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Avian metapneumovirus (aMPV) poses a significant threat to the poultry industry worldwide, primarily affecting turkeys and chickens. The recent detection of aMPV-A and -B subtypes in the United States marks a significant shift after a prolonged period free of aMPV following the eradication of the previously circulating subtype C. Hence, the demand for molecular diagnostic tests for aMPV has arisen due to their limited availability in the US market. In this study, we present the molecular characterization based on the complete genome sequence of aMPV subtype A, which was detected in the US for the first time. Four RT-qPCR positive samples were subjected to next-generation sequencing analysis, resulting in the assembly of one complete and one near-complete genome sequences. Phylogenetic analysis revealed that the isolated strains clustered within the aMPV-A subtype and were most closely related to recent Mexican strains. A detailed amino acid analysis identified unique mutations in the G gene of the US isolates compared to Mexican strains. Additionally, we compared the performance, cross-reactivity, and limit of detection of our revised aMPV subtype-specific RT-qPCR test with two commercial kits, demonstrating similar detection and subtyping capabilities. These findings highlight the importance of accurate diagnostic methods for disease management in the poultry industry, provide valuable insights into the epidemiology of aMPV, and underscore the need for continued vigilance and surveillance to mitigate its impact on poultry production.
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Based on the pathogenicity in chickens, most H1-H16 avian influenza viruses (AIV) cause mild diseases, whereas some of the H5 and H7 AI viruses cause severe, systemic disease. The number of basic amino acids in the haemagglutinin (HA) cleavage site of AIV plays a critical role in pathogenicity. As we gain a greater understanding of the molecular mechanisms of pathogenicity, genome sequencing of the HA0 cleavage site has assumed a greater role in assessment of the potential pathogenicity of H5 and H7 viruses. We validated the use of HA cleavage site motif analysis by comparing molecular pathotyping data against experimental in vivo (intravenous pathogenicity index [IVPI] and lethality) data for determination of both low pathogenicity and high pathogenicity AI virus declaration with the goal of expediting pathotype confirmation and further reducing the reliance on in vivo testing. Our data provide statistical support to the continued use of molecular determination of pathotype for AI viruses based on the HA cleavage site sequence in the absence of an in vivo study determination. This approach not only expedites the declaration process of highly pathogenic AIV (HPAIV) but also reduces the need for experimental in vivo testing of H5 and H7 viruses.
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Pollos , Genoma Viral , Glicoproteínas Hemaglutininas del Virus de la Influenza , Virus de la Influenza A , Gripe Aviar , Animales , Gripe Aviar/virología , Pollos/virología , Virus de la Influenza A/patogenicidad , Virus de la Influenza A/genética , Glicoproteínas Hemaglutininas del Virus de la Influenza/genética , Virulencia , Fenotipo , Enfermedades de las Aves de Corral/virologíaRESUMEN
We report the discovery of two bluetongue virus serotype 6 (BTV-6) reassortants recovered from a domestic sheep and a free-ranging mule deer in northern Colorado. At the time of this publication, whole-genome sequencing of BTV-6 isolates in the Western U.S. have not been undertaken. These findings reflect the incursive movement of geographically distinct BTV serotypes into important agricultural areas of the U.S. and demonstrate reassortment with regionally circulating serotypes.
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Virus de la Lengua Azul , Lengua Azul , Ciervos , Enfermedades de las Ovejas , Ovinos , Animales , Oveja Doméstica , Lengua Azul/epidemiología , Serogrupo , Colorado/epidemiología , EquidaeRESUMEN
We describe the pathology of natural infection with highly pathogenic avian influenza A(H5N1) virus of Eurasian lineage Goose/Guangdong clade 2.3.4.4b in 67 wild terrestrial mammals throughout the United States during April 1âJuly 21, 2022. Affected mammals include 50 red foxes (Vulpes vulpes), 6 striped skunks (Mephitis mephitis), 4 raccoons (Procyon lotor), 2 bobcats (Lynx rufus), 2 Virginia opossums (Didelphis virginiana), 1 coyote (Canis latrans), 1 fisher (Pekania pennanti), and 1 gray fox (Urocyon cinereoargenteus). Infected mammals showed primarily neurologic signs. Necrotizing meningoencephalitis, interstitial pneumonia, and myocardial necrosis were the most common lesions; however, species variations in lesion distribution were observed. Genotype analysis of sequences from 48 animals indicates that these cases represent spillover infections from wild birds.
