Please,dont feel like that. This was just small inattention and I am sure you are very carefull mom. other moms wouldnt even notice that there wasnt cover.
virus cant live outside the body so it cant be transmissed through objects. prolonged contact of blood or body fluids is necessary for hiv transmission and this didnt occur in your case.
If there was injury
it would bleed and then bacterial infections may develop,not viral. . It is extremely hard to injure bowel with thermometer so you dont have to think of it. Just relax and enjoy in your baby.