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Thank you for visiting nature. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser or turn off compatibility mode in Internet Explorer. In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript. Peruvian viruses belong to lineage 2. 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. The recent emergence of highly pathogenic avian influenza HPAI H5N1 viruses in mammals and birds in the Americas 1 , 2 presents a severe threat to wild and endangered species, to poultry production 3 , 4 , and to public health when the virus spills over into humans 3 , 5. The H5N1 clade 2. In October , an apparent mink-to-mink transmission of clade 2. In November , Peruvian pelicans Pelecanus thagus along the coast and in offshore islands began experiencing a mass die-off 10 , This was followed by several spillover events into other domestic and wild birds, including zoo animals and wild raptors 4 , By the beginning of , the Peru outbreak had spread to marine mammals, particularly affecting the South American sea lion Otaria flavescens , which also began to experience a mass die-off The Pacific coast of Peru hosts a rich biodiversity of marine mammals and seabirds In response to a multi-species outbreak starting in November , we collected 69 swabs of external orifices and internal organ tissues from seven species of marine mammals and seabirds common dolphin Delphinus delphis , South American sea lion Otaria flavescens , sanderling Calidris alba , Peruvian pelican Pelecanus thagus , Guanay cormorant Phalacrocorax bougainvillii , Peruvian gull Larus belcheri and Humboldt penguin Spheniscus humboldti in regions representing the northern Piura , central Lima and southern Arequipa and Tacna coast of Peru Supplementary Table 1 , Fig. A Map of Peru showing collection sites representative of the northern, central and southern regions. Mass die-offs of both birds and mammals occurred along the entire coast of Peru, but map only shows positive locations of animals samples in this study. B Photographic record of animals sampled, including common dolphin, South American sea lion, sanderling, Guanay cormorant, Peruvian booby and Peruvian pelican. To date, we have tested 69 samples from a total of 28 individuals by RT-qPCR, confirming 11 individuals 1 dolphin, 4 sea lions and 6 seabirds , plus 1 pooled sample from 5 sea lions, as positive for influenza A. All samples were also tested for coronaviruses, alphaviruses, bunyaviruses and flaviviruses using pan-PCR assays, and all samples were negative for these tests. Influenza A positives were subjected to NGS for subtyping and to generate full genomes for phylogenetic and mutational analysis. It was not possible to type the remaining positive sea lion, as the sample contained very low viral loads or extensive signs of nucleic acid degradation Supplementary Table 1 , likely associated with extensively decomposed tissues in deceased animals Fig. Of the 11 individuals that yielded quality sequence data, we generated complete sequences for most genomic regions in most samples Table 1 and Supplementary Table 1. Most of the H5N1 viruses observed since the summer of in the Americas are reassortants containing various combinations of segments from the Eurasian and American lineages Fig. The Eurasian lineage H5N1 virus that originally invaded North America in has reassorted multiple times with the endemic American lineage since arriving in North America, as evidenced by multiple reassortant clades positioned within the American lineage Fig. A detailed tree is provided for the PB2 segment, including bootstrap values, labels, and a box around the R6 reassortant clade that is presented in greater detail in Fig. Smaller trees are provided for the other 7 segments. R6 reassortants were first detected in North American poultry in March e. The population genetics of H5N1 in the Americas underwent a shift during , as reassortants displaced the original non-reassortant Eurasian H5N1 virus, which has not been detected in the Western hemisphere since June Viruses isolated from poultry in Colombia and Ecuador 21 in November e. The H5N1 viruses isolated from pelicans in Venezuela in November have a different reassortant genotype R7 that is primarily found in the eastern US, including in Florida, and represents a fifth independent H5N1introduction from North to South America during the fall of Fig. Branches shaded by location. South American virus names shaded by country or Peruvian region. Posterior probabilities provided for key nodes. Diamonds indicate the 3 viruses with PB2:DN mutations. B Discrete phylogeographic transition history of R6 viruses at four time points. Red lines with arrows indicate interhemispheric transitions from North America to South America. C Proportion of H5N1 viruses sequenced in the Americas between — that belong to different genotypes Fig. H5N1 viruses from Peru and Chile with the R6 genotype form a single clade, representing the only phylogenetic evidence of H5N1 spread between two South American countries to date Fig. Whether the introduction from North America first arrived in Peru or Chile is difficult to infer from the tree, since the posterior probabilities are similar for both locations at this node 0. Within the Peru-Chile clade, the H5N1 