Pub Date : 2024-06-20DOI: 10.1016/j.meegid.2024.105626
Antonia Sophia Peter , Dieter S. Hoffmann , Johannes Klier , Christina M. Lange , Johanna Moeller , Victoria Most , Christina K. Wüst , Max Beining , Sevilay Gülesen , Hannes Junker , Birke Brumme , Torben Schiffner , Jens Meiler , Clara T. Schoeder
The COVID-19 outbreak has highlighted the importance of pandemic preparedness for the prevention of future health crises. One virus family with high pandemic potential are Arenaviruses, which have been detected almost worldwide, particularly in Africa and the Americas. These viruses are highly understudied and many questions regarding their structure, replication and tropism remain unanswered, making the design of an efficacious and molecularly-defined vaccine challenging. We propose that structure-driven computational vaccine design will contribute to overcome these challenges. Computational methods for stabilization of viral glycoproteins or epitope focusing have made progress during the last decades and particularly during the COVID-19 pandemic, and have proven useful for rational vaccine design and the establishment of novel diagnostic tools. In this review, we summarize gaps in our understanding of Arenavirus molecular biology, highlight challenges in vaccine design and discuss how structure-driven and computationally informed strategies will aid in overcoming these obstacles.
{"title":"Strategies of rational and structure-driven vaccine design for Arenaviruses","authors":"Antonia Sophia Peter , Dieter S. Hoffmann , Johannes Klier , Christina M. Lange , Johanna Moeller , Victoria Most , Christina K. Wüst , Max Beining , Sevilay Gülesen , Hannes Junker , Birke Brumme , Torben Schiffner , Jens Meiler , Clara T. Schoeder","doi":"10.1016/j.meegid.2024.105626","DOIUrl":"10.1016/j.meegid.2024.105626","url":null,"abstract":"<div><p>The COVID-19 outbreak has highlighted the importance of pandemic preparedness for the prevention of future health crises. One virus family with high pandemic potential are Arenaviruses, which have been detected almost worldwide, particularly in Africa and the Americas. These viruses are highly understudied and many questions regarding their structure, replication and tropism remain unanswered, making the design of an efficacious and molecularly-defined vaccine challenging. We propose that structure-driven computational vaccine design will contribute to overcome these challenges. Computational methods for stabilization of viral glycoproteins or epitope focusing have made progress during the last decades and particularly during the COVID-19 pandemic, and have proven useful for rational vaccine design and the establishment of novel diagnostic tools. In this review, we summarize gaps in our understanding of Arenavirus molecular biology, highlight challenges in vaccine design and discuss how structure-driven and computationally informed strategies will aid in overcoming these obstacles.</p></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567134824000777/pdfft?md5=1601ccc92a02607c1db03e7c5b579869&pid=1-s2.0-S1567134824000777-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141441165","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}
The genus Pseudochrobactrum encompasses free-living bacteria phylogenetically close to Ochrobactrum opportunistic pathogens and to Brucella, facultative intracellular parasites causing brucellosis, a worldwide-extended and grave zoonosis. Recently, Pseudochrobactrum strains were isolated from Brucella natural hosts on Brucella selective media, potentially causing diagnostic confusions. Strikingly, P. algeriensis was isolated from cattle lymph nodes, organs that are inimical to bacteria. Here, we analyse P. algeriensis potential virulence factors in comparison with Ochrobactrum and Brucella. Consistent with genomic analyses, Western-Blot analyses confirmed that P. algeriensis lacks the ability to synthesize the N-formylperosamine O-polysaccharide characteristic of the lipopolysaccharide (LPS) of smooth Brucella core species. However, unlike other Pseudochrobactrum but similar to some early diverging brucellae, P. algeriensis carries genes potentially synthetizing a rhamnose-based O-polysaccharide LPS. Lipid A analysis by MALDI-TOF demonstrated that P. algeriensis LPS bears a lipid A with a reduced pathogen-associated molecular pattern, a trait shared with Ochrobactrum and Brucella that is essential to generate a highly stable outer membrane and to delay immune activation. Also, although not able to multiply intracellularly in macrophages, the analysis of P. algeriensis cell lipid envelope revealed the presence of large amounts of cationic aminolipids, which may account for the extremely high resistance of P. algeriensis to bactericidal peptides and could favor colonization of mucosae and transient survival in Brucella hosts. However, two traits critical in Brucella pathogenicity are either significantly different (T4SS [VirB]) or absent (erythritol catabolic pathway) in P. algeriensis. This work shows that, while diverging in other characteristics, lipidic envelope features relevant in Brucella pathogenicity are conserved in Brucellaceae. The constant presence of these features strongly suggests that reinforcement of the envelope integrity as an adaptive advantage in soil was maintained in Brucella because of the similarity of some environmental challenges, such as the action of cationic peptide antibiotics and host defense peptides. This information adds knowledge about the evolution of Brucellaceae, and also underlines the taxonomical differences of the three genera compared.
