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Fall A, Campodónico VL, Howard C, Gallagher N, Bailey G, Kajon AE, Mostafa HH. Dissemination and genome characterization of a human adenovirus F41 in a patient with B-Cell lymphoma. Virol J 2023; 20:141. [PMID: 37415207 PMCID: PMC10327306 DOI: 10.1186/s12985-023-02101-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 06/13/2023] [Indexed: 07/08/2023] Open
Abstract
Adenovirus (HAdV) F41 is a common cause of gastroenteritis and has rarely been reported associated with disseminated disease. In this report, an adult patient with a history of ulcerative colitis, cryptogenic cirrhosis, stage III adenocarcinoma, high-grade diffuse large B-cell lymphoma on chemotherapy was diagnosed with disseminated adenovirus infection. HAdV DNA was quantified in stool, plasma, and urine with viral loads of 7, 4, and 3 log10 copies/mL, respectively. The patient's course was rapidly progressive and he passed away 2 days after initiation of antiviral therapy. The patient's infecting virus was characterized as HAdV-F41 by whole genome sequencing.
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Affiliation(s)
- Amary Fall
- Hopkins Medicine, Department of Pathology, Medical Microbiology, Baltimore, MD, USA
| | | | - Craig Howard
- Department of Pathology, Medical Microbiology, Johns Hopkins Hospital, Baltimore, MD, USA
| | - Nicholas Gallagher
- Hopkins Medicine, Department of Pathology, Medical Microbiology, Baltimore, MD, USA
| | - Gabrielle Bailey
- Hopkins Medicine, Department of Pathology, Medical Microbiology, Baltimore, MD, USA
| | - Adriana E Kajon
- Lovelace Biomedical Research Institute, Albuquerque, NM, USA
| | - Heba H Mostafa
- Hopkins Medicine, Department of Pathology, Medical Microbiology, Baltimore, MD, USA.
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2
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Fukuda D, Aso Y, Nolasco-Hipólito C. Genome and fermentation analyses of Enterococcus faecalis DB-5 isolated from Japanese Mandarin orange: An assessment of potential application in lactic acid production. J Biosci Bioeng 2023:S1389-1723(23)00114-7. [PMID: 37221113 DOI: 10.1016/j.jbiosc.2023.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 04/02/2023] [Accepted: 04/16/2023] [Indexed: 05/25/2023]
Abstract
Enterococcus faecalis strain DB-5 is a lactic acid bacterium newly isolated from the Japanese mandarin orange (mikan). The DB-5 strain produces organic acid from various carbohydrate sources including glycerol and starch. To gain deeper insights into its potential application in lactic acid fermentation (LAF), the genome and fermentation analyses of E. faecalis DB-5 were performed. Whole genome sequencing was carried out using the DNBSEQ platform. After trimming and assembly, the total size of the assembled genome was revealed to be 3,048,630 bp, distributed into 63 contigs with an N50 value of 203,673. The genome has 37.2% GC content, 2928 coding DNA sequences, and 54 putative RNA genes. The DB-5 strain harbored two l-lactate dehydrogenases (L-LDHs), both of which conserved the catalytic domain sequences. The optical purity measurement showed that strain DB-5 is homofermentative and produced only l-lactic acid (LA), which correlated with genome-based pathway analysis. To confirm its LA productivity at high temperatures, open repeated batch fermentation was performed at 45 °C using sucrose as a carbon source. The volumetric LA productivity of DB-5 was averaged at 3.66 g L-1 h-1 for 24 h during the 3rd to 11th fermentation cycles. E. faecalis DB-5 could efficiently convert around 94% of sucrose to LA throughout the fermentation cycles at 45 °C. These genomic characteristics and fermentation properties of E. faecalis DB-5 provide beneficial information for a deeper understanding of the functional properties of future high-temperature LAFs from biomass resources.
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Affiliation(s)
- Daisuke Fukuda
- Medical Affairs and Development, GlaxoSmithKline K.K., 1-8-1 Akasaka, Minato-ku, Tokyo 107-0052, Japan.
| | - Yuji Aso
- Department of Biobased Materials Science, Kyoto Institute of Technology, 1 Hachigami-cho, Sakyo-ku, Kyoto 606-8585, Japan.
| | - Cirilo Nolasco-Hipólito
- Centro de Investigaciones Científicas, Universidad Del Papaloapan Campus Tuxtepec, Circuito Central Nº 200, Col. Parque Industrial, C.P. 68301, Tuxtepec, Oaxaca, Mexico.
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3
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Singh AK, Gupta RK, Purohit HJ, Khardenavis AA. Genomic characterization of denitrifying methylotrophic Pseudomonas aeruginosa strain AAK/M5 isolated from municipal solid waste landfill soil. World J Microbiol Biotechnol 2022; 38:140. [PMID: 35705700 DOI: 10.1007/s11274-022-03311-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 05/15/2022] [Indexed: 11/26/2022]
Abstract
Municipal landfills are known for methane production and a source of nitrate pollution leading to various environmental issues. Therefore, this niche was selected for the isolation of one-carbon (C1) utilizing bacteria with denitrifying capacities using anaerobic enrichment on nitrate mineral salt medium supplemented with methanol as carbon source. Eight axenic cultures were isolated of which, isolate AAK/M5 demonstrated the highest methanol removal (73.28%) in terms of soluble chemical oxygen demand and methane removal (41.27%) at the expense of total nitrate removal of 100% and 33% respectively. The whole genome characterization with phylogenomic approach suggested that the strain AAK/M5 could be assigned to Pseudomonas aeruginosa with close neighbours as type strains DVT779, AES1M, W60856, and LES400. The circular genome annotation showed the presence of complete set of genes essential for methanol utilization and complete denitrification process. The study demonstrates the potential of P. aeruginosa strain AAK/M5 in catalysing methane oxidation thus serving as a methane sink vis-à-vis utilization of nitrate. Considering the existence of such bacteria at landfill site, the study highlights the need to develop strategies for their enrichment and designing of efficient catabolic activity for such environments.
