Spreadsheet: 48ff9836-397d-46b5-8586-a235787c9e55
Sheet: Sheet1

Unnamed: 0 | Supplementary Table 2. Competitive transmission studies in ferrets for wild-type and mutant pandemic H1N1 viruses1 | Unnamed: 2 | Unnamed: 3 | Unnamed: 4 | Unnamed: 5 | Unnamed: 6 | Unnamed: 7 | Unnamed: 8 | Unnamed: 9 | Unnamed: 10 | Unnamed: 11 | Unnamed: 12 | Unnamed: 13 | Unnamed: 14 | Unnamed: 15 | Unnamed: 16 | Unnamed: 17 | Unnamed: 18 | Unnamed: 19 | Unnamed: 20 | Unnamed: 21 | Unnamed: 22 | Unnamed: 23 | Unnamed: 24 | Unnamed: 25 | Unnamed: 26 | Unnamed: 27 | Unnamed: 28 | Unnamed: 29
 |  |  |  |  | Codon set for amino acid at position:
 |  |  |  |  | 591 |  |  |  | 627 |  |  |  | 701
 |  |  |  |  | 1798CGG1800: R (wild-type) |  |  |  | 1906GAA1908: E (wild-type) |  |  |  | 2128GAC2130: D (wild-type)
 |  |  |  |  | 1798CGA1800: R |  |  |  | 1906GAG1908: E |  |  |  | 2128GAT2130: D
 |  |  |  |  | 1798CAG1800: Q |  |  |  | 1906AAA1908: K |  |  |  | 2128AAC2130: N
 |  |  |  |  | 1798CAA1800: Q |  |  |  | 1906AAG1908: K |  |  |  | 2128AAT2130: N
 |  |  | Virus titer in |  | Infected |  |  |  |  |  |  |  |  |  |  |  | Virus titer in |  | Contact
 |  |  | nasal wash |  |  |  |  |  |  |  |  |  |  |  |  |  | nasal wash
Experiment |  |  | (PFU/ml) |  | G1799A | G1800A | Average |  | G1906A | A1908G | Average |  | G2128A | C2130T | Average |  | (PFU/ml) |  | G1799A | G1800A | Average |  | G1906A | A1908G | Average |  | G2128A | C2130T | Average
Wild type vs. 627K | Inoculum |  |  |  |  |  |  |  | 38.94 | 35.62 | 37.28
 |  |  |  |  |  |  |  |  | 37.32 | 29.68 | 33.5
 |  |  |  |  |  |  |  |  |  |  | 35.39
 | Pair 1 | Day 1 | 32000000 |  | <1 | <1 | <1 |  | 22.93 | 20.96 | 21.945 |  | <1 | <1 | <1
 |  | Day 3 | 1000000 |  | <1 | <1 | <1 |  | 21.22 | 19.16 | 20.19 |  | <1 | <1 | <1 |  | 7000000 |  | <1 | 1.61 | <1.3 |  | <1 | <1 | <1 |  | 3.34 | <1 | <2.2
 |  | Day 5 | 80000 |  | <1 | <1 | <1 |  | 8.75 | 8.56 | 8.655000000000001 |  | <1 | <1 | <1 |  | 200000 |  | <1 | 6.07 | <3.6 |  | <1 | <1 | <1 |  | 1.42 | 0.33 | 0.875
 |  | Day 7 |  |  |  |  |  |  |  |  |  |  |  |  |  |  | 120 |  | <1 | 5.99 | <3.5 |  | <1 | <1 | <1 |  | <1 | <1 | <1
 | Pair 2 | Day 1 | 2100000 |  | <1 | <1 | <1 |  | 19.5 | 16.64 | 18.07 |  | <1 | <1 | <1
