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Since October, state and federal court officials have taken extraordinary measures to restart criminal trials in New York City. They have constructed plexiglass boxes with special air filters in court. They have asked witnesses to testify in face shields and have spread jurors out in courtroom galleries.

But those efforts have not stopped the virus from disrupting nearly every step of the process. The state and federal courts in the city have been able to complete only nine criminal jury trials since the pandemic hit in March, officials said. Last year, there were about 800 criminal trials in the city.

Courts are stalled across the country. Federal judges in Nebraska, Nevada, Colorado and several other jurisdictions recently suspended jury trials in response to rising virus cases. A court in McKinney, Texas, a suburb of Dallas, held the state’s first virtual criminal trial last month.

Each court has determined its own protocols. One local courthouse in Orange County, Calif., has completed 114 criminal trials since May, while the federal courthouse across the street has determined it is unsafe to hold any trials at all.

In New York City courts, the challenge of preventing the virus’s spread is magnified by the dense population. In normal times, clerks, court officers and lawyers squeeze into courtroom galleries and line the crowded hallways, waiting for cases to be called.

For months, the logistical problems have threatened the ability of hundreds of defendants to secure their constitutional right to a speedy trial. Now, as a second wave of the virus threatens the New York region, the delays are only worsening — and officials foresee the backlog of unresolved cases continuing to grow.

Some prosecutors, citing safety concerns, have pushed to delay trials because their witnesses live out of state or work in hospitals with Covid-19 patients. In other cases, prosecutors said the fears of catching the virus during trials had been overblown. Defense lawyers told a court in Brooklyn they were unwilling to spend weeks inside a cramped courtroom.

“Is it fair for people to be languishing in pretrial detention and presumed innocent with no prospect of a trial in the future for them?” said New York’s chief administrative judge, Lawrence K. Marks. “A criminal justice system cannot be, in any sense of the word, fully functioning, if it is not conducting jury trials.”

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