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1.
Porcine Health Manag ; 7(1): 22, 2021 Feb 28.
Artigo em Inglês | MEDLINE | ID: mdl-33648592

RESUMO

BACKGROUND: There is limited information on the distribution of virulence-associated genes (VAGs) in U.S. Streptococcus suis isolates, resulting in little understanding of the pathogenic potential of these isolates. This lack also reduces our understanding of the epidemiology associated with S. suis in the United States and thus affects the efficiency of control and prevention strategies. In this study we applied whole genome sequencing (WGS)-based approaches for the characterization of S. suis and identification of VAGs. RESULTS: Of 208 S. suis isolates classified as pathogenic, possibly opportunistic, and commensal pathotypes, the genotype based on the classical VAGs (epf, mrp, and sly encoding the extracellular protein factor, muramidase-release protein, and suilysin, respectively) was identified in 9% (epf+/mrp+/sly+) of the pathogenic pathotype. Using the chi-square test and LASSO regression model, the VAGs ofs (encoding the serum opacity factor) and srtF (encoding sortase F) were selected out of 71 published VAGs as having a significant association with pathotype, and both genes were found in 95% of the pathogenic pathotype. The ofs+/srtF+ genotype was also present in 74% of 'pathogenic' isolates from a separate validation set of isolates. Pan-genome clustering resulted in the differentiation of a group of isolates from five swine production companies into clusters corresponding to clonal complex (CC) and virulence-associated (VA) genotypes. The same CC-VA genotype patterns were identified in multiple production companies, suggesting a lack of association between production company, CC, or VA genotype. CONCLUSIONS: The proposed ofs and srtF genes were stronger predictors for differentiating pathogenic and commensal S. suis isolates compared to the classical VAGs in two sets of U.S. isolates. Pan-genome analysis in combination with metadata (serotype, ST/CC, VA genotype) was illustrated to be a valuable subtyping tool to describe the genetic diversity of S. suis.

2.
J Anim Sci ; 99(1)2021 01 01.
Artigo em Inglês | MEDLINE | ID: mdl-33515482

RESUMO

The effect of hay type on the microbiome of the equine gastrointestinal tract is relatively unexplored. Our objective was to characterize the cecal and fecal microbiome of mature horses consuming alfalfa or Smooth Bromegrass (brome) hay. Six cecally cannulated horses were used in a split-plot design run as a crossover in two periods. The whole plot treatment was ad libitum access to brome or alfalfa hay fed over two 21-d acclimation periods with subplots of sampling location (cecum and rectum) and sampling hour. Each acclimation period was followed by a 24-h collection period where cecal and fecal samples were collected every 3 h for analysis of pH and volatile fatty acids (VFA). Fecal and cecal samples were pooled and sent to a commercial lab (MR DNA, Shallowater, TX) for the amplification of the V4 region of the 16S rRNA gene and sequenced using Illumina HiSeq. The main effects of hay on VFA, pH, and taxonomic abundances were analyzed using the MIXED procedure of SAS 9.4 with fixed effects of hay, hour, location, period, and all possible interactions and random effect of horse. Alpha and beta diversities were analyzed using the R Dame package. Horses fed alfalfa had greater fecal than cecal pH (P ≤ 0.05), whereas horses fed brome had greater cecal than fecal pH (P ≤ 0.05). Regardless of hay type, total VFA concentrations were greater (P ≤ 0.05) in the cecum than in feces, and alfalfa resulted in greater (P ≤ 0.05) VFA concentrations than brome in both sampling locations. Alpha diversity was greater (P ≤ 0.05) in fecal compared with cecal samples. Microbial community structure within each sampling location and hay type differed from one another (P ≤ 0.05). Bacteroidetes were greater (P ≤ 0.05) in the cecum compared with the rectum, regardless of hay type. Firmicutes and Firmicutes:Bacteroidetes were greater (P ≤ 0.05) in the feces compared with cecal samples of alfalfa-fed horses. In all, fermentation parameters and bacterial abundances were impacted by hay type and sampling location in the hindgut.


Assuntos
Ração Animal , Microbiota , Ração Animal/análise , Animais , Ceco/metabolismo , Dieta/veterinária , Fezes , Fermentação , Cavalos , RNA Ribossômico 16S/genética , RNA Ribossômico 16S/metabolismo
3.
Transbound Emerg Dis ; 68(4): 2465-2476, 2021 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-33155439

RESUMO

Porcine epidemic diarrhea virus (PEDV) is a significant global, enteric coronavirus in pigs and was first reported in Colombia in 2014. However, the epidemiology, genetic and antigenic characteristics of the virus have yet to be investigated. In this study, we investigated the dissemination of PEDV by testing 536 samples by RT-PCR over a 33-month period. The 35.8% of positive samples (n = 192) was significantly different (p < .01) between months over time, with a higher number of positives samples occurring at the beginning of the epidemic and during the second epidemic wave within the main pork producing region. The complete PEDV genomes were generated for 21 strains, which shared a high nucleotide and amino acid sequence identity, except for the spike (S) gene. Recombinant regions were identified within the Colombian strains and between Colombian and Asian PEDV strains. Phylogenetic analysis of the 21 Colombian strains demonstrated the presence of 7 lineages that shared common ancestors with PEDV strains from the United States. Moreover, the antigenic analysis demonstrated residue differences in the neutralizing epitopes in the spike and nucleocapsid proteins. Our results illustrated the simultaneous introduction of the two PEDV genotypes (GIIa American pandemic and S-INDEL) into the Colombian swine industry during the 2014 PEDV epidemic and enhanced our understanding of the epidemiology and molecular diversity of PEDV in Colombia.