假核金黄色葡萄球菌属(Pseudochrobactrum)包括自由生活的细菌,在系统发育上与机会致病菌赭曲霉(Ochrobactrum)和布鲁氏菌(Brucella)接近,后者是引起布鲁氏菌病(一种遍及全球的严重人畜共患疾病)的细胞内寄生虫。最近,在布鲁氏菌选择性培养基上从布鲁氏菌自然宿主中分离出假包囊菌株,可能会造成诊断上的混乱。令人震惊的是,从牛的淋巴结中分离出了 P. algeriensis,而淋巴结是不适宜细菌生长的器官。在此,我们分析了 P. algeriensis 与 Ochrobactrum 和布鲁氏菌的潜在毒力因子。与基因组分析一致,Western-Blot 分析证实,P. algeriensis 缺乏合成 N-formylperosamine O 型多糖的能力,而这种多糖是平滑布鲁氏菌核心菌种脂多糖(LPS)的特征。然而,与其他假杆菌不同,但与一些早期分化的布鲁氏菌类似,阿尔及尔假杆菌携带有可能合成鼠李糖基 O 型多糖 LPS 的基因。通过 MALDI-TOF 进行的脂质 A 分析表明,P. algeriensis LPS 所携带的脂质 A 具有较低的病原体相关分子模式,这是与 Ochrobactrum 和布鲁氏菌共有的特性,对于生成高度稳定的外膜和延迟免疫激活至关重要。此外,虽然不能在巨噬细胞内繁殖,但对阿耳戈螺旋体细胞脂质包膜的分析表明,阿耳戈螺旋体存在大量阳离子氨基脂,这可能是阿耳戈螺旋体对杀菌肽具有极强抵抗力的原因,并可能有利于在布鲁氏菌宿主的粘膜上定植和短暂存活。然而,对布鲁氏菌致病性至关重要的两个性状(T4SS [VirB])在阿尔盖氏痢疾杆菌中要么存在显著差异,要么不存在(赤藓糖醇分解途径)。这项工作表明,布鲁氏菌致病性相关的脂质包膜特征虽然在其他特征上存在差异,但在布鲁氏菌科中是保守的。这些特征的持续存在有力地表明,由于某些环境挑战(如阳离子肽抗生素和宿主防御肽的作用)的相似性,布鲁氏菌保持了包膜的完整性,这也是布鲁氏菌在土壤中的一种适应优势。这些信息增加了对布鲁氏菌科演化的了解,同时也强调了所比较的三个属在分类学上的差异。
{"title":"“Phylogenomic insights into brucellaceae: The Pseudochrobactrum algeriensis case”","authors":"Maite Loperena-Barber , Aitor Elizalde-Bielsa , Miriam Salvador-Bescós , Paula Ruiz-Rodríguez , Joaquin Miguel Pellegrini , Chantal Renau-Mínguez , Rebecca Lancaster , Amaia Zúñiga-Ripa , Maite Iriarte , Jose A. Bengoechea , Mireia Coscollá , Jean-Pierre Gorvel , Ignacio Moriyón , Raquel Conde-Álvarez","doi":"10.1016/j.meegid.2024.105625","DOIUrl":"10.1016/j.meegid.2024.105625","url":null,"abstract":"<div><p>The genus <em>Pseudochrobactrum</em> encompasses free-living bacteria phylogenetically close to <em>Ochrobactrum</em> opportunistic pathogens and to <em>Brucella</em>, facultative intracellular parasites causing brucellosis, a worldwide-extended and grave zoonosis. Recently, <em>Pseudochrobactrum</em> strains were isolated from <em>Brucella</em> natural hosts on <em>Brucella</em> selective media, potentially causing diagnostic confusions. Strikingly, <em>P. algeriensis</em> was isolated from cattle lymph nodes, organs that are inimical to bacteria. Here, we analyse <em>P. algeriensis</em> potential virulence factors in comparison with <em>Ochrobactrum</em> and <em>Brucella</em>. Consistent with genomic analyses, Western-Blot analyses confirmed that <em>P. algeriensis</em> lacks the ability to synthesize the N-formylperosamine O-polysaccharide characteristic of the lipopolysaccharide (LPS) of smooth <em>Brucella</em> core species. However, unlike other <em>Pseudochrobactrum</em> but similar to some early diverging brucellae, <em>P. algeriensis</em> carries genes potentially synthetizing a rhamnose-based O-polysaccharide LPS. Lipid A analysis by MALDI-TOF demonstrated that <em>P. algeriensis</em> LPS bears a lipid A with a reduced pathogen-associated molecular pattern, a trait shared with <em>Ochrobactrum</em> and <em>Brucella</em> that is essential to generate a highly stable outer membrane and to delay immune activation. Also, although not able to multiply intracellularly in macrophages, the analysis of <em>P. algeriensis</em> cell lipid envelope revealed the presence of large amounts of cationic aminolipids, which may account for the extremely high resistance of <em>P. algeriensis</em> to bactericidal peptides and could favor colonization of mucosae and transient survival in <em>Brucella</em> hosts. However, two traits critical in <em>Brucella</em> pathogenicity are either significantly different (T4SS [VirB]) or absent (erythritol catabolic pathway) in <em>P. algeriensis</em>. This work shows that, while diverging in other characteristics, lipidic envelope features relevant in <em>Brucella</em> pathogenicity are conserved in <em>Brucellaceae</em>. The constant presence of these features strongly suggests that reinforcement of the envelope integrity as an adaptive advantage in soil was maintained in <em>Brucella</em> because of the similarity of some environmental challenges, such as the action of cationic peptide antibiotics and host defense peptides. This information adds knowledge about the evolution of <em>Brucellaceae</em>, and also underlines the taxonomical differences of the three genera compared.</p></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567134824000765/pdfft?md5=ed938635d1090c67cd11e6f421873841&pid=1-s2.0-S1567134824000765-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141437832","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 : 2024-06-19DOI: 10.1016/j.meegid.2024.105619
Ru Bai , Yanyuan Chen , Junxian Ou , Wenya Dong , Tianhua Zhong , Yiqiang Li , Congrong Li , Chengyi Liu , Cunwei Ji , Huan Li , Yasha Luo , Ya-Fang Mei , Jie Wu , Donald Seto , Aihua Yin , Qiwei Zhang , Mingyong Luo
