scholarly journals Porcine reproductive and respiratory syndrome virus 2 (PRRSV-2) genetic diversity and occurrence of wild type and vaccine-like strains in the United States swine industry

PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0259531
Author(s):  
Mariana Kikuti ◽  
Juan Sanhueza ◽  
Carles Vilalta ◽  
Igor Adolfo Dexheimer Paploski ◽  
Kimberly VanderWaal ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Production Systems ◽  
Sequence Data ◽  
The United States ◽  
Respiratory Syndrome Virus ◽  
Viral Diversity ◽  
Wild Type ◽  
Routine Monitoring ◽  
Genotype 2

Porcine reproductive and respiratory syndrome virus genotype 2 (PRRSV-2) genetic diversity in the U.S. was assessed using a database comprising 10 years’ worth of sequence data obtained from swine production systems routine monitoring and outbreak investigations. A total of 26,831 ORF5 PRRSV-2 sequences from 34 production systems were included in this analysis. Within group mean genetic distance (i.e. mean proportion of nucleotide differences within ORF5) per year according to herd type was calculated for all PRRSV-2 sequences. The percent nucleotide difference between each sequence and the ORF5 sequences from four commercially available PRRSV-2 vaccines (Ingelvac PRRS MLV, Ingelvac PRRS ATP, Fostera PRRS, and Prevacent PRRS) within the same lineage over time was used to classify sequences in wild-type or vaccine-like. The mean ORF5 genetic distance fluctuated from 0.09 to 0.13, being generally smaller in years in which there was a relative higher frequency of dominant lineage. Vaccine-like sequences comprised about one fourth of sequences obtained through routine monitoring of PRRS. We found that lineage 5 sequences were mostly Ingelvac PRRS MLV-like. Lineage 8 sequences up to 2011 were 62.9% Ingelvac PRRS ATP-like while the remaining were wild-type viruses. From 2012 onwards, 51.9% of lineage 8 sequences were Ingelvac PRRS ATP-like, 45.0% were Fostera PRRS-like, and only 3.2% were wild-type. For lineage 1 sequences, 0.1% and 1.7% of the sequences were Prevacent PRRS-like in 2009–2018 and 2019, respectively. These results suggest that repeated introductions of vaccine-like viruses through use of modified live vaccines might decrease within-lineage viral diversity as vaccine-like strains become more prevalent. Overall, this compilation of private data from routine monitoring provides valuable information on PRRSV viral diversity.

scholarly journals Measurement of Genetic Diversity of Chinese Seashore Paspalum Resources through Morphological and Sequence-related Amplified Polymorphism Analysis

2019 ◽  
Vol 144 (6) ◽  
pp. 379-386
Author(s):  
Yan Liu ◽  
Hailin Guo ◽  
Yi Wang ◽  
Jingang Shi ◽  
Dandan Li ◽  
...  
Keyword(s):  
United States ◽  
Genetic Diversity ◽  
Cluster Analysis ◽  
Genetic Variation ◽  
Genetic Distance ◽  
Morphological Characteristics ◽  
The United States ◽  
Germplasm Resources ◽  
Seashore Paspalum ◽  
Chinese Germplasm

Seashore paspalum (Paspalum vaginatum) is a notable warm-season turfgrass. Certain germplasm resources are distributed in the southern regions of China. The objectives of this study were to investigate the genetic diversity and genetic variation of Chinese seashore paspalum resources. Morphological characteristics and sequence-related amplified polymorphism (SRAP) markers were used to assess genetic relationships and genetic variation among 36 germplasm resources from China and six cultivars from the United States. The results showed significant variation for 13 morphological characteristics among 42 tested seashore paspalum accessions, and that the phenotypic cv was, in turn, turf height > turf density > internode length > inflorescence density > leaf width > reproductive branch height > spikelet width > leaf length > spikelet number > inflorescence length > internode diameter > inflorescence width > spikelet length. According to the morphological characteristics and cluster analysis, 42 seashore paspalum accessions were divided into six morphological types. In total, 374 clear bands were amplified using 30 SRAP primer combinations; among these bands, 321 were polymorphic with 85.83% polymorphism. SRAP marker cluster analysis showed that 42 seashore paspalum accessions were grouped into seven major groups, with a genetic similarity coefficient ranging from 0.4385 to 0.9893 and genetic distance values ranging from 0.0108 to 0.8244. The high level of genetic diversity occurred among Chinese germplasm, and the genetic distance was relatively high between Chinese germplasm and cultivars introduced from the United States. The patterns in morphological trait variations and genetic diversity will be useful for the further exploitation and use of Chinese seashore paspalum resources.

