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

Trevisan, Giovani; Sharma, Aditi; Gauger, Phillip C.; Harmon, Karen M.; Zhang, Jianqiang; Main, Rodger; Zeller, Michael A.; Linhares, Leticia; Linhares, Daniel

doi:10.1177/10406387211027221

Cited by 14 publications

(10 citation statements)

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“…Overall data of nt identity and phylogenetic analysis suggest that, for the PRRSV‐2 Category 2, virus detected in clinical samples and their isolates were considered as the same strains in spite of differences in RFLP pattern. This again confirms that RFLP typing, which is dependent exclusively on three restriction enzyme cutting sites, is not a reliable method to truly reflect PRRSV‐2 genetic relatedness as noted previously (Cha et al., 2004; Han et al., 2006; Trevisan et al., 2021; Yoon et al., 2001).…”

Section: Discussionsupporting

confidence: 77%

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Characterization of PRRSV in clinical samples and the corresponding cell culture isolates

Yim-Im

Huang

et al. 2022

Transbounding Emerging Dis

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Isolation of porcine reproductive and respiratory syndrome virus (PRRSV) in cell culture is a primary means of obtaining virus isolates for autogenous vaccine production and other applications. However, it has not been well characterized whether cell culture isolate and the virus in clinical sample are equivalent. This study compared PRRSV ORF5 sequences from 1024 clinical samples (995 PRRSV‐2, 26 PRRSV‐1, and three PRRSV‐1 and PRRSV‐2 PCR‐positive) and their isolates in MARC‐145 and/or ZMAC cells. For three PRRSV‐1 and PRRSV‐2 PCR‐positive clinical samples, both PRRSV‐1 and PRRSV‐2 were isolated in ZMAC cells, whereas either PRRSV‐1 or PRRSV‐2, but not both, was isolated in MARC‐145 cells, with isolate sequences matching the respective viruses in clinical samples. Twenty‐six PRRSV‐1 and most of 995 PRRSV‐2 PCR‐positive clinical samples had matching viral ORF5 sequences with their cell culture isolates. However, 14 out of 995 PRRSV‐2 cases (1.4%) had nonmatching viral sequences between clinical samples and MARC‐145 isolates, although viral sequences from clinical samples and ZMAC isolates matched. This is concerning because, if the MARC‐145 isolate is directly used for autogenous vaccine production without sequencing confirmation against the virus in the clinical sample, it is possible that the produced autogenous vaccine does not include the desired wild‐type virus strain found on the farm and instead contains vaccine‐like virus. Vaccine‐specific PCR and next‐generation sequencing performed on six selected cases indicated presence of ≥2 PRRSV‐2 strains (mixed infection) in such clinical samples. In summary, PRRSV ORF5 sequences from clinical samples and cell culture isolates matched each other for majority of the cases. However, PRRSV sequences between clinical sample and MARC‐145 cell culture isolate could occasionally be different when the clinical sample contains ≥2 PRRSV‐2 strains. Characterizing PRRSV sequences from clinical samples and cell culture isolates should be conducted before using isolates for producing autogenous vaccines or other applications.

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Section: Discussionsupporting

confidence: 77%

“…In the current study, we focused on comparisons of ORF5 sequences that have been widely used to assess the genetic relatedness of PRRSV strains Stadejek et al, 2013). edness as noted previously (Cha et al, 2004;Han et al, 2006;Trevisan et al, 2021;Yoon et al, 2001).…”

Section: Discussionmentioning

confidence: 99%

Characterization of PRRSV in clinical samples and the corresponding cell culture isolates

