OmniVira

Literature detail

Polymerase mutations underlie early adaptation of H5N1 influenza virus to dairy cattle and other mammals.

Vidhi Dholakia1 Jessica L Quantrill2,3 Samuel A S Richardson3 Nunticha Pankaew4 Maryn D Brown2 Jiayun Yang3 Fernando Capelastegui1 Tereza Masonou5 Katie-Marie Case5 Jila Ajeian5 Maximillian N J Woodall5 Callum Magill6 Graham Freimanis3 Amy McCarron3 Ecco Staller7 Carol M Sheppard2 Ian H Brown3 Pablo R Murcia6 Claire M Smith5 Munir Iqbal3 Paul Digard4 Wendy S Barclay2 Rute M Pinto8 Thomas P Peacock9,10 Daniel H Goldhill11
Affiliations 11 institutions
  1. Department of Pathobiology and Population Sciences, Royal Veterinary College, London, UK.
  2. Department of Infectious Disease, Imperial College London, London, UK.
  3. The Pirbright Institute, Woking, UK.
  4. The Roslin Institute, University of Edinburgh, Edinburgh, UK.
  5. Great Ormond Street UCL Institute of Child Health, London, UK.
  6. MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, UK.
  7. Sir William Dunn School of Pathology, The University of Oxford, Oxford, UK.
  8. The Roslin Institute, University of Edinburgh, Edinburgh, UK. [email protected].
  9. Department of Infectious Disease, Imperial College London, London, UK. [email protected].
  10. The Pirbright Institute, Woking, UK. [email protected].
  11. Department of Pathobiology and Population Sciences, Royal Veterinary College, London, UK. [email protected].
PMID 41545362 2026 Nat Commun eng epublish
PubMed DOI Browse context

Article

Publication summary

In 2024, an unprecedented outbreak of H5N1 high pathogenicity avian influenza was detected in dairy cattle in the USA resulting in spillbacks into poultry, wild birds and other mammals including humans. Here, we present molecular and virological evidence that the cattle B3.13 genotype H5N1 viruses rapidly accumulated adaptations in polymerase genes that enabled better replication in bovine cells and tissues, as well as cells of other mammals including humans. We find evidence of several mammalian adaptations in cattle including PB2 M631L, which is found in all cattle sequences, and PA K497R, which is found in the majority. Structurally, PB2 M631L maps to the polymerase-ANP32 interface, an essential host factor for viral genome replication. We show that this mutation adapts the polymerase to better interact with bovine ANP32 proteins, particularly ANP32A, and thereby enhances virus replication in bovine mammary systems and primary human airway cultures. We show that ongoing evolution in the PB2 gene, including E627K and a convergently arising D740N substitution, further increase polymerase activity and virus replication in a range of mammalian cells. Thus, circulation of H5N1 in dairy cattle allows virus adaption improving replicative ability in cattle and poses a continued risk of zoonotic spillover.

Cattle Diseases Influenza A Virus, H5N1 Subtype Orthomyxoviridae Infections RNA-Dependent RNA Polymerase Viral Proteins Adaptation, Physiological Animals Cattle Female Humans Madin Darby Canine Kidney Cells Mutation Virus Replication PB2 protein, Influenzavirus A

Structured evidence records

Evidence records

9 total
Cross Species Transmission 3 records
Cross Species Transmission Extraction confidence 0.90
Key finding

H5N1 avian influenza virus transmitted from birds to dairy cattle and subsequently spilled back from cattle to poultry and wild birds.

Virus
IAV H5N1
Location
United States United States
Supporting text

In 2024, an unprecedented outbreak of H5N1 high pathogenicity avian influenza was detected in dairy cattle in the USA resulting in spillbacks into poultry, wild birds and other mammals including humans.

Method
molecular evidence; virological evidence
Study design
outbreak investigation
Transmission direction
animal-to-animal
Geographic raw
USA
Country inferred
United States
Cross Species Transmission Extraction confidence 0.90
Key finding

H5N1 viruses circulating in dairy cattle spilled back into poultry populations.

Virus
IAV H5N1
Location
United States United States
Supporting text

In 2024, an unprecedented outbreak of H5N1 high pathogenicity avian influenza was detected in dairy cattle in the USA resulting in spillbacks into poultry, wild birds and other mammals including humans.

Method
molecular evidence; virological evidence
Study design
outbreak investigation
Transmission direction
animal-to-animal
Geographic raw
USA
Country inferred
United States
Cross Species Transmission Extraction confidence 0.90
Key finding

H5N1 viruses circulating in dairy cattle spilled back into wild birds.

