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Jaton J, Gómez E, Lucero MS, Rizzi L, Gravisaco MJ, Pinto S, Berinstein A, Chimeno Zoth S. Evasion of maternal antibody protection by an IBDV Argentine variant. Poult Sci 2024; 103:103431. [PMID: 38295501 PMCID: PMC10846382 DOI: 10.1016/j.psj.2024.103431] [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: 11/21/2023] [Revised: 01/02/2024] [Accepted: 01/02/2024] [Indexed: 02/02/2024] Open
Abstract
Infectious bursal disease (IBD) is a viral disease that affects the ability of chickens to produce humoral immune responses. One way to prevent the disease is the passage of maternally derived antibodies (MDA) from dams to offsprings via the yolk. Despite sanitary measures, which include immunization with genogroup 1 (G1) vaccines, infections with IBDV genogroup 4 (G4) in young animals have been detected. The aim of this study was to determine whether a local IBDV isolate belonging to G4 could evade the immunity generated by MDAs. Twelve-day-old animals positive for MDA, were inoculated with G1 or G4 isolates or phosphate buffered saline (PBS) as a control. After 1 wk, the animals were sacrificed and the following parameters were evaluated: bursa-body (BB) ratio, viral load, and histologic damage in the bursa of Fabricius. Results showed that G4-infected animals had significant differences in the BB ratio compared to the PBS group. In addition, viral load was significantly higher in the G4 group than in the G1 group. Histologic damage in the bursa of Fabricius was detected only in G4-infected MDA chickens. Our results suggest that infection with G4 local isolate can circumvent the immunity generated by MDA and, furthermore, that G4 isolate does not differ in its pathogenicity from G1 isolate, which underlines the need to include variant strains in vaccine formulations to reduce potential losses caused by these viruses.
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Affiliation(s)
- Juan Jaton
- Laboratorio de Inmunología y Vacunas Aviares, Instituto de Agrobiotecnología y Biología Molecular, INTA-CONICET, Buenos Aires, Argentina
| | - Evangelina Gómez
- Laboratorio de Inmunología y Vacunas Aviares, Instituto de Agrobiotecnología y Biología Molecular, INTA-CONICET, Buenos Aires, Argentina
| | - María Soledad Lucero
- Laboratorio de Inmunología y Vacunas Aviares, Instituto de Agrobiotecnología y Biología Molecular, INTA-CONICET, Buenos Aires, Argentina
| | - Lucía Rizzi
- Laboratorio de Inmunología y Vacunas Aviares, Instituto de Agrobiotecnología y Biología Molecular, INTA-CONICET, Buenos Aires, Argentina
| | - María José Gravisaco
- Laboratorio de Inmunología y Vacunas Aviares, Instituto de Agrobiotecnología y Biología Molecular, INTA-CONICET, Buenos Aires, Argentina
| | - Silvina Pinto
- Cátedra de Patología, Facultad de Ciencias Veterinarias, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Analía Berinstein
- Laboratorio de Inmunología y Vacunas Aviares, Instituto de Agrobiotecnología y Biología Molecular, INTA-CONICET, Buenos Aires, Argentina
| | - Silvina Chimeno Zoth
- Laboratorio de Inmunología y Vacunas Aviares, Instituto de Agrobiotecnología y Biología Molecular, INTA-CONICET, Buenos Aires, Argentina.
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Volle R, Luo L, Razafindratsimandresy R, Sadeuh-Mba SA, Gouandjika-Valisache I, Horwood P, Duong V, Buchy P, Joffret ML, Huang Z, Duizer E, Martin J, Chakrabarti LA, Dussart P, Jouvenet N, Delpeyroux F, Bessaud M. Neutralization of African enterovirus A71 genogroups by antibodies to canonical genogroups. J Gen Virol 2023; 104. [PMID: 37909282 DOI: 10.1099/jgv.0.001911] [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] [Indexed: 11/03/2023] Open
Abstract
Enterovirus 71 (EV-A71) is a major public health problem, causing a range of illnesses from hand-foot-and-mouth disease to severe neurological manifestations. EV-A71 strains have been phylogenetically classified into eight genogroups (A to H), based on their capsid-coding genomic region. Genogroups B and C have caused large outbreaks worldwide and represent the two canonical circulating EV-A71 subtypes. Little is known about the antigenic diversity of new genogroups as compared to the canonical ones. Here, we compared the antigenic features of EV-A71 strains that belong to the canonical B and C genogroups and to genogroups E and F, which circulate in Africa. Analysis of the peptide sequences of EV-A71 strains belonging to different genogroups revealed a high level of conservation of the capsid residues involved in known linear and conformational neutralization antigenic sites. Using a published crystal structure of the EV-A71 capsid as a model, we found that most of the residues that are seemingly specific to some genogroups were mapped outside known antigenic sites or external loops. These observations suggest a cross-neutralization activity of anti-genogroup B or C antibodies against strains of genogroups E and F. Neutralization assays were performed with diverse rabbit and mouse anti-EV-A71 sera, anti-EV-A71 human standards and a monoclonal neutralizing antibody. All the batches of antibodies that were tested successfully neutralized all available isolates, indicating an overall broad cross-neutralization between the canonical genogroups B and C and genogroups E and F. A panel constituted of more than 80 individual human serum samples from Cambodia with neutralizing antibodies against EV-A71 subgenogroup C4 showed quite similar cross-neutralization activities between isolates of genogroups C4, E and F. Our results thus indicate that the genetic drift underlying the separation of EV-A71 strains into genogroups A, B, C, E and F does not correlate with the emergence of antigenically distinct variants.
