The 2022-2023 outbreak of highly pathogenic avian influenza (HPAI) H5N1 in Chile caused extensive mortality in wild birds, domestic poultry, and marine mammals, highlighting the rapid transboundary spread of this emerging pathogen in South America. However, the evolutionary and ecological processes shaping viral dissemination within Chile have remained insufficiently characterized. Here, we integrated whole-genome sequencing, Bayesian phylogeographic analyses, and ecological modeling to reconstruct introduction routes, diversification patterns, and environmental drivers of H5N1 circulation in Chile. All analyzed genomes belonged to clade 2.3.4.4b, genotype B3.2. Phylogenetic analyses revealed multiple Chilean subclusters, including a lineage characterized by PB2 F323L and D740N substitutions and a single virus carrying the previously mammalian-associated PB2 D701N mutation. Phylogeographic inference identified strongly supported viral movements across South America, with Argentina acting as a major regional connector. Key diffusion pathways linked Peru to Chile and revealed extensive connectivity among Argentina, Chile, Brazil, Uruguay, and the Falkland Islands, delineating three interacting transboundary transfer systems along the Pacific Coast, the Southern Cone, and the Southwest Atlantic. Within Chile, viral population structure reflected ecological segregation. Northern lineages were predominantly associated with coastal and raptor species, whereas southern lineages were mainly linked to freshwater birds. Ecological modeling showed that H5N1 detection probability in wild birds increased with temperature and relative humidity and decreased with human population density, with freshwater species exhibiting the highest infection probability. Together, these results demonstrate how integrating genomic and ecological data provides an integrated framework for risk-based surveillance and early warning, enabling the identification of high-risk host groups, environments, and transboundary corridors critical for anticipating and mitigating the regional spread of emerging avian influenza viruses.

The H5N1 highly pathogenic avian influenza (HPAI) virus has caused severe global losses, reaching South America in 2022 and Antarctica in 2024. Here, we synthesize outbreak reports submitted to the World Organization for Animal Health by South American countries and overseas territories in this continent, and document the virus’s unprecedented expansion into Antarctica, affecting wild birds, wild mammals, and domestic poultry. Phylogenetic and time-calibrated Bayesian analyses were performed on available genomic sequences. Over 6 million domestic birds were lost, mostly from commercial operations. Of the 11 South American countries and overseas territories that reported H5N1 to WOAH, 10 reported infections in wild birds, spanning 104 species, 59.62% of which are migratory and predominantly non-trans-equatorial. Marine mammal outbreaks followed wild bird detections, with the South American sea lion (Otaria flavescens) being the most reported species. Several Antarctic bird species with migratory behavior were also reported in South America. Genomic analyses revealed multiple introduction events, regional viral diversification, and patterns consistent with repeated cross-species spillover events. These findings highlight H5N1’s extensive ecological reach in the Southern Hemisphere and underscore the urgent need for a One Health approach that strengthens wildlife and backyard-poultry surveillance, alongside coordinated regional action to control and prevent further HPAI spread.

The evolution of the Andean orogeny has an impact on the biota diversification of the region due to topographic changes and atmospheric circulation trajectories. Among them are the lizards of the Liolaemidae family and within this, of which Liolaemus is the genus with the most described species up to date, with approximately 290. One of the groups within the genus is the Liolaemus elongatus group, distributed in central-south of Argentina and Chile formed by four clades and a subclade: the L. capillitas subclade. In this work, we describe a new species belonging to the L. capillitas subclade, using an integrative approach, analysing both morphological (lepidosis, morphometrics, colouration and hemipenes characters) and molecular evidence (genetic distances and phylogeny). We made a divergence analysis of the representatives of the L. elongatus group. Furthermore, we correlated the ages of the geological events with the distribution areas for the lineages L. capillitas subclade. This newly described species shows character states (morphological and molecular) that allow its clear distinction from the other members of the L. elongatus group, as well as from the rest of Liolaemus. The divergence analysis places the new species in the L. capillitas subclade and allows us to infer the successive geological events that served as physical barriers to the diversification of the group, besides explaining the current distribution of the group. http://zoobank.org/urn:lsid:zoobank.org:pub:EDFA2340-46D2-460A-AA31-C914E5288883

