(RNS) Hand sanitizer in the pews. A cautionary bow rather than a warm handshake during the Sign of Peace. Empty holy water fonts. Increased absences from religious classes.

The H1N1 flu pandemic is shaking up religious communities and disrupting worship life. But when does caution veer into paranoia, and what is lost when faith becomes fear?

With H1N1 flu being declared a national emergency, religious organizations are issuing guidelines for worship practices and even personal interaction during liturgy. In a reversal of the usual open invitation, some faith communities are asking those who don’t feel well to stay home.

“I have skipped church when the kids were sick,” said Ruth Wynja Gibbons of Whitinsville, Mass., whose 6-year-old son and 3-year-old daughter came down with bad colds. As it turned out, the kids didn’t contract H1N1, or swine flu, but Gibbons has noticed a drop in the number of children in Sunday school at Pleasant Street Christian Reformed Church.

At her church’s Sunday service, congregants are being advised that they need not shake hands when the time comes to greet fellow worshippers. “I personally just greet people verbally, not shake hands,” she said. “I think it’s a good precaution, that people not spread illnesses this time of year. It’s better to be safe than sorry.”

At Gibbons’ church, Communion wine is traditionally passed in individual, disposable cups, but in some denominations, congregants may dip the Communion wafer or bread in wine (known as intinction) or sip from a common cup. Advice varies — some churches have banned the common cup or stopped serving wine altogether since sipping from a shared cup may be a path to sickness.

At Or Shalom Jewish Community in San Francisco, a Reconstructionist congregation, touching is a regular part of worship. “Usually everyone touches the challah (bread) during Shabbat services and we usually break it as a group,” noted administrator Shari Carruthers.

Carruthers said worshippers are being careful to wash their hands before the ritual prayer over the bread. Some are also refraining from sharing the Kiddush cup, a goblet of wine that is passed around after a blessing at the Sabbath meal.

Muslims already incorporate ritual hand-washing, known as wudu, before prayer services, but a notice at the Muslim Community Center in Chicago also advises members that they may wish “salaam,” (peace) to each other verbally and need not shake hands.

Concern about passing along infections is causing changes in style among some clergy. Laurie Wozniak, a parishioner at Trinity Episcopal Church in Buffalo, N.Y., noted that her pastor, the Rev. Cam Miller, is normally a hug-and-shake-hands kind of guy. When he wasn’t feeling up to par recently, he refrained even from meeting parishioners at the door, she said.

“He did not celebrate the Eucharist; he had an associate priest do it,” she said. “He ventured no closer (to the congregation) than the pulpit. He explained … it was to make sure he was not communicating any germs. He stayed in the high altar area, so he could still be there and function.”

Miller said he had upper respiratory symptoms, but didn’t have a definitive diagnosis. “My biggest concern was not being a distraction to other people,” he said.

An Italian inventor has come up with a dispenser that releases a few drops of holy water when worshippers pass their hands under it, to avoid the communal holy water basin. But all these precautions have some people wondering if an essential part of a faith community is getting lost.

Pamela Dempsey DeVries, who attends Fuquay-Varina Baptist Church in Fuquay-Varina, N.C., has kept her three children out of services, though they continue to attend Sunday School. As caretakers of the family, she said, women are bearing the brunt of the flu scare.

At worship, she keeps hand sanitizer in her purse and now is “more reserved” in greeting other parishioners, and worries that she may seem less friendly to newcomers.

“It’s very Southern,” she said. “Everyone gets out of their pew, walks all over the church. It’s a chance to welcome new people or find your friends, and if you know people, give them a kiss or hug.”

The Rev. Tim Schenck, rector of St. John the Evangelist Episcopal Church in Hingham, Mass., is taking all the usual precautions and found himself hurriedly writing a swine flu policy for his church after a parishioner’s child came down with H1N1. But he also mourns the emphasis on avoiding human touch.

“You don’t want to take this lightly or minimize it, but sacramental touch is being lost and that can’t be replaced by being washed in Purell. Sacramental touch is an outward and visible sign of God’s presence. It’s human interaction and communication at its deepest level,” he said.

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As a priest, he said, “the Communion rail is a place of great joy — being able to feed people with the body of Christ.”

“It’s a shame that fear is being brought into the sanctuary,” he said, “because you would hope that the sanctuary is a place where there is no fear.”