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Affiliation(s)
- Romain Volle
- Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Virus Sensing and Signaling Unit, Paris, France
- Present address: Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Lingjie Luo
- Present address: Department of Immunology and Microbiology, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, PR China
- Institut Pasteur, Control of Chronic Viral Infections (CIVIC) Group, Virus and Immunity Unit, Université de Paris Cité, CNRS UMR 3569, Paris, France
| | | | - Serge Alain Sadeuh-Mba
- Present address: Maryland Department of Agriculture, Salisbury Animal Health Laboratory, Salisbury, USA
- Centre Pasteur of Cameroon, Yaounde, Cameroon
| | | | - Paul Horwood
- Present address: James Cook University, Townsville, Australia
- Institut Pasteur of Cambodia, Phnom Penh, Cambodia
| | - Veasna Duong
- Institut Pasteur of Cambodia, Phnom Penh, Cambodia
| | | | - Marie-Line Joffret
- Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Virus Sensing and Signaling Unit, Paris, France
| | - Zhong Huang
- Present address: Fudan University, Shanghai, PR China
- Institut Pasteur of Shanghai - Chinese Academy of Sciences, Shanghai, PR China
| | - Erwin Duizer
- National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Javier Martin
- National Institute for Biological Standards and Control (NIBSC), Potters Bar, UK
| | - Lisa A Chakrabarti
- Institut Pasteur, Control of Chronic Viral Infections (CIVIC) Group, Virus and Immunity Unit, Université de Paris Cité, CNRS UMR 3569, Paris, France
| | | | - Nolwenn Jouvenet
- Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Virus Sensing and Signaling Unit, Paris, France
| | - Francis Delpeyroux
- Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Virus Sensing and Signaling Unit, Paris, France
| | - Maël Bessaud
- Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Virus Sensing and Signaling Unit, Paris, France
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Kariithi HM, Volkening JD, Chiwanga GH, Pantin-Jackwood MJ, Msoffe PLM, Suarez DL. Genome Sequences and Characterization of Chicken Astrovirus and Avian Nephritis Virus from Tanzanian Live Bird Markets. Viruses 2023; 15:1247. [PMID: 37376547 DOI: 10.3390/v15061247] [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: 04/29/2023] [Revised: 05/22/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
The enteric chicken astrovirus (CAstV) and avian nephritis virus (ANV) are the type species of the genus Avastrovirus (AAstV; Astroviridae family), capable of causing considerable production losses in poultry. Using next-generation sequencing of a cloacal swab from a backyard chicken in Tanzania, we assembled genome sequences of ANV and CAstV (6918 nt and 7318 nt in length, respectively, excluding poly(A) tails, which have a typical AAstV genome architecture (5'-UTR-ORF1a-ORF1b-ORF2-'3-UTR). They are most similar to strains ck/ANV/BR/RS/6R/15 (82.72%) and ck/CAstV/PL/G059/14 (82.23%), respectively. Phylogenetic and sequence analyses of the genomes and the three open reading frames (ORFs) grouped the Tanzanian ANV and CAstV strains with Eurasian ANV-5 and CAstV-Aii viruses, respectively. Compared to other AAstVs, the Tanzanian strains have numerous amino acid variations (substitutions, insertions and deletions) in the spike region of the capsid protein. Furthermore, CAstV-A has a 4018 nt recombinant fragment in the ORF1a/1b genomic region, predicted to be from Eurasian CAstV-Bi and Bvi parental strains. These data should inform future epidemiological studies and options for AAstV diagnostics and vaccines.
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Affiliation(s)
- Henry M Kariithi
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, USDA, Athens, GA 30605, USA
- Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, Kaptagat Rd, Nairobi P.O. Box 57811-00200, Kenya
| | | | - Gaspar H Chiwanga
- Tanzania Veterinary Laboratory Agency, South Zone, Mtwara P.O. Box 186, Tanzania
| | - Mary J Pantin-Jackwood
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, USDA, Athens, GA 30605, USA
| | - Peter L M Msoffe
- Department of Veterinary Medicine and Public Health, Sokoine University of Agriculture, Chuo Kikuu, Morogoro P.O. Box 3000, Tanzania
| | - David L Suarez
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, USDA, Athens, GA 30605, USA
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Carannante A, Vacca P, Fontana S, Dal Conte I, Ghisetti V, Cusini M, Prignano G, Vocale C, Barbui AM, Stroppiana E, Busetti M, Mencacci A, Rotondi M, De Francesco MA, Bonanno CL, Innocenti P, Latino MA, Riccobono E, Poletti F, Casonato IC, Soldato G, Ambrosio L, Boros S, Ciammaruconi A, Lista F, Stefanelli P. Seven Years of Culture Collection of Neisseria gonorrhoeae: Antimicrobial Resistance and Molecular Epidemiology. Microb Drug Resist 2023; 29:85-95. [PMID: 36757312 PMCID: PMC10024589 DOI: 10.1089/mdr.2021.0483] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
Abstract
The emergence of Neisseria gonorrhoeae isolates displaying resistance to antimicrobials, in particular to ceftriaxone monotherapy or ceftriaxone plus azithromycin, represents a global public health concern. This study aimed to analyze the trend of antimicrobial resistance in a 7-year isolate collection retrospective analysis in Italy. Molecular typing on a subsample of gonococci was also included. A total of 1,810 culture-positive gonorrhea cases, collected from 2013 to 2019, were investigated by antimicrobial susceptibility, using gradient diffusion method, and by the N. gonorrhoeae multiantigen sequence typing (NG-MAST). The majority of infections occurred among men with urogenital infections and 57.9% of male patients were men who have sex with men. Overall, the cefixime resistance remained stable during the time. An increase of azithromycin resistance was observed until 2018 (26.5%) with a slight decrease in the last year. In 2019, gonococci showing azithromycin minimum inhibitory concentration above the EUCAST epidemiological cutoff value (ECOFF) accounted for 9.9%. Ciprofloxacin resistance and penicillinase-producing N. gonorrhoeae (PPNG) percentages increased reaching 79.1% and 18.7% in 2019, respectively. The most common sequence types identified were 5,441, 1,407, 6,360, and 5,624. The predominant genogroup (G) was the 1,407; moreover, a new genogroup G13070 was also detected. A variation in the antimicrobial resistance rates and high genetic variability were observed in this study. The main phenotypic and genotypic characteristics of N. gonorrhoeae isolates were described to monitor the spread of drug-resistant gonorrhea.
