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Concise and broadly applicable method for determining the genomic sequences of North-American-type porcine reproductive and respiratory syndrome viruses in various clusters.

ABSTRACT: We developed a concise and broadly applicable method for accurate genomic sequencing of North American genotype (NA-type) porcine reproductive and respiratory syndrome viruses (PRRSVs) that overcomes high genetic variability of the viruses. The method, designated "combination of consensus oligonucleotide reverse transcription and multiple displacement amplification" (CORT-MDA), involves reverse-transcription of viral RNA followed by shotgun sequencing after amplification using only 11 degenerate oligonucleotide primers; these primers were designed against consensus regions within the open reading frames of the 124 NA-type PRRSV strains with reported full-length genomic sequences. Sequencing of the 192 shotgun clones generated per virus showed 80% to 94% coverage on the reported PRRSV genomic sequence, such that only 2 or 3 unread regions had to be resequenced after PCR amplification using custom primers. Direct sequencing of RT-PCR products confirmed absolute consistency between sequences determined by the CORT-MDA method and those from RT-PCR. These results suggest that our method is applicable to diverse NA-type viruses.

SUBMITTER: Morozumi T

PROVIDER: S-EPMC4197153 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundPorcine reproductive and respiratory syndrome (PRRS) is one of the most important swine diseases in the world and genetic selection of pigs for increased resistance to PRRS is an attractive method to improve the health status of the swine herd. This study compared phenotypic and genetic responses to infection with one of two genetically distinct type 2 PRRS virus (PRRSV) isolates: NVSL-97-7895 (NVSL) and KS-2006-72109 (KS06), and evaluated whether the single nucleotide polymorphism (SNP) WUR10000125 (WUR) on chromosome 4 that was associated with viral load and weight gain under infection with NVSL also has an effect on response to infection across North American PRRSV isolates. Wood's lactation curve was fitted to repeated viremia measurements to derive five curve characteristics that were evaluated.ResultsInfection with NVSL was characterized by reaching a 14 ± 2 % higher peak viremia (PV) 2.5 ± 0.6 days earlier (time to peak; TP) than KS06, followed by 36 ± 1 % faster virus clearance, which occurred 3.9 ± 0.7 days sooner. Weight gain from 0 to 42 days post-infection (WG) tended to be higher under infection with KS06 than NVSL (3.7 ± 1.5 kg). Estimates of heritability were moderate for both PRRSV isolates for viral load from 0 to 21 days post-infection (VL) (NVSL: 0.31 ± 0.06; KS06: 0.51 ± 0.09) and WG (NVSL: 0.33 ± 0.06; KS06: 0.31 ± 0.09). Strong negative genetic correlations were observed between VL and WG for both NVSL (-0.74 ± 0.10) and KS06 (-0.52 ± 0.17) infected pigs. Pigs with genotype AB at the WUR SNP had a more desirable phenotype than AA pigs for all traits under infection with NVSL, but only for VL and PV with KS06; effects on other traits were smaller and not significantly different from zero (P > 0.05). Genetic correlations of host response between isolates were strong for VL, WG and PV. Accounting for WUR genotype had little impact on these correlations, suggesting that response to PRRSV infection has a substantial polygenic component that is common between these two isolates.ConclusionsThese results suggest that the KS06 PRRSV isolate is less virulent than NVSL but that genetic selection for increased resistance to either of these genetically distinct isolates is expected to increase resistance to the other isolate.

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Concise and broadly applicable method for determining the genomic sequences of North-American-type porcine reproductive and respiratory syndrome viruses in various clusters.

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