Previously Infected Website & SEO

Hello,

I recently rebuilt our company’s website from scratch as the previous one had got severely infected almost beyond repair (according to previous host). The new website is under the same domain name.

Will this have a negative impact on SEO and google rankings? Also I have recently changed permalink structure from default “?=123” to %postname%.
After around a week, i still cannot find the website very well through google even when typing exact page names. I have installed Yoast SEO and renamed page structures.