Pub Date : 2024-01-22DOI: 10.1007/s11262-023-02049-0
L. Ramachandran, S. P. Mangaiyarkarasi, A. Subramanian, S. Senthilkumar
The major dangerous viral infection for cultivated shrimps is WSSV. The virus is extremely dangerous, spreads swiftly, and may result in up to 100% mortality in 3–10 days. The vast wrapped double stranded DNA virus known as WSSV describes a member of the Nimaviridae viral family’s species Whispovirus. It impacts a variety of crustacean hosts but predominantly marine shrimp species that are raised for commercial purposes. The entire age groups are affected by the virus, which leads to widespread mortality. Mesodermal and ectodermal tissues, like the lymph nodes, gills, and cuticular epithelium, represents the centres of infection. Complete genome sequencing related to the WSSV strains from Thailand, China, and Taiwan has identified minute genetic variations amongst them. There exist conflicting findings on the causes of WSSV pathogenicity, which involve variations in the size associated with the genome, the count of tandem repeats, and the availability or lack of certain proteins. Hence, this paper plans to perform the shrimp classification for the WSSV on the basis of novel deep learning methodology. Initially, the data is gathered from the farms as well as internet sources. Next, the pre-processing of the gathered shrimp images is accomplished using the LBP technique. These pre-processed images undergo the segmentation process utilizing the TGVFCMS approach. The extraction of the features from these segmented images is performed by the PLDA technique. In the final step, the classification of the shrimp into healthy shrimp and WSSV affected shrimp is done by the EGRU, in which the parameter tuning is accomplished by the wild GMO algorithm with the consideration of accuracy maximization as the major objective function. Performance indicators for accuracy have been compared with those of various conventional methods, and the results show that the methodology is capable of accurately identifying the shrimp WSSV illness.
{"title":"Shrimp classification for white spot syndrome detection through enhanced gated recurrent unit-based wild geese migration optimization algorithm","authors":"L. Ramachandran, S. P. Mangaiyarkarasi, A. Subramanian, S. Senthilkumar","doi":"10.1007/s11262-023-02049-0","DOIUrl":"https://doi.org/10.1007/s11262-023-02049-0","url":null,"abstract":"<p>The major dangerous viral infection for cultivated shrimps is WSSV. The virus is extremely dangerous, spreads swiftly, and may result in up to 100% mortality in 3–10 days. The vast wrapped double stranded DNA virus known as WSSV describes a member of the Nimaviridae viral family’s species Whispovirus. It impacts a variety of crustacean hosts but predominantly marine shrimp species that are raised for commercial purposes. The entire age groups are affected by the virus, which leads to widespread mortality. Mesodermal and ectodermal tissues, like the lymph nodes, gills, and cuticular epithelium, represents the centres of infection. Complete genome sequencing related to the WSSV strains from Thailand, China, and Taiwan has identified minute genetic variations amongst them. There exist conflicting findings on the causes of WSSV pathogenicity, which involve variations in the size associated with the genome, the count of tandem repeats, and the availability or lack of certain proteins. Hence, this paper plans to perform the shrimp classification for the WSSV on the basis of novel deep learning methodology. Initially, the data is gathered from the farms as well as internet sources. Next, the pre-processing of the gathered shrimp images is accomplished using the LBP technique. These pre-processed images undergo the segmentation process utilizing the TGVFCMS approach. The extraction of the features from these segmented images is performed by the PLDA technique. In the final step, the classification of the shrimp into healthy shrimp and WSSV affected shrimp is done by the EGRU, in which the parameter tuning is accomplished by the wild GMO algorithm with the consideration of accuracy maximization as the major objective function. Performance indicators for accuracy have been compared with those of various conventional methods, and the results show that the methodology is capable of accurately identifying the shrimp WSSV illness.</p>","PeriodicalId":51212,"journal":{"name":"Virus Genes","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139518659","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}
During the Covid-19 pandemic, the resurgence of SARS-CoV-2 was due to the development of novel variants of concern (VOC). Thus, genomic surveillance is essential to monitor continuing evolution of SARS-CoV-2 and to track the emergence of novel variants. In this study, we performed phylogenetic, mutation, and selection pressure analyses of the Spike, nsp12, nsp3, and nsp5 genes of SARS-CoV-2 isolates circulating in Yogyakarta and Central Java provinces, Indonesia from May 2021 to February 2022. Various bioinformatics tools were employed to investigate the evolutionary dynamics of distinct SARS-CoV-2 isolates. During the study period, 213 and 139 isolates of Omicron and Delta variants were identified, respectively. Particularly in the Spike gene, mutations were significantly more abundant in Omicron than in Delta variants. Consistently, in all of four genes studied, the substitution rates of Omicron were higher than that of Delta variants, especially in the Spike and nsp12 genes. In addition, selective pressure analysis revealed several sites that were positively selected in particular genes, implying that these sites were functionally essential for virus evolution. In conclusion, our study demonstrated a distinct evolutionary pattern of SARS-CoV-2 variants circulating in Yogyakarta and Central Java provinces, Indonesia.
