Temporal dynamics and the influence of environmental variables on the prevalence of avian influenza virus in main wetlands in central Chile

Ruíz, Soledad; Jimenez‐Bluhm, Pedro; Pillo, Francisca Di; Baumberger, Cecilia; Galdames, Pablo; Marambio, Victor; Salazar, Carla; Mattar, Cristián; Sanhueza, Juan; Schultz‐Cherry, Stacey; Hamilton‐West, Christopher

doi:10.1111/tbed.13831

Cited by 11 publications

(28 citation statements)

References 48 publications

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“…), show a positive relationship with H5N1 outbreak probabilities in wild birds in Europe. However, a relationship between bird richness and prevalence of avian influenza was not found previously in wetlands of central Chile (Ruiz et al 2021). Studies have shown that the black-headed gull (L. ridibundus) is highly susceptible to avian influenza in Europe, likely contributing to local transmission rather than longdistance spread due to their high mortality to H5N1 (Ramis et al 2014).…”

Section: Discussionmentioning

confidence: 85%

Spatio-temporal dynamics and drivers of Highly Pathogenic Avian Influenza H5N1 in Chile

Soto‐Azat

Alvarado‐Rybak²,

Aguilera

et al. 2023

Preprint

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Highly 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 it was first reported on December 7th, 2022, in a pelican (Pelecanus thagus) found dead in the northern city of Arica. In the following months, lethal H5N1 cases were reported in a wide range of wild bird species, marine mammals, backyard and industrial poultry, and in a human. Despite its high impact and spread, it is not well-known what environmental factors are associated with outbreaks. This study describes the spatio-temporal patterns of the current epizootic of H5N1 in Chile and test ecological and anthropogenic drivers that could be associated with outbreak occurrence. We used H5N1 cases reported by the Chilean national animal health authority to the World Animal Health Information System (WAHIS) from December 9th, 2022, to March 3rd, 2023. These included bird cases confirmed through avian influenza specific real-time PCR assay (qPCR), obtained from passive and active surveillance. Data was analyzed to detect the presence of H5N1 clusters under space-time permutation probability modelling, H5N1 association between distance and days since first outbreak through linear regression, and correlation between H5N1 presence with a range of ecological and anthropogenic variables by general linear modelling. From the 197 H5N1 identified outbreaks, involving 478 individual cases among wild and domestic birds, a wave-like steady spread of H5N1 from north to south was identified, that can help predict hotspots of outbreak risk and establish targeted preventive measures. For instance, 14 statistically significant clusters were identified, with the largest located in central Chile (18-29 km in radius) where poultry production is concentrated. Also, one of the clusters was identified in Tocopilla, location where the H5N1 human case occurred time later. In addition, the presence of H5N1 outbreaks was positively correlated with bird richness, human footprint, precipitation of the wettest month, minimum temperature of the coldest month, and mean diurnal temperature. In contrast, presence of H5N1 was negatively correlated to distance to the closest urban center, precipitation seasonality and isothermality. Preventive actions based on our modeling approach include developing wildlife surveillance diagnostic capabilities in Chilean regions concentrating outbreaks. 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 (i.e., beaches) reporting high wildlife mortalities.

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Section: Discussionmentioning

confidence: 85%

Spatio-temporal dynamics and drivers of Highly Pathogenic Avian Influenza H5N1 in Chile

Soto‐Azat

Alvarado‐Rybak²,

Aguilera

et al. 2023

Preprint

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“…Nevertheless, the probability of isolating a viable AIV sample from fecal biomaterial is, in general, lower than that from freshly taken tracheal and even cloacal swabs [47], so during the sampling of avian feces, special attention has to be paid to their quality in order to maximize the efficacy of live viral strain isolation. A study focusing on the dependence of AIV prevalence on environmental variables, such as bird quantity and species variety along with the temperature, rainfall, vegetation coverage, and water body size, has been performed in wetlands of Chile [49]. The results showed general prevalence of the virus in 4.28% of the droppings, with remarkable seasonal variations, peaking at 30% in summer months.…”

Section: Current Avian Influenza Virus Sampling Analysis and Quantification Methodologymentioning

confidence: 99%

“…where n = required sampling size, N = population size, ∝ = 1 -confidence level, and D = estimated minimum number of positive samples [49].…”