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Affiliation(s)
- Ashish Kumar Singh
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, Maharashtra, 440020, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Rakesh Kumar Gupta
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, Maharashtra, 440020, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Hemant J Purohit
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, Maharashtra, 440020, India
| | - Anshuman Arun Khardenavis
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, Maharashtra, 440020, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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4
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Jha V, Purohit H, Dafale NA. Revealing the potential of Klebsiella pneumoniae PVN-1 for plant beneficial attributes by genome sequencing and analysis. 3 Biotech 2021; 11:473. [PMID: 34777930 DOI: 10.1007/s13205-021-03020-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 10/05/2021] [Indexed: 12/28/2022] Open
Abstract
Genome sequencing of Klebsiella pneumoniae PVN-1, isolated from effluent treatment plant (ETP), generates a 5.064 Mb draft genome with 57.6% GC content. The draft genome assembled into 19 contigs comprises 4783 proteins, 3 rRNA, 44 tRNA, 8 other RNA, 4911 genes, and 73 pseudogenes. Genome information revealed the presence of phosphate metabolism/solubilizing, potassium solubilizing, auxin production, and other plant benefiting attributes like enterobactin and pyrroloquinoline quinone biosynthesis genes. Presence of gcd and pqq genes in K. pneumoniae PVN-1 genome validates the inorganic phosphate solubilizing potential (528.5 mg/L). Pangenome analysis identified a unique 5'-Nucleotidase that further assists in enhanced phosphate acquisition. Additionally, the genetic potential for complete benzoate, catechol, and phenylacetate degradation with stress response and heavy metal (Cu, Zn, Ni, Co) resistance was identified in K. pneumoniae PVN-1. Functioning of annotated plant benefiting genes validates by the metabolic activity of auxin production (7.40 µg/mL), nitrogen fixation, catalase activity, potassium solubilization (solubilization index-3.47), and protease activity (proteolytic index-2.27). In conclusion, the K. pneumoniae PVN-1 genome has numerous beneficial qualities that can be employed to enhance plant growth as well as for phytoremediation. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-03020-2.
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Jha V, Dafale NA, Hathi Z, Purohit H. Genomic and functional potential of the immobilized microbial consortium MCSt-1 for wastewater treatment. Sci Total Environ 2021; 777:146110. [PMID: 33684742 DOI: 10.1016/j.scitotenv.2021.146110] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 06/12/2023]
Abstract
Treatment of wastewater prior to release in water bodies is an imperative need of the current time to address the global water crises. Thus, consortium MCSt-1 was designed for an effective wastewater treatment based on its cellulolytic, proteolytic, lipolytic, phenol and sodium dodecyl sulfate degrading activities along with effective nutrient removal capacity. Performance of the designed consortium was assayed using two differently configured lab-scale bioreactors as subjected to immobilization on two different matrices (pebbles and nylon mesh). Consortium MCSt-1 proficiently removes soluble chemical oxygen demand, nitrate, ammonia and phosphorus with 83%, 67%, 76%, and 62% removal efficiency, respectively. The immobilization on a mesh is recommended as it exhibited better biofilm formation, hence results in significant organic load and nutrient removal. The functional potential of the consortium MCSt-1 explored through genome characterization and reveal the presence of genes responsible for phosphorus metabolism and removal (pst operon and ppk), ammonia assimilation (amt), and nitrate; nitrite reductase (nar, nir, nor). Additionally, consortium members also annotated with the phenol, catechol and benzoate degradation, stress response, heavy metal and antibiotics resistance genes. Hence, the designed consortium MCSt-1 can withstand the harsh condition of treatment plants and serves as the best solution for enhancing wastewater treatment efficiency.
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Affiliation(s)
- Varsha Jha
- Environmental Biotechnology and Genomics Division, CSIR - National Environmental Engineering Research Institute (NEERI), Nagpur 440020, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Nishant A Dafale
- Environmental Biotechnology and Genomics Division, CSIR - National Environmental Engineering Research Institute (NEERI), Nagpur 440020, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
| | - Zubeen Hathi
- City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong Special Administrative Region
| | - Hemant Purohit
- Environmental Biotechnology and Genomics Division, CSIR - National Environmental Engineering Research Institute (NEERI), Nagpur 440020, India
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Boene SS, João ED, Strydom A, Munlela B, Chissaque A, Bauhofer AFL, Nabetse E, Latifo D, Cala A, Mapaco L, Chilaúle J, O'Neill HG, de Deus N. Prevalence and genome characterization of porcine rotavirus A in southern Mozambique. Infect Genet Evol 2020; 87:104637. [PMID: 33232806 DOI: 10.1016/j.meegid.2020.104637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/29/2020] [Accepted: 11/18/2020] [Indexed: 10/22/2022]
Abstract
Rotavirus A (RVA) is an important pathogen causing gastroenteritis in many species, including humans and pigs. The objective of this study was to determine the prevalence of RVA in pigs from smallholdings and commercial farms in southern Mozambique and characterize the complete genomes of selected strains. RVA was detected at a rate of 11.8% (n = 288), of which 7.6% was detected at commercial farms and 4.2% at smallholdings. The whole genomes of eight rotavirus strains were determined using an Illumina MiSeq platform. Seven displayed a G9P[13] and one a G4P[6] genotype combination, all with a typical porcine backbone (I1/5-R1-C1-M1-A1/8-N1-T1/7-E1-H1). Phylogenetic analysis indicated that the seven G9P[13] strains were in fact one strain that circulated on a commercial pig farm. The genome segments of this strain clustered with diverse segments of human and porcine RVA strains from various Asian countries. Analysis of the G4P[6] strain revealed four distinct genome segments (VP2, VP4, VP6 and VP7) and five genome segments closely related to South African porcine rotavirus strains (NSP1, NSP3, NSP4, NSP5 and VP1). These results suggest that both the G4P[6] and the G9P[13] strains possibly emerged through multiple reassortment events. The presence of these strains on the commercial farms and smallholdings calls for a more in-depth surveillance of rotavirus in Mozambique.
