Phylogenetic Analysis of Classical Swine Fever Virus Isolates from Peru

Araínga, Mariluz; Hisanaga, Tamiko; Hills, Kevin; Handel, Katherine; Rivera, G Hermelinda; Pasick, John

doi:10.1111/j.1865-1682.2010.01144.x

Cited by 7 publications

(10 citation statements)

References 21 publications

(22 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Real‐time RT‐PCR for CSF was performed with the Cepheid Smart Cycler II (Cepheid, Sunnyvale, CA, USA) for samples from pigs inoculated with the Peru L8/2008 and LL28/2008 strains, or the ABI 7900 HT (Life Technologies) for samples from pigs inoculated with the Diepholz 1/Han 94 and Honduras 97 strains as per the Standard Operating Procedure at the Canadian Reference Laboratory for CSF (Arainga et al., ). Each reaction had a total volume of 25 μ l and consisted of 9 μ l of RNA added to 16 μ l of master mix.…”

Section: Methodsmentioning

confidence: 99%

“…The primers used were CSF‐Taq‐5′ For (5′‐TCA GTA GTT CGA CGT RRG CAG AA‐3′) and CSF‐Taq‐3′ Rev (5′‐GCA TGC CCT CGT CCA CRT‐3′). The probe used was CSF‐5′UTRMGB‐2 Probe (5′‐6FAM‐CYY RCC TCG AGA TGC‐MGBNFQ‐3′) (Arainga et al., ). Real‐time PCR conditions were 50°C for 30 min, 95°C for 15 min, followed by 40 cycles of 94°C for 30 s and 60°C for 1 min.…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Insulated Isothermal Reverse Transcriptase PCR (iiRT-PCR) for Rapid and Sensitive Detection of Classical Swine Fever Virus

Lung

Pasick

Fisher

et al. 2015

Transbound Emerg Dis

Self Cite

View full text Add to dashboard Cite

Classical swine fever (CSF) is an OIE-listed disease that can have a severe impact on the swine industry. User-friendly, sensitive, rapid diagnostic tests that utilize low-cost field-deployable instruments for CSF diagnosis can be useful for disease surveillance and outbreak monitoring. In this study, we describe validation of a new probe-based insulated isothermal reverse transcriptase PCR (iiRT-PCR) assay for rapid detection of classical swine fever virus (CSFV) on a compact, user-friendly device (POCKIT(™) Nucleic Acid Analyzer) that does not need data interpretation by the user. The assay accurately detected CSFV RNA from a diverse panel of 33 CSFV strains representing all three genotypes plus an additional in vitro-transcribed RNA from cloned sequences representing a vaccine strain. No cross-reactivity was observed with a panel of 18 viruses associated with livestock including eight other pestivirus strains (bovine viral diarrhoea virus type 1 and type 2, border disease virus, HoBi atypical pestivirus), African swine fever virus, swine vesicular disease virus, swine influenza virus, porcine respiratory and reproductive syndrome virus, porcine circovirus 1, porcine circovirus 2, porcine respiratory coronavirus, vesicular exanthema of swine virus, bovine herpes virus type 1 and vesicular stomatitis virus. The iiRT-PCR assay accurately detected CSFV as early as 2 days post-inoculation in RNA extracted from serum samples of experimentally infected pigs, before appearance of clinical signs. The limit of detection (LOD95% ) calculated by probit regression analysis was 23 copies per reaction. The assay has a sample to answer turnaround time of less than an hour using extracted RNA or diluted or low volume of neat serum. The user-friendly, compact device that automatically analyses and displays results could potentially be a useful tool for surveillance and monitoring of CSF in a disease outbreak.

show abstract

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Insulated Isothermal Reverse Transcriptase PCR (iiRT-PCR) for Rapid and Sensitive Detection of Classical Swine Fever Virus

Lung

Pasick

Fisher

et al. 2015

Transbound Emerg Dis

Self Cite

View full text Add to dashboard Cite

show abstract

“…Three regions of the genome, the 5 0 -untranslated region (UTR: 150 nucleotides), E2 (190 nt), and NS5B (409 nt), are useful in classifying CSFV into groups and subgroups [7,12,14]. Understanding the extent of genetic diversity of CSFV can greatly advance our knowledge of its molecular epidemiology in the endemic area.…”

