---
title: "Highly Pathogenic Avian Influenza H5 Detection in Brazilian Cetaceans (2023–2025)"
id: "cdc-emerging-infectious-diseases-journal-5-highly-pathogenic-avian-influenza-virus-subtype-5-in-cetaceans-brazil"
canonical_url: "https://medichelpline.com/clinical-feed/cdc-emerging-infectious-diseases-journal-5-highly-pathogenic-avian-influenza-virus-subtype-5-in-cetaceans-brazil"
content_type: "clinical_feed_article"
specialty: "Infectious Disease"
source_name: "CDC Emerging Infectious Diseases Journal"
source_url: "https://wwwnc.cdc.gov/eid/article/32/10/26-0051_article"
published_at: "2026-09-21T04:00:00.000Z"
evidence_level: "Agency Feed"
license: "CC-BY-NC-4.0 / Informational Use"
---
# Highly Pathogenic Avian Influenza H5 Detection in Brazilian Cetaceans (2023–2025)
## Provenance & Clinical Metadata
- **Canonical URL:** https://medichelpline.com/clinical-feed/cdc-emerging-infectious-diseases-journal-5-highly-pathogenic-avian-influenza-virus-subtype-5-in-cetaceans-brazil
- **Specialty:** [Infectious Disease](https://medichelpline.com/clinical-feed/infectious-disease.md)
- **Primary Source:** CDC Emerging Infectious Diseases Journal
- **Source URL:** [Original Journal Publication](https://wwwnc.cdc.gov/eid/article/32/10/26-0051_article)
- **Published At:** 2026-09-21T04:00:00.000Z
- **Evidence Rating:** Agency Feed
## Executive GIST (TL;DR)
- Surveillance from November 2023–August 2025 screened 45 stranded cetaceans along the Brazilian coast (Rio Grande do Sul, Rio de Janeiro, Ceará) for **influenza A virus** (IAV) using qRT-PCR. - IAV matrix gene RNA was detected in 18 animals across 13 species; positive species included **Franciscana dolphin** (Pontoporia blainvillei), Lahille’s bottlenose dolphin (Tursiops truncatus gephyreus), rough-toothed dolphin, Clymene dolphin, dwarf sperm whale, and Fraser’s dolphin. - Most positive detections were from blowhole swabs; other positive sample types included cerebral, oral, anal, intestinal, tracheal, and ocular tissues. - Viral RNA levels were low (Ct 28–37), approximating the assay limit of detection (≈200–2,000 RNA copies/µL), corresponding to ≈1.3 × 10^5–8.0 × 10^2 RNA copies/µL. - The highly pathogenic avian influenza **H5N1** strain was identified in 2 samples, both with RNA concentrations near the assay limit of detection. - Histopathology performed on six IAV-positive animals did not reveal lesions attributable to influenza infection. - The findings suggest ongoing viral circulation in the marine environment after HPAI H5N1 outbreaks in South America and indicate potential interspecies transmission to cetaceans, including species classified as vulnerable or endangered. - Limitations included sampling only carcasses in decomposition stages 2–4, likely RNA degradation, limited numbers available for histopathology, and potential environmental contamination—although detection in internal tissues supports true infection. - Authors recommend continued, systematic surveillance of marine mammals to monitor pathogen dynamics at the wildlife–marine interface and to assess risks to threatened cetacean species.