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Affiliation(s)
- Anna Carannante
- Department Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Paola Vacca
- Department Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Stefano Fontana
- Department Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Ivano Dal Conte
- Department of Prevention, Sexual Health Center, ASL Città di Torino, Turin, Italy
| | - Valeria Ghisetti
- Laboratory of Microbiology and Virology, ASL Città di Torino, Turin, Italy
| | - Marco Cusini
- Dermatology Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Grazia Prignano
- Molecular Virology, Pathology and Microbiology, IRCCS San Gallicano Dermatological Institute, Rome, Italy
| | - Caterina Vocale
- Regional Reference Center for Microbiological Emergencies (CRREM), Unit of Microbiology, St Orsola Malpighi University Hospital, Bologna, Italy
| | - Anna Maria Barbui
- Microbiology and Virology Laboratory, Molinette Hospital, Turin, Italy
| | - Elena Stroppiana
- Department of Medical Science, Dermatology Clinic, “Città della Salute e della Scienza of Turin,” Turin, Italy
| | - Marina Busetti
- Microbiology Unit, University Hospital of Trieste, Trieste, Italy
| | - Antonella Mencacci
- Medical Microbiology, Department of Medicine, University of Perugia, Perugia, Italy
- Microbiology, Santa Maria della Misericordia Hospital, Perugia, Italy
| | - Marina Rotondi
- Clinical and Microbiological Analysis Laboratory, Marilab s.r.l., Rome, Italy
| | - Maria Antonia De Francesco
- Department of Molecular and Translational Medicine, Institute of Microbiology, University of Brescia-Spedali Civili, Brescia, Italy
| | | | - Patrizia Innocenti
- Microbiology and Virology Laboratory, “Comprensorio Sanitario,” Bolzano, Italy
| | - Maria Agnese Latino
- Unit of Bacteriology, Department of “Medicina di Laboratorio," P. O. Sant'Anna, Città della Salute e della Scienza di Torino,” Turin, Italy
| | - Eleonora Riccobono
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Federica Poletti
- Department Infectious Diseases, Castelli Hospital Verbania, Verbania, Italy
| | | | | | - Luigina Ambrosio
- Department Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Stefano Boros
- Department Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | | | | | - Paola Stefanelli
- Department Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
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Guo J, Ding Y, Sun F, Zhou H, He P, Chen J, Guo J, Zeng H, Long J, Wei Z, Ouyang K, Huang W, Chen Y. Co-circulation and evolution of genogroups I and II of respiratory and enteric feline calicivirus isolates in cats. Transbound Emerg Dis 2022; 69:2924-2937. [PMID: 34982847 PMCID: PMC9787975 DOI: 10.1111/tbed.14447] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 07/31/2021] [Revised: 12/28/2021] [Accepted: 12/28/2021] [Indexed: 12/30/2022]
Abstract
Feline calicivirus (FCV) is a highly infectious pathogen that causes upper respiratory tract disease (URTD), but the enteric FCVs raise concerns regarding their role of an enteric pathogen. In this study, between 2019 and 2020, 101 clinical samples from domestic cats with symptoms of URTD, with or without enteritis, were collected for FCV-specific detection. The FCV-positive rate reached to 42.4% (28/66) in cats with respiratory symptoms. The rates were 11.1% (3/27) and 12.5% (1/8) when faeces and serum samples were measured using reverse transcription polymerase chain reaction (RT-PCR), respectively. Ten FCV strains were successfully isolated from respiratory and enteric sources in domestic cats from Guangxi. Phylogenetic analysis based on the genome sequences of 11 isolates (including GX01-13 isolated in 2013) indicated that the newly characterized FCV strains had two recombinant events in comparison with other FCVs and were of respiratory and enteric origins. These strains displayed high genetic diversity, and they were divided into two genogroups (I and II). Of these, the GXNN02-19 isolate was grouped with previously published Chinese isolates that were identified as genogroup II, which contained three specific amino acid residues (377K, 539V and 557S) in the VP1 protein. In addition, the three enteric viruses appeared genetically heterogeneous to each other. All isolates were found to be more sensitive when exposed to low pH conditions, but they were resistant to treatment with trypsin and bile salts. Furthermore, there were no significant differences between the respiratory and enteric FCVs. Our results showed that the genetically distinct FCV strains with genogroups I and II from respiratory and enteric origins were co-circulating in this geographical area. Also, it was revealed that the potential recombinant events between the enteric and respiratory FCVs suggested an important role of enteric FCV during the evolution.
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Affiliation(s)
- Jinfan Guo
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and TechnologyGuangxi UniversityNanningP. R. China
| | - Yangbao Ding
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and TechnologyGuangxi UniversityNanningP. R. China
| | - Fanyuan Sun
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and TechnologyGuangxi UniversityNanningP. R. China
| | | | - Ping He
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and TechnologyGuangxi UniversityNanningP. R. China
| | - Jiancai Chen
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and TechnologyGuangxi UniversityNanningP. R. China
| | - Jianing Guo
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and TechnologyGuangxi UniversityNanningP. R. China
| | - Hao Zeng
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and TechnologyGuangxi UniversityNanningP. R. China
| | - Jianming Long
- Shenjiu Biological Products Co. Ltd.NanningP. R. China
| | - Zuzhang Wei
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and TechnologyGuangxi UniversityNanningP. R. China
| | - Kang Ouyang
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and TechnologyGuangxi UniversityNanningP. R. China
| | - Weijian Huang
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and TechnologyGuangxi UniversityNanningP. R. China
| | - Ying Chen
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and TechnologyGuangxi UniversityNanningP. R. China
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Batts WN, Capps TR, Crosson LM, Powers RL, Breyta R, Purcell MK. Rapid Diagnostic Test to Detect and Discriminate Infectious Hematopoietic Necrosis Virus (IHNV) Genogroups U and M to Aid Management of Pacific Northwest Salmonid Populations. Animals (Basel) 2022; 12:ani12141761. [PMID: 35883308 PMCID: PMC9311590 DOI: 10.3390/ani12141761] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 11/16/2022] Open
Abstract
Infectious hematopoietic necrosis virus (IHNV) is an acute pathogen of salmonids in North America, Europe, and Asia that is phylogenetically classified into five major virus genogroups (U, M, L, E, and J). The geographic range of the U and M genogroup isolates overlap in the North American Columbia River Basin and Washington Coast region, where these genogroups pose different risks depending on the species of Pacific salmon (Oncorhynchus spp.). For certain management decisions, there is a need to both test for IHNV presence and rapidly determine the genogroup. Herein, we report the development and validation of a U/M multiplex reverse transcription, real-time PCR (RT-rPCR) assay targeting the IHNV nucleocapsid (N) protein gene. The new U/M RT-rPCR is a rapid, sensitive, and repeatable assay capable of specifically discriminating between North American U and M genogroup IHNV isolates. However, one M genogroup isolate obtained from commercially cultured Idaho rainbow trout (O. mykiss) showed reduced sensitivity with the RT-rPCR test, suggesting caution may be warranted before applying RT-rPCR as the sole surveillance test in areas associated with the Idaho trout industry. The new U/M assay had high diagnostic sensitivity (DSe > 94%) and specificity (DSp > 97%) in free-ranging adult Pacific salmon, when assessed relative to cell culture, the widely accepted reference standard, as well as the previously validated universal N RT-rPCR test. The high diagnostic performance of the new U/M assay indicates the test is suitable for surveillance, diagnosis, and confirmation of IHNV in Pacific salmon from the Pacific Northwest regions where the U and M genogroups overlap.
