The afflicted are the wererat things. There are two levels of them - the sewers and the Werereat Cvaes or somethging which you'll find in the NE corner of the sewers.
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SPOILER - highlight to read: You have to kill the wererat boss, too. He's pretty tough. As the_limey said, he is on a lower level than the entrance level, and there are quite a few wererats down there. If you go even further down to the bottom level you will find fire trolls - also difficult. Fire trolls are a quest the wererat boss wants you to deal with if you are friendly to him - too late this time round, but you might keep it in mind for next time.
You get the opportunity when you first enter the sewers to join either the Thieves or the Beggars (wererats). The Beggar/wererat boss wants a cure for his people, because they used to be thieves and got infected. And the Thieves want you to rid the world of wererats. Both have remunerative quests for you to perform. Since you are in the Inquisition, you have made friends with the Thieves until you cleared out the wererats, but hey! who's counting, lol!
There is a fair bit of quite nice loot to be had on all 3 levels, so, even if nobody asks you - and someone WILL! - it's good to clear the trolls and take EVERYTHING you find. One thing down there is a quest item. End SPOILER
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