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Cargnin Faccin F, Cáceres CJ, Gay LC, Seibert B, van Bentem N, Rodriguez LA, Soares Fraiha AL, Cardenas M, Geiger G, Ortiz L, Carnaccini S, Kapczynski DR, Rajao DS, Perez DR. Mass vaccination with reassortment-impaired live H9N2 avian influenza vaccine. NPJ Vaccines 2024; 9:136. [PMID: 39097573 PMCID: PMC11297921 DOI: 10.1038/s41541-024-00923-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 07/12/2024] [Indexed: 08/05/2024] Open
Abstract
Avian influenza poses a severe threat to poultry production and global food security, prompting the development of vaccination programs in numerous countries. Modified live virus (MLV) vaccines, with their potential for mass application, offer a distinct advantage over existing options. However, concerns surrounding reversion, recombination, and unintended transmission have hindered the progress of MLV development for avian influenza in poultry. To address these concerns, we engineered reassortment-impaired, non-transmissible, safe, immunogenic, and protective MLVs through the rearrangement of internal gene segments and additional modifications to the surface gene segments HA and NA. The unique peptide marker aspartic acid-arginine-proline-alanine-valine-isoleucine-alanine-asparragine (DRPAVIAN) was incorporated into HA, while NA was modified to encode the chicken interleukin-18 (ckIL18) gene (MLV-H9N2-IL). In vitro, the MLV-H9N2 and MLV-H9N2-IL candidates demonstrated stability and virus titers comparable to the wild-type H9N2 strain. In chickens, the MLV-H9N2 and MLV-H9N2-IL candidates did not transmit via direct contact. Co-infection studies with wild-type virus confirmed that the altered HA and NA segments exhibited fitness disadvantages and did not reassort. Vaccinated chickens showed no clinical signs upon vaccination, all seroconverted, and the inclusion of ckIL18 in the MLV-H9N2-IL vaccine enhanced neutralizing antibody production. A significant decrease in viral loads post-challenge underscored the protective effect of the MLVs. The MLV-H9N2-IL vaccine, administered via drinking water, proved immunogenic in chickens in a dose-dependent manner, generating protective levels of neutralizing antibodies upon aggressive homologous virus challenge. In summary, this study lays the groundwork for safe MLVs against avian influenza suitable for mass vaccination efforts.
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Affiliation(s)
- Flavio Cargnin Faccin
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - C Joaquin Cáceres
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - L Claire Gay
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Brittany Seibert
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Nick van Bentem
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
- Division of Farm Animal Health, Department Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Luis A Rodriguez
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ana Luiza Soares Fraiha
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
- Departamento de Medicina Veterinária Preventiva, Universidade Federal de Minas Gerais, Belo, Horizonte, Minas Gerais, Brazil
| | - Matias Cardenas
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Ginger Geiger
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Lucia Ortiz
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Silvia Carnaccini
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Darrell R Kapczynski
- Exotic and Emerging Avian Viral Disease Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, USDA, Athens, GA, USA
| | - Daniela S Rajao
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Daniel R Perez
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA.
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Goraichuk IV, Harden M, Spackman E, Suarez DL. The 28S rRNA RT-qPCR assay for host depletion evaluation to enhance avian virus detection in Illumina and Nanopore sequencing. Front Microbiol 2024; 15:1328987. [PMID: 38351914 PMCID: PMC10864109 DOI: 10.3389/fmicb.2024.1328987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/09/2024] [Indexed: 02/16/2024] Open
Abstract
Abundant host and bacterial sequences can obscure the detection of less prevalent viruses in untargeted next-generation sequencing (NGS). Efficient removal of these non-targeted sequences is vital for accurate viral detection. This study presents a novel 28S ribosomal RNA (rRNA) RT-qPCR assay designed to assess the efficiency of avian rRNA depletion before conducting costly NGS for the detection of avian RNA viruses. The comprehensive evaluation of this 28S-test focuses on substituting DNase I with alternative DNases in our established depletion protocols and finetuning essential parameters for reliable host rRNA depletion. To validate the effectiveness of the 28S-test, we compared its performance with NGS results obtained from both Illumina and Nanopore sequencing platforms. This evaluation utilized swab samples from chickens infected with highly pathogenic avian influenza virus, subjected to established and modified depletion protocols. Both methods significantly reduced host rRNA levels, but using the alternative DNase had superior performance. Additionally, utilizing the 28S-test, we explored cost- and time-effective strategies, such as reduced probe concentrations and other alternative DNase usage, assessed the impact of filtration pre-treatment, and evaluated various experimental parameters to further optimize the depletion protocol. Our findings underscore the value of the 28S-test in optimizing depletion methods for advancing improvements in avian disease research through NGS.
