The emergence of the Omicron variant in November 2021 marked a significant turning point in the COVID-19 pandemic due to its unprecedented number of mutations compared to previous variants. To better understand its clinical impact and evolutionary trajectory, we conducted a comprehensive genomic epidemiology study analyzing 528 SARS-CoV-2 samples collected in Iran between March 2021 and March 2023. Using nanopore sequencing with ≥96 % genome coverage and advanced bioinformatics tools including the Nextclade platform, we systematically characterized the mutational profiles of circulating variants with particular focus on the receptor-binding domain (RBD) and ORF9b proteins. Our analysis revealed BA.5.2 as the dominant strain (32.4 % prevalence), followed by XBB.1.9.1 (14.2 %), with only 17.6 % of cases occurring in vaccinated individuals. Through molecular docking and dynamics simulations, we demonstrated that key variants including BA.5.2, XBB.1.5, and XBB.1.9 exhibit enhanced binding affinity to host receptors, with RBD showing stronger interactions with ACE2 and ORF9b variants displaying improved binding to TOM70. Notably, our findings suggest similar pathogenic potential between the XBB.1.5/XBB.1.9 and BA.5 lineages, while highlighting the utility of whole genome entropy analysis for predicting viral evolution patterns. These results provide valuable insights for guiding vaccine development, therapeutic design, and public health strategies against evolving SARS-CoV-2 variants.
{"title":"Next-generation sequencing of Omicron SARS-CoV-2 variants in Hormozgan Province, Iran, and evaluation of the effects of mutations on RBD and ORF9b protein function","authors":"Khadijeh Ahmadi , Soudabeh Kavousipour , Behzad Shahbazi , Farhad Farzin , Zahra Gharibi , Maryam Sadat Pishva , Ali Pishahang , Hamed Gouklani","doi":"10.1016/j.meegid.2025.105812","DOIUrl":"10.1016/j.meegid.2025.105812","url":null,"abstract":"<div><div>The emergence of the Omicron variant in November 2021 marked a significant turning point in the COVID-19 pandemic due to its unprecedented number of mutations compared to previous variants. To better understand its clinical impact and evolutionary trajectory, we conducted a comprehensive genomic epidemiology study analyzing 528 <em>SARS-CoV-2</em> samples collected in Iran between March 2021 and March 2023. Using nanopore sequencing with ≥96 % genome coverage and advanced bioinformatics tools including the Nextclade platform, we systematically characterized the mutational profiles of circulating variants with particular focus on the receptor-binding domain (RBD) and ORF9b proteins. Our analysis revealed BA.5.2 as the dominant strain (32.4 % prevalence), followed by XBB.1.9.1 (14.2 %), with only 17.6 % of cases occurring in vaccinated individuals. Through molecular docking and dynamics simulations, we demonstrated that key variants including BA.5.2, XBB.1.5, and XBB.1.9 exhibit enhanced binding affinity to host receptors, with RBD showing stronger interactions with ACE2 and ORF9b variants displaying improved binding to TOM70. Notably, our findings suggest similar pathogenic potential between the XBB.1.5/XBB.1.9 and BA.5 lineages, while highlighting the utility of whole genome entropy analysis for predicting viral evolution patterns. These results provide valuable insights for guiding vaccine development, therapeutic design, and public health strategies against evolving <em>SARS-CoV-2</em> variants.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"134 ","pages":"Article 105812"},"PeriodicalIF":2.6,"publicationDate":"2025-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144852812","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 : 2025-08-09DOI: 10.1016/j.meegid.2025.105811
Chongli Xu , Yuhan She , Hongli Li , Ling Hou , Wenqiao Ding
Alpha toxin is one of the primary pathogenic factors of Clostridium perfringens and is a metalloenzyme with phospholipase C activity. Currently, the pathogenic mechanism of α toxin is not fully understood. The pathogenicity and significance of α toxin in all toxin-type Clostridium perfringens has not been fully studied. The results of circular dichroism spectroscopy of the α toxin protein at different temperatures in this study showed that the molecular structure of the α toxin protein changed at various temperatures, leading to changes in its biological activity. These findings indicate that the molecular structure of α toxin is essential for maintaining its biological activity. Additionally, recombinant proteins of α toxin, β1 toxin, β2 toxin and ε toxin were individually cloned and expressed. Simultaneously, recombinant protein immunization experiments and animal challenge experiments were conducted. The significant role of alpha toxin in the pathogenicity of various types of Clostridium perfringens has been established, providing mechanistic insight into α toxin function and the development of genetic engineering subunit vaccines in the future.
