Mortality in sea lions is associated with the introduction of the H5N1 clade 2.3.4.4b virus in Brazil October 2023: whole genome sequencing and phylogenetic analysis

Andreina de Carvalho Araujo; Andrew Yong Cho; Laura Morais Nascimento Silva; Thais Camilo Corrêa; Gabriela Cristini de Souza; Adriana Silva Albuquerque; Eduardo Macagnan; Cristiane K M Kolesnikvoas; Rafael Meurer; Jenyffer Vierheller Vieira; Giulia Gaglianone Lemos; André Silva Barreto; Jeferson Luis Dick; Karina Rejane Groch; Pedro Volkmer de Castilho; Deyvid Amgarten; Fernanda Malta; Michael Miller; Erick G Dorlass; Soledad Palameta; Sun-Hak Lee; Clarice Weis Arns; Edison L Durigon; João Renato R Pinho; Dong-Hun Lee; Helena Lage Ferreira

doi:10.1186/s12917-024-04137-1

Mortality in sea lions is associated with the introduction of the H5N1 clade 2.3.4.4b virus in Brazil October 2023: whole genome sequencing and phylogenetic analysis

BMC Vet Res. 2024 Jul 2;20(1):285. doi: 10.1186/s12917-024-04137-1.

Authors

Andreina de Carvalho Araujo^#¹, Andrew Yong Cho^#², Laura Morais Nascimento Silva^#³, Thais Camilo Corrêa¹, Gabriela Cristini de Souza⁴, Adriana Silva Albuquerque⁴, Eduardo Macagnan⁴, Cristiane K M Kolesnikvoas⁵, Rafael Meurer⁵, Jenyffer Vierheller Vieira⁶, Giulia Gaglianone Lemos⁶, André Silva Barreto⁷, Jeferson Luis Dick⁸, Karina Rejane Groch⁹, Pedro Volkmer de Castilho⁴, Deyvid Amgarten¹⁰, Fernanda Malta¹⁰, Michael Miller¹¹, Erick G Dorlass¹⁰, Soledad Palameta¹¹, Sun-Hak Lee², Clarice Weis Arns¹¹, Edison L Durigon^{12

13}, João Renato R Pinho^{10

14}, Dong-Hun Lee^{15

16}, Helena Lage Ferreira^{17

18}

Affiliations

¹ Department of Veterinary Medicine, FZEA- USP, University of São Paulo, 225 Av Duque de Caxias Norte, Pirassununga, SP, 13635900, Brazil.
² Avian Disease Laboratory, College of Veterinary Medicine, Konkuk University, 120 Neungdong-Ro, Gwangjin-Gu, Seoul, 05029, Republic of Korea.
³ Graduate Program in Experimental Epidemiology Applied to Zoonoses, Veterinary Medicine and Animal Science School, University of São Paulo, Av. Prof. Orlando Marques de Paiva, 87, Butantã, São Paulo, SP, 05508270, Brazil.
⁴ Zoology Laboratory, Stabilization Unit, Laguna, UDESC, Av. Colombo Machado Salles 1873, Laguna, SC, 88790-000, Brazil.
⁵ R3 Animal Association, Rod. João Gualberto Soares 11.000, Florianópolis, SC, 88060-000, Brazil.
⁶ Marine Tetrapod Ecology and Conservation Laboratory, Marine Animal Stabilization Unit, São Francisco do Sul, University of the Joinville Region, UNIVILLE, Rod. Duque de Caxias 6.365, São Francisco do Sul, SC, 89240-000, Brazil.
⁷ LIBGeo, UNIVALI, Rua Uruguai 458, Itajaí, SC, 88301-902, Brazil.
⁸ Marine Animal Stabilization Unit, University of Vale do Itajaí - Univali BR, R Maria Emilia, 90, Armação, Penha, SC, 88385-000, Brazil.
⁹ Australis Institute, Av. Atlantica, Sn, Praia de Itapirubá Norte, Imbituba, SC, 88780-000, Brazil.
¹⁰ Albert Einstein Israelite Hospital, Av. Albert Einstein, 627/701, São Paulo, SP, 05652-900, Brazil.
¹¹ BSL-3 Laboratory of Virology and Applied Biotechnology, Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas - UNICAMP, P.O.Box: 6109, Campinas, SP, 13083-862, Brazil.
¹² BSL3+ Laboratory of Clinical and Molecular Virology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes 1374, São Paulo, SP, 05508-000, Brazil.
¹³ Pasteur Institute of São Paulo/USP, University of São Paulo, São Paulo, 05508-020, Brazil.
¹⁴ LIM03/07, Institute of Tropical Medicine and Clinics Hospital, University of São Paulo School of Medicine, São Paulo, 05403-000, Brazil.
¹⁵ Wildlife Health Laboratory, College of Veterinary Medicine, Konkuk University, 120 Neungdong-Ro, Gwangjin-Gu, Seoul, 05029, Republic of Korea.
¹⁶ Konkuk University Zoonotic Diseases Research Center, College of Veterinary Medicine, Konkuk University, 120 Neungdong-Ro, Gwangjin-Gu, Seoul, 05029, Republic of Korea.
¹⁷ Department of Veterinary Medicine, FZEA- USP, University of São Paulo, 225 Av Duque de Caxias Norte, Pirassununga, SP, 13635900, Brazil. [email protected].
¹⁸ Graduate Program in Experimental Epidemiology Applied to Zoonoses, Veterinary Medicine and Animal Science School, University of São Paulo, Av. Prof. Orlando Marques de Paiva, 87, Butantã, São Paulo, SP, 05508270, Brazil. [email protected].

^# Contributed equally.

Abstract

Clade 2.3.4.4b highly pathogenic avian influenza (HPAI) H5N1 virus was detected in the South American sea lions found dead in Santa Catarina, Brazil, in October 2023. Whole genome sequencing and comparative phylogenetic analysis were conducted to investigate the origin, genetic diversity, and zoonotic potentials of the H5N1 viruses. The H5N1 viruses belonged to the genotype B3.2 of clade 2.3.4.4b H5N1 virus, which was identified in North America and disseminated to South America. They have acquired new amino acid substitutions related to mammalian host affinity. Our study provides insights into the genetic landscape of HPAI H5N1 viruses in Brazil, highlighting the continuous evolutionary processes contributing to their possible adaptation to mammalian hosts.

Keywords: High pathogenicity avian influenza; Marine mammal; Public health; South America; Virus; Whole genome sequencing.

MeSH terms

Animals
Brazil
Genetic Variation
Genome, Viral
Genotype
Influenza A Virus, H5N1 Subtype* / classification
Influenza A Virus, H5N1 Subtype* / genetics
Orthomyxoviridae Infections / veterinary
Orthomyxoviridae Infections / virology
Phylogeny*
Sea Lions* / virology
Whole Genome Sequencing*