show Abstracthide AbstractCoxiella burnetii is an intracellular bacterium that causes the zoonosis Q fever. Full-length lipopolysaccharide (LPS), produced by phase I bacteria, is necessary for full virulence by C. burnetii in animal models of infection. Ex vivo or in vitro serial passage results in genetic mutations that direct synthesis of truncated forms of LPS, culminating in the deep-rough LPS of avirulent phase II bacteria. The genome sequences presented here provide a better understanding of the mutational pathways associated with C. burnetii LPS phase variation.