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Subtipo H5N1 del Virus de la Influenza A , Gripe Aviar , Animales , Estados Unidos/epidemiología , Subtipo H5N1 del Virus de la Influenza A/genética , Mephitidae , Gripe Aviar/epidemiología , Mamíferos , Animales Salvajes , ZorrosRESUMEN
Highly pathogenic avian influenza viruses (HPAIVs) of subtype H5 of the Gs/GD/96 lineage remain a major threat to poultry due to endemicity in wild birds. H5N1 HPAIVs from this lineage were detected in 2021 in the United States (U.S.) and since then have infected many wild and domestic birds. We evaluated the pathobiology of an early U.S. H5N1 HPAIV (clade 2.3.4.4b, 2021) and two H5N8 HPAIVs from previous outbreaks in the U.S. (clade 2.3.4.4c, 2014) and Europe (clade 2.3.4.4b, 2016) in chickens and turkeys. Differences in clinical signs, mean death times (MDTs), and virus transmissibility were found between chickens and turkeys. The mean bird infective dose (BID50) of the 2021 H5N1 virus was approximately 2.6 log10 50% embryo infective dose (EID50) in chickens and 2.2 log10 EID50 in turkeys, and the virus transmitted to contact-exposed turkeys but not chickens. The BID50 for the 2016 H5N8 virus was also slightly different in chickens and turkeys (4.2 and 4.7 log10 EID50, respectively); however, the BID50 for the 2014 H5N8 virus was higher for chickens than turkeys (3.9 and ~0.9 log10 EID50, respectively). With all viruses, turkeys took longer to die (MDTs of 2.6-8.2 days for turkeys and 1-4 days for chickens), which increased the virus shedding period and facilitated transmission to contacts.
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Subtipo H5N1 del Virus de la Influenza A , Subtipo H5N8 del Virus de la Influenza A , Virus de la Influenza A , Gripe Aviar , Enfermedades de las Aves de Corral , Animales , Estados Unidos/epidemiología , Subtipo H5N8 del Virus de la Influenza A/genética , Pollos , Subtipo H5N1 del Virus de la Influenza A/genética , Pavos , Virulencia , Virus de la Influenza A/genética , Animales SalvajesRESUMEN
Introduction: The 2022-2023 highly pathogenic avian influenza (HPAI) H5N1 outbreak in the United States (U.S.) is the largest and most costly animal health event in U.S. history. Approximately 70% of commercial farms affected during this outbreak have been turkey farms. Methods: We conducted a case-control study to identify potential risk factors for introduction of HPAI virus onto commercial meat turkey operations. Data were collected from 66 case farms and 59 control farms in 12 states. Univariate and multivariable analyses were conducted to compare management and biosecurity factors on case and control farms. Results: Factors associated with increased risk of infection included being in an existing control zone, having both brooders and growers, having toms, seeing wild waterfowl or shorebirds in the closest field, and using rendering for dead bird disposal. Protective factors included having a restroom facility, including portable, available to crews that visit the farm and workers having access and using a shower at least some of the time when entering a specified barn. Discussion: Study results provide a better understanding of risk factors for HPAI infection and can be used to inform prevention and control measures for HPAI on U.S. turkey farms.
