Virus Genes最新文献

{"title":"Selective inhibition of rabies virus gene expression by human miRNAs: a therapeutic approach using the 7mer-m8 model.","authors":"Aparajita Roy, Supriyo Chakraborty","doi":"10.1007/s11262-025-02155-1","DOIUrl":"https://doi.org/10.1007/s11262-025-02155-1","url":null,"abstract":"<p><p>MicroRNAs, abbreviated as miRNAs, have a substantial impact on viral infections through their ability to control gene expression and influence the interactions between the host and the virus. This work investigates the capacity of miRNAs to selectively inhibit the expression of rabies virus genes, specifically Nucleoprotein N, Phosphoprotein M1 and M2, Transmembrane Glycoprotein G, and L protein. The 7mer-m8 model was utilized to identify human miRNAs that target these viral genes. The interactions between the miRNAs and the genes were then assessed based on binding energy, GC content, and stability. The findings indicated that miRNAs, including miR-1279, miR-4251, miR-4288, and miR-12117, successfully target the N gene. In addition, other miRNAs target the remaining viral genes, indicating their capacity to bind and potentially inhibit viral replication. In addition, docking experiments have verified the stability of miRNA-mRNA duplexes, as evidenced by the high free energy values that indicate strong and reliable contacts between miRNA and gene. These findings indicate that certain human miRNAs have the potential to be effective therapeutic agents against the rabies virus by suppressing gene expression. This offers a new and innovative strategy to fight against this deadly infection.</p>","PeriodicalId":51212,"journal":{"name":"Virus Genes","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2025-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144047470","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic analysis of Varicella zoster virus strains during an outbreak with atypical clinical presentations in Biswanath district of Assam, India.","authors":"Kimmi Sarmah, Ajanta Sharma, Kishore Sarma, Syed Tanwir Alam, Bornali Sarmah Dutta, Eliza Deka, Sahabuddin Ahmed Laskar, Narendra Singh Tishya, Manirangu Sobhana Lakshmi Priya, Achyut Chandra Baishya","doi":"10.1007/s11262-025-02156-0","DOIUrl":"https://doi.org/10.1007/s11262-025-02156-0","url":null,"abstract":"<p><p>Chickenpox, caused by the Varicella Zoster Virus (VZV), presents as varicella (chickenpox) during primary infection and as herpes zoster (shingles) upon reactivation. With a high infectivity rate and transmission through airborne droplets and contact, VZV poses a significant public health challenge. While the disease is self-limiting, complications such as encephalitis and pneumonia can occur, particularly in unimmunized individuals and those with weakened immune systems. The introduction of varicella vaccination has significantly reduced incidence and complications in countries with universal vaccination programs, but India is yet to incorporate this vaccine into its national immunization schedule. In June 2023, an outbreak of varicella was reported in Biswanath district, Assam, affecting 18 individuals. The outbreak highlighted the impact of factors such as overcrowding, poor ventilation, and inadequate medical intervention. Clinical symptoms included fever, vesicular rash, and severe abdominal pain, with three fatalities linked to severe complications. Molecular and serological investigations confirmed VZV infection in the cases, and whole genome sequencing (WGS) identified the strain as belonging to Clade 5. Phylogenetic analysis revealed the strain's similarity to other Indian VZV sequences, aligning with the established VZV clade nomenclature. The outbreak investigation underscored the importance of timely medical intervention and effective vaccination strategies. Enhanced surveillance, community awareness, and a coordinated response involving various health stakeholders are crucial for managing varicella outbreaks and improving vaccination coverage. This study represents the first comprehensive genomic analysis of VZV from Northeast India, providing valuable insights into the strain circulation and reinforcing the need for vaccination and preventive measures.