Highly Pathogenic Avian Influenza A(H5N1) Virus Outbreak in New England Seals, United States

Abstract

We report the spillover of highly pathogenic avian influenza A(H5N1) into marine mammals in the northeastern United States, coincident with H5N1 in sympatric wild birds. Our data indicate monitoring both wild coastal birds and marine mammals will be critical to determine pandemic potential of influenza A viruses.

Keywords: Caniformia; H5N1; New England; United States; avian influenza; ecology; gray seals; harbor seals; influenza; virology; viruses; zoonoses.

Figure 1

Phylogenetic analysis of highly pathogenic avian influenza A(H5N1) viruses from New England birds and seals, United States. Complete genomes of HPAI H5N1 viruses (GISAID database, https://www.gisaid.org) were compared by using IQ-TREE (https://www.iqtree.org) with the Ultrafast bootstrap (n = 10,000) option and A/chicken/NL/FAV-0033/2021 as a reference. Bootstrap support values >80 are shown at nodes. Red text indicates seal-derived sequences, black text avian-derived sequences from New England and Newfoundland, and blue text indicates avian-derived sequences from Europe . Branches are shaded on the basis of lineage groups: primary lineage from North America, pink; New England–specific lineage A, 1st wave blue, 2nd wave light blue; and New England–specific lineage B, green. All newly reported specimens were collected in the New England region during February–July 2022. Scale bar indicates nucleotide substitutions per site.

Figure 2

Amino acid changes in highly pathogenic avian influenza A(H5N1) viruses from New England birds and seals, United States. Each single-nucleotide polymorphism (SNP) that resulted in an amino acid change within ≥1 seal-derived sequence is shown. SNPs were observed in 12 H5N1 virus genes resulting in amino acid changes in corresponding proteins: PB2, PB1, PB1-F2, PA, PA-X, HA, NP, NA, M1, M2, NS1, and NS2. All avian virus reference sequences are shaded gray. A/Sanderling/MA/CW_22–112 (H5N1) (GISAID database, https://www.gisaid.org) (labeled A1) was used as a reference for first wave lineage A sequences; A/common eider/MA/TW_22–1400 (H5N1) (labeled A2) was used as a reference for second wave lineage A sequences; and A/common tern/MA/20220612_1 (H5N1) (labeled B) was used as a reference for lineage B sequences. Four aa differ between first and second wave lineage A viruses and 10 aa differ between first wave lineage A and lineage B. Second wave lineage A and lineage B seal-derived virus sequences, sampling date, and sampling location in Maine, USA, are indicated for each seal as follows: Pv1, MME22-112, 2022 Jun 22, Wells; Pv2, MME22-117, 2022 Jun 24, Yarmouth; Pv3, MME22-121, 2022 Jun 26, Georgetown; Pv4, MME22-122, 2022 Jun 27, New Harbor; Pv5, MME22-131, 2022 Jun 28, Harpswell; Pv6, MME22-133, 2022 Jun 29, S. Portland; Hg1, MME22-144, 2022 Jul 1, Phippsburg; Pv7, MME22-150, 2022 Jul 2, Westport; Pv8, MME22-155, 2022 Jul 2, Falmouth; Pv9, MME22-198, 2022 Jul 9, Wells; Pv10, MME22-230, 2022 Jul 15, Kennebunkport; Pv11, MME22-191, 2022 Jul 8, Harpswell; Pv12, MME22-195, 2022 Jul 9, Harpswell. HA, hemagglutinin; Hg, gray seal; M, matrix; NA, neuraminidase; NP, nucleoprotein; NS, nonstructural; PA, polymerase acidic; PB, polymerase basic; Pv, harbor seal.