RESUMEN
Winter mortality of honey bee colonies represents a major source of economic loss for the beekeeping industry. The objectives of this prospective study were to estimate the incidence risk of winter colony mortality in southwestern Quebec, Canada and to evaluate and quantify the impact of the associated risk factors. A total of 242 colonies from 31 apiaries was selected for sampling in August 2017. The presence of Varroa destructor, Vairimorpha (Nosema) spp., Melissococcus plutonius, deformed wing virus (DWV), and viruses of the acute-Kashmir-Israeli complex (AKI complex) was investigated in each colony. Management practices of the various colonies were obtained from a questionnaire. The incidence risk of colony mortality during the winter of 2017-2018 was estimated to be 26.5% [95% confidence interval (CI): 15.4 to 40.3]. In logistic regression modeling of winter mortality in colonies, an interaction was discovered between V. destructor and DWV; the detection of ≥ 1 V. destructor mites per 100 bees was associated with higher odds of mortality (3.46, 95% CI: 1.35 to 8.90) compared to colonies with < 1 mite per 100 bees, but only in DWV-positive colonies. There were more colony losses in apiaries from beekeepers owning 1 to 5 colonies than in apiaries from beekeepers owning over 100 colonies, which suggests that beekeeper experience and/or type of management are important contributors to winter colony mortality. Assuming a causal relationship, the results of this study suggest that up to 9% of all colony mortalities in the population could have been prevented by reducing the level of V. destructor to < 1 mite per 100 bees in all colonies.
La mortalité hivernale des colonies d'abeilles est une cause importante de pertes économiques en apiculture. Cette étude prospective visait à estimer le risque d'incidence de mortalité hivernale des colonies d'abeilles et les facteurs de risque associés dans le sud-ouest du Québec (Canada). Au total, 242 colonies provenant de 31 ruches ont été sélectionnées en août 2017. La présence de Varroa destructor, de Vairimorpha (Nosema) spp., de Melissococcus plutonius, du virus des ailes déformées (DWV) et des virus du complexe AKI ont été évalués. Les pratiques de régie ont été obtenues selon un questionnaire. Le risque de mortalité des colonies à l'hiver 20172018 a été estimé à 26,5 % (95 % CI : 15,4 à 40,3). Dans un modèle de régression logistique, la détection de ≥ 1 mite de V. destructor par 100 abeilles était associée à des cotes plus élevées de mortalité (3,46, 95 % CI : 1,35 à 8,90) comparativement aux colonies avec < 1 mite par 100 abeilles, mais seulement pour les colonies positives au DWV. Les ruchers d'apiculteurs possédant entre 1 et 5 colonies présentaient une mortalité plus élevée comparativement à ceux d'apiculteurs possédant plus de 100 colonies, suggérant une influence de l'expérience ou du type de régie. En assumant une relation causale, les résultats de cette étude suggèrent que jusqu'à 9 % de toutes les mortalités hivernales observées dans la population auraient pu être prévenues en réduisant le niveau d'infestation par V. destructor à moins d'une mite per 100 abeilles dans toutes les colonies.(Traduit par les auteurs).
Asunto(s)
Estaciones del Año , Varroidae , Animales , Abejas/virología , Abejas/parasitología , Varroidae/virología , Virus ARN/aislamiento & purificación , Quebec/epidemiología , ApiculturaRESUMEN
Honey bees can be affected by a variety of pathogens, which impacts their vital role as pollinators in agriculture. A cross-sectional study was conducted in southwestern Quebec to: i) estimate the prevalence of 11 bee pathogens; ii) assess the agreement between beekeeper suspicion of a disease and laboratory detection of the causative pathogen; and iii) explore the association between observed clinical signs and pathogen detection in a colony. A total of 242 colonies in 31 apiaries owned by 15 beekeepers was sampled in August 2017. The prevalence of Varroa destructor detection was estimated as 48% for colonies and 93% for apiaries. The apparent prevalence of colonies infected by Nosema spp. and Melissococcus plutonius was estimated as 40% and 21%, respectively. At least 180 colonies were tested by polymerase chain reaction (PCR) for deformed wing virus (DWV), acute-Kashmir-Israeli complex (AKI complex), and black queen cell virus (BQCV), which were detected in 33%, 9%, and 95% of colonies, respectively. Acarapis woodi, Paenibacillus larvae, and Aethina tumida were not detected. Varroasis was suspected by beekeepers in 14 of the 15 beekeeping operations in which the mite was detected. However, no correlation was found between suspected European foulbrood and detection of M. plutonius or between suspected nosemosis and detection of Nosema spp. Colony weakness was associated with Nosema spore counts of at least 0.5 × 106 per bee. Melissococcus plutonius was more frequently detected in colonies showing scattered brood.
