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Boxman ILA, Molin R, Persson S, Juréus A, Jansen CCC, Sosef NP, Le Guyader SF, Ollivier J, Summa M, Hautaniemi M, Suffredini E, Di Pasquale S, Myrmel M, Khatri M, Jamnikar-Ciglenecki U, Kusar D, Moor D, Butticaz L, Lowther JA, Walker DI, Stapleton T, Simonsson M, Dirks RAM. An international inter-laboratory study to compare digital PCR with ISO standardized qPCR assays for the detection of norovirus GI and GII in oyster tissue. Food Microbiol 2024; 120:104478. [PMID: 38431324 DOI: 10.1016/j.fm.2024.104478] [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: 10/10/2023] [Revised: 01/10/2024] [Accepted: 01/10/2024] [Indexed: 03/05/2024]
Abstract
An optimized digital RT-PCR (RT-dPCR) assay for the detection of human norovirus GI and GII RNA was compared with ISO 15216-conform quantitative real-time RT-PCR (RT-qPCR) assays in an interlaboratory study (ILS) among eight laboratories. A duplex GI/GII RT-dPCR assay, based on the ISO 15216-oligonucleotides, was used on a Bio-Rad QX200 platform by six laboratories. Adapted assays for Qiagen Qiacuity or ThermoFisher QuantStudio 3D were used by one laboratory each. The ILS comprised quantification of norovirus RNA in the absence of matrix and in oyster tissue samples. On average, results of the RT-dPCR assays were very similar to those obtained by RT-qPCR assays. The coefficient of variation (CV%) of norovirus GI results was, however, much lower for RT-dPCR than for RT-qPCR in intra-laboratory replicates (eight runs) and between the eight laboratories. The CV% of norovirus GII results was in the same range for both detection formats. Had in-house prepared dsDNA standards been used, the CV% of norovirus GII could have been in favor of the RT-dPCR assay. The ratio between RT-dPCR and RT-qPCR results varied per laboratory, despite using the distributed RT-qPCR dsDNA standards. The study indicates that the RT-dPCR assay is likely to increase uniformity of quantitative results between laboratories.
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Affiliation(s)
- Ingeborg L A Boxman
- Wageningen Food Safety Research (WFSR), Wageningen University and Research, Wageningen, the Netherlands.
| | - Ramia Molin
- European Union Reference Laboratory for Foodborne Viruses, Swedish Food Agency, Uppsala, Sweden.
| | - Sofia Persson
- European Union Reference Laboratory for Foodborne Viruses, Swedish Food Agency, Uppsala, Sweden.
| | - Anna Juréus
- European Union Reference Laboratory for Foodborne Viruses, Swedish Food Agency, Uppsala, Sweden.
| | - Claudia C C Jansen
- Wageningen Food Safety Research (WFSR), Wageningen University and Research, Wageningen, the Netherlands.
| | - Nils P Sosef
- Wageningen Food Safety Research (WFSR), Wageningen University and Research, Wageningen, the Netherlands.
| | - Soizick F Le Guyader
- French Research Institute for Exploitation of the Sea (Ifremer) - Laboratoire de Santé, Environnement et Microbiologie, Nantes, France.
| | - Joanna Ollivier
- French Research Institute for Exploitation of the Sea (Ifremer) - Laboratoire de Santé, Environnement et Microbiologie, Nantes, France.
| | | | | | - Elisabetta Suffredini
- Istituto Superiore di Sanità, Department of Food Safety, Nutrition and Veterinary Public Health, Rome, Italy.
| | - Simona Di Pasquale
- Istituto Superiore di Sanità, Department of Food Safety, Nutrition and Veterinary Public Health, Rome, Italy.
| | - Mette Myrmel
- Norwegian University of Life Sciences (NMBU), Faculty of Veterinary Medicine, Virology Unit, Ås, Norway.
