Isolation and complete genomic characterization of pandemic H1N1/2009 influenza viruses from Cuban swine herds

Abstract

The emergence of the pandemic H1N1/2009 influenza virus poses a potential global threat for human and animal health. In this study, we carried out pandemic H1N1/2009 influenza virus surveillance in swine herds in Cuba intending to determine whether the virus was circulating among pig populations. As a result we describe, for the first time, the detection of pandemic H1N1/2009 influenza virus in swine herds in Cuba. In addition, phylogenetic analysis and molecular characterization of three viral isolates were performed. Phylogenetic relationships confirmed that all of the eight genes of the three isolates were derived from the pandemic H1N1/2009 virus. The Cuban isolates, formed an independent cluster within the pandemic H1N1/2009 influenza strains. Different molecular markers, previously described in pandemic H1N1/2009 influenza viruses, related with adaptive evolution, viral evasion from the host-immune response, virulence and dissemination were also present in Cuban pandemic H1N1/2009 isolates.

Introduction

Influenza viruses that circulate continuously in domestic animals are included in the genus Influenza virus A, within the family Orthomyxoviridae and are characterized by a segmented viral genome consisting of eight single-stranded RNA fragments of negative polarity encoding 11 proteins (Webster and Bean, 1978).

In April 2009, a new swine-origin H1N1 influenza virus was identified circulating in humans and rapidly reached pandemic magnitude (Neumann et al., 2009). The newly emergent pandemic H1N1/2009 influenza virus contains ancestral gene segments from triple reassortant swine viruses (H1N1, H3N2, H1N2) that had been circulating in pigs in North America since the late 1990s with an additional reassortment that replaced two gene segments (NA and M) of the North American swine virus with the respective segments of the Eurasian swine virus (Garten et al., 2009, Smith et al., 2009).

To date, there are a number of reports confirming that pandemic H1N1/2009 influenza virus has re-infected swine herds in several countries (Howden et al., 2009, Nagarajan et al., 2010, Song et al., 2010, Vijaykrishna et al., 2010). Swine might serve as reservoirs of this novel influenza virus which can be transmitted to humans and they can also function as switch point for virus infection between different species through reassortment in the pig of avian, swine and/or human viruses (Haß et al., 2011). Therefore, identifying mutations and gene combinations with pandemic potential or virulence determinants are essential to support prevention and control strategies at a global level (Capua and Cattoli, 2010).

In the present study, we carried out pandemic H1N1/2009 influenza virus surveillance in swine herds in Cuba intending to determine whether the virus was circulating among pig populations. As result we obtained three isolates whose complete genome sequences were analyzed to provide useful information for both public and animal health support.