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Pardo-Roa C, Nelson MI, Ariyama N, Aguayo C, Almonacid LI, Munoz G, Navarro C, Avila C, Ulloa M, Reyes R, Luppichini EF, Mathieu C, Vergara R, González Á, González CG, Araya H, Fernández J, Fasce R, Johow M, Medina RA, Neira V. Cross-species transmission and PB2 mammalian adaptations of highly pathogenic avian influenza A/H5N1 viruses in Chile. bioRxiv 2023:2023.06.30.547205. [PMID: 37786724 PMCID: PMC10541606 DOI: 10.1101/2023.06.30.547205] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
H5N1 highly pathogenic avian influenza viruses (HPAIV) emerged in wild birds in Chile in December 2022 and spilled over into poultry, marine mammals, and one human. Between December 9, 2022 - March 14, 2023, a coordinated government/academic response detected HPAIV by real-time RT-PCR in 8.5% (412/4735) of samples from 23 avian and 3 mammal orders. Whole-genome sequences obtained from 77 birds and 8 marine mammals revealed that all Chilean H5N1 viruses belong to lineage 2.3.4.4b and cluster monophyletically with viruses from Peru, indicating a single introduction from North America into Peru/Chile. Mammalian adaptations were identified in the PB2 segment: D701N in two sea lions, one human, and one shorebird, and Q591K in the human and one sea lion. Minor variant analysis revealed that D701N was present in 52.9 - 70.9% of sequence reads, indicating the presence of both genotypes within hosts. Further surveillance of spillover events is warranted to assess the emergence and potential onward transmission of mammalian adapted H5N1 HPAIV in South America.
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Affiliation(s)
- Catalina Pardo-Roa
- Department of Child and Adolescent Health, School of Nursing, Pontificia Universidad Católica de Chile, Santiago, Chile
- Department of Pediatric Infectious Diseases and Immunology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Martha I Nelson
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Naomi Ariyama
- Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile. 11735 Santa Rosa, La Pintana, Santiago, Chile
| | | | - Leonardo I Almonacid
- Molecular Bioinformatics Laboratory, Department of Molecular Genetics and Microbiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | | | - Carlos Navarro
- Servicio Nacional de Pesca y Acuicultura, SERNAPESCA, Chile
| | | | - Mauricio Ulloa
- Servicio Nacional de Pesca y Acuicultura, SERNAPESCA, Chile
- Veterinary Histology and Pathology, Institute of Animal Health and Food Safety, Veterinary School, University of Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - Rodolfo Reyes
- Veterinary Histology and Pathology, Institute of Animal Health and Food Safety, Veterinary School, University of Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - Eugenia Fuentes Luppichini
- Department of Pediatric Infectious Diseases and Immunology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | | | | | | | | | - Hugo Araya
- Servicio Agrícola y Ganadero, SAG, Chile
| | - Jorge Fernández
- Instituto de Salud Pública, ISP, Ministerio de Salud, Santiago, Chile
| | - Rodrigo Fasce
- Instituto de Salud Pública, ISP, Ministerio de Salud, Santiago, Chile
| | | | - Rafael A Medina
- Department of Pediatric Infectious Diseases and Immunology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- Department of Pathology and Laboratory Medicine, School of Medicine, Emory Vaccine Center, Emory University, Atlanta, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Victor Neira
- Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile. 11735 Santa Rosa, La Pintana, Santiago, Chile
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Heritage S, Seiffert ER. Total evidence time-scaled phylogenetic and biogeographic models for the evolution of sea cows (Sirenia, Afrotheria). PeerJ 2022; 10:e13886. [PMID: 36042864 PMCID: PMC9420408 DOI: 10.7717/peerj.13886] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 07/21/2022] [Indexed: 01/18/2023] Open
Abstract
Molecular phylogenetic studies that have included sirenians from the genera Trichechus, Dugong, and Hydrodamalis have resolved their interrelationships but have yielded divergence age estimates that are problematically discordant. The ages of these lineage splits have profound implications for how to interpret the sirenian fossil record-including clade membership, biogeographic patterns, and correlations with Earth history events. In an effort to address these issues, here we present a total evidence phylogenetic analysis of Sirenia that includes living and fossil species and applies Bayesian tip-dating methods to estimate their interrelationships and divergence times. In addition to extant sirenians, our dataset includes 56 fossil species from 106 dated localities and numerous afrotherian outgroup taxa. Genetic, morphological, temporal, and biogeographic data are assessed simultaneously to bring all available evidence to bear on sirenian phylogeny. The resulting time-tree is then used for Bayesian geocoordinates reconstruction analysis, which models ancestral geographic areas at splits throughout the phylogeny, thereby allowing us to infer the direction and timing of dispersals. Our results suggest that Pan-Sirenia arose in North Africa during the latest Paleocene and that the Eocene evolution of stem sirenians was primarily situated in the Tethyan realm. In the late Eocene, some lineages moved into more northern European latitudes, an area that became the source region for a key trans-Atlantic dispersal towards the Caribbean and northern-adjacent west Atlantic. This event led to the phylogenetic and biogeographic founding of crown Sirenia with the Dugongidae-Trichechidae split occurring at the Eocene-Oligocene boundary (~33.9 Ma), temporally coincident with the onset of dropping global sea levels and temperatures. This region became the nexus of sirenian diversification and supported taxonomically-rich dugongid communities until the earliest Pliocene. The Dugonginae-Hydrodamalinae split occurred near Florida during the early Miocene (~21.2 Ma) and was followed by a west-bound dispersal that gave rise to the Pacific hydrodamalines. The late middle Miocene (~12.2 Ma) split of Dugong from all other dugongines also occurred near Florida and our analyses suggest that the Indo-Pacific distribution of modern dugongs is the result of a trans-Pacific dispersal. From at least the early Miocene, trichechid evolution was based entirely in South America, presumably within the Pebas Wetlands System. We infer that the eventual establishment of Amazon drainage into the South Atlantic allowed the dispersal of Trichechus out of South America no earlier than the mid-Pliocene. Our analyses provide a new temporal and biogeographic framework for understanding major events in sirenian evolution and their possible relationships to oceanographic and climatic changes. These hypotheses can be further tested with the recovery and integration of new fossil evidence.
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Affiliation(s)
- Steven Heritage
- Duke Lemur Center Museum of Natural History, Duke University, Durham, NC, USA
| | - Erik R. Seiffert
- Duke Lemur Center Museum of Natural History, Duke University, Durham, NC, USA,Department of Integrative Anatomical Sciences, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA,Department of Mammalogy, Natural History Museum of Los Angeles County, Los Angeles, CA, USA
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