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Affiliation(s)
- Iryna V. Goraichuk
- Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agriculture Research Service, U.S. Department of Agriculture, Athens, GA, United States
| | - Mark Harden
- College of Veterinary Medicine, Tuskegee University, Tuskegee, AL, United States
| | - Erica Spackman
- Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agriculture Research Service, U.S. Department of Agriculture, Athens, GA, United States
| | - David L. Suarez
- Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agriculture Research Service, U.S. Department of Agriculture, Athens, GA, United States
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Nabeshima K, Asakura S, Iwata R, Honjo H, Haga A, Goka K, Onuma M. Sequencing methods for HA and NA genes of avian influenza viruses from wild bird feces using Oxford Nanopore sequencing. Comp Immunol Microbiol Infect Dis 2023; 102:102076. [PMID: 37804607 DOI: 10.1016/j.cimid.2023.102076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/28/2023] [Accepted: 10/02/2023] [Indexed: 10/09/2023]
Abstract
We developed a method to determine the sequences of hemagglutinin (HA) and neuraminidase (NA) from RNA extracted directly from wild bird fecal samples, using Nanopore Flongle. We determined the nucleotide sequences and subtypes of HA and NA in 16 and 15 samples respectively, using Flongle. The results of HA and NA subtyping determined by the conventional method were consistent with their subtypes determined by our method, thereby the applicability of this method in the identification of HA and NA subtypes. In addition, the homology between the HA fragments in this and the Sanger methods ranged from 98.5 % to 100 %. Compared with conventional PCR with the Sanger method, this method can easily determine HA and NA subtypes and sequences directly from the fecal samples. It is easier to implement and has lower running costs (USD100$) than other NGS-based methods, making it a useful tool for avian influenza surveillance in wild birds.
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Affiliation(s)
- Kei Nabeshima
- Biodiversity Division, Ecological Risk Assessment and Control Section, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Shingo Asakura
- Biodiversity Division, Ecological Risk Assessment and Control Section, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki, 305-8506, Japan; Animal Research Center of Hokkaido Research Organization, 5-39 Shintoku, Hokkaido, 081-0038, Japan
| | - Ritsuko Iwata
- Biodiversity Division, Ecological Risk Assessment and Control Section, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Hisako Honjo
- Biodiversity Division, Ecological Risk Assessment and Control Section, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Atsushi Haga
- Biodiversity Division, Ecological Risk Assessment and Control Section, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Koichi Goka
- Biodiversity Division, Ecological Risk Assessment and Control Section, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Manabu Onuma
- Biodiversity Division, Ecological Risk Assessment and Control Section, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki, 305-8506, Japan.
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Carnaccini S, Cáceres CJ, Gay LC, Ferreri LM, Skepner E, Burke DF, Brown IH, Geiger G, Obadan A, Rajao DS, Lewis NS, Perez DR. Antigenic mapping of the hemagglutinin of the H9 subtype influenza A viruses using sera from Japanese quail ( Coturnix c. japonica). J Virol 2023; 97:e0074323. [PMID: 37800947 PMCID: PMC10617583 DOI: 10.1128/jvi.00743-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 08/18/2023] [Indexed: 10/07/2023] Open
Abstract
IMPORTANCE Determining the relevant amino acids involved in antigenic drift on the surface protein hemagglutinin (HA) is critical to understand influenza virus evolution and efficient assessment of vaccine strains relative to current circulating strains. We used antigenic cartography to generate an antigenic map of the H9 hemagglutinin (HA) using sera produced in one of the most relevant minor poultry species, Japanese quail. Key antigenic positions were identified and tested to confirm their impact on the antigenic profile. This work provides a better understanding of the antigenic diversity of the H9 HA as it relates to reactivity to quail sera and will facilitate a rational approach for selecting more efficacious vaccines against poultry-origin H9 influenza viruses in minor poultry species.
