NEW YORK — Crowded bars and house parties have been identified as culprits in spreading the coronavirus. Meat packing plants, prisons and nursing homes are known hot spots. Then there’s the complicated case of America’s churches.

The vast majority of these churches have cooperated with health authorities and successfully protected their congregations. Yet from the earliest phases of the pandemic, and continuing to this day, some worship services and other religious activities have been identified as sources of local outbreaks.

They are by no means at the top of the list of problematic activities across the U.S., but they have posed challenges for government leaders and public health officials whose guidelines and orders are sometimes challenged as encroachments on religious liberty.

“If we wanted to have zero risks, the safest thing would be to never open our doors,” said prominent Dallas megachurch pastor Robert Jeffress. “The question is how can you balance risk with the very real need to worship.”

In the past two weeks alone, there have been two notable church-government confrontations in California.

San Francisco’s city attorney sent a cease-and-desist order in late June to the Catholic archdiocese, alleging that some of its churches had violated a local ban on large indoor gatherings. The archdiocese promised to comply.

A few days later, state officials temporarily banned “indoor singing and chanting activities” at all places of worship, prompting some pastors to defy the rule.

Evangelical pastor Samuel Rodriguez said worshippers at his Sacramento megachurch joined in singing hymns on July 5, even as most of them wore face masks and obeyed social-distancing guidelines.

“To forbid singing in a church is morally reprehensible,” Rodriguez said. “That is how we petition heaven.”

The extent to which religious gatherings have contributed to the pandemic’s toll may never be known with any precision. But there’s no question they have played a role throughout, internationally as well as in the United States, even as myriad houses of worship halted in-person services for safety reasons.

Of the first wave of cases in South Korea in February, several thousand were members of the secretive Shincheonji Church of Jesus. Hundreds of other cases were linked to a Muslim missionary movement event in late February in Malaysia that was attended by about 16,000 people from numerous East Asian countries.

In the second week of March, before warnings and lockdown orders proliferated in the U.S., 35 of the 92 people who attended events at a rural Arkansas church developed COVID-19, and three of them died, according to a Centers for Disease Control and Prevention report issued in May.

More recently, in mid-June, a small-town church in northeastern Oregon became the epicenter of the state’s largest coronavirus outbreak when 236 people linked to the Lighthouse Pentecostal Church tested positive.

According to the Observer newspaper in nearby La Grande, the church in Island City had held religious services, a wedding and a graduation ceremony in the weeks preceding the outbreak, sometimes with more than 100 people in attendance in defiance of state restrictions on gatherings.

Union County, with a population of 25,000 people, had recorded fewer than 25 cases during the pandemic prior to the church outbreak. Within two weeks, it had Oregon’s highest per capita rate of coronavirus infections.

Also in June, West Virginia’s health department announced outbreaks linked to five churches in different parts of the state. The biggest was at Graystone Baptist Church in Lewisburg with 51 cases, three of them fatal.

In several cases, churches that resumed in-person services opted to close again after outbreaks. Among them:

— A church and an administrative office affiliated with the Church of God in Cleveland, Tennessee, which is the home base for the Pentecostal denomination. No official case count has been released, but a senior leader of the denomination, General Overseer Tim Hill, confirmed that the number of verified cases is growing, and that several church leaders were among those seriously ill. One pastor, Ernie Varner of Lenoir City, Tennessee, died Friday, six days after posting on Facebook, “I’m in the ICU with COVID. Please pray for me.”

— Calvary Chapel, an evangelical church in Universal City, Texas. It reopened in early May only to close anew in late June after dozens of staff and churchgoers tested positive, including Pastor Ron Arbaugh and his wife. Arbaugh says he regrets telling worshippers last month they could resume the tradition of hugging each other during an interlude of mid-service socializing.

— Holy Family Catholic Church in Las Vegas. The diocese announced Thursday that the church would be closed indefinitely after a priest who celebrated Mass this week tested positive.

— First Baptist Church of Tillmans Corner in Mobile, Alabama. It resumed in-person services May 17 after the governor gave a statewide green light, but recently canceled them at least through July 31 after more than 20 of the congregation’s 1,500 members tested positive. Pastor Derek Allen wrote a blog post describing the outbreak as a “harrowing and demoralizing journey,” and offering advice to other pastors: “Assume every sniffle is COVID-19, and act quickly. We’ve learned that the tests take too long, and false positives are possible along with false negatives.”

Another Baptist church, First Baptist Dallas, was in the spotlight June 28 when it hosted Vice President Mike Pence at its annual Freedom Sunday celebrations. Most of the 2,400 attendees wore face masks, but some criticism surfaced after the choir sang without masks.

Jeffress, the church’s pastor and a prominent evangelical conservative with close ties to President Donald Trump, said the choir and orchestra had been tested for COVID-19 beforehand. The church said a few who tested positive did not take part in the event.

Jeffress bristled at the idea that choirs should be temporarily banned.

“Choirs will always be a part of worship for us,” he said. “We think it’s possible to still have them but do it in a safe way.”

A few days after the Freedom Sunday event, Texas Gov. Greg Abbott issued an order requiring people wear face masks in most public settings — with several exceptions, including participants in religious services.

Some churches, through their physical attributes and the decisions of their leaders, have been able to minimize risks as worship resumes.

In Incline Village, Nevada, along the north shore of Lake Tahoe, St. Patrick’s Episcopal Church took advantage of a unique feature to relaunch scaled-back, in-person services this month: its outdoor mountain amphitheater chapel shaded by pine trees.

Church officials took precautionary measures such as moving the log-bench pews farther apart, capping attendance at 50 and requiring worshippers have their temperature taken, employ hand sanitizer and wear masks. There was no Eucharist or passing of the peace, and the usual post-service coffee hour was held by video conference.

“Good morning, children of God,” the Rev. Sarah Dunn, the church’s rector, said from behind a plexiglass screen, welcoming parishioners back to the socially distanced service July 5 after 16 Sundays apart. She acknowledged feeling “mixed emotions”: apprehension as the virus remains a threat, but joy at being able to gather in the sacred space.

Associated Press reporters Peter Orsi in Truckee, California, Anthony Izaguirre in Charleston, West Virginia, and Sara Cline in Salem, Oregon, contributed to this report.