Characterization of the 1918 "Spanish" influenza virus neuraminidase gene

Abstract

The "Spanish" influenza pandemic of 1918 was characterized by exceptionally high mortality, especially among young adults. The surface proteins of influenza viruses, hemagglutinin and neuraminidase, play important roles in virulence, host specificity, and the human immune response. The complete coding sequence of hemagglutinin was reported last year. This laboratory has now determined the complete coding sequence of the neuraminidase gene of the 1918 virus. Influenza RNA fragments were isolated from lung tissue of three victims of the 1918 flu; complete sequence was generated from A/Brevig Mission/1/18, with confirmatory sequencing carried out on A/South Carolina/1/18 and A/New York/1/18. The 1918 neuraminidase gene sequence was compared with other N1 subtype neuraminidase genes, including 9 N1 strains newly sequenced for this study. The 1918 neuraminidase shares many sequence and structural characteristics with avian strains, including the conserved active site, wild-type stalk length, glycosylation sites, and antigenic sites. Phylogenetically, the 1918 neuraminidase gene appears to be intermediate between mammals and birds, suggesting that it was introduced into mammals just before the 1918 pandemic.

Figure 1

Complete coding sequence of the NA gene of the 1918 influenza virus. The sequence of A/Brevig Mission/1/18 is shown with a theoretical translation. The numbering of the gene is aligned to A/NJ/8/76 and refers to the sequence in the sense (mRNA) orientation. The sequence coding for the signal peptide is underlined. Boxed amino acids indicate potential glycosylation sites as predicted from the sequence. Circled amino acids indicate the active site residues (3).

Figure 2

Phylogenetic analysis of influenza N1 NA genes. The tree was produced with mega by using neighbor-joining and p distance. Influenza strain abbreviations are given in Table 1. Brevig/18 is identified by an arrow. Bootstrap values are given for selected nodes, and a distance bar is shown below the tree (0.1 p distance is approximately 132 nucleotide differences).

Figure 3

Rate of change of influenza NA genes. One most parsimonious paup N1 protein tree was imported into macclade, and unambiguous amino acid changes were traced in the human (excluding Brevig/18) and swine lineages. The number of changes was plotted vs. year of isolation and regression lines calculated and drawn by using Microsoft Excel (Microsoft, Redmond, WA) and Slide Write (Advanced Graphics, Carlsbad, CA). The regression lines were then extrapolated, and the Brevig/18 data point was plotted. Human viral isolation times were corrected for the 20-year gap in circulation of H1N1 viruses from 1957–1977 (28).