OmniVira

Literature detail

Deciphering transmission dynamics and spillover of avian influenza viruses from avian species to swine populations globally.

Ravendra P Chauhan1 Michelle L Gordon2
Affiliations 2 institutions
  1. School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, 719 Umbilo Road, Durban, 4001, South Africa.
  2. School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, 719 Umbilo Road, Durban, 4001, South Africa. [email protected].
PMID 34625868 2021 Virus Genes eng ppublish
PubMed DOI Browse context

Article

Publication summary

Genome sequences of eleven avian influenza virus (AIV) subtypes have been reported in swine populations from seven countries until August 2020. To unravel the transmission dynamics and spillover events of AIVs from avian reservoirs to swine, full-length hemagglutinin (HA) sequences of AIV subtypes (n = 11) reported from various avian species and swine were retrieved from the 'Influenza Research Database'. Phylogenetic analysis identified closely related avian and swine AIV sequences suggesting potential spillover events from multiple domestic and wild avian species, including chicken, duck, pigeon, goose, quail, and aquatic birds to swine. Furthermore, N-linked glycosylation analysis of these closely related AIV sequences supported the possibility of multiple spillover events of highly pathogenic H5N1 and low pathogenic H9N2 viruses from various avian species to swine. The principal coordinate analysis further validated these findings for H5N1 and H9N2 viruses; however, spillover events of the other nine AIV subtypes were limited. Interestingly, the presence of potential mammalian adaptation markers, particularly in some of the swine H5N1, H7N9, and H9N2 viruses, suggested that these viruses may have already adapted in swine. The occurrence and circulation of these AIVs in swine, especially the H5N1 and H9N2 viruses with numerous spillover events from the avian reservoirs to swine, pose a significant threat in terms of their reassortment with endemic swine viruses or circulating human influenza viruses within the swine which may facilitate the emergence of a novel influenza virus strain with pandemic potential.

Avian influenza virus Avian to swine spillover IAV adaptation Influenza pandemic N-linked glycosylation Phylogenetic analysis Principal coordinate analysis Virus evolution Influenza A Virus, H5N1 Subtype Influenza A Virus, H7N9 Subtype Influenza A Virus, H9N2 Subtype Influenza in Birds Animals Chickens Phylogeny Swine

Structured evidence records

Evidence records

10 total
Genomic Evolution 3 records
Genomic Evolution Extraction confidence 0.93
Key finding

Phylogenetic and glycosylation analyses of full-length HA sequences showed multiple avian-to-swine spillover events of H5N1 and H9N2 avian influenza viruses.

Virus
IAV H5N1
Host
Sus scrofa
Location
Not specified
Supporting text

Phylogenetic analysis identified closely related avian and swine AIV sequences suggesting potential spillover events from multiple domestic and wild avian species, including chicken, duck, pigeon, goose, quail, and aquatic birds to swine. Furthermore, N-linked glycosylation analysis of these closely related AIV sequences supported the possibility of multiple spillover events of highly pathogenic H5N1 and low pathogenic H9N2 viruses from various avian species to swine.

Genes or proteins
hemagglutinin (HA)
Analysis methods
phylogenetic analysis; N-linked glycosylation analysis
Genomic Evolution Extraction confidence 0.93
Key finding

Comparative genomic analysis revealed mammalian adaptation markers in swine H5N1, H7N9, and H9N2 influenza viruses indicating evolutionary adaptation in swine hosts.

Virus
IAV H7N9
Host
Sus scrofa
Location
Not specified
Supporting text

The presence of potential mammalian adaptation markers, particularly in some of the swine H5N1, H7N9, and H9N2 viruses, suggested that these viruses may have already adapted in swine.

Analysis methods
comparative genomic analysis
Genomic Evolution Extraction confidence 0.93
Key finding

Principal coordinate analysis confirmed multiple spillover events of H5N1 and H9N2 avian influenza viruses from birds to swine.

Virus
IAV H9N2
Host
Sus scrofa
Location
Not specified
Supporting text

The principal coordinate analysis further validated these findings for H5N1 and H9N2 viruses; however, spillover events of the other nine AIV subtypes were limited.

