Whole Genome or Single Genes? A Phylodynamic and Bibliometric Analysis of PRRSV

Frias-De-Diego, Alba; Jara, Manuel López; Pecoraro, Brittany M; Crisci, Elisa

doi:10.3389/fvets.2021.658512

Cited by 6 publications

(3 citation statements)

References 51 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…PRRSV exhibits high mutation and recombination rates. Moreover, the transmission mechanism of PRRSV can be explained from multiple perspectives, such as phylogenetic and evolutionary analysis of specific genes ( ORF5,NSP2 ) and varying rates of nucleotide substitution among different sites [ 40 ]. NSP4 plays an important role in antagonizing the innate immune response of the host.…”

Section: Future Perspectivementioning

confidence: 99%

Variations in the NSP4 gene of the type 2 porcine reproductive and respiratory syndrome virus isolated in China from 1996 to 2021

et al. 2022

View full text Add to dashboard Cite

Porcine reproductive and respiratory syndrome virus (PRRSV) has continuously mutated since its first isolation in China in 1996, leading to difficulties in infection prevention and control. Infections caused by PRRSV-2 strains are the main epidemic strains in China, as determined by phylogenetic analysis. In this study, we focused on the prevalence and genetic variations of the non-structural protein 4 (NSP4) from PRRSV-2 over the past 20 years in China. The fundamental biological properties of the NSP4 were predicted, and an analysis and comparison of NSP4 homology at the nucleotide and amino acid levels was conducted using 123 PRRSV-2 strains. The predicted molecular weight of the NSP4 protein was determined to be 21.1 kDa, and it was predicted to be a stable hydrophobic protein that lacks a signal peptide. NSP4 from different strains exhibited a high degree of amino acid (85.8–100%) and nucleotide sequence homology (81.0–100%). Multiple amino acid substitutions were identified in NSP4 among 15 representative PRRSV-2 strains. Phylogenetic analysis showed that the lineage 8 and 1 strains, the most prevalent strains in China, were indifferent clades with a long genetic distance. This analysis will help fully elucidate the parameters of the PRRSV NSP4 epidemic in China to lay a foundation for adequate understanding of the function of NSP4. Genetic information results from the accumulation of conserved and non-conserved sequences. The high conservation of the NSP4 gene determines the most basic life traits and functions of PRRSV. Analyzing the spatial structure of NSP4 protein and studying the genetic evolution of NSP4 not only provide the theoretical basis for how NSP4 participates in the regulation of the innate response of the host but also provide a target for genetic manipulation and a reasonable target molecule and structure for new drug molecules. Supplementary Information The online version contains supplementary material available at 10.1007/s11262-022-01957-x.

show abstract

Section: Future Perspectivementioning

confidence: 99%

Variations in the NSP4 gene of the type 2 porcine reproductive and respiratory syndrome virus isolated in China from 1996 to 2021

et al. 2022

View full text Add to dashboard Cite

show abstract

“…While these findings provide a unique window into the dynamics of between‐farm PRRSV‐2 transmission, one limitation of the analysis is that it focused on the voluntarily submitted ORF5 gene of a specific sub‐lineage within a single, albeit large, swine‐producing region in the U.S., and we do not know the extent to which results can be generalized to other circulating PRRSV‐2 variants or to other regions or countries that may have distinct farming practices. In addition, although we cannot fully elucidate PRRSV‐2 evolutionary dynamics without full‐length genomes, genetic variation and phylogenies estimated from the ORF5 gene can yield comparable results when compared to genomic‐level analysis (Frias‐De‐Diego et al, 2021) and constraining the analysis to highly related genetic variants (>98% pairwise identity) decreases the likelihood that evolutionary analyses would be confounded by recombination.…”

Section: Discussionmentioning

confidence: 99%

Unveiling invisible farm‐to‐farm PRRSV‐2 transmission links and routes through transmission tree and network analysis

