Archives of Virology最新文献

{"title":"Molecular and phylogenetic analysis of transmissible gastroenteritis virus strain VET-16, isolated from piglets in Vietnam","authors":"Soo Hyun Moon,&nbsp;Gyu-Nam Park,&nbsp;SeEun Choe,&nbsp;Sok Song,&nbsp;Van Phan Le,&nbsp;Yun Sang Cho,&nbsp;Dong-Jun An","doi":"10.1007/s00705-024-06101-8","DOIUrl":"10.1007/s00705-024-06101-8","url":null,"abstract":"<div><p>Porcine transmissible gastroenteritis virus (TGEV) is a major pathogen that causes viral enteritis and severe diarrhea in newborn piglets. TGEV strains have been isolated in the USA, Europe, and China, and their molecular characteristics are well known. However, there have been few reports of molecular analysis of TGEV strains isolated in Southeast Asia. In 2016, we isolated TGEV strain VET-16 from fecal samples collected from piglets in Vietnam and determined its complete genome sequence by Sanger sequencing. We found that, while the full genome of the VET-16 strain was 92.4-99.9% identical to those of other TGEV strains, the ORF3 gene showed very little sequence similarity. Phylogenetic analysis suggested that the VET-16 strain belongs to the Purdue subgroup. Comparison of the predicted amino acid (aa) sequence of the spike protein of strain VET-16 with those of other TGEV strains revealed three aa substitutions (V378L, S379T, and D380N) and a 3-aa insertion (F383_F387insWEK) in antigenic site D of the VET-16 strain. Also, a single aa deletion (∆F1413) was found in the transmembrane domain of the spike gene of VET-16. Like the ORF3 gene from the TGEV Miller M60 vaccine strain, the VET-16 strain has a large deletion (∆725 nt) in the ORF3 gene. Previous studies have suggested that these mutations in the spike and ORF3 genes might be associated with a reduction in pathogenicity. The data from this study will facilitate further genetic analysis and research into the evolution of TGEV in pigs in Vietnam.</p></div>","PeriodicalId":8359,"journal":{"name":"Archives of Virology","volume":"169 9","pages":""},"PeriodicalIF":2.5,"publicationDate":"2024-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142008154","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":"Biological characterization and genomic analysis of a novel bacteriophage, MopsHU1, infecting Morganella psychrotolerans","authors":"Shogo Yamaki,&nbsp;Koji Yamazaki","doi":"10.1007/s00705-024-06112-5","DOIUrl":"10.1007/s00705-024-06112-5","url":null,"abstract":"<div><p><i>Morganella psychrotolerans</i> is a histamine-producing bacterium that causes histamine poisoning. In this study, we isolated and characterized a novel phage, MopsHU1, that infects <i>M. psychrotolerans</i>. MopsHU1 is a podovirus with a limited host spectrum. Genomic analysis showed that MopsHU1 belongs to the family <i>Autographiviridae</i>, subfamily <i>Studiervirinae</i>, and genus <i>Kayfunavirus</i>. Comparative analysis revealed that the MopsHU1 genome is similar to those of <i>Citrobacter</i> phage SH3 and <i>Cronobacter</i> phage Dev2. Moreover, the <i>Escherichia coli</i> phage K1F genome is also similar, except for its tailspike gene sequence. These results expand our understanding of the <i>Kayfunavirus</i> phages that infect <i>Morganella</i> spp. Note: The nucleotide sequence data reported here are available in the DDBJ/EMBL/GenBank database under the accession number LC799501.