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Affiliation(s)
- Silvia Carnaccini
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
| | - C. Joaquín Cáceres
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
| | - L. Claire Gay
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
| | - Lucas M. Ferreri
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
| | - Eugene Skepner
- Center for Pathogen Evolution, University of Cambridge, Cambridge, United Kingdom
| | - David F. Burke
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, United Kingdom
| | - Ian H. Brown
- Animal and Plant Health Agency (APHA), Weybridge, United Kingdom
| | - Ginger Geiger
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
| | - Adebimpe Obadan
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
| | - Daniela S. Rajao
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
| | - Nicola S. Lewis
- World Influenza Centre, The Francis Crick Institute, London, United Kingdom
| | - Daniel R. Perez
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
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Ortiz L, Geiger G, Ferreri L, Moran D, Alvarez D, Gonzalez-Reiche AS, Mendez D, Rajao D, Cordon-Rosales C, Perez DR. Evolution and Introductions of Influenza A Virus H1N1 in a Farrow-to-Finish Farm in Guatemala. Microbiol Spectr 2023; 11:e0287822. [PMID: 36475876 PMCID: PMC9927084 DOI: 10.1128/spectrum.02878-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 11/16/2022] [Indexed: 12/12/2022] Open
Abstract
Commercial swine farms provide unique systems for interspecies transmission of influenza A viruses (FLUAVs) at the animal-human interface. Bidirectional transmission of FLUAVs between pigs and humans plays a significant role in the generation of novel strains that become established in the new host population. Active FLUAV surveillance was conducted for 2 years on a commercial pig farm in Southern Guatemala with no history of FLUAV vaccination. Nasal swabs (n = 2,094) from fattening pigs (6 to 24 weeks old) with respiratory signs were collected weekly from May 2016 to February 2018. Swabs were screened for FLUAV by real-time reverse transcriptase PCR (RRT-PCR), and full virus genomes of FLUAV-positive swabs were sequenced by next-generation sequencing (NGS). FLUAV prevalence was 12.0% (95% confidence interval [CI], 10.6% to 13.4%) with two distinct periods of high infection. All samples were identified as FLUAVs of the H1N1 subtype within the H1 swine clade 1A.3.3.2 and whose ancestors are the human origin 2009 H1N1 influenza pandemic virus (H1N1 pdm09). Compared to the prototypic reference segment sequence, 10 amino acid signatures were observed on relevant antigenic sites on the hemagglutinin. The Guatemalan swine-origin FLUAVs show independent evolution from other H1N1 pdm09 FLUAVs circulating in Central America. The zoonotic risk of these viruses remains unknown but strongly calls for continued FLUAV surveillance in pigs in Guatemala. IMPORTANCE Despite increased surveillance efforts, the epidemiology of FLUAVs circulating in swine in Latin America remains understudied. For instance, the 2009 H1N1 influenza pandemic strain (H1N1 pdm09) emerged in Mexico, but its circulation remained undetected in pigs. In Central America, Guatemala is the country with the largest swine industry. We found a unique group of H1N1 pdm09 sequences that suggests independent evolution from similar viruses circulating in Central America. These viruses may represent the establishment of a novel genetic lineage with the potential to reassort with other cocirculating viruses and whose zoonotic risk remains to be determined.
