Maria de Lourdes, Silva's mother, who visits her daughter-in-law regularly in prison, said she was also abused by Portuguese police in Faro in interviews conducted during the Joana investigation.
"The police in Portimão treated us really well," she told ABC News in her home near Lagos. "But the Faro police were awful. They gave us nothing to eat or drink the whole day," said the 57-year-old mother of nine. "They battered us physically and mentally."
Amaral was always present during questioning, de Lourdes said her daughter-in-law told her.
"He controlled everything," she said. "And he kept asking me: 'Did you see blood in the house?' 'I'm sure you cleaned the house with petrol to get rid of the smell.'"
"They have accused us of everything that we killed Joana, that we stabbed her, even that we sold her," de Lourdes said.
But as far as de Lourdes is concerned, the worst thing is not knowing what happened to Joana and then being blamed for her disappearance.
"How can they prove that we had anything to do with her disappearance?"
"If Kate McCann were Portuguese, she would already be in jail," said de Lourdes.
The McCann's circle of friends and savvy contacts have been able to generate the kind of media attention that has made their daughter's face instantly recognizable all over the world. They have also hired top attorneys in Portugal and the U.K., as well as forensic experts to pick apart every DNA sample gathered by investigators.
The couple has also received financial backing from a British millionaire Brian Kennedy, a move that may have saved the 39-year-old doctors from having to sell their home to cover their legal defense.
Still, despite her bitterness over what she believes is her own daughter-in-laws wrongful conviction de Lourdes is convinced of Kate McCann's innocence. In fact the slightest mention of the couple brings empathy from de Lourdes.
"I don't think that that woman is capable of doing something like that to her daughter," she said. "I just don't believe it."
"The same Portuguese press that are now chasing the McCanns are the same journalists who were on my doorstep when Joana disappeared," she said.
And while she knows that she and Kate McCann come from very different worlds their situations are parallel.
"Our plight is not so different anymore," she said. "So I cannot help but feel for that woman. After all we are on the same path."
De Lourdes recalls vividly the day Joana went missing.
"I got the phone call around midnight," said de Lourdes. "My son Leandro was asking me if Joana was here with me." They then went to look for her at the cousin's house where she spent the afternoon.
"When I didn't hear from them again, I assumed they had found her," she said.
But the following morning when de Lourdes was getting ready to pick up her son to go to work, she saw her daughter in law Leonor walking down the street sobbing hysterically.
"'Joana is missing,'" she told me.
The girl's parents called police within an hour of Joana's disappearance. But according to Leandro and his mother, police did not begin searching for his daughter until 48 hours after they reported her missing.
Silva remains convinced of his wife's innocence. But he is particularly bitter about Amaral, against whom he has lodged a formal complaint.
"He (Amaral) should not even be working on this (the McCanns') case," said Silva.