Girl who died of bird flu didn’t have widespread variant

An 11-year-old girl from southern Cambodia who died last week after contracting bird flu A(H5N1) was infected with a different strain than the one causing mass deaths in wild and poultry around the world, scientists say. The scientist who led the effort said virus samples from the girl. Scientists were initially worried that the girl had contracted the now widespread virus. spread in some mammalian species Since 2020, it has infected a small number of people.

Virologist Eric Carlson of the Cambodian Pasteur Institute in Phnom Penh said: Nature How he and his colleagues sequenced the whole genome of a viral sample from a girl in less than a day before sharing the data in the public repository GISAID. He says the sequenced virus belongs to a group that has been found in chickens and ducks in the area for at least her decade, but the girl is the first in her nine years to have her H5N1 in the country. Detected person.

The Cambodian Ministry of Health swabbed 12 of her close contacts and only the 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 the strain has spread among humans. An investigation is underway into how the girl was exposed to the virus.

When did you receive the virus sample from the girl?

The samples were first tested at the National Institute of Public Health in Phnom Penh and then transferred to us. Samples were received on February 22nd around 5pm and sequenced within 24 hours. This highlights how the COVID-19 pandemic has improved our ability to sequence and share data very quickly.

The viral load in the samples was high enough to allow amplification of the entire influenza genome at once. As is often the case, when the viral load was low, we had to wait about 3 days to grow the virus in cells or eggs in order to obtain enough virus for sequencing. Our focus was to sequence the virus and get it into the public domain as soon as possible.

What did you learn from sequences?

The virus belongs to clade 2.3.2.1c and is endemic to this region. It is the same strain that caused a large number of infections in Cambodia in 2013 and 2014, and has since been intermittently detected in poultry, including chickens at live bird markets.

Everyone was worried that the girl had the 2.3.4.4b stock. This strain has now spread all over the world and is causing major problems in Europe, North America and South America. 2.3.4.4b is a new viral clade and we don’t know much about it.

Researchers have been monitoring 2.3.2.1c for quite some time and have the information to make reasonable decisions about its contagiousness and pathogenicity. But whenever a zoonotic spillover occurs, we must treat it with the utmost importance.

What are your concerns about zoonotic spillovers?

Viruses, especially RNA viruses such as influenza, are highly promiscuous and adapt quickly to new hosts. This was seen with the virus that causes COVID-19. Spillovers indicate that viruses have a chance to adapt to new hosts. This is a concern because that adaptation could result in a virus that could be transmitted between people. Understanding is very important and can inform your response to the outbreak.

Are samples from fathers also sequenced?

We are trying to sequence the father’s sample, but his viral load appears to have been low, making it a little harder to get a sequence out of the way quickly. I’ll try some approaches. However, often there is not enough viral load to obtain more than partial sequences.

What do we know about how the girl got infected?

In this case, I have no idea why this virus spread from poultry to humans, even though the virus has been undetected for about a decade. Although many factors still need to be investigated, the COVID-19 pandemic has led to many global changes in agricultural practices that may have created the conditions for spillovers.

Cambodia has seen an increase in backyard poultry farming due to the pandemic. Many people, such as tour guides, were unable to work and had to supplement their income and food sources for their families. People around the world are still struggling, which could result in changes in farming practices and increased contagion risk. Also, changes in people’s health, such as malnutrition and being overweight, can make people more susceptible to infection.

I hope this is an isolated incident, but it may indicate a larger problem.

What further analysis does your team do?

We hope to have more information about the poultry samples involved in the incident soon. Those virus sequences are then compared to historical virus data, for example from monitoring live bird markets from these parts of Cambodia, to see if there have been any major changes or forced viruses. You can see if something is happening in your poultry flock. For example, transforming it into a more dangerous phenotype or putting people at a higher risk.

We also isolate and propagate this virus in a Biosafety Level 3 facility. This will help develop tools to better understand the epidemiology of the virus in this case and the region. can. This is found in samples collected from the father, other people living in the girl’s home, and the wider community. Isolates are also essential for laboratories around the world to study the transmissibility and virulence of viruses, including animal models such as ferrets.

This interview has been edited for length and clarity.