Highly pathogenic influenza A virus (HPIAV) H5N1 within the genetic clade 2.3.4.4b has emerged in wild birds in different regions of the world, leading to the death of >70 million birds. When these strains spread to pinniped species a remarkable mortality has also been observed. A detailed genetic characterization of HPIAV isolated from pinnipeds is essential to understand the potential spread of these viruses to other mammalian species, including humans. To gain insight into these matters a detailed phylogenetic analysis of HPIAV H5N1 2.3.4.4b strains isolated from pinniped species was performed. The results of these studies revealed multiple transmission events from birds to pinnipeds in all world regions. Different evolutionary histories of different genes of HPIAV H5N1 2.3.4.4b strains gave rise to the viruses infecting pinnipeds in different regions of the world. European strains isolated from pinnipeds represent a completely different genetic lineage from strains isolated from South American ones. All strains isolated from pinnipeds bear characteristics of a highly pathogenic form for of avian influenza in poultry. Amino acid substitutions, previously shown to confer an adaptive advantage for infecting mammals, were observed in different genes in all pinniped species studied.
{"title":"Understanding the emergence of highly pathogenic avian influenza A virus H5N1 in pinnipeds: An evolutionary approach","authors":"Mercedes Paz , Valentina Franco-Trecu , Diana Szteren , Alicia Costábile , Cecilia Portela , Alfredo Bruno , Gonzalo Moratorio , Pilar Moreno , Juan Cristina","doi":"10.1016/j.virusres.2024.199472","DOIUrl":"10.1016/j.virusres.2024.199472","url":null,"abstract":"<div><div>Highly pathogenic influenza A virus (HPIAV) H5N1 within the genetic clade 2.3.4.4b has emerged in wild birds in different regions of the world, leading to the death of >70 million birds. When these strains spread to pinniped species a remarkable mortality has also been observed. A detailed genetic characterization of HPIAV isolated from pinnipeds is essential to understand the potential spread of these viruses to other mammalian species, including humans. To gain insight into these matters a detailed phylogenetic analysis of HPIAV H5N1 2.3.4.4b strains isolated from pinniped species was performed. The results of these studies revealed multiple transmission events from birds to pinnipeds in all world regions. Different evolutionary histories of different genes of HPIAV H5N1 2.3.4.4b strains gave rise to the viruses infecting pinnipeds in different regions of the world. European strains isolated from pinnipeds represent a completely different genetic lineage from strains isolated from South American ones. All strains isolated from pinnipeds bear characteristics of a highly pathogenic form for of avian influenza in poultry. Amino acid substitutions, previously shown to confer an adaptive advantage for infecting mammals, were observed in different genes in all pinniped species studied.</div></div>","PeriodicalId":23483,"journal":{"name":"Virus research","volume":"350 ","pages":"Article 199472"},"PeriodicalIF":2.5,"publicationDate":"2024-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142372996","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 : 2024-10-05DOI: 10.1016/j.virusres.2024.199476
Miloš Trifković , Ondřej Hejna , Anna Kuznetsova , Martin Mullett , Libor Jankovský , Leticia Botella
Dothistroma septosporum and Dothistroma pini are severe foliar pathogens of conifers. They infect a broad spectrum of hosts (mainly Pinus spp.), causing chlorosis, defoliation of needles, and eventually the death of pine trees in extreme cases. Mycoviruses represent a novel and innovative avenue for controlling pathogens. To search for possible viruses hosted by Dothistroma spp. we screened a subset of isolates (20 strains of D. septosporum and one D. pini) originating from the Czech Republic, Slovenia, Italy, Austria and Ireland for viral dsRNA segments. Only five of them showed the presence of dsRNA segments. A total of 21 fungal isolates were prepared for total RNA extractions. RNA samples were pooled, and two separate RNA libraries were constructed for stranded total RNA sequencing. RNA-Seq data processing, pairwise sequence comparisons (PASC) and phylogenetic analyses revealed the presence of thirteen novel putative viruses with varying genome types: seven negative-sense single-stranded RNA viruses, including six bunya-like viruses and one new member of the order Mononegavirales; three positive-sense single-stranded RNA viruses, two of which are similar to those of the family Narnaviridae, while the genome of the third correspond to those of the family Gammaflexiviridae; and three double-stranded RNA viruses, comprising two novel members of the family Chrysoviridae and a potentially new species of gammapartitivirus. The results were confirmed with RT-PCR screening that the fungal pathogens hosted all the viruses and showed that particular fungal strains harbour multiple virus infections and that they are transmitted vertically. In this study, we described the narnavirus infecting D. pini. To our knowledge, this is the first virus discovered in D. pini.
