Review
Biochemistry & Molecular Biology
Nash D. Rochman, Yuri Wolf, Eugene Koonin
Summary: This review examines the role of virus genome sequencing in the past half-century and focuses on the molecular mechanisms of several major epidemic viruses in adapting to the human host.
Article
Biochemical Research Methods
Zhi-Jian Zhou, Chen-Hui Yang, Sheng-Bao Ye, Xiao-Wei Yu, Ye Qiu, Xing-Yi Ge
Summary: A novel approach based on information theory was developed to identify viral recombination within highly similar sequences, providing a useful tool for monitoring viral evolution and epidemic control.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemical Research Methods
Zhi-Jian Zhou, Chen-Hui Yang, Sheng-Bao Ye, Xiao-Wei Yu, Ye Qiu, Xing-Yi Ge
Summary: Genomic recombination is an important driver of viral evolution, and it has been observed in SARS-CoV-2 during the COVID-19 pandemic, leading to significant changes in viral infectivity and transmissibility. However, identifying viral recombination is challenging, especially for low-divergence viruses like SARS-CoV-2. In this study, the researchers developed a program called VirusRecom, which uses information theory to efficiently screen recombination events on the viral genome. The program showed good performance in simulated data and accurately identified recombination regions in SARS-CoV-2 variants.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Multidisciplinary Sciences
Alex Varadi, Eszter Kaszab, Gabor Kardos, Eszter Prepost, Krisztina Szarka, Levente Laczko
Summary: This paper introduces a pipeline for reconstructing the dominant consensus genome of viral samples and analyzing their within-host variability. Through benchmarking on multiple datasets, it is shown that the pipeline is reliable and can quickly identify viral samples.
Article
Biochemistry & Molecular Biology
Marios Nikolaidis, Panayotis Markoulatos, Yves van de Peer, Stephen G. Oliver, Grigorios D. Amoutzias
Summary: Research has shown that coronaviruses have a strong ability for intergenomic recombination, where they can exchange genetic material not only within the same subgenus but also across different CoV genera, other viruses, and even hosts. These events often occur at double crossovers surrounding the Spike ORF, indicating the instability and mobility of this genomic region.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Kohei Mishina, Takako Suzuki, Youko Oono, Yoko Yamashita, Hongjing Zhu, Taiichi Ogawa, Masaru Ohta, Kohei Doman, Wenjing Xu, Daichi Takahashi, Taiga Miyazaki, Akemi Tagiri, Chihiro Soma, Harukuni Horita, Shuhei Nasuda, Romain De Oliveira, Etienne Paux, Guoxiong Chen, Mohammad Pourkheirandish, Jianzhong Wu, Cheng Liu, Takao Komatsuda
Summary: Wheat yellow mosaic virus (WYMV) is transmitted by the vector Polymyxa graminis into the roots of its host. The Ym1 and Ym2 genes provide resistance against WYMV, but their mechanisms are not well understood. This study found that Ym1 and Ym2 act in the roots, hindering viral movement or suppressing viral replication. Ym1 reduced viral infection incidence in leaves, while Ym2 did not have an effect. The Ym2 gene was isolated and found to correlate with disease response. Ym2 has undergone structural diversity through translocation and recombination, contributing to the evolution of cultivated wheat.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemistry & Molecular Biology
Maria H. T. Nguyen, Zoe Netter, Angus Angermeyer, Kimberley D. Seed
Summary: Bacteria can acquire mobile genetic elements to combat viral infection. Satellite viruses restrict viral replication for the benefit of their host bacterium. In the arms race against satellite viruses, certain viruses can evade restriction through unknown mechanisms. This study identifies a viral protein that counteracts satellite viruses by exploiting a specific enzyme within the viruses.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Microbiology
Xiaowei Wu, Jing Zhang, Wendong Lan, Lulu Quan, Junxian Ou, Wei Zhao, Jianguo Wu, Patrick C. Y. Woo, Donald Seto, Qiwei Zhang
Summary: This study presents a rapid, simple, and cost-effective method for molecular typing HAdV respiratory pathogens. It allows for the identification of HAdV genotypes and recombinants without the need for whole genome sequencing, making it suitable for real-time surveillance of circulating adenovirus strains in outbreaks and populations.
