H5N1 highly pathogenic avian influenza clade 2.3.4.4b in wild and domestic birds: Introductions into the United States and reassortments, December 2021-April 2022

Emergence of a novel reassortant highly pathogenic avian influenza clade 2.3.4.4b A(H5N2) Virus, 2024

Reassortant highly pathogenic avian influenza A(H5N2) clade 2.3.4.4.b viruses were detected from ducks and environmental samples in Egypt, June 2024. Genomic and phylogenetic analyses revealed a novel genotype produced by the reassortment of an A(H5N1) clade 2.3.3.4b virus with an A(H9N2) G1-like virus. Monitoring the spread of this virus is important.

Replication kinetics, pathogenicity and virus-induced cellular responses of cattle-origin influenza A(H5N1) isolates from Texas, United States

The host range of HPAIV H5N1 was recently expanded to include ruminants, particularly dairy cattle in the United States (US). Shortly after, human H5N1 infection was reported in a dairy worker in Texas following exposure to infected cattle. Herein, we rescued the cattle-origin influenza A/bovine/Texas/24-029328-02/2024(H5N1, rHPbTX) and A/Texas/37/2024(H5N1, rHPhTX) viruses, identified in dairy cattle and human, respectively, and their low pathogenic forms, rLPbTX and rLPhTX, with monobasic HA cleavage sites. Intriguingly, rHPhTX replicated more efficiently than rHPbTX in mammalian and avian cells. Still, variations in the PA and NA proteins didn't affect their antiviral susceptibility to PA and NA inhibitors. Unlike rHPbTX and rLPbTX, both rHPhTX and rLPhTX exhibited higher pathogenicity and efficient replication in infected C57BL/6J mice. The lungs of rHPhTX-infected mice produced higher inflammatory cytokines/chemokines than rHPbTX-infected mice. Our results highlight the potential risk of HPAIV H5N1 virus adaptation in human and/or dairy cattle during the current multistate/multispecies outbreak in the US.

Novel reassortant H2N2 low pathogenic avian influenza virus in live bird markets in the Northeastern United States, 2019-2023

The H2N2 avian influenza viruses (AIV) have been reported in the Northeast United States of America (USA) live bird market (LBM) system since 2014. In this study, we investigated the genetic evolution and characterized molecular markers of the recent H2N2 AIVs in LBMs in the Northeast USA. Phylogenetic analyses revealed that the LBM H2N2 lineage has evolved into three distinct subgroups (groups A.1, A.2, and A.3). The group A.1 viruses and some transient reassortants evolved through several independent reassortment events between the LBM H2N2 lineage and North American wild bird-origin AIVs. Separately, a group of phylogenetically distinct novel H2N2 viruses (group B) identified in LBMs completely originated from wild birds, independent from the previous LBM H2N2 lineage that has persisted since 2014. While no molecular evidence of mammalian adaptation was found, the novel H2N2 viruses in the LBM system underscore the importance of updated risk assessments for potential human transmission.

Highly Pathogenic Avian Influenza A(H5N1) Virus Stability in Irradiated Raw Milk and Wastewater and on Surfaces, United States

We measured stability of infectious influenza A(H5N1) virus in irradiated raw milk and wastewater and on surfaces. We found a relatively slow decay in milk, indicating that contaminated milk and fomites pose transmission risks. Although the risk is low, our results call for caution in milk handling and disposal from infected cattle.

Exposure of Wild Mammals to Influenza A(H5N1) Virus, Alaska, USA, 2020-2023

Serum samples from wild mammals inhabiting Alaska, USA, showed that 4 species, including Ursus arctos bears and Vulpes vulpes foxes, were exposed to influenza A(H5N1) viruses. Results indicated some mammals in Alaska survived H5N1 virus infection. Surveillance efforts may be improved by incorporating information on susceptibility and detectable immune responses among wild mammals.

Antiviral Susceptibility of Influenza A(H5N1) Clade 2.3.2.1c and 2.3.4.4b Viruses from Humans, 2023-2024

During 2023-2024, highly pathogenic avian influenza A(H5N1) viruses from clade 2.3.2.1c caused human infections in Cambodia and from clade 2.3.4.4b caused human infections in the Americas. We assessed the susceptibility of those viruses to approved and investigational antiviral drugs. Except for 2 viruses isolated from Cambodia, all viruses were susceptible to M2 ion channel-blockers in cell culture-based assays. In the neuraminidase inhibition assay, all viruses displayed susceptibility to neuraminidase inhibitor antiviral drugs oseltamivir, zanamivir, peramivir, laninamivir, and AV5080. Oseltamivir was ≈4-fold less potent at inhibiting the neuraminidase activity of clade 2.3.4.4b than clade 2.3.2.1c viruses. All viruses were susceptible to polymerase inhibitors baloxavir and tivoxavir and to polymerase basic 2 inhibitor pimodivir with 50% effective concentrations in low nanomolar ranges. Because drug-resistant viruses can emerge spontaneously or by reassortment, close monitoring of antiviral susceptibility of H5N1 viruses collected from animals and humans by using sequence-based analysis supplemented with phenotypic testing is essential.

PathoSeq-QC: a decision support bioinformatics workflow for robust genomic surveillance

MOTIVATION

Recommendations on the use of genomics for pathogens surveillance are evidence that high-throughput genomic sequencing plays a key role to fight global health threats. Coupled with bioinformatics and other data types (e.g., epidemiological information), genomics is used to obtain knowledge on health pathogenic threats and insights on their evolution, to monitor pathogens spread, and to evaluate the effectiveness of countermeasures. From a decision-making policy perspective, it is essential to ensure the entire process's quality before relying on analysis results as evidence. Available workflows usually offer quality assessment tools that are primarily focused on the quality of raw NGS reads but often struggle to keep pace with new technologies and threats, and fail to provide a robust consensus on results, necessitating manual evaluation of multiple tool outputs.

RESULTS

We present PathoSeq-QC, a bioinformatics decision support workflow developed to improve the trustworthiness of genomic surveillance analyses and conclusions. Designed for SARS-CoV-2, it is suitable for any viral threat. In the specific case of SARS-CoV-2, PathoSeq-QC: (i) evaluates the quality of the raw data; (ii) assesses whether the analysed sample is composed by single or multiple lineages; (iii) produces robust variant calling results via multi-tool comparison; (iv) reports whether the produced data are in support of a recombinant virus, a novel or an already known lineage. The tool is modular, which will allow easy functionalities extension.

AVAILABILITY AND IMPLEMENTATION

PathoSeq-QC is a command-line tool written in Python and R. The code is available at https://code.europa.eu/dighealth/pathoseq-qc.

Highly pathogenic avian influenza H5N1: history, current situation, and outlook

The H5N1 avian panzootic has resulted in cross-species transmission to birds and mammals, causing outbreaks in wildlife, poultry, and US dairy cattle with a range of host-dependent pathogenic outcomes. Although no human-to-human transmission has been observed, the rising number of zoonotic human cases creates opportunities for adaptive mutation or reassortment. This Gem explores the history, evolution, virology, and epidemiology of clade 2.3.4.4b H5N1 relative to its pandemic potential. Pandemic risk reduction measures are urgently required.

mGem: Transmission and exposure risks of dairy cow H5N1 influenza virus

In March 2024, highly pathogenic H5N1 was detected in dairy cows; as of 12 December 2024, it had spread to over 800 herds in 16 states. The ongoing outbreak is a public health crisis affecting both humans and animals, as interspecies transmission has emerged as a common characteristic of this virus. As of 12 December 2024, >30 humans have been infected in the United States related to dairy cow exposure. In this mGem, we discuss transmission modalities between cows within herds, the spread of the virus between dairy farms, and exposure risks for humans. We also highlight major gaps in knowledge constituting barriers to our ability to effectively control the spread of H5N1 in dairy cows and reduce the risks to humans.