Human adenovirus type 41 (HAdV-F41) usually causes pediatrics gastroenteritis. However, it was reported to be associated with the outbreaks of severe acute hepatitis of unknown aetiology (SAHUA) in pediatrics during COVID-19 pandemic. In this study, we investigated the prevalence of enteric HAdV-F41 in 37,920 paediatric gastroenteritis cases from 2017 to 2022 in Guangzhou, China. All children presented were tested negative for SARS-CoV-2 during the “zero-COVID” period. The main clinical symptom of the children was diarrhea (96.5%). No fatalities nor liver abnormal symptoms was found. In 2021, one year since the pandemic of COVID-19, the prevalence of HAdV-F41 abruptly increased from 3.71% to 8.64% (P< 0.001). All of HAdV-F41 circulating worldwide were classified into eight different subtypes (G1-G8) based on the phylogenetic clustering permutation of the four capsid genes of HAdV-F41. G3 was the predominant subtype (56.2%; 77/137). CRV5 isolates from SAHUA cases belong to this subtype, in which N312D and H335D mutations in the short fiber knob were identified in both Guangzhou and CRV5 isolates, presumably changing the virus tropism by directly interacting with the heparin sulfate (HS) receptor. Additionally, a novel recombinant G6 subtype, which is unique and only circulating in China was first identified in this study. This is the first study highlighting the prevalence of HAdV-F41 in paediatric cases of gastroenteritis during COVID-19 pandemic in China. The clinical and viral evolution finding of HAdV-F41 provide insight into the clinical characteristics of children with HAdV-F41 infections as well as the uncertain role of HAdV-F41 in the cause of SAHUA.
{"title":"Clinical characteristics and phylogenetic analysis of human enteric adenovirus type 41 (HAdV-F41) from children with gastroenteritis during SARS-CoV-2 pandemic","authors":"Ru Bai , Yanyuan Chen , Junxian Ou , Wenya Dong , Tianhua Zhong , Yiqiang Li , Congrong Li , Chengyi Liu , Cunwei Ji , Huan Li , Yasha Luo , Ya-Fang Mei , Jie Wu , Donald Seto , Aihua Yin , Qiwei Zhang , Mingyong Luo","doi":"10.1016/j.meegid.2024.105619","DOIUrl":"10.1016/j.meegid.2024.105619","url":null,"abstract":"<div><p>Human adenovirus type 41 (HAdV-F41) usually causes pediatrics gastroenteritis. However, it was reported to be associated with the outbreaks of severe acute hepatitis of unknown aetiology (SAHUA) in pediatrics during COVID-19 pandemic. In this study, we investigated the prevalence of enteric HAdV-F41 in 37,920 paediatric gastroenteritis cases from 2017 to 2022 in Guangzhou, China. All children presented were tested negative for SARS-CoV-2 during the “zero-COVID” period. The main clinical symptom of the children was diarrhea (96.5%). No fatalities nor liver abnormal symptoms was found. In 2021, one year since the pandemic of COVID-19, the prevalence of HAdV-F41 abruptly increased from 3.71% to 8.64% <em>(P</em> <em><</em> 0.001). All of HAdV-F41 circulating worldwide were classified into eight different subtypes (G1-G8) based on the phylogenetic clustering permutation of the four capsid genes of HAdV-F41. G3 was the predominant subtype (56.2%; 77/137). CRV5 isolates from SAHUA cases belong to this subtype, in which N312D and H335D mutations in the short fiber knob were identified in both Guangzhou and CRV5 isolates, presumably changing the virus tropism by directly interacting with the heparin sulfate (HS) receptor. Additionally, a novel recombinant G6 subtype, which is unique and only circulating in China was first identified in this study. This is the first study highlighting the prevalence of HAdV-F41 in paediatric cases of gastroenteritis during COVID-19 pandemic in China. The clinical and viral evolution finding of HAdV-F41 provide insight into the clinical characteristics of children with HAdV-F41 infections as well as the uncertain role of HAdV-F41 in the cause of SAHUA.</p></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567134824000704/pdfft?md5=7948920e8897d000d2b63b674c4cd280&pid=1-s2.0-S1567134824000704-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141437833","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 : 2024-06-18DOI: 10.1016/j.meegid.2024.105624
Bashar Ismael , Morgan Wilson , Dini Miller , Jose E. Pietri
The German cockroach, Blattella germanica, can be a vector of human enteric bacterial pathogens, including Salmonella enterica serovar Typhimurium (S. Typhimurium). Transmission of such pathogens by cockroaches has largely been considered a passive mechanical process, but recent studies have argued against this dogma by demonstrating bacterial proliferation within the cockroach gut and the necessity of specific bacterial genes for successful transmission in the feces, revealing unappreciated biological complexity in the vector-pathogen relationship between cockroaches and S. Typhimurium. However, the influence of naturally occurring variation among cockroach populations on pathogen infection and dissemination has not been investigated. Thus, this study aimed to examine whether distinct strains of B. germanica exhibit differences in their ability to become infected by and disseminate S. Typhimurium. We performed controlled infections of one long-term laboratory strain and three recently field-collected strains reared under identical conditions, then compared bacterial loads in the body and