#Genomic analysis of high pathogenicity avian #influenza viruses from #Antarctica reveals multiple introductions from South #America

 

Abstract

The spread of high pathogenic avian influenza virus (HPAIV) H5N1 clade 2.3.4.4b into Antarctica poses a major threat to polar wildlife. We report the detection of H5N1 in carcasses of eight species during the 2023-2024 and 2024-2025 austral summers in the South Shetland Islands: Antarctic shag, Antarctic tern, kelp gull, pintado petrel, Antarctic petrel, skuas, Antarctic fur seal, and southern elephant seal. Whole-genome sequencing, mutational profiling, and phylogenetic reconstruction revealed that the viruses detected in these hosts descended from distinct introduction events. One group of strains including complete and partial viral genomes from a gull, skuas, fur seals, an Antarctic tern, and a southern elephant seal clustered with H5N1 strains previously detected in marine mammals in South America and formed a polyphyletic lineage consistent with at least two independent introductions into Antarctica. A second group of strains including complete and partial viral genomes from petrels, shags, and skuas clustered with H5N1 strains previously detected in seabirds and marine mammals in South Georgia and with a previously reported HPAIV detection from Torgersen Island, Antarctic Peninsula. These findings reveal extensive epidemiological connectivity between South America and Antarctica, with South Georgia serving as a “stepping stone” for virus spread in the region.

Source: 

Link: https://www.nature.com/articles/s41467-026-71544-3

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Serological and viral #prevalence of #Oropouche virus (OROV): A systematic review and meta-analysis from 2000–24 including #human, #animal, and #vector #surveillance studies

 

Abstract

Background

Oropouche virus (OROV) is an emerging arbovirus primarily transmitted by biting midges and is increasingly recognized as a public health threat in Central and South America. With over 11,000 confirmed cases reported in 2024, a ten-fold increase from the previous year, its transmission dynamics and true burden remain poorly understood due to diagnostic challenges and fragmented surveillance systems.

Objective

This systematic review and meta-analysis (SRMA) synthesizes OROV prevalence data in humans and summarizes the available data for vectors and animal hosts sampled between 2000 and 2024 to provide updated estimates and identify key surveillance gaps.

Methods

We systematically searched Web of Science, PubMed, Embase, Medline, and LILACS for OROV seroprevalence and viral prevalence studies in human, insect, and animal populations, published up to September 12, 2024. The review protocol was registered with PROSPERO (CRD42024551000). Studies were extracted in duplicate, and data were meta-analyzed using generalized linear mixed-effects models. Risk of bias was appraised using a modified Joanna Briggs Institute checklist.

Results

We included 71 articles reporting serological or viral prevalence of OROV across nine countries. Between 2000–2024, pooled human seroprevalence among individuals with febrile illness or suspected of Oropouche infection was 12.6% [95% CI 5.3-26.9%] across four South American countries and seroprevalence of 1.1% [95% CI 0.5-2.3%] was observed in asymptomatic groups. Viral prevalence among individuals with febrile illness or suspected of Oropouche infection was 1.5% [0.8-3.0%] across seven South American countries and Haiti. Most studies used convenience sampling and RT-PCR or hemagglutination assays. In vector populations, positive OROV prevalence in Aedes aegypti and Culex quinquefasciatus was reported in two of 18 sources, while 10.0% and 7.5% animal host prevalence was reported in dogs and cattle, respectively. We found high risk of bias in 11.3% of studies in our critical appraisal, with most animal, human, and vector studies falling in the moderate risk of bias range.

Conclusions

Despite rising numbers of OROV reported cases, prevalence estimates remain limited by sparse surveillance and variable methodology. This review highlights the urgent need for standardized serological assays, community-based studies, and expanded surveillance in animal and vector reservoirs. A One Health approach is essential to monitor OROV transmission and inform regional preparedness efforts.

