“Welcome to the team! It’s great to have you with us.”
You just hired a new employee. She comes in for her first day of work. You say this to welcome her.
Welcome to the team! It’s great to have you with us.
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Use this phrase when a new person joins a team that you're part of: a sports team, a company that you work for, etc. You can even use this phrase jokingly in situations like when someone marries your brother or sister:
Welcome to the team, Frank.
Use the phrase "It's great to ___" in social situations to say that something makes you happy:
It's great to see you.
It's great to finally meet you!
More specifically, you can use the phrase "It's great to have you ___" to talk about someone's current situation:
It's great to have you back.
It's great to have you as part of the family now.
It's great to have you with us.