Virus Genes最新文献_第8页

Analysis of SARS-CoV-2 omicron mutations that emerged during long-term replication in a lung cancer xenograft mouse model 分析肺癌异种移植小鼠模型长期复制过程中出现的 SARS-CoV-2 omicron 突变

IF 1.6 4区医学

Virus Genes Pub Date : 2024-04-08 DOI: 10.1007/s11262-024-02067-6

Kyeongbin Baek, Dongbum Kim, Jinsoo Kim, Bo Min Kang, Heedo Park, Sangkyu Park, Ha-Eun Shin, Myeong-Heon Lee, Sony Maharjan, Minyoung Kim, Suyeon Kim, Man-Seong Park, Younghee Lee, Hyung-Joo Kwon

{"title":"Analysis of SARS-CoV-2 omicron mutations that emerged during long-term replication in a lung cancer xenograft mouse model","authors":"Kyeongbin Baek, Dongbum Kim, Jinsoo Kim, Bo Min Kang, Heedo Park, Sangkyu Park, Ha-Eun Shin, Myeong-Heon Lee, Sony Maharjan, Minyoung Kim, Suyeon Kim, Man-Seong Park, Younghee Lee, Hyung-Joo Kwon","doi":"10.1007/s11262-024-02067-6","DOIUrl":"https://doi.org/10.1007/s11262-024-02067-6","url":null,"abstract":"SARS-CoV-2 Omicron has the largest number of mutations among all the known SARS-CoV-2 variants. The presence of these mutations might explain why Omicron is more infectious and vaccines have lower efficacy to Omicron than other variants, despite lower virulence of Omicron. We recently established a long-term in vivo replication model by infecting Calu-3 xenograft tumors in immunodeficient mice with parental SARS-CoV-2 and found that various mutations occurred majorly in the spike protein during extended replication. To investigate whether there are differences in the spectrum and frequency of mutations between parental SARS-CoV-2 and Omicron, we here applied this model to Omicron. At 30 days after infection, we found that the virus was present at high titers in the tumor tissues and had developed several rare sporadic mutations, mainly in ORF1ab with additional minor spike protein mutations. Many of the mutant isolates had higher replicative activity in Calu-3 cells compared with the original SARS-CoV-2 Omicron virus, suggesting that the novel mutations contributed to increased viral replication. Serial propagation of SARS-CoV-2 Omicron in cultured Calu-3 cells resulted in several rare sporadic mutations in various viral proteins with no mutations in the spike protein. Therefore, the genome of SARS-CoV-2 Omicron seems largely stable compared with that of the parental SARS-CoV-2 during extended replication in Calu-3 cells and xenograft model. The sporadic mutations and modified growth properties observed in Omicron might explain the emergence of Omicron sublineages. However, we cannot exclude the possibility of some differences in natural infection.","PeriodicalId":51212,"journal":{"name":"Virus Genes","volume":"314 1","pages":""},"PeriodicalIF":1.6,"publicationDate":"2024-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140561873","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

Potentials as biomarker and therapeutic target of upregulated long non-coding RNA HLA-F antisense RNA 1 in hepatitis B virus-associated hepatocellular carcinoma 乙型肝炎病毒相关肝细胞癌中上调的长非编码 RNA HLA-F 反义 RNA 1 作为生物标记物和治疗靶点的潜力

