Table 1.
Frequency of stop codon mutations and the numbers of synonymous and nonsynonymous nucleotide substitutions per site for different influenza virusesa
| Virusb | nd | No. truncatede |
dN for: |
dS for: |
ds X-ORF/ ds rest | dN/dS X-ORF frame 0 | dN/dS +1 X-ORFi | ||
|---|---|---|---|---|---|---|---|---|---|
| X-ORF frame 0c | Rest frame 0 | X-ORF frame 0 | Rest frame 0 | ||||||
| Avian influenza | 4,361 (80) | 19 (2) | 0.50 | 0.52 | 4.08 | 16.44 | 0.25 | 0.12 | 3.20 |
| Human H3N2 | 2,296 (49) | 8 (5) | 0.09 | 0.09 | 0.53 | 1.23 | 0.43 | 0.16 | 4.92 |
| Human H1N1s | 853 (50) | 3 (1) | 0.10 | 0.11 | 0.93 | 1.62 | 0.57 | 0.10 | 3.88 |
| Human H1N1pdm | 1,916 (56) | 1,914 (1,914) | 0.09 | 0.10 | 0.68 | 0.57 | 1.19 | 0.13 | 4.36 |
| Swine CS | 121 (52) | 6 (3) | 0.17 | 0.17 | 2.18 | 2.18 | 1.00 | 0.08 | 6.94 |
| Swine CS–stopf | 99 (53) | 98 (98) | 0.15 | 0.16 | 1.95 | 1.67 | 1.17 | 0.08 | 21.29 |
| Swine EA | 152 (60) | 0 (0) | 0.33 | 0.28 | 3.18 | 3.60 | 0.88 | 0.10 | 3.95 |
| Swine TR | 248 (73) | 225 (225) | 0.46 | 0.30 | 3.18 | 2.76 | 1.15 | 0.14 | 5.58 |
| Equine H3N8 | 80 (35) | 0 (0) | 0.12 | 0.09 | 0.25 | 0.73 | 0.34 | 0.49 | 1.15 |
| Equine H7N7g | 2 (2) | 2 (0) | 0.01 | 0.005 | 0.23 | 0.19 | 1.21 | 0.06 | ∞ |
| Bat influenzag | 2 (2) | 2 (0) | 0.01 | 0.005 | 0.14 | 0.13 | 1.08 | 0.05 | 0.59 |
| Canine H3N8 | 26 (6) | 25 (24) | 0.03 | 0.01 | 0.07 | 0.05 | 1.40 | 0.41 | 1.26 |
| Canine H3N2 | 8 (6) | 8 (7) | 0.03 | 0.01 | 0.16 | 0.05 | 3.20 | 0.18 | 4.13 |
| Influenza B | 190 (34) | 190 (AUh) | 0.05 | 0.06 | 1.07 | 1.11 | 0.96 | 0.05 | NAj |
Virus groups with truncated PA-X proteins and associated data are in italics.
Human H1N1s, seasonal H1N1; human H1N1pdm, 2009 pandemic H1N1; swine CS, “classical” swine H1N1; swine EA, Eurasian avian H1N1-like swine H1N1; swine TR, triple-reassortant swine H1N1.
Reading frame encoding the PA protein.
First number is the total data set. The representative sample size used for the analysis of dN and dS is shown in parentheses.
First number is the number of viruses from the total data set that are truncated because of premature stop codons. The number of viruses with stop codon mutations at codon 42 is shown in parentheses.
The classical swine viruses can be divided into two groups representing those with and without the stop codon mutation at codon 42. Note that there has been a single reversion to the non-stop codon state in the stop codon group.
Because the very small sample size these sequences were analyzed with MEGA5 rather than PAML.
AU, sequence alignment is uncertain in this region.
For the full-length X-ORF the analysis of dN/dS was performed on all 61 amino acids present in the protein, while for sequences encoding the truncated protein this analysis was restricted to the 41 amino acids prior to the position corresponding to the stop codon.
NA, contains too many stop codons for meaningful analysis.