Les abeilles mellifères peuvent être affectées par plusieurs agents pathogènes, impactant leur rôle vital de pollinisateur en agriculture. Une étude transversale a été réalisée dans le sud-ouest du Québec afin 1) d'estimer la prévalence de onze agents pathogènes de l'abeille, 2) d'évaluer l'accord entre la suspicion d'une maladie par l'apiculteur et la détection de l'agent causal, 3) d'explorer les associations entre les signes cliniques et la détection d'un agent pathogène dans une colonie. Au total, 242 colonies de 31 ruchers appartenant à 15 apiculteurs ont été échantillonnées en août 2017. La prévalence de Varroa destructor a été estimée à 48 % pour les colonies et à 93 % pour les ruchers. La prévalence apparente de colonies infectées par Nosema spp. ou Melissococcus plutonius a été estimée à respectivement 40 % et 21 %. Le virus des ailes déformées, le complexe viral AKI et le virus de la reine noire ont été détectés dans respectivement 33 %, 9 % et 95 % dans des 180 colonies testées par PCR. Acarapis woodi, Paenibacillus larvae et Aethina tumida n'ont pas été détectés. La varroase était suspectée par les apiculteurs de 14 des 15 entreprises où la mite a été détectée. Aucune corrélation n'a été trouvée entre la suspicion de loque européenne et la détection de M. plutonius ou entre la suspicion de nosémose et la détection de Nosema spp. La faiblesse des colonies a été associée à des comptes de Nosema d'au moins 0,5 × 106 spores par abeille. Melissococcus plutonius était plus fréquemment détecté parmi les colonies présentant du couvain en mosaïque.(Traduit pas les auteurs).
Asunto(s)
Estudios Transversales , Enterococcaceae , Virus ARN , Abejas , Animales , Quebec/epidemiología , PrevalenciaRESUMEN
Swine are an important food source worldwide and producers may not always be aware of the variety of the pathogens infecting their herds, particularly viruses. In this study, 12 enteric viruses were monitored in a total of 181 diarrheic and healthy piglets; namely porcine astrovirus groups 1-5 (poAstV1-5), rotavirus A and C (RVA-RVC), caliciviruses (CaVs), porcine kobuvirus (PoK), hepatitis E virus (HEV), and torque teno sus virus 1 and k2 (TTsuV1-k2). All animals were sampled before 3 weeks of age, and then at 5, 12 and 20 weeks of age. In addition to the 12 targeted viruses, the virome of 12 piglets at 4 different life stages was characterized using a high-throughput sequencing approach. The presence of CaV (sapovirus), poAstV-3 or poAstV-5 was found to be a risk factor for neonatal diarrhea. Co-infections with RVC and poAstV-2, poAstV-3, and poAstV-4 and CaV co-infected with PoK or poAstV-4 were also found to be risk factors for diarrhea in piglets. RVC, PoK, poAstV-3 and poAstV-4 were the most prevalent viruses in piglets below 3 weeks of age. PoAstV-2, poAstV-4, TTsuV1 and TTsuVk2 were found to be the most prevalent viruses infecting piglets of 20 weeks of age. The enteric virome composition varied between healthy and diarrheic piglets. The alpha and beta diversity of the enteric viromes varied from under 3 weeks of age to 20 weeks and was mainly supported by phages. Overall, this study sheds new light on enteric virome dynamics and the virome's relationship with neonatal diarrhea.
Asunto(s)
Kobuvirus , Enfermedades de los Porcinos , Animales , Diarrea/veterinaria , Heces , Filogenia , Porcinos , ViromaRESUMEN
The porcine enteric microbiota is currently extensively studied, taking advantage of developments in high-throughput sequencing technologies. However, the viral part of the microbiota, the virome, is being lightly explored, and the impact of the pretreatments used before sequencing the viruses is barely considered. In this study, the impacts of filtration, RNase and DNase treatments on virus reads recovery and diversity after sequencing on a MiSeq platform were assessed on fecal samples individually taken at <3, 5, 12 and 20 weeks from two piglets. None of the four pretreatment series affected the virus read averages or influenced diversity, but the samples with the higher proportion of reads corresponding to an entry in the "nt" database were those receiving the least number of pretreatments. The enzymatic pretreatments affected the detection of the single-stranded RNA viruses of Aichivirus C, porcine astrovirus, Sapovirus and posavirus, which is worrisome, as these viruses can be involved in swine diarrhea. If enzymatic pretreatments are used when sequencing using a high-throughput method, it may impact single-stranded RNA virus recovery, but not the overall virome diversity. Therefore, filtrated samples may be the better option, reducing the amount of bacterial genetic material while preserving the virus reads.
Asunto(s)
Viroma , Virus , Animales , Diarrea , Heces , Secuenciación de Nucleótidos de Alto Rendimiento , Porcinos , Virus/genéticaRESUMEN
The family Caliciviridae includes viruses with single-stranded, positive-sense RNA genomes of 7.4-8.3 kb. The most clinically important representatives are human noroviruses, which are a leading cause of acute gastroenteritis in humans. Virions are non-enveloped with icosahedral symmetry. Members of seven genera infect mammals (Lagovirus, Norovirus, Nebovirus, Recovirus, Sapovirus, Valovirus and Vesivirus), members of two genera infect birds (Bavovirus and Nacovirus), and members of two genera infect fish (Minovirus and Salovirus). This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Caliciviridae, which is available at ictv.global/report/caliciviridae.
