Credit NIAID
#18,634
Five months ago a new genotype of H5N1 appeared in Canada and the Pacific Northwest - dubbed D1.1 - which very quickly became dominant in wild birds and quickly swept eastward across the United States and Canada.
Over that time, we've seen roughly 20 human infections from this D1.1 genotype, several of them serious or severe (see CDC Statement: First H5 Bird Flu Death Reported in United States).
Recently, genotype D1.1 has been detected in dairy cattle in two states (Nevada & Arizona), further raising concerns over its ability to infect mammals.
Today we've new information - this time from Canada's CFIA and PHAC - describing the detection of a (previously) rare H275Y substitution in the neuraminidase (NA) protein of a number of genotype D1.1 isolates, which is associated with strong resistance to the NA inhibitors oseltamivir and peramivir.
Normally, we only see this mutation appear in a small percentage (1%) of patients receiving antiviral treatment. Because it is thought to exact a `fitness penalty' on influenza A viruses - limiting forward transmission - H275Y in the `wild' is fairly rare.
But, as the following blogs indicate, it is not entirely unheard of:
And in 2008, defying all expectations - H275Y became `fixed' in seasonal H1N1 - rendering Tamiflu all but useless against that subtype (see CIDRAP article With H1N1 resistance, CDC changes advice on flu drugs).
That is, until a new, susceptible pandemic H1N1virus emerged in 2009, supplanting the old resistant subtype.
While we've not seen any reports of H275Y in D1.1 samples collected in the United States, last November the CDC did report finding a far-less impactful mutation (NA-S247N) in 3 poultry workers from Washington State, which they stated may slightly reduce the virus's susceptibility to antivirals.
Due to its length, I've only posted excerpts from the research letter. Follow the link to read it in its entirety. I'll have a bit more after the break.Today's report is concerning because H275Y was discovered on 8 different poultry farms over a period of a couple of weeks, suggesting its `fitness penalty' in genotype D1.1 is less consequential than we've seen in other strains.
Anthony V. Signore,Tomy Joseph,Charlene Ranadheera,Cassidy N.G. ErdelyanORCID Icon,Tamiru N. Alkie,Sugandha Raj, show all
Article: 246964 | Accepted author version posted online: 18 Feb 2025
Cite this article https://doi.org/10.1080/22221751.2025.2469643
Abstract
We report the detection of a clade 2.3.4.4b A(H5N1) reassortant virus with a neuraminidase surface protein derived from a North American lineage low-pathogenic avian influenza virus. This virus caused a widespread and ongoing outbreak across 45 poultry farms in British Columbia, Canada.
Isolates from 8 farms reveal a mutation in the neuraminidase protein (H275Y) that is exceptionally rare among clade 2.3.4.4b viruses (present in 0.045% of publicly available clade 2.3.4.4b isolates). NA-H275Y is a well-known marker of resistance to the neuraminidase inhibitor oseltamivir. We demonstrate that this substitution maintains its resistance phenotype on the genetic background of H5N1 clade 2.3.4.4b viruses.
Main text
The current global outbreak of highly pathogenic avian influenza (HPAI) virus subtype A(H5N1) originated in 2020 from a reassortment event between clade 2.3.4.4b H5N8 viruses and a low pathogenic avian influenza (LPAI) virus circulating in Western Europe[1]. This clade 2.3.4.4b A(H5N1) virus then diversified into two distinct sub-lineages, B1 and B2[2]. Sub-lineage B1 seeded initial North American outbreaks in November 2021 via wild bird migration across the East Atlantic[3]. In January 2022, sub-lineage B2 seeded outbreaks in Western Canada, likely introduced via wild bird migration from Japan[4].
Since the introduction of A(H5N1) to North America, millions of wild and domestic animals have been affected, along with a growing number of human infections. This virus has frequently reassorted with North American lineage LPAI viruses that naturally circulate in wild birds, resulting in the detection of >100 reassortant genotypes[5,6]. However, there has been no evidence of reassortment that would yield an antigenic shift, as the surface protein encoding segments (HA, NA and M2) of all viruses sequenced in North America thus far descend from Eurasian origin viruses.
On October 21, 2024 the Canadian Food Inspection Agency (CFIA) was notified of chicken farms near Chilliwack, British Columbia (BC) suspected to be infected with HPAI virus. Oropharyngeal and cloacal swabs were collected from birds on each premise and sent to the CFIA’s National Centre for Foreign Animal Disease for confirmatory testing and whole-genome sequencing. RT-PCR and sequencing confirmed the virus to be H5 clade 2.3.4.4b HPAI, subtype A(H5N1). However, the neuraminidase (NA) segment appeared to be of North American lineage, rather than Eurasian.
(SNIP)
Discussion
The origin of the current panzootic A(H5N1) HPAI was due to a reassortment event involving the HA segment of clade 2.3.4.4b A(H5N8) HPAI and the NA segment from a LPAI virus circulating in European wild birds. Since then, similar events have been rare, as the only reported reassortment involving the surface protein encoding segments of an H5N1 clade 2.3.4.4b virus was an isolated event in Japan in 2022[12].
Here we report the first detection of a reassortant H5 clade 2.3.4.4b virus with a North American wild bird lineage N1 subtype in Canadian poultry. This virus is estimated to have emerged in Canada at the end of September, 2024 (TMRC: 2024-09-26, 95% HPD: 2024-09-01 - 2024-10-14), shortly before its first detection in British Columbia poultry on October 21, 2024 (Figure 1B).
In the 27 days that followed this initial detection, the virus spread rapidly to 44 farms across the province (see Appendix Figure 1 for collection locations). Viral genome sequencing from swab samples collected on a poultry farm near Abbotsford, BC on November 1, 2024 revealed an exceedingly rare amino acid substitution in the NA gene, H275Y (present in only 8 of 17,698 clade 2.3.4.4b isolates available on GISAID). In agreement with previously published data, we demonstrate that this substitution confers strong resistance to the neuraminidase inhibitor oseltamivir.
Despite evidence to suggest this substitution reduces viral fitness[13], viruses harboring this substitution spread rapidly across 8 farms in the 15 days following its initial detection (Figure 1B). As oseltamivir is the most widely used therapeutic and prophylactic against IAV, the continued circulation of viruses harboring NA-H275Y may necessitate a re-evaluation of influenza treatment strategies in Canada.
While this is obviously unwelcome news, it isn't clear whether this H275Y mutation continues to spread in genotype D1.1, or if it has already died out.
It generally requires other - `permissive' mutations - in the virus to compensate for the `fitness penalty' imposed by H275Y (see PLoS Pathogens: Fitness Advantage From Permissive NA Mutations In Oseltamivir Resistant pH1N1), and those may be transient in H5N1.
But this does remind us that H5N1 doesn't always play by the `rules', and it increases the need for more frequent, and timely, releases of genetic sequencing data on the virus as it spreads and evolves.