4.
PLoS One ; 15(12): e0244498, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-33373390

RESUMO

The genus Rotavirus comprises eight species, designated A to H, and two recently identified tentative species I in dogs and J in bats. Species Rotavirus A, B, C and H (RVA, RVB, RVC and RVH) have been detected in humans and animals. While human and animal RVA are well characterized and defined, complete porcine genome sequences in the GenBank are limited compared to human strains. Here, we used a metagenomic approach to sequence the 11 segments of RVA, RVC and RVH strains from piglets in the United States (US) and explore the evolutionary relations of these RV species. Metagenomics identified Astroviridae, Picornaviridae, Caliciviridae, Coronoviridae in samples MN9.65 and OK5.68 while Picobirnaviridae and Arteriviridae were only identified in sample OK5.68. Whole genome sequencing and phylogenetic analyses identified multiple genotypes with the RVA of strain MN9.65 and OK5.68, with the genome constellation of G5/G9-P[7]/P[13]-I5/I5- R1/R1-C1-M1-A8-N1-T7-E1/E1-H1 and G5/G9-P[6]/P[7]-I5-R1/R1-C1-M1-A8-N1-T1/T7-E1/E1-H1, respectively. The RVA strains had a complex evolutionary relationship with other mammalian strains. The RVC strain OK5.68 had a genome constellation of G9-P[6]-I1-R1-C5-M6-A5-N1-T1-E1-H1, and shared an evolutionary relationship with porcine strains from the US. The RVH strains MN9.65 and OK5.68 had the genome constellation of G5-P1-I1-R1-C1-M1-A5-N1-T1-E4-H1 and G5-P1-I1-R1-C1-M1-A5-N1-T1-E1-H1, indicating multiple RVH genome constellations are circulating in the US. These findings allow us to understand the complexity of the enteric virome, develop improved screening methods for RVC and RVH strains, facilitate expanded rotavirus surveillance in pigs, and increase our understanding of the origin and evolution of rotavirus species.


Assuntos
Genoma Viral/genética , Infecções por Rotavirus/veterinária , Rotavirus/genética , Sus scrofa/virologia , Doenças dos Suínos/virologia , Animais , Evolução Molecular , Metagenômica , Filogenia , Rotavirus/isolamento & purificação , Infecções por Rotavirus/diagnóstico , Infecções por Rotavirus/prevenção & controle , Infecções por Rotavirus/virologia , Suínos , Doenças dos Suínos/diagnóstico , Doenças dos Suínos/prevenção & controle , Estados Unidos , Viroma/genética , Sequenciamento Completo do Genoma
5.
Front Genet ; 11: 828, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32849819

RESUMO

Rotavirus A (RVA) remains one of the most widespread causes of diarrheal disease and mortality in piglets despite decades of research and efforts to boost lactogenic immunity for passive protection. Genetic changes at B cell epitopes (BCEs) may be driving failure of lactogenic immunity, which relies on production of IgA antibodies to passively neutralize RVA within the piglet gut, yet little research has mapped epitopes to swine-specific strains of RVA. Here we describe a bioinformatic approach to predict BCEs on the VP7 outer capsid protein using sequence data alone. We first validated the approach using a previously published dataset of VP7-specific cross-neutralization titers, and found that amino acid changes at predicted BCEs on the VP7 protein allowed for accurate recapitulation of antigenic relationships among the strains. Applying the approach to a dataset of swine RVA sequences identified 9 of the 11 known BCEs previously mapped to swine strains, indicating that epitope prediction can identify sites that are known to drive neutralization escape in vitro. Additional genotype-specific BCEs were also predicted that may be the cause of antigenic differences among strains of RVA on farms and should be targeted for further confirmatory work. The results of this work lay the groundwork for high throughput, immunologically-relevant analysis of swine RVA sequence data, and provide potential sites that can be targeted with vaccines to reduce piglet mortality and support farm health.

