Pub Date : 2025-02-04DOI: 10.1016/j.virusres.2025.199540
Yuji Wada, Ken Ishioka, Tatsuo Suzutani
Human cytomegalovirus (HCMV), a member of the Herpesviridae family, is prevalent worldwide. HCMV is generally asymptomatic but causes severe disease in immunocompromised patients or infants who are congenitally infected. Recent advances in sequencing technology have led to the rapid expansion of the HCMV genetic database, providing a comprehensive resource for studying viral genetics. Although genetic investigations have been vigorously performed in European countries, information on the whole-genome sequence of HCMV in the East Asian region remains limited. In this study, we determined whole-genome sequences of two clinical isolates of HCMV circulating in Japan. Partial genome sequences of 26 genes in UL/b' region were also identified using additional seven clinical isolates. Phylogenetic analysis of the UL148 gene revealed a characteristic genetic clade predominantly constructed from HCMV isolates from Japan and China, suggesting a geographic gene structure in the East Asian region. We consider that this research will contribute to expanding the genetic database of HCMV and unveiling novel genetic characteristics of HCMV in Asia.
{"title":"Determination of whole genome sequence of human cytomegalovirus circulating in Japan and discovery of geographic genome structure in UL148 gene","authors":"Yuji Wada, Ken Ishioka, Tatsuo Suzutani","doi":"10.1016/j.virusres.2025.199540","DOIUrl":"10.1016/j.virusres.2025.199540","url":null,"abstract":"<div><div>Human cytomegalovirus (HCMV), a member of the Herpesviridae family, is prevalent worldwide. HCMV is generally asymptomatic but causes severe disease in immunocompromised patients or infants who are congenitally infected. Recent advances in sequencing technology have led to the rapid expansion of the HCMV genetic database, providing a comprehensive resource for studying viral genetics. Although genetic investigations have been vigorously performed in European countries, information on the whole-genome sequence of HCMV in the East Asian region remains limited. In this study, we determined whole-genome sequences of two clinical isolates of HCMV circulating in Japan. Partial genome sequences of 26 genes in UL/b' region were also identified using additional seven clinical isolates. Phylogenetic analysis of the <em>UL148</em> gene revealed a characteristic genetic clade predominantly constructed from HCMV isolates from Japan and China, suggesting a geographic gene structure in the East Asian region. We consider that this research will contribute to expanding the genetic database of HCMV and unveiling novel genetic characteristics of HCMV in Asia.</div></div>","PeriodicalId":23483,"journal":{"name":"Virus research","volume":"353 ","pages":"Article 199540"},"PeriodicalIF":2.5,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143081179","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}
Pub Date : 2025-02-03DOI: 10.1016/j.virusres.2025.199538
Haiyang Yu, Yudong Zhu, Qiong Wu, Wanjun Zhao, You Wang, Dong Wang, Huaguang Lu, Youxiang Diao, Yijing Li, Yi Tang
In recent years, the infection rate of avian reovirus (ARV) in chicks has been continuously increasing, seriously endangering the healthy development of China's chicken farming industry. However, the pathogenicity of this virus in immune organs has been less studied. In this study, an ARV strain (Chicken/XJ/China/2022/01/16) was isolated from arthritic broiler chicks in Xinjiang province and whole genome sequencing of the ARV strain was performed using next generation sequencing (NGS) technology, and sequence analysis showed that the strain was a type V variant of the ARV gene. In order to further understand the pathogenicity of this strain in terms of immune organs, we randomized 120 healthy 1-day-old broilers equally into 3 groups (oral, footpad inoculation and control), where 2 experimental groups were inoculated with 0.2 mL of ARV (TCID50 of 105.5 /0.1 mL) and the control group was inoculated with an equal amount of sterile saline. The results showed that the footpad inoculation group showed more severe symptoms, which, in addition to causing chick dwarf syndrome and viral arthritis, would also cause serious effects on the immune organs of the chicks. Among them, the spleen and bursa were most seriously damaged, the symptoms of arthritis appeared relatively late, which indicated that the spleen and bursa might be the main target organs preferentially attacked by avian reovirus. This study provides a rationale for the prevention and control of emerging avian reovirus and adds to the evidence of the effects of ARV on immune organs, with the expectation that it will be useful in understanding the immune response-related aspects of the disease in subsequent studies.