| | - Mamata Khatri
- Norwegian University of Life Sciences (NMBU), Faculty of Veterinary Medicine, Virology Unit, Ås, Norway.
| | - Urska Jamnikar-Ciglenecki
- University of Ljubljana Veterinary Faculty, Institute of Food Safety, Feed and Environment, Ljubljana, Slovenia.
| | - Darja Kusar
- University of Ljubljana Veterinary Faculty, Institute of Microbiology and Parasitology, Ljubljana, Slovenia.
| | - Dominik Moor
- Federal Institute of Metrology METAS, Biological Analysis and References Laboratory, Bern, Switzerland.
| | - Lisa Butticaz
- Federal Institute of Metrology METAS, Biological Analysis and References Laboratory, Bern, Switzerland.
| | - James A Lowther
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, United Kingdom.
| | - David I Walker
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, United Kingdom.
| | - Tina Stapleton
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, United Kingdom.
| | - Magnus Simonsson
- European Union Reference Laboratory for Foodborne Viruses, Swedish Food Agency, Uppsala, Sweden.
| | - René A M Dirks
- Wageningen Food Safety Research (WFSR), Wageningen University and Research, Wageningen, the Netherlands.
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Plut J, Jamnikar-Ciglenecki U, Golinar-Oven I, Knific T, Stukelj M. A molecular survey and phylogenetic analysis of porcine circovirus type 3 using oral fluid, faeces and serum. BMC Vet Res 2020; 16:281. [PMID: 32778107 PMCID: PMC7419202 DOI: 10.1186/s12917-020-02489-y] [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: 04/30/2020] [Accepted: 07/22/2020] [Indexed: 11/23/2022] Open
Abstract
Background Porcine circovirus type 3 is the most recently discovered porcine circovirus, and an emerging pathogen. In this study the status of its presence on some Slovenian farms is reported. The effectiveness of the vaccine against porcine circovirus type 2 was assessed against porcine circovirus type 3. Group samples of oral fluid, faeces and individual serum samples were taken from six different pig categories and tested for presence of viral DNA, using both real time and conventional PCR. Positive samples were subjected to direct Sanger sequencing. Nucleotide sequences were analyzed and compared to GenBank PCV3 sequences. Results Positive samples were sent for genome sequencing, which confirmed the presence of virus in all different pig categories on five farms. A high to moderate correlation of strong statistical significance was found between individual serum samples, oral fluid and faeces. Slovenian PCV3 was found to be distributed in a way similar to that of other countries. Slovenian PCV3 nt sequences are highly related, sharing more than 99.5% nt identity. On one farm a commercially available vaccine against porcine circovirus type 2 was used on 3-week-old pigs. It did not affect the presence of porcine circovirus type 3 in oral fluid or sera of any of the seven age groups of pigs, each with two control groups. Conclusions The results constitute the first discovery of the virus in Slovenia. Genome sequencing has revealed a high degree of similarity between Slovenian and GenBank isolates.
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Affiliation(s)
- Jan Plut
- Clinic for Ruminants and Pigs, Clinic for Reproduction and Farm Animals, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia.