6.
BMC Vet Res ; 16(1): 241, 2020 Jul 13.
Artigo em Inglês | MEDLINE | ID: mdl-32660468

RESUMO

BACKGROUND: The present report describes a case of pseudocowpox virus (PCPV) infection in a seven-year-old female bison euthanized due to a history of declining condition and sores on the vulva and udder. CASE PRESENTATION: External examination revealed multifocal, raised, keratinized plaques (0.5-2 cm) covering the skin of the ventral surface of the tail, perineum, caudoventral abdomen, udder, both inguinal recesses, and the medial aspects of both thighs. No significant gross lesions were present in the reminder of the tissues examined. Histopathological examination of the affected skin showed moderate epidermal hyperplasia with rete pegs, marked parakeratotic hyperkeratosis with crusts of degenerate neutrophils and cell debris, and few epithelial cells undergoing ballooning degeneration with occasional eosinophilic intracytoplasmic inclusion bodies (3-5 µm Bollinger body). Negative staining electron microscopy from skin revealed typical Parapoxvirus (PPV) particles, which were also confirmed by real-time PCR (Ct =18.6). Metagenomic analysis of the skin samples revealed only poxviruses. The bison parapox B2L envelope gene clustered with other parapox sequences identified from ruminants. CONCLUSIONS: This is the first report of PCPV virus infection in an American bison. Identification of novel susceptible hosts of parapox viruses sheds light on the viral evolution and highlights the importance of potential economic impact of this disease to the bison industry.


Assuntos
Bison , Infecções por Poxviridae/veterinária , Vírus da Pseudovaríola das Vacas/isolamento & purificação , Animais , DNA Viral/análise , Feminino , Kansas , Microscopia Eletrônica , Infecções por Poxviridae/virologia , Vírus da Pseudovaríola das Vacas/genética , Vírus da Pseudovaríola das Vacas/ultraestrutura , Reação em Cadeia da Polimerase em Tempo Real/veterinária , Dermatopatias Virais/patologia , Dermatopatias Virais/veterinária
7.
Front Microbiol ; 11: 780, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32395116

RESUMO

The increased prevalence of porcine group C rotavirus (PRVC) in suckling piglets and the emergence of new genetically distinct PRVC strains are concerning due to the associated significant economic losses they cause to the swine industry. We sequenced and analyzed two new PRVC strains, RV0104 (G3), and RV0143 (G6) and compared their pathogenesis with that of the historic strain Cowden (G1) in gnotobiotic (Gn) pigs. Near complete genome sequence analysis confirmed that these two strains were distinct from one another and the Cowden strain. VP1, VP2, VP6, NSP1-NSP3, and NSP5 genes were more similar between Cowden and RV0143, whereas VP3, VP7, and NSP4 shared higher nucleotide identity between Cowden and RV0104. Three-day-old and 3-week-old Gn piglets were inoculated with 105 FFU/piglet of Cowden, RV0104 or RV0143, or mock. All 3-day-old piglets developed severe diarrhea, anorexia, and lethargy, with mean PRVC fecal shedding titers peaking and numerically higher in RV0104 and RV0143 piglets on post infection day (PID) 2. Histopathological examination of the small intestine revealed that the 3-day-old Cowden and RV0104 inoculated piglets were mildly affected, while significant destruction of small intestinal villi was observed in the RV0143 inoculated piglets. Consistent with the highest degree of pathological changes in the small intestines, the RV0143 inoculated piglets had numerically higher levels of serum IL-17 and IFN-α cytokines and numerically lower PRVC IgA geometric mean antibody titers. Milder pathological changes and overall higher titers of PRVC IgA antibodies were observed in 3-week-old vs. 3-day-old piglets. Additionally, diarrhea was only observed in RV0104 and RV0143 (but not Cowden) inoculated 3-week-old piglets, while levels of serum IL-10 and PRVC IgA antibodies were higher in Cowden inoculated pigs, consistent with the lack of diarrhea. Thus, we confirmed that these current, genetically heterogeneous PRVC strains possess distinct pathobiological characteristics that may contribute to the increased prevalence of PRVC diarrhea in neonatal suckling piglets.

8.
Viruses ; 12(4)2020 04 07.
Artigo em Inglês | MEDLINE | ID: mdl-32272747

RESUMO

Rotaviruses (RVs) are the leading cause of the acute viral gastroenteritis in young children and livestock animals worldwide. Although live attenuated vaccines have been applied to control RV infection for many years, the underlying mechanisms of RV attenuation following cell culture adaption are unknown. To study these mechanisms at the genomic level, we have sequenced and conducted a comparative analysis of two virulent human (Wa, G1P[8] and M, G3P[8]) and two virulent porcine (Gottfried, G4P[6] and OSU, G5P[7]) RV strains maintained in gnotobiotic piglets for 22, 11, 12 and 9 serial passages, respectively, with their attenuated counterparts serially passaged in MA-104 cell cultures for 25, 43, 54 and 43 passages, respectively. We showed that most of the mutations were clustered in the VP4 gene, with a relatively high nonsynonymous substitution rate (81.2%). Moreover, two amino acid substitutions observed in the VP4 gene were conserved between two or more strain pairs. D385N substitution was found in M, Wa and Gottfried strains, and another one, S471H/L was present in Wa and Gottfried strains. Importantly, D385 was reported previously in another study and may be involved in regulation of virus entry. Of interest, although no 385 substitution was found in OSU strains, the attenuated OSU strain contained a unique D393H substitution within the same VP4 hydrophobic domain. Collectively, our data suggest that the VP4 hydrophobic region may play an important role in RV attenuation and aa385 and aa393 may represent potential targets for RV vaccine development using reverse genetics and site-specific mutagenesis.


