Is this a COVID-19 reference in Kaguya-sama: Love Is War season 2?
Unlikely.

The anime is an adaptation of the manga, which is the canonical source. According to Fandom Wiki, episode 18 (season 2 episode 6) adapts chapter 67-69 of the manga. This particular scene is from chapter 68 titled I Want to Make Miko Iino Smile which was published on 22 June 2017, long before the COVID-19 outbreak happened.

Regarding the term "hot spot", it actually means "conflict hot spot". The original text in Japanese is 紛争地域 which means "disputed territory; conflict area".

The fan translation of this scene is




  My mom's giving vaccines in a war zone,


which gives more context than a general term "hot spot".