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Affiliation(s)
- Lucia Ortiz
- Poultry Diagnostic and Research Center, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
- Centro de Estudios en Salud, Universidad del Valle de Guatemala, Guatemala City, Guatemala
| | - Ginger Geiger
- Poultry Diagnostic and Research Center, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
| | - Lucas Ferreri
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - David Moran
- Centro de Estudios en Salud, Universidad del Valle de Guatemala, Guatemala City, Guatemala
| | - Danilo Alvarez
- Centro de Estudios en Salud, Universidad del Valle de Guatemala, Guatemala City, Guatemala
| | - Ana Silvia Gonzalez-Reiche
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Dione Mendez
- Centro de Estudios en Salud, Universidad del Valle de Guatemala, Guatemala City, Guatemala
| | - Daniela Rajao
- Poultry Diagnostic and Research Center, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
| | - Celia Cordon-Rosales
- Centro de Estudios en Salud, Universidad del Valle de Guatemala, Guatemala City, Guatemala
| | - Daniel R. Perez
- Poultry Diagnostic and Research Center, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
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6
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Blue-Winged Teals in Guatemala and Their Potential Role in the Ecology of H14 Subtype Influenza a Viruses. Viruses 2023; 15:v15020483. [PMID: 36851697 PMCID: PMC9961055 DOI: 10.3390/v15020483] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023] Open
Abstract
Wild aquatic birds are considered the natural hosts of 16 HA (H1-H16) and 9 NA (N1-N9) subtypes of influenza A viruses (FLUAV) found in different combinations. H14 FLUAVs are rarely detected in nature. Since 2011, H14 FLUAVs have been consistently detected in Guatemala, leading to the largest collection of this subtype from a single country. All H14 FLUAVs in Guatemala were detected from blue-winged teal samples. In this report, 17 new full-length H14 FLUAV genome sequences detected from 2014 until 2019 were analyzed and compared to all published H14 sequences, including Guatemala, North America, and Eurasia. The H14 FLUAVs identified in Guatemala were mostly associated with the N3 subtype (n = 25), whereas the rest were paired with either N4 (n = 7), N5 (n = 4), N6 (n = 1), and two mixed infections (N3/N5 n = 2, and N2/N3 n = 1). H14 FLUAVs in Guatemala belong to a distinct H14 lineage in the Americas that is evolving independently from the Eurasian H14 lineage. Of note, the ORF of the H14 HA segments showed three distinct motifs at the cleavage site, two of these containing arginine instead of lysine in the first and fourth positions, not previously described in other countries. The effects of these mutations on virus replication, virulence, and/or transmission remain unknown and warrant further studies.
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Ferreri LM, Geiger G, Seibert B, Obadan A, Rajao D, Lowen AC, Perez DR. Intra- and inter-host evolution of H9N2 influenza A virus in Japanese quail. Virus Evol 2022; 8:veac001. [PMID: 35223084 PMCID: PMC8865083 DOI: 10.1093/ve/veac001] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 12/21/2021] [Accepted: 01/07/2022] [Indexed: 11/13/2022] Open
Abstract
Influenza A viruses (IAVs) are constantly evolving. Crucial steps in the infection cycle, such as sialic acid (SA) receptor binding on the host cell surface, can either promote or hamper the emergence of new variants. We previously assessed the relative fitness in Japanese quail of H9N2 variant viruses differing at a single amino acid position, residue 216 in the hemagglutinin (HA) viral surface protein. This site is known to modulate SA recognition. Our prior study generated a valuable set of longitudinal samples from quail transmission groups where the inoculum comprised different mixed populations of HA 216 variant viruses. Here, we leveraged these samples to examine the evolutionary dynamics of viral populations within and between inoculated and naïve contact quails. We found that positive selection dominated HA gene evolution, but fixation of the fittest variant depended on the competition mixture. Analysis of the whole genome revealed further evidence of positive selection acting both within and between hosts. Positive selection drove fixation of variants in non-HA segments within inoculated and contact quails. Importantly, transmission bottlenecks were modulated by the molecular signature at HA 216, revealing viral receptor usage as a determinant of transmitted diversity. Overall, we show that selection strongly shaped the evolutionary dynamics within and between quails. These findings support the notion that selective processes act effectively on IAV populations in poultry hosts, facilitating rapid viral evolution in this ecological niche.