{"title":"Pathogenicity of avian reovirus variant in the immune organs of broiler chicks.","authors":"Haiyang Yu, Yudong Zhu, Qiong Wu, Wanjun Zhao, You Wang, Dong Wang, Huaguang Lu, Youxiang Diao, Yijing Li, Yi Tang","doi":"10.1016/j.virusres.2025.199538","DOIUrl":"https://doi.org/10.1016/j.virusres.2025.199538","url":null,"abstract":"<p><p>In recent years, the infection rate of avian reovirus (ARV) in chicks has been continuously increasing, seriously endangering the healthy development of China's chicken farming industry. However, the pathogenicity of this virus in immune organs has been less studied. In this study, an ARV strain (Chicken/XJ/China/2022/01/16) was isolated from arthritic broiler chicks in Xinjiang province and whole genome sequencing of the ARV strain was performed using next generation sequencing (NGS) technology, and sequence analysis showed that the strain was a type V variant of the ARV gene. In order to further understand the pathogenicity of this strain in terms of immune organs, we randomized 120 healthy 1-day-old broilers equally into 3 groups (oral, footpad inoculation and control), where 2 experimental groups were inoculated with 0.2 mL of ARV (TCID<sub>50</sub> of 10<sup>5.5</sup> /0.1 mL) and the control group was inoculated with an equal amount of sterile saline. The results showed that the footpad inoculation group showed more severe symptoms, which, in addition to causing chick dwarf syndrome and viral arthritis, would also cause serious effects on the immune organs of the chicks. Among them, the spleen and bursa were most seriously damaged, the symptoms of arthritis appeared relatively late, which indicated that the spleen and bursa might be the main target organs preferentially attacked by avian reovirus. This study provides a rationale for the prevention and control of emerging avian reovirus and adds to the evidence of the effects of ARV on immune organs, with the expectation that it will be useful in understanding the immune response-related aspects of the disease in subsequent studies.</p>","PeriodicalId":23483,"journal":{"name":"Virus research","volume":" ","pages":"199538"},"PeriodicalIF":2.5,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143256770","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}
Pub Date : 2025-02-01DOI: 10.1016/j.virusres.2024.199520
Behzad Hussain , Peizhe Zhao , Yu Liu , Bo Yang , Xiaoxiong Li , Zhichao Zhang , Guoqiang Feng , Demei Zhang , Defen Lu , Wu Changxin
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a single-stranded RNA virus which has resulted in the Coronavirus Disease 2019 (COVID-19) pandemic and has infected millions of people all over the world. SARS-CoV-2 has been mutating rapidly resulting in the emergence of multiple variants to escape the host immune system mainly by mutations in its receptor binding domain (RBD) of the spike protein. The RBD and full-length spike of SARS-CoV-2 are the main targets of the neutralizing antibodies (mainly IgGs). Many SARS-CoV-2 variants are considered to have potential to escape from the host immune system. This rapid evolution of the virus posed a great challenge regarding the efficacy and effectiveness of the current SARS-CoV-2 vaccines. Hence, in this study, RBD of Alpha, Beta, Gamma, Kappa and Omicron BA.1 and full-length spike of BA.1, BA.2, BA.3, BA.4/5, BQ.1.1 and XBB.1.5 Omicron variants were used as coating antigens in an indirect Enzyme Linked Immuno-Sorbent Assay (ELISA) to check the IgG binding capability to the COVID-19 convalescent sera from patients of first wave of infection occurring in Wuhan. Our results show that the currently circulating Omicron BQ.1.1, XBB.1.5 and previous Omicron BA.1, BA.2 and BA.4/5 do not show significant reduction in binding, while Omicron BA.3 and previous variants Alpha, Beta, Gamma, Kappa, and Omicron showed a significantly reduced binding when compared to the wild-type Wuhan strain. These results indicate that the patients recovering from natural infection of early original Wuhan strain may have the potential to resist infection of current circulating variants and the vaccines using the prototype antigen may still work for newly emerged variants.