The H5N1 highly pathogenic avian influenza (HPAI) virus has caused severe global losses, reaching South America in 2022 and Antarctica in 2024. Here we synthesize outbreak reports submitted to the World Organization for Animal Health (WOAH) by South American countries and document the virus’s unprecedented expansion into Antarctica, affecting wild birds, wild mammals, and domestic poultry. More than 6 million domestic birds died or were culled, mostly from commercial operations. Of the 11 South American countries that reported H5N1 to WOAH, 10 reported infections in wild birds, spanning 104 species, 59.62% of which are migratory and predominantly non-trans-equatorial. Marine mammal cases occurred after wild bird detections, with the South American sea lion ( Otaria flavescens ) most affected, and several Antarctic bird species with migratory behavior were also reported in South America. To complement outbreak data, we examined available genomic sequences through phylogenetic and time-calibrated Bayesian analyses, which revealed multiple introduction events, viral diversity across regions, and evidence of interspecies transmission dynamics. These findings highlight the extensive ecological reach of H5N1 in the Southern Hemisphere and underscore the urgent need for a One Health approach that strengthens wildlife and backyard-poultry surveillance while fostering coordinated regional action to control and prevent further spread of HPAI. IMPORTANCE The arrival of H5N1 highly pathogenic avian influenza (HPAI) in South America has caused severe mortality in wild birds, marine mammals, and domestic poultry, and has recently expanded into Antarctica. Understanding how the virus entered and spread across the continent is essential for preparedness and response. Using phylogenetic and time-calibrated analyses, we identify three independent introductions into South America, estimate their temporal windows of entry, and document repeated spillover across species, including into marine mammals and humans. These findings provide novel resolution beyond previous reports and highlight the extensive inter-country connectivity of circulating viruses. The unprecedented detection of HPAI in Antarctica further illustrates the ecological risks posed by ongoing southward spread. Together, this analysis underscores the urgent need for integrated One Health surveillance that bridges wildlife, domestic animal, and human health systems to mitigate the future impacts of HPAI in the region.

Backyard production systems (BPSs) are common in Chile and play an important role in food access and local trade. However, these systems often lack basic biosecurity and disease prevention practices, which increases the risk of disease spreading. In this study, we evaluated the presence of two major avian respiratory viruses, infectious bronchitis virus (IBV) and infectious laryngotracheitis virus (ILTV), in BPSs located near wetlands in central Chile. These areas are known as the country’s main poultry production zones. We collected 449 poultry serum samples from 88 BPSs and performed serological tests using ELISA. Additionally, we analyzed 250 poultry tracheal swabs from 31 BPSs using qPCR. The results showed high seroprevalence levels: 95.5% of BPSs tested positive for IBV and 85.2% for ILTV. At the animal level, 82.2% were positive for IBV and 57.2% for ILTV. Most birds had antibodies to both viruses. However, active infections were less frequent, with 4.3% of tracheal swabs testing positive for IBV and 14.1% for ILTV during 2021 and 0.6% and 3.8% for IBV and ILTV, respectively, during 2024. This is the first serological and molecular evidence of IBV and ILTV circulation in backyard poultry in central Chile. Since this region includes most of the country’s poultry industry, these findings raise concern about the risk of virus transmission to commercial farms. The high circulation rates suggest that backyard poultry could act as reservoirs and may contribute to decreased productivity. Our results highlight the need for improved disease surveillance and enhancement of biosecurity in BPSs in Chile.