{"title":"Sequence analysis of the Spike, RNA-dependent RNA polymerase, and protease genes reveals a distinct evolutionary pattern of SARS-CoV-2 variants circulating in Yogyakarta and Central Java provinces, Indonesia","authors":"Mohamad Saifudin Hakim, Gunadi, Ayu Rahayu, Hendra Wibawa, Laudria Stella Eryvinka, Endah Supriyati, Khanza Adzkia Vujira, Kristy Iskandar, Afiahayati, Edwin Widyanto Daniwijaya, Farida Nur Oktoviani, Luthvia Annisa, Fadila Dyah Trie Utami, Verrell Christopher Amadeus, Setiani Silvy Nurhidayah, Tiara Putri Leksono, Fiqih Vidiantoro Halim, Eggi Arguni, Titik Nuryastuti, Tri Wibawa","doi":"10.1007/s11262-023-02048-1","DOIUrl":"https://doi.org/10.1007/s11262-023-02048-1","url":null,"abstract":"<p>During the Covid-19 pandemic, the resurgence of SARS-CoV-2 was due to the development of novel variants of concern (VOC). Thus, genomic surveillance is essential to monitor continuing evolution of SARS-CoV-2 and to track the emergence of novel variants. In this study, we performed phylogenetic, mutation, and selection pressure analyses of the <i>Spike, nsp12, nsp3,</i> and <i>nsp5</i> genes of SARS-CoV-2 isolates circulating in Yogyakarta and Central Java provinces, Indonesia from May 2021 to February 2022. Various bioinformatics tools were employed to investigate the evolutionary dynamics of distinct SARS-CoV-2 isolates. During the study period, 213 and 139 isolates of Omicron and Delta variants were identified, respectively. Particularly in the <i>Spike</i> gene, mutations were significantly more abundant in Omicron than in Delta variants. Consistently, in all of four genes studied, the substitution rates of Omicron were higher than that of Delta variants, especially in the <i>Spike</i> and <i>nsp12</i> genes. In addition, selective pressure analysis revealed several sites that were positively selected in particular genes, implying that these sites were functionally essential for virus evolution. In conclusion, our study demonstrated a distinct evolutionary pattern of SARS-CoV-2 variants circulating in Yogyakarta and Central Java provinces, Indonesia.</p>","PeriodicalId":51212,"journal":{"name":"Virus Genes","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2024-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139510028","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 : 2023-12-30DOI: 10.1007/s11262-023-02043-6
Tobias Lutz, Gitta Jutta Langer, Cornelia Heinze
From the ascomycete Aspergillus cibarius strain NW-FVA 2590, which was originally isolated from a root, associated with stem collar necrosis of Fraxinus excelsior L., a novel virus was isolated and characterized. Its genome is encoded on three monocistronic dsRNA segments ranging from 3683 bp (dsRNA 1) over 3093 (dsRNA 2) to 2902 bp (dsRNA 3), which are packed in isometric particles of around 35 nm. While the viral RdRp (P1) is encoded on segment 1, protein sequencing showed that two more structural proteins are present which are translated from dsRNA 2 (P2) and dsRNA 3 (P3) and possibly form the viral capsid. Additionally, P2 and P3 may undergo posttranslational modifications since the detected proteins bands deviated from the calculated sizes. Due to its phylogenetic position, the novel virus was grouped in the family of Chrysoviridae and was tentatively denominated as Aspergillus cibarius chrysovirus 1 (AcCV1). Due to its composition, biological properties and phylogenetic position, distant from the genera Alphachrysovirus and Betachrysovirus, we suggest to position AcCV1 in a proposed genus “Gammachrysovirus”.