Aspergillosis in 41 wild bird species in the eastern United States: a 22-year retrospective review

Aspergillosis is the most commonly and widely reported fungal infection in birds. Disease development is often secondary to stressors that cause immunocompromise, and it is typically regarded as a disease of captivity. We retrospectively evaluated data from 133 birds diagnosed with aspergillosis at the Southeastern Cooperative Wildlife Disease Study from 2001-2023 to assess diversity and relative frequency across avian taxa, gross and histologic lesion patterns, and comorbidities. Of 10 taxonomic orders represented, Charadriiformes (shorebirds; n = 35) and Accipitriformes (raptors; n = 32) were most common. Among them, the laughing gull (Leucophaeus atricilla; n = 20) and bald eagle (Haliaeetus leucocephalus; n = 14) were infected most commonly. Gross lesions were most frequent in lung (n = 80), air sac (n = 71), or celomic cavity lining (n = 42). Four distinct gross lesion patterns were identified: 1) tan caseous plaques (n = 106), 2) hollow masses lined with mold (n = 26), 3) red pulmonary nodules (n = 15), and 4) necrotic brown plaques (n = 3). Histologically, fungal hyphae were most common in lung (n = 107) and air sac (n = 49). Comorbidities were diagnosed in 67 birds with a spectrum of viral (n = 19), bacterial (n = 11), parasitic (n = 6), other fungal (n = 4), and non-infectious (n = 50) causes. Six birds each were diagnosed with highly pathogenic avian influenza or salmonellosis. Twenty-two birds were emaciated. Free-ranging birds are susceptible to myriad stressors that can predispose them to the development of aspergillosis.

Living in the city: Angiostrongylus cantonensis is a novel threat to an urban population of Florida burrowing owls (Athene cunicularia floridana) in south Florida

BACKGROUND

Angiostrongylus cantonensis, the rat lungworm, is a metastrongyloid parasite that uses rodents as definitive hosts, mollusks as intermediate hosts, and a wide range of invertebrate and vertebrate species as paratenic hosts. Although this parasite poses a significant public health concern in many regions of the world, it can also cause disease in numerous domestic and wildlife aberrant host species. When parasite larvae are ingested by one of these aberrant hosts, larval migration in the central nervous system causes extensive damage, resulting in spinal cord and/or brain damage and inflammation, leading to potentially fatal neurological disease. We describe A. cantonensis infection in a novel host, the Florida burrowing owl (Athene cunicularia floridana), on Marco Island, Collier County, Florida, USA. The Florida burrowing owl is a state-listed species that has experienced steep population declines across its range, primarily due to habitat loss and fragmentation. Many populations are now restricted to urban environments, which pose novel threats to the owls, such as exposure to anticoagulant rodenticides and novel pathogens, increased risk of predation, vehicular strike, and increased disturbance at nest sites.

METHODS

Through diagnostic evaluation of carcasses and select tissues submitted to the Southeastern Cooperative Wildlife Disease Study from 2019 to 2023, we diagnosed nine confirmed or suspected cases of angiostrongylosis on Marco Island.

RESULTS

Microscopic examination and polymerase chain reaction (PCR) testing confirmed parasite identification. In addition, ancillary testing ruled out other potential causes of neurological disease, such as rodenticides, West Nile virus, and highly pathogenic avian influenza virus.

CONCLUSIONS

This study underscores the importance of surveillance and monitoring efforts for A. cantonensis, particularly in regions where novel hosts may serve as indicators of public health risk. In addition, as urbanization and habitat fragmentation continue encroaching upon wildlife habitats, understanding the dynamics of host-parasite interactions becomes crucial for mitigating the spread of zoonotic diseases.

Dynamics of a Panzootic: Genomic Insights, Host Range, and Epidemiology of the Highly Pathogenic Avian Influenza A(H5N1) Clade 2.3.4.4b in the United States

In late 2021, Eurasian-lineage highly pathogenic avian influenza (HPAI) A(H5N1) viruses from HA clade 2.3.4.4b were first detected in the United States. These viruses have caused severe morbidity and mortality in poultry and have been detected in numerous wild and domestic animals, including cows and humans. Notably, infected cows transmitted the virus to cats, causing extreme pathogenicity and death. While human-to-human spread of the virus has not been recorded, efficient transmission of the bovine-origin virus has also led to extreme pathogenicity and death in ferret models. Recently, markers in PB2 (E627K) and HA (E186D, Q222H), indicating mammalian adaptation mutations, were detected in an H5N1-infected patient manifesting critical illness in Canada. These, combined with instances of interspecies spread of the virus, have raised global public health concerns. This could highlight the potential for the virus to successfully adapt to mammals, posing a serious risk of a global outbreak. A One Health approach is, thereby, necessary to monitor and control the outbreak. This review aims to analyze the epidemiology, transmission, and ecological impacts of HPAI A(H5N1) clade 2.3.4.4b in the U.S., identify knowledge gaps, and inform strategies for effective outbreak management and mitigation.

Exposure and survival of wild raptors during the 2022-2023 highly pathogenic influenza a virus outbreak

The global outbreak of clade 2.3.4.4b H5N1 highly pathogenic influenza A virus (HP H5N1) has had an unprecedented impact on wild birds including raptors, but long-term population impacts have not been addressed. To determine if raptors survive infections with HP H5N1, raptors from the upper Midwest United States were serologically tested for antibodies to influenza A virus (IAV), H5 and N1. Raptors were sampled at The Raptor Center's (University of Minnesota) wildlife rehabilitation hospital and at Hawk Ridge Bird Observatory. Samples were tested for IAV antibodies using a commercially available blocking ELISA, with positive samples tested for antibodies to H5 and N1. Antibodies to IAV were detected in 86 out of 316 individuals representing 7 species. Antibodies to H5 and N1 were detected in 60 individuals representing 6 species. Bald eagles had the highest seroprevalence with 67/97 (69.1%) seropositive for IAV and 52 of these 67 (77.6%) testing positive for antibodies to both H5 and N1. Prevalence of antibodies to IAV observed in this study was higher than reported from raptors sampled in this same region in 2012. The high prevalence of antibodies to H5 and N1 indicates a higher survival rate post-HP H5N1 infection in raptors than previously believed.

A One Health Investigation into H5N1 Avian Influenza Virus Epizootics on Two Dairy Farms

BACKGROUND

In early April 2024 we studied 2 Texas dairy farms that had suffered incursions of H5N1 highly pathogenic avian influenza virus (HPAIV) the previous month.

METHODS

We employed molecular assays, cell and egg culture, Sanger and next generation sequencing to isolate and characterize viruses from multiple farm specimens (cow nasal swab, milk specimens, fecal slurry, and a dead bird).

RESULTS

We detected H5N1 HPAIV in 64% (9/14) of milk specimens, 2.6% (1/39) of cattle nasal swab specimens, and none of 17 cattle worker nasopharyngeal swab specimens. We cultured and characterized virus from 8 H5N1-positive specimens. Sanger and next-generation sequencing revealed the viruses were closely related into other recent Texas epizootic H5N1 strains of clade 2.3.4.4b. Our isolates had multiple mutations associated with increased spillover potential. Surprisingly, we detected severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in a nasal swab from a sick cow. Additionally, 14.3% (2/14) of the farm workers who donated sera were recently symptomatic and had elevated neutralizing antibodies against a related H5N1 strain.

CONCLUSIONS

Although our sampling was limited, these data offer additional insight into the large H5N1 HPAIV epizootic, which has rapidly spread in the United States. Due to fears that research might damage dairy businesses, studies like this one have been few. We need to find ways to work with dairy farms in collecting more comprehensive epidemiological data that are necessary for the design of future interventions against H5N1 HPAIV on cattle farms.

Evaluation of an N1 NA antibody-specific enzyme-linked lectin assay for detection of H5N1 highly pathogenic avian influenza virus infection in vaccinated birds

Unprecedented H5N1 highly pathogenic avian influenza (HPAI) outbreaks are occurring around the world and there is growing interest in the use of vaccines in affected regions. Vaccination when properly applied can contribute to HPAI control by significantly reducing virus shedding and breaking the transmission chain, but it requires robust surveillance to ensure that international trade is not affected. Thus, it is imperative to establish a test to differentiate vaccinated only animals from vaccinated and then infected animals (DIVA). In this study, we applied enzyme-linked lectin assay (ELLA) to specifically detect N1 neuraminidase (NA) antibody by inhibition of NA activity and provide a proof-of-concept bench validation using reference and experimental serum samples. We used a wild-type low pathogenic H7N1 virus of North American lineage as the ELLA antigen. The NA inhibition ELLA (NI-ELLA) was evaluated for its specificity and sensitivity using reference and experimental samples. The results demonstrated that the NI-ELLA was highly specific with low background NI activity against influenza-negative sera from different species although varying level of cross-reactivity was observed against sera of different NA subtypes with highest cross-reactivity against N4 subtype sera. Using a conservative positive cut-off threshold of 50 % NI activity, NI-ELLA provides 100 % specificity with all reference sera of 9 different NA subtypes. The relative sensitivity of NI-ELLA was evaluated in detecting H5N1 infection in vaccinated and then challenged birds and NI-ELLA showed higher detection rate of H5N1 infection compared with commercial NP ELISAs and real-time RT-PCR. Overall, the NI-ELLA shows high specificity and sensitivity and has the potential for application in DIVA surveillance with further validation.