Asunto(s)
Caliciviridae/clasificación , ARN Viral/genética , Virión/ultraestructura , Animales , Aves , Caliciviridae/genética , Caliciviridae/aislamiento & purificación , Caliciviridae/ultraestructura , Infecciones por Caliciviridae/virología , Peces , MamíferosRESUMEN
Porcine kobuviruses are widely distributed in swine, but the clinical significance of these viruses remains unclear, since they have been associated with both diarrheic and healthy pigs. In addition, there is a paucity of data on Kobuvirus prevalence in Canadian pig herds. In this study, a total of 181 diarrheic and healthy piglets were monitored and sampled on four occasions, intended to represent the different stages of production. The piglets were sampled at the nursing farms (birth to weaning stage), at the nursery farms (post-weaning stage), and at finishing farms (at the beginning and the end of the fattening stage). Fecal and environmental samples were collected during each life stage. Following viral extraction, Kobuvirus detection by RT-PCR was conducted, and positive samples were sequenced. During the late-nursing stage (6-21 days old), piglets with diarrhea shed more Kobuvirus than healthy individuals. Piglets shed more Kobuvirus during the post-weaning stage (nursery farms) than during any of the other life stages. This was evidenced in individual samples as well as in environmental samples. Over 97% of the sampled piglets shed Kobuvirus at least once in their lifetime. All piglets shedding a Kobuvirus strain or mix of strains at the nursing stage did not appear to shed another porcine kobuvirus strain at a later life stage. Overall, our findings throw light on Kobuvirus shedding dynamics and their potential role in neonatal diarrhea at the nursing stage, which appears to be the point of entry for kobuviruses into swine production systems.
Asunto(s)
Diarrea/veterinaria , Kobuvirus/fisiología , Infecciones por Picornaviridae/veterinaria , Enfermedades de los Porcinos/virología , Esparcimiento de Virus , Factores de Edad , Animales , Diarrea/virología , Granjas , Heces/virología , Kobuvirus/aislamiento & purificación , Filogenia , Infecciones por Picornaviridae/virología , ARN Viral , Análisis de Secuencia de ADN , Porcinos , DesteteRESUMEN
Mycobacterium avium subspecies paratuberculosis (Map) is the etiological agent of paratuberculosis of domestic and wild ruminants. Map strains are segregated into 2 main groups or strain types referred to as sheep (S) type and cattle (C) type. Few small ruminant Map strains have been genetically characterized to date. The present study was undertaken to genetically characterize a panel of 30 small ruminant Map strains in the province of Quebec, Canada. Mycobacterial Interspersed Repetitive Units - Variable-Number Tandem Repeat analysis (MIRU-VNTR) were used as genetic markers in addition to IS1311 PCR-REA. S-type and C-type strains were found in both sheep and goats, although C-type strains were more frequently isolated from goats and S-type strains were more common in sheep. A total of 12 distinct Map genotypes were uncovered in the present collection of strains using these markers. Considering the genetic diversity reported here, molecular characterization of Map stains in small ruminants using MIRU-VNTR markers represent an interesting avenue for both epidemiological investigations regarding the sources of herd infection and association studies between Map strains and their virulence, persistence and host-specific adaptation characteristics.
Mycobacterium avium subspecies paratuberculosis (Map) est l'agent étiologique de la paratuberculose affectant les ruminants sauvages et domestiques. Les souches de Map se répartissent dans deux grands groupes ou types appelés 'sheep (S)' et 'cattle (C)'. Très peu de souches de Map provenant des petits ruminants ont été caractérisées génétiquement jusqu'à présent. Cette étude a été initiée afin de caractériser un ensemble de 30 souches de Map provenant de 5 troupeaux de moutons et 8 troupeaux de chèvres situés dans la province de Quebec, Canada, et d'évaluer leur diversité génétique. Une analyse répétée en tandem des unités répétitives alternées des mycobactéries (MIRU-VNTR) a été utilisée comme marqueurs génétiques en plus du marqueur IS1311 PCR-REA. Les souches de type S et C ont été retrouvées chez les isolats ovins et caprins, avec une prédominance des souches de type C chez les isolats provenant de chèvres tandis que les souches de type S étaient plus fréquentes chez les moutons. Un total de 12 génotypes distincts de Map ont été retrouvés parmi les isolats d'après les marqueurs utilisés. Considérant la diversité génétique observée, la caractérisation moléculaire des isolats de Map représente une avenue intéressante pour investiguer les sources potentielles d'infection des troupeaux et pour étudier les associations entre les caractéristiques génétiques et pathogéniques des isolats.(Traduit par les auteurs).