{"title":"Study on the pathogenicity of Clostridium perfringens alpha toxin","authors":"Chongli Xu , Yuhan She , Hongli Li , Ling Hou , Wenqiao Ding","doi":"10.1016/j.meegid.2025.105811","DOIUrl":"10.1016/j.meegid.2025.105811","url":null,"abstract":"<div><div>Alpha toxin is one of the primary pathogenic factors of <em>Clostridium perfringens</em> and is a metalloenzyme with phospholipase C activity. Currently, the pathogenic mechanism of α toxin is not fully understood. The pathogenicity and significance of α toxin in all toxin-type <em>Clostridium perfringens</em> has not been fully studied. The results of circular dichroism spectroscopy of the α toxin protein at different temperatures in this study showed that the molecular structure of the α toxin protein changed at various temperatures, leading to changes in its biological activity. These findings indicate that the molecular structure of α toxin is essential for maintaining its biological activity. Additionally, recombinant proteins of α toxin, β<sub>1</sub> toxin, β<sub>2</sub> toxin and ε toxin were individually cloned and expressed. Simultaneously, recombinant protein immunization experiments and animal challenge experiments were conducted. The significant role of alpha toxin in the pathogenicity of various types of <em>Clostridium perfringens</em> has been established, providing mechanistic insight into α toxin function and the development of genetic engineering subunit vaccines in the future.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"134 ","pages":"Article 105811"},"PeriodicalIF":2.6,"publicationDate":"2025-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144823266","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 : 2025-08-09DOI: 10.1016/j.meegid.2025.105810
Xiao-Qing Fan , Shi-Ming Fan , Bi-Ying Dong , Chun-Mei Zhang , Jing Zuo , Dong-Wei Zhang , Xia Xiong , Dan Luo , Xian-Ming Fan
Acute respiratory distress syndrome (ARDS) is a sudden, widespread inflammatory damage to the lungs resulting from multiple etiologies. ARDS is characterized by high sickness rates, mortality, and costly treatments and is a significant global health issue that lacks an effective treatment strategy. The microbiota of the gut is an intricate ecology indispensable for the host's health, immunology, and metabolism. Human immunity and intestinal barrier function depend on gut microbes. Several disorders are linked to gut microbiota dysbiosis. Scientists have been concentrating on the role that gut microbes play in the onset of ARDS. This study examines the relationship between ARDS and intestinal microbiota, specifically addressing two facets: how ARDS affects the composition of the gut microbiota and the integrity of the intestinal barrier, alongside the effects of mechanisms such as bacterial translocation and inflammatory activation resulting from gut microbiota dysregulation on ARDS. Additionally, various therapeutic strategies involving gut microbiota and its metabolites, such as selective digestive decontamination (SDD), fecal microbiota transplantation (FMT), microbiological preparations, and metabolites produced from the microbiota, are explored. It is anticipated that this exploration will make a substantial contribution to the prevention and therapy of ARDS.
{"title":"Recent advances in the interaction between acute respiratory distress syndrome and gut microbiota: A narrative review","authors":"Xiao-Qing Fan , Shi-Ming Fan , Bi-Ying Dong , Chun-Mei Zhang , Jing Zuo , Dong-Wei Zhang , Xia Xiong , Dan Luo , Xian-Ming Fan","doi":"10.1016/j.meegid.2025.105810","DOIUrl":"10.1016/j.meegid.2025.105810","url":null,"abstract":"<div><div>Acute respiratory distress syndrome (ARDS) is a sudden, widespread inflammatory damage to the lungs resulting from multiple etiologies. ARDS is characterized by high sickness rates, mortality, and costly treatments and is a significant global health issue that lacks an effective treatment strategy. The microbiota of the gut is an intricate ecology indispensable for the host's health, immunology, and metabolism. Human immunity and intestinal barrier function depend on gut microbes. Several disorders are linked to gut microbiota dysbiosis. Scientists have been concentrating on the role that gut microbes play in the onset of ARDS. This study examines the relationship between ARDS and intestinal microbiota, specifically addressing two facets: how ARDS affects the composition of the gut microbiota and the integrity of the intestinal barrier, alongside the effects of mechanisms such as bacterial translocation and inflammatory activation resulting from gut microbiota dysregulation on ARDS. Additionally, various therapeutic strategies involving gut microbiota and its metabolites, such as selective digestive decontamination (SDD), fecal microbiota transplantation (FMT), microbiological preparations, and metabolites produced from the microbiota, are explored. It is anticipated that this exploration will make a substantial contribution to the prevention and therapy of ARDS.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"134 ","pages":"Article 105810"},"PeriodicalIF":2.6,"publicationDate":"2025-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144823265","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 : 2025-07-29DOI: 10.1016/j.meegid.2025.105806
Markus Bauswein , Lisa Arnold , David N. Springer , Monika Redlberger-Fritz
Background
Borna disease virus 1 (BoDV-1) is a zoonotic virus with a recently confirmed potential to cause rare but severe cases of encephalitis in humans. While the bicolored white-toothed shrew (Crocidura leucodon), which represents the reservoir, is widely distributed over eastern, central, and southern Europe as well as south-west Asia, human infections have so far only been reported from Germany. As infections in sentinels such as horses indicate the endemic circulation of the virus also in circumscribed regions of neighboring countries (Austria, Liechtenstein, Switzerland), we initiated a retrospective case-finding study to investigate whether there were so far undetected human infections in Austria.