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Affiliation(s)
| | - Ginger Geiger
- Department of Population Health, Poultry Diagnostic and Research Center, College of Veterinary Medicine, University of Georgia, 953 College Station Rd, Athens, GA 30602, USA
| | - Brittany Seibert
- Department of Population Health, Poultry Diagnostic and Research Center, College of Veterinary Medicine, University of Georgia, 953 College Station Rd, Athens, GA 30602, USA
| | | | - Daniela Rajao
- Department of Population Health, Poultry Diagnostic and Research Center, College of Veterinary Medicine, University of Georgia, 953 College Station Rd, Athens, GA 30602, USA
| | - Anice C Lowen
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
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Cáceres CJ, Hu Y, Cárdenas-García S, Wu X, Tan H, Carnaccini S, Gay LC, Geiger G, Ma C, Zhang QY, Rajao D, Perez DR, Wang J. Rational design of a deuterium-containing M2-S31N channel blocker UAWJ280 with in vivo antiviral efficacy against both oseltamivir sensitive and -resistant influenza A viruses. Emerg Microbes Infect 2021; 10:1832-1848. [PMID: 34427541 PMCID: PMC8451667 DOI: 10.1080/22221751.2021.1972769] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 08/16/2021] [Accepted: 08/22/2021] [Indexed: 10/28/2022]
Abstract
Seasonal influenza A virus (IAV) infections are among the most important global health problems. FDA-approved antiviral therapies against IAV include neuraminidase inhibitors, M2 inhibitors, and polymerase inhibitor baloxavir. Resistance against adamantanes (amantadine and rimantadine) is widespread as virtually all IAV strains currently circulating in the human population are resistant to adamantanes through the acquisition of the S31N mutation. The neuraminidase inhibitor-resistant strains also contain the M2-S31N mutant, suggesting M2-S31N is a high-profile antiviral drug target. Here we report the development of a novel deuterium-containing M2-S31N inhibitor UAWJ280. UAWJ280 had broad-spectrum antiviral activity against both oseltamivir sensitive and -resistant influenza A strains and had a synergistic antiviral effect in combination with oseltamivir in cell culture. In vivo pharmacokinetic (PK) studies demonstrated that UAWJ280 had favourable PK properties. The in vivo mouse model study showed that UAWJ280 was effective alone or in combination with oseltamivir in improving clinical signs and survival after lethal challenge with an oseltamivir sensitive IAV H1N1 strain. Furthermore, UAWJ280 was also able to ameliorate clinical signs and increase survival when mice were challenged with an oseltamivir-resistant IAV H1N1 strain. In conclusion, we show for the first time that the M2-S31N channel blocker UAWJ280 has in vivo antiviral efficacy in mice that are infected with either oseltamivir sensitive or -resistant IAVs, and it has a synergistic antiviral effect with oseltamivir.