IF 1.6 4区医学

Virus Genes Pub Date : 2024-04-03 DOI: 10.1007/s11262-024-02065-8

{"title":"Potentials as biomarker and therapeutic target of upregulated long non-coding RNA HLA-F antisense RNA 1 in hepatitis B virus-associated hepatocellular carcinoma","authors":"","doi":"10.1007/s11262-024-02065-8","DOIUrl":"https://doi.org/10.1007/s11262-024-02065-8","url":null,"abstract":"<h3>Abstract</h3> The tissue-specific characteristics have encouraged researchers to identify organ-specific lncRNAs as disease biomarkers. This study aimed to identify the clinical and functional roles of long non-coding RNA HLA-F antisense RNA 1 (HLA-F-AS1) in hepatitis B virus (HBV)-hepatocellular carcinoma (HCC). A total of 121 HBV-HCC, 81 chronic hepatitis B (CHB), and 85 normal liver tissues were evaluated in this study. Real-time quantitative PCR assay was used to evaluate the RNA expression levels. Performance in diagnosis was compared between alpha fetoprotein (AFP) and HLA-F-AS1 using Receiver Operating Characteristic (ROC) curves. Performance in post-hepatectomy prognosis with high or low HLA-F-AS1 was compared using Kaplan–Meier curves. Multi-variable analysis was used to determine the informative predictors. Downstream miRNAs for HLA-F-AS1 were predicted and miR-128-3p was confirmed by luciferase reporter assay and RNA pull-down assay. In vitro functional analysis was performed by MTS reagent for cell proliferation and transwell assay for cell migration. HLA-F-AS1 levels were significantly increased in the HBV-HCC compared to normal healthy tissue and CHB tissues. HLA-F-AS1 exhibited a well potential in making a distinction between HBV-HCC and health, as well as HBV-HCC and CHB. The survival analysis revealed that patients with high levels of HLA-F-AS1 tend to shorter overall survival times. The best prognostic performance was achieved by HLA-F-AS1 after multi-variable analysis (HR 2.290, 95% CI 1.191–4.403, p = 0.013). Functional analysis showed that HLA-F-AS1 promoted cell proliferation and migration via miR-128-3p. Up-regulation of HLA-F-AS1 could serve as a promising diagnostic and prognostic marker for HBV-HCC after surgery, maybe useful in the management of HBV-HCC patients. HLA-F-AS1 can promote the progression of HBV-HCC, may be useful in the targeting treatment of HBV-HCC patients.","PeriodicalId":51212,"journal":{"name":"Virus Genes","volume":"32 1","pages":""},"PeriodicalIF":1.6,"publicationDate":"2024-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140561962","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

Determination of molecular epidemiologic pattern of human T-lymphotropic virus type 1 (HTLV-1) in Alborz province, Iran. 确定伊朗阿尔伯兹省人类 T 淋巴细胞病毒 1 型 (HTLV-1) 的分子流行病学模式。

IF 1.6 4区医学

Virus Genes Pub Date : 2024-04-01 Epub Date: 2024-01-25 DOI: 10.1007/s11262-024-02051-0

Mahshid Safavi, Fariba Habibian-Sezavar, Arash Letafati, Setayesh Solouki, Somayeh Yaslianifard, Parisa Kaboli, Mohammad Mohammadzadeh, Kourosh Kabir, Mehrdad Sadeghi Haj, Sayed-Hamidreza Mozhgani

{"title":"Determination of molecular epidemiologic pattern of human T-lymphotropic virus type 1 (HTLV-1) in Alborz province, Iran.","authors":"Mahshid Safavi, Fariba Habibian-Sezavar, Arash Letafati, Setayesh Solouki, Somayeh Yaslianifard, Parisa Kaboli, Mohammad Mohammadzadeh, Kourosh Kabir, Mehrdad Sadeghi Haj, Sayed-Hamidreza Mozhgani","doi":"10.1007/s11262-024-02051-0","DOIUrl":"10.1007/s11262-024-02051-0","url":null,"abstract":"Human T-cell lymphotropic virus type 1 (HTLV-1) is linked to two debilitating diseases, adult T-cell leukemia/lymphoma (ATLL) and HTLV-1 associated myelopathy tropical spastic paraparesis (HAM/TSP), which are prevalent in various parts of the world, including the Alborz province in Iran. Understanding the prevalence and evolutionary relationships of HTLV-1 infections in these endemic areas is of utmost importance. In the realm of phylogenetic studies, long terminal repeat (LTR) region of HTLV-1 stands out as highly conserved, yet more variable compared to other gene segments. Consequently, it is the primary focus for phylogenetic analyses. Additionally, trans-activator of transcription (Tax), an oncoprotein, holds a pivotal role in the regulation of gene expression. This cross-sectional study delved into the phylogenetic analysis of HTLV-1 among individuals in Alborz province of Iran. To confirm infection, we amplified partial sequence LTR (PLTR) and HTLV-1 bZIP factor (PHBZ). For phylogenetic analysis, we sequenced the full sequence LTR (FLTR) and full Tax sequence (FTax). The FLTR and FTax sequences underwent analysis using BioEdit, and phylogenetic trees were constructed using MEGA-X software. Out of the roughly 15,000 annual blood donors in Alborz, 19 samples tested positive for HTLV-1, indicating a 0.13% HTLV-1 positivity rate among blood donors. Furthermore, the HTLV-1 virus prevalent in the Alborz province belongs to subtype A (cosmopolitan) subgroup A. The findings revealed that while mutations were observed in both the LTR and Tax genes, they were not significant enough to bring about fundamental alterations. Despite positive selection detected in three Alborz isolates, it has not led to mutations affecting Tax function and virulence.","PeriodicalId":51212,"journal":{"name":"Virus Genes","volume":" ","pages":"117-125"},"PeriodicalIF":1.6,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139565158","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