Methods
For this purpose, biobank samples from the Center for Virology in Vienna were selected based on available clinical characteristics consistent with possible neurological symptoms of human BoDV-1 infections to be screened for BoDV-1 RNA (859 cerebrospinal fluid samples) and anti-BoDV-1 IgG antibodies (366 corresponding serum samples).
Results
BoDV-1 RNA or confirmed anti-BoDV-1 IgG antibodies were not detected in any of the cerebrospinal fluid or serum samples, respectively.
Conclusion
Our result demonstrates that if human BoDV-1 infections occur in Austria, they must be very rare even in patients with neurological symptoms. Further research using samples with a more distinct geographical link to the circumscribed endemic rural region in Upper Austria, however, will be necessary to complement the preliminary finding of this study.
{"title":"Screening for Borna disease virus 1 (BoDV-1) in Austria: Absence of human cases in a retrospective case-finding study","authors":"Markus Bauswein , Lisa Arnold , David N. Springer , Monika Redlberger-Fritz","doi":"10.1016/j.meegid.2025.105806","DOIUrl":"10.1016/j.meegid.2025.105806","url":null,"abstract":"<div><h3>Background</h3><div>Borna disease virus 1 (BoDV-1) is a zoonotic virus with a recently confirmed potential to cause rare but severe cases of encephalitis in humans. While the bicolored white-toothed shrew (<em>Crocidura leucodon</em>), which represents the reservoir, is widely distributed over eastern, central, and southern Europe as well as south-west Asia, human infections have so far only been reported from Germany. As infections in sentinels such as horses indicate the endemic circulation of the virus also in circumscribed regions of neighboring countries (Austria, Liechtenstein, Switzerland), we initiated a retrospective case-finding study to investigate whether there were so far undetected human infections in Austria.</div></div><div><h3>Methods</h3><div>For this purpose, biobank samples from the Center for Virology in Vienna were selected based on available clinical characteristics consistent with possible neurological symptoms of human BoDV-1 infections to be screened for BoDV-1 RNA (859 cerebrospinal fluid samples) and anti-BoDV-1 IgG antibodies (366 corresponding serum samples).</div></div><div><h3>Results</h3><div>BoDV-1 RNA or confirmed anti-BoDV-1 IgG antibodies were not detected in any of the cerebrospinal fluid or serum samples, respectively.</div></div><div><h3>Conclusion</h3><div>Our result demonstrates that if human BoDV-1 infections occur in Austria, they must be very rare even in patients with neurological symptoms. Further research using samples with a more distinct geographical link to the circumscribed endemic rural region in Upper Austria, however, will be necessary to complement the preliminary finding of this study.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"134 ","pages":"Article 105806"},"PeriodicalIF":2.6,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144762354","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 : 2025-07-29DOI: 10.1016/j.meegid.2025.105807
Raphael Cavalcante de Medeiros , Késia Thaís Barros dos Santos , Larissa Brasil Skaf , Adriane Meira Mercadante , Matheus Henrique Banchete Rosa , Luiz Eduardo Teixeira de Araújo Pacheco , Sergio Eduardo Longo Fracalanzza , Adriana Lúcia Pires Ferreira , Jennifer L. Reimche , Kim M. Gernert , Ellen N. Kersh , Raquel Regina Bonelli
Neisseria gonorrhoeae poses a significant global public health challenge due to its ability to rapidly evolve antimicrobial resistance. In this study, we analyzed 141 isolates of N. gonorrhoeae obtained between 2015 and 2022 from clinical laboratories in the metropolitan region of Rio de Janeiro. Antimicrobial susceptibility, resistance mechanisms, and clonal diversity were investigated. Whole-genome sequencing and multilocus sequence typing (MLST) revealed the circulation of internationally relevant sequence types (STs) such as ST-1901, ST-7363, and ST-9363. While non-susceptibility rates to penicillin (98 %) and ciprofloxacin (73 %) remained stable compared to earlier data, tetracycline resistance decreased from 67 % (in 2015–2016) to 20 % (in 2019–2020), likely due to the reduced prevalence of ST-1588. However, mainly after 2020, tetM plasmids were detected in ST-7822 and the emerging ST-7363, suggesting the concern of a rising occurrence of these determinants in the near future. Azithromycin non-susceptibility varied between 15 and 33 % in the different time frames, associated with mutations in the mtrR promoter and rrl gene, affecting isolates across eleven STs. While no ceftriaxone non-susceptibility was identified, ST-1901 and ST-7363 isolates harbored unique mosaic penA 34 alleles, and ST-1580/ST-17526 carried semi-mosaic 93 alleles. These findings underscore the persistence of resistance to older antimicrobials, the spread of plasmid-mediated resistance in key clones, and the growing threat of azithromycin resistance, which could compromise the treatment of gonorrhea in patients allergic to beta-lactams.