| | - Urska Jamnikar-Ciglenecki
- Department of Food Safety, Institute of Safe Food, Animal Nutrition and Environment, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Irena Golinar-Oven
- Clinic for Ruminants and Pigs, Clinic for Reproduction and Farm Animals, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Tanja Knific
- Institute of Microbiology and Parasitology, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Marina Stukelj
- Clinic for Ruminants and Pigs, Clinic for Reproduction and Farm Animals, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia
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Plut J, Jamnikar-Ciglenecki U, Stukelj M. Molecular detection of porcine reproductive and respiratory syndrome virus, porcine circovirus 2 and hepatitis E virus in oral fluid compared to their detection in faeces and serum. BMC Vet Res 2020; 16:164. [PMID: 32460762 PMCID: PMC7251745 DOI: 10.1186/s12917-020-02378-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 10/28/2019] [Accepted: 05/14/2020] [Indexed: 02/08/2023] Open
Abstract
Background Porcine Reproductive and Respiratory Syndrome Virus (PRRSV), Porcine Circovirus Type 2 (PCV2) and Hepatitis E virus (HEV) are common and economically important viral disease causative agents detected in pig oral fluid (OF), faeces and serum at some infection stages. The purpose of this study was to detect PRRSV, PCV2 and HEV on six pig farms to determine which of the three sample types, OF, faeces or serum is appropriate for the diagnosis of these viruses in different pig categories. The following pig categories were included: 5 weeks-old (w/o), 7 w/o, 9 w/o, 11 w/o weaners, fatteners and breeding sows. Pursuant to the preliminary detection of each pathogen at the selected farms, OF samples, faeces, serum pools and 10 individual sera were examined, using PCR, for each age category. If any of the viruses were found in pools of faeces and OF, then faeces and OF from positive farms were tested separately for each pig category. The viral nucleic acids were detected using RT-PCR, PCR and real-time RT-PCR, for PRRSV, PCV2 and HEV respectively. Results PRRSV and HEV were detected on one farm and PCV2 on three others, positive results being more often obtained from the OF than from the faeces of the same animals. Ten individual serum samples from pigs from the same group of animals were also tested. The viruses were detected in almost all individual sera and OF in the same pig category with some exceptions: PRRSV was detected in the OF of fatteners but was absent in their sera; on Farm 2, PCV2 was detected in sera of 11 w/o pigs and fatteners but absent in group samples of their OF and, vice versa, in case of 9 w/o animals; HEV was detected in the OF of the youngest, 5 w/o weaners and absent in sera of the same age group. Conclusions The primary finding of the study is that OF is a welfare-friendly, non-invasive and highly efficient matrix for pathogen detection, thus evidencing the usefulness of pig OF as a matrix in which each of the three viruses considered can be detected with the highest probability.
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Affiliation(s)
- Jan Plut
- Clinic for Ruminants and Pigs, Clinic for Reproduction and Farm Animals, Veterinary Faculty University of Ljubljana, Ljubljana, Slovenia.
| | - Urska Jamnikar-Ciglenecki
- Institute of Food Safety, Feed and Environment, Veterinary Faculty University of Ljubljana, Ljubljana, Slovenia
| | - Marina Stukelj
- Clinic for Ruminants and Pigs, Clinic for Reproduction and Farm Animals, Veterinary Faculty University of Ljubljana, Ljubljana, Slovenia
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Abstract
BackgroundClostridioides difficile is an important human and animal intestinal pathogen. Because of increasing indications of an association between C. difficile and food, in 2015, the Administration of the Republic of Slovenia for Food Safety, Veterinary Sector and Plant Protection (UVHVVR) included C. difficile in its national food surveillance.AimWe aim to report the results and experience with a nationwide and long-term testing of food for C. difficile as a part of a regular national food surveillance programme.MethodsRetail minced meat and meat preparations (beef, pork and poultry) were sampled within a three-year period, 2015 to 2017. Selected raw retail vegetables, leaf salads and root vegetables, and ready-to-eat salads were only sampled during 2016 and 2017. Seafood was only sampled in 2017.ResultsAltogether, 434 samples were tested, with 12 of 336 (3.6%) meat samples and 6 of 98 (6.1%) raw vegetables contaminated with C. difficile. Twelve of 18 recovered food isolates were toxigenic (toxinotypes 0, III, V, XII). The isolates belonged to 13 different PCR ribotypes, 001 being most common (5 isolates). Several food types with an increased potential of being contaminated with C. difficile were detected by surveillance.ConclusionThe three-year C. difficile testing within the national food surveillance revealed a low proportion of C. difficile-contaminated food and high genotype variability. Because the risk of C. difficile infection associated with C. difficile-contaminated food is unknown, no measures were recommended in the case of positive results.