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Affiliation(s)
- C. Joaquín Cáceres
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Yanmei Hu
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, USA
| | - Stivalis Cárdenas-García
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Xiangmeng Wu
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, USA
| | - Haozhou Tan
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, USA
| | - Silvia Carnaccini
- Tifton diagnostic laboratory, College of Veterinary Medicine, University of Georgia, Tifton, GA, USA
| | - L. Claire Gay
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Ginger Geiger
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Chunlong Ma
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, USA
| | - Qing-Yu Zhang
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, USA
| | - Daniela Rajao
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Daniel R. Perez
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Jun Wang
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ, USA
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Mo J, Youk S, Pantin-Jackwood MJ, Suarez DL, Lee DH, Killian ML, Bergeson NH, Spackman E. The pathogenicity and transmission of live bird market H2N2 avian influenza viruses in chickens, Pekin ducks, and guinea fowl. Vet Microbiol 2021; 260:109180. [PMID: 34271303 PMCID: PMC8355142 DOI: 10.1016/j.vetmic.2021.109180] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/01/2021] [Indexed: 11/25/2022]
Abstract
H2N2 subtype low pathogenic avian influenza viruses (LPAIVs) have persisted in live bird markets (LBMs) in the Northeastern United States since 2014. Although unrelated to the 1957 pandemic H2N2 lineage, there is concern that the virus could have animal and public health consequences because of high contact with humans and numerous species in the LBM system. The pathogenicity, infectivity, and transmissibility of six LBM H2N2 viruses isolated from three avian species in LBMs were examined in chickens. Two of these isolates were also tested in Pekin ducks and guinea fowl. Full genome sequence was obtained from all 6 isolates and evaluated for genetic markers for host adaptation and pathogenicity in poultry. Clinical signs were not observed in any host with any of the isolates, however one recent isolate was shed at higher titers than the other isolates and had the lowest bird infectious dose of all the isolates tested in all three species. This isolate, A/chicken/NY/19-012787-1/2019, was also the only isolate with a deletion in the stalk region of the neuraminidase protein (NA). This supports the theory that the NA stalk deletion is evidence of adaptation to gallinaceous poultry.
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Affiliation(s)
- Jongseo Mo
- Exotic and Emerging Avian Viral Diseases Unit, US National Poultry Research Center, USDA-Agricultural Research Service, 934 College Station Rd., Athens, GA 30605, USA
| | - Sungsu Youk
- Exotic and Emerging Avian Viral Diseases Unit, US National Poultry Research Center, USDA-Agricultural Research Service, 934 College Station Rd., Athens, GA 30605, USA
| | - Mary J Pantin-Jackwood
- Exotic and Emerging Avian Viral Diseases Unit, US National Poultry Research Center, USDA-Agricultural Research Service, 934 College Station Rd., Athens, GA 30605, USA
| | - David L Suarez
- Exotic and Emerging Avian Viral Diseases Unit, US National Poultry Research Center, USDA-Agricultural Research Service, 934 College Station Rd., Athens, GA 30605, USA
| | - Dong-Hun Lee
- Department of Pathobiology and Veterinary Science, University of Connecticut, 61 North Eagleville Road, Unit-3089 Storrs, CT 06269, USA
| | - Mary Lea Killian
- National Veterinary Services Laboratories, Veterinary Services, United States Department of Agriculture, 1920 Dayton Avenue, Ames, IA 50010, USA
| | - Nichole H Bergeson
- National Veterinary Services Laboratories, Veterinary Services, United States Department of Agriculture, 1920 Dayton Avenue, Ames, IA 50010, USA
| | - Erica Spackman
- Exotic and Emerging Avian Viral Diseases Unit, US National Poultry Research Center, USDA-Agricultural Research Service, 934 College Station Rd., Athens, GA 30605, USA.
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Delgado-Hernández B, Mugica L, Acosta M, Pérez F, Montano DDLN, Abreu Y, Ayala J, Percedo MI, Alfonso P. Knowledge, Attitudes, and Risk Perception Toward Avian Influenza Virus Exposure Among Cuban Hunters. Front Public Health 2021; 9:644786. [PMID: 34368040 PMCID: PMC8342762 DOI: 10.3389/fpubh.2021.644786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 06/28/2021] [Indexed: 11/24/2022] Open
Abstract
A critical step for decreasing zoonotic disease threats is to have a good understanding of the associated risks. Hunters frequently handle potentially infected birds, so they are more at risk of being exposed to zoonotic avian pathogens, including avian influenza viruses (AIVs). The objective of the current study was to gain a better understanding of Cuban hunters' general hunting practices, focusing on their knowledge and risk perception on avian influenza. An anonymous and voluntary semi-structured questionnaire was designed and applied to 398 hunters. Multiple correspondence analyses found relationships with potential exposure of AIVs to people and domestic animals. The main associated risks factors identified were not taking the annual flu vaccine (60.1%) and not cleaning hunting knives (26.3%); Direct contact with water (32.1%), cleaning wild birds at home (33.2%); receiving assistance during bird cleaning (41.9%), keeping poultry at home (56.5%) and feeding domestic animals with wild bird leftovers (30.3%) were also identified as significant risk factors. The lack of use of some protective measures reported by hunters had no relationship with their awareness on avian influenza, which may imply a lack of such knowledge. The results evidenced that more effective risk communication strategies about the consequences of AIVs infecting human or other animals, and the importance of reducing such risks, are urgently needed.