{"title":"Tracking changes in antimicrobial resistance and clone replacement of Neisseria gonorrhoeae in Rio de Janeiro from 2015 to 2022","authors":"Raphael Cavalcante de Medeiros , Késia Thaís Barros dos Santos , Larissa Brasil Skaf , Adriane Meira Mercadante , Matheus Henrique Banchete Rosa , Luiz Eduardo Teixeira de Araújo Pacheco , Sergio Eduardo Longo Fracalanzza , Adriana Lúcia Pires Ferreira , Jennifer L. Reimche , Kim M. Gernert , Ellen N. Kersh , Raquel Regina Bonelli","doi":"10.1016/j.meegid.2025.105807","DOIUrl":"10.1016/j.meegid.2025.105807","url":null,"abstract":"<div><div><em>Neisseria gonorrhoeae</em> poses a significant global public health challenge due to its ability to rapidly evolve antimicrobial resistance. In this study, we analyzed 141 isolates of <em>N. gonorrhoeae</em> obtained between 2015 and 2022 from clinical laboratories in the metropolitan region of Rio de Janeiro. Antimicrobial susceptibility, resistance mechanisms, and clonal diversity were investigated. Whole-genome sequencing and multilocus sequence typing (MLST) revealed the circulation of internationally relevant sequence types (STs) such as ST-1901, ST-7363, and ST-9363. While non-susceptibility rates to penicillin (98 %) and ciprofloxacin (73 %) remained stable compared to earlier data, tetracycline resistance decreased from 67 % (in 2015–2016) to 20 % (in 2019–2020), likely due to the reduced prevalence of ST-1588. However, mainly after 2020, <em>tetM</em> plasmids were detected in ST-7822 and the emerging ST-7363, suggesting the concern of a rising occurrence of these determinants in the near future. Azithromycin non-susceptibility varied between 15 and 33 % in the different time frames, associated with mutations in the <em>mtrR</em> promoter and <em>rrl</em> gene, affecting isolates across eleven STs. While no ceftriaxone non-susceptibility was identified, ST-1901 and ST-7363 isolates harbored unique mosaic <em>penA</em> 34 alleles, and ST-1580/ST-17526 carried semi-mosaic 93 alleles. These findings underscore the persistence of resistance to older antimicrobials, the spread of plasmid-mediated resistance in key clones, and the growing threat of azithromycin resistance, which could compromise the treatment of gonorrhea in patients allergic to beta-lactams.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"134 ","pages":"Article 105807"},"PeriodicalIF":2.6,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144762355","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 : 2025-07-28DOI: 10.1016/j.meegid.2025.105805
Liangning Liao , Yuehong Chen , Yuyang Wang , Ruiwen Ren , Jing Li , Sen Zhang , Xiaoping Kang , Yuchang Li , Ye Feng , Tao Jiang
Human adenovirus (HAdV) is a common pathogen that causes various respiratory illnesses. Human adenovirus type 14 (HAdV-14) emerged in recent decades and has been reported sporadically and unevenly across the globe. In China, the first occurrence of HAdV-14 was reported in 2010, yet its genetic characteristics and transmission patterns remain unclear. This study performed a comprehensive phylogenetic analysis by integrating nine newly sequenced strains with all 67 available complete genome sequences of HAdV-14 strains from GenBank, which were submitted by eight countries where HAdV-14 is endemic. All examined strains were found to belong HAdV-14p1 clade, which was further classified into three major clusters. Notably, all strains identified in China belong to Cluster II and III. This study found that the initial isolates GZ01 and GZ02 from Guangzhou, China, in 2010 belonged to Cluster II, whereas the GZ25 isolate from the same location and year, identified through this study, belonged to Cluster III. Cluster III, which was sporadically epidemic, has formed a transmission circle in China. Despite multiple mutations in key genes between the two clusters, the homology of the Chinese isolates reached as high as 99.7 %. This study revealed that all HAdV-14 strains have highly conserved capsid proteins in China, which exhibit relative genome stability across time and geographic space. This study enhances our understanding of the genetic diversity and genomic characteristics of HAdV-14 and contributes to the prevention and control of HAdV-14 infection in the future.