## Clinical Analysis & Structured Key Points
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[EID Journal](https://wwwnc.cdc.gov/eid/) 2. [Volume 32](https://wwwnc.cdc.gov/eid/early-release) 3. [Early Release](https://wwwnc.cdc.gov/eid/early-release#issue-1346) 4. [Main Article](https://wwwnc.cdc.gov/eid/article/32/10/26-0051_article) * [Facebook](https://www.facebook.com/sharer/sharer.php?u=%2Feid%2Farticle%2F32%2F10%2F26-0051_article "Share to Facebook") * [Twitter](http://twitter.com/share?url=%2Feid%2Farticle%2F32%2F10%2F26-0051_article&text= "Share to Twitter") * [LinkedIn](https://www.linkedin.com/shareArticle?url=%2Feid%2Farticle%2F32%2F10%2F26-0051_article&title= "Share to LinkedIn") * [Syndicate](https://tools.cdc.gov/medialibrary/index.aspx#/sharecontent//eid/article/32/10/26-0051_article "Embed this Page") [ Emerging Infectious Disease journal ISSN: 1080-6059 ](https://wwwnc.cdc.gov/eid/) _Disclaimer: Early release articles are not considered as final versions. Any changes will be reflected in the online version in the month the article is officially released._ #### Volume 32, Number 10—October 2026 ##### _Research Letter_ ### Highly Pathogenic Avian Influenza Virus Subtype 5 in Cetaceans, Brazil On This Page [Research Letter](https://wwwnc.cdc.gov/eid/article/32/10/26-0051_article) * * * [Suggested Citation](https://wwwnc.cdc.gov/eid/article/32/10/26-0051_article) Figures [Figure 1](https://wwwnc.cdc.gov/eid/article/32/10/26-0051-f1) * * * [Figure 2](https://wwwnc.cdc.gov/eid/article/32/10/26-0051-f2) Downloads [Appendix ](https://wwwnc.cdc.gov/eid/article/32/10/26-0051-app1.pdf) * * * [RIS [TXT - 2 KB] ](https://wwwnc.cdc.gov/eid/article/32/10/26-0051.ris) Article Metrics [Metric Details](https://wwwnc.cdc.gov/eid/article/32/10/26-0051_article) Related Articles [The Enduring Influence of Nancy J. Cox (1948–2026)](https://wwwnc.cdc.gov/eid/article/32/10/26-0830_article) * * * [HPAI Clade 2.3.4.4b Virus Infection in Alpacas](https://wwwnc.cdc.gov/eid/article/32/10/26-0491_article) * * * [Divergent HPAI H5N1 Clade 2.3.4.4b Virus, Brazil](https://wwwnc.cdc.gov/eid/article/32/10/26-0723_article) * * * [More articles on Influenza](https://wwwnc.cdc.gov/eid/spotlight/influenza) Alanis S. Melgarejo[![Comments to Author](https://wwwnc.cdc.gov/eid/content/images/icon/email.gif)](https://wwwnc.cdc.gov/eid/article/32/10/26-0051_article#comment) , Mauricio Tavares, Derek B. de Amorim, Sergio C. Estima, Andrine Paiva, Caio R. Soares-Oliveira, Liane A. Dias, Renan C. de Lima, Silvina Botta, Eduardo R. Secchi, Barbara A. Davila, Carlos de Oliveira, Larissa S. Heinzelmann, Martha T. Oliveira, Vitor L. Carvalho, Aline R. Souza, Salvatore Siciliano, Paula Baldassin, Greicy F. Ruenes, Paulo H. Ott, Luciana Sonne, Ana C. Franco, and Larissa R. Oliveira Author affiliation: Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil (A.S. Melgarejo, M. Tavares, D.B. de Amorim, M.T. Oliveira, L. Sonne, A.C. Franco); Núcleo de Educação e Monitoramento Ambiental, Rio Grande, Brazil (S. C. Estima, A. Paiva, C.R. Soares-Oliveira); Universidade Federal do Rio Grande, Rio Grande (L.A. Dias, R.C. de Lima, S. Botta, E.R. Secchi); Universidade do Vale do Rio dos Sinos, São Leopoldo, Brazil (B.A. Davila, C. de Oliveira, L.S. Heinzelmann); Associação de Pesquisa e Preservação de Ecossistemas Aquáticos, Caucaia, Brazil (V.L. Carvalho, A.R. Souza, L.R. Oliveira); Fundação Oswaldo Cruz, Escola Nacional de Saúde Pública, Rio de Janeiro, Brazil (S. Siciliano); Grupo de Estudos da Região dos Lagos, Rio de Janeiro (S. Siciliano, G.F. Ruenes); Instituto BW para a Conservação e Medicina da Fauna Marinha, Araruama, Brazil (P. Baldassin); Universidade Estadual do Rio Grande do Sul, Osório, Brazil (P.H. Ott); Grupo de Estudos de Mamíferos Aquáticos do Rio Grande do Sul, Porto Alegre, Brazil (P.H. Ott, L.R. Oliveira); Marine Vertebrate Evolution and Conservation Lab, Fortaleza, Brazil (L.R. Oliveira). [Suggested citation for this article](https://wwwnc.cdc.gov/eid/article/32/10/26-0051_article#suggestedcitation) ### Abstract We identified highly pathogenic avian influenza virus subtype H5 in stranded dolphins along the coastline of Brazil during 2023–2025. Infected animals included species classified as vulnerable or endangered. Our results highlight the need for ongoing surveillance of cetaceans susceptible to viral infections, which pose an additional threat to threatened species. Marine ecosystems in Brazil have high biodiversity and