viruses collected from northern Peru Piura region and central Peru Lima region cluster together, consistent with transmission in Peru between avian and mammalian species pelican, cormorant, sandpiper, dolphin and sea lion. Both of these viruses have the PB2 DN mutation that is associated with enhanced mammalian transmission in mammals see below , however, these Arequipa viruses were collected in sea lions a month apart February 7, vs. March 6, and they do not cluster together on the same phylogenetic trees. We also performed a detailed SNP and mutational analysis to identify amino acid changes potentially linked to increased virulence, transmission, or mammalian host adaptation, and to assess if we could identify specific differences between host species mammals vs. Within this group, 15 mutations are present in all birds and mammals from Peru 3 cases or present in single individuals from Peru 12 cases. The remaining 8 sites are of particularly high interest because they repeat two or more times. Particularly noteworthy is the PB2 DN mutation, which appears in sea lion samples collected during the late phases of the outbreak in Peru in February and March, and subsequently appears in the virus sequenced from the human case reported in Chile This mutation, along with two other PB2 mutations EK, KR not present in our data, have been specifically linked to mammalian host adaptation and enhanced transmission previously 24 , In addition, despite not finding PB2 EK and KR, we have identified two additional mutations PA MI and NS1 D26K in mammalian samples from Peru that are also present in the human case from Chile 22 , raising the possibility that the viruses are changing in a host-specific manner 24 , 25 that supports mammalian host adaptation. The sea lion viruses contain additional unique mutations, such as PB1 LM and SA, that may warrant further observation, as these are also showing up in Chilean genomes, mostly from birds. Sampling of additional individuals will be needed to fully assess the significance of these uncharacterised variable sites, especially in terms of their pathogenicity to mammals. However, it is clear that most are restricted to sequences reported in Latin America Fig. The arrival of HPAI in regions with less experience managing highly pathogenic viruses in wildlife and poultry is highly concerning. These events should prompt immediate cross-sectoral capacity strengthening and coordinated response activities throughout the region. Here, we rapidly established new surveillance partnerships between government and academia to respond to mass mortality events involving Peruvian pelicans and South American sea lions. We suspect that direct HPAI transmission between sea lions could be occurring, rather than independent spillovers into sea lions from avian sources, but additional sequence data and analysis will be required to further characterise mammal-to-mammal transmission. Within this subset we are particularly concerned by the presence of PB2 DN in 2 sea lion samples, and in a human case reported in Chile 22 , as this mutation has been specifically linked to mammalian host adaptation and enhanced transmission 24 , Two other mutations of concern PB2 EK and KR , linked to mammalian host adaptation and enhanced transmission 24 , 25 , as well as the PB2 TA mutation observed in the mink outbreak in Spain 9 , were not present in our samples. Our analysis has focused on recent non-synonymous mutations, however, other mutations, including synonymous substitutions should be further examined, as these can change viral RNA structure and splicing, which in turn can potentially impact viral pathogenesis and fitness. Our phylogenetic analysis supports a single introduction of 2. There are multiple possible transmission routes for local transmission among species that involve direct contact or indirect environmental transmission. For one, seabirds share feeding spaces with both sea lions and dolphins, providing ample opportunities for direct contact between animals at sea 27 , 28 , 29 , Direct contact also occurs on islands, islets, and guano headlands, especially in protected areas where large and dense breeding colonies of sea lions and seabirds cohabitate, and where indirect transmission is also possible on land and via guano runoff into the surrounding waters 27 , 28 , 30 , Another scenario for transmission involves carnivory and scavenging of infected animal carcasses by marine and terrestrial carnivores, as well as by raptors, gulls, and other scavenger birds 2 , 32 , Fishing docks, where fishermen often dispose of waste by dumping it at sea, attract seabirds, sea lions, marine otters and others that come to feed. Many docks along the Peruvian coast also function as tourist attractions, where seabirds and sea lions are purposely fed to create photo opportunities, building large congregations of wild animals that also increase opportunities for contact with humans. Finally, the Peruvian desert coast is home to large poultry operations with millions of chickens adjacent to infected wild and migratory birds, placing this production industry at risk and furthering the potential for animal and human contact with circulating HPAI lineages in the region. There are outstanding questions about which migratory bird species are