SWINE VIRAL DISEASES PATHOGENESIS AND IMMUNOLOGY
Location: Virus and Prion Research Unit
Title: Swine Influenza Update
Submitted to: Swine Disease Conference Proceedings
Publication Type: Proceedings
Publication Acceptance Date: October 16, 2009
Publication Date: November 5, 2009
Citation: Lager, K.M., Vincent, A.L., Ciacci-Zanella, J.R., Zanella, E.L., Lorusso, A., Faaberg, K.S., Kehrli, Jr., M.E. 2009. Swine influenza update. In: Proceedings of the 17th Annual Swine Disease Conference, November 5-6, 2009, Iowa State University, Ames, Iowa. pp. 128-131.
On April 24, 2009, the Centers for Disease Control (CDC) confirmed an influenza epidemic was occurring in people and the genetic lineage was most closely related to influenza viruses known to be circulating in swine. The outbreak epicenter appeared to be in central Mexico and the virus spread to the United States and Canada by way of infected individuals early in the course of the pandemic. This proclamation that the virus was swine in origin led to a complex series of questions and politics that are still trying to be answered and addressed months later. This paper will summarize our efforts to answer some of the scientific questions with the political debate being left to others.
In mid-April two children in Southern California with influenza like illness (ILI) had tested positive for a swine influenza-like virus . This in and by itself was not unusual since several human swine flu cases have been detected annually over the last few years. What was unique about these two cases is that the children had no known contact with each other nor had visited any common sites or people, yet they were infected with almost identical viruses. Moreover, genetic analysis of the viruses revealed they were composed of a novel set of genes that had not been detected previously anywhere in the world. Within a few days it became clear this virus was transmitting from person to person in the United States and there was an epidemic of ILI in central Mexico that was spreading to the United States and Canada via the movement of infected people. A US Public Health Emergency was declared on April 26th and the CDC began to work closely with World Health Organization staff to try and control the spread of an apparently regional disease. Despite the best efforts of many, the H1N1 virus rapidly moved around the world leading to the declaration of a pandemic by June 11th, 2009.
Since the genetics of the pandemic virus were novel, the obvious question was, would this virus have any unique phenotypic characteristics in swine? The following narrative summarizes research conducted at NADC since the start of the pandemic, followed by concluding statements.
NADC in vivo studies. Beginning on May 1, 2009 we initiated a 4 pig study that followed our usual swine influenza virus challenge model, i.e., giving young pigs an intratracheal inoculation with 1 x 105 CCID50 of the pandemic virus isolate A/CA/04/2009 H1N1 (Vincent, unpublished data). The pigs were euthanized 5 days post inoculation (dpi), a time point that usually provides the peak virus load and extent of lesions when testing swine influenza virus (SIV) isolates. Using virus isolation and a real-time PCR assay, challenge virus was detected in nasal swabs and tissues associated with the respiratory tract in each of the 4 pigs. In contrast, virus was not isolated from sera or any other tissues collected from these pigs, although viral nucleic acid was detected in sera in two pigs and in a lymph node sample from 2 pigs. Pigs were moderately to severely affected following the inoculation having a rapid rise in body temperature and becoming dyspneic to a point of "thumping." Typically, there are few clinical signs following inoculation in our SIV challenge model; however, we have seen a similar response when pigs were given an H1N1 SIV challenge with A/swine/OH/07. The OH/07 virus was isolated from sick swine at an Ohio county fair during which a number of the swine show exhibitors developed ILI. An influenza virus was isolated from a child and parent that matched the swine isolate confirming the exhibitors had become infected with the swine virus. Based on a recent phylogenetic analysis , the OH/07 virus is from a cluster or clade of H1N1 SIV isolates that have emerged in the last few years known as the gamma clade.
In a second animal study we inoculated pigs with the A/CA/4/09 isolate or another human isolate A/Mexico/4108/2009 (Vincent, unpublished data). Pigs were euthanized 3, 5, and 7 dpi. Again, both groups of pigs had a moderate to severe clinical response to challenge as well as extensive lesions upon necropsy at each time point. As in the first study, virus was isolated in tissues associated with respiratory tract only.
NADC in vitro studies. In addition to questions about any unique pathogenic properties of the pandemic virus, there were questions about the specificity of current diagnostic tests. Many state veterinary diagnostic laboratories use a matrix gene based real-time PCR assay developed by ARS scientists at the Southeast Poultry Research Laboratory (SEPRL) to detect influenza virus in field samples. Initial testing with the pandemic virus revealed a loss in sensitivity and specificity with this assay, a problem that was improved following modifications of the assay by SEPRL scientists. NADC scientists developed a matrix based real-time PCR assay that could differentiate the pandemic H1N1 virus from endemic SIV isolates providing a tool that could be used to identify US pigs that might become infected with this virus (Lorusso, unpublished data). SEPRL scientists added to the diagnostic tool kit by developing a real-time PCR assay that could differentiate the neuraminidase gene of the pandemic virus from currently circulating endemic SIV N1 genes. Embryonated chicken eggs and cell culture would be needed for virus isolation since some isolates will replicate better in one substrate or the other.
Studies by others. In England  and Germany  experimental infection of swine with human H1N1 virus isolates produced results similar to the NADC experiments. According to those reports the pigs may not have had as marked of a clinical response to challenge as was observed in the NADC studies. However, this could be attributed to several factors that may reflect differences in methodology as well as inherent differences in virus isolates.
Human to swine transmission of pandemic virus. As of September 22nd, 2009 transmission of the pandemic virus from humans to swine has been reported twice in Canada and in Australia, and once in Argentina, Ireland and Singapore [http://www.oie.int/wahis/public.php?page=weekly_report_index&admin=0]. The first Canadian case was detected in Alberta shortly after the epidemic was recognized in Mexico. Although there was no definitive link between a sick human and the onset of disease in the pigs, it is believed they became infected following contact with people. The second case involved a cluster of herds detected during August in Manitoba. In this case there was linkage between people with an ILI working in a sow barn and the onset of disease in swine. Additional herds were infected and based on what has been made public, some of these infected premises are related to pig flow from the sow barn. However, there may be some sites that were infected without any known linkage to the sow barn. If this is the case, then it is not known if such an event represents indirect area spread or some other source of virus. In Australia, pandemic H1N1 infection of swine was detected in the states of Victoria and New South Wales in July and August, respectively. In each case the clinical disease was reported as mild even though the herds were considered naïve to influenza since Australia was believed to be free of swine flu prior to this species jump. As in the above cases, the case of human to swine transmission of influenza virus in Argentina and Ireland resulted in mild to moderate respiratory disease in affected pigs. In each of these cases the respective governments implemented control measures to restrict movement of swine from the infected premises with the hope of controlling the spread of this virus among swine and reduce the potential risk to people. Since Singapore does not raise swine, the case of pandemic virus infected swine in that country is related to the importation of swine from Indonesia for slaughte