{"title":"Genomic characteristics and phylogenetic analysis of human adenovirus 14 in China during 2010–2016","authors":"Liangning Liao , Yuehong Chen , Yuyang Wang , Ruiwen Ren , Jing Li , Sen Zhang , Xiaoping Kang , Yuchang Li , Ye Feng , Tao Jiang","doi":"10.1016/j.meegid.2025.105805","DOIUrl":"10.1016/j.meegid.2025.105805","url":null,"abstract":"<div><div>Human adenovirus (HAdV) is a common pathogen that causes various respiratory illnesses. Human adenovirus type 14 (HAdV-14) emerged in recent decades and has been reported sporadically and unevenly across the globe. In China, the first occurrence of HAdV-14 was reported in 2010, yet its genetic characteristics and transmission patterns remain unclear. This study performed a comprehensive phylogenetic analysis by integrating nine newly sequenced strains with all 67 available complete genome sequences of HAdV-14 strains from GenBank, which were submitted by eight countries where HAdV-14 is endemic. All examined strains were found to belong HAdV-14p1 clade, which was further classified into three major clusters. Notably, all strains identified in China belong to Cluster II and III. This study found that the initial isolates GZ01 and GZ02 from Guangzhou, China, in 2010 belonged to Cluster II, whereas the GZ25 isolate from the same location and year, identified through this study, belonged to Cluster III. Cluster III, which was sporadically epidemic, has formed a transmission circle in China. Despite multiple mutations in key genes between the two clusters, the homology of the Chinese isolates reached as high as 99.7 %. This study revealed that all HAdV-14 strains have highly conserved capsid proteins in China, which exhibit relative genome stability across time and geographic space. This study enhances our understanding of the genetic diversity and genomic characteristics of HAdV-14 and contributes to the prevention and control of HAdV-14 infection in the future.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"134 ","pages":"Article 105805"},"PeriodicalIF":2.6,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144755167","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 : 2025-07-27DOI: 10.1016/j.meegid.2025.105804
Yan Cardoso Pimenta , Glenda Maria Santos Moreira , Waldemar da Silva Souza , Alberto Ignacio Olivares Olivares , Lennart Svensson , José Paulo Gagliardi Leite , Johan Nordgren , Marcia Terezinha Baroni de Moraes
Noroviruses causes acute gastroenteritis (AGE) worldwide, with children living in low-income areas aged ≤5 years being the most vulnerable. Histo-blood group antigens (HBGA) are recognized as attachment factors for human noroviruses and susceptibility of a given genotype is frequently dependent on the secretor phenotype mediated by FUT2 genotype. This retrospective study involved 734 children aged ≤5 years with AGE (cases group; 66 %, 485/734) or non-AGE (control group; 34 %, 249/734), from the Amazon rainforest (Brazil, Venezuela, and Guyana) and in our previous studies, 87 % of children were positive secretors (641/734). A total of 40.2 % (88/219; GII) and 14.6 % (7/48; GI) of noroviruses were successfully genotyped, being: GII.1 (n = 5), GII.2 (n = 25), GII.4 (n = 32), GII.6 (n = 19), GII.7 (n = 5), GII.14 (n = 2), GI.2 (n = 1), GI.3 (n = 4) and GI.7 (n = 2). Most genotyped GII norovirus including all 32 GII.4, were detected in secretor-positive children (94.3 %, 83/88). Only genotypes GII.2 (n = 2), GII.6 (n = 3), GI.2 (n = 1) and GI.7 (n = 1) were detected in secretor-negative children. Of note, the predominant GII.4 and the GII.6 were not significantly associated with AGE (OR 1.1; 95 % CI 0.5 to 2.4, P = 0.7 and OR 1.4; 95 % CI 0.5 to 4.0, P = 0.4, respectively), in contrast to GII.2 was associated with AGE (OR 6.1; 95 % CI 1.4 to 26.2, P = 0.01). Genotypes GII.2, and GII.4 were detected in all age groups at high frequencies. In conclusion a great diversity of norovirus genotypes circulating in the Amazon region. Only the GII.2 genotype was associated with AGE, while the predominant GII.4 was detected at similar frequencies in both children with AGE and children without AGE.
