IF 1.9 4区医学

Virus Genes Pub Date : 2025-04-01 Epub Date: 2025-02-11 DOI: 10.1007/s11262-025-02135-5

Mustafa Emin Oz, Oguzhan Avci, Muge Dogan

{"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":"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.","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}

引用次数: 0

Gushan virus: a newly discovered virus found in mosquitoes of Shandong, China.

IF 1.9 4区医学

Virus Genes Pub Date : 2025-04-01 Epub Date: 2025-02-11 DOI: 10.1007/s11262-025-02142-6

Long Yuan, Yongchao Yang, Wenbing Zhu, Shuo Feng, Xinbei Li, Jian Song, Yujing Zhu, Guoyu Niu

{"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":"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.","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}

引用次数: 0

Molecular characterization and genetic analysis of highly pathogenic H5N1 clade 2.3.4.4b in seagulls from Dukan Lake, Iraq. 伊拉克杜坎湖海鸥高致病性H5N1进化枝2.3.4.4b的分子特征和遗传分析

IF 1.9 4区医学

Virus Genes Pub Date : 2025-04-01 Epub Date: 2025-01-22 DOI: 10.1007/s11262-025-02133-7

Mohammed Omar Baba Sheikh, Peshnyar M Atta Rashid, Zhino Hussein Rahim, Ari Salahadin Marouf, Star Sharif Saeed

{"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":"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.","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}

引用次数: 0

Genomic and epidemiological surveillance of SARS-CoV-2 variants during the pre-mass vaccination period in Botucatu, Brazil.

IF 1.9 4区医学

Virus Genes Pub Date : 2025-04-01 Epub Date: 2025-02-10 DOI: 10.1007/s11262-025-02137-3

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

{"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":"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.","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}

引用次数: 0

First report of the whole‑genome sequence analysis of Fig badnavirus 2 from China. 中国乙型图病毒2全基因组序列分析首次报道。

IF 1.9 4区医学

Virus Genes Pub Date : 2025-04-01 Epub Date: 2025-01-08 DOI: 10.1007/s11262-024-02132-0

Tuxunaili Aizitili, Yushanjiang Maimaiti, Zhixiang Zhang, Maihemuti Mijiti

{"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":"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).","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}

引用次数: 0

Long non-coding RNA C1RL-AS1 aggravates influenza A virus pneumonia through miR-16-5p/LAMP3. 长链非编码RNA C1RL-AS1通过miR-16-5p/LAMP3加重甲型流感病毒肺炎

IF 1.9 4区医学

Virus Genes Pub Date : 2025-04-01 Epub Date: 2025-01-02 DOI: 10.1007/s11262-024-02131-1

Xingjuan Liao, Qin Liang, Chao Xu, Xinbing Luo

{"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":"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.","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}

引用次数: 0

The complete genomic sequence of Magnaporthe oryzae polymycovirus 1. 米大孔菌多分枝病毒1型全基因组序列。

IF 1.9 4区医学

Virus Genes Pub Date : 2025-04-01 Epub Date: 2024-12-06 DOI: 10.1007/s11262-024-02126-y

Hong Zheng, Cong Li, Yuxin Wu, Xinyi Li, Hongliu An, Shouguo Fang, Songbai Zhang, Qingchao Deng

{"title":"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/s11262-024-02126-y","DOIUrl":"10.1007/s11262-024-02126-y","url":null,"abstract":"A novel double-stranded RNA virus, designated as \"Magnaporthe oryzae polymycovirus 1\" (MoPmV1), was identified in Magnaporthe oryzae strain TM02. MoPmV1 has four dsRNA fragments, ranging from 1324 to 2401 bp in length. DsRNA1, 2, and 3 of MoPmV1 each possess a single large open reading frame (ORF), whereas dsRNA4 contains two ORFs. BLASTp analysis indicated that ORF1a, encoded by dsRNA1, shows 59.2% amino acid sequence identity with the RNA-dependent RNA polymerase (RdRp) of Beauveria bassiana polymycovirus 2; ORF2a, encoded by dsRNA2, shows 42.3% identity with the putative serine protease of Phaeoacremonium minimum tetramycovirus 1; ORF3a, encoded by dsRNA3, shows 40.6% identity with the methyltransferase of Aspergillus fumigatus tetramycovirus 1; ORF4a, encoded by dsRNA4, shows 41.7% identity with the proline-alanine-serine-rich (PASr) protein of Botryosphaeria dothidea virus 1, while ORF4b, encoded by dsRNA4, shows no significant similarity to any known proteins. Phylogenetic analysis of the RdRp domain indicated that MoPmV1 was grouped in a cluster with members of the genus Polymycovirus in the family Polymycoviridae. Based on these characteristics, MoPmV1 is a new member of the genus Polymycovirus in the family Polymycoviridae. This is the first report of a mycovirus of the family Polymycoviridae identified in rice blast fungus M. oryzae.","PeriodicalId":51212,"journal":{"name":"Virus Genes","volume":" ","pages":"204-210"},"PeriodicalIF":1.9,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142787680","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}