Assuntos
Substituição de Aminoácidos , Proteínas do Capsídeo/genética , Técnicas de Cultura de Células , Rotavirus/genética , Cultura de Vírus , Adaptação Fisiológica , Animais , Proteínas do Capsídeo/química , Linhagem Celular , Chlorocebus aethiops , Genoma Viral , Vida Livre de Germes , Humanos , Interações Hidrofóbicas e Hidrofílicas , Mutação , Rotavirus/química , Rotavirus/patogenicidade , Inoculações Seriadas , Suínos/virologia , Sequenciamento Completo do Genoma
9.
J Vet Diagn Invest ; 32(3): 394-400, 2020 May.
Artigo em Inglês | MEDLINE | ID: mdl-32274974

RESUMO

We developed a model to predict the cyclic pattern of porcine reproductive and respiratory syndrome virus (PRRSV) RNA detection by reverse-transcription real-time PCR (RT-rtPCR) from 4 major swine-centric veterinary diagnostic laboratories (VDLs) in the United States and to use historical data to forecast the upcoming year's weekly percentage of positive submissions and issue outbreak signals when the pattern of detection was not as expected. Standardized submission data and test results were used. Historical data (2015-2017) composed of the weekly percentage of PCR-positive submissions were used to fit a cyclic robust regression model. The findings were used to forecast the expected weekly percentage of PCR-positive submissions, with a 95% confidence interval (CI), for 2018. During 2018, the proportion of PRRSV-positive submissions crossed 95% CI boundaries at week 2, 14-25, and 48. The relatively higher detection on week 2 and 48 were mostly from submissions containing samples from wean-to-market pigs, and for week 14-25 originated mostly from samples from adult/sow farms. There was a recurring yearly pattern of detection, wherein an increased proportion of PRRSV RNA detection in submissions originating from wean-to-finish farms was followed by increased detection in samples from adult/sow farms. Results from the model described herein confirm the seasonal cyclic pattern of PRRSV detection using test results consolidated from 4 VDLs. Wave crests occurred consistently during winter, and wave troughs occurred consistently during the summer months. Our model was able to correctly identify statistically significant outbreak signals in PRRSV RNA detection at 3 instances during 2018.


Assuntos
Surtos de Doenças/veterinária , Síndrome Respiratória e Reprodutiva Suína/epidemiologia , Vírus da Síndrome Respiratória e Reprodutiva Suína/fisiologia , Animais , Reação em Cadeia da Polimerase/veterinária , Síndrome Respiratória e Reprodutiva Suína/virologia , RNA Viral/análise , Estações do Ano , Suínos , Estados Unidos/epidemiologia
10.
Transbound Emerg Dis ; 67(1): 18-28, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31461567

RESUMO

Porcine sapoviruses (SaVs) are genetically diverse and widely distributed in pig-producing countries. Eight genogroups of porcine SaV have been identified, and genogroup III is the predominant type. Most of the eight genogroups of porcine SaV are circulating in the United States. In the present study, we report detection of porcine SaVs in pigs at different ages with clinical diarrhoea using next-generation sequencing and genetic characterization. All seven cases have porcine SaV GIII strains detected and one pooled case was found to have a porcine SaV GVI strain IA27912-B-2018. Sequence analysis showed that seven GIII isolates were genetically divergent and formed four different lineages on the trees of complete genome, RdRP, VP1 and VP2. In addition, these seven GIII isolates had three different deletion/insertion patterns in an identified variable region close to the 3' end of VP2. The GVI strain IA27912-B-2018 was closely related to strains previously detected in the United States and Japan. A 3-nt deletion in VP1 region of GVI IA27912-B-2018 was identified. Our study showed that genetically divergent SaVs of different genogroups are co-circulating in pigs in the United States. Future studies comparing the virulence of these different genogroups in pigs are needed to better understand this virus and to determine if surveillance and vaccine development are needed to monitor and control porcine SaVs.


