The suspect in the Pittsburgh synagogue massacre has been indicted by a federal grand jury, four days after 11 people were killed and six wounded in the deadliest attack on Jews in American history.

Wednesday’s indictment, which was expected, charges Robert Bowers with 44 counts, including hate crimes.

US federal prosecutors have previously indicated they plan to seek the death penalty.

The charges were announced on the second day of funerals for the victims.

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A vehicle carrying Robert Bowers with a Pittsburgh Police escort leaves the Federal Courthouse (Gene J. Puskar/AP)

“Today begins the process of seeking justice for the victims of these hateful acts, and healing for the victims’ families, the Jewish community, and our city,” US attorney Scott Brady said in a statement.

“Our office will spare no resource, and will work with professionalism, integrity and diligence, in a way that honours the memories of the victims.”

Bowers, a 46-year-old lorry driver, remained jailed without bail ahead of a preliminary hearing scheduled for Thursday.

Authorities say he raged against Jews during the attack.

Members of Pittsburgh’s grief-stricken Jewish community, meanwhile, endured another round of funerals for the congregants who were gunned down in Saturday’s rampage.

Melvin Wax, 87, Irving Younger, 69, and Joyce Fienberg, 75, were being laid to rest as part of a week-long series of services.

“It can’t be fixed,” Robert Libman said at the funeral of Ms Fienberg, his sister, clutching his chest as he described the pain of losing her.

“My sister is dead. My sister was murdered. There was no one I know like her. Pure goodness. … She was the most tolerant and gentle person that I’ve ever known.”

Her sons, Anthony and Howard said she spent five years caring for their father as he battled cancer, then after his death a few years ago, devoted more of her time and energy to Tree of Life.

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Stones and white flowers, left by President Donald Trump and first lady Melania Trump (Andrew Harnik/AP)

“My mom would be very angry that her funeral wasn’t able to be at Tree of Life, and that her friends lost Saturday couldn’t be here,” Howard Fienberg said.

The funerals for Mr Wax and Mr Younger were to be held later Tuesday.

Six people were wounded in the attack, including four police officers, two of whom remained in hospital with gunshot wounds.

Two congregants were still in the hospital, one in critical condition.

In a bit of good news, hospital officials said the two most seriously injured shooting victims are improving.

A police officer and a congregant remain in intensive care but “are doing much better now,” Dr Donald Yealy, chairman of emergency medicine at UPMC, said Wednesday.

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President Donald Trump, first lady Melania Trump, Ivanka Trump and Jared Kushner visit a memorial outside Pittsburgh’s Tree of Life Synagogue (Matt Rourke/AP)

“I think overall the prognoses are good now.

“But each of them, in a varying way, will have a different trajectory and likely will require a series of ongoing care.”

The first three funerals were held on Tuesday, with thousands of mourners jamming a synagogue, a Jewish community centre and a third, undisclosed site for the funerals of a beloved family doctor, a pillar of the congregation, and two intellectually disabled brothers in the 50s who were known as “the boys”.

Cecil and David Rosenthal were “beautiful souls” who had “not an ounce of hate in them, something we’re terribly missing today”, Rabbi Jeffrey Myers, a survivor of the massacre, said at their funeral at Rodef Shalom, one of the city’s oldest and largest synagogues.

The brothers were both active at Tree of Life, with Cecil the more gregarious of the two, a man with a booming voice who was known as the “mayor” of the city’s Squirrel Hill neighbourhood and the “town crier” for the gossip he managed to gather.

“They were innocent like boys, not hardened like men,” the Rosenthals’ sister, Diane Hirt, told mourners.

On Tuesday afternoon, after the day’s funerals were over, Donald Trump and first lady Melania Trump arrived in Pittsburgh to shouting, chanting protesters with signs such as “It’s your fault” and “Words matter.”

That was a reference to allegations that Mr Trump’s combative language has emboldened bigots.

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Students from the Yeshiva School in the Squirrel Hill neighbourhood of Pittsburgh stand outside Beth Shalom Synagogue after attending the funeral service for Joyce Fienberg (Gene J. Puskar/AP)

Pennsylvania Governor Tom Wolf and Pittsburgh Mayor Bill Peduto, both Democrats, declined to join him during the visit.

“He didn’t pull the trigger, but his verbiage and actions don’t help,” said Squirrel Hill resident Paul Carberry, 55, wearing anti-Trump patches on his hat and jacket.

Another Squirrel Hill resident, Shayna Marcus, a Jewish 34-year-old nurse and Trump supporter who hoped to catch sight of the presidential motorcade, said: “I don’t think focusing on Trump is the answer, or on politics.”

One person was arrested during the protests.

During their visit, Mr Trump and the first lady lit candles at Tree of Life for the victims and laid white roses as well as stones for each of the dead, a Jewish burial tradition.

They later went to a hospital to visit with survivors.

They were joined by Mr Trump’s daughter Ivanka and her husband, Jared Kushner, as well as Mr Myers, the Tree of Life rabbi, and Israeli Ambassador Ron Dermer.

A private funeral was conducted on Tuesday for Daniel Stein, the 71-year-old men’s club president at Tree of Life.

And a service with more than 1,000 people was held for Dr Jerry Rabinowitz at the Jewish Community Centre in Squirrel Hill.

The 66-year-old Dr Rabinowitz was a go-to medic for HIV patients in the epidemic’s early and desperate days, a physician who always hugged his patients as they left his office.

“A lot of people are feeling really angry about this.

“A lot of rage built up inside about this, because of it being a hate crime. Don’t get me wrong; I do.

“But I’m so overwhelmed with sadness right now that I can’t even be angry right now,” said Robin Faulkner, whose family had seen Dr Rabinowitz for 30 years and counted him as a dear friend.

“It’s just such a loss. Just tragic.”

Among the mourners at the Rosenthal brothers’ funeral was Dr Abe Friedman, who typically sat in the back row of Tree of Life with the two men but was late to synagogue on Saturday and was not there when the gunman opened fire.

As he stood in line at the funeral, Dr Friedman wondered why he had been spared.

“Why did things fall into place for me?” he asked.

“I usually sit in the back row. In the last row, everyone got killed.”