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Affiliation(s)
- William N. Batts
- U.S. Geological Survey, Western Fisheries Research Center, Seattle, WA 98115, USA; (W.N.B.); (R.L.P.)
| | - Tony R. Capps
- Washington Department of Fish and Wildlife, Olympia, WA 98501, USA; (T.R.C.); (L.M.C.)
| | - Lisa M. Crosson
- Washington Department of Fish and Wildlife, Olympia, WA 98501, USA; (T.R.C.); (L.M.C.)
| | - Rachel L. Powers
- U.S. Geological Survey, Western Fisheries Research Center, Seattle, WA 98115, USA; (W.N.B.); (R.L.P.)
| | - Rachel Breyta
- School of Aquatic and Fisheries Sciences, University of Washington, Seattle, WA 98195, USA;
| | - Maureen K. Purcell
- U.S. Geological Survey, Western Fisheries Research Center, Seattle, WA 98115, USA; (W.N.B.); (R.L.P.)
- Correspondence:
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Kim SJ, Kim C, Chung HC, Park YH, Park KT. Full-length ORF2 sequence-based genetic and phylogenetic characterization of Korean feline caliciviruses. J Vet Sci 2021; 22:e32. [PMID: 33908206 PMCID: PMC8170210 DOI: 10.4142/jvs.2021.22.e32] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 02/08/2021] [Accepted: 02/21/2021] [Indexed: 11/20/2022] Open
Abstract
Feline calicivirus (FCV) is a highly infectious pathogen in cats and widely distributed worldwide with high genetic variation. Full-length open reading frame 2 of 5 from recently isolated Korean FCV isolates were sequenced and compared with those of global isolates. The results of phylogenetic analysis supported dividing global FCV isolates into two genogroups (type I and II) and demonstrated the presence of genogroup II in Korea, indicating their geographic spread in East Asia. High sequence variations in region E of the FCV isolates emphasizes that a novel vaccine needs to be developed to induce protective immunity against various FCV strains.
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Affiliation(s)
- Sung Jae Kim
- Department of Veterinary Microbiology, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Cheongung Kim
- Department of Veterinary Microbiology, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Hee Chun Chung
- Department of Veterinary Microbiology, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Yong Ho Park
- Department of Veterinary Microbiology, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Kun Taek Park
- Department of Biotechnology, Inje University, Gimhae 50834, Korea.
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Takano T, Watanabe H, Doki T, Kusuhara H. Detection of feline norovirus using commercial real-time RT-PCR kit for the diagnosis of human norovirus infection. J Vet Med Sci 2021; 83:805-808. [PMID: 33692232 PMCID: PMC8182310 DOI: 10.1292/jvms.20-0703] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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] [Indexed: 01/04/2023] Open
Abstract
Feline noroviruses (FNoVs) are potential clinical pathogens in cats. To perform an epidemiological study of FNoV infection, it is necessary to develop a simple and effective method for virus detection. We investigated whether a commercial human NoV quantitative RT-PCR kit for the detection of human NoVs used in medical practice can be applied for FNoV detection. This kit was capable of detecting the FNoV gene regardless of the genogroup (GIV and GVI) in experimental and field samples. Based on the above findings, it is possible to detect FNoVs using human NoV tests. The relationship between FNoV infection and gastroenteritis in cats may be clarified by applying these methods to an epidemiological survey of FNoVs.
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Affiliation(s)
- Tomomi Takano
- School of Veterinary Medicine, Kitasato University, Towada, Aomori 034-8628, Japan
| | - Haruna Watanabe
- School of Veterinary Medicine, Kitasato University, Towada, Aomori 034-8628, Japan
| | - Tomoyoshi Doki
- School of Veterinary Medicine, Kitasato University, Towada, Aomori 034-8628, Japan
| | - Hajime Kusuhara
- Health and Environment Research Institute, Yokkaichi, Mie 512-1211, Japan
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Wulandari PS, Juniastuti, Wahyuni RM, Amin M, Yamani LN, Matondang MQY, Dinana Z, Soetjipto, Utsumi T, Shoji I, Lusida MI. Predominance of norovirus GI.4 from children with acute gastroenteritis in Jambi, Indonesia, 2019. J Med Virol 2020; 92:3165-3172. [PMID: 32445492 DOI: 10.1002/jmv.26057] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 05/18/2020] [Indexed: 12/19/2022]
Abstract
Norovirus (NoV) is one of the most important viral causes of acute gastroenteritis (AGE) in children worldwide. Only a few studies have reported AGE with NoV-positive in some cities in Indonesia. This study aimed to investigate the incidence and clinical characteristic of NoV infection, and also genotype distribution of NoV in children with AGE in Jambi, as the capital and the largest city of Jambi province, Indonesia. Stool samples were collected from children (≤15 years of age) with AGE at three participating hospitals in Jambi from February to April 2019. The detection of NoV and its genotyping were carried out by reverse-transcriptase polymerase chain reaction and direct sequencing. Of the 91 stool samples collected, 14 (15.4%) were positive for NoV. Fever, vomiting, and severe diarrhea were commonly observed in AGE with NoV, while level of dehydration was statistically significant difference between children with NoV-positive and those with NoV-negative. The most prevalent genotype was GI.4 (42.9%), followed by GII.6 (28.6%) and some other genotypes. Interestingly, this study found the predominance of GI.4, differed from previous reports in Indonesia. Continuously investigation of the circulating genotype is needed to control the NoV-infected AGE.
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Affiliation(s)
- Putri Sari Wulandari
- Master Program of Tropical Medicine, School of Medicine, Universitas Airlangga, Surabaya, Indonesia
| | - Juniastuti
- Master Program of Tropical Medicine, School of Medicine, Universitas Airlangga, Surabaya, Indonesia
- Department of Microbiology, Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia
- Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
| | - Rury Mega Wahyuni
- Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
| | - Mochamad Amin
- Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
| | - Laura Navika Yamani
- Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
- Department of Epidemiology, Faculty of Public Health, Universitas Airlangga, Surabaya, Indonesia
| | | | - Zayyin Dinana
- Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
| | - Soetjipto
- Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
- Department of Biochemistry, Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia
| | - Takako Utsumi
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
- Center for Infectious Diseases, Kobe University Graduate School of Medicine, Hyogo, Japan
| | - Ikuo Shoji
- Center for Infectious Diseases, Kobe University Graduate School of Medicine, Hyogo, Japan
| | - Maria Inge Lusida
- Department of Microbiology, Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia
- Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
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10
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Sharif N, Parvez AK, Haque A, Talukder AA, Ushijima H, Dey SK. Molecular and epidemiological trends of human bocavirus and adenovirus in children with acute gastroenteritis in Bangladesh during 2015 to 2019. J Med Virol 2020; 92:3194-3201. [PMID: 32237149 DOI: 10.1002/jmv.25812] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [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: 12/19/2019] [Revised: 03/05/2020] [Accepted: 03/27/2020] [Indexed: 01/11/2023]
Abstract
Virus associated diarrhea remains one of the leading causes of children morbidity and mortality in Bangladesh. Human bocavirus (HBoV) has been reported as a potential pathogen of children's diarrhea worldwide. However, due to its frequent association with other gastroenteric pathogens, its role as diarrhea causative agent remains to be defined. This study focuses to detect the incidence of HBoV and adenovirus (AdV) and to determine the molecular and epidemiological characteristics of HBoV and AdV. Between January 2015 to January 2019, 290 fecal specimens were collected from diarrheal children in Bangladesh. All fecal specimens were tested for HBoV and AdV by conventional polymerase chain reaction and sequencing methods. HBoV was detected in 7.24% (21 of 290) of the stool samples, as a sole virus in 71.42% (15 of 21) of the positive samples. AdV was detected in 4.82% (14 of 290) of the samples. The most common clinical symptoms of HBoV infected patients were diarrhea (100%) and vomiting (57%). All of the isolates of HBoV were from HBoV1 and AdV were from AdV41, AdV5, AdV7, and AdV8. To the best of our knowledge, this is the first epidemiological and molecular analysis report of HBoV from clinical specimens in Bangladesh. In the future, more studies are needed to clarify the role of HBoV as diarrheal pathogens.
