Update: Logan police have identified the body found Wednesday as the remains of 5-year-old Elizabeth “Lizzy” Shelley, according to a tweet from the department.

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Police said they believe they found the body of 5-year-old Elizabeth “Lizzy” Shelley on Wednesday afternoon, after negotiations with her uncle, who has been charged with her murder.

Lizzy had been missing for five days when prosecutors charged 21-year-old Alex Whipple on Wednesday with aggravated murder, child kidnapping, obstructing justice and abuse or desecration of a human body in the disappearance of his niece. Investigators had not found Lizzy’s body when charges were filed Wednesday morning but based the charges on forensic evidence and other information.

“This was the moment we had hoped would come,” Logan Police Chief Gary Jensen told reporters at a news conference Wednesday afternoon. "Obviously, certainly not the way we wanted it to happen. We certainly would have wanted to bring Lizzy home, but this nevertheless is closure and it helps us to be able to now deal with the investigation and help the family through their grief.”

Whipple disclosed the location of Lizzy’s body, buried under leaves and debris in a wooded area about a quarter mile from her home, said Shannon Demler, Whipple’s attorney. Demler said he took police to the site, and the girl’s body was recovered about 1 p.m.; police gave a slightly later timeframe.

Jensen noted that Whipple had offered the information in exchange for prosecutors taking the death penalty “off the table." Investigators have not established a motive for the crime.

Jill Parker, a spokeswoman for the family, held back tears as she read a letter from Jessica Whipple, Lizzy’s mother, at the news conference.

“There are not words to express the sadness and the heartbreak we feel today," she read. "This did not end the way we wanted it to, but in this sadness we are comforted that so many people put forth so much effort to help us find Lizzy. You made the difference and we are so very grateful.”

The statement said Lizzy was a “caring and giving” little girl and requested privacy for the family as they mourn her loss.

On Wednesday, the girl’s grandfather said Jessica Whipple didn’t see her younger brother often but decided to help him when he asked her to pick him up.

He said Alex Whipple had a difficult childhood but had never showed violent tendencies.

"I would never, ever in a million years have thought he was capable of harming such a cute little girl," Bill Whipple said. "I knew he was a thief, but I never labeled him as a murderer."

Alex Whipple’s mother left the family when he was young, leaving his father to raise three children alone while he worked as a truck driver. The young man spent time in foster homes and didn’t graduate from high school.

Charging documents allege that Lizzy’s blood was found on Whipple’s wristwatch and a hooded sweatshirt that he was wearing when he was arrested on Saturday. On the grounds of a nearby charter school, investigators found a broken knife that had Lizzy’s blood on it and matched the brand of a knife that was missing from her family’s kitchen, according to charges.

Officers also found a piece of PVC pipe that carried a partial palm print in a red substance; the palm print matched Whipple’s hand, according to charges. A block from the school, a homeowner found a beer can that had Whipple’s DNA on it, police wrote.

About 50 yards from the parking lot, investigators also found a teal blue skirt — clothing that Lizzy was last seen wearing — “hastily buried” under some dirt and bark. The skirt also had blood on it, according to charges.

Police found Lizzy’s body near 455 W. Center St., “in the general area that we’d found several of the evidence items,” Jensen said Wednesday. "We felt we’d searched that area hard. I’d love to share a picture of the area that her body was found, just because it’s amazing the overgrowth and the difficulty of the scene.”

Lizzy had been missing from her home since Saturday, and police followed “hundreds of tips — thousands of tips,” Jensen said at an earlier news conference Wednesday.

At least two leads turned out to be animals’ remains, Jensen said. The Logan River, which is running fast and high, had posed a particular hazard in the search, he added. Investigators combed through mulch piles after a substance that appeared to be mulch was found on Whipple’s clothing, Jensen said; two semitrailer trucks carrying mulch loads were stopped and searched on their way out of state.

"We’re going on five days of amazing volunteer hours and time, of amazing law enforcement agencies,” Jensen said Wednesday morning, before the girl’s body was uncovered.

Charging documents say that Lizzy’s mother, her mother’s live-in boyfriend and Whipple had stayed up late Friday night drinking beer and rum and playing video games. The couple went to bed and Whipple stayed the night on the couch.

