Full Sequence of Missouri Patient’s H5 Bird Flu May Not Be Available

The concentration of viral RNA obtained from the Missouri patient who contracted H5 bird flu without any known exposure was so low that a full genetic sequence may not be available, federal health officials said.

The CDC has been unable to sequence the neuraminidase gene of the virus, and thus continues to refer to it solely as H5 at this point, Nirav Shah, MD, JD, principal deputy director of the CDC, said during a press briefing Thursday.

Nonetheless, the data “generated thus far show an H5 virus that is closely related to the H5 virus circulating among dairy cows,” Shah said.

Demetre Daskalakis, MD, MPH, director of CDC’s National Center for Immunization and Respiratory Diseases, said the agency “continues to work on the specimen to see if we can maximize the amount of sequence that we have. Ultimately, that’s going to dictate what we’re able to say … specifically about this virus.”

The patient also presented with symptoms that aren’t typical of the flu, but Shah said it’s not considered to be a novel presentation of the virus or an incidental case.

The patient — who had “significant underlying medical conditions,” Shah said — presented to the emergency department on August 22 with acute symptoms of chest pain, nausea, vomiting, diarrhea, and weakness. Further evaluation by medical personnel at the hospital made it “apparent that a respiratory panel was warranted in connection with some other underlying medical conditions,” he noted.

The patient was not severely ill and did not have to go to the intensive care unit, Shah added. They were treated with an antiviral and ultimately discharged and recovered. Shah said that he couldn’t share more, given concerns for revealing protected health information, and the agency had agreed upon the released information with Missouri officials.

It remains unclear how the patient contracted the disease, Shah said, noting, however, that this isn’t unusual for other influenzas, such as swine flu. In the U.S., more than 500 swine flu cases have been detected since 2010, and 8% had no known direct or indirect exposure to pigs, he explained.

Epidemiological questionnaires have asked the Missouri patient about exposure to all types of raw dairy products and contacts with a range of animals, as well as other environmental exposures, but nothing has turned up as a potential source of infection, Shah said.

There’s been no evidence of human-to-human transmission, he added, with no unusual levels of influenza activity in the patient’s area of Missouri, no increases in emergency department visits for flu, and no increase in lab detections of flu in the state.

“Our influenza surveillance system is designed to find needles in haystacks, and as this case and others show, it is working,” Shah said. “In this case we found such a needle, but we don’t know how it got there.”

Missouri hasn’t invited the CDC to participate in its investigation, but Shah said the agency has been in very close contact with health officials there, on almost a daily basis.

As for the perceived delay in reporting the case publicly, Shah explained that the CDC received the sample from Missouri on a Wednesday night, confirmed the results on Thursday, communicated back to Missouri, and then released the information on Friday “as soon as everything was confirmed.”

During the briefing, Eric Deeble, VMD, deputy under secretary for marketing and regulatory programs at the U.S. Department of Agriculture (USDA), gave an update on the H5N1 infections in cattle herds in California that began about 2 weeks ago. Thus far, eight herds have tested positive for the virus, he said.

The virus from the first three affected farms was confirmed to be the same genotype, B3.13, that’s been detected in dairy herds in other states, Deeble said. Sequencing from the remaining five herds will be completed later this week, he said, but thus far there’s “nothing that would lead us to believe it was transmitted in a novel way.”

USDA’s Center for Veterinary Biologics is also seeking groups to apply to conduct vaccine field safety trials of the H5N1 vaccine for cattle, he said.

Shah also said CDC is launching a new program to expedite testing during pandemics. The agency awarded $5 million to five companies, including LabCorp and Quest, to develop H5N1 tests alongside CDC, rather than after CDC. During the initial mpox outbreak in 2022, CDC shared its test with five commercial labs, but it still took 6 weeks from the beginning of the outbreak until testing began in those labs, he noted.

“What this approach does is add the commercial laboratories to the CDC team,” Shah said. “In a sense, they are all wearing the CDC jersey now. In the past, we added them to the team too late in the game. That changes today.”

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