Genetic diversity of porcine reproductive and respiratory syndrome virus 1 in the United States of America from 2010 to 2018

2019 ◽  
Vol 239 ◽  
pp. 108486 ◽  
Author(s):  
Anping Wang ◽  
Jianqiang Zhang ◽  
Huigang Shen ◽  
Ying Zheng ◽  
Qi Feng ◽  
...  
Keyword(s):  
United States ◽  
Genetic Diversity ◽  
United States Of America ◽  
The United States ◽  
Respiratory Syndrome Virus

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

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.

scholarly journals Porcine reproductive and respiratory syndrome virus dissemination across pig production systems in the United States

2020 ◽  
Author(s):  
Manuel Jara ◽  
David A. Rasmussen ◽  
Cesar A. Corzo ◽  
Gustavo Machado
Keyword(s):  
Prevention And Control ◽  
Production Systems ◽  
The United States ◽  
Respiratory Syndrome Virus ◽  
Pig Production ◽  
The North ◽  
Relative Contribution ◽  
Virus Dissemination ◽  
Pig Farms ◽  
And Control

SummaryPorcine reproductive and respiratory syndrome virus (PRRSV) remains widespread in the North American pig population. Despite improvements in virus characterization, it is unclear whether PRRSV infections are a product of viral circulation within a farm, within production systems (local) or across production systems (external). Here we examined the dissemination dynamics of PRRSV and the processes facilitating its spread within and among pig farms in three production systems. Overall, PRRSV genetic diversity declined since 2018, while phylodynamic results support frequent transmission across-production systems. We found that PRRSV dissemination occurred mostly through transmission between farms of different production companies, which were predominant for several months, especially from November until May when PRRSV tends to peak in the studied region. Within production systems, dissemination occurred mainly through regular pig flow (from sow to nursery and then to finisher farms); nevertheless, an important flux of PRRSV dissemination from finisher to sow and nursery farms highlighted the importance of downstream farms as sources of the virus. Farms at areas with pig density from 500 to 1000 pig/km2 and farms located at a range within 0.5 km and 0.7 km from major roads were more likely to infect by PRRSV, whereas farms at elevation between 41 and 61 meters and denser vegetation acted as dissemination barriers. Although remains a challenge, there is a need to disentangle the route of PRRSV transmission, results evidenced that dissemination among commercially unrelated pig production systems was intense, reinforcing the importance of farm proximity on PRRSV spread. Thus, consideration of farm location and their geographic characteristics may help to forecast dissemination. The understanding of PRRSV transmission routes has the potential to inform targeted strategies for its prevention and control. Further studies are needed to quantify the relative contribution of PRRSV transmission routes.

Molecular Epidemiology and Genetic Diversity of Echovirus Type 30 (E30): Genotypes Correlate with Temporal Dynamics of E30 Isolation

1999 ◽  
Vol 37 (12) ◽  
pp. 3928-3933 ◽  
Author(s):  
M. Steven Oberste ◽  
Kaija Maher ◽  
Margery L. Kennett ◽  
Janice J. Campbell ◽  
Michael S. Carpenter ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Aseptic Meningitis ◽  
Temporal Dynamics ◽  
Sequence Data ◽  
Phylogenetic Reconstruction ◽  
The United States ◽  
Molecular Techniques ◽  
Surveillance Data ◽  
Echovirus Type 30 ◽  
Echovirus Type