Targets of influenza human T-cell response are mostly conserved in H5N1

Frequent recent spillovers of subtype H5N1 clade 2.3.4.4b highly pathogenic avian influenza (HPAI) virus into poultry and mammals, especially dairy cattle, including several human cases, increased concerns over a possible future pandemic. Here, we performed an analysis of epitope data curated in the Immune Epitope Database (IEDB). We found that the patterns of immunodominance of seasonal influenza viruses circulating in humans and H5N1 are similar. We further conclude that a significant fraction of the T-cell epitopes is conserved at a level associated with cross-reactivity between avian and seasonal sequences, and we further experimentally demonstrate extensive cross-reactivity in the most dominant T-cell epitopes curated in the IEDB. Based on these observations, and the overall similarity of the neuraminidase (NA) N1 subtype encoded in both HPAI and seasonal H1N1 influenza virus as well as cross-reactive group 1 HA stalk-reactive antibodies, we expect that a degree of pre-existing immunity is present in the general human population that could blunt the severity of human H5N1 infections.IMPORTANCEInfluenza A viruses (IAVs) cause pandemics that can result in millions of deaths. The highly pathogenic avian influenza (HPAI) virus of the H5N1 subtype is presently among the top viruses of pandemic concern, according to the WHO and the National Institute of Allergy and Infectious Diseases (NIAID). Previous exposure by infection and/or vaccination to a given IAV subtype or clade influences immune responses to a different subtype or clade. Analysis of human CD4 and CD8 T-cell epitope conservation between HPAI H5N1 and seasonal IAV sequences revealed levels of identity and conservation conducive to T cell cross-reactivity, suggesting that pre-existing T cell immune memory should, to a large extent, cross-recognize avian influenza viruses. This observation was experimentally verified by testing responses from human T cells to non-avian IAV and their HPAI H5N1 counterparts. Accordingly, should a more widespread HPAI H5N1 outbreak occur, we hypothesize that cross-reactive T-cell responses might be able to limit disease severity.

Genetic diversity of highly pathogenic avian influenza H5N6 and H5N8 viruses in poultry markets in Guangdong, China, 2020-2022

H5 highly pathogenic avian influenza (HPAI) viruses of the A/Goose/Guangdong/1/96 (Gs/Gd) lineage continue to evolve and cause outbreaks in domestic poultry and wild birds, with sporadic spillover infections in mammals. The global spread of clade 2.3.4.4b viruses via migratory birds since 2020 has facilitated the introduction of novel reassortants to China, where avian influenza of various subtypes have been epizootic or enzootic among domestic birds. To determine the impact of clade 2.3.4.4b re-introduction on local HPAI dynamics, we analyzed the genetic diversity of H5N6 and H5N8 detected from monthly poultry market surveillance in Guangdong, China, between 2020 and 2022. Our findings reveal that H5N6 viruses clustered in clades 2.3.4.4b and 2.3.4.4h, while H5N8 viruses were exclusively clustered in clade 2.3.4.4b. After 2020, the re-introduced clade 2.3.4.4b viruses replaced the clade 2.3.4.4h viruses detected in 2020. The N6 genes were divided into two clusters, distinguished by an 11 amino acid deletion in the stalk region, while the N8 genes clustered with clade 2.3.4.4 H5N8 viruses circulating among wild birds. Genomic analysis identified 10 transient genotypes. H5N6, which was more prevalently detected, was also clustered into more genotypes than H5N8. Specifically, H5N6 isolates contained genes derived from HPAI H5Nx viruses and low pathogenic avian influenza in China, while the H5N8 isolates contained genes derived from HPAI A(H5N8) 2.3.4.4b and A(H5N1) 2.3.2.1c. No positive selection on amino acid residues associated with mammalian adaptation was found. Our results suggest expanded genetic diversity of H5Nx viruses in China since 2021 with increasing challenges for pandemic preparedness.IMPORTANCESince 2016/2017, clade 2.3.4.4b H5Nx viruses have spread via migratory birds to all continents except Oceania. Here, we evaluated the impact of the re-introduction of clade of 2.3.4.4b on highly pathogenic avian influenza (HPAI) virus genetic diversity in China. Twenty-two H5N6 and H5N8 HPAI isolated from monthly surveillance in two poultry markets in Guangdong between 2020 and 2022 were characterized. Our findings showed that clade 2.3.4.4h, detected in 2020, was replaced by clade 2.3.4.4b in 2021-2022. H5N6 (n = 18) were clustered into more genotypes than H5N8 (n = 4), suggesting that H5N6 may possess better replication fitness in poultry. Conversely, the H5N8 genotypes are largely derived from the clade 2.3.4.4b wild bird isolates. As clade 2.3.4.4b continues to spread via migratory birds, it is anticipated that the genetic diversity of H5N6 viruses circulating in China may continue to expand in the coming years. Continuous efforts in surveillance, genetic analysis, and risk assessment are therefore crucial for pandemic preparedness.

Pathogenesis of bovine H5N1 clade 2.3.4.4b infection in macaques

Since early 2022, highly pathogenic avian influenza (HPAI) H5N1 virus infections have been reported in wild aquatic birds and poultry throughout the USA with spillover into several mammalian species1-6. In March 2024, HPAIV H5N1 clade 2.3.4.4b was first detected in dairy cows in Texas, USA, and continues to circulate on dairy farms in many states7,8. Milk production and quality are diminished in infected dairy cows, with high virus titres in milk raising concerns of exposure to mammals including humans through consumption9-12. Here we investigated routes of infection with bovine HPAIV H5N1 clade 2.3.4.4b in cynomolgus macaques, a surrogate model for human infection13. We show that intranasal or intratracheal inoculation of macaques could cause systemic infection resulting in mild and severe respiratory disease, respectively. By contrast, infection by the orogastric route resulted in limited infection and seroconversion of macaques that remained subclinical.

Human Health Surveillance During Animal Disease Emergencies: Minnesota Department of Health Response to Highly Pathogenic Avian Influenza Outbreaks, 2015 and 2022-2023

OBJECTIVES

Highly pathogenic avian influenza (HPAI) poses an occupational risk for poultry workers, responders, and others in contact with infected birds. The objective of this analysis was to describe HPAI surveillance methods and outcomes, and highlight the challenges, successes, and lessons learned during the Minnesota Department of Health's (MDH's) public health response to HPAI outbreaks in Minnesota poultry flocks in the years 2015 and 2022-2023.

METHODS

During both outbreaks, MDH staff attempted to contact all potentially exposed people and conduct a standardized interview. People were considered exposed and at risk if they had entered a barn with poultry on any HPAI test-positive premises. With their consent, exposed persons were entered into illness monitoring until 10 days from their last exposure. In 2015, MDH monitored the health of poultry workers only. In the 2022-2023 response, MDH monitored the health of poultry workers, backyard flock owners, responders, and private contract workers. In 2022-2023, interview responses were entered into a REDCap (Research Electronic Data Capture) database in real time, which automatically entered the person into monitoring if they consented. Through REDCap, they received an automated email with a unique link to a short survey asking about any symptom development. Where appropriate, interview responses from poultry workers collected in 2015 were compared to interview responses from poultry workers collected in 2022-2023.

RESULTS

From March 3 to June 5, 2015, MDH epidemiologists interviewed and evaluated 375 (86%) of 435 poultry workers from 110 HPAI-infected flocks. From March 25, 2022 through December 31, 2023, MDH epidemiologists interviewed and evaluated 649 (65%) of 992 poultry workers, responders, contractors, and backyard flock owners associated with 151 HPAI-infected flocks. Among poultry workers, self-reported personal protective equipment (PPE) usage declined significantly from 2015 to 2022-2023 (full PPE usage 51.8% vs. 23.9%, p < .01).

CONCLUSION

MDH's long standing relationships with animal health officials and the poultry industry resulted in strong poultry worker participation rates in surveillance efforts during HPAI outbreaks in 2015 and 2022-2023. Self-reported PPE usage was low, particularly in 2022-2023. Improvements in PPE accessibility and technology are needed to protect workers and responders in the on-going HPAI outbreak.