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Clade 2.3.4.4b highly pathogenic avian influenza (HPAI) A(H5N1) viruses that are responsible for devastating outbreaks in birds and mammals pose a potential threat to public health. Here, we evaluated their susceptibility to influenza antivirals. Of 1,015 sequences of HPAI A(H5N1) viruses collected in the United States during 2022, eight viruses (â¼0.8%) had a molecular marker of drug resistance to an FDA-approved antiviral: three adamantane-resistant (M2-V27A), four oseltamivir-resistant (NA-H275Y), and one baloxavir-resistant (PA-I38T). Additionally, 31 viruses contained mutations that may reduce susceptibility to inhibitors of neuraminidase (NA) (n = 20) or cap-dependent endonuclease (CEN) (n = 11). A panel of 22 representative viruses was tested phenotypically. Overall, clade 2.3.4.4b A(H5N1) viruses lacking recognized resistance mutations were susceptible to FDA-approved antivirals. Oseltamivir was least potent at inhibiting NA activity, while the investigational NA inhibitor AV5080 was most potent, including against NA mutants. A novel NA substitution T438N conferred 12-fold reduced inhibition by zanamivir, and in combination with the known marker N295S, synergistically affected susceptibility to all five NA inhibitors. In cell culture-based assays HINT and IRINA, the PA-I38T virus displayed 75- to 108-fold and 37- to 78-fold reduced susceptibility to CEN inhibitors, baloxavir and the investigational AV5116, respectively. Viruses with PA-I38M or PA-A37T showed 5- to 10-fold reduced susceptibilities. As HPAI A(H5N1) viruses continue to circulate and evolve, close monitoring of drug susceptibility is needed for risk assessment and to inform decisions regarding antiviral stockpiling.
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Subtipo H5N1 del Virus de la Influenza A , Gripe Aviar , Animales , Estados Unidos/epidemiología , Antivirales/farmacología , Oseltamivir/farmacología , Subtipo H5N1 del Virus de la Influenza A/genética , Gripe Aviar/epidemiología , Inhibidores Enzimáticos/farmacología , Aves , Mamíferos , Farmacorresistencia Viral/genética , NeuraminidasaRESUMEN
We report the spillover of highly pathogenic avian influenza A(H5N1) into marine mammals in the northeastern United States, coincident with H5N1 in sympatric wild birds. Our data indicate monitoring both wild coastal birds and marine mammals will be critical to determine pandemic potential of influenza A viruses.
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Subtipo H5N1 del Virus de la Influenza A , Virus de la Influenza A , Gripe Aviar , Phocidae , Animales , Gripe Aviar/epidemiología , Aves , Brotes de Enfermedades , Animales Salvajes , New England/epidemiologíaRESUMEN
As exemplified by the global response to the SARS-CoV-2 pandemic, whole-genome sequencing played an important role in monitoring the evolution of novel viral variants and provided guidance on potential antiviral treatments. The recent rapid and extensive introduction and spread of highly pathogenic avian influenza virus in Europe, North America, and elsewhere raises the need for similarly rapid sequencing to aid in appropriate response and mitigation activities. To facilitate this objective, we investigate a next-generation sequencing platform that uses a portable nanopore sequencing device to generate and present data in real time. This platform offers the potential to extend in-house sequencing capacities to laboratories that may otherwise lack resources to adopt sequencing technologies requiring large benchtop instruments. We evaluate this platform for routine use in a diagnostic laboratory. In this study, we evaluate different primer sets for the whole genome amplification of influenza A virus and evaluate five different library preparation approaches for sequencing on the nanopore platform using the MinION flow cell. A limited amplification procedure and a rapid procedure are found to be best among the approaches taken.
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Live bird market (LBM) surveillance was conducted in the Northeast United States (US) to monitor for the presence of avian influenza viruses (AIV) in domestic poultry and market environments. A total of 384 H2N2 low pathogenicity AIV (LPAIV) isolated from active surveillance efforts in the LBM system of New York, Connecticut, Rhode Island, New Jersey, Pennsylvania, and Maryland during 2013-2019 were included in this analysis. Comparative phylogenetic analysis showed that a wild-bird-origin H2N2 virus may have been introduced into the LBMs in Pennsylvania and independently evolved since March 2012 followed by spread to LBMs in New York City during late 2012-early 2013. LBMs in New York state played a key role in the maintenance and dissemination of the virus to LBMs in the Northeast US including reverse spread to Pennsylvania LBMs. The frequent detections in the domestic ducks and market environment with viral transmissions between birds and environment possibly led to viral adaptation and circulation in domestic gallinaceous poultry in LBMs, suggesting significant roles of domestic ducks and contaminated LBM environment as reservoirs in maintenance and dissemination of H2N2 LPAIV.
