Article
Gastroenterology & Hepatology
Carlota Fernandez-Antunez, Kuan Wang, Ulrik Fahnoe, Lotte S. Mikkelsen, Judith M. Gottwein, Jens Bukh, Santseharay Ramirez
Summary: Understanding the viral determinants that influence antiviral resistance is crucial for preventing the emergence of resistance to direct-acting antiviral treatments. It has been found that NS5A-inhibitor resistance plays a significant role in treatment failure of HCV genotype 3.
Article
Multidisciplinary Sciences
P. Alexander Gunnarsson, M. Madan Babu
Summary: Determining the probability of accessing different sequence variants from a starting sequence can help predict evolutionary trajectories and outcomes. Variant accessibility is influenced by mutational biases and the genetic code's structure. The emergence of a less fit but more accessible variant as adaptation is discussed using influenza A virus as a model. The proposed genotype-accessibility landscape allows predicting the emergence of adaptive genotypes in evolving systems.
Article
Microbiology
Andrew R. Wargo, Gael Kurath, Robert J. Scott, Benjamin Kerr
Summary: The study investigated the association between virus virulence, transmission rate, and duration, finding that higher virulence genotypes had longer transmission durations but small and inconsistent transmission rate differences. Ultimately, more virulent genotypes were found to have an overall fitness advantage, contradicting classical tradeoff theory assumptions.
Article
Biology
Paul Z. Chen, Niklas Bobrovitz, Zahra Premji, Marion Koopmans, David N. Fisman, Frank X. Gu
Summary: Analyzing respiratory viral loads of SARS-CoV-2, SARS-CoV-1, and influenza A(H1N1)pdm09, it was found that the heterogeneity in viral loads is an intrinsic virological factor leading to overdispersion in the transmission of COVID-19. Cases of COVID-19 exhibit broad heterogeneity in transmission risk, with pediatric and asymptomatic infections also being potential sources of transmission.
Article
Multidisciplinary Sciences
Matthew R. Lanahan, Robert W. Maples, Julie K. Pfeiffer
Summary: RNA viruses can mutate to increase replication speed in cultured cells, but this may come at the cost of reduced stability and fitness. Selecting for the earliest viral progeny can reveal unexpected inefficiencies in the viral replication cycle.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Ashish Goyal, Elizabeth R. Duke, E. Fabian Cardozo-Ojeda, Joshua T. Schiffer
Summary: In clinical trials, remdesivir was found to decrease recovery time and prevent hospitalization in patients with SARS-CoV-2. However, it did not reduce nasal viral loads. In animal experiments, early use of remdesivir prevented pneumonia and reduced lung viral loads, but increased viral loads were observed in the nasal passages after a certain period of time. Mathematical models were developed to explain these findings and suggest that a more potent drug could effectively reduce viral loads in both the nasal passages and lungs.
Article
Microbiology
Abdullah A. Alomar, Daniel W. Perez-Ramos, Dongmin Kim, Natalie L. Kendziorski, Bradley H. Eastmond, Barry W. Alto, Eric P. Caragata
Summary: This study aimed to investigate the combined effects of competition stress and Wolbachia infection on host fitness and susceptibility to West Nile virus (WNV) infection in Cx. quinquefasciatus mosquitoes. The results showed that high competition stress prolonged development time, decreased wing length, and increased susceptibility to WNV infection. Additionally, Wolbachia infection reduced WNV load under low competition stress and significantly improved survival rate under high competition stress in larval rearing.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Immunology
Olivia O'Connor, Tey Putita Ou, Fabien Aubry, Stephanie Dabo, Sylvie Russet, Dominique Girault, Saraden In, Marine Minier, Sebastian Lequime, Thavry Hoem, Sebastien Boyer, Philippe Dussart, Nicolas Pocquet, Valerie Burtet-Sarramegna, Louis Lambrechts, Veasna Duong, Myrielle Dupont-Rouzeyrol
Summary: New Caledonia and Cambodia underwent different DENV-1 genotype/lineage replacements, and experimental results showed that these replacements reflected a higher transmission fitness advantage of the replacing DENV genotype/lineage in the mosquito vector.