Testing of Retail Cheese, Butter, Ice Cream, and Other Dairy Products for Highly Pathogenic Avian Influenza in the US

The recent outbreak of highly pathogenic avian influenza (HPAI) in dairy cows has created public health concerns about the potential of consumers being exposed to live virus from commercial dairy products. Previous studies support that pasteurization effectively inactivates avian influenza in milk and an earlier retail milk survey showed viral RNA, but no live virus could be detected in the dairy products tested. Because of the variety of products and processing methods in which milk is used, additional product testing was conducted to determine if HPAI viral RNA could be detected in retail dairy samples, and for positive samples by quantitative real-time RT-PCR (qRT-PCR) further testing for the presence of live virus. Revised protocols were developed to extract RNA from solid dairy products including cheese and butter. The solid dairy product was mechanically liquified with garnet and zirconium beads in a bead beater diluted 1-4 with BHI media. This preprocessing step was suitable in allowing efficient RNA extraction with standard methods. Trial studies were conducted with different cheese types with spiked-in avian influenza virus to show that inoculation of the liquified cheese into embryonating chicken eggs was not toxic to the embryos and allowed virus replication. A total of 167 retail dairy samples, including a variety of cheeses, butter, ice cream, and fluid milk were collected as part of a nationwide survey. A total of 17.4% (29/167) of the samples had detectable viral RNA by qRT-PCR targeting the matrix gene, but all PCR-positive samples were negative for live virus after testing with embryonating egg inoculation. The viral RNA was also evaluated by sequencing part of the hemagglutinin gene using a revised protocol optimized to deal with the fragmented viral RNA. The sequence analysis showed all viral RNA-positive samples were highly similar to previously reported HPAI dairy cow isolates. Using the revised protocols, it was determined that HPAI viral RNA could be detected in a variety of dairy products, but existing pasteurization methods effectively inactivate the virus assuring consumer safety.

Effectiveness of pasteurization for the inactivation of H5N1 influenza virus in raw whole milk

Highly pathogenic avian influenza (HPAI) clade 2.3.4.4b H5Nx viruses continue to cause episodic incursions and have been detected in more than 12 taxonomic orders encompassing more than 80 avian species, terrestrial and marine mammals, including lactating dairy cows. HPAI H5N1 spillover to dairy cattle creates a new interface for human exposure and raises food safety concerns. The presence of H5N1 genetic material in one out of five retail pasteurized milk samples in the USA has prompted the evaluation of the pasteurization processes for the inactivation of influenza viruses. Our study examined whether pasteurization could effectively inactivate HPAI H5N1 spiked into raw whole milk. First, we heated 1 mL of non-homogenized cow milk samples to attain an internal temperature of 63°C or 72°C and spiked with 6.3 log10 EID50 of clade 2.3.4.4b H5N1 virus. Complete inactivation was achieved after incubation of the H5N1 spiked raw milk at 63°C for 30 min. In addition, viral inactivation was observed in seven of eight experimental replicates when treated at 72°C for 15s. In one of the replicates, a 4.44 log10 virus reduction was achieved, which is about 1 log higher than the average viral quantities detected in bulk milk in affected areas. Therefore, we conclude that pasteurization of milk is an effective strategy for mitigation of the risk of human exposure to milk contaminated with H5N1 virus.

Longitudinal screening of retail milk from Canadian provinces reveals no detections of influenza A virus RNA (April-July 2024): leveraging a newly established pan-Canadian network for responding to emerging viruses

Highly pathogenic avian influenza (HPAI) H5N1 has caused the deaths of more than 100 million birds since 2021, and human cases since 1997 have been associated with significant morbidity and mortality. Given recent detections of HPAI H5N1 in dairy cattle and H5N1 RNA detections in pasteurized retail milk in the United States, we established the pan-Canadian Milk Network in April 2024. Through our network of collaborators from across Canada, retail milk was procured longitudinally, approximately every 2 weeks, and sent to a central laboratory to test for the presence of influenza A virus RNA. Between 29 April and 17 July 2024, we tested 109 retail milk samples from all 10 Canadian provinces (NL, NS, PEI, NB, QC, ON, MB, SK, AB, and BC). All samples tested negative for influenza A virus RNA. This nationwide initiative was established for rapid retail milk screening as per the earliest reports of similar undertakings in the United States. Our independent testing results have aligned with reporting from federal retail milk testing initiatives. Despite no known HPAI infections of dairy cattle in Canada to date, H5N1 poses a significant threat to the health of both humans and other animals. By performing routine surveillance of retail milk on a national scale, we have shown that academic networks and initiatives can rapidly establish nationwide emerging infectious disease surveillance that is cost-effective, standardized, scalable, and easily accessible. Our network can serve as an early detection system to help inform containment and mitigation activities if positive samples are identified and can be readily reactivated should HPAI H5N1 or other emerging zoonotic viruses be identified in agricultural or livestock settings, including Canadian dairy cattle.

The global H5N1 influenza panzootic in mammals

Influenza A viruses have caused more documented global pandemics in human history than any other pathogen1,2. High pathogenicity avian influenza viruses belonging to the H5N1 subtype are a leading pandemic risk. Two decades after H5N1 'bird flu' became established in poultry in Southeast Asia, its descendants have resurged3, setting off a H5N1 panzootic in wild birds that is fuelled by: (1) rapid intercontinental spread, reaching South America and Antarctica for the first time4,5; (2) fast evolution via genomic reassortment6; and (3) frequent spillover into terrestrial7,8 and marine mammals9. The virus has sustained mammal-to-mammal transmission in multiple settings, including European fur farms10,11, South American marine mammals12-15 and US dairy cattle16-19, raising questions about whether humans are next. Historically, swine are considered optimal intermediary hosts that help avian influenza viruses adapt to mammals before jumping to humans20. However, the altered ecology of H5N1 has opened the door to new evolutionary pathways. Dairy cattle, farmed mink or South American sea lions may have the potential to serve as new mammalian gateways for transmission of avian influenza viruses to humans. In this Perspective, we explore the molecular and ecological factors driving the sudden expansion in H5N1 host range and assess the likelihood of different zoonotic pathways leading to an H5N1 pandemic.

Dairy cows inoculated with highly pathogenic avian influenza virus H5N1

Highly pathogenic avian influenza (HPAI) H5N1 haemagglutinin clade 2.3.4.4b was detected in the USA in 2021. These HPAI viruses caused mortality events in poultry, wild birds and wild mammals. On 25 March 2024, HPAI H5N1 clade 2.3.4.4b was confirmed in a dairy cow in Texas in response to a multistate investigation into milk production losses1. More than 200 positive herds were identified in 14 US states. The case description included reduced feed intake and rumen motility in lactating cows, decreased milk production and thick yellow milk2,3. The diagnostic investigation revealed viral RNA in milk and alveolar epithelial degeneration and necrosis and positive immunoreactivity of glandular epithelium in mammary tissue. A single transmission event, probably from birds, was followed by limited local transmission and onward horizontal transmission of H5N1 clade 2.3.4.4b genotype B3.13 (ref. 4). Here we sought to experimentally reproduce infection with genotype B3.13 in Holstein yearling heifers and lactating cows. Heifers were inoculated by an aerosol respiratory route and cows by an intramammary route. Clinical disease was mild in heifers, but infection was confirmed by virus detection, lesions and seroconversion. Clinical disease in lactating cows included decreased rumen motility, changes to milk appearance and production losses. Infection was confirmed by high levels of viral RNA detected in milk, virus isolation, lesions in mammary tissue and seroconversion. This study provides the foundation to investigate additional routes of infection, pathogenesis, transmission and intervention strategies.