{"title":"Evaluation of IgG binding capability to SARS-CoV-2 variants in early COVID-19 convalescent sera using an indirect ELISA","authors":"Behzad Hussain , Peizhe Zhao , Yu Liu , Bo Yang , Xiaoxiong Li , Zhichao Zhang , Guoqiang Feng , Demei Zhang , Defen Lu , Wu Changxin","doi":"10.1016/j.virusres.2024.199520","DOIUrl":"10.1016/j.virusres.2024.199520","url":null,"abstract":"<div><div>Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a single-stranded RNA virus which has resulted in the Coronavirus Disease 2019 (COVID-19) pandemic and has infected millions of people all over the world. SARS-CoV-2 has been mutating rapidly resulting in the emergence of multiple variants to escape the host immune system mainly by mutations in its receptor binding domain (RBD) of the spike protein. The RBD and full-length spike of SARS-CoV-2 are the main targets of the neutralizing antibodies (mainly IgGs). Many SARS-CoV-2 variants are considered to have potential to escape from the host immune system. This rapid evolution of the virus posed a great challenge regarding the efficacy and effectiveness of the current SARS-CoV-2 vaccines. Hence, in this study, RBD of Alpha, Beta, Gamma, Kappa and Omicron BA.1 and full-length spike of BA.1, BA.2, BA.3, BA.4/5, BQ.1.1 and XBB.1.5 Omicron variants were used as coating antigens in an indirect Enzyme Linked Immuno-Sorbent Assay (ELISA) to check the IgG binding capability to the COVID-19 convalescent sera from patients of first wave of infection occurring in Wuhan. Our results show that the currently circulating Omicron BQ.1.1, XBB.1.5 and previous Omicron BA.1, BA.2 and BA.4/5 do not show significant reduction in binding, while Omicron BA.3 and previous variants Alpha, Beta, Gamma, Kappa, and Omicron showed a significantly reduced binding when compared to the wild-type Wuhan strain. These results indicate that the patients recovering from natural infection of early original Wuhan strain may have the potential to resist infection of current circulating variants and the vaccines using the prototype antigen may still work for newly emerged variants.</div></div>","PeriodicalId":23483,"journal":{"name":"Virus research","volume":"352 ","pages":"Article 199520"},"PeriodicalIF":2.5,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143161875","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}
Pub Date : 2025-02-01DOI: 10.1016/j.virusres.2024.199524
Peter Erdmann Dougherty , Maja Schmidt Pedersen , Laura Milena Forero-Junco , Alexander Byth Carstens , Jos M. Raaijmakers , Leise Riber , Lars Hestbjerg Hansen
The phyllosphere microbiome can positively or negatively impact plant health and growth, but we currently lack the tools to control microbiome composition. Contributing to a growing collection of bacteriophages (phages) targeting bacteria living in the wheat phyllosphere, we here isolate and sequence eight novel phages targeting common phyllosphere Erwinia and Pseudomonas strains, including two jumbo phages. We characterize genomic, phylogenetic, and morphological traits from these phages and argue for establishing four novel viral genera. We also search the genomes for anti-defense systems and investigate DNA modifications using Nanopore sequencing. In Pseudomonas phage Rembedalsseter we find evidence of 13 motif-associated single-stranded DNA breaks. A bioinformatics search revealed that 60 related Pseudomonas phages are enriched in the same motif, suggesting these single-stranded nicks may be widely distributed in this family of phages. Finally, we also search the Sequence Read Archive for similar phages in public metagenomes. We find close hits to the Erwinia jumbo-phage Kaldavass in a wide variety of plant, food, and wastewater metagenomes including a near-perfect hit from a Spanish spinach sample, illustrating how interconnected geographically distant phages can be.