Source: 

Link: https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0013340

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Overview of high pathogenicity avian #influenza #H5N1 clade 2.3.4.4b in #wildlife from Central and South #America, October 2022 - September 2025

 

Abstract

Between 2022 and 2025, high pathogenicity avian influenza (HPAI) H5N1 clade 2.3.4.4b was detected in poultry and wildlife across most countries in Central and South America. The epizootic peaked in 2023, subsided in 2024, and resurged in 2025. In Central America, outbreaks in wildlife were few and small, and mostly affected pelicans. In contrast, South America experienced unprecedented mass mortality in colonial seabirds and pinnipeds, including endangered and endemic species. Notably, viral adaptation enabled mammal-to-mammal transmission in pinnipeds and rapid viral spread across multiple countries along the Pacific and Atlantic coasts. Subsequent introductions to subantarctic islands and Antarctica stemmed from South American viruses. In February 2025, a novel reassortant virus emerged, recombining HPAI H5N1 B3.2 genotype with South American low pathogenicity avian influenza viruses. In May 2025, HPAI H5N1 viruses re-emerged in Brazil, causing a series of outbreaks in poultry and wild birds. The ongoing circulation and evolution of HPAI H5N1 in this region underscores the need for strengthened surveillance, expanded genomic monitoring, and enhanced integration of wildlife conservation and environmental sectors in regional response frameworks.

Source: Canadian Journal of Microbiology, https://cdnsciencepub.com/doi/10.1139/cjm-2025-0189

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Highly pathogenic avian #influenza in South #America, 2022-25: temporality, affected #species, and southwards #expansion to #Antarctic region.

 

Abstract

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.

Source: BioRxIV, https://www.biorxiv.org/content/10.1101/2025.10.03.680239v1

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Phylogenetic and #Mutation #Analysis of #Hemagglutinin Gene from Highly Pathogenic Avian #Influenza Virus #H5 Clade 2.3.4.4b in South #America

Abstract

The Highly Pathogenic Avian Influenza Virus (HPAIV) H5 clade 2.3.4.4b has caused severe outbreaks in domestic and wild birds worldwide since its emergence in 2014, and especially since 2020, with outbreaks in Europe and North America. The introduction of the virus into South America was reported for the first time in Colombia in October 2022, followed by outbreaks in other South American countries affecting poultry, wild birds, mammals, and humans. In this study, a phylogenetic and mutation analysis of the hemagglutinin (HA) gene of HPAIV H5N1 2.3.4.4b viruses isolated in South America was performed to analyze its evolution and its transmission and zoonotic potential. The analysis shows an increase in the viral effective population size between April and June 2022, which was followed by multiple outbreaks of HPAIV H5N1 clade 2.3.4.4b in South America. Moreover, the virus variants evolved from a recent common ancestor estimated to have existed in June 2017. The mean rate of evolution of the HA gene was 6.95 × 10−3 substitutions per site per year, and the sequence analysis of HA identified a mutation (D171N) located at antibody binding sites and viral oligomerization interfaces, with implications for immune response evasion and new host species infection. Additionally, viral strains from South America share the substitutions L104M, T156A, P181S, and V210A, compared to the vaccine strain A/chicken/Ghana/AVL763/2021. Understanding the dynamics of viral evolution and transmission is essential for effective prevention strategies to mitigate future outbreaks.

Source: Viruses, https://www.mdpi.com/1999-4915/17/7/924

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The spatiotemporal #ecology of #Oropouche virus across Latin #America: a multidisciplinary, laboratory-based, modelling study

Summary

Background

Latin America has been experiencing an Oropouche virus (OROV) outbreak of unprecedented magnitude and spread since 2023–24 for unknown reasons. We aimed to identify risk predictors of and areas at risk for OROV transmission.

Methods

In this multidisciplinary, laboratory-based, modelling study, we retrospectively tested anonymised serum samples collected between 2001 and 2022 for studies on virus epidemiology and medical diagnostics in Bolivia, Brazil, Colombia, Costa Rica, Ecuador, and Peru with nucleoprotein-based commercial ELISAs for OROV-specific IgG and IgM antibodies. Serum samples positive for IgG from different ecological regions and sampling years were tested against Guaroa virus and two OROV glycoprotein reassortants (Iquitos virus and Madre de Dios virus) via plaque reduction neutralisation testing (PRNT) to validate IgG ELISA specificity and support antigenic cartography. Three OROV strains were included in the neutralisation testing, a Cuban OROV isolate from the 2023–24 outbreak, a contemporary Peruvian OROV isolate taken from a patient in 2020, and a historical OROV isolate from Brazil. We analysed the serological data alongside age, sex, cohort, and geographical residence data for the serum samples; reported OROV incidence data; and vector occurrence data to explore OROV transmission in ecologically different regions of Latin America. We used the MaxEnt machine learning methodology to spatially analyse and predict OROV infection risk across Latin America, fitting one model with presence–absence serological data (seropositive results were recorded as presence and seronegative results were recorded as absence) and one model with presence-only, reported incidence data from 2024. We computed marginal dependency plots, variable contribution, and permutation metrics to analyse the impact of socioecological predictors and fitted a generalised linear mixed-effects model with logit link and binary error structure to analyse the potential effects of age, sex, or cohort type bias and interactions between age or sex and cohort type in our serological data. We conducted antigenic cartography and evolutionary characterisations of all available genomic sequences for all three OROV genome segments from the National Center for Biotechnology Information, including branch-specific selection pressure analysis and the construction of OROV phylogenetic trees.