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Affiliation(s)
- Valerija Tkalec
- National Laboratory for Health, Environment and Food, Maribor, Slovenia,Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | - Urska Jamnikar-Ciglenecki
- Institute of Food Safety, Feed and Environment, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Maja Rupnik
- National Laboratory for Health, Environment and Food, Maribor, Slovenia,Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | - Stanka Vadnjal
- Institute of Food Safety, Feed and Environment, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Katja Zelenik
- National Laboratory for Health, Environment and Food, Maribor, Slovenia
| | - Majda Biasizzo
- Institute of Food Safety, Feed and Environment, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia
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Jamnikar-Ciglenecki U, Civnik V, Kirbis A, Kuhar U. A molecular survey, whole genome sequencing and phylogenetic analysis of astroviruses from roe deer. BMC Vet Res 2020; 16:68. [PMID: 32085761 PMCID: PMC7035776 DOI: 10.1186/s12917-020-02289-4] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 02/17/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Although astroviruses (AstV) have been detected in a variety of host species, there are only limited records of their occurrence in deer. One of the most important game species in Europe, due to its meat and antlers, is roe deer. Infected game animals can pose a threat to the health of other animals and of humans, so more attention needs to be focused on understanding the diversity of viruses in wildlife. The complete genome and organization of the roe deer AstV genome have not so far been described. RESULTS In our study, 111 game animals were screened for the presence of AstV. While no AstVs were detected in red deer, wild boar, chamois and mouflon, AstV RNA was present in three samples of roe deer. They were further subjected to whole genome sequencing with next generation sequencing. In this study, two AstV genomes were assembled; one in sample D5-14 and one in sample D12-14, while, in sample D45-14, no AstV sequences were identified. The complete coding sequences of the AstV SLO/D5-14 strain genome and of the almost complete genome of the AstV SLO/D12-14 strain were determined. They showed a typical Mamastrovirus organization. Phylogenetic analyses and amino acid pairwise distance analysis revealed that Slovenian roe deer AstV strains are closely related to each other and, also, related to other deer, bovine, water buffalo, yak, Sichuan takin, dromedary, porcine and porcupine AstV strains - thus forming a highly supported group of currently unassigned sequences. CONCLUSIONS Our findings suggest the existence of a new Mamastrovirus genogroup might be constituted while this aforementioned group is distantly related to Mamastrovirus genogroups I and II. In this study, additional data supporting a novel taxonomic classification are presented.
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Affiliation(s)
- Urska Jamnikar-Ciglenecki
- Institute of Food safety, Feed and Environment, University of Ljubljana, Veterinary faculty, Gerbičeva 60, 1000, Ljubljana, Slovenia.
| | - Vita Civnik
- Institute of Food safety, Feed and Environment, University of Ljubljana, Veterinary faculty, Gerbičeva 60, 1000, Ljubljana, Slovenia
| | - Andrej Kirbis
- Institute of Food safety, Feed and Environment, University of Ljubljana, Veterinary faculty, Gerbičeva 60, 1000, Ljubljana, Slovenia
| | - Urska Kuhar
- Institute of Microbiology and Parasitology, University of Ljubljana, Veterinary faculty, Gerbičeva 60, 1000, Ljubljana, Slovenia
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Kuhar U, Jamnikar-Ciglenecki U. High detection rate and high genetic diversity of genogroup I Picobirnaviruses from roe deer. Infect Genet Evol 2019; 73:210-213. [PMID: 31059785 DOI: 10.1016/j.meegid.2019.05.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 04/26/2019] [Accepted: 05/02/2019] [Indexed: 01/08/2023]
Abstract
Picobirnaviruses (PBVs) have been characterized as opportunistic enteric pathogens detected in various domestic, zoo and wild animals, suggesting a wide host range of these viruses. It is thus important to monitor wild animals for the presence of various human and animal pathogens in order to identify a potential reservoir of infectious diseases. In this study, the first phylogenetic analysis of PBV from roe deer (Capreolus capreolus) was performed with a total of 70 investigated samples of feces from roe deer collected in 2014 and 2015 during a survey throughout Slovenia. A high detection rate of PBVs was observed with newly designed specific primers, 42 samples out of 70 (60%) being positive. Phylogenetic analysis of the partial RdRp gene showed that roe deer PBV sequences were distributed over the whole phylogenetic tree and were distributed between 7 highly supported groups and 12 separate branches within the PBV genogroup I. The animal PBV strain most closely related to roe deer PBV strains was the Rhesus macaque PBV/BGD/PbV-55 strain, with 89.1% nucleotide identity to that of PBV SLO/D80-14. Overall nucleotide sequence identity between PBV strains obtained from roe deer ranged from 60.4 to 100%, confirming the high genetic diversity with no subtypes related to host species or geographic location in general. This first phylogenetic survey of roe deer PBVs provides further knowledge concerning the putative host range and confirms the high genetic diversity of these PBVs.
