Girl who died of bird flu didn't have a widely-spread variant (H5N1)

The Cambodian girl who died of H5N1 this month did not have the worrying 2.3.4.4b virus.Credit: Cambodia Ministry of Health/AP/Shutterstock

An 11-year-old girl in southern Cambodia, who died last week after being infected with avian influenza A (H5N1), had a different strain than the one that caused mass bird deaths wild and domesticated around the world, says the scientist who led the effort to sequence viral samples from the girl. Scientists initially feared the girl might have been infected with the widespread virus that is now spreading in some species of mammals and has infected a handful of people since 2020.

Erik Karlsson, a virologist at the Institut Pasteur du Cambodge in Phnom Penh, told Nature how he and his colleagues sequenced the full genome of the girl's virus sample in less than one year before sharing the data on the GISAID public repository. He says the sequenced virus belongs to a group that has been found in chickens and ducks in the region for at least a decade, although the girl is the first person to be detected with H5N1 in the country in nine years. .

The Cambodian Ministry of Health took 12 of his close contacts, and only his 49-year-old father tested positive. H5N1 infections usually occur in people who have had close contact with poultry, and so far there is no evidence that this strain has spread between people. Investigations into how the girl was exposed to the virus are ongoing.

When did you receive the virus sample from the girl?

The sample was first tested at the National Institute of Public Health in Phnom Penh and then transferred to us. We received the sample around 5 p.m. on February 22, and it was sequenced in 24 hours. This really illustrates how the COVID-19 pandemic has increased our ability to sequence and share data very quickly.

The viral load of the sample was high enough that we could amplify the entire influenza genome at once. If the viral load had been low, which it often is, we would have had to wait about three days to grow it in cells or eggs to get enough virus to sequence. Our goal has been to get the virus sequenced and into the public domain as quickly as possible.

What did you learn from the sequence?

The virus belongs to clade 2.3.2.1c, which is an endemic strain in the region. It's the same strain that caused a number of human infections in 2013 and 2014 in Cambodia, and has been detected intermittently in poultry since then, including chickens at bird markets. alive.

Everyone was worried that the girl might have the 2.3.4.4b strain, which is circulating all over the world and is currently causing big problems in Europe, North America and South America. 2.3.4.4b is a new virus clade, and we don't know much about it.

Researchers have been monitoring 2.3.2.1c for some time and have information about it to make reasonable judgments about its transmissibility and pathogenicity. But whenever there is a zoonotic spillover, we have to treat it with utmost importance.

What's Worrying About Zoonotic Fallout?

Viruses, especially RNA viruses such as influenza, are extremely promiscuous and will quickly adapt to a new host. We have seen it with the virus that causes COVID-19. An overflow indicates that the virus now has a chance to adapt to a new host. This is concerning because this adaptation could result in a virus that could potentially be transmitted between people. Getting ahead and blocking any potential for transmission, as well as understanding what the virus is doing in its new host, is critically important and can inform outbreak response.

Do you also sequence samples from the father?

We are trying to sequence samples from the father, but he seems to have had a lower viral load, which makes it a bit more difficult to get a sequence quickly. We will try other targets...