Guinea pig herpes like virus is a gamma herpesvirus. 豚鼠疱疹病毒是一种伽马疱疹病毒。

IF 1.6 4区医学

Virus Genes Pub Date : 2024-04-01 Epub Date: 2024-02-10 DOI: 10.1007/s11262-024-02054-x

Brent A Stanfield, Emmanuelle Ruiz, Vladimir N Chouljenko, Konstantin G Kousoulas

引用次数: 0

Characterization of a breakthrough vaccine escape strain associated with overt hepatitis B virus infection. 与明显乙型肝炎病毒感染相关的突破性疫苗逃逸株的特征。

IF 1.6 4区医学

Virus Genes Pub Date : 2024-04-01 Epub Date: 2024-02-13 DOI: 10.1007/s11262-024-02055-w

Mohammed El-Mowafy, Mohamed Elegezy, Mohamed El-Mesery, Abdelaziz Elgaml

引用次数: 0

Do HBsAg subdeterminants matter for vaccination against hepatitis B? HBsAg 亚型对乙型肝炎疫苗接种有影响吗？

IF 1.6 4区医学

Virus Genes Pub Date : 2024-04-01 Epub Date: 2024-02-14 DOI: 10.1007/s11262-024-02061-y

Wolfram H Gerlich

引用次数: 0

Isolation and molecular characterization of lumpy skin disease virus from Tamil Nadu, India during the outbreaks from 2020 to 2022. 2020 年至 2022 年疫情爆发期间从印度泰米尔纳德邦分离块状皮肤病病毒并确定其分子特征。

IF 1.6 4区医学

Virus Genes Pub Date : 2024-04-01 Epub Date: 2024-02-12 DOI: 10.1007/s11262-024-02057-8

Manimuthu Prabhu, Shanmugasamy Malmarugan, Sithanandam Rajagunalan, Balakrishnan Govindan, Lakshmi Prasanth Thangavelu, Ganapathi Palanisamy, Revanaiah Yogisharadhya, Kumaragurubaran Karthik

{"title":"Isolation and molecular characterization of lumpy skin disease virus from Tamil Nadu, India during the outbreaks from 2020 to 2022.","authors":"Manimuthu Prabhu, Shanmugasamy Malmarugan, Sithanandam Rajagunalan, Balakrishnan Govindan, Lakshmi Prasanth Thangavelu, Ganapathi Palanisamy, Revanaiah Yogisharadhya, Kumaragurubaran Karthik","doi":"10.1007/s11262-024-02057-8","DOIUrl":"10.1007/s11262-024-02057-8","url":null,"abstract":"Lumpy skin disease (LSD) caused by LSD virus is a WOAH notifiable, high-impact, transboundary poxviral disease of bovines. The first official report of LSDV in India is from Odisha state during August 2019. Since then, cases have been reported from many states including Tamil Nadu, a Southern state of India. The present study deals with isolation and molecular characterization of LSDV from Tamil Nadu during the period August 2020 to July 2022. LSDV was isolated in embryonated chicken eggs (ECE) and BHK 21 cells and was characterized based on P32, RPO30, and GPCR genes. The phylogenetic analysis revealed that Tamil Nadu isolates from India are closely related to other Indian strains, Kenyan strains and strains from neighboring countries such as Bangladesh, Nepal, and Myanmar confirming the common exotic source for the transboundary spread across borders. The presence of unique signature of amino acid (aa) at specific positions (A11, T12, T34, S99, and P199) in the GPCR sequence confirmed the identity of LSDV. A twelve nucleotide (nt94-105) insertion and corresponding aa (TILS) at 30-33 position was found in GPCR sequence and characteristic amino acid proline at 98 position (P98) in the RPO30 gene sequence of our isolates was similar to strains from Bangladesh, Nepal, and Myanmar. Further, dissimilarity of our isolates from Neethling like vaccine strains confirms the circulation of virulent filed strains responsible for the outbreaks.","PeriodicalId":51212,"journal":{"name":"Virus Genes","volume":" ","pages":"159-172"},"PeriodicalIF":1.6,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139724855","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