involved in the long-distance dissemination of HPAI from North to South America, possibly by way of Central America. We detected clade 2. However, Calidris spp. Given the unlikelihood of a successful long-distance migration for a clinically infected bird, we suspect the sanderling was infected locally. Our phylogenetic analysis supports multiple independent introductions of HPAI from North America into South American countries for which sequence data was available at the time of this study, including Peru, Ecuador, and Venezuela. For this reason, and given the uncharacterised variable sites reported here, there is an urgent need to establish pipelines for efficient real-time genomic sequencing of HPAI to track viral evolution and spread across Peru and other countries in South America, as well as funding to support characterisation of possible new mutations. The Peruvian coast is one of the few places in the world where scavenger condors feed on dead marine animals 41 , 42 , putting them at risk of infection if they consume contaminated carcasses. The recent infection and death of several critically endangered California condors Gymnogyps californianus in the United States highlights these risks Similarly, the marine otter 40 is an aquatic mustelid that inhabits the same rocky shores of Peru and Chile inhabited by sea lions. Fortunately, marine otters do not live in large groups 45 , which might limit intraspecies contagion. However, direct mammal to mammal transmission has been suggested as a possible explanation for an outbreak in a Spanish farm among breeding mink, another mustelid, though evidence of mammal-to-mammal transmission was inconclusive 9. Peruvian pelicans have also suffered massive die-offs at the beginning of the outbreak in Peru, later followed by Guanay cormorants and Peruvian boobies. For these reasons, efforts are urgently needed to assess the impact of ongoing mass mortalities on Peruvian marine sea birds and mammals. Finally, an even larger concern is the possibility of spillover into human populations, as has been already documented 22 , 47 , 48 , followed by massive human-to-human transmission. In Peru, the outbreak occurred along the Pacific coast and during the austral summer, when many people go to the beach. It is not uncommon for beachgoers and their pets to interact with sick and disoriented animals without any knowledge of the risks, or for free-roaming dogs in rural and semi-rural coastal areas to encounter sick or dead animals as they scavenge for food. This has led government authorities to relocate live animals that show up in places where they do not belong, or to euthanize sick individuals and appropriately dispose of their carcasses. However, both the pelican and sea lion die-offs have been so massive that it has been very challenging for the authorities to respond in a timely manner. Heightened public awareness campaigns are needed, including educating the public to avoid contact with infected animals Animal workers, particularly municipal personnel tasked with cleaning duties, need additional training in the proper use of personal protective equipment, and on management and disposal of infected carcasses 51 , Subsequent serologic studies of people in close contact with infected animals, especially in outbreak settings, can also inform on the extent of zoonotic spillover and direct future surveillance at important animal-human interfaces. This approach promotes opportunities to strengthen ties among governmental institutions at all levels, expert researchers within academia, and the larger scientific community operationalizing a One Health approach, which are essential for epidemic and pandemic preparedness. Some severely clinically ill animals were humanely euthanized Samples and tissues were collected into cryovials containing 0. Samples positive for influenza A by RT-qPCR were subtyped using a combination of directed amplification with universal primers targeting conserved genomic regions 55 , 56 , 57 , followed by next-generation sequencing NGS. All primer sequences used are provided in Supplementary Table 3. Filtered reads were then re-assembled de-novo using SPAdes 59 to generate complete genomes whenever possible, and to further confirm subtyping by BLAST. Maximum likelihood ML trees were prepared with FastTree 61 incorporating a general time-reversible GTR model of nucleotide substitution with gamma-distributed rate variation among sites. To place the Peruvian viruses in a global context, we downloaded on February 14, an additional background dataset of influenza A virus genomes that included all sequences from avian and mammalian H5 viruses submitted to GISAID since January 1, To keep the dataset up to date, additional South American sequences were added on April 21, Partial sequences were excluded. Phylogenetic relationships were inferred for each of the eight genome segments using the ML methods available in IQ-Tree 2 63 with a GTR model and a gamma distribution as described above. To assess the robustness of each node, a bootstrap resampling process was performed with replicates. Finally, mutation analysis was done using the CDC H5N1 genetic changes inventory for SNP analysis and various other previously published mutations of concern 23 , To examine the evolution of the clade