 |  | Day 3 | 600000 |  | <1 | <1 | <1 |  | 15.02 | 13.59 | 14.305 |  | <1 | <1 | <1 |  | 22000000 |  | <1 | <1 | <1 |  | 1.96 | 1.39 | 1.675 |  | 2.9 | <1 | <2.0
 |  | Day 5 | 100000 |  | <1 | 1.56 | <1.3 |  | 13.94 | 13.43 | 13.685 |  | <1 | <1 | <1 |  | 3500000 |  | <1 | <1 | <1 |  | 2.37 | 1.83 | 2.1 |  | <1 | <1 | <1
 |  | Day 7 |  |  |  |  |  |  |  |  |  |  |  |  |  |  | 290000 |  | <1 | <1 | <1 |  | 11.43 | 8.96 | 10.195 |  | 1.71 | <1 | <1.4
 | Pair 3 | Day 1 | 10000000 |  | <1 | <1 | <1 |  | 27.93 | 23.34 | 25.635 |  | <1 | <1 | <1
 |  | Day 3 | 160000 |  | 3.82 | 3.37 | 3.595 |  | 14.56 | 12.98 | 13.77 |  | 1.05 | 1.7 | 1.375
 |  | Day 5 | 190000 |  | <1 | <1 | <1 |  | 17.05 | 15.26 | 16.155 |  | <1 | <1 | <1 |  | 17000000 |  | <1 | <1 | <1 |  | <1 | <1 | <1 |  | <1 | <1 | <1
 |  | Day 7 |  |  |  |  |  |  |  |  |  |  |  |  |  |  | 300000 |  | <1 | <1 | <1 |  | 2.78 | 2.36 | 2.57 |  | 1.13 | <1 | <2
Wild type vs. 701N | Inoculum |  |  |  |  |  |  |  |  |  |  |  | 44.58 | 51.83 | 48.205
 |  |  |  |  |  |  |  |  |  |  |  |  | 37.44 | 34.19 | 35.815
 |  |  |  |  |  |  |  |  |  |  |  |  |  |  | 42.01
 | Pair 4 | Day 1 | 100000000 |  | <1 | <1 | <1 |  | <1 | <1 | <1 |  | 40.73 | 41.85 | 41.29
 |  | Day 3 | 410000 |  | <1 | <1 | <1 |  | <1 | <1 | <1 |  | 37.14 | 38.2 | 37.67 |  | 8000000 |  | <1 | <1 | <1 |  | <1 | <1 | <1 |  | 38.24 | 38.65 | 38.445
 |  | Day 5 | 90000 |  | <1 | <1 | <1 |  | <1 | <1 | <1 |  | 27.06 | 27.7 | 27.38 |  | 800000 |  | <1 | <1 | <1 |  | <1 | <1 | <1 |  | 19.96 | 19.57 | 19.765
 |  | Day 7 |  |  |  |  |  |  |  |  |  |  |  |  |  |  | 1700 |  | <1 | <1 | <1 |  | <1 | <1 | <1 |  | 27.53 | 28.54 | 28.035
 | Pair 5 | Day 1 | 60000000 |  | <1 | <1 | <1 |  | <1 | <1 | <1 |  | 38.85 | 39.16 | 39.005
 |  | Day 3 | 280000 |  | <1 | <1 | <1 |  | <1 | <1 | <1 |  | 42.77 | 27.99 | 35.38
 |  | Day 5 | 1700000 |  | <1 | <1 | <1 |  | <1 | <1 | <1 |  | 17.98 | 18.11 | 18.045 |  | 1300000 |  | <1 | <1 | <1 |  | <1 | <1 | <1 |  | 33.63 | 33.09 | 33.36
 |  | Day 7 |  |  |  |  |  |  |  |  |  |  |  |  |  |  | 400000 |  | <1 | <1 | <1 |  | <1 | <1 | <1 |  | 23.62 | 23.29 | 23.455
 | Pair 6 | Day 1 | 80000000 |  | <1 | <1 | <1 |  | <1 | <1 | <1 |  | 33.4 | 23.45 | 28.425
 |  | Day 3 | 1200000 |  | <1 | <1 | <1 |  | <1 | <1 | <1 |  | 14.15 | 13.17 | 13.66 |  | 22000000 |  | <1 | <1 | <1 |  | <1 | <1 | <1 |  | 1.51 | 1.94 | 1.725