{"title":"Epidemiological profiles of norovirus genotypes in children with and without acute gastroenteritis from the northwestern Amazon region","authors":"Yan Cardoso Pimenta , Glenda Maria Santos Moreira , Waldemar da Silva Souza , Alberto Ignacio Olivares Olivares , Lennart Svensson , José Paulo Gagliardi Leite , Johan Nordgren , Marcia Terezinha Baroni de Moraes","doi":"10.1016/j.meegid.2025.105804","DOIUrl":"10.1016/j.meegid.2025.105804","url":null,"abstract":"<div><div>Noroviruses causes acute gastroenteritis (AGE) worldwide, with children living in low-income areas aged ≤5 years being the most vulnerable. Histo-blood group antigens (HBGA) are recognized as attachment factors for human noroviruses and susceptibility of a given genotype is frequently dependent on the secretor phenotype mediated by FUT2 genotype. This retrospective study involved 734 children aged ≤5 years with AGE (cases group; 66 %, 485/734) or non-AGE (control group; 34 %, 249/734), from the Amazon rainforest (Brazil, Venezuela, and Guyana) and in our previous studies, 87 % of children were positive secretors (641/734). A total of 40.2 % (88/219; GII) and 14.6 % (7/48; GI) of noroviruses were successfully genotyped, being: GII.1 (<em>n</em> = 5), GII.2 (<em>n</em> = 25), GII.4 (<em>n</em> = 32), GII.6 (<em>n</em> = 19), GII.7 (n = 5), GII.14 (<em>n</em> = 2), GI.2 (<em>n</em> = 1), GI.3 (<em>n</em> = 4) and GI.7 (n = 2). Most genotyped GII norovirus including all 32 GII.4, were detected in secretor-positive children (94.3 %, 83/88). Only genotypes GII.2 (n = 2), GII.6 (<em>n</em> = 3), GI.2 (n = 1) and GI.7 (n = 1) were detected in secretor-negative children. Of note, the predominant GII.4 and the GII.6 were not significantly associated with AGE (OR 1.1; 95 % CI 0.5 to 2.4, <em>P =</em> 0.7 and OR 1.4; 95 % CI 0.5 to 4.0, <em>P</em> = 0.4, respectively), in contrast to GII.2 was associated with AGE (OR 6.1; 95 % CI 1.4 to 26.2, <em>P =</em> 0.01). Genotypes GII.2, and GII.4 were detected in all age groups at high frequencies. In conclusion a great diversity of norovirus genotypes circulating in the Amazon region. Only the GII.2 genotype was associated with AGE, while the predominant GII.4 was detected at similar frequencies in both children with AGE and children without AGE.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"134 ","pages":"Article 105804"},"PeriodicalIF":2.6,"publicationDate":"2025-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144746005","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 : 2025-07-23DOI: 10.1016/j.meegid.2025.105803
Camille Pelletier , Germain Chevignon , Nicole Faury , Isabelle Arzul , Céline Garcia , Bruno Chollet , Tristan Renault , Benjamin Morga , Maude Jacquot
Understanding how pathogens adapt to new hosts is critical to elucidating the evolutionary mechanisms driving disease emergence. This study investigates the evolutionary dynamics of Ostreid herpesvirus 1 (OsHV-1) in two host species—the Pacific oyster Magallana gigas and the European flat oyster Ostrea edulis—to address the question of host specificity and cross-species transmission. While OsHV-1 is primarily associated with mortality in M. gigas, its detection in O. edulis raises concerns about its potential host range and evolutionary trajectory. We aimed to determine whether viral populations in these two hosts show genetic differentiation and to identify the evolutionary forces shaping this divergence. Using high-throughput sequencing, we assembled 40 OsHV-1 genomes from both oyster species and applied comparative genomics, population genetics, and phylodynamic approaches. Our results show that host species significantly influence viral genetic structure, with two distinct lineages emerging after a cross-species transmission event likely following the introduction of M. gigas into Europe. Selection signals were detected in viral genes related to host interaction, replication, and membrane-associated functions, suggesting host-driven adaptation. These findings underscore the importance of host-specific evolutionary pressures in shaping viral diversity and provide a framework for future studies on host-virus coevolution in marine ecosystems.