</p>","PeriodicalId":51212,"journal":{"name":"Virus Genes","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2025-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144008345","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Global population dynamics and evolutionary selection in classical swine fever virus complete genomes: insights from Bayesian coalescent analysis.","authors":"Roopa Mahadevaswamy, Vijay Muruganantham, Varsha Ramesh, Shijili Mambully, Kuralayanapalya Puttahonnappa Suresh, Jagadish Hiremath, Shivasharanappa Nayakvadi, Baldev Gulati, Sharanagouda Patil","doi":"10.1007/s11262-025-02154-2","DOIUrl":"https://doi.org/10.1007/s11262-025-02154-2","url":null,"abstract":"<p><p>Classical swine fever virus (CSFV) is a pathogen that affects pigs and wild boars. This contagious RNA virus is a high threat to swine industries throughout the world because it has high mortality and morbidity rates, leading to economic losses. Although some studies have analyzed whole-genome sequences, but often focus on isolates from only a few countries, while others started with whole-genome analysis before narrowing down to specific gene region like E2. In addition, several studies have predominantly focused on isolated geographic regions. Our study leverages a global dataset of 220 CSFV whole-genome sequences retrieved from the NCBI repository along with two CSFV complete genome sequence from our laboratory (Accession Number: MH734359.1 and OR4282229.1) and carefully curated to 66 sequences. The refined dataset was subjected to Bayesian analysis along with selection pressure analysis. The outcome of this experiment, the mean substitution rate was estimated at 2.06 × 10^-3 substitutions/site/year with the Highest Posterior Density (HPD) (95% HPD 6.8012 × 10^-4 to 3.3044 × 10^-3), and the estimated average time to the most recent common ancestor (tMRCA) for the analyzed dataset was the year 1877 (95% HPD 1833.8181-1932.3176). Among the curated dataset, 2 CSFV complete genome sequences (Accession Number: MH734359.1 and OR428229.1) from our laboratory showed a Chinese origin. In addition, pervasive and episodic selection pressure revealed that both had ongoing diversifying natural positive selection, which could lead to increased genetic diversity and possibly emergence of the new lineage. This potential information could be used for future evaluation of strategies to control emerging new genotypes of CSFV with high mortality and morbidity.</p>","PeriodicalId":51212,"journal":{"name":"Virus Genes","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143812628","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Factors influencing the prevalence of acute bee paralysis virus in Apis mellifera and insights into its phylogenetic relationships.","authors":"Mustafa Emin Oz, Oguzhan Avci, Muge Dogan","doi":"10.1007/s11262-025-02135-5","DOIUrl":"10.1007/s11262-025-02135-5","url":null,"abstract":"<p><p>Acute bee paralysis virus (ABPV) is a notable pathogen frequently detected in managed honeybee (Apis mellifera) colonies. Although infections are often covert, they can lead to severe outcomes in the presence of Varroa destructor infestations. This study aims to evaluate the prevalence of ABPV and its correlation with a range of biotic and abiotic stressors in managed beehives located in the Central Anatolia and Mediterranean Regions of Türkiye during the spring-summer and autumn seasons of 2021. ABPV was identified in 38.6% of the samples (27/70) using real-time RT-PCR. The high prevalence observed was linked to Varroa destructor infestations, elevated temperatures and dry climatic conditions, migratory beekeeping practices, and disruptions in colony management during the COVID-19 pandemic. Phylogenetic relationships among ABPV strains were elucidated through partial sequencing of the capsid and RNA-dependent RNA polymerase protein coding genes, employing maximum likelihood tree construction with the Tamura 3-parameter model. Turkish ABPV strains clustered into a distinct subclade, sharing 98.4-99% nucleotide identity with European strains, indicative of a monophyletic origin and geographic segregation at the regional or continental level. These findings highlight the necessity for robust surveillance and research programs to monitor ABPV prevalence and mitigate its detrimental effects on colony health and productivity. Additionally, the phylogenetic insights provided by this study enhance our understanding of the geographic distribution and evolutionary dynamics of ABPV strains, offering critical information for future molecular epidemiological research and apicultural management strategies.</p>","PeriodicalId":51212,"journal":{"name":"Virus Genes","volume":" ","pages":"220-229"},"PeriodicalIF":1.9,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143400727","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction: The complete genomic sequence of Magnaporthe oryzae polymycovirus 1.","authors":"Hong Zheng, Cong Li, Yuxin Wu, Xinyi Li, Hongliu An, Shouguo Fang, Songbai Zhang, Qingchao Deng","doi":"10.1007/s11262-024-02129-9","DOIUrl":"10.1007/s11262-024-02129-9","url":null,"abstract":"","PeriodicalId":51212,"journal":{"name":"Virus Genes","volume":" ","pages":"211-213"},"PeriodicalIF":1.9,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142924015","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Gushan virus: a newly