{"title":"Novel bacteriophages targeting wheat phyllosphere bacteria carry DNA modifications and single-strand breaks","authors":"Peter Erdmann Dougherty , Maja Schmidt Pedersen , Laura Milena Forero-Junco , Alexander Byth Carstens , Jos M. Raaijmakers , Leise Riber , Lars Hestbjerg Hansen","doi":"10.1016/j.virusres.2024.199524","DOIUrl":"10.1016/j.virusres.2024.199524","url":null,"abstract":"<div><div>The phyllosphere microbiome can positively or negatively impact plant health and growth, but we currently lack the tools to control microbiome composition. Contributing to a growing collection of bacteriophages (phages) targeting bacteria living in the wheat phyllosphere, we here isolate and sequence eight novel phages targeting common phyllosphere <em>Erwinia</em> and <em>Pseudomonas</em> strains, including two jumbo phages. We characterize genomic, phylogenetic, and morphological traits from these phages and argue for establishing four novel viral genera. We also search the genomes for anti-defense systems and investigate DNA modifications using Nanopore sequencing. In Pseudomonas phage Rembedalsseter we find evidence of 13 motif-associated single-stranded DNA breaks. A bioinformatics search revealed that 60 related <em>Pseudomonas</em> phages are enriched in the same motif, suggesting these single-stranded nicks may be widely distributed in this family of phages. Finally, we also search the Sequence Read Archive for similar phages in public metagenomes. We find close hits to the <em>Erwinia</em> jumbo-phage Kaldavass in a wide variety of plant, food, and wastewater metagenomes including a near-perfect hit from a Spanish spinach sample, illustrating how interconnected geographically distant phages can be.</div></div>","PeriodicalId":23483,"journal":{"name":"Virus research","volume":"352 ","pages":"Article 199524"},"PeriodicalIF":2.5,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11780129/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142915651","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}
Pub Date : 2025-02-01DOI: 10.1016/j.virusres.2024.199518
Eva Mazzetto , Alessio Bortolami , Davide Bovo , Matteo Stocchero , Elisa Mazzacan , Alessandra Napolitan , Valentina Panzarin , Maria Rosa Tran , Gianpiero Zamperin , Adelaide Milani , Andrea Fortin , Michela Bigolaro , Paola Pirillo , Matteo Pagliari , Claudia Zanardello , Giuseppe Giordano , Maria Teresa Gervasi , Eugenio Baraldi , Calogero Terregino , Carlo Giaquinto , Francesco Bonfante
Among flaviviruses, Zika virus (ZIKV) is the only arbovirus officially recognized as a teratogenic agent, as a consequence of its ability to infect and cross the placental barrier causing congenital malformation in the fetus. While many studies have focused on understanding ZIKV pathogenesis during pregnancy, the viral mechanisms affecting fetal development remain largely unclear. In this study, we investigated ZIKV virulence in placental trophoblasts, using viruses with distinct lipid profiles. Firstly, we propagated a ZIKV strain belonging to the Asian lineage in either mammalian or mosquito cells, obtaining two viral stocks, which were purified and analyzed to determine their genetic and lipid composition. Successively, we assessed the infectivity of the two stocks in placental cells using both immortalized cell lines and explants. We found that the two viral stocks displayed identical consensus sequences with homogeneous quasispecies composition. However, the lipid composition of their envelope significantly varied depending on the cell of origin, with the mammalian-derived viral stock characterized by a higher content of phosphatidylcholines compared to the virions originating from mosquito cells. Notably, ZIKV stock derived from mammalian cells showed a higher infectivity in immortalized villous trophoblasts and full-term placental explants of human origin. This increased infectivity was linked to enhanced fusion efficiency during the viral uncoating phase in trophoblast cells, as demonstrated using a lipophilic probe. Collectively, our data suggest a potential role of viral lipids as determinants of ZIKV infectivity in full-term placenta, underscoring the importance of lipidomic research in virology.
{"title":"Infectivity in full-term placenta of Zika viruses with different lipid profiles","authors":"Eva Mazzetto , Alessio Bortolami , Davide Bovo , Matteo Stocchero , Elisa Mazzacan , Alessandra Napolitan , Valentina Panzarin , Maria Rosa Tran , Gianpiero Zamperin , Adelaide Milani , Andrea Fortin , Michela Bigolaro , Paola Pirillo , Matteo Pagliari , Claudia Zanardello , Giuseppe Giordano , Maria Teresa Gervasi , Eugenio Baraldi , Calogero Terregino , Carlo Giaquinto , Francesco Bonfante","doi":"10.1016/j.virusres.2024.199518","DOIUrl":"10.1016/j.virusres.2024.199518","url":null,"abstract":"<div><div>Among flaviviruses, Zika virus (ZIKV) is the only arbovirus officially recognized as a teratogenic agent, as a consequence of its ability to infect and cross the placental barrier causing congenital malformation in the fetus. While many studies have focused on understanding ZIKV pathogenesis during pregnancy, the viral mechanisms affecting fetal development remain largely unclear. In this study, we investigated ZIKV virulence in placental trophoblasts, using viruses with distinct lipid profiles. Firstly, we propagated a ZIKV strain belonging to the Asian lineage in either mammalian or mosquito cells, obtaining two viral stocks, which were purified and analyzed to determine their genetic and lipid composition. Successively, we assessed the infectivity of the two stocks in placental cells using both immortalized cell lines and explants. We found that the two viral stocks displayed identical consensus sequences with homogeneous quasispecies composition. However, the lipid composition of their envelope significantly varied depending on the cell of origin, with the mammalian-derived viral stock characterized by a higher content of phosphatidylcholines compared to the virions originating from mosquito cells. Notably, ZIKV stock derived from mammalian cells showed a higher infectivity in immortalized villous trophoblasts and full-term placental explants of human origin. This increased infectivity was linked to enhanced fusion efficiency during the viral uncoating phase in trophoblast cells, as demonstrated using a lipophilic probe. Collectively, our data suggest a potential role of viral lipids as determinants of ZIKV infectivity in full-term placenta, underscoring the importance of lipidomic research in virology.