The suspect in a mass shooting at a synagogue in Pittsburgh that killed 11 worshippers has been charged on a total of 44 counts, up from 29 counts previously, according to a federal indictment filed on Wednesday.

The charges against Robert Bowers, the suspect in what is believed to be the deadliest attack on Jews in the United States in recent history, include religious hate crimes, firearms charges and causing injury to police officers.

Bowers is due to appear at a second hearing in federal court in Pittsburgh on Thursday.

Funerals were being held on Wednesday for three of the victims killed in the massacre at a Pittsburgh synagogue, a day after Donald Trump encountered hundreds of protesters when he paid his respects in the city during the first of the many burials to come.

Pittsburgh shooting: thousands march to remember victims and denounce Trump's visit Read more

Melvin Wax, Irving Younger and Joyce Fienberg will be laid to rest. They were among 11 people who died in the shooting rampage on Saturday at the Tree of Life synagogue. Robert Gregory Bowers, a 46-year-old truck driver who authorities say raged against Jews, was arrested on federal hate-crime charges that could bring the death penalty.

On Wednesday morning, in a tweet that risked further division, the president posted: “Melania and I were treated very nicely yesterday in Pittsburgh. The Office of the President was shown great respect on a very sad and solemn day. We were treated so warmly. Small protest was not seen by us, staged far away. The Fake News stories were just the opposite-Disgraceful!”

Donald J. Trump (@realDonaldTrump) Melania and I were treated very nicely yesterday in Pittsburgh. The Office of the President was shown great respect on a very sad & solemn day. We were treated so warmly. Small protest was not seen by us, staged far away. The Fake News stories were just the opposite-Disgraceful! pic.twitter.com/9B9HgCF1G9

Local reports said yelling protesters were at least within earshot of the president’s party, kept about half a block away by police, and many turned their backs as his motorcade left the area.

Pittsburgh had begun burying the dead on Tuesday, with funerals for a beloved family doctor, a pillar of the congregation, and two fiftysomething brothers known as the Rosenthal “boys”. Thousands of mourners jammed a synagogue, a Jewish community center and a third, undisclosed site for the first in a weeklong series of funerals.

Trump, meanwhile, arrived to shouting, chanting protesters with signs such as “It’s your fault” and “Words matter”, alleging that bigots were being emboldened by his bellicose language. Pennsylvania’s governor and the mayor of Pittsburgh declined to join him during the visit.

With Tree of Life still cordoned off as a crime scene, more than 1,000 people poured into Rodef Shalom, one of the city’s oldest and largest synagogues, to mourn Cecil and David Rosenthal, ages 59 and 54.

The two intellectually disabled men 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.

“The entire world is sharing its grief with you, so you don’t walk alone,” Myers, his voice quivering, told the Rosenthals’ parents and other family members.

The brothers were widely known as “the boys”, the Rosenthals’ sister, Diane Hirt, noted. “They were innocent like boys, not hardened like men,” she said.

She said Cecil, a gregarious man with a booming voice who was lightheartedly known as the mayor of Squirrel Hall and the “town crier” for the gossip he gathered, would have especially enjoyed the media attention this week, a thought that brought laughter from the congregation.

Dr Jerry Rabinowitz’s funeral was held at the Jewish community center in the city’s Squirrel Hill section, the historic Jewish neighborhood where the rampage took place. Two police vehicles were posted at a side door and two at the main entrance.