Intensive transmission in wild, migratory birds drove rapid geographic dissemination and repeated spillovers of H5N1 into agriculture in North America

Since late 2021, a panzootic of highly pathogenic H5N1 avian influenza virus has driven significant morbidity and mortality in wild birds, domestic poultry, and mammals. In North America, infections in novel avian and mammalian species suggest the potential for changing ecology and establishment of new animal reservoirs. Outbreaks among domestic birds have persisted despite aggressive culling, necessitating a re-examination of how these outbreaks were sparked and maintained. To recover how these viruses were introduced and disseminated in North America, we analyzed 1,818 Hemagglutinin (HA) gene sequences sampled from North American wild birds, domestic birds and mammals from November 2021-September 2023 using Bayesian phylodynamic approaches. Using HA, we infer that the North American panzootic was driven by ~8 independent introductions into North America via the Atlantic and Pacific Flyways, followed by rapid dissemination westward via wild, migratory birds. Transmission was primarily driven by Anseriformes, shorebirds, and Galliformes, while species such as songbirds, raptors, and owls mostly acted as dead-end hosts. Unlike the epizootic of 2015, outbreaks in domestic birds were driven by ~46-113 independent introductions from wild birds, with some onward transmission. Backyard birds were infected ~10 days earlier on average than birds in commercial poultry production settings, suggesting that they could act as "early warning signals" for transmission upticks in a given area. Our findings support wild birds as an emerging reservoir for HPAI transmission in North America and suggest continuous surveillance of wild Anseriformes and shorebirds as crucial for outbreak inference. Future prevention of agricultural outbreaks may require investment in strategies that reduce transmission at the wild bird/agriculture interface, and investigation of backyard birds as putative early warning signs.

Recurring incursions and dissemination of novel Eurasian-origin H5Nx avian influenza viruses in Atlantic Canada

Wild birds are important hosts of influenza A viruses (IAVs) and play an important role in their ecology. The emergence of the A/goose/Guangdong/1/1996 H5N1 (Gs/GD) lineage marked a shift in IAV ecology, leading to recurrent outbreaks and mortality in wild birds from 2002 onwards. This lineage has evolved and diversified over time, with a recent important derivative being the 2.3.4.4b sub-lineage, which has caused significant mortality events in wild bird populations. An H5N1 clade 2.3.4.4b virus was transmitted into North America from Eurasia in 2021, with the first detection being in Newfoundland and Labrador in Atlantic Canada, and this virus and its reassortants then spread broadly throughout North America and beyond. Following the first 2021 detection, there have been three additional known incursions of Eurasian-origin strains into Atlantic Canada, a second H5N1 strain in 2022 and two H5N5 strains in 2023. In this study, we document a fifth incursion in Atlantic Canada that occurred in 2023 by another H5N5 strain. This strain spread throughout Atlantic Canada and into Quebec, infecting numerous species of wild birds and mammals. Genomic analysis revealed mammalian-adaptive mutations in some of the detected viruses (PB2-E627K and PB2-D701N) and mutations in the hemagglutinin (HA) and neuraminidase (NA) genes that are associated with enhanced viral fitness and avian transmission capabilities. Our findings indicate that this virus is continuing to circulate in wildlife, and confirms Atlantic Canada is an important North American entry point for Eurasian IAVs. Continued surveillance and genomic analysis of IAVs detected in the region is crucial to monitor the evolution of these viruses and assess potential risks to wildlife and public health.

Charles KM, Hutchinson HC, Schoenbaum M, Marusak R, Culhane MR, Cardona CJ. Estimating the time of Highly Pathogenic Avian Influenza virus introduction into United States poultry flocks during the 2022/24 epizootic

Following confirmation of the first case of the ongoing U.S. HPAI H5N1 epizootic in commercial poultry on February 8, 2022, the virus has continued to devastate the U.S. poultry sector and the pathogen has since managed to cross over to livestock and a few human cases have also been reported. Efficient outbreak management benefits greatly from timely detection and proper identification of the pathways of virus introduction and spread. In this study, we used changes in mortality rates as a proxy for HPAI incidence in a layer, broiler and turkey flock together with diagnostic test results to infer within-flock HPAI transmission dynamics. Mathematical modeling techniques, specifically the Approximate Bayesian Computation algorithm in conjunction with a stochastic within-flock HPAI transmission model were used in the analysis. The time window of HPAI virus introduction into the flock (TOI) and the adequate contact rate (ACR) were estimated. Then, using the estimated TOI together with the day when the first HPAI positive sample was collected from the flock, we calculated the most likely time to first positive sample (MTFPS) which reflects the time to HPAI detection. The estimated joint (i.e., all species combined) median of the MTFPS for different flocks was six days, the joint median most likely ACR was 6.8 newly infected birds per infectious bird per day, the joint median R0 was 13 and the joint median number of test days per flock was two. These results were also grouped by species and by epidemic phase and discussed accordingly. We conclude that this findings from this and other related studies are beneficial for the different stakeholders in outbreak management. We recommend that combining TOI analysis with complementary approaches such as phylogenetic analyses is critically important for improved understanding of disease transmission pathways. The estimated parameters can also be used to parametrize mathematical models that can guide the design of surveillance protocols, risk analyses of HPAI spread, and emergency preparedness for HPAI outbreaks.

Avian influenza A (H5N1) virus in dairy cattle: origin, evolution, and cross-species transmission

Since the emergence of highly pathogenic avian influenza virus (HPAIV) H5N1 of clade 2.3.4.4b as a novel reassortant virus from subtype H5N8, the virus has led to a massive number of outbreaks worldwide in wild and domestic birds. Compared to the parental HPAIV H5N8 clade 2.3.4.4b, the novel reassortant HPAIV H5N1 displayed an increased ability to escape species barriers and infect multiple mammalian species, including humans. The virus host range has been recently expanded to include ruminants, particularly dairy cattle in the United States, where cattle-to-cattle transmission was reported. As with the avian 2.3.4.4.b H5N1 viruses, the cattle-infecting virus was found to transmit from cattle to other contact animals including cats, raccoons, rodents, opossums, and poultry. Although replication of the virus in cows appears to be mainly confined to the mammary tissue, with high levels of viral loads detected in milk, infected cats and poultry showed severe respiratory disease, neurologic signs, and eventually died. Furthermore, several human infections with HPAIV H5N1 have also been reported in dairy farm workers and were attributed to exposures to infected dairy cattle. This is believed to represent the first mammalian-to-human transmission report of the HPAIV H5N1. Fortunately, infection in humans and cows, as opposed to other animals, appears to be mild in most cases. Nevertheless, the H5N1 bovine outbreak represents the largest outbreak of the H5N1 in a domestic mammal close to humans, increasing the risk that this already mammalian adapted H5N1 further adapts to human-to-human transmission and starts a pandemic. Herein, we discuss the epidemiology, evolution, pathogenesis, and potential impact of the recently identified HPAIV H5N1 clade 2.3.4.4b in dairy cattle in the United States. Eventually, interdisciplinary cooperation under a One Health framework is required to be able to control this ongoing HPAIV H5N1 outbreak to stop it before further expansion of its host range and geographical distribution.

A single mutation in bovine influenza H5N1 hemagglutinin switches specificity to human receptors

In 2024, several human infections with highly pathogenic clade 2.3.4.4b bovine influenza H5N1 viruses in the United States raised concerns about their capability for bovine-to-human or even human-to-human transmission. In this study, analysis of the hemagglutinin (HA) from the first-reported human-infecting bovine H5N1 virus (A/Texas/37/2024, Texas) revealed avian-type receptor binding preference. Notably, a Gln226Leu substitution switched Texas HA binding specificity to human-type receptors, which was enhanced when combined with an Asn224Lys mutation. Crystal structures of the Texas HA with avian receptor analog LSTa and its Gln226Leu mutant with human receptor analog LSTc elucidated the structural basis for this preferential receptor recognition. These findings highlight the need for continuous surveillance of emerging mutations in avian and bovine clade 2.3.4.4b H5N1 viruses.

Analysis of the Monophyletic Lineage of Avian Influenza H5N1 Which Circulated in Venezuelan Birds During the 2022-2023 Outbreak

Avian influenza subtype H5N1 has caused outbreaks worldwide since 1996, with the emergence of the Guandong lineage in China. The current clade 2.3.4.4b has evolved from this lineage, with increased virulence and mass mortality events in birds and mammals. The objective of this study was the analysis of 17 viral genomes of H5N1 avian influenza isolated in Venezuela during the 2022-2023 outbreak. The eight viral genomic segments were amplified using universal primers and sequenced via next-generation sequencing. The sequences were analyzed to confirm the H5 hemagglutinin clade, identify possible genetic reassortments, and perform a phylogenetic and docking analysis of the viral isolates. The viruses found in Venezuela belonged, as expected, to clade 2.3.4.4b and formed a monophyletic clade with North American influenza viruses, with no evidence of further reassortment. The introduction of the virus in South America is associated with bird migration through the Atlantic (Venezuela), Atlantic/Mississippi (Choco, Colombia), and Pacific migratory flyways, with the emergence of several viral lineages. Several mutations were found in all segments of the genome, although none of the key mutations was involved in mammalian adaptation. Moreover, in silico structural analysis suggests, as expected, that the viral hemagglutinin maintained a predilection for avian α2,3-linked sialic acid. The unprecedented pathogenic outbreak of avian influenza disease in South America was associated with the circulation of three different lineages, which maintain a lower affinity for the mammalian receptor.