discovered virus found in mosquitoes of Shandong, China.","authors":"Long Yuan, Yongchao Yang, Wenbing Zhu, Shuo Feng, Xinbei Li, Jian Song, Yujing Zhu, Guoyu Niu","doi":"10.1007/s11262-025-02142-6","DOIUrl":"10.1007/s11262-025-02142-6","url":null,"abstract":"<p><p>Arboviruses persist as a significant threat to global public and human health. The advent of macrogenomics technology has substantially expanded our understanding of mosquito-borne viruses by facilitating the direct identification and characterization of viruses from diverse environmental samples. In 2022, we conducted mosquito surveillance in the Shandong region of China and discovered a novel virus, tentatively named Gushan virus based on the site of discovery. In this study, a total of 3170 mosquitoes were collected and divided into 62 pools based on species and collection locations. Quantitative reverse transcription PCR (qRT-PCR) and nested PCR were employed to detect Gushan virus nucleic acids in all samples. The results revealed that 16 pools were positive, with a minimum infection rate (MIR) of 0.5% (16/3,170). Concurrently, we successfully obtained one complete genome sequence and six partial sequences. Nucleotide homology analysis demonstrated a high degree of sequence identity, indicating that Gushan virus may maintain a stable genetic profile in the region. Phylogenetic analyses revealed that Gushan virus is most closely related to Drosophila immigrans Nora virus of the family Noroviridae. Taxonomically, Gushan virus belongs to the order Picornavirales, family Noroviridae, and genus Orthonoravirus. This study contributes new insights into the diversity of mosquito-associated viruses.</p>","PeriodicalId":51212,"journal":{"name":"Virus Genes","volume":" ","pages":"230-238"},"PeriodicalIF":1.9,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143400733","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular characterization and genetic analysis of highly pathogenic H5N1 clade 2.3.4.4b in seagulls from Dukan Lake, Iraq.","authors":"Mohammed Omar Baba Sheikh, Peshnyar M Atta Rashid, Zhino Hussein Rahim, Ari Salahadin Marouf, Star Sharif Saeed","doi":"10.1007/s11262-025-02133-7","DOIUrl":"10.1007/s11262-025-02133-7","url":null,"abstract":"<p><p>Avian influenza virus (AIV) remains a significant global threat, with periodic reemergence in Iraq. This study marks the first molecular characterization of the highly pathogenic avian influenza (HPAI) H5N1 clade 2.3.4.4b in seagulls. The H5N1 AIV was identified during outbreaks in 2024 at Dukan Lake in Sulaimani province. Phylogenetic analysis of the HA gene revealed that the Dukan Lake strain belongs to subclade 2.3.4.4b, clustering closely with Kazakhstan HPAI strains (A/mute swan/Mangystau/1-S24R-2/2024(H5N1) and (A/Cygnus cygnus/Karakol lake/01/2024(H5N1)), with DNA identities of 99.38% and 98.82%, respectively. Genetic analysis showed a polybasic amino acid cleavage site motif (PLREKRRKRGLF) in the HA gene. Additionally, receptor-binding domain (RBD) analysis indicated a preference for the avian α-2, 3 Sialic acid (SA) receptor over the mammalian α-2, 6 SA receptor. The NA gene analysis revealed amino acid residues D199, I223, S247, and H275, which are susceptible to antiviral drugs. The molecular analysis of the H5N1 Dukan Lake seagull strain provides insights into how the virus spreads among different species and countries, which is crucial for global health security and the development of effective control measures.</p>","PeriodicalId":51212,"journal":{"name":"Virus Genes","volume":" ","pages":"193-203"},"PeriodicalIF":1.9,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143015636","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic and epidemiological surveillance of SARS-CoV-2 variants during the pre-mass vaccination period in Botucatu, Brazil.","authors":"Felipe Allan da Silva da Costa, Patricia Akemi Assato, Karen Ingrid Tasca, Leonardo Nazário de Moraes, Drielle Baptista Dos Santos Figueiredo, Gabriela Ribeiro, Alex Ranieri Jerônimo Lima, Sandra Coccuzzo Sampaio, Maria Carolina Quartim Barbosa Elias Sabbaga, Carlos Magno Castelo Branco Fortaleza, Jayme Augusto de Souza-Neto, Rejane Maria Tommasini Grotto","doi":"10.1007/s11262-025-02137-3","DOIUrl":"10.1007/s11262-025-02137-3","url":null,"abstract":"<p><p>The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has caused an unprecedented pandemic in human history. To date, more than 6.5 million lives have been lost to COVID-19 (coronavirus disease 2019). Following widespread efforts for COVID-19 vaccination in Brazil, there has been a drastic reduction in COVID-19 deaths, which was particularly evident in the city of Botucatu, SP, Brazil, after a campaign to a mass vaccination. Our objective was to assess the temporal and epidemiological spread of variants