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Affiliation(s)
- Nadim Sharif
- Department of Microbiology, Jahangirnagar University, Dhaka, Bangladesh
| | | | - Aynul Haque
- Department of Physiology, Pabna Medical College, Pabna, Bangladesh
| | - Ali Azam Talukder
- Department of Microbiology, Jahangirnagar University, Dhaka, Bangladesh
| | - Hiroshi Ushijima
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University, Tokyo, Japan
| | - Shuvra Kanti Dey
- Department of Microbiology, Jahangirnagar University, Dhaka, Bangladesh
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11
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Maj-Paluch J, Matras M, Borzym E, Stachnik M, Reichert M. Phylogenetic characterization of Polish isolates of infectious pancreatic necrosis virus in salmonid fish. J Fish Dis 2020; 43:1443-1451. [PMID: 32851666 DOI: 10.1111/jfd.13249] [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] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 07/31/2020] [Accepted: 08/03/2020] [Indexed: 06/11/2023]
Abstract
INTRODUCTION Infectious pancreatic necrosis virus belongs to the genus Aquabirnavirus and family Birnaviridae. By VP2 gene similarity, aquatic birnavirus is clustered into seven genogroups. The aim of this study was to genetically analyse IPN viruses occurring on Polish fish farms. MATERIALS AND METHODS Samples from freshwater fish mostly from 2012 to 2013 and from northern Poland were examined for the presence of IPN virus using isolation on cell cultures, real-time RT-PCR and RT-PCR. Fragments of 1,377 and 1,079 bp of the VP2 and VP5 genes, respectively, were sequenced, and the results were assembled into one consensus and analysed by Geneious software. The same VP2 gene region was compared and a phylogenetic tree generated by the neighbour-joining method and MEGA6 software. RESULTS All tested Polish isolates belonged to genogroup 5, like other European Spajurup isolates. CONCLUSION Our findings prove that there is only one IPN virus genogroup in Poland. Polish isolates show close relationships with each other. There is a close relationship between Polish isolates and isolates from Turkey, Spain and Iran. Isolate 57 is a separate branch related to isolates from the United States and Taiwan. This points to the likelihood of past virus introduction via import of stock from those countries.
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Affiliation(s)
- Joanna Maj-Paluch
- Department of Fish Diseases, National Veterinary Research Institute, Pulawy, Poland
| | - Marek Matras
- Department of Fish Diseases, National Veterinary Research Institute, Pulawy, Poland
| | - Ewa Borzym
- Department of Fish Diseases, National Veterinary Research Institute, Pulawy, Poland
| | - Magdalena Stachnik
- Department of Fish Diseases, National Veterinary Research Institute, Pulawy, Poland
| | - Michal Reichert
- Department of Fish Diseases, National Veterinary Research Institute, Pulawy, Poland
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12
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Li F, Zeng Y, Zhang R, Peng K, Jiang C, Xu Z, Zhu L. Genetic variations in S gene of porcine epidemic diarrhoea virus from 2018 in Sichuan Province, China. Vet Med Sci 2020; 6:910-918. [PMID: 32885908 PMCID: PMC7738707 DOI: 10.1002/vms3.326] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 10/31/2019] [Revised: 05/28/2020] [Accepted: 07/06/2020] [Indexed: 11/17/2022] Open
Abstract
Porcine epidemic diarrhoea virus (PEDV) belongs to the family Coronavirus, a genus of coronavirus, a highly contact‐infectious intestinal disease pathogen. In this study, we downloaded 62 PEDV S gene sequences uploaded to GenBank, including 10 uploaded by our laboratory from 2018, and constructed a PEDV S gene evolution tree using MEGA V7.0 software. Phylogenetic tree analysis indicated that the genogroup of PEDV in Sichuan Province was divided into three coexisting genogroups (GII‐a, GII‐b and GI‐a), of them, GII‐a has become the main genogroup in the province due to its prevalence and range of spread. Amino acid sequence analysis showed that there were amino acid insertions and deletions in the S protein encoded by the amplified S gene, and there were amino acid mutations in the COE and SS6 of the epitope in the amplified S protein. These results provide a basic research theory for understanding the prevalence of PEDV variation and controlling PED in Sichuan.