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Affiliation(s)
- Simone S Boene
- Instituto Nacional de Saúde (INS), Maputo, Mozambique; Centro de Biotecnologia, Universidade Eduardo Mondlane, Maputo, Mozambique.
| | - Eva D João
- Instituto Nacional de Saúde (INS), Maputo, Mozambique; Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal.
| | - Amy Strydom
- Department of Microbial, Biochemical and Food Biotechnology, University of Free State, Bloemfontein, South Africa.
| | - Benilde Munlela
- Instituto Nacional de Saúde (INS), Maputo, Mozambique; Centro de Biotecnologia, Universidade Eduardo Mondlane, Maputo, Mozambique
| | - Assucênio Chissaque
- Instituto Nacional de Saúde (INS), Maputo, Mozambique; Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Adilson Fernando Loforte Bauhofer
- Instituto Nacional de Saúde (INS), Maputo, Mozambique; Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Elvino Nabetse
- Departamento de Pecuária, Ministério de Agricultura e Desenvolvimento Rural, Maputo, Mozambique
| | - Dalilo Latifo
- Departamento de Pecuária, Ministério de Agricultura e Desenvolvimento Rural, Maputo, Mozambique
| | - Aida Cala
- Direcção de Ciências Animais, Agrarian Investigation Institute of Mozambique (DCA-IIAM), Maputo, Mozambique
| | - Lourenço Mapaco
- Direcção de Ciências Animais, Agrarian Investigation Institute of Mozambique (DCA-IIAM), Maputo, Mozambique
| | | | - Hester G O'Neill
- Department of Microbial, Biochemical and Food Biotechnology, University of Free State, Bloemfontein, South Africa.
| | - Nilsa de Deus
- Instituto Nacional de Saúde (INS), Maputo, Mozambique; Departamento de Ciências Biológicas, Universidade Eduardo Mondlane, Maputo, Mozambique
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7
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Willemsen A, van den Boom A, Dietz J, Bilge Dagalp S, Dogan F, Bravo IG, Ehrhardt A, Ehrke-Schulz E. Genomic and phylogenetic characterization of ChPV2, a novel goat PV closely related to the Xi-PV1 species infecting bovines. Virol J 2020; 17:167. [PMID: 33126890 PMCID: PMC7602357 DOI: 10.1186/s12985-020-01440-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 10/21/2020] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Papillomaviruses (PVs) infecting artiodactyls are very diverse, and only second in number to PVs infecting primates. PVs associated to lesions in economically important ruminant species have been isolated from cattle and sheep. METHODS Potential PV DNA from teat lesions of a Damascus goat was isolated, cloned and sequenced. The PV genome was analyzed using bioinformatics approaches to detect open reading frames and to predict potential features of encoded proteins as well as putative regulatory elements. Sequence comparison and phylogenetic analyses using the concatenated E1E2L2L1 nucleotide and amino acid alignments was used to reveal the relationship of the new PV to the known PV diversity and its closest relevants. RESULTS We isolated and characterized the full-genome of novel Capra hircus papillomavirus. We identified the E6, E7, E1, E2, L2, L1 open reading frames with protein coding potential and putative active elements in the ChPV2 proteins and putative regulatory genome elements. Sequence similarities of L1 and phylogenetic analyses using concatenated E1E2L2L1 nucleotide and amino acid alignments suggest the classification as a new PV type designated ChPV2 with a phylogenetic position within the XiPV genus, basal to the XiPV1 species. ChPV2 is not closely related to ChPV1, the other known goat PV isolated from healthy skin, although both of them belong confidently into a clade composed of PVs infecting cervids and bovids. Interestingly, ChPV2 contains an E6 open reading frame whereas all closely related PVs do not CONCLUSION: ChPV2 is a novel goat PV closely related to the Xi-PV1 species infecting bovines. Phylogenetic relationships and genome architecture of ChPV2 and closely related PV types suggest at least two independent E6 losses within the XiPV clade.
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Affiliation(s)
- Anouk Willemsen
- Centre National de La Recherche Scientifique (CNRS), Laboratory MIVEGEC (CNRS IRD Uni Montpellier), Montpellier, France.,Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Alexander van den Boom
- Chair for Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department for Human Medicine, Faculty of Health, Witten/Herdecke University, Stockumer Strasse 10, 58453, Witten, Germany
| | - Julienne Dietz
- Chair for Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department for Human Medicine, Faculty of Health, Witten/Herdecke University, Stockumer Strasse 10, 58453, Witten, Germany
| | - Seval Bilge Dagalp
- Faculty of Veterinary Medicine, Department of Virology, Ankara University, Ankara, Turkey
| | - Firat Dogan
- Faculty of Veterinary Medicine, Department of Virology, Hatay Mustafa Kemal University, Hatay, Turkey
| | - Ignacio G Bravo
- Centre National de La Recherche Scientifique (CNRS), Laboratory MIVEGEC (CNRS IRD Uni Montpellier), Montpellier, France.,Center for Research on the Ecology and Evolution of Diseases (CREES), Montpellier, France
| | - Anja Ehrhardt
- Chair for Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department for Human Medicine, Faculty of Health, Witten/Herdecke University, Stockumer Strasse 10, 58453, Witten, Germany
| | - Eric Ehrke-Schulz
- Chair for Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department for Human Medicine, Faculty of Health, Witten/Herdecke University, Stockumer Strasse 10, 58453, Witten, Germany.
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8
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Romanutti C, Keller L, La Torre J, Panzera Y, Fuques E, Pérez R, Gallo Calderon M. Virus isolation and full-length genome sequencing of a representative canine distemper virus wild type strain of the South America 2 clade. J Virol Methods 2020; 279:113857. [PMID: 32205180 DOI: 10.1016/j.jviromet.2020.113857] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 02/17/2020] [Accepted: 03/14/2020] [Indexed: 11/20/2022]
Abstract
Canine Distemper Virus (CDV) is a highly contagious pathogen of dogs that causes severe respiratory, gastrointestinal and nervous signs. Although vaccines have been used to prevent infections, CDV has been reported worldwide, even in vaccinated animals. In the present study, a representative wild type CDV strain (Arg24) was isolated from a sick vaccinated dog and its genome was completely sequenced using Illumina technology. This strain produced a strong cytopathic effect in Vero SLAM (Signaling Lymphocyte Activation Molecule) cells with a higher titer of 1.1 × 105 Median Tissue Culture Infectious Dose (TCID50/mL) at 32 h post infection, in cell-associated virus. The Arg24 strain genome, showed values of 97.1, 90.3, 96.7, 90.6, 89.8 and 97.3 % of amino acid identity with respect to the Onderstepoort vaccine strain (Nucleoprotein, Phosphoprotein, Matrix, Fusion, Hemagglutinin and Large polymerase, respectively). Focusing on the Hemagglutinin gene, which is the target for genetic characterization, Arg24 showed four additional potential glycosylation sites, with respect to the Onderstepoort. The availability of Arg24 strain, which can be easily grown in Vero SLAM cells, is an important tool to perform immunological and antigenic comparative studies, between wild type and vaccine CDV strains.