Assuntos
Infecções por Caliciviridae/veterinária , Diarreia/veterinária , Variação Genética , Sapovirus/genética , Doenças dos Suínos/virologia , Animais , Infecções por Caliciviridae/epidemiologia , Infecções por Caliciviridae/virologia , Diarreia/epidemiologia , Diarreia/virologia , Fezes/virologia , Feminino , Genótipo , Sequenciamento de Nucleotídeos em Larga Escala/veterinária , Filogenia , Sapovirus/isolamento & purificação , Suínos , Doenças dos Suínos/epidemiologia , Estados Unidos/epidemiologia
11.
J Gen Virol ; 101(2): 175-187, 2020 02.
Artigo em Inglês | MEDLINE | ID: mdl-31859611

RESUMO

Senecavirus A (SVA) is an emerging picornavirus that causes vesicular disease (VD) in swine. The virus has been circulating in swine in the United Stated (USA) since at least 1988, however, since 2014 a marked increase in the number of SVA outbreaks has been observed in swine worldwide. The factors that led to the emergence of SVA remain unknown. Evolutionary changes that accumulated in the SVA genome over the years may have contributed to the recent increase in disease incidence. Here we compared full-genome sequences of historical SVA strains (identified before 2010) from the USA and global contemporary SVA strains (identified after 2011). The results from the genetic analysis revealed 6.32 % genetic divergence between historical and contemporary SVA isolates. Selection pressure analysis revealed that the SVA polyprotein is undergoing selection, with four amino acid (aa) residues located in the VP1 (aa 735), 2A (aa 941), 3C (aa 1547) and 3D (aa 1850) coding regions being under positive/diversifying selection. Several aa substitutions were observed in the structural proteins (VP1, VP2 and VP3) of contemporary SVA isolates when compared to historical SVA strains. Some of these aa substitutions led to changes in the surface electrostatic potential of the structural proteins. This work provides important insights into the molecular evolution and epidemiology of SVA.


Assuntos
Doenças Transmissíveis Emergentes , Infecções por Picornaviridae/veterinária , Picornaviridae/genética , Doenças dos Suínos/virologia , Substituição de Aminoácidos/genética , Animais , Doenças Transmissíveis Emergentes/veterinária , Doenças Transmissíveis Emergentes/virologia , Surtos de Doenças , Evolução Molecular , Variação Genética , Genoma Viral , Filogenia , Infecções por Picornaviridae/epidemiologia , Suínos , Doenças dos Suínos/epidemiologia , Estados Unidos/epidemiologia , Proteínas Virais/genética , Proteínas Estruturais Virais/genética
12.
J Microbiol Methods ; 169: 105817, 2020 02.
Artigo em Inglês | MEDLINE | ID: mdl-31881288

RESUMO

In recent years, high-throughput sequencing has revolutionized disease diagnosis by its powerful ability to provide high resolution genomic information. The Oxford Nanopore MinION sequencer has unparalleled potential as a rapid disease diagnostic tool due to its high mobility, accessibility, and short turnaround time. However, there is a lack of rigorous quality assessment and control processes standardizing the testing on the MinION, which is necessary for incorporation into a diagnostic workflow. Thus, our study examined the use of the MinION sequencer for bacterial whole genome generation and characterization. Using Streptococcus suis as a model, we optimized DNA isolation and treatments to be used for MinION sequencing and standardized de novo assembly to quickly generate a full-length consensus sequence achieving a 99.4% average accuracy. The consensus genomes from MinION sequencing were able to accurately predict the multilocus sequence type in 8 out of 10 samples and identified antimicrobial resistance profiles for 100% of the samples, despite the concern of a high error rate. The inability to unequivocally predict sequence types was due to difficulty in differentiating high identity alleles, which was overcome by applying additional error correction methods to increase consensus accuracy. This manuscript provides methods for the use of MinION sequencing for identification of S. suis genome sequence, sequence type, and antibiotic resistance profile that can be used as a framework for identification and classification of other pathogens.


Assuntos
Farmacorresistência Bacteriana/genética , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Tipagem de Sequências Multilocus/métodos , Streptococcus suis/genética , Sequenciamento Completo do Genoma/métodos , Animais , Antibacterianos/farmacologia , Genoma Bacteriano/genética , Humanos , Testes de Sensibilidade Microbiana/métodos , Análise de Sequência de DNA/métodos , Infecções Estreptocócicas/diagnóstico , Infecções Estreptocócicas/microbiologia , Infecções Estreptocócicas/veterinária , Streptococcus suis/classificação , Suínos , Doenças dos Suínos/diagnóstico , Doenças dos Suínos/microbiologia
13.
PLoS One ; 14(10): e0223544, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31618236

