of cis-encoded sRNAs in Campylobacter jejuni, where CJnc190 and CJnc180 interact with each other and impact the regulation of the colonization factor PtmG.
Article
Virology
Olesya N. Gusachenko, Luke Woodford, Katharin Balbirnie-Cumming, Ewan M. Campbell, Craig R. Christie, Alan S. Bowman, David J. Evans
Article
Multidisciplinary Sciences
Giles E. Budge, Nicola K. Simcock, Philippa J. Holder, Mark D. F. Shirley, Mike A. Brown, Pauline S. M. Van Weymers, David J. Evans, Steve P. Rushton
NATURE COMMUNICATIONS
(2020)
Article
Multidisciplinary Sciences
Olesya N. Gusachenko, Luke Woodford, Katharin Balbirnie-Cumming, Eugene V. Ryabov, David J. Evans
SCIENTIFIC REPORTS
(2020)
Article
Infectious Diseases
Glenn A. Marsh, Alexander J. McAuley, Sheree Brown, Elizabeth A. Pharo, Sandra Crameri, Gough G. Au, Michelle L. Baker, Jennifer A. Barr, Jemma Bergfeld, Matthew P. Bruce, Kathie Burkett, Peter A. Durr, Clare Holmes, Leonard Izzard, Rachel Layton, Suzanne Lowther, Matthew J. Neave, Timothy Poole, Sarah-Jane Riddell, Brenton Rowe, Elisha Soldani, Vittoria Stevens, Willy W. Suen, Vinod Sundaramoorthy, Mary Tachedjian, Shawn Todd, Lee Trinidad, Sinead M. Williams, Julian D. Druce, Trevor W. Drew, Seshadri S. Vasan
Summary: Researchers made efforts early in the SARS-CoV-2 outbreak to propagate and characterize an Australian isolate of the virus in vitro and in an ex vivo model of human airway epithelium, as well as to demonstrate the susceptibility of domestic ferrets to SARS-CoV-2 infection following intranasal challenge.
TRANSBOUNDARY AND EMERGING DISEASES
(2022)
Article
Virology
Agathe M. G. Colmant, Jody Hobson-Peters, Teun A. P. Slijkerman, Jessica J. Harrison, Gorben P. Pijlman, Monique M. van Oers, Peter Simmonds, Roy A. Hall, Jelke J. Fros
Summary: The study found that the zinc-finger antiviral protein (ZAP) in vertebrate cells effectively prevents insect-specific flaviviruses (ISF) from replicating in vertebrate cells. This research reveals how ISFs are inhibited, providing new insights into flavivirus evolution and mechanisms associated with host switching.
Article
Ecology
Olesya N. Gusachenko, Luke Woodford, Katharin Balbirnie-Cumming, David J. Evans
Summary: Deformed wing virus (DWV) is a globally distributed pathogen of honey bees, which when vectored by Varroa destructor can lead to high levels of colony losses. Different DWV types may compete and interact within colonies, with the ability to outcompete existing infections correlated to genetic divergence. Genetic recombination within the DWV genome results in recombinants accounting for a small portion of the population.
Article
Microbiology
Kirsten Bentley, Fadi Ghassan Alnaji, Luke Woodford, Sian Jones, Andrew Woodman, David J. Evans
Summary: The study reveals that positive-sense RNA viruses undergo repeated rounds of recombination until precise, wild type length genomes are selected. The survival of viruses with wild type genomes is determined by their overall fitness in the virus population.
Article
Microbiology
Heli Harvala, Kimberley S. M. Benschop, Natasa Berginc, Sofie Midgley, Katja Wolthers, Peter Simmonds, Susan Feeney, Jean-Luc Bailly, Audrey Mirand, Thea K. Fischer
Summary: ENPEN has developed standardized protocols for a multi-center study in Europe to collect data on EV and PeV infections, providing guidance for future prevention measures and policy making.
Article
Virology
Kirsten Bentley, Han Kang Tee, Ashley Pearson, Kym Lowry, Sheila Waugh, Sian Jones, Yoke Fun Chan, David J. Evans
Summary: Recombination plays a significant role in the evolution of viruses, with common occurrences between closely related viruses but rare inter-species recombination. Despite the ubiquitous nature of recombination, not all recombinant genomes result in infectious progeny virus. This study demonstrates the propensity for inter-species recombination at the genome level but suggests significant sequence plasticity is needed to overcome blocks in the virus life cycle.
Article
Virology
Fadi G. Alnaji, Kirsten Bentley, Ashley Pearson, Andrew Woodman, Jonathan Moore, Helen Fox, Andrew J. Macadam, David J. Evans
Summary: Genetic recombination is an important evolutionary mechanism in RNA viruses, affecting population diversity, host/tissue adaptation, and vaccine efficacy. Studies using an in vitro recombination assay and next-generation sequencing revealed that sequence identity and RNA structure do not determine the location of recombination junctions. Instead, genome function and fitness play a greater role in determining the identity of recombinant progeny.
Article
Pharmacology & Pharmacy
Qianyu Chen, Shenna Langenbach, Meina Li, Yuxiu C. Xia, Xumei Gao, Matthew J. Gartner, Elizabeth A. Pharo, Sinead M. Williams, Shawn Todd, Nadeene Clarke, Sarath Ranganathan, Michelle L. Baker, Kanta Subbarao, Alastair G. Stewart
Summary: This study established a physiologically relevant airway epithelial model for investigating therapeutics for COVID-19. ACE2 was mainly localized in ciliated and basal epithelial cells, and asthma and smoking status had no consistent marked influence on ACE2 expression or distribution.
FRONTIERS IN PHARMACOLOGY
(2022)
Article
Virology
Luke Woodford, Craig R. Christie, Ewan M. Campbell, Giles E. Budge, Alan S. Bowman, David J. Evans
Summary: Varroa destructor is a parasitic mite associated with honeybee losses and the transmission of pathogenic viruses. Studies have shown that removing mites from infected colonies can rapidly reduce virus load, while placing mite-free colonies in mite-infested apiaries leads to mite acquisition and changes in the virus population. These findings have implications for strategies in Varroa control planning.
Article
Biochemistry & Molecular Biology
Morgan R. R. Herod, Joseph C. C. Ward, Andrew Tuplin, Mark Harris, Nicola J. J. Stonehouse, Christopher J. J. McCormick
Summary: Genome replication of positive strand RNA viruses requires the production of a complementary negative strand RNA, but evidence of structural RNA elements in the negative strand is limited. This study found that different viruses have different capacities for the folding of the negative strand RNA, which may explain the limited observation.
Article
Biodiversity Conservation
Luke Woodford, Graeme Sharp, Fiona Highet, David J. Evans
Summary: This study demonstrates the benefits of coordinated treatment of Varroa mites in improving honey bee colony health and reducing virus infection and mite numbers in a geographically isolated environment.
JOURNAL OF APPLIED ECOLOGY
(2023)
Article
Biology
Luke Woodford, Pieter C. Steketee, David J. Evans
Summary: Varroa destructor is a parasite that vectors pathogenic viruses, including Deformed wing virus (DWV), in honeybees. This study investigates the replication, competition, and morbidity of DWV genotypes in drones, finding that drones are highly susceptible to both predominant genotypes. Using an in-silico model, the research also examines bottlenecks during virus acquisition by mites and injection into the host, providing insights into virus diversity in the mite-virus-bee system.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)