Virus
IAV H5N1
Location
United States United States
Supporting text

In 2024, an unprecedented outbreak of H5N1 high pathogenicity avian influenza was detected in dairy cattle in the USA resulting in spillbacks into poultry, wild birds and other mammals including humans.

Method
molecular evidence; virological evidence
Study design
outbreak investigation
Transmission direction
animal-to-animal
Geographic raw
USA
Country inferred
United States
Host Range Experiment 2 records
Host Range Experiment Extraction confidence 0.80
Key finding

H5N1 viruses from dairy cattle replicated more efficiently in bovine mammary systems and primary human airway cultures, indicating adaptation for improved replication in mammalian hosts.

Virus
IAV H5N1
Location
Not specified
Supporting text

We show that this mutation adapts the polymerase to better interact with bovine ANP32 proteins, particularly ANP32A, and thereby enhances virus replication in bovine mammary systems and primary human airway cultures.

Method
replication assay; polymerase activity assay
Sample type
bovine mammary systems
Experimental system
in vitro cell culture
Host Range Experiment Extraction confidence 0.80
Key finding

The cattle genotype H5N1 viruses replicated more efficiently in bovine cells and tissues, demonstrating host adaptation of avian influenza to cattle.

Virus
IAV H5N1
Location
Not specified
Supporting text

We present molecular and virological evidence that the cattle B3.13 genotype H5N1 viruses rapidly accumulated adaptations in polymerase genes that enabled better replication in bovine cells and tissues.

Method
replication assay
Sample type
bovine tissues
Experimental system
in vitro cell culture
Molecular Adaptation 2 records
Molecular Adaptation Extraction confidence 1.00
Key finding

PB2 M631L and PA K497R mutations in the polymerase of H5N1 influenza viruses circulating in cattle enhance viral replication in bovine cells by improving interaction with host factor ANP32A.

Virus
IAV H5N1
Host
Not specified
Location
Not specified
Supporting text

We find evidence of several mammalian adaptations in cattle including PB2 M631L, which is found in all cattle sequences, and PA K497R, which is found in the majority. Structurally, PB2 M631L maps to the polymerase-ANP32 interface, an essential host factor for viral genome replication. We show that this mutation adapts the polymerase to better interact with bovine ANP32 proteins, particularly ANP32A, and thereby enhances virus replication in bovine mammary systems and primary human airway cultures.

Genes or proteins
PB2; PA
Host factors
ANP32A
Mutations
PB2 M631L; PA K497R
Mechanism types
polymerase_activity; host_factor_interaction; replication_efficiency
Molecular Adaptation Extraction confidence 1.00
Key finding

PB2 E627K and D740N mutations further increased polymerase activity and replication of H5N1 viruses in mammalian cells.

Virus
IAV H5N1
Host
Not specified
Location
Not specified
Supporting text

We show that ongoing evolution in the PB2 gene, including E627K and a convergently arising D740N substitution, further increase polymerase activity and virus replication in a range of mammalian cells.

Genes or proteins
PB2
Mutations
PB2 E627K; PB2 D740N
Mechanism types
polymerase_activity; replication_efficiency
Genomic Evolution 1 records
Genomic Evolution Extraction confidence 0.85
Key finding

Genomic analysis revealed polymerase mutations PB2 M631L, PA K497R, E627K, and D740N that enhance the mammalian adaptation of H5N1 influenza virus circulating in dairy cattle.

Virus
IAV H5N1
Host
Bos taurus
Location
Not specified
Supporting text

We find evidence of several mammalian adaptations in cattle including PB2 M631L, which is found in all cattle sequences, and PA K497R, which is found in the majority. Structurally, PB2 M631L maps to the polymerase-ANP32 interface, an essential host factor for viral genome replication. We show that ongoing evolution in the PB2 gene, including E627K and a convergently arising D740N substitution, further increase polymerase activity and virus replication in a range of mammalian cells.

Genes or proteins
PB2; PA
Analysis methods
genomic analysis; evolutionary analysis
Spillover Event 1 records
Spillover Event Extraction confidence 0.95
Key finding

H5N1 avian influenza virus spilled over from infected animals into humans during the 2024 outbreak in dairy cattle in the USA.

Virus
IAV H5N1
Location
United States United States
Supporting text

In 2024, an unprecedented outbreak of H5N1 high pathogenicity avian influenza was detected in dairy cattle in the USA resulting in spillbacks into poultry, wild birds and other mammals including humans.

Method
molecular analysis; virological evidence; sequencing
Study design
outbreak investigation
Transmission direction
animal-to-human
Geographic raw
USA
Country inferred
United States