Educational farms provide students with hands-on experience in agricultural and animal practices. However, the close contact between humans and farm animals creates a significant interface for zoonotic disease transmission, yet research on infectious diseases in such settings remains limited. This study investigates the ongoing spillovers of human-origin influenza A virus (IAV) into swine at an educational farm in central Chile, describing IAV prevalence, outbreak dynamics, and the genomic characterization of detected strains. The Menesianos educational farm, located in Melipilla, central Chile, houses approximately 40 swine alongside other domestic animals, such as horses and cows. As part of an active IAV surveillance project, monthly nasal swab samples were collected from pigs between June 2019 and September 2023 for IAV detection via RT-qPCR targeting the M gene, with positive samples subsequently sequenced. During the study period, monthly IAV prevalence ranged from 0% to 52.5%, with a notable outbreak detected between May and June 2023. The outbreak lasted 5 weeks, peaking at 52.5% prevalence during week 3. Nine IAV strains were isolated over the study period, eight of which were obtained during weeks 2 and 3 of the outbreak. Phylogenetic analysis revealed that all strains were closely related to the pandemic H1N1 2009 influenza virus, with the closest related strains being those circulating in humans in Chile during the same years. These findings highlight the importance of conducting regular IAV surveillance on educational farms, where close interactions between animals and individuals—particularly children and young people—can facilitate viral spillovers and potential reverse zoonosis events.

AIM:Backyard production systems (BPS) represent an interface of contact between people, domestic and wild animals. Studies conducted in Chile during the last decade have provided extensive evidence of influenza A virus (IAV) circulation in backyard poultry and swine. The aim of this study was to investigate exposure practices of humans to animal-origin IAV within backyards. METHODS AND RESULTS:Backyard farmers and household members of a total of 101 BPS in the proximity of wetlands located throughout Chile were interviewed between 2021 and 2022. Data were collected on the nature of human-animal contacts through participation in productive activities conducted within backyards, which was used to estimate participants' exposure risk to animal-origin IAV. Additionally, RT-qPCR and serologic IAV active surveillance was carried out in backyard animals. Multilinear regression was used to identify factors associated with exposure risk. Overall, IAV prevalence was 10.1% (95% CI: 4.7%-15.5%) and seroprevalence was 43.5% (95% CI: 29.7%-54.2%), both at the BPS level. Of 180 interviewees, 86% reported participating regularly in poultry or swine exposure activities within the backyard. A greater participation of male participants was observed when evaluating swine exposure activities, while female participation was greater for some activities related to poultry handling. Handwashing was a very extended hygiene practice; however, the use of personal protective equipment was uncommon. Different factors related to participants, households and backyards were associated with an increased exposure risk of participants to animal-origin IAV: (i) older age, (ii) less years of education, (iii) no off-farm work, (iv) greater backyard production value and (v) greater household consumption of backyard products. CONCLUSION:These results indicate the circulation of IAV in BPS and the frequent human-animal contact at this interface, highlighting the need for awareness campaigns and educational programmes aimed at backyard farmers on prevention and biosecurity measures in the management of backyard animals.

The Lluta River is the northernmost coastal wetland in Chile, representing a unique ecosystem and an important source of water in the extremely arid Atacama Desert. During peak season, the wetland is home to more than 150 species of wild birds and is the first stopover point for many migratory species that arrive in the country along the Pacific migratory route, thereby representing a priority site for avian influenza virus (AIV) surveillance in Chile. The aim of this study was to determine the prevalence of influenza A virus (IAV) in the Lluta River wetland, identify subtype diversity, and evaluate ecological and environmental factors that drive the prevalence at the study site. The wetland was studied and sampled from September 2015 to October 2020. In each visit, fresh fecal samples of wild birds were collected for IAV detection by real-time RT-PCR. Furthermore, a count of wild birds present at the site was performed and environmental variables, such as temperature, rainfall, vegetation coverage (Normalized Difference Vegetation Index—NDVI), and water body size were determined. A generalized linear mixed model (GLMM) was built to assess the association between AIV prevalence and explanatory variables. Influenza positive samples were sequenced, and the host species was determined by barcoding. Of the 4349 samples screened during the study period, overall prevalence in the wetland was 2.07% (95% CI: 1.68 to 2.55) and monthly prevalence of AIV ranged widely from 0% to 8.6%. Several hemagglutinin (HA) and neuraminidase (NA) subtypes were identified, and 10 viruses were isolated and sequenced, including low pathogenic H5, H7, and H9 strains. In addition, several reservoir species were recognized (both migratory and resident birds), including the newly identified host Chilean flamingo (Phoenicopterus chilensis). Regarding environmental variables, prevalence of AIV was positively associated with NDVI (OR = 3.65, p < 0.05) and with the abundance of migratory birds (OR = 3.57, p < 0.05). These results emphasize the importance of the Lluta wetland as a gateway to Chile for viruses that come from the Northern Hemisphere and contribute to the understanding of AIV ecological drivers.