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We detected Eurasian-origin highly pathogenic avian influenza A(H5N1) virus belonging to the Gs/GD lineage, clade 2.3.4.4b, in wild waterfowl in 2 Atlantic coastal states in the United States. Bird banding data showed widespread movement of waterfowl within the Atlantic Flyway and between neighboring flyways and northern breeding grounds.
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Subtipo H5N1 del Virus de la Influenza A , Virus de la Influenza A , Gripe Aviar , Gripe Humana , Animales , Animales Salvajes , Aves , Humanos , Virus de la Influenza A/genética , Gripe Aviar/epidemiología , Filogenia , Estados Unidos/epidemiologíaRESUMEN
We report whole-genome sequencing of influenza A virus (IAV) with 100% diagnostic sensitivity and results available in <24-48 h using amplicon-based nanopore sequencing technology (MinION) on clinical material from wild waterfowl (n = 19), commercial poultry (n = 4), and swine (n = 3). All 8 gene segments of IAV including those from 14 of the 18 recognized hemagglutinin subtypes and 9 of the 11 neuraminidase subtypes were amplified in their entirety at >500× coverage from each of 16 reference virus isolates evaluated. Subgenomic viral sequences obtained in 3 cases using Sanger sequencing as the reference standard were identical to those obtained when sequenced using the MinION approach. An inter-laboratory comparison demonstrated reproducibility when comparing 2 independent laboratories at ≥99.8% across the entirety of the IAV genomes sequenced.
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Enfermedades de las Aves/diagnóstico , Virus de la Influenza A/aislamiento & purificación , Gripe Aviar/diagnóstico , Secuenciación de Nanoporos/veterinaria , Infecciones por Orthomyxoviridae/veterinaria , Enfermedades de los Porcinos/diagnóstico , Secuenciación Completa del Genoma/veterinaria , Animales , Animales Salvajes , Enfermedades de las Aves/virología , Pollos , Patos , Virus de la Influenza A/genética , Gripe Aviar/virología , Secuenciación de Nanoporos/métodos , Infecciones por Orthomyxoviridae/diagnóstico , Infecciones por Orthomyxoviridae/virología , Enfermedades de las Aves de Corral/diagnóstico , Enfermedades de las Aves de Corral/virología , Sus scrofa , Porcinos , Enfermedades de los Porcinos/virología , Pavos , Secuenciación Completa del Genoma/métodosRESUMEN
In August 2020, outbreaks of coronavirus disease were confirmed on mink farms in Utah, USA. We surveyed mammals captured on and around farms for evidence of infection or exposure. Free-ranging mink, presumed domestic escapees, exhibited high antibody titers, suggesting a potential severe acute respiratory syndrome coronavirus 2 transmission pathway to native wildlife.
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Animales Salvajes/virología , Visón/virología , SARS-CoV-2/aislamiento & purificación , Animales , COVID-19/diagnóstico , COVID-19/epidemiología , COVID-19/transmisión , COVID-19/veterinaria , Granjas , Mamíferos/virología , SARS-CoV-2/genética , SARS-CoV-2/inmunología , Utah/epidemiología , Zoonosis/diagnóstico , Zoonosis/epidemiología , Zoonosis/transmisiónRESUMEN
Low pathogenicity avian influenza (H5N2) virus was detected in poultry in the Dominican Republic in 2007 and re-emerged in 2017. Whole-genome sequencing and phylogenetic analysis show introduction of an H5N2 virus lineage from Mexico into poultry in the Dominican Republic, then divergence into 3 distinct genetic subgroups during 2007-2019.
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Subtipo H5N2 del Virus de la Influenza A , Gripe Aviar , Enfermedades de las Aves de Corral , Animales , República Dominicana/epidemiología , Gripe Aviar/epidemiología , México , Filogenia , Aves de Corral , VirulenciaRESUMEN
An outbreak of low-pathogenicity avian influenza A(H7N3) virus of North American wild bird lineage occurred on commercial turkey farms in North Carolina and South Carolina, USA, during March-April 2020. The virus mutated to the highly pathogenic form in 1 house on 1 farm via recombination with host 28S rRNA.