excreta of individual insects. Separately, we also compared rates of necrophagy, a behavior known to contribute to the horizontal spread of S. Typhimurium among cockroaches. Our data show significant differences in infection susceptibility, pathogen shedding in the excreta, and necrophagy between laboratory and field strains as well as between some field strains. These observations represent the first evidence that genomic variation among cockroach populations may influence their ability to become infected by and disseminate pathogens, providing further support for the hypothesis that German cockroaches are active biological vectors rather than passive mechanical vectors of S. Typhimurium. Additional studies are needed to identify the genomic drivers of vector competence for S. Typhimurium in B. germanica.
{"title":"Differences in Salmonella Typhimurium infection and excretion among laboratory and field strains of the German cockroach suggest a genomic basis for vector competence","authors":"Bashar Ismael , Morgan Wilson , Dini Miller , Jose E. Pietri","doi":"10.1016/j.meegid.2024.105624","DOIUrl":"10.1016/j.meegid.2024.105624","url":null,"abstract":"<div><p>The German cockroach, <em>Blattella germanica</em>, can be a vector of human enteric bacterial pathogens, including <em>Salmonella enterica</em> serovar Typhimurium (<em>S.</em> Typhimurium)<em>.</em> Transmission of such pathogens by cockroaches has largely been considered a passive mechanical process, but recent studies have argued against this dogma by demonstrating bacterial proliferation within the cockroach gut and the necessity of specific bacterial genes for successful transmission in the feces, revealing unappreciated biological complexity in the vector-pathogen relationship between cockroaches and <em>S.</em> Typhimurium. However, the influence of naturally occurring variation among cockroach populations on pathogen infection and dissemination has not been investigated. Thus, this study aimed to examine whether distinct strains of <em>B. germanica</em> exhibit differences in their ability to become infected by and disseminate <em>S.</em> Typhimurium. We performed controlled infections of one long-term laboratory strain and three recently field-collected strains reared under identical conditions, then compared bacterial loads in the body and excreta of individual insects. Separately, we also compared rates of necrophagy, a behavior known to contribute to the horizontal spread of <em>S.</em> Typhimurium among cockroaches. Our data show significant differences in infection susceptibility, pathogen shedding in the excreta, and necrophagy between laboratory and field strains as well as between some field strains. These observations represent the first evidence that genomic variation among cockroach populations may influence their ability to become infected by and disseminate pathogens, providing further support for the hypothesis that German cockroaches are active biological vectors rather than passive mechanical vectors of <em>S.</em> Typhimuriu<em>m</em>. Additional studies are needed to identify the genomic drivers of vector competence for <em>S.</em> Typhimurium in <em>B. germanica.</em></p></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567134824000753/pdfft?md5=3e5ad2503243f9f4bc60f93da50d923c&pid=1-s2.0-S1567134824000753-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141433422","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 : 2024-06-18DOI: 10.1016/j.meegid.2024.105623
Victoria G. Castiglioni , María J. Olmo-Uceda , Susana Martín , Marie-Anne Félix , Rubén González , Santiago F. Elena
The discovery of Orsay virus (OrV), the first virus infecting wild populations of Caenorhabditis elegans, has boosted studies of viral immunity pathways in this nematode. Considering the many advantages that C. elegans offers for fundamental research in host-pathogen interactions, this pathosystem has high potential to become a model system for experimental virus evolution studies. However, the evolutionary constraints – i.e, the balance between genetic variation, selection, drift and historical contingency- operating in this pathosystem have barely been explored. Here we describe for the first time an evolution experiment of two different OrV strains in C. elegans. Comparison of the two ancestral strains showed differences in infectivity and sequence, and highlighted the importance of consistently normalize viral inocula for meaningful comparisons among strains. After 10 serial passages of evolution, we report slight changes in infectivity and non-synonymous mutations fixed in the evolved viral populations. In addition, we observed numerous minor variants emerging in the viral population. These minor variants were not randomly distributed along the genome but concentrated in polymorphic genomic regions. Overall, our work established the grounds for future experimental virus evolution studies using Caenorhabditis nematodes.