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Affiliation(s)
- Fei Li
- College of Veterinary Medicine, Sichuan Agricultural University - Chengdu Campus, Chengdu, Sichuan, China
| | - Yubing Zeng
- College of Veterinary Medicine, Sichuan Agricultural University - Chengdu Campus, Chengdu, Sichuan, China
| | - Rubo Zhang
- College of Veterinary Medicine, Sichuan Agricultural University - Chengdu Campus, Chengdu, Sichuan, China
| | - Kenan Peng
- College of Veterinary Medicine, Sichuan Agricultural University - Chengdu Campus, Chengdu, Sichuan, China
| | - Chaoyuan Jiang
- College of Veterinary Medicine, Sichuan Agricultural University - Chengdu Campus, Chengdu, Sichuan, China
| | - Zhiwen Xu
- College of Veterinary Medicine, Sichuan Agricultural University - Chengdu Campus, Chengdu, Sichuan, China
| | - Ling Zhu
- College of Veterinary Medicine, Sichuan Agricultural University - Chengdu Campus, Chengdu, Sichuan, China
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13
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Chhabra P, de Graaf M, Parra GI, Chan MCW, Green K, Martella V, Wang Q, White PA, Katayama K, Vennema H, Koopmans MPG, Vinjé J. Updated classification of norovirus genogroups and genotypes. J Gen Virol 2020; 100:1393-1406. [PMID: 31483239 DOI: 10.1099/jgv.0.001318] [Citation(s) in RCA: 440] [Impact Index Per Article: 110.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Noroviruses are genetically diverse RNA viruses associated with acute gastroenteritis in mammalian hosts. Phylogenetically, they can be segregated into different genogroups as well as P (polymerase)-groups and further into genotypes and P-types based on amino acid diversity of the complete VP1 gene and nucleotide diversity of the RNA-dependent RNA polymerase (RdRp) region of ORF1, respectively. In recent years, several new noroviruses have been reported that warrant an update of the existing classification scheme. Using previously described 2× standard deviation (sd) criteria to group sequences into separate clusters, we expanded the number of genogroups to 10 (GI-GX) and the number of genotypes to 48 (9 GI, 27 GII, 3 GIII, 2 GIV, 2 GV, 2 GVI and 1 genotype each for GVII, GVIII, GIX [formerly GII.15] and GX). Viruses for which currently only one sequence is available in public databases were classified into tentative new genogroups (GNA1 and GNA2) and genotypes (GII.NA1, GII.NA2 and GIV.NA1) with their definitive assignment awaiting additional related sequences. Based on nucleotide diversity in the RdRp region, noroviruses can be divided into 60 P-types (14 GI, 37 GII, 2 GIII, 1 GIV, 2 GV, 2 GVI, 1 GVII and 1 GX), 2 tentative P-groups and 14 tentative P-types. Future classification and nomenclature updates will be based on complete genome sequences and will be coordinated and disseminated by the international norovirus classification-working group.
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Affiliation(s)
- Preeti Chhabra
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Miranda de Graaf
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Gabriel I Parra
- Division of Viral Products, Food and Drug Administration, Silver Spring, MD, USA
| | - Martin Chi-Wai Chan
- Department of Microbiology, Stanley Ho Centre for Emerging Infectious Diseases and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, PR China
| | - Kim Green
- Caliciviruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Vito Martella
- Department of Veterinary Medicine, University of Bari Aldo Moro, Bari, Italy
| | - Qiuhong Wang
- Department of Veterinary Preventive Medicine, The Ohio State University, Wooster, OH, USA
| | - Peter A White
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney 2052, Australia
| | - Kazuhiko Katayama
- Laboratory of Viral infection I, Kitasato Institute for Life Sciences Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
| | - Harry Vennema
- Division for Virology, Centre for Infectious Diseases Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Marion P G Koopmans
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jan Vinjé
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
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Abstract
Bursa tissue samples from a pullet flock in New York State that was experiencing immune suppression related disease were sent to our laboratory in 2018. A very virulent infectious bursal disease virus (vvIBDV) was identified in those samples through molecular and pathogenicity studies and designated 1/chicken/USA/1054NY/18. Phylogenetic analyses of the hypervariable VP2 nucleotide sequence region indicated that this strain belonged to genogroup 3 which comprises the vvIBDV. Partial sequence data of the VP1 gene indicated this virus also had a VP1 typical of vvIBDV. While vvIBDV have previously been identified in the United States in California and Washington State, the 1054NY vvIBDV was most closely related to isolates from Ethiopia, suggesting it is a new introduction into the U.S. The 1054NY vvIBDV was used to challenge four-week old specific-pathogen-free (SPF) layer chicks where it caused 100% morbidity and 68.7% mortality within 4 days. Upon necropsy, gross pathological findings in infected SPF birds included small yellowish coloured bursas, some with haemorrhages on the serosal and mucosal surfaces. Microscopic lesions included inflammation, severe lymphocyte necrosis, atrophy of the follicles and follicular depletion of lymphocytes. RESEARCH HIGHLIGHTS A very virulent infectious bursal disease virus (vvIBDV) was detected in a pullet flock in New York state, USA. Nucleotide sequence analysis of the vvIBDV VP2 gene indicates it is not related to previous US vvIBDV isolates and appears to be a new introduction into the US. The New York vvIBDV caused 100% morbidity and 68.7% mortality in four-week-old specific-pathogen-free chicks.
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Affiliation(s)
- Linda O Michel
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University , Wooster , OH , USA
| | | | - Daral J Jackwood
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University , Wooster , OH , USA
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15
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Stoute ST, Jackwood DJ, Crossley BM, Michel LO, Blakey JR. Molecular epidemiology of endemic and very virulent infectious bursal disease virus genogroups in backyard chickens in California, 2009-2017. J Vet Diagn Invest 2019; 31:371-377. [PMID: 30943870 DOI: 10.1177/1040638719842193] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Pathogenic strains of infectious bursal disease virus (IBDV) are associated with increased morbidity, mortality, and immunosuppression in susceptible chickens. Backyard poultry is increasing in popularity in the United States, but very little is known about the prevalence and molecular epidemiology of IBDV within these flocks. We performed a retrospective study and phylogenetic analyses of IBDV detected in backyard chickens (BYCs) submitted to the California Animal Health and Food Safety (CAHFS) diagnostic laboratory system in 2009-2017. There were 17 CAHFS autopsy cases of very virulent IBDV (vvIBDV) segment A detected by RT-rtPCR in BYC flocks from 7 counties in California from 2009-2017. During this same time period, non-vvIBDV genotypes were detected by RT-rtPCR in 16 autopsy cases originating from BYC premises in 10 counties in California. Subsequent RT-PCR and phylogenetic analysis of a segment of the hvVP2 and VP1 gene identified vvIBDV, interserotypic reassortant IBDV (vvIBDV segment A and serotype 2 segment B), and non-vvIBDV (variant/subclinical IBDV and classic IBDV) strains in BYC flocks in California.