MiR-339-5p inhibits replication of porcine reproductive and respiratory syndrome virus by targeting viral gene regions. MiR-339-5p 通过靶向病毒基因区域抑制猪繁殖与呼吸综合征病毒的复制。

IF 1.6 4区医学

Virus Genes Pub Date : 2024-04-01 Epub Date: 2024-02-18 DOI: 10.1007/s11262-024-02059-6

Cuifang Ye, Xinyan Cao, Jinliang Sheng, Yanming Sun, Guang Li, Wenbin Fang, Yanbing Zhang

{"title":"MiR-339-5p inhibits replication of porcine reproductive and respiratory syndrome virus by targeting viral gene regions.","authors":"Cuifang Ye, Xinyan Cao, Jinliang Sheng, Yanming Sun, Guang Li, Wenbin Fang, Yanbing Zhang","doi":"10.1007/s11262-024-02059-6","DOIUrl":"10.1007/s11262-024-02059-6","url":null,"abstract":"Porcine reproductive and respiratory syndrome virus (PRRSV) is a variable virus, whose spread cannot be totally stopped by vaccination. PRRSV infection results in abortion and respiratory symptoms in pregnant pigs. One crucial component of the anti-viral infection strategy is microRNA (miRNA), a class of multifunctional small molecules. It is unknown whether miR-339-5p can specifically target the PRRSV gene and prevent the virus from replicating, despite the fact that miR-339-5p is markedly up-regulated during the PRRSV infection. In this pursuit, the present study revealed that the two PRRSV areas targeted by miR-339-5p were PRRSV nsp2-3378 to 3403 and PRRSV nsp2-3112 to 3133 using the miRanda program. Dual luciferase reporter assays showed that the miR-339-5p target region of the PRRSV gene sequence exhibited 100% homology and was highly conserved. Furthermore, the ability of miR-339-5p to target PRRSV gene areas was verified. It was found that the overexpression of miR-339-5p markedly reduced the PRRSV replication through PRRSV infection trials. The precursor sequence of ssc-miR-339-5p was amplified using the DNA of pig lung tissue as a template in order to create a fragment of 402 bp of porcine-derived miR-339-5p precursor sequence, which was then used to produce the eukaryotic expression plasmid of miR-339-5p. In conclusion, miR-339-5p can target the specific PRRSV gene areas and prevent PRRSV replication, offering fresh perspectives for the creation of medications that combat the PRRSV infection.","PeriodicalId":51212,"journal":{"name":"Virus Genes","volume":" ","pages":"186-193"},"PeriodicalIF":1.6,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139898331","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

Characterization and complete genome analysis of Klebsiella phage Kp109 with lytic activity against Klebsiella pneumoniae. 对肺炎克雷伯氏菌具有溶菌活性的克雷伯氏菌噬菌体 Kp109 的特征和全基因组分析。

IF 1.6 4区医学

Virus Genes Pub Date : 2024-04-01 Epub Date: 2024-01-27 DOI: 10.1007/s11262-024-02053-y

