The sea and the Kansas prairie: simile
"For the next eight days, no wind, just a glassy sea as flat as the Kansas Prairie, and the sun beating down on our heads" is an example of simile as it uses as to compare the glassy sea and the flat Kansas prairie. Yancey includes this to build a sense of place and to paint a picture in readers' minds of the setting of the novel and the places his characters inhabit.
Horror and wonder: simile
"It was not horror that seized my imagination so much as wonder" is an example of simile because it uses "as" to compares the effect horror and wonder had on the speaker's imagination. This sentence is used to characterize Erasmus, the man with whom Will and Dr. Warthrope work with to fight against the Anthropophagi invasion.
Infectious diseases and the Anthropophagi: metaphor
The novel compares two seemingly unlike things: infectious diseases and the Anthropophagi. Both are invasive organisms which wreak havoc on the ecosystems and people they come near. Similarly, both kill those who they, in the case of infectious diseases, infect and in the case of the Anthropophagi, they attack.
A shark: metaphor
A character in the novel tells another character that he is a "shark." He does this to compare who he is, the steps he takes, and some of his characteristics to sharks, which are known for their intelligence, intense bite, and lust for blood.