ya...sidenote to my above post
I didn't understand any of that technical jargon in those twitter posts...I only understood outbreak has been going on for weeks undetected
Hes looking at virus proteins. Virus all over shows variation quickly at rather non important points (vaccines can still work, still attacks humans the same etc). With that, you can look an determine where the virus came from. it should be consistent with the person's history.
In this case, he's claiming the person just diagnosed is in the virus evolution very direct linked to a case 6 weeks ago. This would suggest this person caught it from that other case. But if there is no direct transmission, then that first case has been infecting a chain of others until now.
The thing is this is built on a lot of assumptions that you really need to be an expert to judge.