{"title":"Dothistroma septosporum and Dothistroma pini, the causal agents of Dothistroma needle blight, are infected by multiple viruses","authors":"Miloš Trifković , Ondřej Hejna , Anna Kuznetsova , Martin Mullett , Libor Jankovský , Leticia Botella","doi":"10.1016/j.virusres.2024.199476","DOIUrl":"10.1016/j.virusres.2024.199476","url":null,"abstract":"<div><div><em>Dothistroma septosporum</em> and <em>Dothistroma pini</em> are severe foliar pathogens of conifers. They infect a broad spectrum of hosts (mainly <em>Pinus</em> spp.), causing chlorosis, defoliation of needles, and eventually the death of pine trees in extreme cases. Mycoviruses represent a novel and innovative avenue for controlling pathogens. To search for possible viruses hosted by <em>Dothistroma</em> spp<em>.</em> we screened a subset of isolates (20 strains of <em>D. septosporum</em> and one <em>D. pini</em>) originating from the Czech Republic, Slovenia, Italy, Austria and Ireland for viral dsRNA segments. Only five of them showed the presence of dsRNA segments. A total of 21 fungal isolates were prepared for total RNA extractions. RNA samples were pooled, and two separate RNA libraries were constructed for stranded total RNA sequencing. RNA-Seq data processing, pairwise sequence comparisons (PASC) and phylogenetic analyses revealed the presence of thirteen novel putative viruses with varying genome types: seven negative-sense single-stranded RNA viruses, including six bunya-like viruses and one new member of the order <em>Mononegavirales</em>; three positive-sense single-stranded RNA viruses, two of which are similar to those of the family <em>Narnaviridae</em>, while the genome of the third correspond to those of the family <em>Gammaflexiviridae;</em> and three double-stranded RNA viruses, comprising two novel members of the family <em>Chrysoviridae</em> and a potentially new species of gammapartitivirus. The results were confirmed with RT-PCR screening that the fungal pathogens hosted all the viruses and showed that particular fungal strains harbour multiple virus infections and that they are transmitted vertically. In this study, we described the narnavirus infecting <em>D. pini</em>. To our knowledge, this is the first virus discovered in <em>D. pini</em>.</div></div>","PeriodicalId":23483,"journal":{"name":"Virus research","volume":"350 ","pages":"Article 199476"},"PeriodicalIF":2.5,"publicationDate":"2024-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142366712","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 : 2024-10-01DOI: 10.1016/j.virusres.2024.199473
Qian Wang , Ran Chen , Hui Liu , Yue Liu , Jinmei Li , Yueling Wang , Yan Jin , Yuanyuan Bai , Zhen Song , Xinglun Lu , Changyin Wang , Yingying Hao
The global health threat posed by carbapenem-resistant Klebsiella pneumoniae (CRKP) is exacerbated by the limited availability of effective treatments. Bacteriophages are promising alternatives to conventional antimicrobial agents. However, current phage databases are limited. Thus, identifying and characterizing new phages could provide biological options for the treatment of multi-drug resistant bacterial infections. Here, we report the characterization of a novel lytic phage, vB_KpnP_23, isolated from hospital sewage. This phage exhibited potent activity against carbapenemase-producing CRKP strains and was characterised by an icosahedral head, a retractable tail, and a genome comprising 40,987 base pairs, with a G + C content of 51 %. Capable of targeting and lysing nine different capsule types (K-types) of CRKP, including the clinically relevant ST11-K64, it demonstrated both high bacteriolytic efficiency and stability in various environmental contexts. Crucially, vB_KpnP_23 lacks virulence factors, antimicrobial resistance genes, or tRNA, aligning with the key criteria for therapeutic application. In vitro evaluation of phage-antibiotic combinations revealed a significant synergistic effect between vB_KpnP_23 and meropenem, levofloxacin, or amikacin. This synergy could lead to an 8-fold reduction in the minimum inhibitory concentration (MIC), suggesting that integrated treatments combining this phage with the aforementioned antibiotics may substantially enhance drug effectiveness. This approach not only extends the clinical utility of these antibiotics but also presents a strategic advance in combating antibiotic resistance. Specifically, it underscores the potential of phage-antibiotic combinations as a powerful tool in the treatment of infections caused by CRKP, offering a promising avenue to mitigate the public health challenges of antibiotic-resistant pathogens.
