In January, a federal judge ruled against the group's legal maneuver to block the city policy.
"As enacted, the regulation does no more than ensure that parents can make an informed decision whether to grant or deny such consent," Judge Nami Reice Buchwald said at the time, according to the New York Daily News.
Some estimate that 70 percent of the general population is infected with the Type 1 herpes I (HSV-1), which can be transmitted from the mouth to the child, causing painful ulcers. It is different from Type 2 or genital herpes (HSV-2), which is a sexually transmitted disease and can cause deadly infections of the brain when a newborn passes through an infected birth canal.
"A herpes infection in a newborn baby has the risk of leading to severe illness and death," said Varma. "The reason is that the baby doesn't have the same fully developed immune system as an adult. Instead of staying in the genital area, it extends throughout different organs in the body."
The health department had issued alerts about the two latest cases -- on in January and one in March -- to urge all medical providers and laboratory staff to inquire about "direct oral suction" during a circumcision when evaluating newborn males for sepsis and to consider herpes.
The more than 5,000-year-old religious practice of circumcision is performed during a Jewish religious ceremony known as the bris, which is observed by Jews of all denominations around the world.
The modern Jewish community uses a sterile aspiration device or pipette to clean the wound in a circumcision. About two-thirds of boys born in New York City's Hasidic communities are circumcised in the oral suction manner, according to Rabbi David Zwiebel, executive vice president of Agudath Israel of America.
In 2003 and 2004, three babies, including a set of twins, were infected with Type 1 herpes; the cases were linked to circumcision, and one boy died. Another died in 2010. In the last decade, 13 babies in the city have contracted the virus, and two have had brain damage, according to health officials. All were circumcised by the metzitzah b'peh method.
"Social health policy is art of the possible and [New York City's] Bloomberg administration and the department of health worked with the [ultra-Orthodox] community to develop a policy that it hoped was both acceptable and effective," said infectious disease expert Schaffner. "That was the hope."
"It's clear the implementation of policy is not completely effective and that it resulted in serious, but preventable infections," he said. "Perhaps the policy needs to be revisited."
Varma said changing traditional practices in New York's ultra-Orthodox community will take time.
"We developed this law ... to balance the right of people to practice religion with the requirements of a health agency to protect everybody, especially the most vulnerable.
"We require their cooperation and it's a challenge," said Varma.
The health department could take no action against the rabbi who performed the circumcision because the parents would not reveal his identity.