 |  | Day 5 | 130000 |  | <1 | <1 | <1 |  | 1.42 | 1.12 | 1.27 |  | 21.22 | 21.37 | 21.295 |  | 110000 |  | <1 | <1 | <1 |  | <1 | <1 | <1 |  | <1 | <1 | <1
 |  | Day 7
Wild type vs. 591Q | Inoculum |  |  |  | 39.73 | 37.48 | 38.605
 |  |  |  |  | 38.17 | 32.87 | 35.52
 |  |  |  |  |  |  | 37.0625
 | Pair 7 | Day 1 | 480000000 |  | 36.23 | 34.18 | 35.205 |  | <1 | <1 | <1 |  | <1 | <1 | <1
 |  | Day 3 | 4800000 |  | 31.63 | 28.48 | 30.055 |  | <1 | <1 | <1 |  | 2.38 | <1 | <1.7 |  | 4000000 |  | 93.57 | 87.37 | 90.47 |  | <1 | <1 | <1 |  | <1 | <1 | <1
 |  | Day 5 | 600000 |  | 5.31 | 5.48 | 5.395 |  | <1 | <1 | <1 |  | 2.23 | <1 | <1.6 |  | 90000 |  | 60.92 | 55.96 | 58.44 |  | 1.99 | 1.99 | 1.99 |  | 1.41 | 2.82 | 2.115
 |  | Day 7
 | Pair 8 | Day 1 | 390000000 |  | 40.91 | 38.96 | 39.935 |  | <1 | <1 | <1 |  | <1 | <1 | <1 |  | 230 |  | 24.51 | 22.6 | 23.555 |  | 12.62 | 12.12 | 12.37 |  | <1 | 1.67 | <1.4
 |  | Day 3 | 210000 |  | 42.33 | 40.18 | 41.255 |  | <1 | <1 | <1 |  | <1 | <1 | <1 |  | 28000000 |  | 2.09 | 1.94 | 2.015 |  | <1 | <1 | <1 |  | <1 | <1 | <1
 |  | Day 5 | 90000 |  | 9.09 | 8.26 | 8.675 |  | <1 | <1 | <1 |  | <1 | <1 | <1 |  | 200000 |  | 2.06 | 2.15 | 2.105 |  | <1 | <1 | <1 |  | <1 | <1 | <1
 |  | Day 7
 | Pair 9 | Day 1 | 200000000 |  | 44.8 | 42.89 | 43.845 |  | <1 | <1 | <1 |  | <1 | <1 | <1
 |  | Day 3 | 160000 |  | 23.38 | 23.02 | 23.2 |  | <1 | <1 | <1 |  | <1 | <1 | <1 |  | 1200000 |  | 79.71 | 77.34 | 78.525 |  | <1 | <1 | <1 |  | <1 | <1 | <1
 |  | Day 5 | 50000 |  | 12.56 | 11.59 | 12.075 |  | <1 | <1 | <1 |  | <1 | <1 | <1 |  | 250000 |  | 40.88 | 38.68 | 39.78 |  | <1 | <1 | <1 |  | <1 | <1 | <1
 |  | Day 7 |  |  |  |  |  |  |  |  |  |  |  |  |  |  | 11000 |  | 12.99 | 12.18 | 12.585 |  | 1.16 | 1.05 | 1.105 |  | 1.05 | 1.52 | 1.285
 | [NAME] amplicons spanning the three codons of interest were pyrosequenced on a Roche/454 GS FLX. The data shown here are summarized in Figure 3. The percentage of variant sequence at each nucleotide residue is shown. Since two nucleotide sites are affected in each of the three codons, the mutant frequency plotted in Figure 3 is based on the mean perecentage of variants detected at both positions. The limit of sensitivity was arbitrarily defined at 1%; mutations observed in less than 1% of reads are denoted '<1'.