Deeksha Singh, Shilpee Pal, Srikrishna Subramanian, Natesan Manickam

{"title":"Characterization and complete genome analysis of Klebsiella phage Kp109 with lytic activity against Klebsiella pneumoniae.","authors":"Deeksha Singh, Shilpee Pal, Srikrishna Subramanian, Natesan Manickam","doi":"10.1007/s11262-024-02053-y","DOIUrl":"10.1007/s11262-024-02053-y","url":null,"abstract":"Klebsiella pneumonia is a serious pathogen involved in a range of infections. The increasing frequency of infection associated with K. pneumoniae and accelerated development of antimicrobial resistance has limited the available options of antibiotics for the treatment of infection. Bacteriophages are an attractive substitute to alleviate the problem of antibiotic resistance. In this study, isolation, microbiological and genomic characterization of bacteriophage Kp109 having the ability to infect K. pneumoniae has been shown. Phage Kp109 showed good killing efficiency and tolerance to a broad range of temperatures (4-60 °C) and pH (3-9). Transmission electron microscopy and genomic analysis indicated that phage Kp109 belongs to the genus Webervirus and family Drexlerviridae. Genomic analysis showed that the Kp109 has a 51,630 bp long double-stranded DNA genome with a GC content of 51.64%. The absence of known lysogenic, virulence, and antibiotic-resistant genes (ARGs) in its genome makes phage Kp109 safer to be used as a biocontrol agent for different purposes including phage therapy. The computational analysis of the putative endolysin gene revealed a binding energy of - 6.23 kcal/mol between LysKp109 and ligand NAM-NAG showing its potential to be used as an enzybiotic. However, future research is required for experimental validation of the in silico work to further corroborate the results obtained in the present study. Overall, phenotypic, genomic, and computational characterization performed in the present study showed that phages Kp109 and LysKp109 are promising candidates for future in vivo studies and could potentially be used for controlling K. pneumoniae infection.","PeriodicalId":51212,"journal":{"name":"Virus Genes","volume":" ","pages":"222-234"},"PeriodicalIF":1.6,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139571220","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

Comparison of HVT-ND recombinant and convection-based Newcastle disease vaccination programs in the protection against the genotype VII NDV challenges: an experimental study. 比较 HVT-ND 重组疫苗接种计划和基于对流的新城疫疫苗接种计划对基因型 VII NDV 挑战的保护作用：一项实验研究。

IF 1.6 4区医学

Virus Genes Pub Date : 2024-04-01 Epub Date: 2024-01-30 DOI: 10.1007/s11262-023-02038-3

Mohammad Kazem Rajab, Mohmmad Hassan Bozorgmehri Fard, Arash Ghalyanchilangeroudi, Hossein Hosseini, Saeed Charkhkar

{"title":"Comparison of HVT-ND recombinant and convection-based Newcastle disease vaccination programs in the protection against the genotype VII NDV challenges: an experimental study.","authors":"Mohammad Kazem Rajab, Mohmmad Hassan Bozorgmehri Fard, Arash Ghalyanchilangeroudi, Hossein Hosseini, Saeed Charkhkar","doi":"10.1007/s11262-023-02038-3","DOIUrl":"10.1007/s11262-023-02038-3","url":null,"abstract":"Newcastle disease virus (NDV) belongs to the Avulavirus genus and Paramyxoviridae family virus that causes acute, highly infectious Newcastle disease in poultry. The two proteins of haemagglutinin neuraminidase (HN) and fusion (F) are key virulence factors with an important role in its immunogenicity. Genotype VII NDV is still among the most serious viral hazards to the poultry industry worldwide. In this study, a commercial vector vaccine (HVT-NDV) was evaluated compared to the conventional vaccination strategy against Iranian genotype VII. This experiment showed that the group receiving the conventional vaccination strategy had higher antibodies, fewer clinical signs, and lower viral loads in tracheal swabs and feces. Also, two vaccine groups showed significant difference, which could have resulted from two extra vaccine doses in the conventional group. However, except for antibody levels in commercial chickens in the Iran new-generation vaccine, this difference was minor. Further, both groups showed 100% protection in the challenge study. Despite the phylogenetic gap between the NDV-F gene placed in the vector vaccine and the challenge virus (genotypes I and VII, respectively), the rHVT-NDV vaccine offered strong clinical protection and decreased challenge virus shedding considerably.","PeriodicalId":51212,"journal":{"name":"Virus Genes","volume":" ","pages":"126-133"},"PeriodicalIF":1.6,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139576298","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