{"title":"Experimental evolution of an RNA virus in Caenorhabditis elegans","authors":"Victoria G. Castiglioni , María J. Olmo-Uceda , Susana Martín , Marie-Anne Félix , Rubén González , Santiago F. Elena","doi":"10.1016/j.meegid.2024.105623","DOIUrl":"10.1016/j.meegid.2024.105623","url":null,"abstract":"<div><p>The discovery of Orsay virus (OrV), the first virus infecting wild populations of <em>Caenorhabditis elegans</em>, has boosted studies of viral immunity pathways in this nematode. Considering the many advantages that <em>C. elegans</em> offers for fundamental research in host-pathogen interactions, this pathosystem has high potential to become a model system for experimental virus evolution studies. However, the evolutionary constraints – <em>i.e</em>, the balance between genetic variation, selection, drift and historical contingency- operating in this pathosystem have barely been explored. Here we describe for the first time an evolution experiment of two different OrV strains in <em>C. elegans</em>. Comparison of the two ancestral strains showed differences in infectivity and sequence, and highlighted the importance of consistently normalize viral inocula for meaningful comparisons among strains. After 10 serial passages of evolution, we report slight changes in infectivity and non-synonymous mutations fixed in the evolved viral populations. In addition, we observed numerous minor variants emerging in the viral population. These minor variants were not randomly distributed along the genome but concentrated in polymorphic genomic regions. Overall, our work established the grounds for future experimental virus evolution studies using <em>Caenorhabditis</em> nematodes.</p></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567134824000741/pdfft?md5=c6e70c067014f412de4de57be5bfd483&pid=1-s2.0-S1567134824000741-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141433423","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 : 2024-06-18DOI: 10.1016/j.meegid.2024.105622
Ágnes Dencs , Andrea Hettmann , Erzsébet Barcsay , Erzsébet Rusvai , Emese Kozma , Mária Takács
Men who have sex with men (MSM) are at high risk of acquiring hepatitis A virus (HAV) and in recent years several HAV outbreaks mostly affecting MSM have been described. These outbreaks were caused by subtype IA strains circulating in this high-risk population. After years of low incidence, an outbreak among MSM in Hungary caused a significant increase in reported HAV infections in 2022.
Samples from 224 HAV IgM-positive patients diagnosed in 2022 were tested for HAV RNA and positive samples were genotyped by sequencing. In 171 patients a unique subtype IB virus was detected with 99.8–100% sequence identity in the VP1/P2A junction. It was distinct from previously published strains, but most closely related to an Egyptian isolate. Sequence analysis revealed one dominant and three minor variants based on VP1/P2A. Whole genome sequencing revealed limited variation among these variants, suggesting a recent common origin. Epidemiological data indicated that sexual transmission was driving the outbreak for most of the year, suggested by the high male to female ratio and the large number of coinfections with HIV and other sexually transmitted infections among the patients. The outbreak was also associated with a restaurant cluster, in which one of the variants was detected and frozen berries were implicated as the source of infections. The outbreak strain was also detected in other countries around Europe and remained frequently detectable in Hungary in 2023.
This study provides insights into the molecular and epidemiological characteristics of the described HAV outbreak. The results show that sequencing is not only useful in connecting cases to an outbreak, but also helps to clarify the relatedness of detected variants. Prevention strategies focusing on vulnerable communities may reduce the burden of HAV infections in the future.