引用次数: 0

First detection and diversity of astroviruses in wild migratory birds of Sakhalin Island, North Pacific. 北太平洋库页岛野生候鸟中星状病毒的首次检测及其多样性。

IF 1.9 4区医学

Virus Genes Pub Date : 2025-04-01 Epub Date: 2024-12-27 DOI: 10.1007/s11262-024-02130-2

Dmitry Zhirov, Nikita Dubovitskiy, Anastasiya Derko, Arina Loginova, Ivan Sobolev, Pavel Ktitorov, Olga Kulikova, Guimei He, Zhenghuan Wang, Wen Wang, Alexander Alekseev, Alexander Shestopalov, Kirill Sharshov

{"title":"First detection and diversity of astroviruses in wild migratory birds of Sakhalin Island, North Pacific.","authors":"Dmitry Zhirov, Nikita Dubovitskiy, Anastasiya Derko, Arina Loginova, Ivan Sobolev, Pavel Ktitorov, Olga Kulikova, Guimei He, Zhenghuan Wang, Wen Wang, Alexander Alekseev, Alexander Shestopalov, Kirill Sharshov","doi":"10.1007/s11262-024-02130-2","DOIUrl":"10.1007/s11262-024-02130-2","url":null,"abstract":"Researchers have identified Avastrovirus as a significant genus of bird viruses, linked to various avian diseases such as enteritis, growth retardation, nephritis and hepatitis. These infections can cause substantial economic losses in agrocultureand have a widespread impact on global food production. Although there have been numerous studies on these viruses, most of them-mainly focuses on poultry. Research on astroviruses in wild bird populations has revealed a wide genetic diversity of these viruses, yet our understanding of their biological and ecological characteristics remains limited. In this study, we for the first time detected avastrovirus in wild migratory birds of the families Anatidae and Columbidae from Sakhalin Island, North Pacific Ocean. Phylogenetic analysis revealed the presence of Avastrovirus 2 in wild doves and Avastrovirus 3 in wild ducks. These findings provide valuable insights into the circulation of astroviruses in wild bird populations of Sakhalin Island, which lies along the East Asian-Australasian Flyway.","PeriodicalId":51212,"journal":{"name":"Virus Genes","volume":" ","pages":"244-248"},"PeriodicalIF":1.9,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142900059","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}

引用次数: 0

Effect of thymidine kinase-deficiency (∆ORF38) on neuropathogenicity of equine herpesvirus-1 in the mouse model and expression of neighboring genes. 胸苷激酶缺乏（∆ORF38）对马疱疹病毒-1小鼠模型神经致病性及邻近基因表达的影响

IF 1.9 4区医学

Virus Genes Pub Date : 2025-04-01 Epub Date: 2024-12-16 DOI: 10.1007/s11262-024-02128-w

Samy Kasem, Ahmed S Abdel-Moneim, Hideto Fukushi

引用次数: 0

Pooled screening for endogenous HHV-6 in subjects with coronary artery disease.

IF 1.9 4区医学

Virus Genes Pub Date : 2025-04-01 Epub Date: 2025-01-31 DOI: 10.1007/s11262-025-02134-6

Rie Koide, Yoshie Nakashima, Shohei Kojima, Yohei Sotomi, Yasushi Sakata, Yasuhiko Sakata, Kaoru Ito, Nicholas F Parrish

引用次数: 0

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