RESUMO

This project investigates the macroepidemiological aspects of porcine reproductive and respiratory syndrome virus (PRRSV) RNA detection by veterinary diagnostic laboratories (VDLs) for the period 2007 through 2018. Standardized submission data and PRRSV real-time reverse-transcriptase polymerase chain reaction (RT-qPCR) test results from porcine samples were retrieved from four VDLs representing 95% of all swine samples tested in NAHLN laboratories in the US. Anonymized data were retrieved and organized at the case level using SAS (SAS® Version 9.4, SAS® Institute, Inc., Cary, NC) with the use of PROC DATA, PROC MERGE, and PROC SQL scripts. The final aggregated and anonymized dataset comprised of 547,873 unique cases was uploaded to Power Business Intelligence-Power BI® (Microsoft Corporation, Redmond, Washington) to construct dynamic charts. The number of cases tested for PRRSV doubled from 2010 to 2018, with that increase mainly driven by samples typically used for monitoring purposes rather than diagnosis of disease. Apparent seasonal trends for the frequency of PRRSV detection were consistently observed with a higher percentage of positive cases occurring during fall or winter months and lower during summer months, perhaps due to increased testing associated with well-known seasonal occurrence of swine respiratory disease. PRRSV type 2, also known as North American genotype, accounted for 94.76% of all positive cases and was distributed across the US. PRRSV type 1, also known as European genotype, was geographically restricted and accounted for 2.15% of all positive cases. Co-detection of both strains accounted for 3.09% of the positive cases. Both oral fluid and processing fluid samples, had a rapid increase in the number of submissions soon after they were described in 2008 and 2017, respectively, suggesting rapid adoption of these specimens by the US swine industry for PRRSV monitoring in swine populations. As part of this project, a bio-informatics tool defined as Swine Disease Reporting System (SDRS) was developed. This tool has real-time capability to inform the US swine industry on the macroepidemiological aspects of PRRSV detection, and is easily adaptable for other analytes relevant to the swine industry.


Assuntos
Síndrome Respiratória e Reprodutiva Suína/diagnóstico , Síndrome Respiratória e Reprodutiva Suína/virologia , Vírus da Síndrome Respiratória e Reprodutiva Suína , Animais , Serviços de Laboratório Clínico , Geografia Médica , Laboratórios Hospitalares , Síndrome Respiratória e Reprodutiva Suína/epidemiologia , Vírus da Síndrome Respiratória e Reprodutiva Suína/classificação , Vírus da Síndrome Respiratória e Reprodutiva Suína/genética , Reação em Cadeia da Polimerase em Tempo Real , Sensibilidade e Especificidade , Suínos
14.
Viruses ; 11(10)2019 09 26.
Artigo em Inglês | MEDLINE | ID: mdl-31561462

RESUMO

Porcine deltacoronavirus (δ-CoV) is the object of extensive research in several countries including the United States. In contrast, the epidemiology of δ-CoVs in wild birds in the US is largely unknown. Our aim was to comparatively assess the prevalence of δ- and γ-CoVs in wild migratory terrestrial and aquatic birds in Arkansas, Illinois, Indiana, Maryland, Mississippi, Missouri, Ohio, Tennessee and Wisconsin. A total of 1236 cloacal/fecal swabs collected during the period 2015-2018 were tested for γ- and δ-CoVs using genus-specific reverse transcription-PCR assays. A total of 61 (4.99%) samples were γ-CoV positive, with up to 29 positive samples per state. In contrast, only 14 samples were positive for δ-CoV (1.14%) with only 1-4 originating from the same state. Thus, unlike previous reports from Asia, γ-CoVs are more prevalent than δ-CoVs in the US, suggesting that δ-CoVs may spread in birds with lower efficiency. This may indicate δ-CoV emerging status and incomplete adaptation to new host species limiting its spread. Phylogenetic analysis of the partial N gene revealed that the newly identified δ-CoV strains were most closely related to the HKU20 (wigeon) strain. Further studies are necessary to investigate the role of aquatic bird δ-CoVs in the epidemiology of δ-CoVs in swine and terrestrial birds.


Assuntos
Doenças das Aves/epidemiologia , Aves/virologia , Infecções por Coronavirus/veterinária , Coronavirus/isolamento & purificação , Animais , Animais Selvagens , Doenças das Aves/virologia , Coronavirus/classificação , Coronavirus/genética , Infecções por Coronavirus/epidemiologia , Infecções por Coronavirus/virologia , Gammacoronavirus/classificação , Gammacoronavirus/genética , Gammacoronavirus/isolamento & purificação , Especificidade de Hospedeiro , Filogenia , Prevalência , RNA Viral/genética , Estados Unidos/epidemiologia
15.
Viruses ; 11(9)2019 08 23.
Artigo em Inglês | MEDLINE | ID: mdl-31450796

RESUMO

A distinct Russian Mammalian orthorubulavirus 5 (PIV5) was detected in cell culture exhibiting cytopathic effect and hypothesized to be contaminated by a scientist with respiratory symptoms. The identification of the divergent strain indicated a lack of knowledge on the diversity of PIV5 strains and calls for surveillance of global PIV5 strains.