</div></div>","PeriodicalId":23483,"journal":{"name":"Virus research","volume":"352 ","pages":"Article 199518"},"PeriodicalIF":2.5,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11761821/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142903617","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}
Pub Date : 2025-02-01DOI: 10.1016/j.virusres.2025.199536
Jia Li , Deming Ren , Xiangxu Meng , Yiyun He , Lixian Wang , Xihui Sheng , Ligang Wang
The genetic foundations underlying the observed disease resistance in certain indigenous pig breeds, notably the Min pigs of China, present a compelling underexplored subject of study. Exploring the mechanisms of disease resistance in these breeds could lay the groundwork for genetic improvements in pig immunity, potentially augmenting overall pig productivity. In this study, whole blood samples were collected from pre- and post- swine fever vaccinated Min and Large White pigs for transcriptome sequencing. The mRNA and lncRNA in both pig breeds were analyzed, and intra-group and inter-group comparisons were also conducted. The results indicated that a greater number of immune-related pathways such as the JAK-STAT and PI3K-AKT signaling were enriched in Min pigs. Furthermore, genes involved in inflammation and antiviral responses, including IL16, IL27, USP18, and DHX58, were upregulated in post-vaccination Min pigs compared to post-vaccination Large White pigs. This heightened immune responsiveness could contribute to the observed differences in disease resistance between Min pigs and Large White pigs.
{"title":"Transcriptomics-based investigation of resistance differences to swine fever between large white pigs and min pigs","authors":"Jia Li , Deming Ren , Xiangxu Meng , Yiyun He , Lixian Wang , Xihui Sheng , Ligang Wang","doi":"10.1016/j.virusres.2025.199536","DOIUrl":"10.1016/j.virusres.2025.199536","url":null,"abstract":"<div><div>The genetic foundations underlying the observed disease resistance in certain indigenous pig breeds, notably the Min pigs of China, present a compelling underexplored subject of study. Exploring the mechanisms of disease resistance in these breeds could lay the groundwork for genetic improvements in pig immunity, potentially augmenting overall pig productivity. In this study, whole blood samples were collected from pre- and post- swine fever vaccinated Min and Large White pigs for transcriptome sequencing. The mRNA and lncRNA in both pig breeds were analyzed, and intra-group and inter-group comparisons were also conducted. The results indicated that a greater number of immune-related pathways such as the JAK-STAT and PI3K-AKT signaling were enriched in Min pigs. Furthermore, genes involved in inflammation and antiviral responses, including IL16, IL27, USP18, and DHX58, were upregulated in post-vaccination Min pigs compared to post-vaccination Large White pigs. This heightened immune responsiveness could contribute to the observed differences in disease resistance between Min pigs and Large White pigs.</div></div>","PeriodicalId":23483,"journal":{"name":"Virus research","volume":"353 ","pages":"Article 199536"},"PeriodicalIF":2.5,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143060869","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}
Interest in bacteriophages (phages) as sustainable biocontrol agents in the agri-food industry has increased because of growing worries about food safety and antimicrobial resistance (AMR). The phage manufacturing process is examined in this review, with particular attention paid to the crucial upstream and downstream processes needed for large-scale production. Achieving large phage yields requires upstream procedures, including fermentation and phage amplification. In the meantime, downstream procedures, including purification, endotoxin removal, and formulation, is essential for guaranteeing product quality and regulatory compliance. Despite advances in upstream and downstream process optimization of phage production processes, these methods are not effectively utilized in manufacturing processes. Additionally, the commercialization of phage products is hindered by fragmented rules and inconsistent regulations. Emerging technologies such as enhanced chromatography, continuous processing, and encapsulating techniques provide prospects for increased stability, efficiency, and scalability to fill these gaps. Furthermore, by facilitating real-time process optimization, predictive quality control (QC), and unique phage product creation, the integration of artificial intelligence (AI) and machine learning has the potential to transform the phage manufacturing industry completely. In order to provide consistent standards, encourage innovation, and bridge the gap between academic research and commercial applications, this review identifies gaps and highlights the necessity of cooperation between academia, industry, and regulatory agencies. To effectively utilize phages' potential to improve food safety, fight AMR, and promote sustainable agricultural practices, the agri-food industry must advance phage manufacturing techniques and harmonize regulatory frameworks.