{"title":"Phylogenomic evidence for host specialization and genetic divergence in OsHV-1 infecting Magallana gigas and Ostrea edulis","authors":"Camille Pelletier , Germain Chevignon , Nicole Faury , Isabelle Arzul , Céline Garcia , Bruno Chollet , Tristan Renault , Benjamin Morga , Maude Jacquot","doi":"10.1016/j.meegid.2025.105803","DOIUrl":"10.1016/j.meegid.2025.105803","url":null,"abstract":"<div><div>Understanding how pathogens adapt to new hosts is critical to elucidating the evolutionary mechanisms driving disease emergence. This study investigates the evolutionary dynamics of <em>Ostreid herpesvirus 1</em> (OsHV-1) in two host species—the Pacific oyster <em>Magallana gigas</em> and the European flat oyster <em>Ostrea edulis</em>—to address the question of host specificity and cross-species transmission. While OsHV-1 is primarily associated with mortality in <em>M. gigas</em>, its detection in <em>O. edulis</em> raises concerns about its potential host range and evolutionary trajectory. We aimed to determine whether viral populations in these two hosts show genetic differentiation and to identify the evolutionary forces shaping this divergence. Using high-throughput sequencing, we assembled 40 OsHV-1 genomes from both oyster species and applied comparative genomics, population genetics, and phylodynamic approaches. Our results show that host species significantly influence viral genetic structure, with two distinct lineages emerging after a cross-species transmission event likely following the introduction of <em>M. gigas</em> into Europe. Selection signals were detected in viral genes related to host interaction, replication, and membrane-associated functions, suggesting host-driven adaptation. These findings underscore the importance of host-specific evolutionary pressures in shaping viral diversity and provide a framework for future studies on host-virus coevolution in marine ecosystems.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"134 ","pages":"Article 105803"},"PeriodicalIF":2.6,"publicationDate":"2025-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144719179","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}
There are four major lineages of Mycobacterium tuberculosis (Mtb) whose geographic ranges vary considerably. Mtb lineage 2 (L2) or the East Asia lineage is particularly common in East and Southeast Asia, and also reported worldwide. Most L2 isolates belong to a sublineage L2.2 while L2.1 is more restricted to the Southern part of East Asia. It was reported that the L2.1 isolates in Thailand usually resisted isoniazid, rifampin and fluoroquinolones, i.e., being pre-XDR strains. It is, therefore, of particular public health concern. Our previous study in a limited number of available complete genomes of L2.1 suggested unique structural variations of some pe-ppe genes. The gene family plays roles in immune evasion and host-pathogen interactions and, hence, is integral to the bacterium's virulence. Here we examine the identified structural variations of the pe-ppe gene family among all 180 L2.1 samples from eight countries, whose WGS data with high-quality are available in GenBank. We identified the deletion of the esxR-esxS gene segment in 26 L2.1 genomes, 19 of which, primarily restricted to Vietnam, Thailand, and China, belonged to a single clade. Additionally, we confirmed the deletions of four pe-ppe genes, wag22, ppe38, ppe50 and ppe66, in all L2.1 samples. These genetic deletions may contribute to the virulence, pathogenesis, and evolutionary dynamics of the L2.1 strains, with significant implications for understanding the molecular mechanisms underlying the persistence and spread of this lineage.