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9
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Lecis R, Mucedda M, Pidinchedda E, Zobba R, Pittau M, Alberti A. Genomic characterization of a novel bat-associated Circovirus detected in European Miniopterus schreibersii bats. Virus Genes 2020; 56:325-328. [PMID: 32088806 PMCID: PMC7088871 DOI: 10.1007/s11262-020-01747-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 02/13/2020] [Indexed: 11/21/2022]
Abstract
Circoviruses are small circular DNA viruses causing severe pig and poultry disease, recently identified in various bat species worldwide. We report the detection and full-genome molecular characterization of a novel bat-associated Circovirus identified in faecal samples of Miniopterus schreibersii bats (Schreiber’s bent-winged bats) from Sardinia, Italy. Full-genomic sequencing revealed a new putative member of Circoviridae family, with a genome size of 2063 nt. Sequencing allowed the characterization of the two major ORFs, inversely arranged, encoding replicase and capsid proteins, as well as the finding of a polythymidine tract within the genome, and highlighted phylogenetic relationships of the novel virus. This is the first report of circovirus in European bats. Giving the high level of genetic diversity of bat circoviruses, it is paramount to further investigate the relationships between these viruses and bats.
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Affiliation(s)
- Roberta Lecis
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100, Sassari, Italy. .,Mediterranean Centre for Disease Control, University of Sassari, Via Vienna 2, 07100, Sassari, Italy.
| | - Mauro Mucedda
- Centro Pipistrelli Sardegna, Via G. Leopardi 1, 07100, Sassari, Italy
| | | | - Rosanna Zobba
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100, Sassari, Italy
| | - Marco Pittau
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100, Sassari, Italy.,Mediterranean Centre for Disease Control, University of Sassari, Via Vienna 2, 07100, Sassari, Italy
| | - Alberto Alberti
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100, Sassari, Italy.,Mediterranean Centre for Disease Control, University of Sassari, Via Vienna 2, 07100, Sassari, Italy
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Sun YF, Jiang X, Zhang A, Ma JF, Yu XX, Li LA, Yu H. Early infection of Streptococcus suis serotype 2 increases the virulence of highly pathogenic porcine reproductive and respiratory syndrome MLV-like virus in pigs. Res Vet Sci 2020; 130:68-72. [PMID: 32146377 DOI: 10.1016/j.rvsc.2020.02.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 01/20/2020] [Accepted: 02/18/2020] [Indexed: 11/19/2022]
Abstract
Modified-live virus (MLV) vaccines derived from highly pathogenic porcine reproductive and respiratory syndrome virus (HP-PRRSV) were wildly used in China, which resulted in the emergence of MLV-like strains in pigs. Previous studies demonstrated that secondary bacterial infection could enhance HP-PRRSV infection-mediated inflammatory responses, but it is unknown whether early bacterial infection could enhance the HP-PRRSV MLV-like infection-mediated pathological reaction. In this paper, to gain the evidence for infection of pigs with MLV-like strains in China, we firstly analyzed the genetic characterization of the HP-PRRSV MLV-like isolate (TJxq1701) and further evaluated whether the early Streptococcus suis infection synergizes HP-PRRSV MLV-like infection-mediated pathological reaction. Our results showed that the whole genome of TJxq1701 shared the highest homology with JXA1-P80 and a total of 16 amino acids residues unique to JXA1-P80 in ORF1a, ORF1b, GP2, GP3, GP4, and GP5 were found in the corresponding locations. The results of infection experiments in pigs revealed that TJxq1701 caused transitional fever, moderate respiratory clinical sign and microscopic lung lesions in piglets, but early infection with low virulence Streptococcus suis serotype 2 (SS2) exhibited seriously clinical signs, including high fever, anorexia, and respiratory distress, leading to 60% mortality within four weeks in comparison with alone infected group. Taken together, our findings reveal that early bacterial infection could enhance the HP-PRRSV MLV-like infection-mediated pathological reaction, which provide an important clue for understanding that streptococcus infection increases the pathogenicity of MLV-like virus and a new thought for prevention and control of PRRSV.
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Affiliation(s)
- Ying-Feng Sun
- Tianjin Key Laboratory of Agricultural Animal Breeding and Healthy Husbandry, College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, Tianjin 300384, PR China
| | - Xuan Jiang
- Tianjin Key Laboratory of Agricultural Animal Breeding and Healthy Husbandry, College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, Tianjin 300384, PR China
| | - Ao Zhang
- Tianjin Key Laboratory of Agricultural Animal Breeding and Healthy Husbandry, College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, Tianjin 300384, PR China
| | - Ji-Fei Ma
- Tianjin Key Laboratory of Agricultural Animal Breeding and Healthy Husbandry, College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, Tianjin 300384, PR China
| | - Xiao-Xue Yu
- Tianjin Key Laboratory of Agricultural Animal Breeding and Healthy Husbandry, College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, Tianjin 300384, PR China
| | - Liu-An Li
- Tianjin Key Laboratory of Agricultural Animal Breeding and Healthy Husbandry, College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, Tianjin 300384, PR China.
| | - Hai Yu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, PR China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou 225009, PR China.
