Detection and phylogenetic analysis of highly pathogenic A/H5N1 avian influenza clade 2.3.4.4b virus in Chile, 2022

Jimenez‐Bluhm, Pedro; Siegers, Jurre Y.; Tan, Shaoyuan; Sharp, Bridgett; Freiden, Pamela; Johow, Magdalena; Orozco, Katherinne; Ruíz, Soledad; Baumberger, Cecilia; Galdames, Pablo; Gonzalez, Maria Antonieta; Rojas, Camila; Karlsson, Erik A.; Hamilton‐West, Christopher; Schultz‐Cherry, Stacey

doi:10.1080/22221751.2023.2220569

Cited by 19 publications

(8 citation statements)

References 8 publications

(10 reference statements)

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“…This wide host range has facilitated the transmission of the lineage across a large geographic area, including from Europe to North America 9, 10 , where it has since rapidly expanded its range southward into South America via migratory avian species. Incursion into South American countries, starting in November of 2022, represented the first recorded instances of GsGd-lineage H5 HPAIV in the region 11, 12, 13 . Mass mortality events in the region have been particularly severe and reported across several different bird species in addition to marine mammals 3, 11, 14, 15 , highlighting the extensive ecological impact of HPAIV and the ongoing threat it presents to naïve hosts.…”

Section: Introductionmentioning

confidence: 99%

Detection and spread of high pathogenicity avian influenza virus H5N1 in the Antarctic Region

Bennison,

Byrne,

Reid

et al. 2023

Preprint

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The Antarctic is the only major geographical region in which high pathogenicity avian influenza virus (HPAIV) has never previously been detected. The current panzootic of H5N1 HPAIV has decimated wild bird populations across Europe, North America and South America. Here we report on the emergence of clade 2.3.4.4b H5N1 HPAIV in the Antarctic and sub-Antarctic regions of South Georgia and the Falkland Islands respectively. We initially detected H5N1 HPAIV in samples collected from brown skuas at Bird Island, South Georgia on 8thOctober 2023. Since this detection, increased mortalities were observed in brown skuas, kelp gulls, elephant seals and fur seal at multiple sites across South Georgia. We confirmed H5N1 HPAIV in multiple brown skuas and kelp gulls across four different sampling locations in South Georgia. Simultaneously, we also confirmed H5N1 HPAIV in a southern fulmar in the Falkland Islands. Genetic assessment of the virus indicates spread from South America, likely through movement of migratory birds. Here we describe the emergence, species impact and genetic composition of the virus and propose both introductory routes and potential long-term impact on avian and mammalian species across the Antarctic region.

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Section: Introductionmentioning

confidence: 99%

Detection and spread of high pathogenicity avian influenza virus H5N1 in the Antarctic Region

Bennison,

Byrne,

Reid

et al. 2023

Preprint

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“…In the present analysis, PB2-591K and PB2-701N were restricted to the clade 5 comprised of three sea lions collected in March 2023 from Chile and Peru, a human case from Chile, and Uruguayan sea lions, fur seals, and terns (Figure 1A and https://microreact.org/project/nSinj3LbMRme4gqussrTaU-influenzasea-lionurug). The phylogenetic similarity, the 591K/701N residues, and the ancestral state reconstruction suggest that Uruguayan viruses originated from similar strains circulating in pinnipeds from the Chilean and Peruvian coasts (45,46). The expansion of this successful lineage might be related to the combined residues that enhance the geographic spreading ability of the virus through mammalian hosts.…”

Section: Discussionmentioning

confidence: 92%

Highly pathogenic avian influenza H5N1 virus infections in pinnipeds and seabirds in Uruguay: a paradigm shift to virus transmission in South America