{"title":"Bridging the gap: Phage manufacturing processes from laboratory to agri-food industry","authors":"Elham Mohammadi , Mohammadreza Rahimian , Bahman Panahi","doi":"10.1016/j.virusres.2025.199537","DOIUrl":"10.1016/j.virusres.2025.199537","url":null,"abstract":"<div><div>Interest in bacteriophages (phages) as sustainable biocontrol agents in the agri-food industry has increased because of growing worries about food safety and antimicrobial resistance (AMR). The phage manufacturing process is examined in this review, with particular attention paid to the crucial upstream and downstream processes needed for large-scale production. Achieving large phage yields requires upstream procedures, including fermentation and phage amplification. In the meantime, downstream procedures, including purification, endotoxin removal, and formulation, is essential for guaranteeing product quality and regulatory compliance. Despite advances in upstream and downstream process optimization of phage production processes, these methods are not effectively utilized in manufacturing processes. Additionally, the commercialization of phage products is hindered by fragmented rules and inconsistent regulations. Emerging technologies such as enhanced chromatography, continuous processing, and encapsulating techniques provide prospects for increased stability, efficiency, and scalability to fill these gaps. Furthermore, by facilitating real-time process optimization, predictive quality control (QC), and unique phage product creation, the integration of artificial intelligence (AI) and machine learning has the potential to transform the phage manufacturing industry completely. In order to provide consistent standards, encourage innovation, and bridge the gap between academic research and commercial applications, this review identifies gaps and highlights the necessity of cooperation between academia, industry, and regulatory agencies. To effectively utilize phages' potential to improve food safety, fight AMR, and promote sustainable agricultural practices, the agri-food industry must advance phage manufacturing techniques and harmonize regulatory frameworks.</div></div>","PeriodicalId":23483,"journal":{"name":"Virus research","volume":"353 ","pages":"Article 199537"},"PeriodicalIF":2.5,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143068312","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}
Pub Date : 2025-01-31DOI: 10.1016/j.virusres.2025.199541
Ra Mi Cha, Min-Ji Park, Yoon-Gi Baek, Yu-Na Lee, Yunyoung Jang, Yong-Myung Kang, Gyeong-Beom Heo, Se-Hee An, Kwang-Nyeong Lee, Jae-Kyeom Kim, Hye-Ryoung Kim, Youn-Jeong Lee, Eun-Kyoung Lee
During the 2022-2023 winter season in South Korea, a novel clade 2.3.4.4b H5N1 HPAIV was first detected in wild birds, which then subsequently caused multiple outbreaks in poultry farms and wild birds. This study aimed to investigate the genetic characteristics of H5N1 HPAIVs isolated during the 2022-2023, along with their pathogenicity and transmissibility in chickens and ducks. The clade 2.3.4.4b H5N1 HPAIV viruses caused outbreaks in 75 poultry farms and detected in 174 wild bird cases. Phylogenetic analysis of hemagglutinin genes revealed that the South Korean H5N1 HPAIV isolates were closely related to Eurasian and American HPAIVs isolated between 2022 and 2023. In total, 21 diverse genotypes (22G0-22G20) were identified in virus isolates from poultry and wild birds, among which 22G7 was the dominant genotype. The 22G1 genotype (A/duck/Korea/H493/2022(H5N1)) caused high virulence and pathogenicity, with a 100% mortality rate in specific-pathogen-free chickens. Ducks inoculated with genotypes 22G1 or 22G7 (A/duck/Korea/H537/2022(H5N1)) showed neurological signs, with 60%-80% mortality rate. In the contact groups of ducks, 100% of transmissibility was observed. Notably, in the 22G7-inoculated group, viral shedding via the cloacal route was longer, and viral replication in the cecal tonsil was higher than that in the 22G1-inoculated group, which may have contributed to the dominancy of the 22G7 genotype. Therefore, better understanding of the genetic and pathogenic features of HPAI viruses is important for effective virus control in the field.