FRONTIERS IN MICROBIOLOGY
(2022)
Review
Virology
Xi Yu, Huicheng Shi, Gong Cheng
Summary: Mpox, previously known as monkeypox, is an infectious viral illness caused by the mpox virus. The recent spread of mpox across Africa and other parts of the world has raised concerns about its natural evolution and the potential for a global pandemic. This review provides an overview of the mpox virus, including its genome, hosts and reservoirs, and virus-host interaction and immunology, as well as phylogenetic analysis on available mpox virus genomes with a focus on human evolution.
Article
Virology
Shi-Jia Le, Gen-Yang Xin, Wei-Chen Wu, Mang Shi
Summary: In this study, the global diversity of all known cat viruses was comprehensively analyzed, with a focus on their geographic expansion patterns, temporal dynamics, and recombination frequencies. The findings deepen our understanding of the evolutionary and epidemiological features of cat viruses and provide important insight into the prevention and control of cat pathogens.
Article
Virology
Larissa G. Zanardo, Tiago A. Trindade, Talita B. Mar, Tarsiane M. C. Barbosa, Diogo F. Milanesi, Murilo S. Alves, Roberta R. P. N. Lima, F. Murilo Zerbini, Arne Janssen, Eduardo S. G. Mizubuti, Simon L. Elliot, Claudine M. Carvalho
Summary: The study demonstrates the in vivo molecular evolution of an RNA plant virus and highlights the role of genetic recombination in driving the emergence of new variants and the reduction in virulence. Virulence reduction was associated with specific sites in ORF1, indicating a potential link between genetic recombination and changes in virulence.
Review
Genetics & Heredity
Rodrigo P. Baptista, Garrett W. Cooper, Jessica C. Kissinger
Summary: Cryptosporidiosis ranks sixth among the most important food-borne parasites globally, contributing significantly to mortality in infants and immunosuppressed individuals. The lack of an optimal in vitro culture system for replicating the parasite's lifecycle makes it challenging to work with, hindering the cloning of isolates. The current sequencing method using oocysts as the lifecycle stage presents difficulties in accurately representing the population due to each oocyst containing multiple progeny.
Article
Virology
Juan Song, Huanhuan Lu, Lin Ma, Shuangli Zhu, Dongmei Yan, Jun Han, Yong Zhang
Summary: This study determined the global genetic diversity and transmission dynamics of enterovirus B83 (EV-B83). The study collected blood samples from a patient with viral myocarditis and obtained the complete genome sequence of the viral isolate. Bioinformatics methods, including evolutionary dynamics, recombination event analysis, and phylogeographic analysis, were used to analyze the genetic diversity and transmission dynamics of global EV-B83. The study found that EV-B83 is globally distributed and added to our understanding of EV-B83 epidemiology.
Article
Multidisciplinary Sciences
Anastasiya D. Kirichenko, Anastasiya A. Poroshina, Dmitry Yu Sherbakov, Michael G. Sadovsky, Konstantin Krutovsky
Summary: Understanding the origin, evolution, and phylogenetic relationships of viruses is crucial for studying their pathogenicity and developing antiviral drugs and vaccines. This research compared two methods for identifying relationships between coronavirus genomes, showing well-resolved robust classifications. The alignment-free methods proved to be efficient and provided valuable alternative information on the genomes relationships.
Article
Virology
Chuang Yuan, Cheng Wang, Kongfu Zhu, Song Li, Zengmin Miao
Summary: The study found a positive correlation between population density and measles incidence, while negative correlations were observed between measles incidence and healthcare condition as well as average routine vaccination rate. The predominant lineage of MeV in Shandong Province, China was formed by genotype H1 strains, and the most recent common ancestor of the N gene of MeV genotype H1 in Shandong traced back to around 1987 with relatively rapid evolution. The genetic diversity of MeV N gene increased before 2005 and remained relatively high and stable.
JOURNAL OF MEDICAL VIROLOGY
(2022)