Yim-Im

Huang

et al. 2022

Transbounding Emerging Dis

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“…Within the whole‐PRRSV genome, the specific region ORF5b, also known and herein identified as ORF5, encodes the virus envelope protein and has been extensively used in molecular epidemiology and evolutionary studies to characterize distinct isolates (Brar et al., 2015 ; Lambert et al., 2019 ; Larochelle et al., 2003 ; Paploski et al., 2019 ; Paploski et al., 2021 ; Shi et al., 2010 ; Trevisan et al., 2021b ; Wan et al., 2019b ). The ORF5 gene comprises 603 nucleotide base pairs (bp) for PRRSV‐2 and 606 bp for PRRSV‐1, representing approximately 4% of the whole PRRSV genome and has been primarily used in the Americas to classify PRRSV‐2 strains according to restriction fragment length polymorphism (RFLP) patterns (Wesley et al., 1998 ) and genetic lineages (Lambert et al., 2019 ; Paploski et al., 2019 ; Paploski et al., 2021 ; Shi et al., 2010 ; Wang et al., 2019b ), and to charactherize PRRSV strains in diversity studies (Alkhamis et al., 2016 ; Arruda et al., 2017 ; Brar et al., 2015 ; Ramos et al., 2018 ; Ramírez et al., 2019 ; Trevisan et al., 2021b ). In U.S. veterinary diagnostic laboratories, sequencing of the PRRSV ORF5 region is performed using the Sanger technique (Sanger et al., 1977 ) which determines the consensus gene sequence in a sample and is not an efficient tool to sequence multiple viruses if more than one PRRSV strain is present (Harmon et al., 2019 ).…”

Section: Introductionmentioning

confidence: 99%

Implementing a user‐friendly format to analyze PRRSV next‐generation sequencing results and associating breeding herd production performance with number of PRRSV strains and recombination events

Trevisan

Zeller

et al. 2022

Transbounding Emerging Dis

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The open reading frames (ORF)5 represents approximately 4% of the porcine reproductive and respiratory syndrome virus (PRRSV)-2 genome (whole-PRRSV) and is often determined by the Sanger technique, which rarely detects >1 PRRSV strain if present in the sample. Next-generation sequencing (NGS) may provide a more appropriate method of detecting multiple PRRSV strains in one sample. This work assessed the effect of PRRSV genetic variability and recombination events, using NGS, on the time-to-low prevalence (TTLP) and total losses in breeding herds (n 20) that detected a PRRSV outbreak and adopted measures to eliminate PRRSV. Serum, lung or live virus inoculation material collected within 3-weeks of outbreak, and subsequently, processing fluids (PFs) were tested for PRRSV by RT-qPCR and NGS. Recovered whole-PRRSV or partial sequences were used to characterize within and between herd PRRSV genetic variability. Whole-PRRSV was recovered in five out of six (83.3%) lung, 16 out of 22 (72.73%) serum and in five out of 95 (5.26%) PF. Whole-PRRSV recovered from serum or lung were used as farm referent strains in 16 out of 20 (80%) farms.In four farms, only partial genome sequences were recovered and used as farm referent strains. At least two wild-type PRRSV strains (wt-PRRSV) were circulating simultaneously in 18 out of 20 (90%) and at least one vaccine-like strain co-circulating in eight out of 20 (40%) farms. PRRSV recombination events were detected in 12 farms (59%), been 10 out of 12 between wt-PRRSV and two out of 12 between wt-PRRSV and vaccine-like strains. Farms having ≥3 strains had a 12-week increase TTLP versus herds ≤2 strains detected. Farms with ≤2 strains (n 10) had 1837 and farms with no recombination events detected (n 8) had 1827 fewer piglet losses per 1000 sows versus farms with ≥3 PRRSV strains (n 8) or detected recombination (n 10), respectively. NGS outcomes and novel visualization methods provided more thorough insightThis is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

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“…We further classified the NADC34-like PRRSV strains on this farm according to restriction fragment length polymorphism (RFLP) of the ORF5 gene [25][26][27]. The RFLP pattern of ORF5 of TZJ1277 is 1-4-4, while those of the others are 1-7-4.…”

Section: Sequence Analysis Of Nadc34-like Prrsvsmentioning

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

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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.

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

Cited by 14 publications

References 59 publications

Characterization of PRRSV in clinical samples and the corresponding cell culture isolates

Characterization of PRRSV in clinical samples and the corresponding cell culture isolates

Implementing a user‐friendly format to analyze PRRSV next‐generation sequencing results and associating breeding herd production performance with number of PRRSV strains and recombination events

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

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