Assuntos
Vírus da Parainfluenza 5 , Células Vero/virologia , Animais , Linhagem Celular , Chlorocebus aethiops , Efeito Citopatogênico Viral , Genoma Viral , Humanos , Mamíferos/virologia , Vírus da Parainfluenza 5/classificação , Vírus da Parainfluenza 5/genética , Vírus da Parainfluenza 5/isolamento & purificação , Filogenia , Infecções por Rubulavirus/virologia , Federação Russa , Sequenciamento Completo do Genoma
16.
Viruses ; 11(8)2019 07 31.
Artigo em Inglês | MEDLINE | ID: mdl-31370351

RESUMO

Viruses belonging to the genus Bocaparvovirus (BoV) are a genetically diverse group of DNA viruses known to cause respiratory, enteric, and neurological diseases in animals, including humans. An intestinal sample from an alpaca (Vicugna pacos) herd with reoccurring diarrhea and respiratory disease was submitted for next-generation sequencing, revealing the presence of a BoV strain. The alpaca BoV strain (AlBoV) had a 58.58% whole genome nucleotide percent identity to a camel BoV from Dubai, belonging to a tentative ungulate BoV 8 species (UBoV8). Recombination events were lacking with other UBoV strains. The AlBoV genome was comprised of the NS1, NP1, and VP1 proteins. The NS1 protein had the highest amino acid percent identity range (57.89-67.85%) to the members of UBoV8, which was below the 85% cut-off set by the International Committee on Taxonomy of Viruses. The low NS1 amino acid identity suggests that AlBoV is a tentative new species. The whole genome, NS1, NP1, and VP1 phylogenetic trees illustrated distinct branching of AlBoV, sharing a common ancestor with UBoV8. Walker loop and Phospholipase A2 (PLA2) motifs that are vital for virus infectivity were identified in NS1 and VP1 proteins, respectively. Our study reports a novel BoV strain in an alpaca intestinal sample and highlights the need for additional BoV research.


Assuntos
Bocavirus/classificação , Camelídeos Americanos/virologia , Genoma Viral , Filogenia , Animais , Bocavirus/isolamento & purificação , Diarreia/virologia , Fezes/virologia , Sequenciamento de Nucleotídeos em Larga Escala , Metagenômica , Infecções por Parvoviridae/virologia , Infecções Respiratórias/virologia , Análise de Sequência de DNA , Estados Unidos
17.
J Clin Microbiol ; 57(9)2019 09.
Artigo em Inglês | MEDLINE | ID: mdl-31243086

RESUMO

Streptococcus suis is a significant cause of mortality in piglets and growing pigs worldwide. The species contains pathogenic and commensal strains, with pathogenic strains causing meningitis, arthritis, endocarditis, polyserositis, and septicemia. Serotyping and multilocus sequence typing (MLST) are primary methods to differentiate strains, but the information is limited for strains found in the United States. The objective of this study was to characterize the diversity of 208 S. suis isolates collected between 2014 and 2017 across North America (mainly the United States) by serotyping and MLST and to investigate associations between subtype and pathotype classifications (pathogenic, possibly opportunistic, and commensal), based on clinical information and site of isolation. Twenty serotypes were identified, and the predominant serotypes were 1/2 and 7. Fifty-eight sequence types (STs) were identified, and the predominant ST was ST28. Associations among serotypes, STs, and pathotypes were investigated using odds ratio and clustering analyses. Evaluation of serotype and ST with pathotype identified a majority of isolates of serotypes 1, 1/2, 2, 7, 14, and 23 and ST1, ST13, ST25, ST28, ST29, ST94, ST108, ST117, ST225, ST373, ST961, and ST977 as associated with the pathogenic pathotype. Serotypes 21 and 31, ST750, and ST821 were associated with the commensal pathotype, which is composed of isolates from farms with no known history of S. suis-associated disease. Our study demonstrates the use of serotyping and MLST to differentiate pathogenic from commensal isolates and establish links between pathotype and subtype, thus increasing the knowledge about S. suis strains circulating in the United States.


Assuntos
Genótipo , Sorogrupo , Infecções Estreptocócicas/veterinária , Streptococcus suis/classificação , Streptococcus suis/patogenicidade , Doenças dos Suínos/microbiologia , Animais , Tipagem de Sequências Multilocus , América do Norte , Sorotipagem , Infecções Estreptocócicas/microbiologia , Streptococcus suis/genética , Streptococcus suis/isolamento & purificação , Suínos
18.
Sci Rep ; 9(1): 3953, 2019 03 08.
Artigo em Inglês | MEDLINE | ID: mdl-30850666

RESUMO

The epidemiology and genetic diversity of transmissible gastroenteritis virus (TGEV) in the United States (US) was investigated by testing clinical cases for TGEV by real time RT-PCR between January 2008 and November 2016. Prevalence of TGEV ranged between 3.8-6.8% and peaked during cold months until March 2013, in which prevalence decreased to < 0.1%. Nineteen complete TGEV genomes and a single strain of porcine respiratory coronavirus (PRCV) from the US were generated and compared to historical strains to investigate the evolution of these endemic coronaviruses. Sixteen of our TGEV strains share 8 unique deletions and 119 distinct amino acid changes, which might greatly affect the biological characteristics of the variant TGEV, and resulted in a "variant" genotype of TGEV. The "variant" genotype shared similar unique deletions and amino acid changes with the recent PRCV strain identified in this study, suggesting a recombination event occurred between the ''variant'' TGEV and PRCV. Moreover, the results indicate the "variant" genotype is the dominant genotype circulating in the US. Therefore, this study provides insight into the occurrence, origin, genetic characteristics, and evolution of TGEV and PRCV circulating in the US.