Pamornchainavakul,

Makau,

Paploski

et al. 2023

Evolutionary Applications

View full text Add to dashboard Cite

The United States (U.S.) swine industry has struggled to control porcine reproductive and respiratory syndrome (PRRS) for decades, yet the causative virus, PRRSV‐2, continues to circulate and rapidly diverges into new variants. In the swine industry, the farm is typically the epidemiological unit for monitoring, prevention, and control; breaking transmission among farms is a critical step in containing disease spread. Despite this, our understanding of farm transmission still is inadequate, precluding the development of tailored control strategies. Therefore, our objective was to infer farm‐to‐farm transmission links, estimate farm‐level transmissibility as defined by reproduction numbers (R), and identify associated risk factors for transmission using PRRSV‐2 open reading frame 5 (ORF5) gene sequences, animal movement records, and other data from farms in a swine‐dense region of the U.S. from 2014 to 2017. Timed phylogenetic and transmission tree analyses were performed on three sets of sequences (n = 206) from 144 farms that represented the three largest genetic variants of the virus in the study area. The length of inferred pig‐to‐pig infection chains that corresponded to pairs of farms connected via direct animal movement was used as a threshold value for identifying other feasible transmission links between farms; these links were then transformed into farm‐to‐farm transmission networks and calculated farm‐level R‐values. The median farm‐level R was one (IQR = 1–2), whereas the R value of 28% of farms was more than one. Exponential random graph models were then used to evaluate the influence of farm attributes and/or farm relationships on the occurrence of farm‐to‐farm transmission links. These models showed that, even though most transmission events cannot be directly explained by animal movement, movement was strongly associated with transmission. This study demonstrates how integrative techniques may improve disease traceability in a data‐rich era by providing a clearer picture of regional disease transmission.

show abstract

“…Whole-genome sequencing (WGS) can reveal more information about PRRSV than traditional Sanger sequencing analysis of ORF5 [29]. To explore the evolutionary relationships of all of the isolated PRRSV strains with the representative strains, we sequenced two complete genomes from NADC34-like PRRSVs from this farm.…”

Section: Whole Genome Analysismentioning

confidence: 99%

First Detection of NADC34-like PRRSV as a Main Epidemic Strain on a Large Farm in China

Gong

Sun

et al. 2021

Pathogens

View full text Add to dashboard Cite

The newly emerged sublineage 1.5 (NADC34-like) porcine reproductive and respiratory syndrome virus (PRRSV) has posed a direct threat to the Chinese pig industry since 2018. However, the prevalence and impact of NADC34-like PRRSV on Chinese pig farms is unclear. In the present study, we continuously monitored pathogens—including PRRSV, African swine fever virus (ASFV), classical swine fever virus (CSFV), pseudorabies virus (PRV), and porcine circovirus 2 (PCV2)—on a fattening pig farm with strict biosecurity practices located in Heilongjiang Province, China, from 2020 to 2021. The results showed that multiple types of PRRSV coexisted on a single pig farm. NADC30-like and NADC34-like PRRSVs were the predominant strains on this pig farm. Importantly, NADC34-like PRRSV—detected during the period of peak mortality—was one of the predominant strains on this pig farm. Sequence alignment suggested that these strains shared the same 100 aa deletion in the NSP2 protein as IA/2014/NADC34 isolated from the United States (U.S.) in 2014. Phylogenetic analysis based on open reading frame 5 (ORF5) showed that the genetic diversity of NADC34-like PRRSV on this farm was relatively singular, but it had a relatively high rate of evolution. Restriction fragment length polymorphism (RFLP) pattern analysis showed that almost all ORF5 RFLPs were 1-7-4, with one 1-4-4. In addition, two complete genomes of NADC34-like PRRSVs were sequenced. Recombination analysis and sequence alignment demonstrated that both viruses, with 98.9% nucleotide similarity, were non-recombinant viruses. This study reports the prevalence and characteristics of NADC34-like PRRSVs on a large-scale breeding farm in northern China for the first time. These results will help to reveal the impact of NADC34-like PRRSVs on Chinese pig farms, and provide a reference for the detection and further prevention and control of NADC34-like PRRSVs.

show abstract

Whole Genome or Single Genes? A Phylodynamic and Bibliometric Analysis of PRRSV

Cited by 6 publications

References 51 publications

Variations in the NSP4 gene of the type 2 porcine reproductive and respiratory syndrome virus isolated in China from 1996 to 2021

Variations in the NSP4 gene of the type 2 porcine reproductive and respiratory syndrome virus isolated in China from 1996 to 2021

Unveiling invisible farm‐to‐farm PRRSV‐2 transmission links and routes through transmission tree and network analysis

First Detection of NADC34-like PRRSV as a Main Epidemic Strain on a Large Farm in China

Contact Info

Product

Resources

About