Hemidactylus mabouia (Moreau de Jonnès, 1818) is an African species introduced and widely distributed in South America. We report H. mabouia for the first time in the municipal campsite of Colonia Carlos Pellegrini (province of Corrientes, Argentina) and in Salvador Mazza (province of Salta, Argentina). These new records increase the known distribution in Argentina of this invasive species, and they are the first from Salta, and only the second from Corrientes.

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.

Highly pathogenic avian influenza (HPAI) A/H5N1 viruses continue to pose a significant threat to animal and human health worldwide. In late 2022, the first confirmed case of HPAI A/H5N1 infection in wild birds in Chile near the Chilean-Peruvian border was reported. Active surveillance by our group in the adyacent Lluta river estuary revealed an increase in A/H5N1 prevalence coinciding with the arrival of migratory birds from the Northern Hemisphere. Genomic analysis of A/H5N1-positive samples demonstrated a close genetic relationship to strains detected in Peru during the same period, which originated from A/H5N1 viruses causing outbreaks in North America. Notably, we identified genetic mutations that did not correlate with known enhanced transmission or binding traits to mammalian receptors. In summary, this study provides valuable genomic insights into the A/H5N1 Clade 2.3.4.4b viruses in wild birds in Chile, emphasizing the need for enhanced surveillance and response strategies to mitigate the threat posed by these highly pathogenic avian influenza viruses in South America.

Little is known about the prevalence of avian influenza viruses (AIV) in wildlife and domestic animals in Polynesia. Here, we present the results of active AIV surveillance performed during two sampling seasons in 2019 on Easter Island (Rapa Nui). Tracheal and cloacal swabs as well as sera samples were obtained from domestic backyard poultry, while fresh faeces were collected from wild birds. In addition to detecting antibodies against AIV in 46% of the domestic chickens in backyard production systems tested, we isolated a novel low pathogenic H6N1 virus from a chicken. Phylogenetic analysis of all genetic segments revealed that the virus was closely related to AIV’s circulating in South America. Our analysis showed different geographical origins of the genetic segments, with the PA, HA, NA, NP, and MP gene segments coming from central Chile and the PB2, PB1, and NS being closely related to viruses isolated in Argentina. While the route of introduction can only be speculated, our analysis shows the persistence and independent evolution of this strain in the island since its putative introduction between 2015 and 2016. The results of this research are the first evidence of AIV circulation in domestic birds on a Polynesian island and increase our understanding of AIV ecology in region, warranting further surveillance on Rapa Nui and beyond.

Salmonella spp. is a relevant foodborne pathogen with worldwide distribution. To mitigate Salmonella infections, bacteriophages represent an alternative to antimicrobials and chemicals in food animals and food in general. Bacteriophages (phages) are viruses that infect bacteria, which interact constantly with their host. Importantly, the study of these interactions is crucial for the use of phages as a mitigation strategy. In this study, experimental coevolution of Salmonella Enteritidis (S. Enteritidis) and a lytic phage was conducted in tryptic soy broth for 21 days. Transfer to fresh media was conducted daily and every 24 hours, 2 mL of the sample was collected to quantify Salmonella OD600 and phage titter. Additionally, time-shift experiments were conducted on 20 colonies selected on days 1, 12, and 21 to evaluate the evolution of resistance to past (day 1), present (day 12), and future (day 21) phage populations. The behavior of the dynamics was modeled and simulated with mathematical mass-action models. Bacteria and phage from days 1 and 21 were sequenced to determine the emergence of mutations. We found that S. Enteritidis grew for 21 days in the presence and absence of the phage and developed resistance to the phage from day 1. Also, the phage was also able to survive in the media for 21 days, however, the phage titer decreased in approx. 3 logs PFU/mL. The stability of the lytic phage population was consistent with the leaky resistance model. The time-shift experiments showed resistance to phages from day 1 of at least 85% to the past, present, and future phages. Sequencing of S. Enteritidis showed mutations in genes involved in lipopolysaccharide biosynthesis genes rfbP and rfbN at day 21. The phage showed mutations in the tail phage proteins responsible for recognizing the cell surface receptors. These results suggest that interactions between bacteria and phage in a rich resource media generate a rapid resistance to the infective phage but a fraction of the population remains susceptible. Interactions between Salmonella and lytic phages are an important component for the rational use of phages to control this important foodborne pathogen.