{"title":"A virus from Aspergillus cibarius with features of alpha- and betachrysoviruses","authors":"Tobias Lutz, Gitta Jutta Langer, Cornelia Heinze","doi":"10.1007/s11262-023-02043-6","DOIUrl":"https://doi.org/10.1007/s11262-023-02043-6","url":null,"abstract":"<p>From the ascomycete <i>Aspergillus cibarius</i> strain NW-FVA 2590, which was originally isolated from a root, associated with stem collar necrosis of <i>Fraxinus excelsior</i> L., a novel virus was isolated and characterized. Its genome is encoded on three monocistronic dsRNA segments ranging from 3683 bp (dsRNA 1) over 3093 (dsRNA 2) to 2902 bp (dsRNA 3), which are packed in isometric particles of around 35 nm. While the viral RdRp (P1) is encoded on segment 1, protein sequencing showed that two more structural proteins are present which are translated from dsRNA 2 (P2) and dsRNA 3 (P3) and possibly form the viral capsid. Additionally, P2 and P3 may undergo posttranslational modifications since the detected proteins bands deviated from the calculated sizes. Due to its phylogenetic position, the novel virus was grouped in the family of <i>Chrysoviridae</i> and was tentatively denominated as Aspergillus cibarius chrysovirus 1 (AcCV1). Due to its composition, biological properties and phylogenetic position, distant from the genera <i>Alphachrysovirus</i> and <i>Betachrysovirus</i>, we suggest to position AcCV1 in a proposed genus “<i>Gammachrysovirus</i>”<i>.</i></p>","PeriodicalId":51212,"journal":{"name":"Virus Genes","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2023-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139068934","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 : 2023-12-16DOI: 10.1007/s11262-023-02041-8
Sıla Erkmen, Ergin Sahin, Ilgaz Akata
Members of the genus Armillaria belong to the group of pathogenic and facultative saprotrophic fungi that are generally known as one of the causative agents of white root rot in infected plants including deciduous and evergreen trees and shrubs. Although several single-stranded RNA mycoviruses were previously described in different Armillaria species, there is no report on mitoviruses (one of the simplest RNA viruses of fungal hosts) known to infect Armillaria taxa. In this study, a new mitovirus denominated “Armillaria mellea mitovirus 1” (AmMV1) was identified in the sporophore samples of Armillaria mellea, commonly known as honey mushroom. AmMV1 has a genome length of 4440 nucleotides and a G + C content of 48%. It encompasses a single open reading frame (ORF) that encodes an RNA-dependent RNA polymerase (RdRp). Comparison through BLASTp analysis revealed that the RdRp domain of AmMV1 shares a sequence identity ranging from 33.43% to 43.27% with RdRp domains of Duamitovirus genus members, having the highest similarity (43.27%) to Rhizoctonia solani mitovirus 94. According to phylogenetic analysis, AmMV1 is classified as a member of the genus Duamitovirus belonging to the Mitoviridae family. This marks the initial instance of a mitovirus identified in Armillaria spp..