Section: Current Avian Influenza Virus Sampling Analysis and Quantification Methodologymentioning

confidence: 99%

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Avian Influenza in Wild Birds and Poultry: Dissemination Pathways, Monitoring Methods, and Virus Ecology

et al. 2021

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Avian influenza is one of the largest known threats to domestic poultry. Influenza outbreaks on poultry farms typically lead to the complete slaughter of the entire domestic bird population, causing severe economic losses worldwide. Moreover, there are highly pathogenic avian influenza (HPAI) strains that are able to infect the swine or human population in addition to their primary avian host and, as such, have the potential of being a global zoonotic and pandemic threat. Migratory birds, especially waterfowl, are a natural reservoir of the avian influenza virus; they carry and exchange different virus strains along their migration routes, leading to antigenic drift and antigenic shift, which results in the emergence of novel HPAI viruses. This requires monitoring over time and in different locations to allow for the upkeep of relevant knowledge on avian influenza virus evolution and the prevention of novel epizootic and epidemic outbreaks. In this review, we assess the role of migratory birds in the spread and introduction of influenza strains on a global level, based on recent data. Our analysis sheds light on the details of viral dissemination linked to avian migration, the viral exchange between migratory waterfowl and domestic poultry, virus ecology in general, and viral evolution as a process tightly linked to bird migration. We also provide insight into methods used to detect and quantify avian influenza in the wild. This review may be beneficial for the influenza research community and may pave the way to novel strategies of avian influenza and HPAI zoonosis outbreak monitoring and prevention.

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“…HPAI A/H5Nx viruses in South America have only been detected in shorebirds and Charadriiformes hosts so far, likely due to passive detection systems. Active, longitudinal surveillance, especially in known AIV hotspots [7,8] should also focus on Anseriformes, given year long AIV circulation and genetic diversity in these species in Chile [8]. Further sequencing of A/H5Nx and non-A/H5 positive samples is critical to identify possible reassortment events with locally circulating AIV strains.…”

Section: Main Textmentioning

confidence: 99%

Detection and Phylogenetic Analysis of Highly Pathogenic A/H5N1 Avian Influenza Clade 2.3.4.4b Virus in Chile, 2022

Jimenez‐Bluhm

Siegers

Tan

et al. 2023

Preprint

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Since the emergence of the Highly Pathogenic Avian Influenza H5N1 goose/Guangdong (Gs/GD) lineage in China in 1996, these viruses have spread globally. This includes the recent introduction of the Gs/GD lineage 2.3.4.4b in the Americas in 2021, which has affected both wild and domestic bird populations causing high mortality. Since November 2022, reports of mortality in wild birds in numerous South American countries along the Pacific Migratory Flyway have been attributed to this lineage. Through an ongoing longitudinal avian influenza virus (AIV) surveillance, we determined that AIV prevalence remained below 1% in the Lluta river wetland from August through October 2022. However, there was a significant increase in prevalence to 2.6% and 11.7% in November and December respectively, coinciding with the arrival of migratory birds from the Northern Hemisphere. Of the AIV RT-qPCR positive environmental feces samples 7 were identified as A/H5. Sequencing of the COI gene demonstrated that the H5 positive samples were obtained from Peruvian pelican (n=1), Franklin’s gull (n=1), Gray gull (n=1), Elegant tern (n=2) and Black skimmer (n=2). Full genomes were obtained from 3 samples and the putative cleavage site composition of the HA was polybasic REKRRKR/GLF for all. Phylogenetic analysis of the samples revealed them to belong to the H5 2.3.4.4b clade, closely related to isolates obtained in Peru in late November. The emergence of H5 clade 2.3.4.4b in South America has an immediate impact on public health, animal production and wildlife, hence increased active surveillance is warranted.

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Temporal dynamics and the influence of environmental variables on the prevalence of avian influenza virus in main wetlands in central Chile

Cited by 11 publications

References 48 publications

Spatio-temporal dynamics and drivers of Highly Pathogenic Avian Influenza H5N1 in Chile

Spatio-temporal dynamics and drivers of Highly Pathogenic Avian Influenza H5N1 in Chile

Avian Influenza in Wild Birds and Poultry: Dissemination Pathways, Monitoring Methods, and Virus Ecology

Detection and Phylogenetic Analysis of Highly Pathogenic A/H5N1 Avian Influenza Clade 2.3.4.4b Virus in Chile, 2022

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