Fixation and reversion of mutations in the receptor-binding domain of the SARS-CoV-2 spike protein: A 2020–2024 analysis by Daniele Focosi, Pietro Giorgio Spezia, Fabrizio Maggi

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Geographical distribution and evolutionary dynamics of H4Nx avian influenza viruses by Ye Ge, Jing Liu, Yuanguo Li, Peng Peng, Yan Zhou, Jiantao Yu, Miaotong Huo, Xiaodong Liang, Yuwei Gao, Qiucheng Yao

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Dataset of SARS-CoV-2 spike protein receptor binding domain variants in complex with antigen-binding fragments targeting COVID-19 vaccine-referenced variantsModel Archive by Ferdinando Spagnolo, Florigio Lista, Claudia Curcio

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Order reduction for an RNA virus evolution model by Andrei Korobeinikov, Aleksei Archibasov, Vladimir Sobolev

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A novel isothermal whole genome sequencing approach for Monkeypox Virus by Matthias Licheri, Manon Flore Licheri, Lukas Probst, Cora Sägesser, Pascal Bittel, Franziska Suter-Riniker, Ronald Dijkman

“…Whole genome sequencing (WGS) has been successfully used to keep track of viral evolution during outbreaks or for surveillance of multiple pathogens of public health significance. …”
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Detection and Phylogenetic Analysis of an Exotic Strain of Porcine Epidemic Diarrhea Virus and Its Effect on an Affected Herd Immunized Against the Endemic Strain in Thailand by Christopher James Stott, Patumporn Jermsutjarit, Pornchai Pornpanom, Hongyao Lin, Angkana Tantituvanont, Dachrit Nilubol

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NOVEL MUTATIONS IN THE NON-STRUCTURE PROTEIN 2 OF SARS-CoV-2 by Mohsen Nakhaei, Zohreh-Al-Sadat Ghoreshi, Mohammad Rezaei Zadeh Rukerd, Hedyeh Askarpour, Nasir

“…Conclusion: Our study suggested that the mutations as K337D and G392D modulate the stability of nsp2 and tracking viral evolution should be implemented and vaccine development updated. …”
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Phylodynamic reconstruction of major chicken infectious anemia virus clades epidemiology, dispersal, and evolution by Giovanni Franzo, Matteo Legnardi, Francesca Poletto, Riccardo Baston, Giulia Faustini, Mattia Cecchinato, Claudia Maria Tucciarone

“…Accordingly, although significant selective pressures were shaping viral evolution, comparable strengths were estimated in the two viral populations. …”
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Development of a differentiating of infected from vaccinated animal (DIVA) ELISA to detect antibodies against Senecavirus A in pigs using two expression systems of non-structural p... by Parin Watcharavongtip, Patumporn Jermsutjarit, Angkana Tantituvanont, Dachrit Nilubol

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Rotavirus in Calves and Its Zoonotic Importance by Umer Seid Geletu, Munera Ahmednur Usmael, Fufa Dawo Bari

“…Reassortment is one of the important mechanisms for generating genetic diversity of rotaviruses and eventually for viral evolution. So, the primary strategy is to reduce the burden of rotavirus infections by practicing early colostrum’s feeding in newborn calves, using vaccine, and improving livestock management. …”
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The R203M and D377Y mutations of the nucleocapsid protein promote SARS-CoV-2 infectivity by impairing RIG-I-mediated antiviral signaling. by Yongkui Li, Moran Li, Heng Xiao, Feng Liao, Miaomiao Shen, Weiwei Ge, Junxian Ou, Yuqing Liu, Lumiao Chen, Yue Zhao, Pin Wan, Jinbiao Liu, Jun Chen, Xianwu Lan, Shaorong Wu, Qiang Ding, Geng Li, Qiwei Zhang, Pan Pan

“…However, its biological function in viral evolution is not well understood. SARS-CoV-2 N protein mutations were analyzed in Delta, Omicron, and original strains. …”
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Antivirals and monoclonal antibody combination therapy in haematological patients in the omicron era by Serena Vita, Emanuela Giombini, Patrizia De Marco, Martina Rueca, Cesare Ernesto Maria Gruber, Alessia Beccacece, Laura Scorzolini, Valentina Mazzotta, Carmen Pinnetti, Priscilla Caputi, Daniele Focosi, Enrico Girardi, Andrea Antinori, Fabrizio Maggi, Alessandra D'Abramo, Emanuele Nicastri, Investigation Team Spallanzani COVID-19 case