{"title":"Full-length genome characterization of a novel mitovirus isolated from the root rot fungus Armillaria mellea","authors":"Sıla Erkmen, Ergin Sahin, Ilgaz Akata","doi":"10.1007/s11262-023-02041-8","DOIUrl":"https://doi.org/10.1007/s11262-023-02041-8","url":null,"abstract":"<p>Members of the genus <i>Armillaria</i> belong to the group of pathogenic and facultative saprotrophic fungi that are generally known as one of the causative agents of white root rot in infected plants including deciduous and evergreen trees and shrubs. Although several single-stranded RNA mycoviruses were previously described in different <i>Armillaria</i> species, there is no report on mitoviruses (one of the simplest RNA viruses of fungal hosts) known to infect <i>Armillaria</i> taxa. In this study, a new mitovirus denominated “Armillaria mellea mitovirus 1” (AmMV1) was identified in the sporophore samples of <i>Armillaria mellea</i>, commonly known as honey mushroom. AmMV1 has a genome length of 4440 nucleotides and a G + C content of 48%. It encompasses a single open reading frame (ORF) that encodes an RNA-dependent RNA polymerase (RdRp). Comparison through BLASTp analysis revealed that the RdRp domain of AmMV1 shares a sequence identity ranging from 33.43% to 43.27% with RdRp domains of <i>Duamitovirus</i> genus members, having the highest similarity (43.27%) to Rhizoctonia solani mitovirus 94. According to phylogenetic analysis, AmMV1 is classified as a member of the genus <i>Duamitovirus</i> belonging to the <i>Mitoviridae</i> family. This marks the initial instance of a mitovirus identified in <i>Armillaria</i> spp..</p>","PeriodicalId":51212,"journal":{"name":"Virus Genes","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2023-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138690891","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}
Rotavirus A infects many mammalian species, including humans and causes diarrhea and gastrointestinal diseases. The virus also infects various bird species, including chickens, although information of avian rotavirus A (ARVA) infection in chicken populations in Japan is scarce. In this study, we report for the first time the whole-genome sequences of ARVA strains from Japanese chicken populations. The virus strains were inoculated to MA104 cells and cultured viruses were used to obtain the sequences with the MiSeq system, and genetic analysis demonstrated the genotype constellation of G19-P[30]-I11-R6-C6-M7-A16-N6-T8-E10-H8 of the Japanese chicken ARVA isolates. Phylogenetic analyses demonstrated that the VP1, VP2, VP3, VP4, VP7, NSP2, and NSP4 coding gene sequences of the Japanese strains were closer to those of Korean than the European ARVA strains, although such relationship was not clear for other genes. The data suggest that the Japanese ARVA strains and the ones in Korea have genetically close relationship, although the origin is not clear at this point. Further information including the whole-genome sequences of the Korean strains and sequences of other Japanese chicken ARVA strains will be necessary for elucidation of their origin.
{"title":"First report of the whole-genome sequence analysis of avian rotavirus A from Japanese chickens","authors":"Ayana Okamoto, Hitoshi Takemae, Makoto Nagai, Shinichiro Hashimoto, Tetsuya Mizutani, Tetsuya Furuya","doi":"10.1007/s11262-023-02040-9","DOIUrl":"https://doi.org/10.1007/s11262-023-02040-9","url":null,"abstract":"<p>Rotavirus A infects many mammalian species, including humans and causes diarrhea and gastrointestinal diseases. The virus also infects various bird species, including chickens, although information of avian rotavirus A (ARVA) infection in chicken populations in Japan is scarce. In this study, we report for the first time the whole-genome sequences of ARVA strains from Japanese chicken populations. The virus strains were inoculated to MA104 cells and cultured viruses were used to obtain the sequences with the MiSeq system, and genetic analysis demonstrated the genotype constellation of G19-P[30]-I11-R6-C6-M7-A16-N6-T8-E10-H8 of the Japanese chicken ARVA isolates. Phylogenetic analyses demonstrated that the VP1, VP2, VP3, VP4, VP7, NSP2, and NSP4 coding gene sequences of the Japanese strains were closer to those of Korean than the European ARVA strains, although such relationship was not clear for other genes. The data suggest that the Japanese ARVA strains and the ones in Korea have genetically close relationship, although the origin is not clear at this point. Further information including the whole-genome sequences of the Korean strains and sequences of other Japanese chicken ARVA strains will be necessary for elucidation of their origin.</p>","PeriodicalId":51212,"journal":{"name":"Virus Genes","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2023-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138690894","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 : 2023-12-01Epub Date: 2023-09-20DOI: 10.1007/s11262-023-02031-w