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Gripe Aviar , Enfermedades de las Aves de Corral , Aves de Corral , Animales , Aves , Brotes de Enfermedades , Subtipo H7N3 del Virus de la Influenza A , Gripe Aviar/epidemiología , North Carolina , Aves de Corral/virología , Enfermedades de las Aves de Corral/epidemiología , Estados Unidos/epidemiologíaRESUMEN
Wild bird migration and illegal trade of infected poultry, eggs, and poultry products have been associated with the spread of avian influenza viruses (AIV). During 1992-1996, H7N1 and H7N8 low pathogenic AIV (LPAIV) were identified from captive wild birds; such as Pekin robin (Leiothrix lutea), magpie robin (Copsychus saularis), flycatcher sp. (genus Empidonax), a species of softbill and parakeet, sun conure (Aratinga solstitialis), painted conure (Pyrrhura picta), fairy bluebird (Irena puella), and common iora (Aegithina tiphia), kept in aviaries or quarantine stations in England, The Netherlands, Singapore and the United States (U.S.). In this study, we sequenced these H7 viruses isolated from quarantine facilities and aviaries using next-generation sequencing and conducted a comparative phylogenetic analysis of complete genome sequences to elucidate spread patterns. The complete genome sequencing and phylogenetic analysis suggested that H7 viruses originated from a common source, even though they were obtained from birds in distant geographical regions. All H7N1 and H7N8 viruses were LPAIV, except a H7N1 highly pathogenic AIV (HPAIV), A/Pekin robin/California/30412/1994(H7N1) virus. Our results support the continued need for regulation of the captive wild bird trade to reduce the risk of introduction and dissemination of both LPAIV and HPAIV throughout the world.
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Aves/virología , Subtipo H7N1 del Virus de la Influenza A , Subtipo H7N9 del Virus de la Influenza A , Gripe Aviar/transmisión , Gripe Aviar/virología , Animales , Animales Salvajes , Comercio , Genoma Viral , Salud Global , Historia del Siglo XX , Subtipo H7N1 del Virus de la Influenza A/genética , Subtipo H7N1 del Virus de la Influenza A/patogenicidad , Subtipo H7N9 del Virus de la Influenza A/genética , Subtipo H7N9 del Virus de la Influenza A/patogenicidad , Gripe Aviar/epidemiología , Gripe Aviar/historia , Internacionalidad , VirulenciaRESUMEN
In late 2016, an H7N6 low pathogenic avian influenza virus outbreak occurred in domestic turkeys in Central Chile. We characterized the genetic and antigenic properties of the outbreak virus and its experimental transmission in chickens. Our studies demonstrate that the outbreak virus is a reassortment of genes identified from Chilean wild bird viruses between 2013 and 2017 and displays molecular adaptations to poultry and antiviral resistance to adamantanes. Further, these wild bird viruses are also able to transmit in experimentally infected chickens highlighting the need for continued surveillance and improvement of biosecurity in poultry farms.
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Brotes de Enfermedades , Virus de la Influenza A/clasificación , Virus de la Influenza A/aislamiento & purificación , Gripe Aviar/epidemiología , Gripe Aviar/virología , Virus Reordenados/clasificación , Virus Reordenados/aislamiento & purificación , Adamantano/farmacología , Adaptación Biológica , Animales , Animales Domésticos , Antivirales/farmacología , Chile/epidemiología , Farmacorresistencia Viral , Virus de la Influenza A/genética , Virus de la Influenza A/inmunología , Virus Reordenados/genética , Virus Reordenados/inmunología , PavosRESUMEN
In 2017, outbreaks of low and highly pathogenic avian H7N9 viruses were reported in four States in the United States. In total, over 270 000 birds died or were culled, causing significant economic loss. The potential for avian-to-swine transmission of the U.S. avian H7N9 was unknown. In an experimental challenge in swine using a representative low pathogenic H7N9 (A/chicken/Tennessee/17-007431-3/2017; LPAI TN/17) isolated from these events, no infectious virus in the upper and minimal virus in the lower respiratory tract was detected, nor was lung pathology or evidence of transmission in pigs observed, indicating that the virus cannot efficiently infect swine.
