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]