Lu Yang, Di Zhou, Kächele Martin, Jun Wu, Mingfa Chen, Mengji Lu, Dongliang Yang, Ulrike Protzer, Michael Roggendorf, Jingjiao Song
Due to the limited host range of HBV, research progress has been hindered by the absence of a suitable animal model. The natural history of woodchuck hepatitis virus (WHV) infection in woodchuck closely mirrors that of HBV infection in human, making this species a promising candidate for establishing both in vivo and in vitro HBV infection models. Therefore, this animal may be a valuable species to evaluate HBV vaccines and anti-HBV drugs. A significant milestone in HBV and hepatitis D virus (HDV) infection is the discovery of sodium taurocholate cotransporting polypeptide (NTCP) as the functional receptor. In an effort to enhance susceptibility to HBV infection, we introduced hNTCP into the woodchuck hepatocytes by multiple approaches including transduction of vLentivirus-hNTCP in woodchuck hepatocytes, transfection of p-lentivirus-hNTCP-eGFP plasmids into these cells, as well as transduction of vAdenovirus-hNTCP-eGFP. Encouragingly, our findings demonstrated the successful introduction of hNTCP into woodchuck hepatocytes. However, it was observed that these hNTCP-expressing hepatocytes were only susceptible to HDV infection but not HBV. This suggests the presence of additional crucial factors mediating early-stage HBV infection that are subject to stringent species-specific restrictions.
{"title":"Aborted infection of human sodium taurocholate cotransporting polypeptide (hNTCP) expressing woodchuck hepatocytes with hepatitis B virus (HBV).","authors":"Lu Yang, Di Zhou, Kächele Martin, Jun Wu, Mingfa Chen, Mengji Lu, Dongliang Yang, Ulrike Protzer, Michael Roggendorf, Jingjiao Song","doi":"10.1007/s11262-023-02031-w","DOIUrl":"10.1007/s11262-023-02031-w","url":null,"abstract":"<p><p>Due to the limited host range of HBV, research progress has been hindered by the absence of a suitable animal model. The natural history of woodchuck hepatitis virus (WHV) infection in woodchuck closely mirrors that of HBV infection in human, making this species a promising candidate for establishing both in vivo and in vitro HBV infection models. Therefore, this animal may be a valuable species to evaluate HBV vaccines and anti-HBV drugs. A significant milestone in HBV and hepatitis D virus (HDV) infection is the discovery of sodium taurocholate cotransporting polypeptide (NTCP) as the functional receptor. In an effort to enhance susceptibility to HBV infection, we introduced hNTCP into the woodchuck hepatocytes by multiple approaches including transduction of vLentivirus-hNTCP in woodchuck hepatocytes, transfection of p-lentivirus-hNTCP-eGFP plasmids into these cells, as well as transduction of vAdenovirus-hNTCP-eGFP. Encouragingly, our findings demonstrated the successful introduction of hNTCP into woodchuck hepatocytes. However, it was observed that these hNTCP-expressing hepatocytes were only susceptible to HDV infection but not HBV. This suggests the presence of additional crucial factors mediating early-stage HBV infection that are subject to stringent species-specific restrictions.</p>","PeriodicalId":51212,"journal":{"name":"Virus Genes","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41158880","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 : 2023-12-01Epub Date: 2023-08-17DOI: 10.1007/s11262-023-02024-9
Nikola Sklenovská, Mandy Bloemen, Valentijn Vergote, Anne-Sophie Logist, Bert Vanmechelen, Lies Laenen, Emmanuel André, Jean-Jacques Muyembe-Tamfum, Elke Wollants, Marc Van Ranst, Piet Maes, Tony Wawina-Bokalanga
Mpox is a viral zoonosis with endemic circulation in animals and humans in some West and Central African countries. The disease was imported a few times in the past to countries outside the African continent through infected animals or travelers, one of which resulted in an unprecedented global outbreak sustained by human-to-human transmission in 2022. Although timely and reliable diagnosis is a cornerstone of any disease control, availability of accurate diagnostic assays and comparative performance studies of diagnostic assays remains limited despite of the long-known identification of monkeypox virus (MPXV) as a human pathogen since 1970. We laboratory-developed a real-time PCR test (LDT) and evaluated its performance against the commercial TaqMan™ Monkeypox Virus Microbe Detection Assay (Applied Biosystems, Cat A50137). The limit of detection of the LDT was established at 1.2 genome copies/ml. The sensitivity and specificity of both assays were 99.14% and 100%, respectively, and both are capable of detecting both clade I and clade II of MPXV. Our results demonstrate the validity and accuracy of the LDT for confirmation of MPXV infection from lesion swabs samples.