EMERGING MICROBES & INFECTIONS
(2021)
Article
Biochemical Research Methods
Sylvain Blois, Benjamin M. Goetz, James J. Bull, Christopher S. Sullivan
Summary: The concept of nucleic acid barcodes in pathogen genomes is easy to understand, but implementing it may be challenging due to potential issues like fitness alteration, mutation accumulation, and unintended barcode generation. In this study, approximately 5000 randomized barcodes were generated in the genome of a small DNA virus, and a post-sequencing method was developed to interpret the barcode sequences. These findings may have implications for the use of randomized barcodes in other microbial systems and provide a useful approach for future studies involving nucleic acid barcoded pathogens.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Biochemical Research Methods
Shion Hosoda, Tsukasa Fukunaga, Michiaki Hamada
Summary: This study developed a novel microbial interaction inference method Umibato that can estimate time-varying microbial interaction networks and outperformed existing methods. Umibato showed superior performance on synthetic datasets and a mouse gut microbiota dataset in providing new insights into the relationship between consumed diets and gut microbiota.
Article
Immunology
Sarah C. Kuchinsky, Francesca Frere, Nora Heitzman-Breen, Jacob Golden, Ana Vazquez, Christa F. Honaker, Paul B. Siegel, Stanca M. Ciupe, Tanya LeRoith, Nisha K. Duggal
Summary: Usutu virus (USUV) is an emerging zoonotic arbovirus that causes severe neuroinvasive disease in humans and has been linked to decline in breeding bird populations in Europe. By infecting commercial ISA Brown chickens, researchers found that chickens with high and low antibody production had different responses to USUV infection, with low antibody producers showing higher viral titers and lower neutralizing antibody responses. This avian model provides insights into USUV pathogenesis in birds and transmission dynamics between hosts and vectors.
EMERGING MICROBES & INFECTIONS
(2021)
Article
Microbiology
Yuta Shirogane, Elsa Rousseau, Jakub Voznica, Yinghong Xiao, Weiheng Su, Adam Catching, Zachary J. Whitfield, Igor M. Rouzine, Simone Bianco, Raul Andino
Summary: This study investigates the interactions between viruses and defective interfering genomes (DI) during replication using a mathematical model and experimental validation. The efficiency of DI genome replication and encapsidation are identified as critical parameters that determine the outcome of wild-type (WT) virus replication. Despite the establishment of equilibrium, allowing WT virus to replicate, the replication levels are reduced.
Article
Biochemistry & Molecular Biology
Nergis Imprachim, Yuliana Yosaatmadja, Joseph A. Newman
Summary: NSP14 is a dual function enzyme, consisting of an N-terminal exonuclease domain (ExoN) and a C-terminal guanine-N7-methyltransferase (N7-MTase) domain. The interaction between NSP14 and NSP10 enhances the nuclease activity. Structural analysis reveals conformational changes in the NSP14 ExoN domain upon binding of NSP10, which explains the stimulation of nuclease activity. Additionally, structural insights into the viral mRNA capping process are gained through the structure of NSP14 in complex with cap analogue (7Me)GpppG.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Zhike Feng, Jun-ichi Inaba, Peter D. Nagy
Summary: Biogenesis of viral replication organelles (VROs) is critical for positive-strand RNA viruses replication. The study shows that tomato bushy stunt virus (TBSV) and carnation Italian ringspot virus (CIRV) hijack the retromer complex to build VROs. The viruses recruit cellular enzymes by retargeting the retromer, essential for lipid production and enrichment within VROs.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Gastroenterology & Hepatology
Wataru Hirose, Makoto Horiuchi, Donghan Li, Ikuko N. Motoike, Lin Zhang, Hafumi Nishi, Yusuke Taniyama, Takashi Kamei, Mikiko Suzuki, Kengo Kinoshita, Fumiki Katsuoka, Keiko Taguchi, Masayuki Yamamoto
Summary: A model of coexisting NRF2-activated and KEAP1-normal cells was established in the esophageal epithelium using Keap1 conditional knockout mice. NRF2-activated cells are selectively eliminated through cell competition, but loser NRF2-activated cells leave a memory for the remaining winner KEAP1-normal cells.