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Affiliation(s)
- Beatriz Delgado-Hernández
- Epidemiology Group, National Center for Animal and Plant Health (CENSA), World Organisation for Animal Health (OIE) Collaborating Center for the Reduction of the Risk of Disaster in Animal Health, San José de las Lajas, Cuba
| | - Lourdes Mugica
- Bird Ecology Group, Biology Faculty, Havana University, Vedado, Cuba
| | - Martin Acosta
- Bird Ecology Group, Biology Faculty, Havana University, Vedado, Cuba
| | - Frank Pérez
- Epidemiology Group, National Center for Animal and Plant Health (CENSA), World Organisation for Animal Health (OIE) Collaborating Center for the Reduction of the Risk of Disaster in Animal Health, San José de las Lajas, Cuba.,Department of Veterinary Medicine, Faculty of Agricultural Sciences, University of Granma, Bayamo, Cuba
| | - Damarys de Las Nieves Montano
- Epidemiology Group, National Center for Animal and Plant Health (CENSA), World Organisation for Animal Health (OIE) Collaborating Center for the Reduction of the Risk of Disaster in Animal Health, San José de las Lajas, Cuba
| | - Yandy Abreu
- Epidemiology Group, National Center for Animal and Plant Health (CENSA), World Organisation for Animal Health (OIE) Collaborating Center for the Reduction of the Risk of Disaster in Animal Health, San José de las Lajas, Cuba
| | - Joel Ayala
- Epidemiology Group, National Center for Animal and Plant Health (CENSA), World Organisation for Animal Health (OIE) Collaborating Center for the Reduction of the Risk of Disaster in Animal Health, San José de las Lajas, Cuba
| | - María Irian Percedo
- Epidemiology Group, National Center for Animal and Plant Health (CENSA), World Organisation for Animal Health (OIE) Collaborating Center for the Reduction of the Risk of Disaster in Animal Health, San José de las Lajas, Cuba
| | - Pastor Alfonso
- Epidemiology Group, National Center for Animal and Plant Health (CENSA), World Organisation for Animal Health (OIE) Collaborating Center for the Reduction of the Risk of Disaster in Animal Health, San José de las Lajas, Cuba
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11
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Development of a Novel Live Attenuated Influenza A Virus Vaccine Encoding the IgA-Inducing Protein. Vaccines (Basel) 2021; 9:vaccines9070703. [PMID: 34198994 PMCID: PMC8310050 DOI: 10.3390/vaccines9070703] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/19/2021] [Accepted: 06/22/2021] [Indexed: 11/26/2022] Open
Abstract
Live attenuated influenza virus (LAIV) vaccines elicit a combination of systemic and mucosal immunity by mimicking a natural infection. To further enhance protective mucosal responses, we incorporated the gene encoding the IgA-inducing protein (IGIP) into the LAIV genomes of the cold-adapted A/Leningrad/134/17/57 (H2N2) strain (caLen) and the experimental attenuated backbone A/turkey/Ohio/313053/04 (H3N2) (OH/04att). Incorporation of IGIP into the caLen background led to a virus that grew poorly in prototypical substrates. In contrast, IGIP in the OH/04att background (IGIP-H1att) virus grew to titers comparable to the isogenic backbone H1att (H1N1) without IGIP. IGIP-H1att- and H1caLen-vaccinated mice were protected against lethal challenge with a homologous virus. The IGIP-H1att vaccine generated robust serum HAI responses in naïve mice against the homologous virus, equal or better than those obtained with the H1caLen vaccine. Analyses of IgG and IgA responses using a protein microarray revealed qualitative differences in humoral and mucosal responses between vaccine groups. Overall, serum and bronchoalveolar lavage samples from the IGIP-H1att group showed trends towards increased stimulation of IgG and IgA responses compared to H1caLen samples. In summary, the introduction of genes encoding immunomodulatory functions into a candidate LAIV can serve as natural adjuvants to improve overall vaccine safety and efficacy.