{"title":"Design and validation of a laboratory-developed diagnostic assay for monkeypox virus.","authors":"Nikola Sklenovská, Mandy Bloemen, Valentijn Vergote, Anne-Sophie Logist, Bert Vanmechelen, Lies Laenen, Emmanuel André, Jean-Jacques Muyembe-Tamfum, Elke Wollants, Marc Van Ranst, Piet Maes, Tony Wawina-Bokalanga","doi":"10.1007/s11262-023-02024-9","DOIUrl":"10.1007/s11262-023-02024-9","url":null,"abstract":"<p><p>Mpox is a viral zoonosis with endemic circulation in animals and humans in some West and Central African countries. The disease was imported a few times in the past to countries outside the African continent through infected animals or travelers, one of which resulted in an unprecedented global outbreak sustained by human-to-human transmission in 2022. Although timely and reliable diagnosis is a cornerstone of any disease control, availability of accurate diagnostic assays and comparative performance studies of diagnostic assays remains limited despite of the long-known identification of monkeypox virus (MPXV) as a human pathogen since 1970. We laboratory-developed a real-time PCR test (LDT) and evaluated its performance against the commercial TaqMan™ Monkeypox Virus Microbe Detection Assay (Applied Biosystems, Cat A50137). The limit of detection of the LDT was established at 1.2 genome copies/ml. The sensitivity and specificity of both assays were 99.14% and 100%, respectively, and both are capable of detecting both clade I and clade II of MPXV. Our results demonstrate the validity and accuracy of the LDT for confirmation of MPXV infection from lesion swabs samples.</p>","PeriodicalId":51212,"journal":{"name":"Virus Genes","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10667130/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10005544","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 : 2023-12-01Epub Date: 2023-09-04DOI: 10.1007/s11262-023-02027-6
Mária Neoralová, Sára Brázdová, Aleš Eichmeier, Karel Petrzik
The newly discovered Xanthomonas phage M29 (Xp M29) is the first lytic phage infecting Xanthomonas campestris pv. campestris (Xcc) that was isolated from cabbage leaves in the Czech Republic. The phage consists of icosahedral head approximately 60 nm in diameter and a probably contractile tail of 170 nm. The complete genome size was 42 891 bp, with a G + C content of 59.6%, and 69 ORFs were predicted on both strands. Pairwise nucleotide comparison showed the highest similarity with the recently described Xanthomonas phage FoX3 (91.2%). Bacteriophage Xp M29 has a narrow host range infecting 5 out of 21 isolates of Xcc. Xp M29 is a novel species in a newly formed genus Foxunavirus assigned directly to the class Caudoviricetes.