Section: Introductionmentioning

confidence: 99%

“…During recent decades, CSF has been prevalent in Asia, Europe, Central and South America, and parts of Africa [3][4][5][6]. Serious outbreaks of CSF in Peru were reported by the OIE between 2005 and 2009, in which the genotype of the responsible CSF viral strains was genotyped to genetic subgroup 1.1 [7]. Classical swine fever virus (CSFV) is the causative agent of CSF disease, belonging to the genus Pestivirus within the family Flaviviridae [8].…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity and positive selection analysis of classical swine fever virus isolates in south China

et al. 2011

View full text Add to dashboard Cite

Classical swine fever virus (CSFV) causes a highly contagious disease that leads to significant economic losses in the pig industry worldwide. However, there is a paucity of knowledge on the accurate genotyping of CSFV isolates in south China. This study genotyped the E2 gene of 14 CSFV strains isolated during 2008-2010 from domestic pigs in different districts of south China. Phylogenetic analyses revealed that all of the 14 CSFV isolates were clustered into genetic subgroup 1.1. This contrasts with most parts of China, where group 2 isolates are predominant. Furthermore, the positive selection pressures acting on the E(rns) and E2 envelope protein genes of CSFV were assessed and a site-by-site analysis of the dN/dS ratio was performed to identify specific codons that undergo diversification under positive selection. While no significant evidence for positive selection was observed in E(rns), two positively selected sites at amino acid residues 49 and 72 in the E2 encoding region were identified. Our results revealed that a predominance of subgroup 1.1 CSFV isolates is currently circulating in some districts of south China, which appear to be unrelated to the Chinese C-strain vaccine. Moreover, the envelope protein gene, E2, has undergone positive selection in 14 CSFV strains and two positively selected sites have been identified in this study. Understanding the molecular epidemiology and functional importance of these positively selected amino acid positions could help to predict possible changes in virulence, the development of vaccines and disease control.

show abstract

“…GenBank contains nucleic acid sequences from CSFVs collected since 1945, and according to an evolutionary study by Lowings, Ibata, Needham, and Paton (), there are two main parental strains, ALD from the United States (1946) and Brescia from Italy (1945), which can be associated to genotypes 1 and 2, respectively. With the exception of a few Colombian strains from 2005 to 2006, most outbreaks reported in the Americas correspond to CSFV genotype 1, which consist of subgenotypes 1.1 to 1.6 (Arainga et al., ; Pereda et al., ; Sabogal, Mogollon, Rincon, & Clavijo, ; Silva et al., ). There is no direct association between genotype and virulence for CSFV, but the majority of highly virulent strains and all vaccine strains fall within genotype 1, while genotypes 2 and 3 mostly include strains that are moderately to low virulent (Leifer, Hoeper, Blome, Beer, & Ruggli, ).…”

Section: Introductionmentioning

confidence: 99%

Phylodynamics of classical swine fever virus with emphasis on Ecuadorian strains

Garrido

Valle

Acosta

et al. 2018

Transbound Emerg Dis

View full text Add to dashboard Cite

Classic swine fever virus (CSFV) is a Pestivirus from the Flaviviridae family that affects pigs worldwide and is endemic in several Latin American countries. However, there are still some countries in the region, including Ecuador, for which CSFV molecular information is lacking. To better understand the epidemiology of CSFV in the Americas, sequences from CSFVs from Ecuador were generated and a phylodynamic analysis of the virus was performed. Sequences for the full-length glycoprotein E2 gene of twenty field isolates were obtained and, along with sequences from strains previously described in the Americas and from the most representative strains worldwide, were used to analyse the phylodynamics of the virus. Bayesian methods were used to test several molecular clock and demographic models. A calibrated ultrametric tree and a Bayesian skyline were constructed, and codons associated with positive selection involving immune scape were detected. The best model according to Bayes factors was the strict molecular clock and Bayesian skyline model, which shows that CSFV has an evolution rate of 3.2 × 10 substitutions per site per year. The model estimates the origin of CSFV in the mid-1500s. There is a strong spatial structure for CSFV in the Americas, indicating that the virus is moving mainly through neighbouring countries. The genetic diversity of CSFV has increased constantly since its appearance, with a slight decrease in mid-twentieth century, which coincides, with eradication campaigns in North America. Even though there is no evidence of strong directional evolution of the E2 gene in CSFV, codons 713, 761, 762 and 975 appear to be selected positively and could be related to virulence or pathogenesis. These results reveal how CSFV has spread and evolved since it first appeared in the Americas and provide important information for attaining the goal of eradication of this virus in Latin America.

show abstract

Phylogenetic Analysis of Classical Swine Fever Virus Isolates from Peru

Cited by 7 publications

References 21 publications

Insulated Isothermal Reverse Transcriptase PCR (iiRT-PCR) for Rapid and Sensitive Detection of Classical Swine Fever Virus

Insulated Isothermal Reverse Transcriptase PCR (iiRT-PCR) for Rapid and Sensitive Detection of Classical Swine Fever Virus

Genetic diversity and positive selection analysis of classical swine fever virus isolates in south China

Phylodynamics of classical swine fever virus with emphasis on Ecuadorian strains

Contact Info

Product

Resources

About