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Affiliation(s)
- Simone T Stoute
- California Animal Health & Food Safety Laboratory System, School of Veterinary Medicine, University of California, Davis branch (Crossley).,California Animal Health & Food Safety Laboratory System, School of Veterinary Medicine, University of California, Turlock branch (Stoute, Blakey).,Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH (Jackwood, Michel)
| | - Daral J Jackwood
- California Animal Health & Food Safety Laboratory System, School of Veterinary Medicine, University of California, Davis branch (Crossley).,California Animal Health & Food Safety Laboratory System, School of Veterinary Medicine, University of California, Turlock branch (Stoute, Blakey).,Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH (Jackwood, Michel)
| | - Beate M Crossley
- California Animal Health & Food Safety Laboratory System, School of Veterinary Medicine, University of California, Davis branch (Crossley).,California Animal Health & Food Safety Laboratory System, School of Veterinary Medicine, University of California, Turlock branch (Stoute, Blakey).,Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH (Jackwood, Michel)
| | - Linda O Michel
- California Animal Health & Food Safety Laboratory System, School of Veterinary Medicine, University of California, Davis branch (Crossley).,California Animal Health & Food Safety Laboratory System, School of Veterinary Medicine, University of California, Turlock branch (Stoute, Blakey).,Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH (Jackwood, Michel)
| | - Julia R Blakey
- California Animal Health & Food Safety Laboratory System, School of Veterinary Medicine, University of California, Davis branch (Crossley).,California Animal Health & Food Safety Laboratory System, School of Veterinary Medicine, University of California, Turlock branch (Stoute, Blakey).,Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH (Jackwood, Michel)
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16
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Mlynarczyk-Bonikowska B, Malejczyk M, Majewski S, Unemo M. Antibiotic resistance and NG-MAST sequence types of Neisseria gonorrhoeae isolates in Poland compared to the world. Postepy Dermatol Alergol 2018; 35:346-551. [PMID: 30618519 PMCID: PMC6320495 DOI: 10.5114/ada.2018.79780] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 06/12/2018] [Indexed: 11/17/2022] Open
Abstract
Gonorrhoea is one of the most common sexually transmitted infections and in 2012, the World Health Organization estimated about 78 million of new global urogenital cases among adults per year. The main concern during the latest decade has been the emergence and spread of multidrug-resistant strains of Neisseria gonorrhoeae. Resistance has emerged internationally to the extended-spectrum cephalosporins, ceftriaxone and cefixime, which are the last remaining options for empiric first-line monotherapy of gonorrhoea. In Poland, the levels of resistance to ciprofloxacin, benzylpenicillin and tetracycline are high, and the prevalence of azithromycin resistance has increased. However, no resistance to ceftriaxone has been identified. The currently spread multidrug-resistant strains frequently represent epidemic clones. The present paper reviews and describes the antimicrobial resistance and N. gonorrhoeae multiantigen sequence typing (NG-MAST) sequence types of N. gonorrhoeae strains spreading in Poland compared to the world.
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Affiliation(s)
| | - Magdalena Malejczyk
- Department of Diagnostics of Sexually Transmitted Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Sławomir Majewski
- Department of Diagnostics of Sexually Transmitted Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Magnus Unemo
- World Health Organization (WHO) Collaborating Centre for Gonorrhoea and other STIs, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
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17
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Delfino CM, Cerrudo CS, Biglione M, Oubiña JR, Ghiringhelli PD, Mathet VL. A comprehensive bioinformatic analysis of hepatitis D virus full-length genomes. J Viral Hepat 2018; 25:860-869. [PMID: 29406571 DOI: 10.1111/jvh.12876] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 01/02/2018] [Indexed: 12/15/2022]
Abstract
In association with hepatitis B virus (HBV), hepatitis delta virus (HDV) is a subviral agent that may promote severe acute and chronic forms of liver disease. Based on the percentage of nucleotide identity of the genome, HDV was initially classified into three genotypes. However, since 2006, the original classification has been further expanded into eight clades/genotypes. The intergenotype divergence may be as high as 35%-40% over the entire RNA genome, whereas sequence heterogeneity among the isolates of a given genotype is <20%; furthermore, HDV recombinants have been clearly demonstrated. The genetic diversity of HDV is related to the geographic origin of the isolates. This study shows the first comprehensive bioinformatic analysis of the complete available set of HDV sequences, using both nucleotide and protein phylogenies (based on an evolutionary model selection, gamma distribution estimation, tree inference and phylogenetic distance estimation), protein composition analysis and comparison (based on the presence of invariant residues, molecular signatures, amino acid frequencies and mono- and di-amino acid compositional distances), as well as amino acid changes in sequence evolution. Taking into account the congruent and consistent results of both nucleotide and amino acid analyses of GenBank available sequences (recorded as of January, 2017), we propose that the eight hepatitis D virus genotypes may be grouped into three large genogroups fully supported by their shared characteristics.
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Affiliation(s)
- C M Delfino
- Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET) - Universidad de Buenos Aires (UBA), Instituto de Investigaciones en Microbiología y Parasitología Médica, (IMPAM), Ciudad Autónoma de Buenos Aires, Argentina
| | - C S Cerrudo
- Departamento de Ciencia y Tecnología, Laboratorio de Ingeniería Genética y Biología Celular y Molecular - Área Virosis de Insectos (LIGBCM-AVI), Instituto de Microbiología Básica y Aplicada (IMBA), Universidad Nacional de Quilmes, Bernal, Provincia de Buenos Aires, Argentina
| | - M Biglione
- Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET) - Universidad de Buenos Aires (UBA), Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), Ciudad Autónoma de Buenos Aires, Argentina
| | - J R Oubiña
- Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET) - Universidad de Buenos Aires (UBA), Instituto de Investigaciones en Microbiología y Parasitología Médica, (IMPAM), Ciudad Autónoma de Buenos Aires, Argentina
| | - P D Ghiringhelli
- Departamento de Ciencia y Tecnología, Laboratorio de Ingeniería Genética y Biología Celular y Molecular - Área Virosis de Insectos (LIGBCM-AVI), Instituto de Microbiología Básica y Aplicada (IMBA), Universidad Nacional de Quilmes, Bernal, Provincia de Buenos Aires, Argentina
| | - V L Mathet
- Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET) - Universidad de Buenos Aires (UBA), Instituto de Investigaciones en Microbiología y Parasitología Médica, (IMPAM), Ciudad Autónoma de Buenos Aires, Argentina
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18
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Teng JLL, Martelli P, Chan WM, Lee HH, Hui SW, Lau CCY, Tse H, Yuen KY, Lau SKP, Woo PCY. Two novel noroviruses and a novel norovirus genogroup in California sea lions. J Gen Virol 2018; 99:777-782. [PMID: 29722646 DOI: 10.1099/jgv.0.001071] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [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] [Indexed: 01/09/2023] Open
Abstract
In this study, two novel noroviruses (NoVs) were discovered from faecal samples from California sea lions from an oceanarium in Hong Kong, and named California sea lion NoV 1 (Csl/NoV1) and California sea lion NoV 2 (Csl/NoV2). Whole-genome sequencing showed that the genome organization and amino acid motifs of both Csl/NoV1 and Csl/NoV2 were typical of those of other NoVs in their open reading frames (ORFs). Csl/NoV1 possessed only 52.6-52.8 % amino acid identity in VP1 to the closest matches in genogroup GII. Therefore, Csl/NoV1 should constitute a novel genogroup of NoV. Shifting of the phylogenetic position of Csl/NoV1 in the RdRp, VP1 and VP2 trees was observed, which may have been due to recombination events and/or biased mutations. Csl/NoV2 possessed 55.4-56.2 % amino acid identity in VP1 to its closest relatives in genogroup GVI, which means that it represents a new genotype in genogroup GVI. Further studies will reveal what diseases these NoVs can cause in marine mammals.