新发现的黄单胞菌噬菌体M29 (Xanthomonas phage M29, Xp M29)是第一个感染油菜黄单胞菌的裂解噬菌体。从捷克共和国的卷心菜叶子中分离出的campestris (Xcc)。噬菌体由直径约60纳米的二十面体头部和直径约170纳米的可收缩尾部组成。全基因组大小为42 891 bp, G + C含量为59.6%,两条链上预测有69个orf。两两核苷酸比对显示,该菌株与最近报道的黄单胞菌噬菌体FoX3相似度最高(91.2%)。噬菌体Xp M29具有狭窄的宿主范围,感染21株Xcc中的5株。Xp M29是新形成的Foxunavirus属中的一个新种,直接归属于尾状病毒纲。
{"title":"Complete genome sequence of Xanthomonas phage M29, a new member of Foxunavirus isolated in the Czech Republic.","authors":"Mária Neoralová, Sára Brázdová, Aleš Eichmeier, Karel Petrzik","doi":"10.1007/s11262-023-02027-6","DOIUrl":"10.1007/s11262-023-02027-6","url":null,"abstract":"<p><p>The newly discovered Xanthomonas phage M29 (Xp M29) is the first lytic phage infecting Xanthomonas campestris pv. campestris (Xcc) that was isolated from cabbage leaves in the Czech Republic. The phage consists of icosahedral head approximately 60 nm in diameter and a probably contractile tail of 170 nm. The complete genome size was 42 891 bp, with a G + C content of 59.6%, and 69 ORFs were predicted on both strands. Pairwise nucleotide comparison showed the highest similarity with the recently described Xanthomonas phage FoX3 (91.2%). Bacteriophage Xp M29 has a narrow host range infecting 5 out of 21 isolates of Xcc. Xp M29 is a novel species in a newly formed genus Foxunavirus assigned directly to the class Caudoviricetes.</p>","PeriodicalId":51212,"journal":{"name":"Virus Genes","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10507771","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 : 2023-12-01Epub Date: 2023-10-05DOI: 10.1007/s11262-023-02030-x
Helena Beatriz de Carvalho Ruthner Batista, Luiz Fernando Pereira Vieira, Juliana Galera Castilho Kawai, Willian de Oliveira Fahl, Camila Mosca Barboza, Samira Achkar, Rafael de Novaes Oliveira, Paulo Eduardo Brandão, Pedro Carnieli Junior
Rabies is worldwide zoonosis caused by Lyssavirus rabies (RABV) a RNA negative sense virus with low level of fidelity during replication cycle. Nucleoprotein of RABV is the most conserved between all five proteins of the virus and is the most used gene for phylogenetic and phylogeographic studies. Despite of rabies been very important in Public Health concern, it demands continuous prophylactic care for herbivores with economic interest, such as cattle and horses. The main transmitter of RABV for these animals in Brazil is the hematophagous bats Desmodus rotundus. The aim of this study was to determine the dispersion over time and space of RABV transmitted by D. rotundus. Samples of RABV from the State of São Paulo (SP), Southeast Brazil isolated from the central nervous system (CNS) of cattle, were submitted to RNA extraction, RT-PCR, sequencing and phylogeographic analyzes with BEAST (Bayesian Evolutionary Analysis Sampling Trees) v 2.5 software. Was possible to identify high rate of diversification in starts sublineages of RABV what are correlated with a behavior of D. rotundus, the main transmitter of rabies to cattle. This study also highlights the importance of continuous monitoring of genetic lineages of RABV in Brazil.
