But New York's The Jewish Week exclusively reports that the protocols that were agreed upon by a "broad array" of orthodox rabbis and health officials after the 2004 death were rescinded only a year later in 2007.
The city required one of three things, at the mohel's option: continue abstaining from the practice until he could be ruled out as the source of infection; agree to take anti-viral medication for the rest of his life; or take medication for three days before the circumcision.
The state health department dropped those protocols when a new governor --- then Democrat Eliot Spitzer -- took office and a new health commissioner was appointed.
The newspaper reports that the metzitzah b'peh practice is still "in widespread use."
The numbers of ultra-Orthodox Jews are growing rapidly, according to a study by University of Florida geography professor Joshua Comenetz, mostly because they have so many children.
He completed the first population survey based on the 2010 U.S. Census, estimating there were about 180,000 or 3 percent of the total number of Jews in the U.S.
In New York City, home to about 100,000 Orthodox Jews, the communities are reclusive, but they're also powerful voting blocks. Public officials try to work closely with their leaders to educate them about modern health practices and to encourage changes in a religious practice that is largely unregulated.
"Reluctance is a matter of respect," said Schaffner. "But then we have the occasional infant who succumbs."
If the mohel has an infection in the mouth and throat, the virus is transmitted to a baby's circumcision wound directly through saliva. From an inflamed wound, it can get into the bloodstream and travel to the brain, causing dangerous encephalitis and either brain damage or death.
The herpes virus is so contagious that when medical professionals give mouth care to patients, they wear gloves, according to Schaffner.
"If they don't, nicks around the nails can be infected with the patient's herpes virus," he said. "They can get bad infections on the fingers."
During the investigation of the 2004 death, rabbis proposed health safeguards, "but none of them provide assurances of safety," according to Schaffner.
One was to use an antiviral medication on the infant's wound, treatments that have not been tested for that purpose. The other was to use an antibiotic cream, which is ineffective against a virus.
"The standard is looking for zero infection and even if there is one, it's unacceptable," said Schaffner. "[The orthodox community] has a hard time getting their brains around this. The ancients are simply wrong about this."