</p></div>","PeriodicalId":8359,"journal":{"name":"Archives of Virology","volume":"169 9","pages":""},"PeriodicalIF":2.5,"publicationDate":"2024-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141995194","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 of a novel mitovirus from the plant-pathogenic fungus Nigrospora oryzae","authors":"Lei Wu,&nbsp;Qinxiang Wu,&nbsp;Jiwu Cao,&nbsp;Xizhi Wu,&nbsp;Manguo Yang,&nbsp;Hong Liu","doi":"10.1007/s00705-024-06110-7","DOIUrl":"10.1007/s00705-024-06110-7","url":null,"abstract":"<div><p>Here, we characterized a novel mitovirus from the fungus <i>Nigrospora oryzae</i>, which was named “Nigrospora oryzae mitovirus 3” (NoMV3). The NoMV3 genome is 2,492 nt in length with a G + C content of 33%, containing a single large open reading frame (ORF) using the fungal mitochondrial genetic code. The ORF encodes an RNA-dependent RNA polymerase (RdRp) of 775 amino acids with a molecular mass of 88.75 kDa. BLASTp analysis revealed that the RdRp of NoMV3 had 68.6%, 50.6%, and 48.6% sequence identity to those of Nigrospora oryzae mitovirus 2, Suillus luteus mitovirus 6, and Fusarium proliferatum mitovirus 3, respectively, which belong to the genus <i>Unuamitovirus</i> within the family <i>Mitoviridae</i>. Phylogenetic analysis based on amino acid sequences supported the classification of NoMV3 as a member of a new species in the genus <i>Unuamitovirus</i> within the family <i>Mitoviridae</i>.</p></div>","PeriodicalId":8359,"journal":{"name":"Archives of Virology","volume":"169 9","pages":""},"PeriodicalIF":2.5,"publicationDate":"2024-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141987339","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":"The first report of porcine parvovirus 8 (PPV8) on the American continent is associated with pigs in Colombia with porcine respiratory disease","authors":"Diana S. Vargas-Bermudez,&nbsp;Jairo Jaime","doi":"10.1007/s00705-024-06099-z","DOIUrl":"10.1007/s00705-024-06099-z","url":null,"abstract":"<div><p>Seven novel porcine parvoviruses (PPV2 to PPV8) have been discovered in the last two decades. The last one reported was PPV8 in China in 2022, which was proposed to be a member of the genus <i>Protoparvovirus</i>. Here, we report the first detection of PPV8 outside China – in two provinces from Colombia. Six out of 146 (4.1%) pigs showing porcine respiratory disease (PRD) tested positive for PPV8. Sequencing and phylogenetic analysis of two Colombian PPV8 isolates (GenBank database accession numbers PP335559 and PP335560) showed them to be members of the genus <i>Protoparvovirus</i>. Furthermore, PPV8 was detected in coinfections with porcine circovirus type 2 (PCV2) and porcine reproductive and respiratory syndrome virus (PRRSV), which are associated with PRD.</p></div>","PeriodicalId":8359,"journal":{"name":"Archives of Virology","volume":"169 9","pages":""},"PeriodicalIF":2.5,"publicationDate":"2024-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11329616/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141987341","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Complete genome sequence of a new virus, a tentative member of the family Geminiviridae, infecting hedge bindweed (Calystegia sepium) in South Korea","authors":"Do Yeon Kim,&nbsp;Jeong A Kwon,&nbsp;Se Eun Kim,&nbsp;Davaajargal Igori,&nbsp;Hualin Nie,&nbsp;Suk-Yoon Kwon,&nbsp;Young Kwon Park,&nbsp;Jae Sun Moon,&nbsp;Sun Hyung Kim","doi":"10.1007/s00705-024-06087-3","DOIUrl":"10.1007/s00705-024-06087-3","url":null,"abstract":"<div><p>The family Convolvulaceae comprises approximately 50–60 genera with approximately 1600–1700 species, exhibiting a rich diversity of morphological characteristics and occupying a broad range of ecological habitats. High-throughput sequencing identified a tentative new virus in the family <i>Geminiviridae</i> infecting <i>Calystegia sepium</i> var<i>. japonica</i> in South Korea. The 2,706 nt long genome comprises six open reading frames (ORFs). The analysis of the nucleotide sequence of the genome and the putative amino acid sequences of ORFs indicated that the virus was closely related to the members of the family <i>Geminiviridae</i>. The genome organization of the virus was similar to that of members of the genus <i>Topilevirus</i> in terms of the number of ORFs and splicing signal. However, the virus, tentatively named bindweed mottle virus (BWMV), may not be assigned to current genera into the family <i>Geminiviridae</i>.