Genomic characterization of highly pathogenic H5 avian influenza viruses from Alaska during 2022 provides evidence for genotype-specific trends of spatiotemporal and interspecies dissemination

The ongoing panzootic of highly pathogenic H5 clade 2.3.4.4b avian influenza (HPAI) spread to North America in late 2021, with detections of HPAI viruses in Alaska beginning in April 2022. HPAI viruses have since spread across the state, affecting many species of wild birds as well as domestic poultry and wild mammals. To better understand the dissemination of HPAI viruses spatiotemporally and among hosts in Alaska and adjacent regions, we compared the genomes of 177 confirmed HPAI viruses detected in Alaska during April-December 2022. Results suggest multiple viral introductions into Alaska between November 2021 and August or September 2022, as well as dissemination to areas within and outside of the state. Viral genotypes differed in their spatiotemporal spread, likely influenced by timing of introductions relative to population immunity. We found evidence for dissemination of HPAI viruses between wild bird species, wild birds and domestic poultry, as well as wild birds and wild mammals. Continued monitoring for and genomic characterization of HPAI viruses in Alaska can improve our understanding of the evolution and dispersal of these economically costly and ecologically relevant pathogens.

Descriptive epidemiology and phylogenetic analysis of highly pathogenic avian influenza H5N1 clade 2.3.4.4b in British Columbia (B.C.) and the Yukon, Canada, September 2022 to June 2023

Surveillance data from wildlife and poultry was used to describe the spread of highly pathogenic avian influenza (HPAI) H5N1 clade 2.3.4.4b in British Columbia (B.C.) and the Yukon, Canada from September 2022 - June 2023 compared to the first "wave" of the outbreak in this region, which occurred April - August 2022, after the initial viral introduction. Although the number of HPAI-positive poultry farms and wildlife samples was greater in "Wave 2", cases were more tightly clustered in southwestern B.C. and the most commonly affected species differed, likely due to an influx of overwintering waterfowl in the area. Eight HPAI genetic clusters, representing seven genotypes and two inter-continental viral incursions, were detected, with significant variation in the relative abundance of each cluster between the waves. Phylogenetic data suggests multiple spillover events from wild birds to poultry and mammals but could not rule out transmission among farms and among mammals.

DIAGNOSTIC INVESTIGATION OF AMERICAN ROBINS (TURDUS MIGRATORIUS) WITH FATAL ETHYLENE GLYCOL TOXICOSIS AND CONCURRENT PLASMODIUM SPP. INFECTION WITH RETROSPECTIVE REVIEW OF 44 YEARS OF DIAGNOSTIC DATA

We describe a mortality event involving at least 44 adult American robins (Turdus migratorius) that were found dead on the morning of February 25, 2023 in a residential backyard in Natchitoches Parish, Louisiana. Five carcasses were submitted for diagnostic evaluation. All five robins were in good nutritional and feather condition with no external indicators of injury or illness. Grossly, kidneys were diffusely pale in all robins and 4/5 also had splenomegaly. Consistent histologic lesions included severe, multifocal to coalescing, renal tubular degeneration and necrosis with intraluminal, birefringent calcium oxalate crystals and calcified concretions. Toxicologic testing revealed a markedly elevated calcium concentration (10,000 parts per million) in a pooled kidney sample. Collectively, these findings support a diagnosis of ethylene glycol toxicosis. Ethylene glycol, an ingredient in antifreeze, is a hazardous toxicant in domestic and wild animals living in residential areas, although confirmed reports in songbirds are scarce. In the present case, the circumstances of ethylene glycol exposure are unknown but most likely anthropogenic in origin. Additionally, splenomegaly prompted molecular testing, which detected Plasmodium unalis in three robins and P. vaughani in one robin. Both Plasmodium spp. can infect a wide range of hosts, and although infections likely were subclinical, their detection raises awareness of their potential pathogenicity in wild birds. This mortality event underscores the need to recognize health risks posed by environmental contaminants and vector-borne pathogens to wildlife, and reinforces that wildlife, especially peridomestic species, can serve as sentinels for risks to domestic animal and human health.

Understanding the emergence of highly pathogenic avian influenza A virus H5N1 in pinnipeds: An evolutionary approach

Highly pathogenic influenza A virus (HPIAV) H5N1 within the genetic clade 2.3.4.4b has emerged in wild birds in different regions of the world, leading to the death of >70 million birds. When these strains spread to pinniped species a remarkable mortality has also been observed. A detailed genetic characterization of HPIAV isolated from pinnipeds is essential to understand the potential spread of these viruses to other mammalian species, including humans. To gain insight into these matters a detailed phylogenetic analysis of HPIAV H5N1 2.3.4.4b strains isolated from pinniped species was performed. The results of these studies revealed multiple transmission events from birds to pinnipeds in all world regions. Different evolutionary histories of different genes of HPIAV H5N1 2.3.4.4b strains gave rise to the viruses infecting pinnipeds in different regions of the world. European strains isolated from pinnipeds represent a completely different genetic lineage from strains isolated from South American ones. All strains isolated from pinnipeds bear characteristics of a highly pathogenic form for of avian influenza in poultry. Amino acid substitutions, previously shown to confer an adaptive advantage for infecting mammals, were observed in different genes in all pinniped species studied.

The Arrival of Highly Pathogenic Avian Influenza Viruses in North America, Ensuing Epizootics in Poultry and Dairy Farms and Difficulties in Scientific Naming

The highly pathogenic avian influenza virus (HPAIV) H5N1, first isolated in 1996 in China, spread rapidly across Eurasia and caused major epizootics in wild and domesticated birds, as well as spillover infections in humans characterised by high mortality. Avian influenza viruses are therefore candidate viruses for a human pandemic. Surprisingly, HPAIV was not isolated in North America until 2014. With the help of intensive biological sampling and viral genome sequencing, the intrusion of HPAIV into North America could be retraced to two separate events. First, migratory birds carried HPAIV from East Siberia via Beringia and dispersed the virus along the Pacific flyway. After reassortment with genes of local low pathogenic avian influenza viruses, HPAIV H5 caused 2015 a major epizootic on poultry farms in the US Mid-West. After costly containment, HPAIV dropped below the detection limit. In 2021, Eurasian HPAIV H5 viruses arrived a second time in North America, carried by migratory birds to Canada via the Atlantic flyway, using Iceland as a stop. The H5 virus then spread with water birds along the East Coast of the United States and dispersed across the United States. In contrast to the 2015 poultry outbreak, spillover infections into diverse species of mammals were now observed. The events culminated in the 2024 HPAIV H5 epizootic in dairy cows affecting 300 dairy herds in 14 US states. The cattle epizootic was spread mainly by milking machinery and animal transport. On affected farms infected cats developed fatal neurological diseases. Retail milk across the United States frequently contains viral RNA, but so far only a few milk farm workers have developed mild symptoms. The tracing of HPAIV with viral genome sequencing complicated the taxonomical naming of influenza viruses raising fundamental problems in how to mirror biological complexity in written plain language, rendering communication with the lay public difficult.

Evolution of H7N9 highly pathogenic avian influenza virus in the context of vaccination

Human infections with the H7N9 influenza virus have been eliminated in China through vaccination of poultry; however, the H7N9 virus has not yet been eradicated from poultry. Carefully analysis of H7N9 viruses in poultry that have sub-optimal immunity may provide a unique opportunity to witness the evolution of highly pathogenic avian influenza virus in the context of vaccination. Between January 2020 and June 2023, we isolated 16 H7N9 viruses from samples we collected during surveillance and samples that were sent to us for disease diagnosis. Genetic analysis indicated that these viruses belonged to a single genotype previously detected in poultry. Antigenic analysis indicated that 12 of the 16 viruses were antigenically close to the H7-Re4 vaccine virus that has been used since January 2022, and the other four viruses showed reduced reactivity with the vaccine. Animal studies indicated that all 16 viruses were nonlethal in mice, and four of six viruses showed reduced virulence in chickens upon intranasally inoculation. Importantly, the H7N9 viruses detected in this study exclusively bound to the avian-type receptors, having lost the capacity to bind to human-type receptors. Our study shows that vaccination slows the evolution of H7N9 virus by preventing its reassortment with other viruses and eliminates a harmful characteristic of H7N9 virus, namely its ability to bind to human-type receptors.