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Transmisión de Enfermedad Infecciosa , Especificidad del Huésped , Subtipo H7N9 del Virus de la Influenza A/aislamiento & purificación , Gripe Aviar/transmisión , Infecciones por Orthomyxoviridae/veterinaria , Virus Reordenados/aislamiento & purificación , Enfermedades de los Porcinos/virología , Experimentación Animal , Animales , Pollos , Subtipo H7N9 del Virus de la Influenza A/genética , Subtipo H7N9 del Virus de la Influenza A/crecimiento & desarrollo , Gripe Aviar/epidemiología , Gripe Aviar/virología , Infecciones por Orthomyxoviridae/patología , Infecciones por Orthomyxoviridae/virología , Virus Reordenados/genética , Virus Reordenados/crecimiento & desarrollo , Porcinos , Estados Unidos/epidemiologíaRESUMEN
In March 2017, a novel highly pathogenic avian influenza A(H7N9) virus was detected at two commercial broiler breeder facilities in Tennessee, United States. In this study, a wild bird low pathogenic avian influenza A virus, A/blue-winged teal/Wyoming/AH0099021/2016(H7N9), was shown to be the probable precursor of the novel H7N9 virus; this low pathogenic virus has eight possible progenitor genes sharing >â¯99% sequence identity with the novel H7N9 virus. Phylogeographic analyses showed that viral gene constellations that formed and circulated among dabbling ducks contributed to the emergence of the novel H7N9 virus. This is in contrast to the virus that caused the 2016 H7N8 outbreak, which had more genetic contributions from viruses circulating among diving ducks. Study findings support the need for ongoing wild bird surveillance to monitor circulating viruses and to understand possible evolutionary pathways of virus emergence in poultry.
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Evolución Molecular , Subtipo H7N9 del Virus de la Influenza A/patogenicidad , Gripe Aviar/virología , Animales , Animales Domésticos , Animales Salvajes , Aves , Genotipo , Subtipo H7N9 del Virus de la Influenza A/genética , Gripe Aviar/epidemiología , Filogenia , Alineación de Secuencia , Tennessee/epidemiología , Factores de TiempoRESUMEN
Between December 2014 and June 2015, North America experienced the largest recorded foreign animal disease outbreak with over 47 million poultry dead or euthanized from viral exposure to a clade 2.3.4.4 H5 highly pathogenic avian influenza (HPAI) epizootic. Soon after the epizootic began, the U.S. Department of Agriculture (USDA) began testing the efficacy of different vaccines as a possible future control strategy. The aim of these studies were to evaluate the efficacy three H5 vaccines to aid in control of HPAI in commercial turkeys. Three different vaccine technologies were evaluated for efficacy: 1) inactivated reverse genetic laboratory-generated virus encoding a clade 2.3.4.4 H5 hemagglutinin (HA) gene (rgH5), 2) recombinant turkey herpesvirus encoding a clade 2.2. H5 HA (rHVT-AI), and 3) recombinant replication-deficient alphavirus RNA particle vaccine encoding a clade 2.3.4.4 H5 HA (RP-H5). All vaccines tested significantly (P<0.01) increased survival rates between vaccinated and sham vaccinated groups of poults challenged with A/turkey/Minnesota/12582/2015 clade 2.3.4.4 H5N2 HPAI. The rgH5 vaccine had detectable serum hemagglutination inhibition (HI) antibody against the challenge virus, and significantly reduced the frequency and level of viral shedding from oropharyngeal and cloacal swabs at days 2 and 4 post-challenge. Vaccination with only rHVT-AI or RP-H5 was not 100% protective, and failed to significantly reduce viral shedding post-challenge. A combined prime and boost strategy with the rHVT-AI and RP-H5, or rHVT-AI and rgH5, was 100% protective against lethal H5N2 HPAI challenge. Results of these studies led to USDA conditional approval of commercially available recombinant vaccines for use in turkeys as a control measure for clade 2.3.4.4 H5 HPAI epizootics.