{"title":"Global genetic diversity of Mycobacterium tuberculosis L2.1 based on pe-ppe gene family","authors":"Olabisi Flora Davies-Bolorunduro , Bharkbhoom Jaemsai , Wuthiwat Ruangchai , Thanakron Noppanamas , Manon Boonbangyang , Prasit Palittapongarnpim","doi":"10.1016/j.meegid.2025.105802","DOIUrl":"10.1016/j.meegid.2025.105802","url":null,"abstract":"<div><div>There are four major lineages of <em>Mycobacterium tuberculosis</em> (Mtb) whose geographic ranges vary considerably. Mtb lineage 2 (L2) or the East Asia lineage is particularly common in East and Southeast Asia, and also reported worldwide. Most L2 isolates belong to a sublineage L2.2 while L2.1 is more restricted to the Southern part of East Asia. It was reported that the L2.1 isolates in Thailand usually resisted isoniazid, rifampin and fluoroquinolones, <em>i.e.</em>, being pre-XDR strains. It is, therefore, of particular public health concern. Our previous study in a limited number of available complete genomes of L2.1 suggested unique structural variations of some <em>pe-ppe</em> genes. The gene family plays roles in immune evasion and host-pathogen interactions and, hence, is integral to the bacterium's virulence. Here we examine the identified structural variations of the <em>pe-ppe</em> gene family among all 180 L2.1 samples from eight countries, whose WGS data with high-quality are available in GenBank. We identified the deletion of the <em>esxR-esxS</em> gene segment in 26 L2.1 genomes, 19 of which, primarily restricted to Vietnam, Thailand, and China, belonged to a single clade. Additionally, we confirmed the deletions of four <em>pe-ppe</em> genes, <em>wag22, ppe38, ppe50</em> and <em>ppe66</em>, in all L2.1 samples. These genetic deletions may contribute to the virulence, pathogenesis, and evolutionary dynamics of the L2.1 strains, with significant implications for understanding the molecular mechanisms underlying the persistence and spread of this lineage.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"134 ","pages":"Article 105802"},"PeriodicalIF":2.6,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144709942","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}
Mammalian cells from embryonic mouse 3 T3 and bovine trachea (EBTr) lines were incubated in in vitro-conditions. A sub-population of from the EBTr cells was inoculated with low initial infectious titers of the vaccine avipoxviral strains FK (fowl), and another - with vaccine avipoxviral strain Dessau (pigeon) (Poxviridae family). Analogically, a subpopulation from the 3 T3 cells was pre-incubated in cultural fluid from transfected by recombinant DNA-plasmid P3-X63-Ag8 mouse malignant myeloma cells and cocultivated with them, another – co-cultivated with the same malignant cells. Although cytopathogenic effect, cell inclusions and mature virions were not observed, different methods of microscopic observations revealed molecular, structural and ultra-structural differences in the inoculated cells compared to the non-inoculated. Light microscopy observations of fixed and semi-thin slides revealed membrane excrescences, changed cell shape, size and nucleus-cytoplasm ratio, as well as activated lipid and protein synthesis (particularly of collagen and elastin). Transmission electron microscopy (TEM) of ultra-thin slides indicated cytoplasmic vacuolation and granulation, changes in the cytoplasmic organelles and in the nuclear chromatin. These changes were suggested as initial markers of cell (infectious, malignant or degenerative) injury and are underlining the initial cellular protective mechanisms. As one of the manifestations of these protective systems was proposed the production of immune molecules by non-immune cells in appropriate conditions. Also, a possibility about transfer of nucleotide (DNA- and/or RNA-) fragments between cellular and viral genomes was suggested. This phenomenon is probably due to activated fusion processes on the influence of organic detergent and drastic temperature changes.
{"title":"Detection of initial intra-cellular functional, structural and ultra-structural changes in virus-inoculated cells: A pilot study","authors":"Iskra Sainova , Radka Hadjiolova , Andrey Petrov , Dimitrina Dimitrova-Dikanarova , Tzvetanka Markova","doi":"10.1016/j.meegid.2025.105801","DOIUrl":"10.1016/j.meegid.2025.105801","url":null,"abstract":"<div><div>Mammalian cells from embryonic mouse 3 T3 and bovine trachea (EBTr) lines were incubated in <em>in vitro</em>-conditions. A sub-population of from the EBTr cells was inoculated with low initial infectious titers of the vaccine avipoxviral strains FK (fowl), and another - with vaccine avipoxviral strain Dessau (pigeon) (Poxviridae family). Analogically, a subpopulation from the 3 T3 cells was pre-incubated in cultural fluid from transfected by recombinant DNA-plasmid P3-X63-Ag8 mouse malignant myeloma cells and cocultivated with them, another – co-cultivated with the same malignant cells. Although cytopathogenic effect, cell inclusions and mature virions were not observed, different methods of microscopic observations revealed molecular, structural and ultra-structural differences in the inoculated cells compared to the non-inoculated. Light microscopy observations of fixed and semi-thin slides revealed membrane excrescences, changed cell shape, size and nucleus-cytoplasm ratio, as well as activated lipid and protein synthesis (particularly of collagen and elastin). Transmission electron microscopy (TEM) of ultra-thin slides indicated cytoplasmic vacuolation and granulation, changes in the cytoplasmic organelles and in the nuclear chromatin. These changes were suggested as initial markers of cell (infectious, malignant or degenerative) injury and are underlining the initial cellular protective mechanisms. As one of the manifestations of these protective systems was proposed the production of immune molecules by non-immune cells in appropriate conditions. Also, a possibility about transfer of nucleotide (DNA- and/or RNA-) fragments between cellular and viral genomes was suggested. This phenomenon is probably due to activated fusion processes on the influence of organic detergent and drastic temperature changes.</div></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":"134 ","pages":"Article 105801"},"PeriodicalIF":2.6,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144686156","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}
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