“…Keywords: immunocompromised; SARS-CoV-2 infection; monoclonal antibodies; antivirals; persistent infection; viral evolution …”
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Two Years of SARS-CoV-2 Omicron Genomic Evolution in Brazil (2022–2024): Subvariant Tracking and Assessment of Regional Sequencing Efforts by Ueric José Borges de Souza, Fernando Rosado Spilki, Amilcar Tanuri, Paulo Michel Roehe, Fabrício Souza Campos

“…The emergence of new subvariants in this new epidemiological scenario underscores the importance of ongoing genomic surveillance to track viral evolution and inform public health strategies, providing valuable information to update vaccines and implement other measures, such as lockdowns, mask usage, social distancing, health education, and self-testing.…”
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Diversity and Potential Cross-Species Transmission of Rotavirus A in Wild Animals in Yunnan, China by Xiang Le, Yinzhu Tao, Binghui Wang, Yutong Hou, Yuting Ning, Junjie Hou, Ruimei Wang, Qian Li, Xueshan Xia

“…This study provides critical data for understanding the transmission mechanisms and the RVA host range, and highlights the pivotal role of wildlife in viral evolution and dissemination. These findings have significant implications for public health policies and emphasize the need for enhanced surveillance to prevent interspecies RVA transmission.…”
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Low-Level Zoonotic Transmission of Clade C MERS-CoV in Africa: Insights from Scoping Review and Cohort Studies in Hospital and Community Settings by Andrew Karani, Cynthia Ombok, Silvia Situma, Robert Breiman, Marianne Mureithi, Walter Jaoko, M. Kariuki Njenga, Isaac Ngere

“…Ongoing research focuses on genomic comparisons between clade C and the more virulent clades A and B, alongside the surveillance of viral evolution. This study highlights the need for continuous monitoring but indicates that MERS-CoV clade C currently poses a minimal public health threat in Africa.…”
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A novel approach to analyzing the evolution of SARS-CoV-2 based on visualization and clustering of large genetic data compactly represented in operative memory by A. Yu. Palyanov, N. V. Palyanova

“…Finally, the evolution of distributions of the number of changes (editing distance between each genome and reference sequence) caused by substitutions, deletions and insertions was visualized as 3D surfaces, which clearly show the process of viral evolution over 4.5 years, with a time step = 1 week. …”
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p18 encoded by FgGMTV1 is responsible for asymptomatic infection in Fusarium graminearum by Lihang Zhang, Pengfei Li, Yanfei Wang, Shuangchao Wang, Lihua Guo

“…This work not only expands our knowledge of the genomovirus proteome but also provides insights into the strategies of viral evolution and adaptation. Moreover, we propose an innovative approach for creating hypovirulent strains utilizing engineered mycoviruses for the biocontrol of plant pathogenic fungi.IMPORTANCEMycovirus-fungus interplay often leads to asymptomatic infections. …”
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Insight into the codon usage patterns and adaptation of Tembusu Virus by Fucheng Guo, Huiming Tan, Jinjin Yang, Rumin Jia, Ruichen Wang, Lie Wu, Fengzhi Pan, Kai Kang, Weitian Xie, Youquan Li, Kewei Fan

“…Codon adaptation index (CAI) analysis reveals that this lineage of TMUV show best adapted to the CUPs of duck than other lineages, underscoring the role of natural selection in shaping viral evolution, a finding in line with evidence that CUPs in the TMUV genome is predominantly shaped by natural selection. …”
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Fc-binding nanodisc restores antiviral efficacy of antibodies with reduced neutralizing effects against evolving SARS-CoV-2 variants by Jaehyeon Hwang, Soyun Choi, Beom Kyu Kim, Sumin Son, Jeong Hyeon Yoon, Kyung Won Kim, Wonbeom Park, Hyunjoo Choo, Suhyun Kim, Soomin Kim, Seokhyeon Yu, Sangwon Jung, Sang Taek Jung, Min-Suk Song, Sang Jick Kim, Dae-Hyuk Kweon

“…Notably, Sotrovimab, an FDA-approved monoclonal antibody that has experienced a significant decline in neutralizing potency due to viral evolution, exhibited robust antiviral activity when complexed with the nanodisc against all tested Omicron variants. …”
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Exploring the recombinant evolution and hosts of crucivirus based on novel oyster-associated viruses by Hong-Sai Zhang, Hong-Sai Zhang, Chang Liu, Guang-Feng Liu, Yu-Yu Chen, Peng Zhu, Peng Zhu, Xin Xu, Bing-Xin Yin, Jing-Zhe Jiang, Jing-Zhe Jiang

“…“Crucivirus” represents a group of viruses with chimeric genomes, significant for viral evolution and recombination studies. Their capsid proteins share homology with the RNA virus tombusvirus, while their replicase-associated proteins are homologous to a class of single-stranded DNA viruses, namely CRESS DNA viruses. …”
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