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11
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Dey KK, Sugikawa J, Kerr C, Melzer MJ. Air potato (Dioscorea bulbifera) plants displaying virus-like symptoms are co-infected with a novel potyvirus and a novel ampelovirus. Virus Genes 2018; 55:117-121. [PMID: 30460477 DOI: 10.1007/s11262-018-1616-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 11/10/2018] [Indexed: 01/27/2023]
Abstract
Air potato (Dioscorea bulbifera) plants being grown at the Florida Department of Agriculture and Consumer Services Division of Plant Industry Biological Control Laboratory II in Alachua County, Florida were observed exhibiting foliar mosaic symptoms characteristic of virus infection. A double-stranded RNA library generated from a symptomatic plant underwent high-throughput sequencing to determine if viral pathogens were present. Sequence data revealed the presence of two viral genomes, one with properties congruent with members of the genus Potyvirus (family Potyviridae), and the other with members of the genus Ampelovirus (family Closteroviridae). Sequence comparisons and phylogenetic placement indicate that both viruses represent novel species. The names "dioscorea mosaic virus" and "air potato virus 1" are proposed for the potyvirus and ampelovirus, respectively.
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Affiliation(s)
- Kishore K Dey
- Division of Plant Industry, Florida Department of Agriculture and Consumer Services, Gainesville, FL, 32608, USA
| | - Jaylinn Sugikawa
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI, 96822, USA
| | - Christopher Kerr
- Division of Plant Industry, Florida Department of Agriculture and Consumer Services, Gainesville, FL, 32608, USA
| | - Michael J Melzer
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI, 96822, USA.
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12
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Zhang Z, Zhou L, Ge X, Guo X, Han J, Yang H. Evolutionary analysis of six isolates of porcine reproductive and respiratory syndrome virus from a single pig farm: MLV-evolved and recombinant viruses. Infect Genet Evol 2018; 66:111-119. [PMID: 30261264 DOI: 10.1016/j.meegid.2018.09.024] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 09/21/2018] [Accepted: 09/24/2018] [Indexed: 01/27/2023]
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) is one of the most important pathogens with economic significance for swine industry globally. The virus is characterized by its genetically extraordinary variability and diversified strains due to high mutation frequency and recombination rates. In the current study, we analyzed the genomes of six PRRSV strains isolated in different years from a single pig farm practicing HP-PRRSV-derived modified-live virus (MLV) vaccination in China, and in detail dissected their evolutionary relationship to MLV vaccines. The results show that all the six isolates belong to type 2 PRRSV, and are clustered into two lineages (lineage 1 and 8) based on their ORF5 genes. Further comparative analyses of genomes and the characteristic amino acid sites show that both HeN1201 and HeN1502 are MLV-like strains evolved from the MLV HuN4-F112. Recombination analyses reveal that HeN1301 is a recombinant virus emerged from the recombination event between two MLV-like strains evolved from the MLV TJM-F92 and HuN4-F112, and HeN1501 is a recombinant virus between two MLV-like strains evolved from HuN4-F112, while HeN1401 and HeN1601 are recombinant viruses derived from the recombination between NADC30-like and a MLV-like strain evolved from TJM-F92. Our findings provide more evidence for the fact that MLV-derived from the Chinese HP-PRRSV can be evolved and reversed in the field and enrich the data about the recombination between the viruses evolved from MLV and newly infected strain of PRRSV. This study stresses the necessity for pig producers to restrain the use of HP-PRRSV MLV vaccines in the field.
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Affiliation(s)
- Zhendong Zhang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, People's Republic of China
| | - Lei Zhou
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, People's Republic of China
| | - Xinna Ge
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, People's Republic of China
| | - Xin Guo
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, People's Republic of China
| | - Jun Han
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, People's Republic of China
| | - Hanchun Yang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, People's Republic of China.
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13
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Abstract
Comparative immunology, studying both vertebrates and invertebrates, provided the earliest descriptions of phagocytosis as a general immune mechanism. However, the large scale of animal diversity challenges all-inclusive investigations and the field of immunology has developed by mostly emphasizing study of a few vertebrate species. In addressing the lack of comprehensive understanding of animal immunity, especially that of invertebrates, comparative immunology helps toward management of invertebrates that are food sources, agricultural pests, pathogens, or transmit diseases, and helps interpret the evolution of animal immunity. Initial studies showed that the Mollusca (second largest animal phylum), and invertebrates in general, possess innate defenses but lack the lymphocytic immune system that characterizes vertebrate immunology. Recognizing the reality of both common and taxon-specific immune features, and applying up-to-date cell and molecular research capabilities, in-depth studies of a select number of bivalve and gastropod species continue to reveal novel aspects of molluscan immunity. The genomics era heralded a new stage of comparative immunology; large-scale efforts yielded an initial set of full molluscan genome sequences that is available for analyses of full complements of immune genes and regulatory sequences. Next-generation sequencing (NGS), due to lower cost and effort required, allows individual researchers to generate large sequence datasets for growing numbers of molluscs. RNAseq provides expression profiles that enable discovery of immune genes and genome sequences reveal distribution and diversity of immune factors across molluscan phylogeny. Although computational de novo sequence assembly will benefit from continued development and automated annotation may require some experimental validation, NGS is a powerful tool for comparative immunology, especially increasing coverage of the extensive molluscan diversity. To date, immunogenomics revealed new levels of complexity of molluscan defense by indicating sequence heterogeneity in individual snails and bivalves, and members of expanded immune gene families are expressed differentially to generate pathogen-specific defense responses.
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Affiliation(s)
- Jonathan H Schultz
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Coen M Adema
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA.