The description of Liolaemus shitan was made based on an exhaustive morphological diagnosis.However, due to the lack of molecular evidence, a later phylogeographic study suggested thatL. shitan would not be a valid species, but rather a synonym for L. elongatus. Here, after carefulexamination, we show numerous evidences of external morphology, coloration, physiologicaldata and distribution, which would indicate that L. shitan is a valid species different from L.elongatus. Therefore, we consider L. shitan as a valid species.

As companion animals, dogs and cats live in close contact with humans, generating the possibility of interspecies pathogen transmission events. Equine origin H3N8 and avian origin H5N1 influenza virus have been reported in dogs and cats respectively since 2004 with outbreaks associated with different strains recorded for both species in Asia and North America. To date, there have been no reports of influenza viruses from companion animals in South America. To fill this gap in knowledge, we performed active epidemiological surveillance in shelters that received abandoned animals, backyard production systems and veterinary clinics between May 2017 and January 2019 to estimate the burden of influenza infection in cats and dogs in the central region of Chile. Blood samples, oropharyngeal swabs or both were collected for influenza A virus detection by RT-qPCR, NP-ELISA, and hemagglutination inhibition assay. Logistic regression models were performed to assess the association between NP-ELISA-positivity and variables including sex and animal origin. The percentage of ELISA-positive samples was 43.5 % (95 % CI: 37.0-50.1) and 23.3 % (95 % CI: 10.6-42.7) for dogs and cats, respectively. No association was found between NP-ELISA results and sex or animal origin for either dogs or cats. Two ELISA positive samples showed hemagglutination inhibition titers against pandemic H1N1 influenza. One dog sample tested positive by RT-qPCR, indicating an overall RT-qPCR positivity in dogs of 1.1 % (95 % CI: 0.05-6.7). None of the tested cat samples were positive by this assay.

Andean orogeny is one of the main factors that promoted the diversification of many groups of animals. Among them are the lizards of the Liolaemidae family and within this, Liolaemus is the genus with the most described species up to date, with approximately 277 species. One of the groups within the genus is the Liolaemus ornatus group, distributed in the south of Central Andes mountain chain. In this work, we describe a new species belonging to the L. ornatus group, using an integrative approach, analyzing both morphological (lepidosis, morphometric, coloration and hemipenes characters) and molecular evidence. We made a divergence analysis of the representatives of the L. ornatus group. Furthermore, we correlated the ages of the geological events with the distribution areas for the L. ornatus group. This newly described species shows character states (morphological and molecular) that allow its clear distinction from the other members of the L. ornatus group, as well as from the rest of Liolaemus. The divergence analysis places the new species in the L. ornatus group and allows us to infer the successive geological events that served as physical barriers for the diversification of the group, besides explaining the current distribution of the group. (c) 2021 Elsevier GmbH. All rights reserved.