Influenza A Virus Antibodies in Ducks and Introduction of Highly Pathogenic Influenza A(H5N1) Virus, Tennessee, USA

Testing of ducks in Tennessee, United States, before introduction of highly pathogenic influenza A(H5N1) virus demonstrated a high prevalence of antibodies to influenza A virus but very low prevalence of antibodies to H5 (25%) or H5 and N1 (13%) subtypes. Antibody prevalence increased after H5N1 introduction.

Genomic characterization of highly pathogenic avian influenza A H5N1 virus newly emerged in dairy cattle

In March 2024, the emergence of highly pathogenic avian influenza (HPAI) A (H5N1) infections in dairy cattle was detected in the United Sates for the first time. We genetically characterize HPAI viruses from dairy cattle showing an abrupt drop in milk production, as well as from two cats, six wild birds, and one skunk. They share nearly identical genome sequences, forming a new genotype B3.13 within the 2.3.4.4b clade. B3.13 viruses underwent two reassortment events since 2023 and exhibit critical mutations in HA, M1, and NS genes but lack critical mutations in PB2 and PB1 genes, which enhance virulence or adaptation to mammals. The PB2 E627 K mutation in a human case associated with cattle underscores the potential for rapid evolution post infection, highlighting the need for continued surveillance to monitor public health threats.

Genotypic Clustering of H5N1 Avian Influenza Viruses in North America Evaluated by Ordination Analysis

The introduction of HPAI H5N1 clade 2.3.4.4b viruses to North America in late 2021 resulted in avian influenza outbreaks in poultry, mortality events in many wild bird species, and spillovers into many mammalian species. Reassortment events with North American low-pathogenic virus were identified as early as February 2022 and over 100 genotypes have been characterized. Such diversity increases the complexity and time required for monitoring virus evolution. Here, we performed ordination and clustering analyses on sequence data from H5N1 viruses identified in North America between January 2020 and December 2023 to visualize the genotypic diversity of viruses in poultry and wildlife populations. Our results reveal that ordination- and cluster-based approaches can complement traditional phylogenetic analyses specifically for the preliminary assignment of H5N1 viruses to genotypic groups or to identify novel genotypes. Our study expands current knowledge on the genotypic diversity of H5N1 viruses in North America and describes a rapid approach for early virus genotype assignment.

Highly Pathogenic H5N1 Influenza A Virus (IAV) in Blue-Winged Teal in the Mississippi Flyway Is Following the Historic Seasonal Pattern of Low-Pathogenicity IAV in Ducks

Highly pathogenic H5N1 (HP H5N1) influenza A virus (IAV) has been detected annually in North American ducks since its introduction during 2021, but it is unknown if this virus will follow the same seasonal and geographic patterns that have been observed with low-pathogenicity (LP) IAV in this reservoir. We monitored blue-winged teal in the Mississippi flyway prior to the detection of HP H5N1 and during two post-introduction migration cycles from spring 2022 to spring 2024, testing birds for infection and antibodies to IAV nucleoprotein (NP), hemagglutinin subtype H5, and neuraminidase subtype N1. Antigens representing clade 2.3.4.4b HP H5 and LP North American H5 were used for hemagglutination inhibition (HI) and virus neutralization (VN) tests for H5 antibodies. Virologic results were consistent with historic seasonal and geographic patterns reported for LP IAV with peak infections occurring in pre-migration staging areas in Minnesota during fall 2022. However, the high prevalence of the H5 subtype was exceptional compared to historic prevalence estimates at this same site and for the Mississippi flyway. HP H5N1 was detected on wintering areas in Louisiana and Texas during the fall of that same year and this was followed by an increase in estimated antibody prevalence to NP, H5, and N1 with no HP H5N1 detections during the wintering or spring migration periods of 2022/2023. HP H5N1 was not detected in Minnesota during fall 2023 but was detected from a single bird in Louisiana. However, a similar increase in antibody prevalence was observed during the winter and spring period of 2023 and 2024. Over the two migration cycles, there was a temporal shift in observed prevalence and relative titers against the H5 antigens with a higher proportion of ducks testing positive to the 2.3.4.4b H5 antigen and higher relative titer to that antigen compared to the representative LP North American H5 antigen. The seasonal and geographic patterns observed appear to be driven by population immunity during the migration cycle. Results support an initial high infection rate of HP H5N1 in blue-winged teal in the Mississippi flyway followed by a high prevalence of antibodies to NP, H5, and N1. Although prevalence was much reduced in the second migration cycle following introduction, it is not known if this pattern will persist in the longer term or affect historic patterns of subtype diversity in this reservoir.

Multi-Year Mortality Due to Staphylococcal Arthritis and Osteomyelitis with Sandspur-Associated Injury in Juvenile Black Skimmers (Rynchops niger) at Nesting Colonies in Southwest Florida, USA

The black skimmer (Rynchops niger) is a state-threatened, colonially nesting seabird in Florida, USA. Conservation threats include habitat alteration, human disturbances, severe weather, and predation. During nest monitoring (May-September, 2020-2022), black skimmer juveniles at colonies on Fort Myers Beach and Marco Island, Florida, had polyarthritis and died or were euthanized due to severe illness. Similarly-aged skimmers from geographically distant (considered unaffected) colonies were evaluated for comparison (2021-2023). We documented field, clinical, radiographical, and pathological findings to characterize disease and purported pathogenesis. The majority were lame and lethargic, in poor nutritional condition, and dehydrated. Additionally, 8/23 of the skimmers with dermatitis and arthritis from affected colonies also had penetrating sandspurs associated with skin ulceration, scabbing, and/or hemorrhage. The affected joints were often in limbs (interphalangeal and hock; less commonly stifle, elbow, carpus). A postmortem evaluation and bacteriology revealed Staphylococcal aureus-associated dermatitis, arthritis, tenosynovitis, and/or osteomyelitis in 21/22 of the juvenile skimmers from southwestern nest colonies. Staphylococcus aureus dissemination to internal organs occurred in 10/13 of the skimmers tested. Among skimmers evaluated from distant colonies, 5/10 that were examined histologically had skin crusting and inflammation but lacked arthritis. Occasional coinfections were documented (e.g., West Nile virus, Gram-negative bacilli). The results suggest that staphylococcal joint disease originated from sandspur-induced skin damage, followed by hematogenous dissemination to the joints and, occasionally, the internal organs. Additional nest sites should be tested to evaluate disease risk and potentially contributing environmental factors. We recommend that site managers employ techniques that reduce the risk of skimmer interactions with sandspurs.

Epidemiological data of an influenza A/H5N1 outbreak in elephant seals in Argentina indicates mammal-to-mammal transmission

H5N1 high pathogenicity avian influenza virus has killed thousands of marine mammals in South America since 2022. Here we report epidemiological data and full genome characterization of clade 2.3.4.4b H5N1 HPAI viruses associated with a massive outbreak in southern elephant seals (Mirounga leonina) at Península Valdés, Argentina, in October 2023. We also report on H5N1 viruses in concurrently dead terns. Our genomic analysis shows that viruses from pinnipeds and terns in Argentina form a distinct clade with marine mammal viruses from Peru, Chile, Brazil and Uruguay. Additionally, these marine mammal clade viruses share an identical set of mammalian adaptation mutations which were also present in tern viruses. Our combined ecological and phylogenetic data support mammal-to-mammal transmission and occasional mammal-to-bird spillover and suggest multinational transmission of H5N1 viruses in mammals. We reflect that H5N1 viruses becoming more evolutionary flexible and adapting to mammals in new ways could have global consequences for wildlife, humans, and/or livestock.

Global influenza threatens conservation

How avian influenza virus will continue to spread and circulate among wildlife is unclear.