{"title":"Isolation and characterization of lytic bacteriophage vB_KpnP_23: A promising antimicrobial candidate against carbapenem-resistant Klebsiella pneumoniae","authors":"Qian Wang , Ran Chen , Hui Liu , Yue Liu , Jinmei Li , Yueling Wang , Yan Jin , Yuanyuan Bai , Zhen Song , Xinglun Lu , Changyin Wang , Yingying Hao","doi":"10.1016/j.virusres.2024.199473","DOIUrl":"10.1016/j.virusres.2024.199473","url":null,"abstract":"<div><div>The global health threat posed by carbapenem-resistant <em>Klebsiella pneumoniae</em> (CRKP) is exacerbated by the limited availability of effective treatments. Bacteriophages are promising alternatives to conventional antimicrobial agents. However, current phage databases are limited. Thus, identifying and characterizing new phages could provide biological options for the treatment of multi-drug resistant bacterial infections. Here, we report the characterization of a novel lytic phage, vB_KpnP_23, isolated from hospital sewage. This phage exhibited potent activity against carbapenemase-producing CRKP strains and was characterised by an icosahedral head, a retractable tail, and a genome comprising 40,987 base pairs, with a G + C content of 51 %. Capable of targeting and lysing nine different capsule types (K-types) of CRKP, including the clinically relevant ST11-K64, it demonstrated both high bacteriolytic efficiency and stability in various environmental contexts. Crucially, vB_KpnP_23 lacks virulence factors, antimicrobial resistance genes, or tRNA, aligning with the key criteria for therapeutic application. In vitro evaluation of phage-antibiotic combinations revealed a significant synergistic effect between vB_KpnP_23 and meropenem, levofloxacin, or amikacin. This synergy could lead to an 8-fold reduction in the minimum inhibitory concentration (MIC), suggesting that integrated treatments combining this phage with the aforementioned antibiotics may substantially enhance drug effectiveness. This approach not only extends the clinical utility of these antibiotics but also presents a strategic advance in combating antibiotic resistance. Specifically, it underscores the potential of phage-antibiotic combinations as a powerful tool in the treatment of infections caused by CRKP, offering a promising avenue to mitigate the public health challenges of antibiotic-resistant pathogens.</div></div>","PeriodicalId":23483,"journal":{"name":"Virus research","volume":"350 ","pages":"Article 199473"},"PeriodicalIF":2.5,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142354764","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 : 2024-09-27DOI: 10.1016/j.virusres.2024.199474
Eun-A Ko , Tong Zhou , Jae-Hong Ko
Influenza A virus (IAV) induces acute respiratory infections in birds and various mammals, including humans, and presents a significant global public health concern, with considerable economic consequences. Recently, researchers have shown keen interest in noncanonical small noncoding RNAs (sncRNAs) as carriers of epigenetic information, including tRNA-derived small RNAs (tsRNAs), rRNA-derived small RNA (rsRNAs), and Y RNA-derived small RNAs (ysRNAs). Particularly, tsRNAs and rsRNAs are detected in diverse species and demonstrate evolutionary conservation. We analyzed sncRNAs sequencing data in the pulmonary tissue of two genetically distinct mouse strains, C57BL/6J and DBA/2J, to explore strain-specific variations of sncRNAs in response to IAV infection. We systematically compiled information on noncanonical sncRNAs in these two strains and investigated the tsRNAs/rsRNAs/ysRNAs profiles influenced by IAV infection. Specifically, four noncanonical sncRNA families, including rsRNA-12S, GtsRNA-Arg-CCT, GtsRNA-Arg-TCT, and GtsRNA-Lys-TTT, exhibited upregulation upon IAV infection. Notably, DBA/2J mice showed earlier systemic differential expression of noncanonical sncRNAs after IAV infection compared to C57BL/6J mice. Additionally, our study revealed a strain-specific biogenesis of MtsRNAs in response to IAV infection. Also, distinct co-expression patterns of MtsRNAs were observed between C57BL/6J and DBA/2J mice, with DBA/2J mice showing broader positive co-expression of MtsRNAs with various sncRNA families compared to C57BL/6J mice. Our study provides a novel insight into noncanonical sncRNAs and their implications in IAV pathology and mouse strain specificity.
{"title":"Insight into noncanonical small noncoding RNAs in Influenza A virus infection","authors":"Eun-A Ko , Tong Zhou , Jae-Hong Ko","doi":"10.1016/j.virusres.2024.199474","DOIUrl":"10.1016/j.virusres.2024.199474","url":null,"abstract":"<div><div>Influenza A virus (IAV) induces acute respiratory infections in birds and various mammals, including humans, and presents a significant global public health concern, with considerable economic consequences. Recently, researchers have shown keen interest in noncanonical small noncoding RNAs (sncRNAs) as carriers of epigenetic information, including tRNA-derived small RNAs (tsRNAs), rRNA-derived small RNA (rsRNAs), and Y RNA-derived small RNAs (ysRNAs). Particularly, tsRNAs and rsRNAs are detected in diverse species and demonstrate evolutionary conservation. We analyzed sncRNAs sequencing data in the pulmonary tissue of two genetically distinct mouse strains, C57BL/6J and DBA/2J, to explore strain-specific variations of sncRNAs in response to IAV infection. We systematically compiled information on noncanonical sncRNAs in these two strains and investigated the tsRNAs/rsRNAs/ysRNAs profiles influenced by IAV infection. Specifically, four noncanonical sncRNA families, including rsRNA-12S, GtsRNA-Arg-CCT, GtsRNA-Arg-TCT, and GtsRNA-Lys-TTT, exhibited upregulation upon IAV infection. Notably, DBA/2J mice showed earlier systemic differential expression of noncanonical sncRNAs after IAV infection compared to C57BL/6J mice. Additionally, our study revealed a strain-specific biogenesis of MtsRNAs in response to IAV infection. Also, distinct co-expression patterns of MtsRNAs were observed between C57BL/6J and DBA/2J mice, with DBA/2J mice showing broader positive co-expression of MtsRNAs with various sncRNA families compared to C57BL/6J mice. Our study provides a novel insight into noncanonical sncRNAs and their implications in IAV pathology and mouse strain specificity.