I'm a little tired and my brain isn't quite at full speed yet this morning, but I don't recall Holmes having any phobia like that. I could have forgotten some lines somewhere though. There are some episodes I haven't seen in while and some stories it's been even longer since I read. I wouldn't be surprised though as Watson has pointed out Holmes' "cat like" approach to personal cleanliness. But on the other hand he doesn't seem to hesitate getting his hands dirty if a case calls for it, or touching something nasty like a dead body. Off the top of my head I can think of a couple of instances where he did shake hands, such as Captain Croker in The Abbey Grange and Lestrade in that great scene from The Six Napoleons. The few examples I can think of where he didn't shake hands seemed, in my opinion, like attempts to highlight how unusual Holmes was. Sometimes I think he doesn't care for such niceties (he's not the most sociable guy at times), or is too focused on the problem or impatient to bother with the gesture. In A Scandal In Bohemia I think he just doesn't care for the Grand Duke too much, plus not shaking his hand sort of underlines the idea that Holmes isn't impressed with the fact that he's royalty and doesn't stand on ceremony. In the story it kind of seems to me that he didn't even notice the outstretched hand, saying he left the room without observing the outstretched hand. Which could be taken multiple ways I guess, either he didn't notice it (though Holmes seems to notice everything) or that he just didn't acknowledge/return the gesture.
"Dan Marino should die of gonorrhea and rot in hell. Would you like a cookie son?"
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