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Affiliation(s)
- Urska Kuhar
- Institute of Microbiology and Parasitology, Veterinary faculty, University of Ljubljana, Gerbičeva 60, 1000 Ljubljana, Slovenia.
| | - Urska Jamnikar-Ciglenecki
- Institute of Food safety, Feed and Environment, Veterinary faculty, University of Ljubljana, Gerbičeva 60, 1000 Ljubljana, Slovenia
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Jamnikar-Ciglenecki U, Pislak Ocepek M, Toplak I. Genetic Diversity of Deformed Wing Virus From Apis mellifera carnica (Hymenoptera: Apidae) and Varroa Mite (Mesostigmata: Varroidae). J Econ Entomol 2019; 112:11-19. [PMID: 30285237 DOI: 10.1093/jee/toy312] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Indexed: 06/08/2023]
Abstract
Deformed wing virus (DWV) is one of the most widespread viruses that infect honey bee colonies. The route of infection is directly through contaminated food, feces, and air, or indirectly through the varroa mite, which acts as a vector. Positive DWV samples were obtained from Carniolan honey bee (Apis mellifera carnica) colonies and of varroa mites from the whole territory of Slovenia during a survey between 2007 and 2014. Nucleotide sequences of 471 nucleotides for the L protein gene and 573 nucleotides for the helicase gene were compared. High genetic diversity was observed among these Slovenian Carniolan honey bee DWV field samples, as well as with almost all the strains previously found in other countries in Europe. Phylogenetic analyses in two regions of the viral genome show that several of the DWV strains obtained from honey bees and varroa are genetically very closely related, confirming the important role of varroa in the transmission of DWV. Identification of closely related sequences also confirmed that the same strains of DWV have been successfully transmitted between various honey bee colonies and apiaries. It has also been established that simultaneous infection, in one apiary, of honey bees with two or more different strains of DWV is quite frequent. This is phylogenetic study that compares honey bee and varroa DWV strains from Carniolan honeybees.