Tomás,

Marandino,

Panzera

et al. 2023

Preprint

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The highly pathogenic avian influenza viruses of the clade 2.3.4.4b have caused unprecedented deaths in South American wild birds, poultry, and marine mammals. In September 2023, pinnipeds and seabirds appeared dead on the Uruguayan Atlantic coast. Sixteen influenza virus strains were characterized by real-time reverse transcription PCR and genome sequencing in samples from sea lions (Otaria flavescens), fur seals (Arctocephalus australis), and terns (Sterna hirundinacea). Phylogenetic and ancestral reconstruction analysis showed that these strains have pinnipeds as the most likely ancestral host, representing a recent introduction of the clade 2.3.4.4b in Uruguay. The Uruguayan and closely related strains from Peru (sea lions) and Chile (sea lions and a human case) carry mammalian adaptative residues 591K and 701N in the viral polymerase basic protein 2 (PB2). Our findings suggest that the clade 2.3.4.4b strains in South America may have spread from mammals to mammals and seabirds, revealing a new transmission route.

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“…Genetic sequencing of Chilean H5N1 samples indicates that they all cluster together within the clade 2.3.4.4b ( 20 , 41 , 42 ), suggesting that the outbreaks in the country all belong to the same viral lineage (with potentially minor variations) that is globally widespread. This virus arrived in Chile from neighboring Peru, and previously from North America ( 2 , 36 ).…”

Section: Discussionmentioning

confidence: 99%

Spatio-temporal dynamics and drivers of highly pathogenic avian influenza H5N1 in Chile

Azat,

Alvarado-Rybak,

Aguilera

et al. 2024

Front. Vet. Sci.

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IntroductionHighly pathogenic avian influenza A H5N1 clade 2.3.4.4b (hereafter H5N1) is causing vast impacts on biodiversity and poultry around the globe. In Chile, lethal H5N1 cases have been reported in a wide range of wild bird species, marine mammals, backyard and industrial poultry, and humans. This study describes the spatio-temporal patterns of the current epizootic of H5N1 in Chile and test drivers that could be associated with outbreak occurrence.MethodsWe used H5N1 cases reported by the Chilean National Animal Health Authority from 5 December 2022 to 5 April 2023. These included wild bird cases confirmed through an avian influenza-specific real-time reverse transcription PCR assay (RT-qPCR), obtained from passive and active surveillance. Data were analyzed to detect the presence of H5N1 clusters under space–time permutation probability modeling, the association of H5N1 with distance and days since the first outbreak through linear regression, and the correlation of H5N1 presence with a number of ecological and anthropogenic variables using general linear modeling.ResultsFrom 445 H5N1 identified outbreaks involving 613 individual cases in wild birds, a consistent wave-like spread of H5N1 from north to south was identified, which may help predict hotspots of outbreak risk. For instance, seven statistically significant clusters were identified in central and northern Chile, where poultry production and wildlife mortality are concentrated. The presence of outbreaks was correlated with landscape-scale variables, notably temperature range, bird richness, and human footprint.DiscussionIn less than a year, H5N1 has been associated with the unusual mortality of >100,000 individuals of wild animals in Chile, mainly coastal birds and marine mammals. It is urgent that scientists, the poultry sector, local communities, and national health authorities co-design and implement science-based measures from a One Health perspective to avoid further H5N1 spillover from wildlife to domestic animals and humans, including rapid removal and proper disposal of wild dead animals and the closure of public areas (e.g., beaches) reporting high wildlife mortalities.

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Detection and phylogenetic analysis of highly pathogenic A/H5N1 avian influenza clade 2.3.4.4b virus in Chile, 2022

Cited by 19 publications

References 8 publications

Detection and spread of high pathogenicity avian influenza virus H5N1 in the Antarctic Region

Detection and spread of high pathogenicity avian influenza virus H5N1 in the Antarctic Region

Highly pathogenic avian influenza H5N1 virus infections in pinnipeds and seabirds in Uruguay: a paradigm shift to virus transmission in South America

Spatio-temporal dynamics and drivers of highly pathogenic avian influenza H5N1 in Chile

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