Findings

In total, 9420 serum samples were included in this study, representing 76 provinces in the six Latin American countries previously mentioned. The sex distribution across the combined cohorts was 48% female (4237 of 8910 samples with available data) and 52% male (4673 of 8910 samples) and the mean age was 29·5 years (range 0–95 years). The samples were collected from census-based cohorts, cohorts of healthy individuals, and cohorts of febrile patients receiving routine health care. The average OROV IgG antibody detection rate was 6·3% (95% CI 5·8–6·8), with substantial regional heterogeneity. The presence–absence, serology-based model predicted high-risk areas for OROV transmission in the Amazon River basin, around the coastal and southern areas of Brazil, and in parts of central America and the Caribbean islands, consistent with case data from the 2023–24 outbreak reported by the Pan American Health Organization. Areas with a high predicted risk of OROV transmission with the serology-based model showed a statistically significant positive correlation with state-level incidence rates per 100 000 people in 2024 (generalised linear model, p=0·0003). The area under the curve estimates were 0·79 (95% CI 0·78–0·80) for the serology-based model and 0·66 (95% CI 0·65–0·66) for the presence-only incidence-based model. Longitudinal diagnostic testing of serum samples from cohorts of febrile patients suggested constant circulation of OROV in endemic regions at varying intensity. Climate variables accounted for more than 60% of variable contribution in both the serology-based and incidence-based models. Antigenic cartography, evolutionary analyses, and in-vitro growth comparisons showed clear differentiation between OROV and its glycoprotein reassortants, but not between the three different OROV strains. PRNT titres of OROV-neutralising serum samples were strongly correlated between all three tested OROV isolates (r>0·83; p<0·0001) but were not correlated with the two glycoprotein reassortants.

Interpretation

Our data suggest that climatic factors are major drivers of OROV spread and were potentially exacerbated during 2024 by extreme weather events. OROV glycoprotein reassortants, but not individual OROV strains, probably have distinct antigenicity. Preparedness for OROV outbreaks requires enhanced diagnostics, surveillance, and vector control in current and future endemic areas, which could all be informed by the risk predictions presented in this Article.

Source: Lancet Infectious Diseases, https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(25)00110-0/fulltext?rss=yes

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Cross-species and #mammal-to-mammal #transmission of clade 2.3.4.4b highly pathogenic avian #influenza A #H5N1 with #PB2 adaptations

Abstract

Highly pathogenic H5N1 avian influenza viruses (HPAIV) belonging to lineage 2.3.4.4b emerged in Chile in December 2022, leading to mass mortality events in wild birds, poultry, and marine mammals and one human case. We detected HPAIV in 7,33% (714/9745) of cases between December 2022–April 2023 and sequenced 177 H5N1 virus genomes from poultry, marine mammals, a human, and wild birds spanning >3800 km of Chilean coastline. Chilean viruses were closely related to Peru’s H5N1 outbreak, consistent with north-to-south spread down the Pacific coastline. One human virus and nine marine mammal viruses in Chile had the rare PB2 D701N mammalian-adaptation mutation and clustered phylogenetically despite being sampled 5 weeks and hundreds of kilometers apart. These viruses shared additional genetic signatures, including another mammalian PB2 adaptation (Q591K, n = 6), synonymous mutations, and minor variants. Several mutations were detected months later in sealions in the Atlantic coast, indicating that the pinniped outbreaks on the west and east coasts of South America are genetically linked. These data support sustained mammal-to-mammal transmission of HPAIV in marine mammals over thousands of kilometers of Chile’s Pacific coastline, which subsequently continued through the Atlantic coastline.

Source: Nature Communications, https://www.nature.com/articles/s41467-025-57338-z

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