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14
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Wang B, Yang XL, Li W, Zhu Y, Ge XY, Zhang LB, Zhang YZ, Bock CT, Shi ZL. Detection and genome characterization of four novel bat hepadnaviruses and a hepevirus in China. Virol J 2017; 14:40. [PMID: 28222808 PMCID: PMC5320732 DOI: 10.1186/s12985-017-0706-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 02/04/2017] [Indexed: 01/28/2023] Open
Abstract
Background In recent years, novel hepadnaviruses, hepeviruses, hepatoviruses, and hepaciviruses have been discovered in various species of bat around the world, indicating that bats may act as natural reservoirs for these hepatitis viruses. In order to further assess the distribution of hepatitis viruses in bat populations in China, we tested the presence of these hepatitis viruses in our archived bat liver samples that originated from several bat species and various geographical regions in China. Methods A total of 78 bat liver samples (involving two families, five genera, and 17 species of bat) were examined using nested or heminested reverse transcription PCR (RT-PCR) with degenerate primers. Full-length genomic sequences of two virus strains were sequenced followed by phylogenetic analyses. Results Four samples were positive for hepadnavirus, only one was positive for hepevirus, and none of the samples were positive for hepatovirus or hepacivirus. The hepadnaviruses were discovered in the horseshoe bats, Rhinolophus sinicus and Rhinolophus affinis, and the hepevirus was found in the whiskered bat Myotis davidii. The full-length genomic sequences were determined for one of the two hepadnaviruses identified in R. sinicus (designated BtHBVRs3364) and the hepevirus (designated BtHEVMd2350). A sequence identity analysis indicated that BtHBVRs3364 had the highest degree of identity with a previously reported hepadnavirus from the roundleaf bat, Hipposideros pomona, from China, and BtHEVMd2350 had the highest degree of identity with a hepevirus found in the serotine bat, Eptesicus serotinus, from Germany, but it exhibited high levels of divergence at both the nucleotide and the amino acid levels. Conclusions This is the first study to report that the Chinese horseshoe bat and the Chinese whiskered bat have been found to carry novel hepadnaviruses and a novel hepevirus, respectively. The discovery of BtHBVRs3364 further supports the significance of host switches evolution while opposing the co-evolutionary theory associated with hepadnaviruses. According to the latest criterion of the International Committee on Taxonomy of Viruses (ICTV), we hypothesize that BtHEVMd2350 represents an independent genotype within the species Orthohepevirus D of the family Hepeviridae.
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Affiliation(s)
- Bo Wang
- CAS Key Laboratory of Special Pathogens and Biosafety and Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,Department of Infectious Diseases, Robert Koch Institute, Berlin, Germany
| | - Xing-Lou Yang
- CAS Key Laboratory of Special Pathogens and Biosafety and Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Wen Li
- CAS Key Laboratory of Special Pathogens and Biosafety and Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Yan Zhu
- CAS Key Laboratory of Special Pathogens and Biosafety and Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Xing-Yi Ge
- CAS Key Laboratory of Special Pathogens and Biosafety and Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Li-Biao Zhang
- Guangdong Institute of Applied Biological Resource, Guangzhou, 510260, China
| | - Yun-Zhi Zhang
- Laboratory for Zoonosis Control and Prevention, Yunnan Institute of Endemic Diseases Control and Prevention, Dali, 671000, China
| | - Claus-Thomas Bock
- Department of Infectious Diseases, Robert Koch Institute, Berlin, Germany
| | - Zheng-Li Shi
- CAS Key Laboratory of Special Pathogens and Biosafety and Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.
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15
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Peng Z, Liang W, Wang Y, Liu W, Zhang H, Yu T, Zhang A, Chen H, Wu B. Experimental pathogenicity and complete genome characterization of a pig origin Pasteurella multocida serogroup F isolate HN07. Vet Microbiol 2016; 198:23-33. [PMID: 28062004 DOI: 10.1016/j.vetmic.2016.11.028] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 10/31/2016] [Accepted: 11/27/2016] [Indexed: 01/17/2023]
Abstract
Pasteurella multocida serotype F isolates are predominately prevalent in avian hosts, but rarely seen in pigs. However, we isolated several strains of P. multocida serotype F from clinical samples of pigs in China. To understand the pathogenicity of these strains, one of the serotype F isolates designated HN07, was used to challenge experimental chickens, as P. multocida of this serotype is predominately prevalent in avian hosts. However, strain HN07 could not resulted in significant clinical signs in experimental chickens even at an infective dose of ∼109 CFU, suggesting the isolate was avirulent to chickens and therefore raising the possibility that the porcine serotype F isolate is not transmitted by chickens. We then used HN07 to challenge experimental pigs, as this strain was isolated from pigs. As expected, the strain led to the clinical signs and the pathological lesions in experimental pigs that are similar to the pasteurellosis disease. We then determined the complete genome sequence of the pig origin serogroup F isolate HN07 for the first time. Genome comparison between HN07 and the avian serotype F P. multocida Pm70 identified a novel integrative conjugative element (ICE) ICEpmcn07 which was likely to harbor a series of genes responsible for a putative type IV secretion system (T4SS) in HN07. This is the first time that we determined an ICE carrying a T4SS in P. multocida. Besides, comparative analysis also defined a number of virulence-associated genes in HN07 but absent in Pm70 which may have a contribution to the pathogenicity of the strain. This is the first report of the pathogenicity and genome characterization of a pig origin Pasteurella multocida serogroup F isolate. The pathogenic and genomic definition of the pig origin P. multocida serogroup F in our study would have significance on the pathogenesis and genetic diversity and virulence variability of P. multocida.
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Affiliation(s)
- Zhong Peng
- State Key Laboratory of Agricultural Microbiology, College of Animal Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China; The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Wan Liang
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yuanguo Wang
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, United States
| | - Wenjing Liu
- State Key Laboratory of Agricultural Microbiology, College of Animal Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China; The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Hongfeng Zhang
- State Key Laboratory of Agricultural Microbiology, College of Animal Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China; The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Teng Yu
- State Key Laboratory of Agricultural Microbiology, College of Animal Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China; The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Anding Zhang
- State Key Laboratory of Agricultural Microbiology, College of Animal Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China; The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Huanchun Chen
- State Key Laboratory of Agricultural Microbiology, College of Animal Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China; The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Bin Wu
- State Key Laboratory of Agricultural Microbiology, College of Animal Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China; The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
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16
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Dong N, Fang L, Yang H, Liu H, Du T, Fang P, Wang D, Chen H, Xiao S. Isolation, genomic characterization, and pathogenicity of a Chinese porcine deltacoronavirus strain CHN-HN-2014. Vet Microbiol 2016; 196:98-106. [PMID: 27939164 PMCID: PMC7117368 DOI: 10.1016/j.vetmic.2016.10.022] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 10/14/2016] [Accepted: 10/17/2016] [Indexed: 02/07/2023]
Abstract
Porcine deltacoronavirus (PDCoV) is an emerging swine coronavirus that causes diarrhea in piglets. Since the first outbreak of PDCoV in the United States in 2014, this novel porcine coronavirus has been detected in South Korea, Canada, Mexico, Thailand, and China. In this study, a Chinese PDCoV strain, designated CHN-HN-2014, was isolated from piglets with severe diarrhea on a pig farm in Henan Province, China, and examined with a specific immunofluorescence assay and electron microscopy. Genomic analysis showed that CHN-HN-2014 shares 91.6%-99.4% nucleotide identity with other known PDCoV strains. The pathogenicity of CHN-HN-2014 was further investigated in 5-day-old and 21-day-old piglets. Both kinds of piglets developed clear clinical symptoms, including vomiting, anorexia, lethargy, and severe diarrhea, by 2days postinoculation (DPI), and diarrhea persisted for about 5-6 days. Viral shedding was detected in rectal swabs until 14 DPI in challenged 5-day-old pigs and until 18 DPI in challenged 21-day-old pigs. At necropsy at 4 DPI, macroscopic and microscopic lesions were observed and viral antigen was detected in the small intestines with immunohistochemical staining. These data demonstrate that Chinese PDCoV strain CHN-HN-2014 shares high nucleotide identity with previously reported PDCoV strains and is pathogenic in 5-day-old and 21-day-old piglets.