Asunto(s)
Enfermedades de las Cabras/microbiología , Mycobacterium avium subsp. paratuberculosis/clasificación , Paratuberculosis/microbiología , Enfermedades de las Ovejas/microbiología , Alelos , Animales , Bovinos , Enfermedades de los Bovinos/epidemiología , Enfermedades de los Bovinos/microbiología , ADN Bacteriano/genética , Genotipo , Enfermedades de las Cabras/epidemiología , Cabras , Repeticiones de Minisatélite , Mycobacterium avium subsp. paratuberculosis/genética , Paratuberculosis/epidemiología , Quebec , Ovinos , Enfermedades de las Ovejas/epidemiologíaRESUMEN
Paratuberculosis is a chronic infectious enteritis of ruminants caused by Mycobacterium avium subsp. paratuberculosis (MAP). In sheep, the antemortem detection of the infection is challenging given the slow progression of the disease and the lack of sensitive, specific, and cost-effective validated tests. We adapted an in-house real-time PCR (rtPCR) assay targeting the multi-copy IS 900 element of MAP. The sensitivity and specificity of this essay for the detection of MAP infection were estimated in a convenience sample of culled ewes from 7 infected flocks and compared to a commercial fecal rtPCR, a commercial ELISA, and fecal culture. An infected ewe was defined as a ewe with a positive culture of the ileum and/or mesenteric lymph node. A non-infected ewe was defined as a ewe negative in intestinal tissue culture, negative in fecal culture, and with no lesions consistent with paratuberculosis. The in-house rtPCR had a sensitivity estimate of 84% (95% confidence interval [CI]: 59%, 97%) among the 44 infected ewes, which was significantly higher ( p ⩽ 0.05) than the sensitivity of a commercial fecal rtPCR (52%, 95% CI: 27%, 76%; or 63%, 95% CI: 35%, 87% depending on the cutoff used), an ELISA (14%, 95% CI:2.0%, 41%), and fecal culture (21%, 95% CI: 2.7%, 59%). No statistical difference in assay specificities was observed for the 30 non-infected ewes. The in-house rtPCR is a promising tool that could be used advantageously for the antemortem detection of MAP infection in sheep.
Asunto(s)
Pruebas Diagnósticas de Rutina/veterinaria , Ensayo de Inmunoadsorción Enzimática/veterinaria , Heces/microbiología , Mycobacterium avium subsp. paratuberculosis/aislamiento & purificación , Paratuberculosis/diagnóstico , Reacción en Cadena en Tiempo Real de la Polimerasa/veterinaria , Enfermedades de las Ovejas/diagnóstico , Animales , Pruebas Diagnósticas de Rutina/métodos , Ensayo de Inmunoadsorción Enzimática/métodos , Femenino , Paratuberculosis/microbiología , Reacción en Cadena en Tiempo Real de la Polimerasa/métodos , Sensibilidad y Especificidad , Ovinos , Enfermedades de las Ovejas/microbiologíaRESUMEN
Modern swine production systems represent complex and dynamic networks involving numerous stakeholders. For instance, livestock transporters carry live animals between fattening sites, abattoirs, and other premises on a daily basis. This interconnected system may increase the risk of microbial spread within and between networks, although little information is available in that regard. In the present study, a swine network composed of 10 finishing farms, one abattoir, and three types of stakeholders (veterinarians, livestock transporters, and nutritional technicians) in Quebec, Canada, was selected to investigate specific vectors and reservoirs of enteric viruses. Environmental samples were collected from the premises over a 12-month period. Samples were screened using targeted reverse transcription-PCR and sequencing of two selected viral markers, group A rotaviruses (RVA) and porcine astroviruses (PoAstV), both prevalent and genetically heterogeneous swine enteric viruses. The results revealed frequent contamination of farm sites (21.4 to 100%), livestock transporter vehicles (30.6 to 68.8%) and, most importantly, the abattoir yard (46.7 to 94.1%), depending on the sample types. Although high levels of strain diversity for both viruses were found, identical PoAstV and RVA strains were detected in specific samples from farms, the abattoir yard, and the livestock transporter vehicle, suggesting interconnections between these premises and transporters. Overall, the results from this study underscore the potential role of abattoirs and livestock transport as a reservoir and transmission route for enteric viruses within and between animal production networks, respectively. IMPORTANCE: Using rotaviruses and astroviruses as markers of enteric contamination in a swine network has revealed the potential role of abattoirs and livestock transporters as a reservoir and vectors of enteric pathogens. The results from this study highlight the importance of tightening biosecurity measures. For instance, implementing sanitary vacancy between animal batches and emphasizing washing, disinfection, and drying procedures on farms and for transportation vehicles, as well as giving limited access and circulation of vehicles throughout the production premises, are some examples of measures that should be applied properly. The results also emphasize the need to closely monitor the dynamics of enteric contamination in the swine industry in order to better understand and potentially prevent the spread of infectious diseases. This is especially relevant when a virulent and economically damaging agent is involved, as seen with the recent introduction of the porcine epidemic diarrhea virus in the country.
