OmniVira

Highly pathogenic avian influenza A (H5N1) in marine mammals and seabirds in Peru.

Mariana Leguia1,2 Alejandra Garcia-Glaessner3,4 Breno Muñoz-Saavedra3,4 Diana Juarez3,4 Patricia Barrera3,4 Carlos Calvo-Mac4 Javier Jara5 Walter Silva5 Karl Ploog5 Lady Amaro5 Paulo Colchao-Claux6 Christine K Johnson4,7 Marcela M Uhart4,7 Martha I Nelson8 Jesus Lescano5
Affiliations 8 institutions
  1. Laboratorio de Genómica, Pontificia Universidad Católica del Perú (PUCP), Lima, Peru. [email protected].
  2. EpiCenter for Emerging Infectious Disease Intelligence, Centers for Research in Emerging Infectious Diseases, Lima, Peru. [email protected].
  3. Laboratorio de Genómica, Pontificia Universidad Católica del Perú (PUCP), Lima, Peru.
  4. EpiCenter for Emerging Infectious Disease Intelligence, Centers for Research in Emerging Infectious Diseases, Lima, Peru.
  5. Servicio Nacional Forestal y de Fauna Silvestre (SERFOR), Ministerio de Desarrollo Agrario y Riego (MIDAGRI) del Perú, Lima, Peru.
  6. Wildlife Conservation Society (WCS) - Perú, Lima, Peru.
  7. One Health Institute, School of Veterinary Medicine, University of California, Davis, CA, USA.
  8. National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, MD, USA.
PMID37679333 DOI10.1038/s41467-023-41182-0 Year2023 Journal Nature communications Nat Commun Languageeng Statusepublish

Abstract

Highly pathogenic avian influenza (HPAI) A/H5N1 viruses (lineage 2.3.4.4b) are rapidly invading the Americas, threatening wildlife, poultry, and potentially evolving into the next global pandemic. In November 2022 HPAI arrived in Peru, triggering massive pelican and sea lion die-offs. We report genomic characterization of HPAI/H5N1 in five species of marine mammals and seabirds (dolphins, sea lions, sanderlings, pelicans and cormorants). Peruvian viruses belong to lineage 2.3.4.4b, but they are 4:4 reassortants where 4 genomic segments (PA, HA, NA and MP) position within the Eurasian lineage that initially entered North America from Eurasia, while the other 4 genomic segments (PB2, PB1, NP and NS) position within the American lineage (clade C) that circulated in North America. These viruses are rapidly accruing mutations, including mutations of concern, that warrant further examination and highlight an urgent need for active local surveillance to manage outbreaks and limit spillover into other species, including humans.

Supporting text Virus Host Location
Caniformia 3 Influenza A virus 186 Influenza A Virus, H5N1 Subtype 300 Influenza in Birds 341 Influenza, Human 286 Animals 1948 Birds 212 Cetacea 3 Humans 1440 Peru 6

Evidence records

4 total
Zoonotic Surveillance
1 records · 1 evidence types
Evidence type Viral Detection
1 records
OVE7335 Viral Detection
Key finding

Highly pathogenic avian influenza A/H5N1 virus was genomically detected in dolphins, sea lions, sanderlings, pelicans, and cormorants in Peru.

Virus
Influenza A virus H5N1
Host
marine dolphins Delphinidae Natural host fur seals & sea lions Otariidae Natural host sanderling Calidris alba Natural host pelicans Pelecanidae Natural host cormorants and shags Phalacrocoracidae Natural host
Location
Peru
Supporting text

Highly pathogenic avian influenza A (H5N1) in marine mammals and seabirds in Peru. We report genomic characterization of HPAI/H5N1 in five species of marine mammals and seabirds (dolphins, sea lions, sanderlings, pelicans and cormorants).

Method
genomic characterization
Geographic raw
Peru
Country inferred
PER
Transmission Evidence
1 records · 1 evidence types
Evidence type Outbreak Investigation
1 records
OVE7338 Outbreak Investigation
Key finding

Arrival of HPAI A/H5N1 in Peru in November 2022 was linked to an outbreak causing massive die-offs among pelicans and sea lions.

Virus
Influenza A virus H5N1
Host
pelicans Pelecanidae Natural host fur seals & sea lions Otariidae Natural host
Location
Peru
Supporting text

In November 2022 HPAI arrived in Peru, triggering massive pelican and sea lion die-offs.

Method
field outbreak investigation | mortality monitoring
Transmission direction
unknown
Geographic raw
Peru
Country inferred
PER
Outbreak setting
wildlife along the Peruvian coast
Outbreak time
November 2022
Outbreak scale
massive pelican and sea lion die-offs
Genomic Evolution
2 records · 2 evidence types
Evidence type Recombination or Reassortment
1 records
OVE7336 Recombination or Reassortment
Key finding

Peruvian highly pathogenic avian influenza A/H5N1 viruses were identified as 4:4 reassortants combining Eurasian and American lineage genome segments.

Virus
Influenza A virus H5N1
Host
Not specified
Location
Not specified
Supporting text

Peruvian viruses belong to lineage 2.3.4.4b, but they are 4:4 reassortants where 4 genomic segments (PA, HA, NA and MP) position within the Eurasian lineage ... while the other 4 genomic segments (PB2, PB1, NP and NS) position within the American lineage (clade C).

Event type
reassortment
Genes or segments
PA | HA | NA | MP | PB2 | PB1 | NP | NS
Evidence type Phylogenetic Evolution
1 records
OVE7337 Phylogenetic Evolution
Key finding

Peruvian HPAI A/H5N1 viruses belong to lineage 2.3.4.4b and exhibit rapid evolutionary change through accumulation of mutations, including mutations of concern.

Virus
Influenza A virus H5N1
Host
Not specified
Location
Not specified
Supporting text

Peruvian viruses belong to lineage 2.3.4.4b ... These viruses are rapidly accruing mutations, including mutations of concern, that warrant further examination.

Analysis methods
phylogenetic analysis | genomic characterization