Abstract
The genome of a porcine H1N1 influenza A strain is reported in this study. The strain proved to be a monoreassortant strain with a typical porcine N1 gene on the genetic backbone of the pandemic H1N1 influenza A virus strain. Monitoring of descendants of the pandemic 2009 H1N1 strain is needed because of concerns that more-virulent strains may emerge in forthcoming epidemic seasons.
GENOME ANNOUNCEMENT
Influenza A virus is classified based on differences in the neutralization antigens, the hemagglutinin (HA) and the neuraminidase (NA) (7). To date, 17 HA and 10 NA subtypes have been described, with the greatest heterogeneity in migratory birds and lower diversity in secondary hosts, e.g., pigs and humans (6, 7). Unlike the devastating pandemics in the 20th century, the 2009 swine-origin H1N1 influenza A virus was associated with lower mortality (2). This new pandemic H1N1 virus was also detected from humans and pigs in Hungary (1). Detection of the pandemic H1N1 virus in Hungarian piggeries prompted us to strengthen influenza strain surveillance in swine and monitor possible genetic and phenotypic changes of this emerging strain.
In May 2011, an H1N1 influenza A virus was isolated from the nasal swab of an adult domestic swine with lethargy, fever, labored breathing, coughing, nasal discharge, and conjunctivitis in a farm southwest of Budapest, the capital of Hungary. To further characterize this strain, the whole genome was sequenced. In brief, PCR amplicons were generated using primers and protocols described previously (1, 3, 4) and an ABI PRISM 3130 genetic analyzer was utilized to generate sequence chromatograms. Sequences were assembled using the DNAStar 7 software.
The eight genome segments encoded 10 proteins (length of PB2, 759 amino acids [aa]; PB1, 757 aa; PA, 716 aa; HA, 566 aa; NP, 498 aa; NA, 469 aa; M1, 252 aa; M2, 97 aa; NS1, 219 aa; NS2, 121 aa). The strain A/Swine/Hungary/362/2011/H1N1 shared transmission-, virulence-, and resistance-related markers with typical 2009 pandemic H1N1 viruses. These included a T271A substitution in PB2 that is associated with enhanced polymerase activity, the substitutions S409N in PA and C55F in M2, both being associated with increased transmissibility, and the substitution 31N in M2 that is responsible for increased resistance to amantadine. The HA protein displayed no accumulation of basic amino acids in the cleavage region, whereas the NA protein had no particular resistance motifs (i.e., R292K, H274Y, or E119V).
Phylogenetic analyses showed relatedness of the HA gene with those of the 2009 swine-origin pandemic strains (up to 99% nucleotide [nt] identity with reference strains), including the pandemic Hungarian porcine and human isolates (>98%), whereas the NA gene was more similar to those of a Hungarian porcine strain from 2006 (96%) and some other European strains detected in Spain, Belgium, Italy, and France during the early and mid-2000s (96% to 97%) and those isolated in Germany during 2010 (95%) (5). The backbone genes were able to be derived from the pandemic swine H1N1 strain, with >97% nt identities (depending on the gene) to local porcine and human strains from 2009 to 2010 (1) and with comparable sequence identities to international strains isolated from the same period. These findings suggest that strain A/Swine/Hungary/362/2011/H1N1 evolved from the pandemic H1N1 strain and a true porcine strain through natural reassortment. This study reaffirms that the pandemic 2009 H1N1 strain is evolving and likely to become enzootic in European pig herds.
Nucleotide sequence accession numbers.
The genome sequence of A/Swine/Hungary/362/2011/H1N1 has been deposited in GenBank under accession numbers JX397999 to JX398006.
ACKNOWLEDGMENTS
We gratefully acknowledge the excellent technical assistance of Ágnes Juhász and Ernőné Ottinger.
This work was financially supported by the ESNIP3 (European Surveillance Network for Influenza in Pigs 3), FP7-INFLUENZA-2010, contract no. 259949. K.B. was supported by the Momentum program (Hungarian Academy of Sciences).
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