</p></div>","PeriodicalId":8359,"journal":{"name":"Archives of Virology","volume":"169 9","pages":""},"PeriodicalIF":2.5,"publicationDate":"2024-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141987337","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":"Genetic characterization and phylogenetic analysis of the S genes of porcine epidemic diarrhea virus isolates from China from 2020 to 2023","authors":"Yi Wang,&nbsp;Jiali Qian,&nbsp;Yupeng Li,&nbsp;Dandan Wang,&nbsp;Xu Song,&nbsp;Shuo Tian,&nbsp;Jinzhu Zhou,&nbsp;Wei Wang,&nbsp;Rongli Guo,&nbsp;Jizong Li,&nbsp;Xuehan Zhang,&nbsp;Xianwei Wang,&nbsp;Baochao Fan,&nbsp;Bin Li","doi":"10.1007/s00705-024-06109-0","DOIUrl":"10.1007/s00705-024-06109-0","url":null,"abstract":"<div><p>Porcine epidemic diarrhea virus (PEDV) is an enteric coronavirus that has been the main cause of diarrhea in piglets since 2010 in China. The aim of this study was to investigate sequence variation and recombination events in the spike (S) gene of PEDV isolates from China. Thirty complete S gene sequences were obtained from PEDV-positive samples collected in six provinces in China from 2020 to 2023. Phylogenetic analysis showed that 10% (3/30) belonged to subtype GII-a, 6.67% (2/30) were categorized as subtype GII-b, 66.67% (20/30) were categorized as subtype GII-c, and 16.66% (5/30) were clustered with the S-INDEL strains. Amino acid sequence alignments showed that, when compared to strains of other subtypes, the GII-c strains had two characteristic amino acid substitutions (N139D and I289M). Five S-INDEL subtype strains had a single amino acid deletion (139N) and four amino acid substitutions (N118G, T137S, A138S, and D141G). Recombination analysis allowed six putative recombination events to be identified, one involving recombination between GII-c strains, two involving GII-c and GII-b strains, two involving GII-c and GI-a strains, and one involving GII-a and GI-b strains. These results suggest that recombination between PEDV strains has been common and complex in recent years and is one of the main reasons for the continuous variation of PEDV strains.</p></div>","PeriodicalId":8359,"journal":{"name":"Archives of Virology","volume":"169 9","pages":""},"PeriodicalIF":2.5,"publicationDate":"2024-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141987338","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":"Spectrum detection and analysis of the epidemiological characteristics of infectious pathogens in the feline respiratory tract","authors":"Houbin Ju,&nbsp;Dequan Yang,&nbsp;Jizexiao Jin,&nbsp;Jian Wang,&nbsp;Xin Li,&nbsp;Xianchao Yang,&nbsp;Jie Ge,&nbsp;Jiuchao Zhu,&nbsp;Haixiao Shen,&nbsp;Jun Lu,&nbsp;Xiujuan Wu,&nbsp;Xiaoxu Wang,&nbsp;Yanting Tang,&nbsp;Qi Chen","doi":"10.1007/s00705-024-06093-5","DOIUrl":"10.1007/s00705-024-06093-5","url":null,"abstract":"<div><p>Our study was designed to investigate the original spectrum of feline respiratory tract infection and to provide a scientific basis for the clinical diagnosis and treatment of feline respiratory infections and for precise prevention and control measures. A total of 400 cats with upper respiratory tract infections from animal hospitals in 12 provinces in China were examined from November 2022 to October 2023 to investigate the epidemiology of feline calicivirus (FCV), feline herpes virus type 1 (FHV-1), influenza A virus (IAV), <i>Mycoplasma felis</i>, <i>Chlamydia felis</i>, and <i>Bordetella