{"title":"Hepatitis A virus subtype IB outbreak among MSM in Hungary with a link to a frozen berry source","authors":"Ágnes Dencs , Andrea Hettmann , Erzsébet Barcsay , Erzsébet Rusvai , Emese Kozma , Mária Takács","doi":"10.1016/j.meegid.2024.105622","DOIUrl":"10.1016/j.meegid.2024.105622","url":null,"abstract":"<div><p>Men who have sex with men (MSM) are at high risk of acquiring hepatitis A virus (HAV) and in recent years several HAV outbreaks mostly affecting MSM have been described. These outbreaks were caused by subtype IA strains circulating in this high-risk population. After years of low incidence, an outbreak among MSM in Hungary caused a significant increase in reported HAV infections in 2022.</p><p>Samples from 224 HAV IgM-positive patients diagnosed in 2022 were tested for HAV RNA and positive samples were genotyped by sequencing. In 171 patients a unique subtype IB virus was detected with 99.8–100% sequence identity in the VP1/P2A junction. It was distinct from previously published strains, but most closely related to an Egyptian isolate. Sequence analysis revealed one dominant and three minor variants based on VP1/P2A. Whole genome sequencing revealed limited variation among these variants, suggesting a recent common origin. Epidemiological data indicated that sexual transmission was driving the outbreak for most of the year, suggested by the high male to female ratio and the large number of coinfections with HIV and other sexually transmitted infections among the patients. The outbreak was also associated with a restaurant cluster, in which one of the variants was detected and frozen berries were implicated as the source of infections. The outbreak strain was also detected in other countries around Europe and remained frequently detectable in Hungary in 2023.</p><p>This study provides insights into the molecular and epidemiological characteristics of the described HAV outbreak. The results show that sequencing is not only useful in connecting cases to an outbreak, but also helps to clarify the relatedness of detected variants. Prevention strategies focusing on vulnerable communities may reduce the burden of HAV infections in the future.</p></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S156713482400073X/pdfft?md5=8e2480defbdf74b54464b5c2ba77a316&pid=1-s2.0-S156713482400073X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141433424","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 : 2024-06-13DOI: 10.1016/j.meegid.2024.105620
András Surján, Balázs Harrach, Márton Z. Vidovszky
The Eurasian beaver (Castor fiber), native to Hungary, faced local extinction in 1865 and was successfully reintroduced between mid-1980s and 2008. Despite screening programs focusing on animal health during reintroduction in other countries, information about viruses in the Hungarian beaver population remains limited. Polyomaviruses (PyVs) have been identified in various rodents, and have been detected just recently in beavers by us. In this paper we present the full genome analysis of the first PyV detected in Eurasian beaver. The novel PyV was discovered in the kidney tissues of two specimens. The genome is 5244 bp, and contains four genes. Small T-antigen (STAg) and alternative large T ORF (ALTO) genes are directly fused together forming the middle T-antigen (MTAg). VP3 is absent from the genome. Its large T-antigen (LTAg) coding sequence exhibited over 15% genetic divergence from known PyVs, supporting its classification into a new species within the genus Alphapolyomavirus, suggesting to be named Alphapolyomavirus castoris. Phylogenetic analysis, based on the LTAg gene showed, that the beaver PyV forms a distinct clade with primate PyVs within the genus Alphapolyomavirus, separate from other rodent PyVs. Phylogenetic study of the VP1 gene however showed this virus to belong in a distinct clade with the same primate PyVs, and additionally PyVs from rodents and a myocastor, which suggest host virus co-evolution. The virus detection of the euthanized beavers suggests an apathogenic persistent infections. The aquatic lifestyle of beavers may influence virus transmission, warranting further exploration of undiscovered viruses in beavers.
{"title":"Complete genome characterization and phylogenetic analysis of a novel polyomavirus detected in Eurasian beavers (Castor fiber)","authors":"András Surján, Balázs Harrach, Márton Z. Vidovszky","doi":"10.1016/j.meegid.2024.105620","DOIUrl":"10.1016/j.meegid.2024.105620","url":null,"abstract":"<div><p>The Eurasian beaver (<em>Castor fiber</em>), native to Hungary, faced local extinction in 1865 and was successfully reintroduced between mid-1980s and 2008. Despite screening programs focusing on animal health during reintroduction in other countries, information about viruses in the Hungarian beaver population remains limited. Polyomaviruses (PyVs) have been identified in various rodents, and have been detected just recently in beavers by us. In this paper we present the full genome analysis of the first PyV detected in Eurasian beaver. The novel PyV was discovered in the kidney tissues of two specimens. The genome is 5244 bp, and contains four genes. Small T-antigen (STAg) and alternative large T ORF (ALTO) genes are directly fused together forming the middle T-antigen (MTAg). VP3 is absent from the genome. Its large T-antigen (LTAg) coding sequence exhibited over 15% genetic divergence from known PyVs, supporting its classification into a new species within the genus <em>Alphapolyomavirus</em>, suggesting to be named <em>Alphapolyomavirus castoris</em>. Phylogenetic analysis, based on the LTAg gene showed, that the beaver PyV forms a distinct clade with primate PyVs within the genus <em>Alphapolyomavirus</em>, separate from other rodent PyVs. Phylogenetic study of the VP1 gene however showed this virus to belong in a distinct clade with the same primate PyVs, and additionally PyVs from rodents and a myocastor, which suggest host virus co-evolution. The virus detection of the euthanized beavers suggests an apathogenic persistent infections. The aquatic lifestyle of beavers may influence virus transmission, warranting further exploration of undiscovered viruses in beavers.</p></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2024-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567134824000716/pdfft?md5=6ae538405c74fe5562623a7fced72c5d&pid=1-s2.0-S1567134824000716-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141321962","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 : 2024-06-08DOI: 10.1016/j.meegid.2024.105617
Jie Ma, Jinjin Liu, Chaohong Fu, Yuqi Huo
Unlike pandemic GII.4 norovirus, GII.6 norovirus shows limited sequence variation in its major capsid protein VP1. In this study, we investigated the VP1 expression profiles, binding abilities, and cross-blocking effects of three GII.6 norovirus strains derived from three distinct variants. Norovirus VP1 was expressed using a recombinant baculovirus expression system and characterized by transmission electron microscopy, mass spectrometry, salivary histo-blood group antigen (HBGA)-virus like particles (VLPs) binding and binding blockade assays. Mass spectrometry revealed the expected molecular weight (MW) of full-length proteins and degraded or cleaved fragments of all three VP1 proteins. Peptide mapping showed loss of 2 and 3 amino acids from the N- and C-terminus, respectively. Further, the co-expression of VP1 and VP2 proteins did not lead to extra fragmentation during mass spectrometry. Salivary HBGA-VLP binding assay revealed similar binding patterns of the three GII.6 VP1 proteins. Salivary HBGA-VLP binding blockade assay induced cross-blocking effects. Our results demonstrate similar binding abilities against salivary HBGAs and specific cross-blocking effects for GII.6 norovirus strains derived from distinct variants, suggesting that fewer GII.6 strains from different evolutionary variants are needed for the development of norovirus vaccines.