support numerous top predators, including marine mammals. Along the coast of Brazil, >46 cetacean species have been recorded, several of which are classified as threatened or near threatened ([_1_](https://wwwnc.cdc.gov/eid/article/32/10/26-0051_article#r1 "1")). Influenza A viruses (IAV) infect a wide range of hosts, including marine mammals ([_2_](https://wwwnc.cdc.gov/eid/article/32/10/26-0051_article#r2 "2")). The highly pathogenic avian influenza (HPAI) H5N1 virus is causing a widespread panzootic, including outbreaks with high mortality rates among birds and pinnipeds ([_3_](https://wwwnc.cdc.gov/eid/article/32/10/26-0051_article#r3 "3")). Reports of IAV in cetaceans remain rare and limited to a few species, and large-scale outbreaks have not been reported ([_4_](https://wwwnc.cdc.gov/eid/article/32/10/26-0051_article#r4 "4")). We screened swab samples from cetaceans stranded along the coast of Brazil during November 2023–August 2025 for IAV by using quantitative reverse transcription PCR (qRT-PCR). Figure 1 ![Temporal and spatial distribution of cetacean species collected along the coast of Brazil during a study of influenza A virus from November 2023–August 2025. A–D\) Sampling locations along the coast of Brazil. Insets show sampling locations in the states of Rio Grande do Sul \(B\), Rio de Janeiro \(C\) , and Ceará \(D\). Each dot represents an analyzed sample from the cetacean. E\) Temporal distribution of sampled cetaceans. Each point represents an individual animal; red points indicate detection of influenza A virus matrix gene RNA, and blue points indicate no detectable viral RNA.](https://wwwnc.cdc.gov/eid/images/26-0051-F1-tn.jpg) [Figure 1](https://wwwnc.cdc.gov/eid/article/32/10/26-0051-f1 "Figure 1"). Temporal and spatial distribution of cetacean species collected along the coast of Brazil during a study of influenza A virus from November 2023–August 2025. A–D) Sampling locations along the coast... During November 2023–August 2025, we recorded stranded marine mammals along the Brazil coastlines of Rio Grande do Sul (≈485 km), Rio de Janeiro (317 km), and Ceará (573 km) ([Figure 1](https://wwwnc.cdc.gov/eid/article/32/10/26-0051-f1), panels A–D). Moreover, we conducted systematic surveys along the beaches of Rio Grande do Sul and responded to stranding notifications across all coastal regions. For each animal, we recorded standardized data including date, location, species, sex, and decomposition stage ([_5_](https://wwwnc.cdc.gov/eid/article/32/10/26-0051_article#r5 "5")). Ethical approval for this study was granted by the Animal Ethics Committee of the Universidade do Vale do Rio dos Sinos (protocol no. PPECEUA 02.2025). We collected swab samples exclusively from carcasses in decomposition stages 2–4, which include the bloated stage, active decay, and advanced decay ([_5_](https://wwwnc.cdc.gov/eid/article/32/10/26-0051_article#r5 "5")). We collected and fixed tissue samples (brain, lungs, trachea, spleen, intestine and liver) from carcasses in earlier decomposition stages ([_2_](https://wwwnc.cdc.gov/eid/article/32/10/26-0051_article#r2 "2"),[_3_](https://wwwnc.cdc.gov/eid/article/32/10/26-0051_article#r3 "3")) in 10% buffered formalin and routinely processed the fixed tissues for histology. We extracted total nucleic acids by using the MagMAX CORE Nucleic Acid Purification Kit (Thermo Fisher Scientific, [External Link](https://www.thermofisher.com)) with the KingFisher Flex system (Thermo Fisher Scientific). We performed qRT-PCR amplification of the IAV matrix gene for IAV detection ([_6_](https://wwwnc.cdc.gov/eid/article/32/10/26-0051_article#r6 "6")), and we detected the H5N1 strain by using World Health Organization molecular protocols ([_7_](https://wwwnc.cdc.gov/eid/article/32/10/26-0051_article#r7 "7")). We set the fluorescence threshold at 0.09 and classified samples with cycle threshold (Ct) values <37 as positive. We evaluated the sensitivity of the IAV qRT-PCR by using RNA from MDCK cells infected with H1N1, cloned into a plasmid as a positive control. We assessed the sensitivity of the H5N1 qRT-PCR assay by using a pEz plasmid and performed 10-fold serial dilutions to determine the qRT-PCR limit of detection. Figure 2 ![Influenza A viral RNA detected by quantitative reverse transcription PCR in stranded cetaceans from Brazil, November 2023–August 2025. A\) Influenza A virus M gene RNA concentration \(copies/µL\) in positive animals by sample type. B\) H5 subtype RNA concentrations \(copies/µL\) in cetaceans positive for H5 influenza A virus by sample type. ID, identification; M, matrix.](https://wwwnc.cdc.gov/eid/images/26-0051-F2-tn.jpg) [Figure 2](https://wwwnc.cdc.gov/eid/article/32/10/26-0051-f2 "Figure 2"). Influenza A viral RNA detected by quantitative reverse transcription PCR in stranded cetaceans from Brazil, November 2023–August 2025. A) Influenza A virus M gene RNA concentration (copies/µL) in positive animals... We analyzed 45 stranded cetaceans, representing 13 species ([Figure 1](https://wwwnc.cdc.gov/eid/article/32/10/26-0051-f1), panel E; [Appendix](https://wwwnc.cdc.gov/eid/article/32/10/26-0051-app1.pdf) Table 1). We detected the IAV matrix gene RNA in 18 animals, including Franciscana dolphins (_Pontoporia blainvillei_), Lahille’s bottlenose dolphins (_Tursiops truncatus gephyreus_), rough-toothed dolphins (_Steno bredanensis_), Clymene dolphins (_Stenella clymene_), dwarf sperm whales (_Kogia sima_), and Fraser’s dolphins (_Lagenodelphis hosei_). Samples positive for IAV RNA were from multiple tissues, most frequently blowhole swab samples, followed by cerebral, oral, anal, intestinal, tracheal, and ocular tissue samples. Overall, viral RNA levels were low, and Ct values ranged from 28–37, corresponding to ≈1.3 × 105 –8.0 × 102 RNA copies/µL ([Figure 2](https://wwwnc.cdc.gov/eid/article/32/10/26-0051-f2), panel A), approaching the assay limit of detection (200–2,000 RNA copies/µL). We only detected the H5N1 strain in 2 samples, both with viral RNA levels near the assay limit of detection ([Figure 2](https://wwwnc.cdc.gov/eid/article/32/10/26-0051-f2), panel B; [Appendix](https://wwwnc.cdc.gov/eid/article/32/10/26-0051-app1.pdf) Table 2). Our histopathologic examination of the 6 samples positive for IAV (animals 11, 16, 17, 35, 37 and 39; [Appendix](https://wwwnc.cdc.gov/eid/article/32/10/26-0051-app1.pdf) Tables 1, 2) did not reveal lesions associated with influenza infection. We detected IAV in samples from cetaceans along the coastline of Brazil after large HPAI H5N1 outbreaks that caused high mortality rates in pinnipeds along the coastline of South American were reported in 2023, which suggests enduring viral circulation in the marine environment and interspecies transmission ([_3_](https://wwwnc.cdc.gov/eid/article/32/10/26-0051_article#r3 "3"),[_9_](https://wwwnc.cdc.gov/eid/article/32/10/26-0051_article#r9 "9")). Cetaceans with samples positive for IAV included the Franciscana dolphin, which is classified as vulnerable, and Lahille’s bottlenose dolphin, which is classified as endangered ([_8_](https://wwwnc.cdc.gov/eid/article/32/10/26-0051_article#r8 "8")). Our results underscore a new potential threat to species already at risk for extinction along the coast of Brazil, particularly for Franciscana and Lahille’s bottlenose dolphins, native to the southwestern Atlantic Ocean. Moreover, we detected the HPAI H5N1 strain in Franciscana and Clymene dolphins, highlighting the potential for viral dissemination in coastal and offshore waters. We observed high Ct values, corresponding with low viral RNA copy numbers. Those results likely reflect RNA degradation associated with postmortem autolysis and advanced carcass decomposition, which can reduce RNA integrity and limit viral detection ([_10_](https://wwwnc.cdc.gov/eid/article/32/10/26-0051_article#r10 "10")). Indeed, the likelihood of identifying lesions associated with influenza infection was likely reduced by the limited number of animals available for histopathologic evaluation because of the advanced stage of decomposition in most of the carcasses analyzed. Environmental contamination from seabirds and shorebirds cannot be excluded in stranded carcasses. However, we detected viral RNA in internal tissues, which indicates true infection rather than surface contamination. Our results underscore the importance of continued and systematic surveillance of marine mammals to understand pathogen dynamics at the wildlife–marine interface. Miss Melgarejo is a master’s researcher at the Federal University of Rio Grande do Sul, Brazil, working in molecular virology and wildlife disease surveillance. Her research focuses on the surveillance and monitoring of influenza viruses in wildlife, with emphasis on viral detection and public health relevance. [TopExternal Link](javascript:void\(0\)) ### Acknowledgments We are very grateful to the staff, students, and vo
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