</div></div>","PeriodicalId":23483,"journal":{"name":"Virus research","volume":"350 ","pages":"Article 199474"},"PeriodicalIF":2.5,"publicationDate":"2024-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142326427","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 : 2024-09-25DOI: 10.1016/j.virusres.2024.199471
Jin Sun No , Ji Yeong Noh , Chae Young Lee , Il-Hwan Kim , Jeong-Ah Kim , Yu Jeong Ahn , Hyeokjin Lee , Jeong-Min Kim , Nam-Joo Lee , Dong-Wook Lee , Jeong-Hoon Kwon , JeeEun Rhee , Eun-Jin Kim
As COVID-19 has become endemic, SARS-CoV-2 variants are becoming increasingly diverse, underscoring the escalating importance of global genomic surveillance. This study analyzed 86,762 COVID-19 samples identified in the Republic of Korea from September 2022 to November 2023. The results revealed a consistent increase in the prevalence of the XBB variants following the dominance of BN.1, with various XBB sub-lineages co-circulating in the Republic of Korea. The overall nucleotide diversity (π) among the SARS-CoV-2 genomes was 0.00155. Evolutionary analysis revealed that the average time interval between the first detection and estimated date of the most recent common ancestor of Korean XBB sub-lineages was 47 d, suggesting that the novel variants were efficiently identified in the Korean surveillance system. The mutation rate was determined to be in the range of 5.6 × 10–4 to 9.1 × 10–4 substitutions/site/year. In conclusion, this study provides insights into the genetic diversity and evolutionary interpretation of the XBB sub-lineages during the XBB wave in the Republic of Korea, highlighting the importance of continued genomic surveillance for emerging variants.
{"title":"Dynamics of SARS-CoV-2 variants during the XBB wave in the Republic of Korea","authors":"Jin Sun No , Ji Yeong Noh , Chae Young Lee , Il-Hwan Kim , Jeong-Ah Kim , Yu Jeong Ahn , Hyeokjin Lee , Jeong-Min Kim , Nam-Joo Lee , Dong-Wook Lee , Jeong-Hoon Kwon , JeeEun Rhee , Eun-Jin Kim","doi":"10.1016/j.virusres.2024.199471","DOIUrl":"10.1016/j.virusres.2024.199471","url":null,"abstract":"<div><div>As COVID-19 has become endemic, SARS-CoV-2 variants are becoming increasingly diverse, underscoring the escalating importance of global genomic surveillance. This study analyzed 86,762 COVID-19 samples identified in the Republic of Korea from September 2022 to November 2023. The results revealed a consistent increase in the prevalence of the XBB variants following the dominance of BN.1, with various XBB sub-lineages co-circulating in the Republic of Korea. The overall nucleotide diversity (π) among the SARS-CoV-2 genomes was 0.00155. Evolutionary analysis revealed that the average time interval between the first detection and estimated date of the most recent common ancestor of Korean XBB sub-lineages was 47 d, suggesting that the novel variants were efficiently identified in the Korean surveillance system. The mutation rate was determined to be in the range of 5.6 × 10<sup>–4</sup> to 9.1 × 10<sup>–4</sup> substitutions/site/year. In conclusion, this study provides insights into the genetic diversity and evolutionary interpretation of the XBB sub-lineages during the XBB wave in the Republic of Korea, highlighting the importance of continued genomic surveillance for emerging variants.</div></div>","PeriodicalId":23483,"journal":{"name":"Virus research","volume":"350 ","pages":"Article 199471"},"PeriodicalIF":2.5,"publicationDate":"2024-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142296528","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}
This study aims to screen and identify linear B-cell epitopes on the structural proteins of African Swine Fever Virus (ASFV) to assist in the development of peptide-based vaccines. In experiments, 66 peptides of 12 structural proteins of ASFV were predicted as potential linear B-cell epitopes using bioinformatics tools and were designed; the potential epitope proteins carried the GST tag were expressed, purified, and subjected to antigenicity analysis with porcine antiserum against ASFV, and further identified based on their immunogenicity in mice. A total of 22 potential linear B-cell epitopes showed immunoreactivity and immunogenicity. Of these epitopes, 13 epitopes were firstly identified including 4 epitopes located in p72 (352–363, 416–434, 424–439, 496–530 aa), 3 epitopes located in pE248R (121–136, 138–169, 158–185 aa), and only one epitope of each protein of pH108R (33–46 aa), p17 (63–86 aa), pE120R (65–117 aa), pE199L (175–189 aa), p12 (36–56 aa) as well as pB438L (211–230 aa). Notably, the immunoreactivity of the epitopes from the 63-86 aa of p17 and the 65–117 aa of pE120R were the highest amongst identified epitopes, while the immunogenicity of epitopes from the 36–56 aa of p12, the 211–230 aa of pB438L, the 352–363 aa of p72 and the 63–86 aa of p17 were the best strong. The other 9 epitopes are partly overlapped with previous researches. These epitopes identified here will further enrich the database of ASFV epitope, as well as help to develop safe, effective epitope-based ASF vaccines and ASF diagnostic reagents.
