Heuermann has already been charged with murdering three other escorts. Like Megan Waterman, Amber Costello and Melissa Barthelemy, the remains of Brainard-Barnes were found in a desolate spot along the ocean near Gilgo Beach in 2010.
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The four women, who were discovered within days of each other, came to be known as the "Gilgo Four."
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"Today, Defendant Rex A. Heuermann stands before this Court charged by the Grand Jury in a Superseding Indictment, which incorporates not only the above counts, but the additional charge of: MURDER IN THE SECOND DEGREE, in violation of New York State Penal Law Section 125.25(1), a class A-I violent felony for the death of Maureen Brainard-Barnes on or about July 9, 2007," prosecutors wrote in a court filing.
Heuermann pleaded not guilty Tuesday to the new second-degree murder charge.
Authorities have previously said that Heuermann was the prime suspect in Brainard-Barnes' disappearance.
Brainard-Barnes was 25 years old when she was last seen in July 2007. She was found three years later wrapped with a belt, which had a buckle bearing the initial "WH," which possibly stands for Hiermann's father, according to ABC News.
Prosecutors said Heuermann's now-estranged wife, Asa Ellerup, and his children were out of town when Brainard-Barnes disappeared and was killed, fitting an alleged pattern of Heuermann being home alone when the other three killed.
"As set forth in Exhibit A, travel and cellular telephone billing records had previously established that Defendant Heuermann's wife and children were out of the state during the disappearances and murders of three of the four victims, specifically, Melissa Barthelemy, Megan Waterman, and Amber Costello," prosecutors said, citing documents they obtained during a search of a storage unit leased by Heuermann.
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The documents include a credit card statement that shows Ellerup checked into an Atlantic City hotel on July 6, 2007, and stayed through July 20.
"Based on the foregoing, the murders of all four victims occurred at times when Defendant Heuermann's wife and children were traveling out of state, which allowed Defendant Heuermann unfettered time to execute his plans for each victim without any fear that his family would uncover or learn of his involvement in these crimes," prosecutors said.
The new filing also revealed that prosecutors seized two phones from Heuermann at the time of his arrest that they said were held by him "in fictitious names and used for illicit activities." Prosecutors said Heuermann "utilized these phones in furtherance of hundreds of contacts with sex workers between 2020 and 2023."
Prosecutors additionally revealed Tuesday they seized hundreds of electronic devices from Heuermann's Massapequa Park home and Manhattan office following his arrest.
Heuermann used the devices to search for the deceased victims and their family members; the status of the instant investigation; for software that would assist in wiping or erasing data from computers and other similar digital devices and purchase digital masking and forensic wiping tools, prosecutors said.
"Defendant's devices also contained the following: A collection of violent, bondage, and torture pornography preceding, during, and subsequent to the disappearances and murders of the aforementioned victims between 2007 and 2010; and prostitution-related searches preceding, during, and subsequent to the disappearances and murders of the aforementioned victims between 2007 and 2010."
The new court filing also outlines the lengths prosecutors went to obtain DNA from Heuermann's family, including tracking his daughter on a Long Island Railroad train drinking from a gold-colored "Monster Java" can. Investigators saw her toss the can into the trash. They recovered it and took it for analysis, prosecutors said.
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Last summer, a special task force zeroed in on Heuermann, an architect whom investigators linked to the women through DNA evidence, including a sample taken from pizza crust in the trash outside his Manhattan office.
Heuermann also faces three counts of first-degree murder for the 2009 killings of Barthelemy and Waterman, as well as Costello in 2010, according to the Suffolk County District Attorney's Office.
Barthelemy's remains were the first set of female remains found in bushes along an isolated strip of waterfront property in December 2010. At the time, authorities were searching for another missing woman, Shannan Gilbert, a 23-year-old from New Jersey who hadn't been seen since May 2010.
He has pleaded not guilty in the three other charges.
There are six other women whose bodies were discovered near Gilgo Beach, whose deaths remain unsolved.
ABC News and CNN contributed to this post.