She told the 12 jurors the case stands and falls on whether they believed the complainant's evidence.
If they trusted that the man didn't have unprotected sex with any other HIV-infected person during the transmission period, they must find Filitonga guilty.
But if they were unsure, the jury had to take into account all the other evidence, Judge Sharp said.
On Tuesday, the court heard from the man who said he asked Filitonga about his health status when he met him in February 2014.
Filitonga told him he'd had an HIV test three months earlier and said it was negative, the man said.
After two months of dating and during a holiday to the Philippines with friends, the man grew ill with nausea, aches, a fever and a rash that spread across his body.
He said he figured it was probably a tropical virus but later learned these were symptoms of seroconversion; when a person first develops antibodies for HIV.
However, medical experts told the court this could not pinpoint when the man was infected as the seroconversion wasn't confirmed.
The experts gave evidence the risk of transmission for each individual intercourse act between an infected man and a non-infected man was between one in 200 and one in 30.
The pair continued their relationship until it broke down in August 2013 over allegations of infidelity, although they continued to have intercourse for several months.
The court was shown texts the man sent Filitonga in October 2013.
"So please tell me now for real, have you got HIV or something? You have to tell me if you do. Something's not been said, I know it. Is that why you avoid having sex?"
A later text read: "Will you promise me to get that test and never take risks with your own or anybody else's life again?"
The man said the only other people he had intercourse with were three men who have all tested negative.
It was for the jurors to decide on the first charge whether Filitonga was guilty of infecting the man with HIV.
But it is a matter of law that to infect someone else with the virus is to cause grievous bodily harm, the judge said.
The Crown's case in relation to the criminal nuisance charge was that Filitonga, knowing himself to be positive and advised it was his legal duty to inform partners, "decided to continue on anyway", the judge said.
Judge Sharp told the jurors the defence case was that the man was not a truthful and accurate witness whom they could not believe. The complainant's drug use and that he'd been "promiscuous" and had unprotected casual sex raised enough doubt that Filitonga should not be convicted.
The jury was sent to deliberate at 11am.
