If you click the orange notification bubble at the end of the conversation’s title, the bubble will disappear and the thread will be considered Read. If you hover over where the bubble was, you will see a gray notification bubble. You can click the gray bubble to mark the conversation Unread.
You can also mark all conversations in a space as read at once. When joining a new space, after unhiding a space, or returning to Kona after an extended period of time away, like vacation, your account may have several unread new comments, and this can be overwhelming. So, you can clear all new notifications at the space level. From the Spaces section on the left sidebar of Kona, click the drop-down arrow next to the space name and select “Mark all read.”