本研究旨在筛选和鉴定非洲猪瘟病毒（ASFV）结构蛋白上的线性B细胞表位，以帮助开发基于多肽的疫苗。在实验中，利用生物信息学工具预测了非洲猪瘟病毒 12 种结构蛋白中的 66 个肽段，并设计了潜在的线性 B 细胞表位；对这些潜在表位蛋白进行了 GST 标记表达、纯化，并用猪抗血清对非洲猪瘟病毒进行了抗原性分析，根据其在小鼠中的免疫原性进一步鉴定。共有 22 个潜在的线性 B 细胞表位显示出免疫反应性和免疫原性。在这些表位中，首先确定了 13 个表位，包括位于 p72 的 4 个表位（352-363、416-434、424-439、496-530 aa）、位于 pE248R 的 3 个表位（121-136、138-169、158-185 aa），pH108R（33-46 aa）、p17（63-86 aa）、pE120R（65-117 aa）、pE199L（175-189 aa）、p12（36-56 aa）和 pB438L（211-230 aa）的每个蛋白质只有一个表位。值得注意的是，在已鉴定的表位中，p17 的 63-86 aa 表位和 pE120R 的 65-117 aa 表位的免疫活性最高，而 p12 的 36-56 aa 表位、pB438L 的 211-230 aa 表位、p72 的 352-363 aa 表位和 p17 的 63-86 aa 表位的免疫原性最强。其他 9 个表位与之前的研究有部分重叠。这些表位的发现将进一步丰富 ASFV 表位数据库，并有助于开发安全、有效的基于表位的 ASF 疫苗和 ASF 诊断试剂。
{"title":"Screening and identification of linear B-cell epitopes on structural proteins of African Swine Fever Virus","authors":"Haiyan Lu, Junjun Shao, Wei Liu, Shandian Gao, Guangqing Zhou, Xiaoyu Ning, Haiyan Huang, Yijia Liu, Huiyun Chang","doi":"10.1016/j.virusres.2024.199465","DOIUrl":"10.1016/j.virusres.2024.199465","url":null,"abstract":"<div><div>This study aims to screen and identify linear B-cell epitopes on the structural proteins of African Swine Fever Virus (ASFV) to assist in the development of peptide-based vaccines. In experiments, 66 peptides of 12 structural proteins of ASFV were predicted as potential linear B-cell epitopes using bioinformatics tools and were designed; the potential epitope proteins carried the GST tag were expressed, purified, and subjected to antigenicity analysis with porcine antiserum against ASFV, and further identified based on their immunogenicity in mice. A total of 22 potential linear B-cell epitopes showed immunoreactivity and immunogenicity. Of these epitopes, 13 epitopes were firstly identified including 4 epitopes located in p72 (352–363, 416–434, 424–439, 496–530 aa), 3 epitopes located in pE248R (121–136, 138–169, 158–185 aa), and only one epitope of each protein of pH108R (33–46 aa), p17 (63–86 aa), pE120R (65–117 aa), pE199L (175–189 aa), p12 (36–56 aa) as well as pB438L (211–230 aa). Notably, the immunoreactivity of the epitopes from the 63-86 aa of p17 and the 65–117 aa of pE120R were the highest amongst identified epitopes, while the immunogenicity of epitopes from the 36–56 aa of p12, the 211–230 aa of pB438L, the 352–363 aa of p72 and the 63–86 aa of p17 were the best strong. The other 9 epitopes are partly overlapped with previous researches. These epitopes identified here will further enrich the database of ASFV epitope, as well as help to develop safe, effective epitope-based ASF vaccines and ASF diagnostic reagents.</div></div>","PeriodicalId":23483,"journal":{"name":"Virus research","volume":"350 ","pages":"Article 199465"},"PeriodicalIF":2.5,"publicationDate":"2024-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142296529","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}
Canine distemper virus (CDV) is responsible for a highly contagious and often fatal neurological disease that affects various carnivores, including domestic dogs. In Nepal, recent reports of CDV exposure and illness in leopards (Panthera pardus) have raised concerns about the transmission of the virus among domestic dogs and wild carnivores. To investigate the genetic lineage and spread of CDV, our study utilized archived post-mortem samples from four leopards that exhibited clinical signs suggestive of canine distemper infection. These leopards were rescued in the Palpa, Dolakha, Kathmandu, and Parbat districts. Our phylogenetic analysis revealed that the CDV strains circulating among the leopards belong to the Asia-5 lineage, which is also prevalent among dogs and wild carnivores in Nepal and neighboring India. The genetic relatedness between the leopard CDV sequences and those from both dogs and other carnivores within the Asia-5 lineage suggests that leopards in Nepal may have acquired the virus from multiple sources, potentially facilitated by their generalist dietary habits preying on dogs and even mesocarnivores. Furthermore, we inspected specific amino acid substitution in the hemagglutinin gene of leopard CDV, which also suggests possible transmission from both domestic dogs and non-canid hosts, although further research is needed to draw definitive conclusions. Given the vulnerable state of the leopard population in Nepal, already threatened by poaching and retaliatory killing, the emergence of CDV as a potential novel threat is deeply concerning. Comprehensive surveillance studies are essential to understand the dynamics of CDV spillover and to develop informed interventions. Urgent measures, including vaccination programs and effective control of the dog population, are needed to mitigate the impact of this disease and safeguard the future of Nepal's leopards and other wild carnivores.