{"title":"GII.6 norovirus major capsid protein VP1 derived from distinct clusters induce cross-blocking effects","authors":"Jie Ma, Jinjin Liu, Chaohong Fu, Yuqi Huo","doi":"10.1016/j.meegid.2024.105617","DOIUrl":"10.1016/j.meegid.2024.105617","url":null,"abstract":"<div><p>Unlike pandemic GII.4 norovirus, GII.6 norovirus shows limited sequence variation in its major capsid protein VP1. In this study, we investigated the VP1 expression profiles, binding abilities, and cross-blocking effects of three GII.6 norovirus strains derived from three distinct variants. Norovirus VP1 was expressed using a recombinant baculovirus expression system and characterized by transmission electron microscopy, mass spectrometry, salivary histo-blood group antigen (HBGA)-virus like particles (VLPs) binding and binding blockade assays. Mass spectrometry revealed the expected molecular weight (MW) of full-length proteins and degraded or cleaved fragments of all three VP1 proteins. Peptide mapping showed loss of 2 and 3 amino acids from the N- and C-terminus, respectively. Further, the co-expression of VP1 and VP2 proteins did not lead to extra fragmentation during mass spectrometry. Salivary HBGA-VLP binding assay revealed similar binding patterns of the three GII.6 VP1 proteins. Salivary HBGA-VLP binding blockade assay induced cross-blocking effects. Our results demonstrate similar binding abilities against salivary HBGAs and specific cross-blocking effects for GII.6 norovirus strains derived from distinct variants, suggesting that fewer GII.6 strains from different evolutionary variants are needed for the development of norovirus vaccines.</p></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2024-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567134824000686/pdfft?md5=a20e6ff365a060e85aae767bd8ccfa1f&pid=1-s2.0-S1567134824000686-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141302176","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}
Hepatitis B virus (HBV) belongs to the family Hepadnaviridae and is the smallest human DNA virus, with a genome that is only 3200 nucleotides long. The absence of proofreading function in HBV reverse transcriptase provides a wide range of genetic variants for targeted outgrowth at different stages of infection. A number of sub genotypes and ten HBV genotypes (A through J) have been identified through analyses of the divergence of HBV genomic sequences. Numerous clinical outcomes, including the emergence of chronicity, the course of the disease, the effectiveness of treatment, and the response to vaccination, have been related to differences in genotype between HBV isolates. There are just seven studies that have been done in Ethiopia that examine the molecular epidemiology of HBV. Moreover, these studies haven't been compiled and reviewed yet. In this review, we looked at the genetic diversity and molecular epidemiology of HBV, the relationship between HBV genotypes and clinical outcomes, the immunopathogenesis of HBV, and finally the molecular epidemiology of HBV in Ethiopia. PubMed, Embase, and Google Scholar search engines were used to find relevant articles for the review. By using HBV genotyping, clinicians can better tailor vaccination decisions and antiviral therapy for patients with chronic hepatitis B who are more likely to experience the disease's progression.
