Novel approaches for Spatial and Molecular Surveillance of Porcine Reproductive and Respiratory Syndrome Virus (PRRSv) in the United States

A recent outbreak of particularly virulent disease caused by porcine reproductive and respiratory syndrome virus has occurred in swine herds across the United States. We report here the complete genome sequence of eight viral isolates from four Nebraska herds experiencing an outbreak of severe disease in 2016.

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Surveillance of porcine reproductive and respiratory syndrome virus in the United States using risk mapping and species distribution modeling

Preventive Veterinary Medicine ◽

10.1016/j.prevetmed.2017.11.011 ◽

2018 ◽

Vol 150 ◽

pp. 135-142 ◽

Cited By ~ 5

Author(s):

Moh A. Alkhamis ◽

Andreia G. Arruda ◽

Carles Vilalta ◽

Robert B. Morrison ◽

Andres M. Perez

Keyword(s):

United States ◽

Species Distribution ◽

Species Distribution Modeling ◽

The United States ◽

Risk Mapping ◽

Respiratory Syndrome Virus ◽

Distribution Modeling

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Unraveling the contact patterns and network structure of pig shipments in the United States and its association with porcine reproductive and respiratory syndrome virus (PRRSV) outbreaks

Preventive Veterinary Medicine ◽

10.1016/j.prevetmed.2017.02.001 ◽

2017 ◽

Vol 138 ◽

pp. 113-123 ◽

Cited By ~ 29

Author(s):

Kyuyoung Lee ◽

Dale Polson ◽

Erin Lowe ◽

Rodger Main ◽

Derald Holtkamp ◽

...

Keyword(s):

United States ◽

Network Structure ◽

The United States ◽

Respiratory Syndrome Virus ◽

Contact Patterns

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Genetic and Epidemiologic Trends of Norovirus Outbreaks in the United States from 2013 to 2016 Demonstrated Emergence of Novel GII.4 Recombinant Viruses

Journal of Clinical Microbiology ◽

10.1128/jcm.00455-17 ◽

2017 ◽

Vol 55 (7) ◽

pp. 2208-2221 ◽

Cited By ~ 107

Author(s):

Jennifer L. Cannon ◽

Leslie Barclay ◽

Nikail R. Collins ◽

Mary E. Wikswo ◽

Christina J. Castro ◽

...

Keyword(s):

United States ◽

Acute Gastroenteritis ◽

The United States ◽

Rna Polymerases ◽

Common Ancestry ◽

Molecular Surveillance ◽

Recombinant Viruses

ABSTRACT Noroviruses are the most frequent cause of epidemic acute gastroenteritis in the United States. Between September 2013 and August 2016, 2,715 genotyped norovirus outbreaks were submitted to CaliciNet. GII.4 Sydney viruses caused 58% of the outbreaks during these years. A GII.4 Sydney virus with a novel GII.P16 polymerase emerged in November 2015, causing 60% of all GII.4 outbreaks in the 2015-2016 season. Several genotypes detected were associated with more than one polymerase type, including GI.3, GII.2, GII.3, GII.4 Sydney, GII.13, and GII.17, four of which harbored GII.P16 polymerases. GII.P16 polymerase sequences associated with GII.2 and GII.4 Sydney viruses were nearly identical, suggesting common ancestry. Other common genotypes, each causing 5 to 17% of outbreaks in a season, included GI.3, GI.5, GII.2, GII.3, GII.6, GII.13, and GII.17 Kawasaki 308. Acquisition of alternative RNA polymerases by recombination is an important mechanism for norovirus evolution and a phenomenon that was shown to occur more frequently than previously recognized in the United States. Continued molecular surveillance of noroviruses, including typing of both polymerase and capsid genes, is important for monitoring emerging strains in our continued efforts to reduce the overall burden of norovirus disease.

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The United States Swine Pathogen Database: integrating veterinary diagnostic laboratory sequence data to monitor emerging pathogens of swine

10.1101/2021.04.16.439882 ◽

2021 ◽

Author(s):

Tavis K Anderson ◽

Blake K Inderski ◽

Diego G Diel ◽

Benjamin M Hause ◽

Elizabeth Porter ◽

...

Keyword(s):

