ORF 5 vs whole genome sequencing for PRRSv

For epidemiological investigations, ORF-5 sequence has been the standard to differentiate PRRSv isolates. In the field people have used different cut offs to differentiate viruses (related vs non-related), the most common being to consider that isolates with 97 to 99% ORF 5 nucleotide similarity (within a year) to be related (Christopher-Hennings et al., JSHAP 2002; Murtaugh, Leman 2012).

However, studies comparing ORF5 sequences have failed to identify RNA segments correlated with virulence. Therefore, some PRRSv-researchers are now studying the whole genome (ORFs 1 to 7) to try to find "the million dollar answer", that is, what makes one isolate relatively avirulent and other isolates "highly pathogenic".

Some examples of PRRSv whole-genome studies that came out this week:

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J Virol. 2012 Dec;86(24):13883-4. doi: 10.1128/JVI.02731-12.

Complete genome sequence of a moderately pathogenic porcine reproductive and respiratory syndrome virus variant strain.

Du Y, Lu Y, Qi J, Wu J, Wang G, Wang J.

Source

Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China.

Abstract

Porcine reproductive and respiratory syndrome (PRRS) has become one of the most economically important diseases to the global pork industry. The etiological agent is the PRRS virus (PRRSV). In the spring of 2006, a highly pathogenic porcine reproductive and respiratory syndrome virus (HP-PRRSV) appeared in China and caused heavy economic losses. Here we report the complete genomic sequence of a novel PRRSV variant with 174 amino acid deletions in the nonstructural protein 2 (nsp2) gene.

PMID:

 

23166276

 

[PubMed - in process]

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J Virol. 2012 Dec;86(24):13882. doi: 10.1128/JVI.02729-12.

Complete Genome Sequence of Porcine Reproductive and Respiratory Syndrome Virus Strain ZCYZ Isolated from Hybrid Wild Boars.

Wu J, Liu S, Du Y, Gao Y, Wang G, Wang J.

Source

Shandong Key Lab of Animal Disease Control and Breeding, Shandong Academy of Agricultural Sciences, Jinan, People's Republic of China.

Abstract

A serologic investigation of porcine reproductive and respiratory syndrome virus (PRRSV) in hybrid wild boar herds was conducted during 2008-2009. PRRSV isolates with novel genetic markers were recovered. Experimental infection of pigs indicated that hybrid wild boars are involved in the epidemiology of PRRSV.

PMID:

 

23166275

 

[PubMed - in process]

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J Virol. 2012 Dec;86(24):13863-4. doi: 10.1128/JVI.02642-12.

Complete Genome Sequence of a Highly Pathogenic Porcine Reproductive and Respiratory Syndrome Virus NM1 Strain from Northern China.

Li Z, Leng X, Qi Q, Wang F, Wen Y, Tan B, He Y, Xia M, Lu W, Chen L, Cheng S, Wu H.

Source

Division of Zoonoses, Institute of Special Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Jilin, China.

Abstract

NM1 is a highly pathogenic North American-type porcine reproductive and respiratory syndrome virus (PRRSV). The complete genome sequence shows that NM1 shares high sequence identity (99.2 to 99.4%) to other HP-PRRSV isolates, containing two discontinuous deletions, a 1-amino-acid deletion at position 481 and a 29-amino-acid deletion at positions 533 to 651, in nonstructural protein 2.

PMID:

 

23166263

 

[PubMed - in process]

Investigation of strategies for the introduction and transportation of replacement gilts

ABSTRACT:

BACKGROUND: Porcine reproductive and respiratory syndrome (PRRS) is of major concern to the swine industry; infection with the virus can lead to production losses, morbidity, and mortality within swine operations. Biosecurity practices related to the management of replacement animals are important for the prevention and control of the PRRS virus, as well as other diseases. The objectives of this study were: (i) to describe individual biosecurity practices related to the introduction and transportation of replacement gilts on southern Ontario sow farms, and (ii) to understand patterns in the implementation of these practices. The second objective was accomplished using multiple correspondence analysis (MCA), which allows visualization of the relationships between individual practices and provides information about which practices frequently occur together, and which practices rarely occur together. These patterns constitute strategies for the implementation of biosecurity practices related to the introduction and transportation of replacement gilts. Data were collected using version 2 of the Production Animal Disease Risk Assessment Program's survey for the breeding herd. Two subsets of variables were retained for analysis; one subset pertained to how replacements were managed upon arrival to the farm, and the other pertained to the transportation of genetic animals.

RESULTS:

For both subsets of variables, the results of the MCA procedure were similar; in both solutions the 1st dimension separated herds that were closed with respect to replacement animals from herds that were open, and the 2nd dimension described how open herds managed replacements. The most interesting finding of this study was that, in some cases where a risky practice was being implemented, it was closely associated with other biosecurity practices that may mitigate that risk.

CONCLUSIONS:

The findings from this approach suggest that one cannot always examine biosecurity on a variable-by-variable basis. Even if a practice that is generally considered high-risk is being implemented, it may be balanced by other practices that mitigate that risk. Thus, the overall biosecurity strategy on a farm must be considered instead of only examining the implementation of individual practices.

PMID:

 

23140357

 

[PubMed - as supplied by publisher]

Bottoms K, Poljak Z, Dewey C, Deardon R, Holtkamp D, Friendship R. Investigation of strategies for the introduction and transportation of replacement gilts on southern Ontario sow farms. BMC veterinary research 2012;8(1):217-217.