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Affiliation(s)
- Nan Dong
- Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Liurong Fang
- Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Hao Yang
- Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Han Liu
- Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Ting Du
- Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Puxian Fang
- Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Dang Wang
- Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Huanchun Chen
- Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Shaobo Xiao
- Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China.
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17
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Zhai SL, Chen SN, Liu W, Li XP, Deng SF, Wen XH, Luo ML, Lv DH, Wei WK, Chen RA. Molecular detection and genome characterization of porcine circovirus type 2 in rats captured on commercial swine farms. Arch Virol 2016; 161:3237-44. [PMID: 27530112 DOI: 10.1007/s00705-016-3004-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 07/26/2016] [Indexed: 11/27/2022]
Abstract
Porcine circovirus type 2 (PCV2) is considered the major etiological pathogen of porcine circovirus-associated diseases (PCVADs) in pigs. Recently, PCV2 was also found in non-porcine animals such as cattle, rats, and mice. However, there was no record of PCV2 in rats in China. The goal of this study was to investigate whether PCV2 was present in rats (Rattus norvegicus, RN) on three swine farms, using molecular tools. PCR results showed that 30 of 95 (31.6 %) rat samples were positive for PCV2. Moreover, further genotype analysis suggested that 10 of 30 (33.3 %) were positive for PCV2a, 19 of 30 (63.3 %) were positive for PCV2b, and only one sample (1/30, 3.33 %) was co-infected by PCV2a and PCV2b. To determine the possible origin of PCV2, 60 serum samples were also collected from weaned pigs on those swine farms, and 23 out of 60 samples were positive for PCV2. In addition, two distinct RN-origin and two distinct porcine-origin PCV2 full-length nucleotide sequences were obtained from the farms. Sequence and phylogenetic analysis indicated that they had the highest nucleotide similarity and closest genetic relationships to each other. In this study, we report the infection and genome characterization of PCV2 in rats and compare RN-origin and porcine-origin PCV2 sequences obtained from the same pig farm, revealing possible cross-species transmission of PCV2.
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Affiliation(s)
- Shao-Lun Zhai
- Animal Disease Diagnostic Center, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.,Guangdong Key Laboratory of Animal Disease Prevention and Guangdong Open Laboratory of Veterinary Public Health, Guangzhou, 510640, China
| | - Sheng-Nan Chen
- Guangdong Wens Dahuanong Biotechnology Co., Ltd., Xinxing, 527400, China
| | - Wei Liu
- Guangdong Wens Dahuanong Biotechnology Co., Ltd., Xinxing, 527400, China
| | - Xiao-Peng Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Su-Fang Deng
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Xiao-Hui Wen
- Animal Disease Diagnostic Center, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.,Guangdong Key Laboratory of Animal Disease Prevention and Guangdong Open Laboratory of Veterinary Public Health, Guangzhou, 510640, China
| | - Man-Lin Luo
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Dian-Hong Lv
- Animal Disease Diagnostic Center, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China. .,Guangdong Key Laboratory of Animal Disease Prevention and Guangdong Open Laboratory of Veterinary Public Health, Guangzhou, 510640, China.
| | - Wen-Kang Wei
- Animal Disease Diagnostic Center, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China. .,Guangdong Key Laboratory of Animal Disease Prevention and Guangdong Open Laboratory of Veterinary Public Health, Guangzhou, 510640, China.
| | - Rui-Ai Chen
- Guangdong Wens Dahuanong Biotechnology Co., Ltd., Xinxing, 527400, China. .,College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.
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18
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François-Souquière S, Makuwa M, Bisvigou U, Kazanji M. Epidemiological and molecular features of hepatitis B and hepatitis delta virus transmission in a remote rural community in central Africa. Infect Genet Evol 2015; 39:12-21. [PMID: 26747245 DOI: 10.1016/j.meegid.2015.12.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 12/21/2015] [Accepted: 12/29/2015] [Indexed: 02/06/2023]
Abstract
Hepatitis B virus (HBV) and hepatitis delta virus (HDV) occur worldwide and are prevalent in both urban and remote rural communities. In a remote village in Gabon, central Africa, we observed a high prevalence of HBsAg carriage and HDV infection, particularly in children and adolescents. The prevalence of HBsAg differed significantly by gender and age, females being more likely than males to carry the HBsAg during the first 10 years of life, while the prevalence was higher among males than females aged 11-20 years. We also characterised HBV and HDV strains circulating in the village. The principal HBV strains belonged to genotype HBV-E and subgenotype QS-A3. Complete genome analysis revealed for the first time the presence of the HBV-D genotype in Gabon, in the form of an HBV-D/E recombinant. Molecular analysis of HDV strains and their complete genomic characterisation revealed two distinct groups within the dominant HDV clade 8. Molecular analysis of HBV and HDV strains did not reveal vertical transmission within the families studied but rather horizontal, intrafamilial transmission among children aged 0-10 years. Our findings indicate that HBV is transmitted in early childhood by body fluids rather than by sexual contact. Health education adapted to the different age groups might therefore help to reduce HBV transmission. Young children should be vaccinated to control HBV infection in areas of extremely high prevalence.
