Sequencing reveals Asian H5N1 avian flu clade in Cambodian cases

DNA testing

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Over the weekend, Cambodia's health ministry announced that genetic analysis has revealed that the Asian clade H5N1 avian influenza clade was involved in the two recent human infections, which involved an 11-year-old girl who died and her father who is still hospitalized.

The cases raise concerns that the more recent Eurasian H5N1 clade, which has sickened birds, mammals, and a few people in multiple world regions, may be expanding. At a World Health Organization (WHO) briefing on Feb 24, the group's flu experts said multiple H5N1 clades are circulating in Cambodian poultry, including as well as more localized lineages.

In an update yesterday, the WHO said an outbreak investigation is still under way to determine how the girl and her father were exposed to the virus.

Clues from speedy sequencing

The WHO said Cambodia shared the genetic sequencing data with GISAID, the publicly available flu virus sharing database, which showed the virus belongs to the clade and that the virus is similar to one that has been circulating in Southeast Asia's poultry since 2014.

Cambodia has reported sporadic human cases since 2003, but not since 2014. The WHO said that, aside from the girl's father, who tested positive, samples from 11 other contacts were negative.

Erik Karlsson, PhD, with the National Influenza Center and Pasteur Institute in Cambodia, on Twitter said the genetic sequencing took less than 24 hours after receiving the original sample, and he credited collaborating partners in and outside of Cambodia with their role in advancing the technology and tools to analyze the virus so quickly. He added that the finding is critical to understanding, which has been endemic in Southeast Asia for about a decade.

"All zoonotic spillover is concerning," he said in a separate tweet. "Response needs to be coordinated and swift to get ahead of any potential further spread, and limit exposure to a common source. It is critical to monitor the situation in an active, longitudinal #OneHealth manner."

More contacts test negative

Cambodia's health ministry said today on its Facebook page that the girl's father, who had been receiving antiviral treatment in the hospital, has now tested negative for H5N1. He will remain hospitalized while his treatment is completed.

Officials also said 29 people have been tested, including 16 close contacts and 13 people with flulike illness. All results were negative.

CDC weighs in on Cambodia cases

The US Centers for Disease Control and Prevention (CDC) weighed in on the cases and new genetic findings, noting that the clade has circulated in birds and poultry in Cambodia for many years, which have resulted in rare human cases. It said the father had a fever and a cough.

"To date, no indication of person-to-person spread has been found. There is no indication at this time that these two human cases of H5N1 in Cambodia pose a threat to the U.S. public," the CDC said, adding the caveat that people with occupational or recreational exposure to sick birds and mammals should take precautions, such as avoiding contact with animals that are sick or dead.

The agency said a CDC rapid response team is supporting Cambodia in its outbreak response and that the CDC has developed a H5 candidate vaccine virus that is identical or nearly identical to the hemagglutinin protein in the clade H5N1 viruses, which could be used to make a vaccine for humans, if needed.

More outbreaks in US poultry

In its latest updates, the US Department of Agriculture (USDA) Animal and Plant Health Inspection Service (APHIS) reported more highly pathogenic avian influenza outbreaks in four states: Colorado, Illinois, Pennsylvania, and Virginia. Colorado's outbreak appears to involve backyard birds, but in the other states hundreds to thousands of birds are involved in each event, likely indicating commercial farms.

The outbreak in Illinois occurred at a turkey farm in Wayne County housing more than 18,000 birds, and the event in Virginia's Alexandria County occurred at a live bird and slaughterhouse facility that had 800 birds. The latest outbreaks in Pennsylvania affected flocks of 3,400; 4,000; and 4,200 poultry in Chester and Lancaster counties.

Since the Eurasian H5N1 strain was first detected in US poultry more than a year ago, the outbreaks have led to the loss of a record 58.5 million birds in 47 states.

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