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Affiliation(s)
- Urska Jamnikar-Ciglenecki
- Institute of Food safety, Feed and Environment, Veterinary faculty, University of Ljubljana, Gerbiceva, Ljubljana, Slovenia
| | - Metka Pislak Ocepek
- Institute of Pathology, Wild Animals, Fish and Bees, Veterinary faculty, University of Ljubljana, Gerbiceva, Ljubljana, Slovenia
| | - Ivan Toplak
- Institute of Microbiology and Parasitology, Veterinary faculty, University of Ljubljana, Gerbiceva, Ljubljana, Slovenia
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Biasizzo M, Vadnjal S, Henigman U, Krizman M, Kirbis A, Jamnikar-Ciglenecki U. Development and Validation of a New Protocol for Detecting and Recovering Clostridium difficile from Meat Samples. J Food Prot 2018; 81:561-568. [PMID: 29517350 DOI: 10.4315/0362-028x.jfp-17-354] [Citation(s) in RCA: 2] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
There is no recommended protocol for detecting and isolating Clostridium difficile present in food samples. Here, we have evaluated the recovery of C. difficile in meat samples after incubating them in various enrichment broths. The media were as follows: cycloserine-cefoxitin fructose broth supplemented with taurocholic acid, d-cycloserine, cefoxitin, and lysozyme; cycloserine-cefoxitin mannitol broth with taurocholate and lysozyme; and cycloserine-cefoxitin fructose broth supplemented with taurocholic acid, C. difficile moxalactam norfloxacin selective supplement, and lysozyme. Samples were inoculated with various strains and quantities of C. difficile and then enriched in the different broths for 1, 4, and 7 days. C. difficile was isolated on agar plates and detected with quantitative real-time PCR (qPCR). The procedure using enrichment in cycloserine-cefoxitin fructose broth supplemented with taurocholic acid, d-cycloserine, cefoxitin, and lysozyme and incubation for 4 days for qPCR detection and 7 days for isolation (plating on C. difficile agar base with added C. difficile selective supplement and 7% [v/v] defibrinated horse blood after alcoholic shock and centrifugation) was validated. Samples of different kinds of meat and meat preparation were contaminated and used for validation of the chosen protocol. The sensitivity of detection with qPCR was 100%, and the sensitivity of the isolation method was 96%.
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Affiliation(s)
- Majda Biasizzo
- Institute of Food Safety, Feed and Environment, Veterinary Faculty, University of Ljubljana, Gerbičeva 60, 1000 Ljubljana, Slovenia
| | - Stanka Vadnjal
- Institute of Food Safety, Feed and Environment, Veterinary Faculty, University of Ljubljana, Gerbičeva 60, 1000 Ljubljana, Slovenia
| | - Urska Henigman
- Institute of Food Safety, Feed and Environment, Veterinary Faculty, University of Ljubljana, Gerbičeva 60, 1000 Ljubljana, Slovenia
| | - Manja Krizman
- Institute of Food Safety, Feed and Environment, Veterinary Faculty, University of Ljubljana, Gerbičeva 60, 1000 Ljubljana, Slovenia
| | - Andrej Kirbis
- Institute of Food Safety, Feed and Environment, Veterinary Faculty, University of Ljubljana, Gerbičeva 60, 1000 Ljubljana, Slovenia
| | - Urska Jamnikar-Ciglenecki
- Institute of Food Safety, Feed and Environment, Veterinary Faculty, University of Ljubljana, Gerbičeva 60, 1000 Ljubljana, Slovenia
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Jamnikar-Ciglenecki U, Kuhar U, Steyer A, Kirbis A. Whole genome sequence and a phylogenetic analysis of the G8P[14] group A rotavirus strain from roe deer. BMC Vet Res 2017; 13:353. [PMID: 29178883 PMCID: PMC5702219 DOI: 10.1186/s12917-017-1280-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [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: 05/18/2017] [Accepted: 11/16/2017] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Group A rotaviruses (RVA) are associated with acute gastroenteritis in children and in young domestic and wild animals. A RVA strain was detected from a roe deer for the first time during a survey of game animals in Slovenia in 2014. A further RVA strain (SLO/D110-15) was detected from a roe deer during 2015. The aim of this study was to provide a full genetic profile of the detected RVA strain from roe deer and to obtain additional information about zoonotic transmitted strains and potential reassortments between human rotavirus strains and zoonotic transmitted rotavirus strains. The next generation sequencing (NGS) analysis on Ion Torrent was performed and the whole genome sequence has been determined together with a phylogenetic analysis. RESULTS The whole genome sequence of SLO/D110-15 was obtained by NGS analyses on an IonTorrent platform. According to the genetic profile, the strain SLO/D110-15 clusters with the DS-1-like group and expresses the G8-P[14]-I2-R2-C2-M2-A3-N2-T6-E2-H3 genome constellation. Phylogenetic analysis shows that this roe deer G8P[14] strain is most closely related to RVA strains found in sheep, cattle and humans. A human RVA strain with the same genotype profile was detected in 2009 in Slovenia. CONCLUSIONS The G8P[14] genotype has been found, for the first time, in deer, a newly described host from the order Artiodactyla for this RVA genotype. The finding of a rotavirus with the same genome segment constellation in humans indicates the possible zoonotic potential of this virus strain.