{"title":"Molecular epidemiology of hepatitis B virus (HBV) in Ethiopia: A review article","authors":"Ayenew Assefa , Molla Getie , Birhanu Getie , Takilosimeneh Yazie , Aklesya Enkobahry","doi":"10.1016/j.meegid.2024.105618","DOIUrl":"10.1016/j.meegid.2024.105618","url":null,"abstract":"<div><p>Hepatitis B virus (HBV) belongs to the family Hepadnaviridae and is the smallest human DNA virus, with a genome that is only 3200 nucleotides long. The absence of proofreading function in HBV reverse transcriptase provides a wide range of genetic variants for targeted outgrowth at different stages of infection. A number of sub genotypes and ten HBV genotypes (A through J) have been identified through analyses of the divergence of HBV genomic sequences. Numerous clinical outcomes, including the emergence of chronicity, the course of the disease, the effectiveness of treatment, and the response to vaccination, have been related to differences in genotype between HBV isolates. There are just seven studies that have been done in Ethiopia that examine the molecular epidemiology of HBV. Moreover, these studies haven't been compiled and reviewed yet. In this review, we looked at the genetic diversity and molecular epidemiology of HBV, the relationship between HBV genotypes and clinical outcomes, the immunopathogenesis of HBV, and finally the molecular epidemiology of HBV in Ethiopia. PubMed, Embase, and Google Scholar search engines were used to find relevant articles for the review. By using HBV genotyping, clinicians can better tailor vaccination decisions and antiviral therapy for patients with chronic hepatitis B who are more likely to experience the disease's progression.</p></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2024-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567134824000698/pdfft?md5=166804aa463fb39667c6d7eb6687bea7&pid=1-s2.0-S1567134824000698-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141302129","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}
Glanders, a highly contagious and often fatal disease affecting equids, is caused by Burkholderia mallei. Although sporadic cases of equine glanders have recently been documented in Mongolia, genome sequencing and molecular studies of the bacteria within this region are lacking. This study provided the first molecular characterization of B. mallei isolated from four native Mongolian horses from two different provinces in 2019 and 2022 by applying whole-genome sequencing with two SNP types (previously developed genotyping with 15 SNP markers that provide global coverage of the B. mallei population and the core genome coding SNP typing developed in this study). The Mongolian isolates were located within the L3B1 cluster, which was previously associated with the V-120 strain from Russia. Within the L3B1 cluster shared by neighboring countries, they were in a unique subbranch. In this study, specific SNP markers unique to the Mongolian strains were identified to track these strains using a high-resolution melting analysis (HRMA). This study revealed the unique phylogenetic background of Mongolian strains isolated from the eastern part of Mongolia. HRMA specific to the Mongolian subbranch may contribute to the molecular epidemiological monitoring of glanders in Mongolia and surrounding countries.
马传染性软疣是一种由马伯克霍尔德氏菌(Burkholderia mallei)引起的传染性极强的疾病,通常会致命。虽然最近在蒙古发现了零星的马传染性单核细胞增多症病例,但该地区缺乏对这种细菌的基因组测序和分子研究。本研究首次采用全基因组测序和两种 SNP 类型(之前开发的 15 个 SNP 标记的基因分型可提供 B. mallei 群体的全球覆盖范围,以及本研究开发的核心基因组编码 SNP 分型),对 2019 年和 2022 年从两个不同省份的四匹本地蒙古马中分离出的 B. mallei 进行了分子鉴定。蒙古分离物位于 L3B1 群组中,该群组以前与来自俄罗斯的 V-120 株相关联。在邻国共享的 L3B1 群中,它们属于一个独特的亚支。在本研究中,利用高分辨率熔解分析(HRMA)确定了蒙古菌株特有的SNP标记,以追踪这些菌株。这项研究揭示了分离自蒙古东部地区的蒙古菌株的独特系统发育背景。蒙古亚支特有的高分辨率熔解分析(HRMA)可能有助于对蒙古及周边国家的传染性单核细胞增多症进行分子流行病学监测。
{"title":"First molecular characterization of Burkholderia mallei strains isolated from horses in Mongolia","authors":"Yoshiki Ichikawa , Liushiqi Borjigin , Batchuluun Enkhtuul , Ochirbat Khurtsbaatar , Keisuke Aoshima , Atsushi Kobayashi , Vanaabaatar Batbaatar , Takashi Kimura","doi":"10.1016/j.meegid.2024.105616","DOIUrl":"10.1016/j.meegid.2024.105616","url":null,"abstract":"<div><p>Glanders, a highly contagious and often fatal disease affecting equids, is caused by <em>Burkholderia mallei</em>. Although sporadic cases of equine glanders have recently been documented in Mongolia, genome sequencing and molecular studies of the bacteria within this region are lacking. This study provided the first molecular characterization of <em>B. mallei</em> isolated from four native Mongolian horses from two different provinces in 2019 and 2022 by applying whole-genome sequencing with two SNP types (previously developed genotyping with 15 SNP markers that provide global coverage of the <em>B. mallei</em> population and the core genome coding SNP typing developed in this study). The Mongolian isolates were located within the L3B1 cluster, which was previously associated with the V-120 strain from Russia. Within the L3B1 cluster shared by neighboring countries, they were in a unique subbranch. In this study, specific SNP markers unique to the Mongolian strains were identified to track these strains using a high-resolution melting analysis (HRMA). This study revealed the unique phylogenetic background of Mongolian strains isolated from the eastern part of Mongolia. HRMA specific to the Mongolian subbranch may contribute to the molecular epidemiological monitoring of glanders in Mongolia and surrounding countries.</p></div>","PeriodicalId":54986,"journal":{"name":"Infection Genetics and Evolution","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2024-06-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567134824000674/pdfft?md5=14809ce6db554fa9a4d281a2455cd70f&pid=1-s2.0-S1567134824000674-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141297318","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}