Identification and characterization of H2N3 avian influenza virus from backyard poultry and comparison to novel H2N3 swine influenza virus

There are currently 16 identified H subtypes of influenza A; all 16 are known to infect avian species. In 2006 a novel influenza subtype (H2N3) was identified in a swine herd in Missouri. The hemagglutinin (HA) and neuraminidase (NA) genes were found to be avian in origin, raising concern regarding the potential for inter-species transmission of avian viruses to swine and humans. In early 2007, H2N3 influenza virus was isolated from a duck and a chicken from two separate backyard poultry flocks in Ohio. The nearly coincidental isolation of the same subtype in unnatural hosts in the Midwest United States raised the question about the origin of the viruses and the potential for these viruses to adapt to a new host and easily spread to nearby flocks or herds. Therefore, the viruses were further characterized by DNA sequencing and in vivo chicken pathogenicity testing. The virus sequences were compared to those from the 2006 swine isolates. In addition, the avian viruses were tested for cross-reactivity by virus neutralization (VN) and hemagglutination-inhibition (HI) using a panel of H2 reference sera including serum from the Missouri swine virus. Serologic survey on swine herds and poultry flocks in Ohio for H2 virus infection was also conducted to assess virus spreading. Sequence comparisons for the H and N genes demonstrated that the avian viruses were similar, but not identical, to the swine viruses. Accordingly, the avian and swine isolates were also antigenically related as determined by HI and VN assays, suggesting that both avian and swine viruses originated from the same group of H2N3 avian influenza viruses. Although serological surveys using the HI assay on poultry flocks and swine herds in Ohio did not reveal further spreading of H2 virus from the index flocks, continuous surveillance will be necessary. Contemporary H2N3 avian influenza viruses appear to be easily adaptable to poultry and swine, raising concern regarding the potential for inter-species transmission of H2N3 avian virus to humans

An Evaluation of Avian Influenza Virus Whole-Genome Sequencing Approaches Using Nanopore Technology

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

Outbreak of H7N8 Low Pathogenic Avian Influenza in Commercial Turkeys with Spontaneous Mutation to Highly Pathogenic Avian Influenza

Highly pathogenic avian influenza (HPAI) subtype H7N8 was detected in commercial turkeys in January 2016. Control zone surveillance discovered a progenitor low pathogenic avian influenza (LPAI) virus in surrounding turkey flocks. Data analysis supports a single LPAI virus introduction followed by spontaneous mutation to HPAI on a single premises

Outbreak of H7N8 Low Pathogenic Avian Influenza in Commercial Turkeys with Spontaneous Mutation to Highly Pathogenic Avian Influenza

Highly pathogenic avian influenza (HPAI) subtype H7N8 was detected in commercial turkeys in January 2016. Control zone surveillance discovered a progenitor low pathogenic avian influenza (LPAI) virus in surrounding turkey flocks. Data analysis supports a single LPAI virus introduction followed by spontaneous mutation to HPAI on a single premises

H7N1 Low Pathogenicity Avian Influenza Viruses in Poultry in the United States During 2018

Here, we report three detections of H7N1 low pathogenicity avian influenza viruses (LPAIV) from poultry in Missouri (n¼2) and Texas (n¼1) during February and March 2018. Complete genome sequencing and comparative phylogenetic analysis suggest that the H7 LPAIV precursor viruses were circulating in wild birds in North America during the fall and winter of 2017 and spilled over into domestic poultry in Texas and Missouri independently during the spring of 2018. RESUMEN. Nota de investigacio´n—Virus de la influenza aviar de baja patogenicidad H7N1 en avicultura, Estados Unidos, 2018. En este art´ıculo se reportan tres detecciones del virus de influenza aviar de baja patogenicidad H7N1 (LPAIV) en avicultura en Missouri (n¼2) y Texas (n¼1) durante febrero y marzo del 2018. La secuenciacio´n completa del genoma y el ana´lisis filogene´tico comparativo sugieren que precursores de este virus de influenza de baja patogenicidad H7 circulaban en aves silvestres en Ame´rica del Norte durante el oton˜o y el invierno de 2017 y se propagaron a las aves comerciales en Texas y Missouri de forma independiente durante la primavera del 2018