{"title":"Genetic characteristics and pathogenesis of clade 2.3.4.4b H5N1 high pathogenicity avian influenza virus isolated from poultry in South Korea, 2022-2023.","authors":"Ra Mi Cha, Min-Ji Park, Yoon-Gi Baek, Yu-Na Lee, Yunyoung Jang, Yong-Myung Kang, Gyeong-Beom Heo, Se-Hee An, Kwang-Nyeong Lee, Jae-Kyeom Kim, Hye-Ryoung Kim, Youn-Jeong Lee, Eun-Kyoung Lee","doi":"10.1016/j.virusres.2025.199541","DOIUrl":"https://doi.org/10.1016/j.virusres.2025.199541","url":null,"abstract":"<p><p>During the 2022-2023 winter season in South Korea, a novel clade 2.3.4.4b H5N1 HPAIV was first detected in wild birds, which then subsequently caused multiple outbreaks in poultry farms and wild birds. This study aimed to investigate the genetic characteristics of H5N1 HPAIVs isolated during the 2022-2023, along with their pathogenicity and transmissibility in chickens and ducks. The clade 2.3.4.4b H5N1 HPAIV viruses caused outbreaks in 75 poultry farms and detected in 174 wild bird cases. Phylogenetic analysis of hemagglutinin genes revealed that the South Korean H5N1 HPAIV isolates were closely related to Eurasian and American HPAIVs isolated between 2022 and 2023. In total, 21 diverse genotypes (22G0-22G20) were identified in virus isolates from poultry and wild birds, among which 22G7 was the dominant genotype. The 22G1 genotype (A/duck/Korea/H493/2022(H5N1)) caused high virulence and pathogenicity, with a 100% mortality rate in specific-pathogen-free chickens. Ducks inoculated with genotypes 22G1 or 22G7 (A/duck/Korea/H537/2022(H5N1)) showed neurological signs, with 60%-80% mortality rate. In the contact groups of ducks, 100% of transmissibility was observed. Notably, in the 22G7-inoculated group, viral shedding via the cloacal route was longer, and viral replication in the cecal tonsil was higher than that in the 22G1-inoculated group, which may have contributed to the dominancy of the 22G7 genotype. Therefore, better understanding of the genetic and pathogenic features of HPAI viruses is important for effective virus control in the field.</p>","PeriodicalId":23483,"journal":{"name":"Virus research","volume":" ","pages":"199541"},"PeriodicalIF":2.5,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143081181","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}
Pub Date : 2025-01-31DOI: 10.1016/j.virusres.2025.199530
Hamza GHAMMAZ , Marouane MELLOUL , Ahlam MBARKI , Mouhssine HEMLALI , Taha CHOUATI , Hicham EL ANNAZ , Nadia TOUIL , Mostafa ELOUENNASS , Khalid ENNIBI , Elmostafa EL FAHIME
This study investigates the evolution and genetic diversity of SARS-CoV-2 strains circulating in Morocco to track the spread, clade distributions and mutations of the virus across various regions from February 2020 to June 2024. The genome sequences were retrieved from the GISAID database. A total of 2630 SARS-CoV-2 genome sequences were analyzed using bioinformatic tools such as Nextclade, followed by phylogenetic and statistical analyses. The study highlights the predominance of the GRA clade (Omicron variant) since November 2021, while clades such as G, GH, GR, and GRY were identified earlier. The GRA clade exhibited the highest number of non-synonymous mutations, particularly in the Spike (S) gene, suggesting strong evolutionary pressure. The correlation analysis between structural and non-structural proteins revealed key interactions between S and NSP5, providing insights into the viral replication and assembly processes. This work gives new insights to the dynamics of SARS-CoV-2 in Morocco and underscores the importance of ongoing genomic surveillance to respond to emerging variants and potential future outbreaks.