{"title":"Phylogenetic analysis linked fatal neurologic disease in leopards (Panthera pardus) to Asia-5 lineage of canine distemper virus in Nepal","authors":"Amir Sadaula , Prajwol Manandhar , Bijaya Kumar Shrestha , Parbat Jung Thapa , Suresh Nepali , Janardan Dev Joshi , Babu Ram Lamichhane , Rachana Shah , Madhu Chetri , Kiran Raj Rijal , Kamal Prasad Gairhe , Naresh Subedi , Chiranjibi Prasad Pokheral , Roji Raut , Purushottam Pandey , Bikalpa Karki , Gita Pandey","doi":"10.1016/j.virusres.2024.199463","DOIUrl":"10.1016/j.virusres.2024.199463","url":null,"abstract":"<div><div>Canine distemper virus (CDV) is responsible for a highly contagious and often fatal neurological disease that affects various carnivores, including domestic dogs. In Nepal, recent reports of CDV exposure and illness in leopards (<em>Panthera pardus</em>) have raised concerns about the transmission of the virus among domestic dogs and wild carnivores. To investigate the genetic lineage and spread of CDV, our study utilized archived post-mortem samples from four leopards that exhibited clinical signs suggestive of canine distemper infection. These leopards were rescued in the Palpa, Dolakha, Kathmandu, and Parbat districts. Our phylogenetic analysis revealed that the CDV strains circulating among the leopards belong to the Asia-5 lineage, which is also prevalent among dogs and wild carnivores in Nepal and neighboring India. The genetic relatedness between the leopard CDV sequences and those from both dogs and other carnivores within the Asia-5 lineage suggests that leopards in Nepal may have acquired the virus from multiple sources, potentially facilitated by their generalist dietary habits preying on dogs and even mesocarnivores. Furthermore, we inspected specific amino acid substitution in the hemagglutinin gene of leopard CDV, which also suggests possible transmission from both domestic dogs and non-canid hosts, although further research is needed to draw definitive conclusions. Given the vulnerable state of the leopard population in Nepal, already threatened by poaching and retaliatory killing, the emergence of CDV as a potential novel threat is deeply concerning. Comprehensive surveillance studies are essential to understand the dynamics of CDV spillover and to develop informed interventions. Urgent measures, including vaccination programs and effective control of the dog population, are needed to mitigate the impact of this disease and safeguard the future of Nepal's leopards and other wild carnivores.</div></div>","PeriodicalId":23483,"journal":{"name":"Virus research","volume":"350 ","pages":"Article 199463"},"PeriodicalIF":2.5,"publicationDate":"2024-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142308616","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 : 2024-09-20DOI: 10.1016/j.virusres.2024.199464
Jake D'Addiego , Sonal Shah , Ayşe Nur Pektaş , Bi̇nnur Köksal Bağci , Murtaza Öz , Sasha Sebastianelli , Nazif Elaldı , David J Allen , Roger Hewson
Crimean-Congo haemorrhagic fever (CCHF) is the most prevalent human tick-borne viral disease, with a reported case fatality rate of 30 % or higher. The virus contains a tri-segmented, negative-sense RNA genome consisting of the small (S), medium (M) and large (L) segments encoding respectively the nucleoprotein (NP), the glycoproteins precursor (GPC) and the viral RNA-dependent RNA polymerase (RDRP). CCHFV is one of the most genetically diverse arboviruses, with seven distinct lineages named after the region they were first reported in and based on S segment phylogenetic analysis.
Due to the high genetic divergence of the virus, a single targeted tiling PCR strategy to enrich for viral nucleic acids prior to sequencing is difficult to develop, and previously we have developed and validated a tiling PCR enrichment method for the Europe 1 genetic lineage.
We have developed a targeted, probe hybridisation capture method and validated its performance on clinical as well as cell-cultured material of CCHFV from different genetic lineages, including Europe 1, Europe 2, Africa 2 and Africa 3. The method produced over 95 % reference coverages with at least 10x sequencing depth. While we were only able to recover a single complete genome sequence from the tested Europe 1 clinical samples with the capture hybridisation protocol, the data provides evidence of its applicability to different CCHFV genetic lineages.
CCHFV is an important tick-borne human pathogen with wide geographical distribution. Environmental as well as anthropogenic factors are causing increased CCHFV transmission. Development of strategies to recover CCHFV sequences from genetically diverse lineages of the virus is of paramount importance to monitor the presence of the virus in new areas, and in public health responses for CCHFV molecular surveillance to rapidly detect, diagnose and characterise currently circulating strains.