Genes or proteins
hemagglutinin (HA)
Analysis methods
principal coordinate analysis
Molecular Adaptation 3 records
Molecular Adaptation Extraction confidence 0.90
Key finding

Swine isolates of H5N1, H7N9, and H9N2 avian influenza viruses contain potential mammalian adaptation markers, indicating molecular adaptation to swine hosts.

Virus
IAV H5N1
Host
Not specified
Location
Not specified
Supporting text

The presence of potential mammalian adaptation markers, particularly in some of the swine H5N1, H7N9, and H9N2 viruses, suggested that these viruses may have already adapted in swine.

Mechanism types
mammalian_adaptation
Molecular Adaptation Extraction confidence 0.90
Key finding

Swine isolates of H5N1, H7N9, and H9N2 avian influenza viruses contain potential mammalian adaptation markers, indicating molecular adaptation to swine hosts.

Virus
IAV H7N9
Host
Not specified
Location
Not specified
Supporting text

The presence of potential mammalian adaptation markers, particularly in some of the swine H5N1, H7N9, and H9N2 viruses, suggested that these viruses may have already adapted in swine.

Mechanism types
mammalian_adaptation
Molecular Adaptation Extraction confidence 0.90
Key finding

Swine isolates of H5N1, H7N9, and H9N2 avian influenza viruses contain potential mammalian adaptation markers, indicating molecular adaptation to swine hosts.

Virus
IAV H9N2
Host
Not specified
Location
Not specified
Supporting text

The presence of potential mammalian adaptation markers, particularly in some of the swine H5N1, H7N9, and H9N2 viruses, suggested that these viruses may have already adapted in swine.

Mechanism types
mammalian_adaptation
Cross Species Transmission 2 records
Cross Species Transmission Extraction confidence 0.85
Key finding

Avian influenza viruses H5N1 and H9N2 were transmitted from domestic and wild avian species to swine populations, as supported by phylogenetic relationships between avian and swine isolates.

Virus
IAV H5N1
Location
globally
Supporting text

Phylogenetic analysis identified closely related avian and swine AIV sequences suggesting potential spillover events from multiple domestic and wild avian species, including chicken, duck, pigeon, goose, quail, and aquatic birds to swine.

Method
phylogenetic analysis; N-linked glycosylation analysis
Study design
phylogenetic analysis
Transmission direction
animal-to-animal
Geographic raw
globally
Cross Species Transmission Extraction confidence 0.85
Key finding

Low pathogenic H9N2 avian influenza viruses have undergone multiple transmission events from avian hosts to swine, consistent with molecular and phylogenetic evidence.

Virus
IAV H9N2
Location
globally
Supporting text

N-linked glycosylation analysis of these closely related AIV sequences supported the possibility of multiple spillover events of highly pathogenic H5N1 and low pathogenic H9N2 viruses from various avian species to swine.

Method
phylogenetic analysis; N-linked glycosylation analysis
Study design
phylogenetic analysis
Transmission direction
animal-to-animal
Geographic raw
globally
Spillover Event 2 records
Spillover Event Extraction confidence 0.97
Key finding

Evidence supports multiple spillover events of avian influenza H5N1 and H9N2 viruses from domestic and wild avian species to swine.

Virus
IAV H5N1
Location
seven countries
Supporting text

Phylogenetic analysis identified closely related avian and swine AIV sequences suggesting potential spillover events from multiple domestic and wild avian species, including chicken, duck, pigeon, goose, quail, and aquatic birds to swine. Furthermore, N-linked glycosylation analysis supported the possibility of multiple spillover events of highly pathogenic H5N1 and low pathogenic H9N2 viruses from various avian species to swine.

Method
phylogenetic analysis; N-linked glycosylation analysis
Study design
phylogenetic analysis
Transmission direction
animal-to-human
Geographic raw
seven countries
Spillover Event Extraction confidence 0.97
Key finding

Evidence supports spillover of avian influenza H9N2 viruses from multiple avian species to swine.

Virus
IAV H9N2
Location
seven countries
Supporting text

N-linked glycosylation analysis of these closely related AIV sequences supported the possibility of multiple spillover events of low pathogenic H9N2 viruses from various avian species to swine.

Method
phylogenetic analysis; N-linked glycosylation analysis
Study design
phylogenetic analysis
Transmission direction
animal-to-human
Geographic raw
seven countries