Highly Pathogenic Avian Influenza Viruses and Generation of Novel Reassortants, United States, 2014–2015

Asian highly pathogenic avian influenza A(H5N8) viruses spread into North America in 2014 during autumn bird migration. Complete genome sequencing and phylogenetic analysis of 32 H5 viruses identified novel H5N1, H5N2, and H5N8 viruses that emerged in late 2014 through reassortment with North American low-pathogenicity avian influenza viruses

Highly Pathogenic Avian Influenza Viruses and Generation of Novel Reassortants, United States, 2014–2015

Asian highly pathogenic avian influenza A(H5N8) viruses spread into North America in 2014 during autumn bird migration. Complete genome sequencing and phylogenetic analysis of 32 H5 viruses identified novel H5N1, H5N2, and H5N8 viruses that emerged in late 2014 through reassortment with North American low-pathogenicity avian influenza viruses

Characterization of co-circulating swine influenza A viruses in North America and the identification of a novel H1 genetic clade with antigenic significance.

Multiple genetically and antigenically distinct hemagglutinin genes of the H1 and H3 influenza A virus (IAV) subtypes co-circulate in North American swine. This diversity has evolved by repeated transmission of IAVs from humans to swine and subsequent antigenic drift in swine. To understand the evolutionary dynamics of these diverse HA lineages in North American swine, we undertook a phylogenetic analysis of 1576 H1 and 607 H3 HA gene segments, as well as 834 N1 and 1293 N2 NA gene segments, and 2126 M gene segments. These data revealed yearly co-circulation of H1N1, H1N2, and H3N2 viruses, with three HA clades representing the majority of the HA sequences: of the H1 viruses, 42% were classified as H1δ1 and 40.6% were classified as H1γ; and of the H3 viruses 53% were classified as cluster IV-A H3N2. We detected a genetically distinct minor clade consisting of 37 H1 viruses isolated between 2003 and 2013, which we classified as H1γ-2. We estimated that this clade circulated in swine since approximately 1995, but it was not detected in swine until 2003. Though this clade only represents 1.07% of swine H1 sequences reported over the past 10 years, hemagglutination inhibition (HI) assays demonstrated that representatives of this clade of viruses are antigenically distinct, and, when measured using antigenic cartography, were as many as 7 antigenic units from other H1γ viruses. Therefore vaccines against the contemporary H1γ viruses are not likely to cross-protect against γ-2 viruses. The long-term circulation of these γ-2 viruses suggests that minor populations of viruses may be underreported in the national dataset given the long branch lengths and gaps in detections. The identification of these γ-2 viruses demonstrates the need for robust surveillance to capture the full diversity IAVs in swine in the USA and the importance of antigenic drift in the diversification and emergence of new antigenic variants in swine, which complicates vaccine design.Funding was provided by USDA-ARS and USDA355 APHIS-VS by the Supplemental Appropriations Act of 2009. NSL was funded by USDA-ARS SCA agreement number 58-3625-2-103F and the EC FP7 award number 259949. TKA was funded by USDA ARS SCA agreement number 58-3625-4-070.This is the accepted manuscript. The final version is available at http://www.sciencedirect.com/science/article/pii/S0168170215000799

Intercontinental Movement of Highly Pathogenic Avian Influenza A(H5N1) Clade 2.3.4.4 Virus to the United States, 2021

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

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

Highly pathogenic avian influenza viruses (HPAIVs) of the A/goose/Guangdong/1/1996 lineage H5 clade 2.3.4.4b continue to have a devastating effect on domestic and wild birds. Full genome sequence analyses using 1369 H5N1 HPAIVs detected in the United States (U.S.) in wild birds, commercial poultry, and backyard flocks from December 2021 to April 2022, showed three phylogenetically distinct H5N1 virus introductions in the U.S. by wild birds. Unreassorted Eurasian genotypes A1 and A2 entered the Northeast Atlantic states, whereas a genetically distinct A3 genotype was detected in Alaska. The A1 genotype spread westward via wild bird migration and reassorted with North American wild bird avian influenza viruses. Reassortments of up to five internal genes generated a total of 21 distinct clusters; of these, six genotypes represented 92% of the HPAIVs examined. By phylodynamic analyses, most detections in domestic birds were shown to be point-source transmissions from wild birds, with limited farm-to-farm spread