CELLULAR AND MOLECULAR GASTROENTEROLOGY AND HEPATOLOGY
(2023)
Article
Virology
Mohamed S. H. Hassan, Ahmed Ali, Motamed Elsayed Mahmoud, Danah Altakrouni, Shahnas M. Najimudeen, Mohamed Faizal Abdul-Careem
Summary: This study compared the efficacy of different vaccination programs against Canadian DMV/1639 IBV and found that the autogenous inactivated DMV/1639 vaccine was more effective in reducing viral loads and boosting virus neutralization titers. Both vaccination programs provided significant protection against pathological effects.
Article
Virology
Wanda Christ, Jonas Klingstrom, Janne Tynell
Summary: The integrated stress response (ISR) is activated in response to SARS-CoV-2 infection, triggering translational arrest and inhibiting stress granule formation. However, the stress-responsive transcription factors ATF4 and CHOP are not induced. Different SARS-CoV-2 variants show variant-specific differences in ISR activation, suggesting potential impacts on pathogenesis and treatment strategies.
Article
Virology
Xiao Han, Hankun Xu, Yifan Weng, Rong Chen, Jidong Xu, Tong Cao, Renjie Sun, Ying Shan, Fang He, Weihuan Fang, Xiaoliang Li
Summary: Classical swine fever virus (CSFV) can inhibit the host innate immunity by decreasing the level of high mobility group box 1 (HMGB1), and CSFV Npro can evade host antiviral immune response through upregulating HMGB1 acetylation.
Article
Virology
Sunjian Lyu, Fulei Xiong, Tianpeng Qi, Weifeng Shen, Qi Guo, Mingming Han, Li Liu, Weishao Bu, Julin Yuan, Bao Lou
Summary: This study identified and characterized a novel temperate A. hydrophila phage, P05B, which has strong lytic ability and stability across different temperatures and pH values.
Article
Virology
Siyuan Liu, Wei Chen, Raphael Nyaruaba, Shunlong Wang, Cihan Yang, Qun Wu, Ying Liu, Puyu Liu, Fei Wang, Jingling Wang, Zhiming Yuan, Dingwei Sun, Han Xia
Summary: Specific, sensitive, and reliable RT-qPCR assays for the detection of OYAV and EBIV have been successfully developed in this study. These assays hold great promise for their potential application in clinical and field samples in the future.
Article
Virology
Rui Wang, Qiang Sun, Jinbo Xiao, Congcong Wang, Xiaoliang Li, Jichen Li, Yang Song, Huanhuan Lu, Ying Liu, Shuangli Zhu, Zhijun Liu, Yong Zhang
Summary: Coxsackievirus A6 (CVA6) has emerged as an important agent causing hand, foot, and mouth disease (HFMD). Mutations in residue 64 of the virus have been found to increase resistance to ribavirin and decrease sensitivity to guanidine hydrochloride. This mutation also leads to increased replication fidelity and reduced pathogenicity. These findings provide a foundation for the development of a safe and effective live attenuated CVA6 vaccine.
Article
Virology
Yao Xiong, Keran Ma, Xiao Zou, Yantao Liang, Kaiyang Zheng, Tiancong Wang, Hong Zhang, Yue Dong, Ziyue Wang, Yundan Liu, Hongbing Shao, Andrew Mcminn, Min Wang
Summary: This study isolated a novel virus, vB_VviC_ZQ26, infecting Vibrio cyclitrophicus from coastal waters near Qingdao, China. It was found that vB_VviC_ZQ26 belongs to a new vibriophage-specific family, Coheviridae, and is mainly found in temperate and tropical epipelagic zones.
Article
Virology
Xing Li, Zhiping Ye, Ewan P. Plant
Summary: By analyzing clinical and cultured samples using the same bioinformatic pipeline, it was found that 5' copyback DVGs are prevalent in human clinical samples but not in cultured samples. Furthermore, there are differences in DVG production and composition between in vivo and in vitro infections.