Asunto(s)
Crianza de Animales Domésticos/métodos , Astroviridae/aislamiento & purificación , Diarrea/veterinaria , Enterovirus Porcinos/aislamiento & purificación , Rotavirus/aislamiento & purificación , Enfermedades de los Porcinos/epidemiología , Porcinos/virología , Mataderos , Animales , Astroviridae/genética , Canadá , Diarrea/virología , Infecciones por Enterovirus/veterinaria , Infecciones por Enterovirus/virología , Enterovirus Porcinos/genética , Granjas , Contaminación de Alimentos , Ganado/virología , Rotavirus/genética , Enfermedades de los Porcinos/virologíaRESUMEN
Viral contamination along the production chain is a significant concern in both food safety and livestock health. Pigs have been reported to act as a reservoir for zoonotic viruses, sometimes emerging ones, and epidemiological studies have shown direct links between the consumption of uncooked pork offal and cases of hepatitis caused by the hepatitis E virus (HEV) genotype 3 in humans. The presence of HEV in swine herds has been reported, but its dissemination in pork production environments is still unknown. To investigate viral contamination sources in the swine industry, 452 environment and fecal samples, including samples from livestock transportation vehicles, were collected over a period of 11 months from ten farms and one slaughterhouse that together represent a single production network. Hepatitis E virus RNA was detected by nested RT-PCR in 32 samples from both inside and outside farm buildings, on trucks, and, mostly, from fomites collected in the slaughterhouse yard, such as on a utility vehicle. Phylogenetic analysis showed a wide diversity of HEV genotype 3 strains, similar to human and swine strains previously found. According to the results of this study, the movements of trucks and utility vehicles might play an important role in HEV dissemination on a slaughterhouse site and throughout an entire network.
Asunto(s)
Virus de la Hepatitis E/clasificación , Virus de la Hepatitis E/aislamiento & purificación , Hepatitis E/veterinaria , Filogenia , Enfermedades de los Porcinos/virología , Animales , Canadá , Heces/virología , Contaminación de Alimentos/análisis , Inocuidad de los Alimentos , Genotipo , Hepatitis E/virología , Virus de la Hepatitis E/genética , Humanos , Carne/virología , PorcinosRESUMEN
Pan-viral DNA array (PVDA) and high-throughput sequencing (HTS) are useful tools to identify novel viruses of emerging diseases. However, both techniques have difficulties to identify viruses in clinical samples because of the host genomic nucleic acid content (hg/cont). Both propidium monoazide (PMA) and ethidium bromide monoazide (EMA) have the capacity to bind free DNA/RNA, but are cell membrane-impermeable. Thus, both are unable to bind protected nucleic acid such as viral genomes within intact virions. However, EMA/PMA modified genetic material cannot be amplified by enzymes. In order to assess the potential of EMA/PMA to lower the presence of amplifiable hg/cont in samples and improve virus detection, serum and lung tissue homogenates were spiked with porcine reproductive and respiratory virus (PRRSV) and were processed with EMA/PMA. In addition, PRRSV RT-qPCR positive clinical samples were also tested. EMA/PMA treatments significantly decreased amplifiable hg/cont and significantly increased the number of PVDA positive probes and their signal intensity compared to untreated spiked lung samples. EMA/PMA treatments also increased the sensitivity of HTS by increasing the number of specific PRRSV reads and the PRRSV percentage of coverage. Interestingly, EMA/PMA treatments significantly increased the sensitivity of PVDA and HTS in two out of three clinical tissue samples. Thus, EMA/PMA treatments offer a new approach to lower the amplifiable hg/cont in clinical samples and increase the success of PVDA and HTS to identify viruses.
Asunto(s)
Azidas/metabolismo , Etidio/metabolismo , Técnicas de Diagnóstico Molecular/métodos , Análisis de Secuencia por Matrices de Oligonucleótidos/métodos , Síndrome Respiratorio y de la Reproducción Porcina/diagnóstico , Virus del Síndrome Respiratorio y Reproductivo Porcino/aislamiento & purificación , Propidio/análogos & derivados , Animales , Ensayos Analíticos de Alto Rendimiento , Pulmón/virología , Propidio/metabolismo , Sensibilidad y Especificidad , Suero/virología , PorcinosRESUMEN
The molecular epidemiology of small ruminant lentiviruses (SRLVs) is constantly changing due to animal movements, cross species transmission and because of their rapid evolutionary rate. This study reports a comprehensive genetic and phylogenetic analysis based on consensus gag and pol sequences covering 3kb of the SRLV genome from small ruminants in Québec, Canada. A group of strains obtained from goats originating from different flocks, segregated in a unique clade distinct from currently known SRLV groups. Genetic dissection of the gag gene from these strains revealed that it originated as a result of a recombination event between parental strains currently circulating in small ruminants of the country. Following HIV nomenclature, we propose to call this group of strains, circulating recombinant form 1 SRLV, or CRF01_AB SRLV. In addition, the study confirms the existence of genetically distinct and homogeneous populations of SRLVs infecting sheep and goats housed in single species flocks.
