TABLE 2

Within-host variants identified by deep sequencinga

SampleVariantFrequency
WSPHL1NS1-G47S0.042
WSPHL3HA-D513Y0.035
WSPHL4NA-E83K0.32
WSPHL4PB2-E40G0.035
WSPHL4PB2-R175K0.042
WSPHL4HA-E325K0.06
WSPHL6PB1-M372I0.038
WSPHL6PB1-H562Y0.059
WSPHL7PB1-F254F0.34
WSPHL7PA-P238P0.119
WSPHL7HA-I202V0.115
WSPHL7NP-P419P0.268
WSPHL8NA-F42F0.153
WSPHL8NA-N86T0.204
WSPHL8PB2-M631V0.061
WSPHL8PB1-I392M0.079
WSPHL8HA-R208S0.081
WSPHL8HA-A425A0.161
WSPHL9PB1-N518N0.248
WSPHL9PB1-E731E0.21
  • a Sites were called as variable if a nonconsensus base exceeded a frequency of 0.03, given a sequencing coverage of at least 100×, in both sequencing replicates.