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

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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Regulatory power, post-crisis transatlantic disputes, and the network structure of the financial industry

Business and Politics ◽

10.1017/bap.2017.1 ◽

2017 ◽

Vol 19 (2) ◽

pp. 241-266 ◽

Cited By ~ 5

Author(s):

Lucia Quaglia

Keyword(s):

United States ◽

European Union ◽

Network Structure ◽

Hedge Funds ◽

Financial Regulation ◽

The United States ◽

The European Union ◽

Financial Industry ◽

Active Involvement ◽

Bank Structure

AbstractThe international financial crisis was followed by waves of domestic regulatory reforms, first and foremost, in the United States and the European Union. Post-crisis financial regulation was sometimes different across jurisdictions. Moreover, the United States and the European Union sought in various ways to (re)assert their regulatory power not only vis-à-vis the market, but also with regard to other jurisdictions, which often resisted the projection of regulatory power beyond national borders. Consequently, a handful of important post-crisis transatlantic regulatory disputes emerged concerning E.U. rules on hedge funds, U.S. rules on bank structure and E.U. and U.S. rules on over-the-counter (OTC) derivatives. These disputes mainly involved the terms of access to each other's markets, the equivalence between domestic rules, and the extraterritorial effects of those rules. Some of these disputes were also intra-E.U. disagreements, whenever the preferences of the United Kingdom were different from those of Continental countries and similar to those of the United States. The network structure of the financial industry and the patterns of financial interdependence across the Atlantic amplified the extra territorial effects of domestic reforms, but at the same time triggered an active involvement of the transnational financial industry in the management and, eventually, the settlement of these disputes.

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The network structure of the United States input-output table

Empirical Economics ◽

10.1007/bf01764564 ◽

1978 ◽

Vol 3 (1) ◽

pp. 49-70 ◽

Cited By ~ 12

Author(s):

P. Slater

Keyword(s):

United States ◽

Network Structure ◽

The United States ◽

Input Output ◽

Output Table

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Contact surveys reveal heterogeneities in age-group contributions to SARS-CoV-2 dynamics in the United States

10.1101/2021.09.25.21264082 ◽

2021 ◽

Author(s):

Taylor Chin ◽

Dennis M. Feehan ◽

Caroline O. Buckee ◽

Ayesha S. Mahmud

Keyword(s):

United States ◽

Age Groups ◽

The United States ◽

Contact Rate ◽

Age Group ◽

Contact Rates ◽

Contact Patterns ◽

Age Structured ◽

The Impact ◽

Over Time

SARS-CoV-2 is spread primarily through person-to-person contacts. Quantifying population contact rates is important for understanding the impact of physical distancing policies and for modeling COVID-19, but contact patterns have changed substantially over time due to shifting policies and behaviors. There are surprisingly few empirical estimates of age-structured contact rates in the United States both before and throughout the COVID-19 pandemic that capture these changes. Here, we use data from six waves of the Berkeley Interpersonal Contact Survey (BICS), which collected detailed contact data between March 22, 2020 and February 15, 2021 across six metropolitan designated market areas (DMA) in the United States. Contact rates were low across all six DMAs at the start of the pandemic. We find steady increases in the mean and median number of contacts across these localities over time, as well as a greater proportion of respondents reporting a high number of contacts. We also find that young adults between ages 18 and 34 reported more contacts on average compared to other age groups. The 65 and older age group consistently reported low levels of contact throughout the study period. To understand the impact of these changing contact patterns, we simulate COVID-19 dynamics in each DMA using an age-structured mechanistic model. We compare results from models that use BICS contact rate estimates versus commonly used alternative contact rate sources. We find that simulations parameterized with BICS estimates give insight into time-varying changes in relative incidence by age group that are not captured in the absence of these frequently updated estimates. We also find that simulation results based on BICS estimates closely match observed data on the age distribution of cases, and changes in these distributions over time. Together these findings highlight the role of different age groups in driving and sustaining SARS-CoV-2 transmission in the U.S. We also show the utility of repeated contact surveys in revealing heterogeneities in the epidemiology of COVID-19 across localities in the United States.

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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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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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