Asunto(s)
Enfermedades de las Cabras/virología , Infecciones por Lentivirus/veterinaria , Lentivirus Ovinos-Caprinos/genética , Lentivirus Ovinos-Caprinos/aislamiento & purificación , Enfermedades de las Ovejas/virología , Secuencia de Aminoácidos , Animales , ADN Viral/genética , Proteínas de Fusión gag-pol/química , Proteínas de Fusión gag-pol/genética , Variación Genética , Enfermedades de las Cabras/epidemiología , Cabras , Infecciones por Lentivirus/epidemiología , Infecciones por Lentivirus/virología , Lentivirus Ovinos-Caprinos/clasificación , Datos de Secuencia Molecular , Filogenia , Quebec/epidemiología , Alineación de Secuencia , Pruebas Serológicas , Ovinos , Enfermedades de las Ovejas/epidemiologíaRESUMEN
Canonical human astroviruses (HAstVs) are important enteric pathogens that can be classified genetically and antigenically into eight types. Sequence analysis of small diagnostic regions at either the 5' or 3' end of ORF2 (capsid precursor) is a good proxy for prediction of HAstV types and for distinction of intratypic genetic lineages (subtypes), although lineage diversification/classification has not been investigated systematically. Upon sequence and phylogenetic analysis of the full-length ORF2 of 86 HAstV strains selected from the databases, a detailed classification of HAstVs into lineages was established. Three main lineages could be defined in HAstV-1, four in HAstV-2, two in HAstV-3, three in HAstV-4, three in HAstV-5 and two in HAstV-6. Intratypic (inter-lineages) ORF2 recombinant strains were identified in type 1 (1b/1d) and type 2 (2c/2b) with distinct crossover points. Other potential intratypic recombinant strains were identified in type 3, type 5 and type 6. In addition, a type-1b strain with a large insertion (~600 bp) of heterologous RNA in the N-terminal region and a type-6 strain with a large RNA rearrangement in the hypervariable region were identified. The classification scheme was integrated in a novel nomenclature system suitable for designation of HAstV strains.
Asunto(s)
Reordenamiento Génico , Mamastrovirus/clasificación , Mamastrovirus/genética , Recombinación Genética , Proteínas Virales/genética , Análisis por Conglomerados , Biología Computacional , Genotipo , Humanos , Filogenia , Análisis de Secuencia de ADN , Homología de SecuenciaRESUMEN
Mycobacterium avium subsp. paratuberculosis is the etiological agent of paratuberculosis, a granulomatous enteritis affecting a wide range of domestic and wild ruminants worldwide. A variety of molecular typing tools are used to distinguish M. avium subsp. paratuberculosis strains, contributing to a better understanding of M. avium subsp. paratuberculosis epidemiology. In the present study, PCR-based typing methods, including mycobacterial interspersed repetitive units/variable-number tandem repeats (MIRU-VNTR) and small sequence repeats (SSR) in addition to IS1311 PCR-restriction enzyme analysis (PCR-REA), were used to investigate the genetic heterogeneity of 200 M. avium subsp. paratuberculosis strains from dairy herds located in the province of Quebec, Canada. The majority of strains were of the "cattle type," or type II, although 3 strains were of the "bison type." A total of 38 genotypes, including a novel one, were identified using a combination of 17 genetic markers, which generated a Simpson's index of genetic diversity of 0.876. Additional analyses revealed no differences in genetic diversity between environmental and individual strains. Of note, a spatial and spatiotemporal cluster was evidenced regarding the distribution of one of the most common genotypes. The population had an overall homogeneous genetic structure, although a few strains stemmed out of the consensus cluster, including the bison-type strains. The genetic structure of M. avium subsp. paratuberculosis populations within most herds suggested intraherd dissemination and microevolution, although evidence of interherd contamination was also revealed. The level of genetic diversity obtained by combining MIRU-VNTR and SSR markers shows a promising avenue for molecular epidemiology investigations of M. avium subsp. paratuberculosis transmission patterns.
Asunto(s)
Variación Genética , Tipificación Molecular , Mycobacterium avium subsp. paratuberculosis/clasificación , Mycobacterium avium subsp. paratuberculosis/genética , Paratuberculosis/epidemiología , Paratuberculosis/microbiología , Reacción en Cadena de la Polimerasa , Animales , Bovinos , Análisis por Conglomerados , Evolución Molecular , Genotipo , Epidemiología Molecular , Mycobacterium avium subsp. paratuberculosis/aislamiento & purificación , Quebec/epidemiología , Análisis Espacio-TemporalRESUMEN
Group A rotaviruses (RVA) in pigs have been poorly investigated in Canada. In a continued effort to fill this gap, ten finisher swine farms in Quebec, Canada, were sampled over a nine-month period. The presence of RVA was detected in healthy pigs on all farms investigated during the entire sampling period. The genotypes detected included G2, G5, G9 and G11; P[6], P[7], P[13], P[27] and P[34]; and I5 and I14. The predominant types were G2, P[13] and I5, which is different from previous global reports. Various fomites were consistently contaminated by RVA, suggesting that a resident viral flora remains in the farm environment and may play a role in the infection of incoming pigs. The results also suggest temporal or geographical specificities regarding strain distribution on pig farms.