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Affiliation(s)
- Jade L L Teng
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong SAR
- State Key Laboratory of Emerging Infectious Diseases, Hong Kong SAR
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong SAR
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR
| | | | - Wan-Mui Chan
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR
| | - Hwei Huih Lee
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR
| | | | - Candy C Y Lau
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR
| | - Herman Tse
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR
- State Key Laboratory of Emerging Infectious Diseases, Hong Kong SAR
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong SAR
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong SAR
| | - Kwok-Yung Yuen
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Hong Kong SAR
- State Key Laboratory of Emerging Infectious Diseases, Hong Kong SAR
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong SAR
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong SAR
| | - Susanna K P Lau
- State Key Laboratory of Emerging Infectious Diseases, Hong Kong SAR
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong SAR
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong SAR
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Hong Kong SAR
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR
| | - Patrick C Y Woo
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Hong Kong SAR
- State Key Laboratory of Emerging Infectious Diseases, Hong Kong SAR
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong SAR
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong SAR
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR
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Rupprom K, Chavalitshewinkoon-Petmitr P, Diraphat P, Kittigul L. Evaluation of real-time RT-PCR assays for detection and quantification of norovirus genogroups I and II. Virol Sin 2017; 32:139-146. [PMID: 28224385 DOI: 10.1007/s12250-016-3863-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [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: 09/05/2016] [Accepted: 01/13/2017] [Indexed: 12/31/2022] Open
Abstract
Noroviruses are the leading cause of acute gastroenteritis in humans. Real-time reverse transcription-polymerase chain reaction (real-time RT-PCR) is a promising molecular method for the detection of noroviruses. In this study, the performance of three TaqMan real-time RT-PCR assays was assessed, which were one commercially available real-time RT-PCR kit (assay A: Norovirus Real Time RT-PCR kit) and two in-house real-time RT-PCR assays (assay B: LightCycler RNA Master Hybprobe and assay C: RealTime ready RNA Virus Master). Assays A and B showed higher sensitivity than assay C for norovirus GI, while they all had the same sensitivity (103 DNA copies/mL) for GII DNA standard controls. Assay B had the highest efficiency for both genogroups. No cross-reactivity was observed among GI and GII noroviruses, rotavirus, hepatitis A virus, and poliovirus. The detection rates of these assays in GI and GII norovirus-positive fecal samples were not significantly different. However, the mean quantification cycle (Cq) value of assay B for GII was lower than assays A and C with statistical significance (P-value, 0.000). All three real-time RT-PCR assays could detect a variety of noroviruses including GI.2, GII.2, GII.3, GII.4, GII.6, GII.12, GII.17, and GII.21. This study suggests assay B as a suitable assay for the detection and quantification of noroviruses GI and GII due to good analytical sensitivity and higher performance to amplify norovirus on DNA standard controls and clinical samples.
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Affiliation(s)
- Kitwadee Rupprom
- Department of Microbiology, Faculty of Public Health, Mahidol University, Bangkok, 10400, Thailand
| | | | - Pornphan Diraphat
- Department of Microbiology, Faculty of Public Health, Mahidol University, Bangkok, 10400, Thailand
| | - Leera Kittigul
- Department of Microbiology, Faculty of Public Health, Mahidol University, Bangkok, 10400, Thailand.
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Parida M, Dash PK, Kumar JS, Joshi G, Tandel K, Sharma S, Srivastava A, Agarwal A, Saha A, Saraswat S, Karothia D, Malviya V. Emergence of influenza A (H1N1)pdm09 genogroup 6B and drug resistant virus, India, January to May 2015. ACTA ACUST UNITED AC 2016; 21:6-11. [PMID: 26876980 DOI: 10.2807/1560-7917.es.2016.21.5.30124] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [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: 12/11/2015] [Accepted: 02/04/2016] [Indexed: 11/20/2022]
Abstract
To investigate the aetiology of the 2015 A(H1N1)pdm09 influenza outbreak in India, 1,083 nasopharyngeal swabs from suspect patients were screened for influenza A(H1N1)pdm09 in the state of Madhya Pradesh. Of 412 positive specimens, six were further characterised by phylogenetic analysis of haemagglutinin (HA) sequences revealing that they belonged to genogroup 6B. A new mutation (E164G) was observed in HA2 of two sequences. Neuraminidase genes in two of 12 isolates from fatal cases on prior oseltamivir treatment harboured the H275Y mutation.
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Affiliation(s)
- Manmohan Parida
- Division of Virology, Defence Research & Development Establishment (DRDE), Gwalior, India
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Hoffmann D, Mauroy A, Seebach J, Simon V, Wantia N, Protzer U. New norovirus classified as a recombinant GII.g/GII.1 causes an extended foodborne outbreak at a university hospital in Munich. J Clin Virol 2013; 58:24-30. [PMID: 23849648 DOI: 10.1016/j.jcv.2013.06.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 05/24/2013] [Accepted: 06/11/2013] [Indexed: 11/22/2022]
Abstract
BACKGROUND Noroviruses are among the most prevalent causative agents for gastroenteritis worldwide. The low infectious dose, its stability in the environment, and its genetic variability enable the virus to cause outbreaks, especially in health care facilities and other similar settings. Genotype II.4 has been most prevalent over the last years. OBJECTIVES To characterize an extended norovirus outbreak at a university hospital in Munich, Germany, molecularly and epidemiologically. STUDY DESIGN The outbreak affecting more than 100 persons within 3 days was monitored by real time PCR. The rapid onset indicated a food-borne outbreak. Rigorous hygienic measures, including disinfection procedures and closure of wards helped contain the outbreak within 6 days. A 2193 nt sequence covering polymerase (825 nt) and capsid gene (1388 nt) was characterized from 4 specimens derived from different wards and the catering facility. RESULTS Our polymerase sequences were classified GII.g, whereas the capsid belonged to GII.1. Recombination analysis revealed a putative breakpoint at a typical location. Our sequenced region clustered with GIIg/GII.1 sequences first detected in Hungary, Belgium, and the US in 2010. p-Distances on nucleic acid level were 0.18 and 0.21, respectively. CONCLUSIONS Our data establish a novel strain classified as GII.g/GII.1 as the causative agent for an extended outbreak.
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