Research and interest in avian influenza virus have increased considerably in recent decades in response to highly pathogenic avian influenza outbreaks in poultry and its zoonotic potential. Wild waterfowl are the main reservoir of the virus, therefore studying the dynamics of influenza A virus (IAV) infection in these populations is essential in order to understand its potential persistence in the environment and transmission to poultry and humans. It has been identified that environmental factors (such as temperature, rainfall, vegetation and landscape characteristics, among others) can play an important role in the maintenance and dissemination of the virus in the areas of concentration of wild birds. However, studies that include ecological aspects of the virus and explore the interaction between the prevalence of IAV in wild birds and environmental factors remain scarce. This review summarizes research efforts that have been made to identify the environmental factors involved in the persistence and transmission of IAV in areas of wild bird concentration and how these factors may influence the prevalence of the virus in these populations, generating differences in the presentation of the infection among different geographical areas.

La investigación y el interés por el virus influenza aviar han aumentado considerablemente en las últimas décadas en respuesta a los brotes de influenza aviar de alta patogenicidad en aves de corral y a su potencial zoonótico. Las aves silvestres acuáticas son el principal reservorio del virus en la naturaleza, por lo tanto, la comprensión de la dinámica de infección del virus influenza A (VIA) en estas poblaciones es fundamental para entender su potencial de persistencia en el ambiente y sus posibilidades de transmisión hacia aves domésticas y humanos. Se ha identificado que factores ambientales (como temperatura, precipitaciones, vegetación y características del paisaje, entre otros) pueden tener un importante rol en el mantenimiento y diseminación del virus en las zonas de concentración de aves silvestres. Sin embargo, los estudios que incluyen aspectos ecológicos del virus y que exploran la interacción entre la prevalencia del VIA en aves silvestres y el ambiente, continúan siendo escasos. En esta revisión se resumen los esfuerzos de investigación que se han realizado para identificar a los factores ambientales involucrados en la persistencia y transmisión del VIA en lugares de concentración de aves silvestres y cómo estos factores pueden incidir en la prevalencia del virus en estas poblaciones, generando diferencias en la presentación de la infección entre distintas zonas geográficas.

The genus Liolaemus includes 268 species, classified in two subgenera, Eulaemus and Liolaemus sensu stricto. The latter is formed by 12 monophyletic groups; one of them being the Liolaemus elongatus group, distributed in South America. We studied the biogeographic history of the L. elongatus group. We obtained a phylogenetic hypothesis recovering five main clades: the L. punmahuida, L. elongatus sensu stricto, L. kriegi, L. petrophilus and L. capillitas clades. Based on that hypothesis we obtained a time calibrated tree. The ancestral ranges were estimated applying three methodologies: DEC, DEC+j (using predefined areas) and GEM (using explicit geographical data). Our results show that the ancestral area of the L. elongatus group was located in central Argentina, and its divergence began around 11.5 Mya. From here, a combination of events (founder events and/or vicariances) led the species to their current distribution. Despite their differences, DEC+j and GEM show congruent results.

Although wild birds are considered the main reservoir of the influenza A virus (IAV) in nature, empirical investigations exploring the interaction between the IAV prevalence in these populations and environmental drivers remain scarce. Chile has a coastline of more than 4000 kilometres with hundreds of wetlands, which are important habitats for both resident and inter-hemispheric migratory species. The aim of this study was to characterize the temporal dynamics of IAV in main wetlands in central Chile and to assess the influence of environmental variables on AIV prevalence. For that purpose, four wetlands were studied from September 2015 to June 2018. Fresh faecal samples of wild birds were collected for IAV detection by real-time RT-PCR. Furthermore, a count of wild birds present at the site was performed and environmental variables, such as temperature, rainfall, vegetation coverage (Normalized Difference Vegetation Index (NDVI)) and water body size, were determined. A generalized linear mixed model was built to assess the association between IAV prevalence and explanatory variables. An overall prevalence of 4.28% ± 0.28% was detected with important fluctuations among seasons, being greater during summer (OR = 4.87, 95% CI 2.11 to 11.21) and fall (OR = 2.59, 95% CI 1.12 to 5.97). Prevalence was positively associated with minimum temperature for the month of sampling and negatively associated with water body size measured two months before sampling, and NDVI measured three months before sampling. These results contribute to the understanding of IAV ecological drivers in Chilean wetlands providing important considerations for the global surveillance of IAV.