Thread by @angie_rasmussen

Okay, so. I don’t know how much of a heads up this is when it’s just a notice about these 2 mutations. Do they really raise serious concerns about “increased transmission?”

Sort of. It’s more complex than D701N & E626K, omg pandemic bird flu.

What do these mutations do in H5N1?

https://twitter.com/covid19_disease/status/1894924526150119625

Flu is a segmented, negative sense RNA virus. This means its genome is divided into 8 pieces and they are negative coding sense and serve as a template for transcribing (copying) mRNA from each segment.

D701N and E672K are in a segment called PB2.

PB2 is one of 3 subunits (with PA and PB1) that make up the viral RNA-dependent RNA polymerase (RdRp). The RdRp both makes mRNA that’s translated into viral proteins and copies the viral genome segments in the process of virus replication to package into progeny virus particles.

Mutations that result in an amino acid change are named for their position in the protein sequence & the change from wild type.

D701N is a change from aspartic acid (D) to asparagine (N) at PB2 pos 701.

E672K is a change from glutamic acid (E) to lysine (K) at PB2 pos 672.

So what do these mutations do? Well, because they are in the PB2 subunit of the RdRp, they change how the RdRp works.

D701N increases polymerase (RNA copying) activity & enhances viral replication, as shown by virology legend Hans-Dieter Klenk et al.

journals.asm.org/doi/10.1128/jv…

And for those of you gain of function haters who say there’s no benefit to this work, we know that E672K is required for respiratory transmission between mammalian hosts thanks to Ron Fouchier’s GOF work in ferrets.

pmc.ncbi.nlm.nih.gov/articles/PMC48…

I talked a lot more about E672K in the context of H5N1’s viral replication cycle & pandemic potential in this thread (which I see I wrote on my last birthday because my work-life balance is unhealthy 😭). E672K interacts with ANP32, a host protein, to enhance virus replication.

https://twitter.com/angie_rasmussen/status/1858144535290806496

All a virus “wants” is to make more viruses. Both of these mutations make it easier for flu viruses to replicate their genome segments, make more viral RNA encoding viral proteins, and thus make more viral progeny.

D701N & E672K both increase viral fitness in mammalian hosts.

A key barrier H5N1 must overcome to be pandemic-capable is transmission between human hosts. But does increased fitness equal increased transmission between humans or are there other barriers?

There are other barriers, starting with hemagglutinin (HA—the H5 part of H5N1).

HA is analogous to SARS-CoV-2 spike in that it binds to the cellular receptor to enter and infect a host cell. If HA can’t efficiently enter a host cell, that host is not susceptible.

No entry = no infection.

If a virus can’t efficiently infect humans, it’s not a pandemic virus

Flu viruses use a sugar molecule called sialic acid as a receptor. There are 2 types of sialic acid—a “bird” SA used by avian viruses like H5 or H7 subtypes & a “human” SA used by seasonal flu viruses. More details on that are in the thread below:

https://twitter.com/angie_rasmussen/status/1622291626264788992

A pandemic virus has to infect human cells efficiently in order for it to transmit between humans easily. For that to happen, HA must bind the human receptors in the upper respiratory tract (nose). Upper tract infection results in lots of virus shedding & easy access to new hosts

Productive infection of the upper respiratory tract is an absolute requirement for increased transmissibility and pandemic capabilities. A virus needs to infect a host cell before it can benefit from mutations that enhance viral fitness.

And a pandemic H5N1 with would need to have both enhanced fitness in humans (make more virus) & the ability to use the human receptor (infect cells). Mutations in PB2 or other RdRp subunits/viral proteins confer fitness. Mutations in HA are needed to use the human receptor still.

Mutations in HA associated with binding the human receptor have been seen in human H5N1 cases. However, as far as we know, they haven’t been transmitted onward (fortunately).

More discussion on that in this thread 👇🏻

https://twitter.com/angie_rasmussen/status/1872431698149003493

So yes, it’s a concern we are seeing known human-adaptive mutations in PB2, but we aren’t seeing circulating virus with the infectivity-enhancing HA mutations that are also required to increase transmission.

And that’s good news, but…(there’s always a but)

We have had 70 confirmed H5N1 human cases, with (many?) more undetected. Every time the virus replicates in a human, it can acquire mutations in HA or PB2 (or any of the other gene segments) that adapt the virus to replicating & transmitting between human hosts.

It can also reassort with human seasonal viruses in a co-infected human host, which is very dangerous because it is unpredictable & has caused flu pandemics in the past. I covered this in thread below:

https://twitter.com/angie_rasmussen/status/1892172061898092892

Combined acquisition of mutations in HA and fitness-enhancing mutations coupled with reassortment could produce viruses that are very capable of causing a pandemic. This could happen in a human co-infected with H5N1 & seasonal flu. Seasonal flu is declining but still lots around.

Here’s a scenario: dairy/poultry gets H5N1 then gets seasonal H1N1 or H3N2. The H5N1 acquires mutations in HA allowing human receptor usage. Reassortment produces viruses with HA mutations & increased fitness from seasonal flu segments. Person isn’t very sick & transmits onward.

More people get infected with this reassortant & it continues to adapt, causing new human-adaptive mutations to be fixed. More transmission leads to more adaptation & eventually severe illness occurs. When enough people get infected, more cases of severe disease occur.

By the time hospitals are filled with H5 reassortant patients, the infection will have spread & been exported to other parts of the world. It will be impossible to contain. We will suddenly find ourselves in a bird flu pandemic that is likely to be worse than COVID-19.

So is the news of these mutations an “Important Public Health Update”? Not in my opinion. They are steps along the way to pandemic-capable H5N1 & a warning that we need to reduce human cases to prevent reassortment & emergence of pandemic viruses down the line.

We need to reduce opportunities for human infection, so we need to control cow and poultry outbreaks that increase human exposure risk. Viruses don’t get mutations or reassort in the environment—they need to replicate & they need a host to do that.

Let’s stop being hosts.