Echovirus type 30 (E30) (genus, Enterovirus; family,Picornaviridae) has caused large outbreaks of aseptic meningitis in many regions of the world in the last 40 years. U.S. enterovirus surveillance data for the period 1961 to 1998 indicated that the annual proportion of E30 isolations relative to total enterovirus isolations has fluctuated widely, from a low of 0% in 1966 to a high of 42% in 1998. Peaks of E30 isolations occurred in the years 1968 to 1969, 1981 to 1984, 1990 to 1993, and 1997 to 1998, coincident with large nationwide outbreaks of E30-associated aseptic meningitis. Analysis of the complete VP1 sequence (876 nucleotides) of 136 E30 strains isolated in geographically dispersed regions of the United States and nine other countries between 1956 and 1998 indicated that the currently circulating E30 strains are genetically distinct from those isolated 30 to 40 years ago. Phylogenetic reconstruction demonstrated the existence of at least four distinct genetic groups, three of which have not been isolated in North America since 1981. Two of the three groups disappeared during periods when E30 was isolated infrequently. All North American E30 strains isolated after 1988 were closely related to one another, and all post-1993 isolates were of the same lineage within this group. Surveillance data indicate that E30 causes large national outbreaks of 2- to 4-year durations, separated by periods of relative quiescence. Our results show that shifts in the overall genetic diversity of E30 and the predominant genetic type correlate temporally with the dynamics of E30 isolation. The sequence data also provide a basis for the application of molecular techniques for future epidemiologic investigations of E30 disease.

scholarly journals Genetic Diversity Analysis of Genotype 2 Porcine Reproductive and Respiratory Syndrome Viruses Emerging in Recent Years in China

2014 ◽  
Vol 2014 ◽  
pp. 1-13 ◽  
Author(s):  
Lei Zhou ◽  
Xiaorong Yang ◽  
Yuan Tian ◽  
Shuoyan Yin ◽  
Gang Geng ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Hypervariable Region ◽  
Clinical Samples ◽  
Respiratory Syndrome Virus ◽  
Diversity Analysis ◽  
Coding Region ◽  
Genotype 2 ◽  
Orf5 Sequences ◽  
Complete Genomic

Porcine reproductive and respiratory syndrome virus (PRRSV) is characterized by its extensive genetic diversity. Here we analyzed 101 sequences of NSP2 hypervariable region, 123 ORF3 sequences, and 118 ORF5 sequences from 128 PRRSV-positive clinical samples collected in different areas of China during 2008–early 2012. The results indicated that the amino acid identities of the three genes among these sequences were 87.6%–100%, 92.5%–100%, and 77%–100%, respectively. Meanwhile, 4 novel patterns of deletion and insertion in NSP2 region or GP5 were first found. The phylogenetic analysis on these 3 genes revealed that the Chinese PRRSV strains could be divided into three subgroups; majority of genes analyzed here were clustered in subgroup 3 with multiple branches; the strains with 30-aa deletion in NSP2-coding region were still the dominant virus in the field. Further phylogenetic analysis on four obtained complete genomic sequences showed that they were clustered into different branches with the Chinese corresponding representative strains. Our analyses suggest that the genetic diversity of genotype 2 PRRSV in the field displays a tendency of increasing in recent years in China, and the 30-aa deletion in NSP2-coding region should be no longer defined as the molecular marker of the Chinese HP-PRRSV.

scholarly journals Phylogenetic Structure and Sequential Dominance of Sub-Lineages of PRRSV Type-2 Lineage 1 in the United States

Vaccines ◽  
2021 ◽  
Vol 9 (6) ◽  
pp. 608
Author(s):  
Igor A. D. Paploski ◽  
Nakarin Pamornchainavakul ◽  
Dennis N. Makau ◽  
Albert Rovira ◽  
Cesar A. Corzo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Evolutionary Dynamics ◽  
The United States ◽  
Amino Acid Sequences ◽  
Respiratory Syndrome Virus ◽  
Effective Population ◽  
Phylogenetic Structure ◽  
The U.S

The genetic diversity and frequent emergence of novel genetic variants of porcine reproductive and respiratory syndrome virus type-2 (PRRSV) hinders control efforts, yet drivers of macro-evolutionary patterns of PRRSV remain poorly documented. Utilizing a comprehensive database of >20,000 orf5 sequences, our objective was to classify variants according to the phylogenetic structure of PRRSV co-circulating in the U.S., quantify evolutionary dynamics of sub-lineage emergence, and describe potential antigenic differences among sub-lineages. We subdivided the most prevalent lineage (Lineage 1, accounting for approximately 60% of available sequences) into eight sub-lineages. Bayesian coalescent SkyGrid models were used to estimate each sub-lineage’s effective population size over time. We show that a new sub-lineage emerged every 1 to 4 years and that the time between emergence and peak population size was 4.5 years on average (range: 2–8 years). A pattern of sequential dominance of different sub-lineages was identified, with a new dominant sub-lineage replacing its predecessor approximately every 3 years. Consensus amino acid sequences for each sub-lineage differed in key GP5 sites related to host immunity, suggesting that sub-lineage turnover may be linked to immune-mediated competition. This has important implications for understanding drivers of genetic diversity and emergence of new PRRSV variants in the U.S.

