Phenotypes of the Reassortant viruses observed in this study
#18,894
Over the past 3 years we've seen a dizzying array of reports and studies showing that many clade 2.3.4.4b H5Nx viruses circulating today exhibit vastly different behaviors from the viruses that circulated prior to 2022.
A few of many ominous changes include:
- First, we've seen numerous spillovers into mammals, often presenting with severe neurological manifestations (see Cell: The Neuropathogenesis of HPAI H5Nx Viruses in Mammalian Species Including Humans)
- Second, tens of thousands of marine mammals - in North and South America, and Europe - have been killed (see Nature Comms: Cross-species and mammal-to-mammal transmission of clade 2.3.4.4b HPAI A/H5N1 with PB2 adaptations)
- Third, nearly 1,100 dairy herds - and a smattering of other ruminants - have been infected with HPAI H5N1
- Fourth, the CDC lists 70 confirmed and 7 probable human H5N1 infections since the spring of 2024, most - but not all - with exposure to either infected cattle or poultry.
- And hundreds of cats - both household pets and strays - have succumbed (see One Health: Outbreak of HPAI a(H5N1) Among House Cats: A Case Series Involving Oseltamivir Treatment
HPAI H5N1 is not a single viral strain, as there are literally hundreds of genotypes circulating around the world. Some are more dangerous than others. But exactly what makes one genotype more dangerous - while others are relatively benign - remains poorly understood.
Regular readers know we often look for a handful of mutations (e.g. PB2 mutations like E627K, D701N, Q591K, and M631L and HA mutations like Q226L and E190D) which may favor mammalian adaptation, but new ones (see Sci. Adv.: PB2 and NP of North American H5N1 Virus Drive Immune Cell Replication and Systemic Infections) continue to be discovered.
Today we have a fascinating preprint (not yet peer reviewed) from Universities and Institutes in the UK, the Netherlands, and Italy which may end up changing the way we look for H5N1 adaptation signatures.
Fair warning, this is a lengthy (60 page) and highly technical report, and I can only cover the high points. First the link, and abstract, after which I'll try to break out some of the highlights.
The potential of H5N1 viruses to adapt to bovine cells varies throughout evolution
Matthew L Turnbull, Mohammad Khalid Zakaria, Nicole S Upfold, Siddharth Bakshi, Callum Magill, Udeet Ranjan Das, Andrew T Clarke, Laura Mojsiejczuk, Vanessa Herder, Kieran Dee, Nancy Liu, Monika Folwarczna, Georgios Ilia, Wilhelm Furnon, Verena Schultz, Hanting Chen, Ryan Devlin, Jack McCowan, Alex L Young, Wai-Wai Po, Katherine Smollett, Muhammad Ahsan Yaseen, Rebecca Ros, Avanti Bhide, Bianca van Kekem, Ron Fouchier, Ana Da Silva Filipe, Munir Iqbal, Ed Roberts, Joseph Hughes, Dirk Werling, Pablo R Murcia, Massimo Palmarini
doi: https://doi.org/10.1101/2024.11.29.626120
This article is a preprint and has not been certified by peer review [what does this mean?].
Preview PDF
Abstract
Avian influenza H5N1 clade 2.3.4.4b viruses caused a global panzootic and, unexpectedly, widespread outbreaks in dairy cattle, therefore representing a pandemic threat. To inform effective control strategies, it is critical to determine whether the potential to adapt to bovine cells is a generalised feature of H5N1 viruses, or is specific to clade 2.3.4.4b, or even more restricted to specific genotypes within this clade (e.g., B3.13 and D1.1).
Using a large panel of H5N1 viruses representing >60 years of their natural history and other IAV for comparative purposes, we demonstrate that virus adaptation to bovine cells is: (i) highly variable across 2.3.4.4b genotypes, (ii) limited in viruses predating the global expansion of this clade, (iii) determined by the viral internal gene cassette, and (iv) not restricted to udder epithelial cells.
Mutations in the PB2 polymerase subunit, particularly M631L, emerge as key determinants of adaptation, although their phenotypic effects are context dependent and have limited enhanced viral polymerase activity in human cells.
Bovine B3.13 and some avian genotypes also exhibit enhanced modulation of bovine interferon-induced antiviral responses, determined by at least the viral PB2, nucleoprotein, and the non-structural protein NS1.
Our results highlight the polygenic nature of IAV host range and reveal that the potential to cross the species barrier varies during the evolutionary trajectory of H5N1, with some avian viruses more predisposed to spillover than others.
Essentially this study looked at whether HPAI H5N1 viruses have always had the ability to infect cattle, or if something had recently changed to enable that capability.
They used reverse genetics to generate an array of reassortant viruses (using the HA and NA from H1N1 Puerto Rico/8/34 (PR8)) with the internal genes from 12 different H5N1 viruses going back 60 years.
Using bovine cell models they showed that only viruses with the internal cassette from recent H5N1 viruses (particularly genotypes B3.13 and D1.1) replicated efficiently in bovine respiratory, skin, and udder cells.
Previously known mutations - like PB2 M631L - enhanced replication but were only fully effective when combined with these recently emerged internal gene cassettes.
These findings suggest that mammalian adaptation in H5N1 appears highly depended on permissive-compensatory changes across multiple internal gene segments - making our current surveillance based on a handful of `signature' mutations insufficient.
It also suggest that H5's arrival in North America - and its subsequent reassortment with N.A. LPAI viruses - signaled a major turning point in its evolution.
I've only covered the less technical highlights of this preprint, so follow the link to read it in its entirety.
None of this means that a B3.13 or D1.1 pandemic is inevitable, only that the North American branch of the H5N1 virus has become better adapted to mammalian hosts than its Eurasian cousins.
Where H5 goes from here is unknown. It could fizzle - or run into an insurmountable species barrier.
But we continue to treat this virus as if it is the same pathogen that tried - and failed - to spark a pandemic 20 years ago. It isn't, and what we may be faced with six months - or six years - from now, will almost certainly have changed even more.
A reminder that evolution never stops, and Nature always bats last.