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Affiliation(s)
- Urska Jamnikar-Ciglenecki
- Institute of Food safety, Feed and Environment, Veterinary Faculty, University of Ljubljana, Gerbičeva 60, 1000, Ljubljana, Slovenia.
| | - Urska Kuhar
- Institute of Microbiology and Parasitology, Veterinary Faculty, University of Ljubljana, Gerbičeva 60, 1000, Ljubljana, Slovenia
| | - Andrej Steyer
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška 4, 1000, Ljubljana, Slovenia
| | - Andrej Kirbis
- Institute of Food safety, Feed and Environment, Veterinary Faculty, University of Ljubljana, Gerbičeva 60, 1000, Ljubljana, Slovenia
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Jamnikar-Ciglenecki U, Kuhar U, Sturm S, Kirbis A, Racki N, Steyer A. The first detection and whole genome characterization of the G6P[15] group A rotavirus strain from roe deer. Vet Microbiol 2016; 191:52-9. [PMID: 27374907 DOI: 10.1016/j.vetmic.2016.05.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [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: 04/01/2016] [Revised: 05/25/2016] [Accepted: 05/26/2016] [Indexed: 01/23/2023]
Abstract
Although rotaviruses have been detected in a variety of host species, there are only limited records of their occurrence in deer, where their role is unknown. In this study, group A rotavirus was identified in roe deer during a study of enteric viruses in game animals. 102 samples of intestinal content were collected from roe deer (56), wild boars (29), chamois (10), red deer (6) and mouflon (1), but only one sample from roe deer was positive. Following whole genome sequence analysis, the rotavirus strain D38/14 was characterized by next generation sequencing. The genotype constellation, comprising 11 genome segments, was G6-P[15]-I2-R2-C2-M2-A3-N2-T6-E2-H3. Phylogenetic analysis of the VP7 genome segment showed that the D38/14 rotavirus strain is closely related to the various G6 zoonotic rotavirus strains of bovine-like origin frequently detected in humans. In the VP4 segment, this strain showed high variation compared to that in the P[15] strain found in sheep and in a goat. This finding suggests that rotaviruses from deer are similar to those in other DS-1 rotavirus groups and could constitute a source of zoonotically transmitted rotaviruses. The epidemiological status of group A rotaviruses in deer should be further investigated.
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Affiliation(s)
- Urska Jamnikar-Ciglenecki
- Institute of Food Safety, Feed and Environment, Veterinary Faculty, University of Ljubljana, Gerbičeva 60, 1000 Ljubljana, Slovenia.
| | - Urska Kuhar
- Institute of Microbiology and Parasitology, Veterinary Faculty, University of Ljubljana, Gerbičeva 60, 1000 Ljubljana, Slovenia
| | - Sabina Sturm
- Institute of Food Safety, Feed and Environment, Veterinary Faculty, University of Ljubljana, Gerbičeva 60, 1000 Ljubljana, Slovenia
| | - Andrej Kirbis
- Institute of Food Safety, Feed and Environment, Veterinary Faculty, University of Ljubljana, Gerbičeva 60, 1000 Ljubljana, Slovenia
| | - Nejc Racki
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Andrej Steyer
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška 4,1000 Ljubljana, Slovenia
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