bronchiseptica</i> through loop-mediated isothermal amplification (LAMP) with microfluidic chip detection. The results showed that 396 of the 400 samples tested were positive for at least one of these pathogens, with an overall detection rate of 99.00%. The detection rates were as follows: FCV, 36.00% (144/400); <i>M. felis</i>, 34.00% (136/400); FHV-1, 21.50% (86/400); <i>C. felis</i>, 15.75% (63/400); <i>B. b</i>, 13.00% (52/400); IAV, 4.50% (18/400). There were no statistically significant differences in the detection rates of respiratory pathogens between different sexes, ages, seasons, breeds, or regions (<i>P</i> &gt; 0.05). There were 88 mixed infections, giving a total mixed infection rate of 22.00% (88/400). It is worth noting that the detection rate of FCV at different ages and of FHV-1 in different sexes showed significant differences (<i>P</i> &lt; 0.05). The highest rate of FCV infection was found in animals that were 1 to 2 years old, and the rate of FHV-1 infection in male cats was higher than that in female cats. The results showed that the spectrum of feline respiratory pathogens is complex, with diverse epidemiological characteristics and mixed infections, and some differences among different respiratory pathogens were found with regard to the sex, age, and breed of the cat. Studies should be continued to provide a scientific basis for precise prevention and control of feline respiratory diseases.</p></div>","PeriodicalId":8359,"journal":{"name":"Archives of Virology","volume":"169 9","pages":""},"PeriodicalIF":2.5,"publicationDate":"2024-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141987340","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":"2024 taxonomy update for the family Circoviridae","authors":"Arvind Varsani,&nbsp;Balázs Harrach,&nbsp;Philippe Roumagnac,&nbsp;Mária Benkő,&nbsp;Mya Breitbart,&nbsp;Eric Delwart,&nbsp;Giovanni Franzo,&nbsp;Darius Kazlauskas,&nbsp;Karyna Rosario,&nbsp;Joaquim Segalés,&nbsp;Emily Dunay,&nbsp;Joshua Rukundo,&nbsp;Tony L. Goldberg,&nbsp;Enikő Fehér,&nbsp;Eszter Kaszab,&nbsp;Krisztián Bányai,&nbsp;Mart Krupovic","doi":"10.1007/s00705-024-06107-2","DOIUrl":"10.1007/s00705-024-06107-2","url":null,"abstract":"<div><p>Circovirids have a circular single-stranded DNA genome packed into a small icosahedral capsid. They are classified within two genera, <i>Circovirus</i> and <i>Cyclovirus</i>, in the family <i>Circoviridae</i> (phylum <i>Cressdnaviricota</i>, class <i>Arfiviricetes</i>, order <i>Cirlivirales</i>). Over the last five years, a number of new circovirids have been identified, and, as a result, 54 new species have been created for their classification based on the previously established species demarcation criterion, namely, that viruses classified into different species share less than 80% genome-wide pairwise sequence identity<i>.</i> Of note, one of the newly created species includes a circovirus that was identified in human hepatocytes and suspected of causing liver damage. Furthermore, to comply with binomial species nomenclature, all new and previously recognized species have been (re)named in binomial format with a freeform epithet. Here, we provide a summary of the properties of circovirid genomes and their classification as of June 2024 (65 species in the genus <i>Circovirus</i> and 90 species in the genus <i>Cyclovirus</i>). Finally, we provide reference datasets of the nucleotide and amino acid sequences representing each of the officially recognized circovirid species to facilitate further classification of newly discovered members of the <i>Circoviridae</i>.