of reassortant R6 viruses in Peru and other locations in greater detail, we performed a time-scaled Bayesian analysis on a dataset of 98 PB2 sequences from the R6 clade. The dataset included all South American sequences, all mammalian sequences, and a representative subsample of North American avian sequences, including one representative virus from each cluster of viruses from the same US or Canadian state that were sampled from the same avian species on the same date. Each tip was assigned a location state and we performed a phylogeographic discrete trait analysis 66 to examine the routes of viral spatial dissemination between North America and South America, within South America, and within Peru. The MCMC chain was run separately four times for each dataset using the BEAGLE 3 67 library to improve computational performance, until all parameters reached convergence, as assessed visually using Tracer v. Further information on research design is available in the Nature Portfolio Reporting Summary linked to this article. We also provide GenBank accession numbers with hyperlinks for all the sequences generated as part of this study in Supplementary Table 4. Ramey, A. Highly pathogenic avian influenza is an emerging disease threat to wild birds in North America. Wildlife Manag. Google Scholar. Vreman, S. Zoonotic mutation of highly pathogenic avian influenza H5N1 virus identified in the brain of multiple wild carnivore species. Pathogens 12 , Alders, R. Impact of avian influenza on village poultry production globally. Ecohealth 11 , 63—72 PubMed Google Scholar. Ministerio de Salud del Peru, M. Kalthoff, D. Highly pathogenic avian influenza as a zoonotic agent. Caliendo, V. Transatlantic spread of highly pathogenic avian influenza H5N1 by wild birds from Europe to North America in Elsmo, E. Pathology of natural infection with highly pathogenic avian influenza virus H5N1 clade 2. Alkie, T. Virus Evol. Miloslavich, P. Marine biodiversity in the Atlantic and Pacific coasts of South America: knowledge and gaps. PLoS One 6 , e Schulenberg, T. Nelson, M. The genetic diversity of influenza A viruses in wild birds in Peru. PLoS One 11 , e Rimondi, A. Evidence of a fixed internal gene constellation in influenza A viruses isolated from wild birds in Argentina — Microbes Infect. Wild birds in Chile Harbor diverse avian influenza A viruses. Lee, D. Highly pathogenic Avian Influenza Viruses and generation of novel reassortants, United States, — Harfoot, R. H5 influenza, a global update. Bruno, A. Phylogenetic analysis reveals that the H5N1 avian influenza A outbreak in poultry in Ecuador in November is associated with the highly pathogenic clade 2. World Health Organization, W. Centers for Disease Control Prevention, C. Suttie, A. Inventory of molecular markers affecting biological characteristics of avian influenza A viruses. Virus Genes 55 , — Bordes, L. Highly pathogenic avian influenza H5N1 virus infections in wild red foxes Vulpes vulpes show neurotropism and adaptive virus mutations. Spectrum 11 , e— Bevins, S. Intercontinental movement of highly pathogenic avian influenza A H5N1 Clade 2. Crespo, E. Schramm 93— Springer International Publishing, Reperant, L. Avian influenza viruses in mammals. Thiebault, A. How to capture fish in a school? Effect of successive predator attacks on seabird feeding success. Weimerskirch, H. Foraging in Guanay cormorant and Peruvian booby, the major guano-producing seabirds in the Humboldt Current System. Marine Ecol. ADS Google Scholar. Martin, G. Environmental persistence of influenza H5N1 is driven by temperature and salinity: insights from a bayesian meta-analysis. US Department of Agriculture, A. Highly pathogenic avian influenza virus H5N1 infection in red foxes fed infected bird carcasses. Kurmi, B. Survivability of highly pathogenic avian influenza H5N1 virus in poultry faeces at different temperatures. Indian J. Kandun, I. Chicken faeces garden fertilizer: possible source of human avian influenza H5N1 infection. Zoonoses Public Health 57 , — Hall, J. Experimental challenge and pathology of highly pathogenic avian influenza virus H5N1 in dunlin Calidris alpina , an intercontinental migrant shorebird species. Influenza Other Respir. Viruses 5 , — Highly pathogenic avian influenza virus H5N1 infection in a long-distance migrant shorebird under migratory and non-migratory states. PLOS One 6 , e International Union for Conservation of Nature, I. Wallace, M. Competitive interactions within and between species in a guild of avian scavengers. The Auk , — Stucchi, M. National Parks Service, N. Servicio Nacional de Pesca y Acuicultura, S. Valqui, J. The marine otter Lontra felina Molina, : A review of its present status and implications for future conservation. Article Google Scholar. Lai, S. Global epidemiology of avian influenza A H5N1 virus infection in humans, — a systematic review of individual case data. Lancet Infect. Assessment of risk associated with recent influenza A H5N1 clade 2. Geraci, J. Marine mammals ashore: a field guide for strandings National Aquarium in Baltimore, Miller, L. Carcass management guidelines: effective disposal of animal carcasses and contaminated materials on small to medium-sized farms , Vol. Underwood, W. AV MA guidelines for the euthanasia of animals: edition. Shu, B. Multiplex real-time reverse transcription PCR for influenza A virus, influenza B virus, and severe acute respiratory syndrome coronavirus 2. Hoffmann, E. Universal primer set for the full-length amplification of all influenza A viruses. Zhou, B. Single-reaction genomic amplification accelerates sequencing and vaccine production for classical and swine origin human influenza A viruses. Hurtado, R. Molecular characterization of subtype H11N9 avian influenza virus isolated from shorebirds in Brazil. PLoS One 10 , e Bushnell, B. Bankevich, A. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. Katoh, K. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Price, M. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Smith, G. Nomenclature updates resulting from the evolution of avian influenza A H5 virus clades 2. Viruses 9 , — Nguyen, L. Suchard, M. Gill, M. Improving Bayesian population dynamics inference: a coalescent-based model for multiple loci. Lemey, P. Bayesian phylogeography finds its roots. PLoS Comput. Ayres, D. BEAGLE 3: improved performance, scaling, and usability for a high-performance computing library for statistical phylogenetics. Rambaut, A. Posterior summarization in bayesian phylogenetics using tracer 1. Nahata, K. Download references. The funders had no role in study design, sample collection, data collection and analysis, decision to publish, or preparation of the article. You can also search for this author in PubMed Google Scholar. Study Design: M. Field work and sample collection: J. Lab work and sample processing: A. Bioinformatics processing and data analysis: M. Manuscript preparation: M. Manuscript editing: all authors. Review and approval of final manuscript: all authors. Correspondence to Mariana Leguia. Nature Communications thanks the anonymous reviewer s for their contribution to the peer review of this work. A peer review file is available. Reprints and permissions. Leguia, M. Highly pathogenic avian influenza A H5N1 in marine mammals and seabirds in Peru. Nat Commun 14 , Download citation. Received : 08 March Accepted : 23 August Published : 07 September Anyone you share the following link with will be able to read this content:. Sorry, a shareable link is not currently available for this article. Provided by the Springer Nature SharedIt content-sharing initiative. Current Infectious Disease Reports Sign up for the Nature Briefing: Translational Research newsletter — top stories in biotechnology, drug discovery and pharma. Skip to main content Thank you for visiting nature. Download PDF. Subjects Genomics Influenza virus Public health Viral infection. The global H5N1 influenza panzootic in mammals Article 24 September Highly pathogenic avian influenza virus H5N1 clade 2. Introduction The recent emergence of highly pathogenic avian influenza HPAI H5N1 viruses in mammals and birds in the Americas 1 , 2 presents a severe threat to wild and endangered species, to poultry production 3 , 4 , and to public health when the virus spills over into humans 3 , 5. Results Detection of HPAI positive samples in mammals and seabirds in Peru In response to a multi-species outbreak starting in November , we collected 69 swabs of external orifices and internal organ tissues from seven species of marine mammals and seabirds common dolphin Delphinus delphis , South American sea lion Otaria flavescens , sanderling Calidris alba , Peruvian pelican Pelecanus thagus , Guanay cormorant Phalacrocorax bougainvillii , Peruvian gull Larus belcheri and Humboldt penguin Spheniscus humboldti in regions representing the northern Piura , central Lima and southern Arequipa and Tacna coast of Peru Supplementary Table 1 , Fig. Full size image. Influenza A subtyping Samples positive for influenza A by RT-qPCR were subtyped using a combination of directed amplification with universal primers targeting conserved genomic regions 55 , 56 , 57 , followed by next-generation sequencing NGS. Bayesian analysis To examine the evolution of the clade of reassortant R6 viruses in Peru and other locations in greater detail, we performed a time-scaled Bayesian analysis on a dataset of 98 PB2 sequences from the R6 clade. Reporting summary Further information on research design is available in the Nature Portfolio Reporting Summary linked to this article. References Ramey, A. Google Scholar Vreman, S. Google Scholar Bevins, S. Google Scholar Stucchi, M. Nelson Authors Mariana Leguia View author publications. View author publications. Ethics declarations Competing interests The authors declare no competing interests. Peer review Peer review information Nature Communications thanks the anonymous reviewer s for their contribution to the peer review of this work. Supplementary information. Supplementary Information. Peer Review File. Reporting Summary. About this article. Cite this article Leguia, M. Copy to clipboard. Webby Communications Biology Mortality in sea lions is associated with the introduction of the H5N1 clade 2. Search Search articles by subject, keyword or author. Show results from All journals This journal. Advanced search. Close banner Close. Email address Sign up. Get what matters in translational research, free to your inbox weekly. Sign up for Nature Briefing: Translational Research.

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