{"title":"Dispersion and diversification of Lyssavirus rabies transmitted from haematophagous bats Desmodus rotundus: a phylogeographical study.","authors":"Helena Beatriz de Carvalho Ruthner Batista, Luiz Fernando Pereira Vieira, Juliana Galera Castilho Kawai, Willian de Oliveira Fahl, Camila Mosca Barboza, Samira Achkar, Rafael de Novaes Oliveira, Paulo Eduardo Brandão, Pedro Carnieli Junior","doi":"10.1007/s11262-023-02030-x","DOIUrl":"10.1007/s11262-023-02030-x","url":null,"abstract":"<p><p>Rabies is worldwide zoonosis caused by Lyssavirus rabies (RABV) a RNA negative sense virus with low level of fidelity during replication cycle. Nucleoprotein of RABV is the most conserved between all five proteins of the virus and is the most used gene for phylogenetic and phylogeographic studies. Despite of rabies been very important in Public Health concern, it demands continuous prophylactic care for herbivores with economic interest, such as cattle and horses. The main transmitter of RABV for these animals in Brazil is the hematophagous bats Desmodus rotundus. The aim of this study was to determine the dispersion over time and space of RABV transmitted by D. rotundus. Samples of RABV from the State of São Paulo (SP), Southeast Brazil isolated from the central nervous system (CNS) of cattle, were submitted to RNA extraction, RT-PCR, sequencing and phylogeographic analyzes with BEAST (Bayesian Evolutionary Analysis Sampling Trees) v 2.5 software. Was possible to identify high rate of diversification in starts sublineages of RABV what are correlated with a behavior of D. rotundus, the main transmitter of rabies to cattle. This study also highlights the importance of continuous monitoring of genetic lineages of RABV in Brazil.</p>","PeriodicalId":51212,"journal":{"name":"Virus Genes","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41151968","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 : 2023-12-01Epub Date: 2023-10-19DOI: 10.1007/s11262-023-02033-8
Guangye Zhang, Yucong Liu, Jinhong Wang, Nan Li, Pengjun Han, Yiming Chen, Weijian Xu, Changxia Liu
Bacteriophages are a type of virus widely distributed in nature that demonstrates a remarkable aptitude for selectively recognizing and infecting bacteria. In particular, Klebsiella pneumoniae is acknowledged as a clinical pathogen responsible for nosocomial infections and frequently develops multidrug resistance. Considering the increasing prevalence of antibiotic-resistant bacteria, bacteriophages have emerged as a compelling alternative therapeutic approach. In this study, a novel phage named BUCT_49532 was isolated from sewage using K. pneumoniae K1119 as the host. Electron microscopy revealed that BUCT_49532 belongs to the Caudoviricetes class. Further analysis through whole genome sequencing demonstrated that BUCT_49532 is a Jedunavirus comprised of linear double-stranded DNA with a length of 49,532 bp. Comparative genomics analysis based on average nucleotide identity (ANI) values revealed that BUCT_49532 should be identified as a novel species. Characterized by a good safety profile, high environmental stability, and strong lytic performance, phage BUCT_49532 presents an interesting case for consideration. Although its host range is relatively narrow, its application potential can be expanded by utilizing phage cocktails, making it a promising candidate for biocontrol approaches.
{"title":"Characterization and genomic analysis of a novel bacteriophage BUCT_49532 lysing Klebsiella pneumoniae.","authors":"Guangye Zhang, Yucong Liu, Jinhong Wang, Nan Li, Pengjun Han, Yiming Chen, Weijian Xu, Changxia Liu","doi":"10.1007/s11262-023-02033-8","DOIUrl":"10.1007/s11262-023-02033-8","url":null,"abstract":"<p><p>Bacteriophages are a type of virus widely distributed in nature that demonstrates a remarkable aptitude for selectively recognizing and infecting bacteria. In particular, Klebsiella pneumoniae is acknowledged as a clinical pathogen responsible for nosocomial infections and frequently develops multidrug resistance. Considering the increasing prevalence of antibiotic-resistant bacteria, bacteriophages have emerged as a compelling alternative therapeutic approach. In this study, a novel phage named BUCT_49532 was isolated from sewage using K. pneumoniae K1119 as the host. Electron microscopy revealed that BUCT_49532 belongs to the Caudoviricetes class. Further analysis through whole genome sequencing demonstrated that BUCT_49532 is a Jedunavirus comprised of linear double-stranded DNA with a length of 49,532 bp. Comparative genomics analysis based on average nucleotide identity (ANI) values revealed that BUCT_49532 should be identified as a novel species. Characterized by a good safety profile, high environmental stability, and strong lytic performance, phage BUCT_49532 presents an interesting case for consideration. Although its host range is relatively narrow, its application potential can be expanded by utilizing phage cocktails, making it a promising candidate for biocontrol approaches.</p>","PeriodicalId":51212,"journal":{"name":"Virus Genes","volume":null,"pages":null},"PeriodicalIF":1.6,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49684807","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}