Clinical influenza A isolates are frequently not sequenced directly. Instead, a majority of these isolates (~70% in 2015) are first subjected to passaging for amplification, most commonly in non-human cell culture. Here, we find that this passaging leaves distinct signals of adaptation in the viral sequences, which can confound evolutionary analyse...

Sequence amplification via cell passaging creates spurious signals of positive adaptation in influenza H3N2 hemagglutinin

10.1101/038364