Genetic assessment of VDL SIV isolate pool for evidence of the swine flu strain reported to be infecting people and development of a high-throughput differential test for the novel strain
A novel H1N1 influenza virus (initially named “Swine Flu” and now referred to as “2009 pandemic H1N1”) emerged and caused widespread clinical disease in US and other countries. The novel virus is a reassortant between North American lineage and Eurasian lineage of swine influenza viruses (SIVs) which has not been reported in human and swine populations throughout the world previously. Although human-to-human transmission was the main mode after initial outbreak, the potential and perception that pigs might have been the initial source of the novel strain had detrimental impact on both domestic and export markets of U.S. pigs and pork products. Although preliminary tests indicated otherwise, uncertainty existed as to whether or not the novel strain had been circulating undetected in the US swine population. The following study was conducted to address this concern through retrospective and proactive surveys.
First, archived H1N1 SIV isolates (n=118) and H1N1-positive clinical specimens from cases submitted from Iowa and major swine producing states to the Iowa State University Veterinary Diagnostic Laboratory during 2008 and the first quarter of 2009 were sequenced and analyzed for HA, NA and M genes in comparison to those of the novel H1N1 strain. Sequence analyses did not reveal the presence of novel H1N1 virus among the 118 banked H1N1 SIV isolates and H1N1-positive clinical specimens, strongly suggesting that 2009 pandemic H1N1 was unlikely circulating undetected in the US swine population prior to its emergence in humans. Second, the effort was made to develop a multiplex PCR assay for rapid detection and differentiation of the novel H1N1 strain from endemic SIVs which have been circulated in the US swine population. As a differential PCR was successfully developed, specimens collected from 165 animals after the emergence of the novel H1N1 virus in humans were examined by the test. In contrast to the observation on the archived isolates/samples, the novel H1N1 strain was detected in various animal species (pigs, cats and dog) although its incidence was low (3%).
In conclusion, evidence that the novel H1N1 virus was circulating undetected in US swine population prior to its emergence in human is lacking. Cross-species transmission of the novel H1N1 strain from affected humans to animals including pigs were apparent, suggesting that good biosecurity measure and farm personnel management should be practiced when an influenza epidemic occurs in humans. Development of PCR-based assay for rapid detection and differentiation of the novel H1N1 strain would be of help for a proactive surveillance program as its incidence in pigs is expected to continue to increase. Please contact Dr. Yoon for details and further information.
Dr. Kyoung-Jin Yoon
Iowa State University
College of Veterinary Medicine
Veterinary Medical Research Institute, #1
1802 University Boulevard, Ames, IA 50011
515-294-1083 (Voice) / 515-294-6619 (FAX) / firstname.lastname@example.org
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