Asunto(s)
Variación Genética , Infecciones por Rotavirus/veterinaria , Rotavirus/genética , Enfermedades de los Porcinos/virología , Animales , Antígenos Virales/genética , Antígenos Virales/metabolismo , Secuencia de Bases , Proteínas de la Cápside/genética , Proteínas de la Cápside/metabolismo , Heces/virología , Regulación Viral de la Expresión Génica , Datos de Secuencia Molecular , Filogenia , Quebec/epidemiología , Rotavirus/clasificación , Infecciones por Rotavirus/epidemiología , Infecciones por Rotavirus/virología , Alineación de Secuencia/veterinaria , Porcinos , Enfermedades de los Porcinos/epidemiologíaRESUMEN
Previous molecular analyses of small ruminant lentivirus (SRLV) populations in single species herds in Quebec, Canada, have revealed a relatively simple structure where goats and sheep appeared exclusively infected with B1 and A2 subtypes respectively. The present work aimed at extending these earlier findings with the analysis of SRLVs in mixed flocks. Molecular analyses revealed a more complex picture of SRLV population structure in mixed herds compared to single species herds. Notably, phylogenetic analyses of long gag sequences strongly support transmission of A2 subtype from sheep to goats as well as transmission of B1 subtype from goats to sheep. Hence, this work uncovered for the first time natural transmission between sheep and goats of North American subtype A2. In addition, multiple evidences of mixed infection of sheep and goats with A2 and B1 subtypes were found. The data reported in this study reinforces the concept of a genetic continuum of SRLVs where strains are exchanged between sheep and goats under favourable conditions and in the absence of specific species barriers. Most interestingly, this study suggests that dual infection, which is a hallmark of the lentivirus paradigm HIV, may not be such rare events in small ruminants but may simply be understudied and underreported. Overall, the present data shows that sheep and goats in Canada can be infected with both SRLV A and B types, sometimes simultaneously, and that mixed flocks may represent a breeding ground for their evolution.
Asunto(s)
Coinfección/virología , Cabras/virología , Infecciones por Lentivirus/virología , Lentivirus/clasificación , Ovinos/virología , Animales , Anticuerpos Antivirales/sangre , Coinfección/transmisión , Coinfección/veterinaria , ADN Viral/sangre , ADN Viral/genética , Lentivirus/genética , Lentivirus/aislamiento & purificación , Infecciones por Lentivirus/transmisión , Infecciones por Lentivirus/veterinaria , FilogeniaRESUMEN
BACKGROUND: A publicly funded, group A rotavirus (RVA) vaccination program was implemented in Quebec in November 2011. OBJECTIVES: To evaluate trends in RVA infections and describe circulating genotypes before the implementation of a publicly funded vaccination program. METHODS: The Montreal Children's Hospital (Montreal, Quebec) virology laboratory database was reviewed for RVA ELISA performed between July 2006 and June 2011. A five-week moving average was used to follow the proportion of positive RVA ELISA test results. A season was defined as starting with the first two and ending with the final two consecutive weeks in which the percentage of specimens testing positive for RVA was ≥10%. Duplicate tests were excluded. A random sample of 39 RVA-positive fecal samples from the final season (2010/2011) was genetically characterized: VP4, VP6, VP7 and NSP4 gene segments were genotyped using sequence analysis. RESULTS: Of the 3403 nonduplicate tests, 433 were RVA positive: 15.1% (2006/2007) to 9.3% (2010/2011) of the samples were positive during the study period, with a proportionally larger decrease in the percentage of positive tests compared with the decrease in the number of tests performed. The most common RVA strain types detected were G9P[8]I1 (n=19) and G1P[8]I1 (n=14), followed by G2P[4]I2 (n=4), G3P[6]I1 (n=1) and G4P[8]I2 (n=1). Mixed RVA infection was observed in two samples. CONCLUSION: Before the implementation of the vaccination program, the proportion of positive RVA tests had already begun to steadily decline. The present study was the first to report the genetic makeup of human RVA collected from a Canadian hospital based on the genotyping of four gene segments. The present study provided a baseline with which to monitor the impact of the universal vaccination program.