Article
Virology
Shreya Banerjee, Rakesh Sarkar, Arpita Mukherjee, Suvrotoa Mitra, Animesh Gope, Mamta Chawla-Sarkar
Summary: Rotavirus is a major cause of viral gastroenteritis in infants and continues to be a severe issue in underdeveloped nations. Recent research has shown that a long non-coding RNA called SLC7A11-AS1 is upregulated during rotavirus infection and plays a role in facilitating the virus's propagation by regulating intracellular glutathione and lipid peroxidation.
Article
Virology
Eiichi Hondo, Tetsufumi Katta, Ayato Sato, Naoya Kadofusa, Tomoki Ishibashi, Hiroshi Shimoda, Hirokazu Katoh, Atsuo Iida
Summary: Bat-borne emerging viruses, such as the Ebola virus and Nipah virus, pose a significant threat to public health. In this study, we identified micafungin as a potential antiviral drug against Pteropine orthoreovirus (PRV) and found that it inhibits viral release in human cells through activating the endoplasmic reticulum stress response pathway. This research provides valuable insights into the development of effective treatments for future virus pandemics.
Article
Virology
M. Joubert, N. van den Berg, J. Theron, V. Swart
Summary: This study investigated the host gene expression in asymptomatic avocado nursery trees infected with Avocado sunblotch viroid (ASBVd) using RNA sequencing. The results showed that 631 genes were differentially expressed during infection, with 63% upregulated. ASBVd infection significantly affected plant defence responses, phytohormone networks, gene expression pathways, secondary metabolism, cellular transport, as well as protein modification and degradation. This study provides insights into the molecular interactions underlying avsunviroid-host interactions.
Article
Virology
Wanling Zhang, Haiyan Yang, Zhengyun Liu, Shengyu Wang, Tianyang Chen, Hong Song, Yunbin Xu, Fajin Li, Guo Luo, Huan Wang
Summary: EV71 infection leads to changes in mitochondrial morphology and dynamics in human neuroblastoma cells, resulting in mitochondrial dysfunction that may contribute to nervous system dysfunction.
Article
Virology
Mikhail Oliveira Leastro, Elliot Watanabe Kitajima, Vicente Pallas, Jesus Angel Sanchez- Navarro
Summary: This study reports the construction and validation of an infectious cDNA clone of Citrus leprosis virus C (CiLV-C) based on an agroinfection system. Agro-injected Nicotiana benthamiana plants showed localized lesions similar to the natural infection process. The virus recovered from the infected plant tissue could be mechanically transmitted between plants. The CiLV-C reverse genetic system provides a powerful molecular tool for unraveling the peculiarities of the citrus leprosis pathosystem.
Article
Virology
Manel Essaidi-Laziosi, Francisco J. Perez-Rodriguez, Catia Alvarez, Pascale Sattonnet-Roche, Giulia Torriani, Meriem Bekliz, Kenneth Adea, Matthias Lenk, Tasnim Suliman, Wolfgang Preiser, Marcel A. Mueller, Christian Drosten, Laurent Kaiser, Isabella Eckerle
Summary: This study found that the Omicron variant has different replication characteristics compared to other variants of concern, being able to efficiently produce infectious virus in nasal cells but not lung cells. In addition, the Delta and Omicron variants showed increased infection efficiency in A549 cells. These findings suggest that the variants of concern have better adaptation to humans but do not have an extended host range.
Article
Virology
Martin Faye, Modeste Name Faye, Babacar Ndiaye, Moussa Moise Diagne, Safietou Sankhe, Ndeye Marieme Top, Amadou Diallo, Cheikh Loucoubar, Ndongo Dia, Amadou Alpha Sall, Ousmane Faye
Summary: Genomic surveillance in Senegal since March 2020 has detected the emergence of Omicron BA.4 and BA.5 sublineages in June 2022. Next-generation sequencing and phylogeny analysis of isolates from a cluster of cases in Northern Senegal in July 2022 revealed that the BA.4 cases originated from a XAS recombinant, marking the first reported sequence of this variant from Senegal. Continuous genomic surveillance of positive SARS-CoV-2 samples is crucial.