Genetic and pathogenic potential of highly pathogenic avian influenza H5N8 viruses from live bird markets in Egypt in avian and mammalian models

Since its first isolation from migratory birds in Egypt in 2016, highly pathogenic avian influenza (HPAI) H5N8 has caused several outbreaks among domestic poultry in various areas of the country affecting poultry health and production systems. However, the genetic and biological properties of the H5N8 HPAI viruses have not been fully elucidated yet. In this study, we aimed to monitor the evolution of circulating H5N8 viruses and identify the pathogenicity and mammalian adaptation in vitro and in vivo. Three H5N8 HPAI viruses were used in this study and were isolated in 2021-2022 from poultry and wild birds during our routine surveillance. RNA extracts were subjected to full genome sequencing. Genetic, phylogenetic, and antigenic analyses were performed to assess viral characteristics and similarities to previously isolated viruses. Phylogenetic analysis showed that the hemagglutinin genes of the three isolates belonged to clade 2.3.4.4b and grouped with the 2019 viruses from G3 with high similarity to Russian and European lineages. Multiple basic amino acids were observed at cleavage sites in the hemagglutinin proteins of the H5N8 isolates, indicating high pathogenicity. In addition, several mutations associated with increased virulence and polymerase activity in mammals were observed. Growth kinetics assays showed that the H5N8 isolate is capable of replicating efficiently in mammalian cells lines. In vivo studies were conducted in SPF chickens (White Leghorn), mice, and hamsters to compare the virological characteristics of the 2022 H5N8 isolates with previous H5N8 viruses isolated in 2016 from the first introduction. The H5N8 viruses caused lethal infection in all tested chickens and transmitted by direct contact. However, we showed that the 2016 H5N8 virus causes a higher mortality in chickens compared to 2022 H5N8 virus. Moreover, the 2022 virus can replicate efficiently in hamsters and mice without preadaptation causing systemic infection. These findings underscore the need for continued surveillance of H5 viruses to identify circulating strains, determine the commercial vaccine's effectiveness, and identify zoonotic potential.

Licensed H5N1 vaccines generate cross-neutralizing antibodies against highly pathogenic H5N1 clade 2.3.4.4b influenza virus

The emergence of highly pathogenic avian influenza (HPAI) H5N1 clade 2.3.4.4b viruses and their transmission to dairy cattle and animals, including humans, poses a major global public health threat. Therefore, the development of effective vaccines and therapeutics against H5N1 clade 2.3.4.4b virus is considered a public health priority. In the United States, three H5N1 vaccines derived from earlier strains of HPAI H5N1 (A/Vietnam, clade 1, and A/Indonesia, clade 2.1) virus, with (MF59 or AS03) or without adjuvants, are licensed and stockpiled for pre-pandemic preparedness, but whether they can elicit neutralizing antibodies against circulating H5N1 clade 2.3.4.4b viruses is unknown. In this study, we evaluated the binding, hemagglutination inhibition and neutralizing antibody response generated after vaccination of adults with the three licensed vaccines. Individuals vaccinated with the two adjuvanted licensed H5N1 vaccines generated cross-reactive binding and cross-neutralizing antibodies against the HPAI clade 2.3.4.4b A/Astrakhan/3212/2020 virus. Seroconversion rates of 60-95% against H5 clade 2.3.4.4b were observed after two doses of AS03-adjuvanted-A/Indonesia or three doses of MF59-adjuvanted-A/Vietnam vaccine. These findings suggest that the stockpiled US-licensed adjuvanted H5N1 vaccines generate cross-neutralizing antibodies against circulating HPAI H5N1 clade 2.3.4.4b in humans and may be useful as bridging vaccines until updated H5N1 vaccines become available.

Spillover of highly pathogenic avian influenza H5N1 virus to dairy cattle

The highly pathogenic avian influenza (HPAI) H5N1 virus clade 2.3.4.4b has caused the death of millions of domestic birds and thousands of wild birds in the USA since January 2022 (refs. 1-4). Throughout this outbreak, spillovers to mammals have been frequently documented5-12. Here we report spillover of the HPAI H5N1 virus to dairy cattle across several states in the USA. The affected cows displayed clinical signs encompassing decreased feed intake, altered faecal consistency, respiratory distress and decreased milk production with abnormal milk. Infectious virus and viral RNA were consistently detected in milk from affected cows. Viral distribution in tissues via immunohistochemistry and in situ hybridization revealed a distinct tropism of the virus for the epithelial cells lining the alveoli of the mammary gland in cows. Whole viral genome sequences recovered from dairy cows, birds, domestic cats and a raccoon from affected farms indicated multidirectional interspecies transmissions. Epidemiological and genomic data revealed efficient cow-to-cow transmission after apparently healthy cows from an affected farm were transported to a premise in a different state. These results demonstrate the transmission of the HPAI H5N1 clade 2.3.4.4b virus at a non-traditional interface, underscoring the ability of the virus to cross species barriers.

Infection of South American coatis (Nasua nasua) with highly pathogenic avian influenza H5N1 virus displaying mammalian adaptive mutations

Deadly outbreaks among poultry, wild birds, and carnivorous mammals by the highly pathogenic H5N1 virus of the clade 2.3.4.4b have been reported in South America. The increasing virus incidence in various mammal species poses a severe zoonotic and pandemic threat. In Uruguay, the clade 2.3.4.4b viruses were first detected in February 2023, affecting wild birds and backyard poultry. Three months after the first reported case in Uruguay, the disease affected a population of 23 coatis (Nasua) in an ecological park. Most animals became infected, likely directly or indirectly from wild birds in the park, and experienced sudden death. Five animals from the colony survived, and four of them developed antibodies. The genomes of the H5N1 strains infecting coatis belonged to the B3.2 genotype of the clade 2.3.4.4b. Genomes from coatis were closely associated with those infecting backyard poultry, but transmission likely occurred through wild birds. Notable, two genomes have a 627K substitution in the RNA polymerase PB2 subunit, a hallmark amino acid linked to mammalian adaptation. Our findings support the ability of the avian influenza virus of the 2.3.4.4b clade to infect and transmit among terrestrial mammals with high pathogenicity and undergo rapid adaptive changes. It also highlights the coatis' ability to develop immunity and naturally clear the infection.

Hot topic: Influenza A H5N1 virus exhibits a broad host range, including dairy cows

The widespread circulation of highly pathogenic avian influenza (HPAI) H5N1 clade 2.3.4.4b in wild birds in North America since late 2021 has resulted in multiple outbreaks in commercial and backyard poultry leading to major economic losses. Since the emergence of the virus in North America, multiple reassortment events have led to the emergence of many new variant genotypes that have been isolated from wild birds, with several viruses spilling over into poultry and other terrestrial and aquatic mammalian hosts. Notably, the most recent emerging HPAI H5N1 reassortant genotype B3.13 spilled over into dairy cattle (Bos taurus), resulting in unprecedented efficient transmission of the virus in this species, the first case of sustained transmission in a mammalian species. The transmission pathways involved in the spread of the virus from its first detection in Texas to several other states are complex. However, movement of subclinically infected cattle likely played a major role in virus spread. Infection in dairy cattle is characterized by the virus's tropism for milk-secreting cells in the mammary gland, leading to high viral load and shedding in milk. Replication of the virus in milk-secreting cells results in destruction of infected cells leading to severe viral mastitis, which is characterized by marked changes in milk quality (altered consistency and color) and pronounced decline in milk production by clinically affected animals. Here, we provide an overview of the HPAI H5N1 panzootic virus and discuss its host range and the current knowledge of its pathogenesis in the new bovine host.

Review of the Highly Pathogenic Avian Influenza in Argentina in 2023: Chronicle of Its Emergence and Control in Poultry

Highly pathogenic avian influenza (HPAI) is a highly contagious viral disease that represents a significant threat to poultry production worldwide. Variants of the HPAI virus (HPAIV) H5A/Goose/GuangDong/1/96 (H5 Gs/GD/96) lineage have caused five intercontinental epizootic waves, with the most recent, clade 2.3.4.4b, reaching Argentina in February 2023. Initially detected in wild birds, the virus quickly spread to backyard and commercial poultry farms, leading to economic losses, including the loss of influenza-free status (IFS). By March/April 2023 the epidemic had peaked and vaccination was seriously considered. However, the success of strict stamping-out measures dissuaded the National Animal Health Authority (SENASA) from authorizing any vaccine. Suspected cases sharply declined by May, and the last detection in commercial poultry was reported in June. The effective control and potential eradication of HPAIV in Argentina were due to SENASA's early detection and rapid response, supported by private companies, veterinarians, and other stakeholders. Stamping-out measures have been effective for virus elimination and reduced farm-to-farm transmission; however, as the virus of this clade may remain present in wild birds, the risk of reintroduction into poultry production is high. Therefore, maintaining continuous active surveillance will be crucial for promptly detecting any new HPAIV incursion and taking appropriate action to contain virus dissemination.