HISTORIQUE: En novembre 2011, le Québec a commencé à financer un programme de vaccination contre le rotavirus du groupe A (RVA). OBJECTIFS: Évaluer les tendances des infections par le RVA et décrire les génotypes en circulation avant la mise en Åuvre d'un programme de vaccination financé par le gouvernement. MÉTHODOLOGIE: Les chercheurs ont analysé la base de données du laboratoire de virologie de L'Hôpital de Montréal pour enfants de Montréal, au Québec, pour en extraire les tests ELISA du RVA effectués entre juillet 2006 et juin 2011. Ils ont utilisé une moyenne mobile de cinq semaines pour suivre la proportion de résultats de tests ELISA positifs au RVA. Ils ont défini une saison comme commençant avec les deux premières semaines consécutives au cours desquelles au moins 10 % des échantillons étaient positifs au RVA et se terminant avec les deux dernières semaines présentant ces caractéristiques. Ils ont exclu les tests dédoublés. Ils ont procédé à la caractérisation génétique d'un échantillon aléatoire de 39 coprocultures positives au RVA de la dernière saison (2010-2011) : ils ont génotypé les segments de gène VP4, VP6, VP7 et NSP4 au moyen de l'analyse séquentielle. RÉSULTATS: Sur les 3 403 tests non dédoublés, 433 étaient positifs au RVA : de 15,1 % (2006-2007) à 9,3 % (2010-2011) des échantillons étaient positifs pendant la période de l'étude, la diminution étant proportionnellement plus importante en matière de pourcentage de tests positifs que de nombre de tests effectués. Les types de souches de RVA les plus décelés étaient le G9P[8]I1 (n=19) et le G1P[8]I1 (n=14), suivis du G2P[4]I2 (n=4), du G3P[6]I1 (n=1) et du G4P[8]I2 (n=1). Dans deux échantillons, les chercheurs ont observé une infection à RVA mixte. CONCLUSION: Avant la mise en Åuvre du programme de vaccination, la proportion de tests positifs au RVA avait déjà commencé à subir une baisse constante. La présente étude est la première à avoir rendu compte de la constitution génétique du RVA humain prélevé dans un hôpital canadien d'après le génotypage de quatre segments de gène. Elle fournit un point de départ pour surveiller les répercussions du programme de vaccination universelle.
RESUMEN
Group A rotaviruses with G2 and G9 VP7 specificity are common in humans, while G11 strains have been detected only sporadically. G2, G9 and G11 rotaviruses also circulate in pigs and swine rotaviruses have been suspected of interspecies and zoonotic transmissions in numerous studies. However, the complete gene constellation of G2 and G9 porcine rotaviruses has not yet been determined. In order to start filling this gap, the genomic make up of two G2, one G9 and one G11 porcine rotavirus strains, detected in Canada in 2005-2007, was determined. With the exception of a G2P[34] strain, with E9 NSP4 type and mixed I5+I14 VP6 type, the constellation of genomic segments was rather conserved and were closely related to prototype porcine strains in the four viruses characterized (I5-R1-C1-M1-A8-N1-T7-E1-H1). Most notably, all the viruses displayed a rare NSP3 genotype, T7, which has also been identified in rare human reassortant strains and in the reference strain RVA/Cow-tc/GBR/UK/1973/G6P[5]. This study provides crucial genetic data on these complex viruses and will help understand the origin and ecological niche of gene segments and the role played by pigs in their evolution.
Asunto(s)
Genoma Viral , Infecciones por Rotavirus/veterinaria , Rotavirus/genética , Enfermedades de los Porcinos/virología , Animales , Bovinos , Genotipo , Humanos , Filogenia , Rotavirus/clasificación , Rotavirus/aislamiento & purificación , Infecciones por Rotavirus/virología , Análisis de Secuencia de ADN , PorcinosRESUMEN
Emerging viruses represent a continuous threat to human health and to farmed animals, as evidenced on multiple occasions by outbreaks of influenza, henipavirus and SARS. Knowledge about the diversity of viromes present in reservoir species can lead to a better understanding of the origin of emerging pathogens. In this study, we extend the knowledge of astrovirus diversity in pigs by reporting the genetic characterization of an unknown astrovirus lineage. Phylogenetic analyses provided evidence that this porcine astrovirus lineage is unique and does not appear to share a recent common ancestor with any known mamastrovirus. The data reported in this study extend the number of porcine astrovirus lineages to a total of five, all of which most likely represent distinct species of different origins.
Asunto(s)
Infecciones por Astroviridae/veterinaria , Infecciones por Astroviridae/virología , Astroviridae/genética , Astroviridae/aislamiento & purificación , Variación Genética , Enfermedades de los Porcinos/virología , Animales , Astroviridae/clasificación , Humanos , Datos de Secuencia Molecular , Filogenia , Sus scrofa , PorcinosRESUMEN
BACKGROUND: Small Ruminant Lentiviruses (SRLV) are widespread in Canadian sheep and goats and represent an important health issue in these animals. There is however no data about the genetic diversity of Caprine Arthritis Encephalitis Virus (CAEV) or Maedi Visna Virus (MVV) in this country. FINDINGS: We performed a molecular and phylogenetic analysis of sheep and goat lentiviruses from a small geographic area in Canada using long sequences from the gag region of 30 infected sheep and 36 infected goats originating from 14 different flocks. Pairwise DNA distance and phylogenetic analyses revealed that all SRLV sequences obtained from sheep clustered tightly with prototypical Maedi visna sequences from America. Similarly, all SRLV strains obtained from goats clustered tightly with prototypical US CAEV-Cork strain. CONCLUSIONS: The data reported in this study suggests that Canadian and US SRLV strains share common origins. In addition, the molecular data failed to bring to light any evidence of past cross species transmission between sheep and goats, which is consistent with the type of farming practiced in this part of the country where single species flocks predominate and where opportunities of cross species transmissions are proportionately low.