{"title":"Development of targeted whole genome sequencing approaches for Crimean-Congo haemorrhagic fever virus (CCHFV)","authors":"Jake D'Addiego , Sonal Shah , Ayşe Nur Pektaş , Bi̇nnur Köksal Bağci , Murtaza Öz , Sasha Sebastianelli , Nazif Elaldı , David J Allen , Roger Hewson","doi":"10.1016/j.virusres.2024.199464","DOIUrl":"10.1016/j.virusres.2024.199464","url":null,"abstract":"<div><div>Crimean-Congo haemorrhagic fever (CCHF) is the most prevalent human tick-borne viral disease, with a reported case fatality rate of 30 % or higher. The virus contains a tri-segmented, negative-sense RNA genome consisting of the small (S), medium (M) and large (L) segments encoding respectively the nucleoprotein (NP), the glycoproteins precursor (GPC) and the viral RNA-dependent RNA polymerase (RDRP). CCHFV is one of the most genetically diverse arboviruses, with seven distinct lineages named after the region they were first reported in and based on S segment phylogenetic analysis.</div><div>Due to the high genetic divergence of the virus, a single targeted tiling PCR strategy to enrich for viral nucleic acids prior to sequencing is difficult to develop, and previously we have developed and validated a tiling PCR enrichment method for the Europe 1 genetic lineage.</div><div>We have developed a targeted, probe hybridisation capture method and validated its performance on clinical as well as cell-cultured material of CCHFV from different genetic lineages, including Europe 1, Europe 2, Africa 2 and Africa 3. The method produced over 95 % reference coverages with at least 10x sequencing depth. While we were only able to recover a single complete genome sequence from the tested Europe 1 clinical samples with the capture hybridisation protocol, the data provides evidence of its applicability to different CCHFV genetic lineages.</div><div>CCHFV is an important tick-borne human pathogen with wide geographical distribution. Environmental as well as anthropogenic factors are causing increased CCHFV transmission. Development of strategies to recover CCHFV sequences from genetically diverse lineages of the virus is of paramount importance to monitor the presence of the virus in new areas, and in public health responses for CCHFV molecular surveillance to rapidly detect, diagnose and characterise currently circulating strains.</div></div>","PeriodicalId":23483,"journal":{"name":"Virus research","volume":"350 ","pages":"Article 199464"},"PeriodicalIF":2.5,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0168170224001576/pdfft?md5=0befa523815397549149ae9521981693&pid=1-s2.0-S0168170224001576-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142296532","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 : 2024-09-18DOI: 10.1016/j.virusres.2024.199461
Jia-Hao Zheng , Zhi-Jian Zhou , Zheng-Chan Liao , Ye Qiu , Xing-Yi Ge , Xun Huang
Human parechovirus (HPeV) is a common virus that can cause severe infections in newborns. Due to the limited knowledge of the prevalence of HPeV in different cities in China and the unknown association between HPeV infection and clinical characteristics of newborns, this research investigated the epidemiological and clinical characteristics of HPeV infection in hospitalized neonates in Changsha. From August to October 2023, 145 anal swab samples from 96 newborns and 38 pharyngeal swab samples from 33 newborns in the neonatal intensive care unit (NICU) were collected. The prevalence of HPeV was detected by reverse transcription-polymerase chain reaction (RT-PCR). The genomes of HPeV were sequenced and the viral protein 1 (VP1) region was used for genotyping. Phylogenetic analysis and recombination analysis of HPeV genome were performed. Finally, HPeV was detected in 10 out of 44 patients in October, all of them were HPeV-1. The sequenced 4 genomes of HPeV showed high genetic diversity with known strains. Additionally, a HPeV-1 recombinant strain was detected. Compared with HPeV negative patients, HPeV patients had higher prevalence of abdominal pain and diarrhea, intracranial hemorrhage, and purulent meningitis. Compared with HPeV negative patients, HPeV patients had higher peripheral blood lymphocytes, albumin, globulin, pH and lower peripheral blood neutrophils and hemoglobin. HPeV is an important viral cause of newborn infections and appears to be increasing in prevalence in recent years. Characteristic clinical pictures exist in HPeV infections, and further research is needed to accumulate more cases to obtain a comprehensive understanding of HPeV infections.