The girl’s mother told police she last saw her daughter in her bed around midnight, and said the girl was wearing a teal skirt with white lace and a Fourth of July-themed shirt.

When the couple woke up at around 9:30 a.m. the next morning, Lizzy and Whipple were gone — and the front door was wide open. They called police.

The mother told investigators that she didn’t know where Whipple would have taken Lizzy, according to charges, and said he didn’t have a vehicle and often walked or rode a skateboard. His skateboard and cellphone had been left at the home.

Authorities focused their search on a 10-mile stretch from Logan to Hyrum, particularly along 1200 West. While some video surveillance turned over to police has captured Whipple’s movements on Friday, Jensen said there has been no footage so far of Lizzy. Police asked anyone who may have seen him on Friday night or Saturday morning to come forward.

(Photo courtesy of Logan Police) This photo of Alex Whipple shows him on Friday. He's the primary suspect in the disappearance of his 5-year-old niece, Elizabeth Shelley.

Police found Whipple walking alone in a rural area near Hyrum on Saturday around 3 p.m. and discovered a metal baseball bat tucked in his back pocket and hidden in his jacket along his back, according to a probable cause statement filed with the jail. They also allegedly found a pipe and what they suspected was marijuana, and an unopened can of beer. Whipple’s hands were “filthy” and had several cuts, according to the charges.

As Whipple waited in the interview room, he began to lick his hands and trying to wipe them clean, investigators wrote. He initially denied that he had gone to his sister’s house the night before Lizzy disappeared but later conceded that he had been there that night, investigators wrote. He said he had left just before sunrise to take a walk in Hyrum and enjoy the scenery, the charges state.

During the interview, Whipple “would allude to how evil the world we live in is,” and said he had struggles as a child and that his family has mistreated him throughout his life, police wrote. He said alcohol makes him “black out” and that sometimes he does “criminal things” while he’s blacked out, police wrote.

But Whipple would not elaborate on those crimes, and he neither admitted nor denied being involved with Lizzy’s disappearance, police wrote.

Prosecutors looked at “the totality of all of the evidence that we have,” when they charged Whipple before locating the girl’s body, Jensen said.

“The blood, the knife, the ... distance from ... Lizzy’s home, where these items of evidence were found, and it’s been five days now — yeah, we believe it [met] the elements of the crime,” Jensen said.

For the charge of abuse or desecration of a human body, prosecutors looked at statutory language that defines the crime as when a person “disturbs, moves, removes, conceals, or destroys a dead human body or any part of it,” Jensen said.

“Alex has taken substantial steps to move, remove or conceal Elizabeth’s body,” Jensen said.

A judge has ordered Whipple be kept in the Cache County jail without bail, at least until a Monday court hearing.

Demler would not discuss how Whipple intends to plead. But, Demler said, "He knows he’s done a terrible thing and obviously something he can’t fix.

“He’s very emotional about it, and feels he’s done something terrible," Demler said. "Based on that, he felt it was appropriate to tell the authorities where the body was located so at least the family could have some closure as to that part of the case, knowing where the body was.”

Demler said Whipple did not say why he didn’t disclose the location of the girl’s body while police searched for five days.

“We didn’t talk about that,” said Demler, who said he has represented Whipple in previous cases. “I think he was in a very emotional state. I think it took him some time to come to grips with what’s happened and decide it would be best to do that.”

Whipple made a court appearance Tuesday via video conference related to minor charges that appear to be unrelated to Lizzy’s disappearance.

Whipple was not supposed to have alcohol as part of his probation. Court records show he is on probation for two cases — a 2017 drug possession conviction in Logan’s justice court and another case where he pleaded guilty to felonies after leading police on a chase in a stolen vehicle in September 2017.

An account to collect donations for Lizzy’s family has been opened at Zions Bank, the Cache County Attorney’s office said Wednesday.

The name of the account is Elizabeth Shelley Donation and it is the only account authorized by the family, said Parker, who is also the spokeswoman for victim advocates in the county attorney’s office.

Tribune reporter Jessica Miller and The Associated Press contributed to this report.