</p></div>","PeriodicalId":8359,"journal":{"name":"Archives of Virology","volume":"169 9","pages":""},"PeriodicalIF":2.5,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141981503","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":"A time series transcriptome profiling of host cell responses to Newcastle disease virus infection","authors":"B. Nagaraj Nayak,&nbsp;Preethi Palanisamy,&nbsp;Sangita Venkataraman,&nbsp;Madhuri Subbiah","doi":"10.1007/s00705-024-06100-9","DOIUrl":"10.1007/s00705-024-06100-9","url":null,"abstract":"<div><p>Newcastle disease virus (NDV), an avian paramyxovirus, causes major economic losses in the poultry industry worldwide. NDV strains are classified as avirulent, moderately virulent, or virulent according to the severity of the disease they cause. In order to gain a deeper understanding of the molecular mechanisms of virus-host interactions, we conducted Illumina HiSeq-based RNA-Seq analysis on chicken embryo fibroblast (DF1) cells during the first 24 hours of infection with NDV strain Komarov. Comparative analysis of uninfected DF1 cells versus NDV-infected DF1 cells at 6, 12, and 24 h postinfection identified 462, 459, and 410 differentially expressed genes, respectively. The findings revealed an increase in the expression of genes linked to the MAPK signalling pathway in the initial stages of NDV infection. This overexpression potentially aids viral multiplication while hindering pathogen detection and subsequent immune responses from the host. Our findings provide initial insights into the early responses of DF1 cells to NDV infection.</p></div>","PeriodicalId":8359,"journal":{"name":"Archives of Virology","volume":"169 9","pages":""},"PeriodicalIF":2.5,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141905813","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":"Prevalence and molecular analysis of some important viruses in honey bee colonies in Türkiye: the status of multiple infections","authors":"Rahsan Akpinar,&nbsp;Emre Ozan,&nbsp;Semanur Celik,&nbsp;Yunus Bayram,&nbsp;Ayhan Akman,&nbsp;Gulnur Kalayci,&nbsp;Abdurrahman Anil Cagirgan,&nbsp;Hamza Kadi,&nbsp;Omer Faruk Kucukkalem,&nbsp;Mustafa Emin Oz,&nbsp;Resul Emre Yilmazer,&nbsp;Arif Bozdeveci,&nbsp;Bilal Kucukoglu,&nbsp;Gokhan Guven,&nbsp;Murat Yaldiz,&nbsp;Sengul Alpay Karaoglu","doi":"10.1007/s00705-024-06103-6","DOIUrl":"10.1007/s00705-024-06103-6","url":null,"abstract":"<div><p>In this study, seven bee viruses of significant importance for bee health in Türkiye were investigated using one-step RT-PCR. For this purpose, larvae from 1183 hives and adult bees from 1196 hives were sampled from 400 apiaries in 40 provinces. The prevalence of viral infections in hives was as follows: acute bee paralysis virus (ABPV), 6.4%; black queen cell virus (BQCV), 77%; chronic bee paralysis virus (CBPV), 3.2%; deformed wing virus (DWV), 63.8%; Israel acute bee paralysis virus (IAPV), 7%; Kashmir bee virus (KBV), 2.7%; sacbrood virus (SBV), 49.7%. Moreover, 50 different combinations of viral infections were identified in the hives. While dual infections (36.1%) were the most common in hives, triple infections with BQCV, DWV, and SBV were found to have the highest prevalence (22.1%). At least one viral infection was detected in all of the apiaries tested. Phylogenetic analysis showed that the isolates from this study generally exhibited the highest similarity to previously reported Turkish isolates. When similarity ratios and the locations and types of amino acid mutations were analyzed, it was observed that the isolates from our study exhibited high similarity to isolates from various countries, including China, the United Kingdom, Syria, and Germany.</p></div>","PeriodicalId":8359,"journal":{"name":"Archives of Virology","volume":"169 9","pages":""},"PeriodicalIF":2.5,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141892764","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}