United States ◽

Sequence Data ◽

The United States ◽

Content Management ◽

Biological Data ◽

Amino Acid Sequences ◽

Control Measures ◽

Clinical Samples ◽

Respiratory Syndrome Virus ◽

Genomic Information

Veterinary diagnostic laboratories annually derive thousands of nucleotide sequences from clinical samples of swine pathogens such as porcine reproductive and respiratory syndrome virus (PRRSV), Senecavirus A, and swine enteric coronaviruses. In addition, next generation sequencing has resulted in the rapid production of full-length genomes. Presently, sequence data are released to diagnostic clients for the purposes of informing control measures, but are not publicly available as data may be associated with sensitive information. However, public sequence data can be used to objectively design field-relevant vaccines; determine when and how pathogens are spreading across the landscape; identify virus transmission hotspots; and are a critical component in genomic surveillance for pandemic preparedness. We have developed a centralized sequence database that integrates a selected set of previously private clinical data, using PRRSV data as an exemplar, alongside publicly available genomic information. We implemented the Tripal toolkit, using the open source Drupal content management system and the Chado database schema. Tripal consists of a collection of Drupal modules that are used to manage, visualize, and disseminate biological data stored within Chado. Hosting is provided by Amazon Web Services (AWS) EC2 cloud instance with resource scaling. New sequences sourced from diagnostic labs contain at a minimum four data items: genomic information; date of collection; collection location (state or province level); and a unique identifier. Users can download annotated genomic sequences from the database using a customized search interface that incorporates data mined from published literature; search for similar sequences using BLAST-based tools; and explore annotated reference genomes. Additionally, because the bulk of data presently are PRRSV sequences, custom curation and annotation pipelines have determined PRRSV genotype (Type 1 or 2), the location of open reading frames and nonstructural proteins, generated amino acid sequences, the occurrence of putative frame shifts, and restriction fragment length polymorphism (RFLP) classification of GP5 genes. Genomic data from seven major swine pathogens have been curated and annotated. The resource provides researchers timely access to sequences discovered by veterinary diagnosticians, allowing for epidemiological and comparative virology studies. The result will be a better understanding on the emergence of novel swine viruses in the United States (US), and how these novel strains are disseminated in the US and abroad.

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Addressing Domestic Regulation Affecting Trade in Services in CETA, CPTPP, and USMCA: Revolution or Timid Steps?

The Journal of World Investment & Trade ◽

10.1163/22119000-12340152 ◽

2019 ◽

Vol 20 (5) ◽

pp. 680-704 ◽

Cited By ~ 1

Author(s):

Federico Ortino ◽

Emily Lydgate

Keyword(s):

United States ◽

Trade Agreement ◽

Trade Agreements ◽

The United States ◽

The European Union ◽

Trade In Services ◽

Novel Approaches ◽

United States Mexico ◽

Domestic Regulation ◽

The Eu

Abstract The number of international agreements purporting to liberalise trade, mainly focused on reducing protectionist measures through the imposition of general principles, has increased greatly over the last 25 years. More recently, the United States and the European Union (EU) concluded comprehensive agreements covering trade in goods, trade in services, and foreign investment. This article inquires whether, and the extent to which, such agreements represent a departure from previous practice. It focuses on (a) the instruments employed to address domestic regulation affecting trade in services and (b) three specific agreements concluded between 2016 and 2018: the EU-Canada Comprehensive Economic and Trade Agreement, the Comprehensive and Progressive Agreement for Trans-Pacific Partnership, and the United States-Mexico-Canada Agreement. While these recent Preferential Trade Agreements put forward novel approaches to regulatory diversity affecting trade in services, it is too early to ascertain whether these will have any ground-breaking impact in terms of services trade liberalisation.

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Phylogeny-Based Evolutionary, Demographical, and Geographical Dissection of North American Type 2 Porcine Reproductive and Respiratory Syndrome Viruses

Journal of Virology ◽

10.1128/jvi.02551-09 ◽

2010 ◽

Vol 84 (17) ◽

pp. 8700-8711 ◽

Cited By ~ 178

Author(s):

Mang Shi ◽

Tommy Tsan-Yuk Lam ◽

Chung-Chau Hon ◽

Michael P. Murtaugh ◽

Peter R. Davies ◽

...

Keyword(s):

United States ◽

North American ◽

Phylogenetic Analyses ◽

The United States ◽

Respiratory Syndrome Virus ◽

Viral Spread ◽

Comprehensive Picture ◽

North American Type ◽

Orf5 Sequences

ABSTRACT Type 2 (or North American-like) porcine reproductive and respiratory syndrome virus (PRRSV) was first recorded in 1987 in the United States and now occurs in most commercial swine industries throughout the world. In this study, we investigated the epidemiological and evolutionary behaviors of type 2 PRRSV. Based on phylogenetic analyses of 8,624 ORF5 sequences, we described a comprehensive picture of the diversity of type 2 PRRSVs and systematically classified all available sequences into lineages and sublineages, including a number of previously undescribed lineages. With the rapid growth of sequence deposition into the databases, it would be technically difficult for veterinary researchers to genotype their sequences by reanalyzing all sequences in the databases. To this end, a set of reference sequences was established based on our classification system, which represents the principal diversity of all available sequences and can readily be used for further genotyping studies. In addition, we further investigated the demographic histories of these lineages and sublineages by using Bayesian coalescence analyses, providing evolutionary insights into several important epidemiological events of type 2 PRRSV. Moreover, by using a phylogeographic approach, we were able to estimate the transmission frequencies between the pig-producing states in the United States and identified several states as the major sources of viral spread, i.e., “transmission centers.” In summary, this study represents the most extensive phylogenetic analyses of type 2 PRRSV to date, providing a basis for future genotyping studies and dissecting the epidemiology of type 2 PRRSV from phylogenetic perspectives.

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