{"title":"Genomic evolution of SARS-CoV-2 in Morocco: Insights from whole genome sequences collected from 2020 to 2024","authors":"Hamza GHAMMAZ , Marouane MELLOUL , Ahlam MBARKI , Mouhssine HEMLALI , Taha CHOUATI , Hicham EL ANNAZ , Nadia TOUIL , Mostafa ELOUENNASS , Khalid ENNIBI , Elmostafa EL FAHIME","doi":"10.1016/j.virusres.2025.199530","DOIUrl":"10.1016/j.virusres.2025.199530","url":null,"abstract":"<div><div>This study investigates the evolution and genetic diversity of SARS-CoV-2 strains circulating in Morocco to track the spread, clade distributions and mutations of the virus across various regions from February 2020 to June 2024. The genome sequences were retrieved from the GISAID database. A total of 2630 SARS-CoV-2 genome sequences were analyzed using bioinformatic tools such as Nextclade, followed by phylogenetic and statistical analyses. The study highlights the predominance of the GRA clade (Omicron variant) since November 2021, while clades such as G, GH, GR, and GRY were identified earlier. The GRA clade exhibited the highest number of non-synonymous mutations, particularly in the Spike (S) gene, suggesting strong evolutionary pressure. The correlation analysis between structural and non-structural proteins revealed key interactions between S and NSP5, providing insights into the viral replication and assembly processes. This work gives new insights to the dynamics of SARS-CoV-2 in Morocco and underscores the importance of ongoing genomic surveillance to respond to emerging variants and potential future outbreaks.</div></div>","PeriodicalId":23483,"journal":{"name":"Virus research","volume":"353 ","pages":"Article 199530"},"PeriodicalIF":2.5,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143048109","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}
Pub Date : 2025-01-31DOI: 10.1016/j.virusres.2025.199531
Chongwei Xie , Bing Zhou , Da Yao , Xin Wang , Lihong Zhong , Chuanghua Qiu , Junfang Zhang
Hepatitis B virus (HBV) represents one of the major pathogenic factor that leads to chronic liver diseases and the development of hepatocellular carcinoma (HCC). The currently approved anti-HBV drugs cannot eradicate the virus or block the development of HCC. HBV nucleocapsid consists of the hepatitis B core antigen (HBcAg) and the HBV relaxed-circular partially double-stranded DNA (rcDNA), indispensable in virus replication. The present study reported a cell-penetrating bispecific antibody targeting HBcAg and preS1, fused with the cell-penetrating peptide R9TAT, named Anti-preS1 × Anti-HBcAg-R9TAT. The antibody could recognize preS1 and HBcAg and internalize into living cells efficiently, suppressing the extracellular hepatitis B surface antigen (HBsAg) and hepatitis B envelope antigen, and the intracellular HBsAg and HBcAg in vitro. This cell-penetrating bispecific antibody is a novel approach to suppressing HBV replication and secretion and is a promising anti-HBV therapeutic antibody candidate.
{"title":"A cell-penetrating bispecific antibody suppresses hepatitis B virus replication and secretion","authors":"Chongwei Xie , Bing Zhou , Da Yao , Xin Wang , Lihong Zhong , Chuanghua Qiu , Junfang Zhang","doi":"10.1016/j.virusres.2025.199531","DOIUrl":"10.1016/j.virusres.2025.199531","url":null,"abstract":"<div><div>Hepatitis B virus (HBV) represents one of the major pathogenic factor that leads to chronic liver diseases and the development of hepatocellular carcinoma (HCC). The currently approved anti-HBV drugs cannot eradicate the virus or block the development of HCC. HBV nucleocapsid consists of the hepatitis B core antigen (HBcAg) and the HBV relaxed-circular partially double-stranded DNA (rcDNA), indispensable in virus replication. The present study reported a cell-penetrating bispecific antibody targeting HBcAg and preS1, fused with the cell-penetrating peptide R9TAT, named Anti-preS1 × Anti-HBcAg-R9TAT. The antibody could recognize preS1 and HBcAg and internalize into living cells efficiently, suppressing the extracellular hepatitis B surface antigen (HBsAg) and hepatitis B envelope antigen, and the intracellular HBsAg and HBcAg <em>in vitro</em>. This cell-penetrating bispecific antibody is a novel approach to suppressing HBV replication and secretion and is a promising anti-HBV therapeutic antibody candidate.</div></div>","PeriodicalId":23483,"journal":{"name":"Virus research","volume":"353 ","pages":"Article 199531"},"PeriodicalIF":2.5,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143041678","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}
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