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Affiliation(s)
- Sandrine François-Souquière
- Laboratoire de Virologie, Centre International de Recherches Médicales de Franceville, BP 769, Franceville, Gabon
| | - Maria Makuwa
- Laboratoire de Virologie, Centre International de Recherches Médicales de Franceville, BP 769, Franceville, Gabon
| | - Ulrich Bisvigou
- Laboratoire de Virologie, Centre International de Recherches Médicales de Franceville, BP 769, Franceville, Gabon
| | - Mirdad Kazanji
- Laboratoire de Virologie, Centre International de Recherches Médicales de Franceville, BP 769, Franceville, Gabon; Réseau International des Instituts Pasteur, Institut Pasteur de la Guyane, French Guiana, France.
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19
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Abstract
The complete mitochondrial sequence of the capped langur (Trachypithecus pileatus) has been determined using long amplification polymerase chain reaction (LA-PCR). The total sequence length is 16,526 bp and includes 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and 1 D-loop locus. The base composition of H-strand is 31.9% A, 29.1% T, 26.2% C and 12.8% G, with an AT content of 55.3%. The arrangement of genes in T. pileatus is identical to that of other primate species. All genes are encoded on the heavy strand with the exception of ND6 and eight tRNA genes. The mitochondrial genome of T. pileatus presented here will contribute to a better understanding of the species' population genetics, helping to protect its genetic diversity and resolve phylogenetic relationships within the family.
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Affiliation(s)
- Fang-Lei Shi
- a College of Nature Conservation, Beijing Forestry University , Beijing , China and.,b Key Laboratory of Animal Ecology and Conservation Biology , Institute of Zoology, Chinese Academy of Sciences , Beijing , China
| | - Bo-Shi Wang
- b Key Laboratory of Animal Ecology and Conservation Biology , Institute of Zoology, Chinese Academy of Sciences , Beijing , China
| | - Hui-Juan Pan
- a College of Nature Conservation, Beijing Forestry University , Beijing , China and
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20
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Kasthuri SR, Wan Q, Umasuthan N, Bathige SDNK, Lim BS, Jung HB, Lee J, Whang I. Genomic characterization, expression analysis, and antimicrobial function of a glyrichin homologue from rock bream, Oplegnathus fasciatus. Fish Shellfish Immunol 2013; 35:1406-1415. [PMID: 23968692 DOI: 10.1016/j.fsi.2013.08.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 08/08/2013] [Accepted: 08/08/2013] [Indexed: 06/02/2023]
Abstract
Antimicrobial peptides are important innate effector molecules, playing a vital role in antimicrobial immunity in all species. Glyrichin is a transmembrane protein and an antibacterial peptide, exerting its functions against a wide range of pathogenic bacteria. In this study, cDNA and a BAC clone harboring the glyrichin gene were identified from rock bream and characterized. Genomic characterization showed that the OfGlyrichin gene exhibited a 3 exon-2 intron structure. OfGlyrichin is a 79-amino-acid protein with a transmembrane domain at (22)GFMMGFAVGMAAGAMFGTFSCLR(44). Pairwise and multiple sequence alignments showed high identity and conservation with mammalian orthologues. Phylogenetic analysis showed a close relationship with fish species. Higher levels of OfGlyrichin transcripts were detected in the liver from healthy rock bream which were induced by immunogens like lipopolysaccharide, poly I:C, rock bream irido virus, Edwardsiella tarda and Streptococcus iniae. The synthetic peptide (pOf19) showed antibacterial activity against Escherichia coli, E. tarda, and S. iniae. Analysis of the bacterial morphological features after pOf19 peptide treatment showed breakage of the cell membrane, affirming that antibacterial function is accomplished through membrane lysis. The pOf19 peptide also showed antiviral activity against RBIV infection. The high conservation of the genomic structure and protein, together with the antimicrobial roles of OfGlyrichin, provide evidence for the evolutionary existence of this protein playing a vital role in innate immune defense in rock bream.
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Affiliation(s)
- Saranya Revathy Kasthuri
- Department of Marine Life Sciences, School of Marine Biomedical Sciences, Jeju National University, Jeju Self-Governing Province 690-756, Republic of Korea
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21
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Pachler K, Růžek D, Nowotny N. Molecular characterization of the African orthobunyavirus Ilesha virus. Infect Genet Evol 2013; 20:124-30. [PMID: 23988729 DOI: 10.1016/j.meegid.2013.08.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2013] [Revised: 08/07/2013] [Accepted: 08/20/2013] [Indexed: 11/17/2022]
Abstract
Ilesha virus is an arthropod-borne virus belonging to the genus Orthobunyavirus of the Bunyaviridae family. Ilesha virus has been isolated from humans in several African countries, mostly in relation with febrile illness and erythema, though there are reported cases of fatal meningoencephalitis and hemorrhagic fever. In the present study, we report the complete genomic sequence of all three Ilesha virus segments (S, M, L) and characterize the open reading frames. The nucleoprotein encoded by segment S contains 59 conserved orthobunyavirus amino acids putatively critical for protein function. For the polyprotein encoded by segment M, potential proteolytic cleavage sites and N-glycosylation sites as well as conserved cysteines are described in reference to other orthobunyaviruses. Within the C terminal glycoprotein Gc a putative fusion peptide could be localized. In the RNA-dependent RNA polymerase encoded by segment L, all strictly conserved amino acids within the four conserved regions known to be catalytically active are present. Phylogenetic analyses conducted for each Ilesha virus genomic segment confirm the classification of Ilesha virus within the Bunyamwera serogroup of orthobunyaviruses. Ilesha virus segments S and L exhibit highest genetic conservation with Bunyamwera virus and Ngari virus, with maximum sequence identities of 88% for segment S and 82% for segment L. However, the M segment was found to be more diverse with a maximum nucleotide identity of 72% to Bunyamwera serogroup viruses.
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Affiliation(s)
- Karin Pachler
- Viral Zoonoses, Emerging and Vector-Borne Infections Group, Institute of Virology, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria.
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