{"title":"Prevalence and genetic diversity of Parechovirus","authors":"Jia-Hao Zheng , Zhi-Jian Zhou , Zheng-Chan Liao , Ye Qiu , Xing-Yi Ge , Xun Huang","doi":"10.1016/j.virusres.2024.199461","DOIUrl":"10.1016/j.virusres.2024.199461","url":null,"abstract":"<div><p>Human parechovirus (HPeV) is a common virus that can cause severe infections in newborns. Due to the limited knowledge of the prevalence of HPeV in different cities in China and the unknown association between HPeV infection and clinical characteristics of newborns, this research investigated the epidemiological and clinical characteristics of HPeV infection in hospitalized neonates in Changsha. From August to October 2023, 145 anal swab samples from 96 newborns and 38 pharyngeal swab samples from 33 newborns in the neonatal intensive care unit (NICU) were collected. The prevalence of HPeV was detected by reverse transcription-polymerase chain reaction (RT-PCR). The genomes of HPeV were sequenced and the viral protein 1 (VP1) region was used for genotyping. Phylogenetic analysis and recombination analysis of HPeV genome were performed. Finally, HPeV was detected in 10 out of 44 patients in October, all of them were HPeV-1. The sequenced 4 genomes of HPeV showed high genetic diversity with known strains. Additionally, a HPeV-1 recombinant strain was detected. Compared with HPeV negative patients, HPeV patients had higher prevalence of abdominal pain and diarrhea, intracranial hemorrhage, and purulent meningitis. Compared with HPeV negative patients, HPeV patients had higher peripheral blood lymphocytes, albumin, globulin, pH and lower peripheral blood neutrophils and hemoglobin. HPeV is an important viral cause of newborn infections and appears to be increasing in prevalence in recent years. Characteristic clinical pictures exist in HPeV infections, and further research is needed to accumulate more cases to obtain a comprehensive understanding of HPeV infections.</p></div>","PeriodicalId":23483,"journal":{"name":"Virus research","volume":"349 ","pages":"Article 199461"},"PeriodicalIF":2.5,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0168170224001540/pdfft?md5=b494f505e3990f48bb40a8798443ee6e&pid=1-s2.0-S0168170224001540-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142242284","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}
Respiratory syncytial virus (RSV) is the most predominant viral pathogen worldwide in children with lower respiratory tract infections. The coronavirus disease 2019 (COVID-19) pandemic and resulting non-pharmaceutical interventions perturbed the transmission pattern of respiratory pathogens in South Africa. A seasonality shift and RSV resurgence was observed in 2020 and 2021, with several infected children observed.
Conventional RSV-positive nasopharyngeal swabs were collected from various hospitals in the Free State province, Bloemfontein, South Africa, from children suffering from respiratory distress and severe acute respiratory infection between 2020 to 2021. Overlapping genome fragments were amplified and complete genomes were sequenced using the Illumina MiSeq platform. Maximum likelihood phylogenetic and evolutionary analysis were performed on both RSV-A/-B G-genes with published reference sequences from GISAID and GenBank. Our study strains belonged to the RSV-A GA2.3.2 and RSV-B GB5.0.5a clades. The upsurge of RSV was due to pre-existing strains that predominated in South Africa and circulating globally also driving these off-season RSV outbreaks during the COVID-19 pandemic. The variants responsible for the resurgence were phylogenetically related to pre-pandemic strains and could have contributed to the immune debt resulting from pandemic imposed restrictions. The deviation of the RSV season from the usual pattern affected by the COVID-19 pandemic highlights the need for ongoing genomic surveillance and the identification of genetic variants to prevent unforeseen outbreaks in the future.
{"title":"Corrigendum to “Whole genome molecular analysis of respiratory syncytial virus pre and during the COVID-19 pandemic in Free State province, South Africa” [Virus Research, Volume 347, September 2024, 199421]","authors":"Hlengiwe Sondlane , Ayodeji Ogunbayo , Celeste Donato , Milton Mogotsi , Mathew Esona , Ute Hallbauer , Phillip Bester , Dominique Goedhals , Martin Nyaga","doi":"10.1016/j.virusres.2024.199449","DOIUrl":"10.1016/j.virusres.2024.199449","url":null,"abstract":"<div><div>Respiratory syncytial virus (RSV) is the most predominant viral pathogen worldwide in children with lower respiratory tract infections. The coronavirus disease 2019 (COVID-19) pandemic and resulting non-pharmaceutical interventions perturbed the transmission pattern of respiratory pathogens in South Africa. A seasonality shift and RSV resurgence was observed in 2020 and 2021, with several infected children observed.</div><div>Conventional RSV-positive nasopharyngeal swabs were collected from various hospitals in the Free State province, Bloemfontein, South Africa, from children suffering from respiratory distress and severe acute respiratory infection between 2020 to 2021. Overlapping genome fragments were amplified and complete genomes were sequenced using the Illumina MiSeq platform. Maximum likelihood phylogenetic and evolutionary analysis were performed on both RSV-A/-B G-genes with published reference sequences from GISAID and GenBank. Our study strains belonged to the RSV-A GA2.3.2 and RSV-B GB5.0.5a clades. The upsurge of RSV was due to pre-existing strains that predominated in South Africa and circulating globally also driving these off-season RSV outbreaks during the COVID-19 pandemic. The variants responsible for the resurgence were phylogenetically related to pre-pandemic strains and could have contributed to the immune debt resulting from pandemic imposed restrictions. The deviation of the RSV season from the usual pattern affected by the COVID-19 pandemic highlights the need for ongoing genomic surveillance and the identification of genetic variants to prevent unforeseen outbreaks in the future.</div></div>","PeriodicalId":23483,"journal":{"name":"Virus research","volume":"349 ","pages":"Article 199449"},"PeriodicalIF":2.5,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0168170224001424/pdfft?md5=257099debe7b71b54f3e0e68a6b619f2&pid=1-s2.0-S0168170224001424-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142296531","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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