PRRSV2 genetic diversity defined by RFLP patterns in the United States from 2007 to 2019

2021 ◽  
pp. 104063872110272
Author(s):  
Giovani Trevisan ◽  
Aditi Sharma ◽  
Phillip Gauger ◽  
Karen M. Harmon ◽  
Jianqiang Zhang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Genetic Difference ◽  
The United States ◽  
Respiratory Syndrome Virus ◽  
Control Programs ◽  
Geographic Space ◽  
Different Strains ◽  
Orf5 Sequences ◽  
Over Time

The genetic diversity of porcine reproductive and respiratory syndrome virus (PRRSV) increases over time. In 1998, restriction-fragment length polymorphism (RFLP) pattern analysis was introduced to differentiate PRRSV wild-type strains from VR2332, a reference strain from which a commercial vaccine (Ingelvac PRRS MLV) was derived. We have characterized here the PRRSV genetic diversity within selected RFLP families over time and U.S. geographic space, using available ISU-VDL data from 2007 to 2019. The 40,454 ORF5 sequences recovered corresponded to 228 distinct RFLPs. Four RFLPs [2-5-2 (21.2%), 1-7-4 (15.6%), 1-4-4 (11.8%), and 1-8-4 (9.9%)] represented 58.5% of all ORF5 sequences and were used for cluster analysis. Over time, there was increased detection of RFLPs 2-5-2, 1-7-4, 1-3-4, 1-3-2, and 1-12-4; decreased detection of 1-4-2, 1-18-4, 1-18-2, and 1-2-2; and different detection trends for 1-8-4, 1-4-4, 1-26-1, 1-22-2, and 1-2-4. An over-time cluster analysis revealed a single cluster for RFLP 2-5-2, supporting that sequences within RFLP 2-5-2 are still relatively conserved. For 1-7-4, 1-4-4, and 1-8-4, there were multiple clusters. State-wise cluster analysis demonstrated 4 main clusters for RFLP 1-7-4 and 1-8-4, and 6 for RFLP 1-4-4. For the other RFLPs, there was a significant genetic difference within them, particularly between states. RFLP typing is limited in its ability to discriminate among different strains of PRRSV. Understanding the magnitude of genetic divergence within RFLPs helps develop PRRSV regional control programs, placement, herd immunization strategies, and design of appropriate animal movements across borders to minimize the risk of PRRSV transmission.

Hydrophobic Particle Films Improve Tree Fruit Productivity

HortScience ◽  
1998 ◽  
Vol 33 (3) ◽  
pp. 548a-548 ◽  
Author(s):  
D.M. Glenn ◽  
G. Puterka ◽  
T. Baugher ◽  
T. Unruh ◽  
S. Drake
Keyword(s):  
West Virginia ◽  
Production Systems ◽  
Fruit Size ◽  
The United States ◽  
Fruit Production ◽  
Red Color ◽  
Tree Fruit ◽  
Fruit Productivity ◽  
Leaf Level ◽  
Hydrophobic Particle

Hydrophobic particle film technology (HPF) is a developing pest control system for tree fruit production systems. Studies were established in Chile, and Washington, Pennsylvania, and West Virginia in the United States, to evaluate the effect of HPF technology on tree fruit yield and quality. Studies in Chile, Washington, and West Virginia demonstrated increased photosynthetic rate at the leaf level. Yield was increased in peaches (Chile) and apples (West Virginia), and fruit size was increased in apples (Washington and Pennsylvania). Increased red color in apple was demonstrated at all sites with reduced russetting and `Stayman' cracking in Pennsylvania. HPF technology appears to be an effective tool in reducing water and heat stress in tree fruit resulting in increased fruit quality.

Sign in / Sign up

Export Citation Format

Share Document