of concern (VOC) of SARS-CoV-2 in the four weeks preceding the massive vaccination campaign in the municipality. After randomizing 400 samples, Next-Generation Sequencing was used to produce sequences and determine the variants. Among high-quality sequences, 98.4% belonged to the VOC Gamma, with P.1 and P.1.14 being the most prevalent lineages. P.1 was more frequent in both men and women, and in younger individuals and adults (0-59 years) compared to P.1.14. There was no correlation between the variants and the presence of comorbidities or between them and moderate to severe clinical cases of COVID-19 or death. However, P.1 was more frequent than P.1.14 in people with mild forms of the disease and in those who exhibited symptoms. In the phylogenetic analyses, a small cluster of 9 P.1.14 samples containing mutations in ORF1a: M584V and A3620V was observed, which had not been found in any Gamma sequences to date. The importance of genomic surveillance of SARS-CoV-2 is evident in assisting public health decision-making and the management of COVID-19 and other diseases.</p>","PeriodicalId":51212,"journal":{"name":"Virus Genes","volume":" ","pages":"153-166"},"PeriodicalIF":1.9,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143384040","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"First report of the whole‑genome sequence analysis of Fig badnavirus 2 from China.","authors":"Tuxunaili Aizitili, Yushanjiang Maimaiti, Zhixiang Zhang, Maihemuti Mijiti","doi":"10.1007/s11262-024-02132-0","DOIUrl":"10.1007/s11262-024-02132-0","url":null,"abstract":"<p><p>A novel plant virus was identified in fig trees exhibiting ring spot symptoms through high-throughput sequencing (HTS). The complete genome sequence was successfully determined using PCR and RT-PCR techniques. The virus features a circular DNA genome of 7233 nucleotides (nt) in length, encompassing four open reading frames (ORFs). ORF1 and ORF2 encode hypothetical proteins, while ORF3 encodes a putative polyprotein with conserved domains, including a zinc finger, aspartic protease, reverse transcriptase (RT), and RNase H. ORF4 encodes a putative protein of unknown function. Comparative nucleotide sequence analysis of the RT + RNase H region reveals 84.46% and 78.82% identity with grapevine badnavirus 1 (GBV-1, MF781082.1) and fig badnavirus 1 (FBV-1, MK348055.1), respectively. Notably, this virus's genomic organization diverges from GBV-1 but is similar to FBV-1. Phylogenetic analysis demonstrates that the three isolates of this virus form a distinct clade within the badnaviruses. Based on genomic structure and phylogenetic relationships, this novel virus represents a new member of the genus Badnavirus and is proposed to be named \"Fig badnavirus 2\" (FBV-2).</p>","PeriodicalId":51212,"journal":{"name":"Virus Genes","volume":" ","pages":"214-219"},"PeriodicalIF":1.9,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142958399","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Long non-coding RNA C1RL-AS1 aggravates influenza A virus pneumonia through miR-16-5p/LAMP3.","authors":"Xingjuan Liao, Qin Liang, Chao Xu, Xinbing Luo","doi":"10.1007/s11262-024-02131-1","DOIUrl":"10.1007/s11262-024-02131-1","url":null,"abstract":"<p><p>Influenza A viruses continue to pose a serious threat to public health and economic stability. To investigate the role of C1RL-AS1 in influenza A virus (IAV) pneumonia. Using RT-qPCR analysis, we determined C1RL-AS1 expression levels in children with IAV-infected pneumonia and A549 cells. C1RL-AS1 expression levels in children were subjected to ROC analysis. C1RL-AS1 was knocked down to investigate its role in IAV-infected A549 cells, including effects on viral nucleoprotein (NP) production, cell survival, and apoptosis. Downstream miRNAs of C1RL-AS1 were predicted and validated. MiR-16-5p target genes were predicted and validated. C1RL-AS1 was up-regulated in IAV-infected children and A549 cells. C1RL-AS1 expression levels distinguished children with IAV pneumonia from healthy children. Knockdown of C1RL-AS1 attenuated viral NP production, promoted A549 cell survival, and inhibited apoptosis. MiR-16-5p was a downstream C1RL-AS1 miRNA. miR-16-5p counteracted the anti-IAV infection effect brought about by C1RL-AS1 knockdown. LAMP3 was a miR-16-5p target gene associated with pneumonia. LAMP3 restored the cellular effects brought about by C1RL-AS1/miR-16-5p co-knockdown. C1RL-AS1 is a possible diagnostic factor for IAV pneumonia in children. C1RL-AS1 may participate in IAV pneumonia by sponging miR-16-5p and then moderating LAMP3.</p>","PeriodicalId":51212,"journal":{"name":"Virus Genes","volume":" ","pages":"145-152"},"PeriodicalIF":1.9,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142924016","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}