Assuntos
Evolução Molecular , Gastroenterite Suína Transmissível/epidemiologia , Coronavirus Respiratório Porcino , Vírus da Gastroenterite Transmissível , Animais , Infecções por Coronavirus/epidemiologia , Infecções por Coronavirus/veterinária , Infecções por Coronavirus/virologia , Gastroenterite Suína Transmissível/virologia , Genoma Viral/genética , Mutação INDEL/genética , Filogenia , Coronavirus Respiratório Porcino/genética , Reação em Cadeia da Polimerase em Tempo Real , Recombinação Genética/genética , Alinhamento de Sequência/veterinária , Suínos/virologia , Vírus da Gastroenterite Transmissível/genética , Estados Unidos/epidemiologia
19.
Zoonoses Public Health ; 66(5): 546-557, 2019 08.
Artigo em Inglês | MEDLINE | ID: mdl-30848076

RESUMO

Rotavirus C (RVC) causes enteric disease in multiple species, including humans, swine, bovines, and canines. To date, the evolutionary relationships of RVC populations circulating in different host species are poorly understood, owing to the low availability of genetic sequence data. To address this gap, we sequenced 45 RVC complete genomes from swine samples collected in the United States and Mexico. A phylogenetic analysis of each genome segment indicates that RVC populations have been evolving independently in human, swine, canine, and bovine hosts for at least the last century, with inter-species transmission events occurring deep in the phylogenetic tree, and none in the last 100 years. Bovine and canine RVC populations clustered together nine of the 11 gene segments, indicating a shared common ancestor centuries ago. The evolutionary relationships of RVC in humans and swine were more complex, due to the extensive genetic diversity and multiple RVC clades identified in pigs, which were not structured geographically. Topological differences between trees inferred for different genome segments occurred frequently, including at nodes deep in the tree, indicating that RVC's evolutionary history includes multiple reassortment events that occurred a long time ago. Overall, we find that RVC is evolving within host-defined lineages, but the evolutionary history of RVC is more complex than previously recognized due to the high genetic diversity of RVC in swine, with a common ancestor dating back centuries. Pigs may act as a reservoir host for RVC, and a source of the lineages identified in other species, including humans, but additional sequencing is needed to understand the full diversity of this understudied pathogen across multiple host species.


Assuntos
Evolução Biológica , Doenças dos Bovinos/virologia , Infecções por Rotavirus/veterinária , Rotavirus/genética , Doenças dos Suínos/virologia , Animais , Bovinos , Doenças dos Bovinos/epidemiologia , Humanos , México/epidemiologia , Infecções por Rotavirus/epidemiologia , Infecções por Rotavirus/virologia , Seleção Genética , Suínos , Doenças dos Suínos/epidemiologia , Estados Unidos/epidemiologia , Proteínas Virais/genética
20.
Transbound Emerg Dis ; 66(3): 1420-1425, 2019 May.
Artigo em Inglês | MEDLINE | ID: mdl-30806022

RESUMO

Porcine Pegivirus (PPgV) and Atypical Porcine Pestivirus (APPV) are two recently identified porcine viruses. In this study, the identification of two viruses by metagenomic sequencing, and a duplex semi-quantitative RT-PCR was developed to detect these pathogens simultaneously. The PPgV strain Minnesota-1/2016 had a 95.5%-96.3% nucleotide identity and clustered with the recently identified US PPgV strains, which is a distant clade from the German PPgV strains. The APPV strain Minnesota-1/2016 shared an 87.3%-92.0% nucleotide identity with the other global APPV strains identity but only shared an 82.8%-83.0% nucleotide identity with clade II consisting of strain identified in China. Detection of both PPgV and APPV was 9.0% of the diagnostic cases. Co-infection of PPgV and APPV was identified in 7.5% of the diagnostic cases. The occurrence and genetic characterization of PPgV and APPV further enhance our knowledge regarding these new pathogens in the United States.


Assuntos
Coinfecção/veterinária , Infecções por Flaviviridae/veterinária , Flaviviridae/isolamento & purificação , Metagenômica , Doenças dos Suínos/epidemiologia , Animais , Flaviviridae/genética , Infecções por Flaviviridae/epidemiologia , Infecções por Flaviviridae/virologia , Minnesota/epidemiologia , Pestivirus/genética , Pestivirus/isolamento & purificação , Infecções por Pestivirus/epidemiologia , Infecções por Pestivirus/veterinária , Infecções por Pestivirus/virologia , Filogenia , Reação em Cadeia da Polimerase Via Transcriptase Reversa/veterinária , Suínos , Doenças dos Suínos/virologia , Estados Unidos/epidemiologia
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