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12
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Bakre AA, Jones LP, Kyriakis CS, Hanson JM, Bobbitt DE, Bennett HK, Todd KV, Orr-Burks N, Murray J, Zhang M, Steinhauer DA, Byrd-Leotis L, Cummings RD, Fent J, Coffey T, Tripp RA. Molecular epidemiology and glycomics of swine influenza viruses circulating in commercial swine farms in the southeastern and midwest United States. Vet Microbiol 2020; 251:108914. [PMID: 33181438 DOI: 10.1016/j.vetmic.2020.108914] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 10/26/2020] [Indexed: 12/14/2022]
Abstract
Tracking the genetic diversity and spread of swine influenza viruses (SIVs) in commercial swine farms is central for control and to reduce the potential emergence of SIV reassortants. We analyzed the diversity of SIVs in nasal washes or oral fluids from commercial swine farms in North Carolina using influenza M qRT-PCR and hemagglutinin (HA) and neuraminidase (NA) subtyping. We found a predominance of H1 HAs and N2 NAs in the samples examined. The majority of the H1 HAs could be further classified into gamma and delta subclusters. We also identified HAs of the H1 alpha cluster, and those of human novel pandemic origin. Glycan binding profiles from a representative subset of these viruses revealed broad α2,6 sialylated glycan recognition, though some strains exhibited the ability to bind to α2,3 sialic acid. These data show that SIV surveillance can aid our understanding of viral transmission dynamics and help uncover the diversity at the human-swine interface.
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Affiliation(s)
| | - Les P Jones
- Department of Infectious Diseases, Athens, GA, United States
| | | | - Jarod M Hanson
- Department of Infectious Diseases, Athens, GA, United States
| | - Davis E Bobbitt
- Department of Infectious Diseases, Athens, GA, United States
| | | | - Kyle V Todd
- Department of Infectious Diseases, Athens, GA, United States
| | | | - Jackelyn Murray
- Department of Infectious Diseases, Athens, GA, United States
| | - Ming Zhang
- Department of Epidemiology and Biostatistics, University of Georgia, Athens, GA, United States
| | | | | | - Richard D Cummings
- Beth Israel Deaconess Medical Center, Department of Surgery and Harvard Medical School Center for Glycoscience, Harvard Medical School, Boston, MA, United States
| | - Joseph Fent
- Smithfield Foods, Rose Hill, NC, United States
| | | | - Ralph A Tripp
- Department of Infectious Diseases, Athens, GA, United States.
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13
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Hopken MW, Piaggio AJ, Pabilonia KL, Pierce J, Anderson T, Pierce C, Abdo Z. Population genomic transformations induced by isolation of wild bird avian influenza viruses (Orthomyxoviridae) in embryonated chicken eggs. INFECTION GENETICS AND EVOLUTION 2020; 90:104505. [PMID: 32827730 DOI: 10.1016/j.meegid.2020.104505] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 08/09/2020] [Accepted: 08/13/2020] [Indexed: 12/21/2022]
Abstract
Isolation and cultivation of wild-type viruses in model organism cells or tissues is standard practice in virology. Oftentimes, the virus host species is distantly related to the species from which the culture system was developed. Thus, virus culture in these tissues and cells basically constitutes a host jump, which can lead to genomic changes through genetic drift and/or adaptation to the culture system. We directly sequenced 70 avian influenza virus (Orthomyxoviridae) genomes from oropharyngeal/cloacal swabs collected from wild bird species and paired virus isolates propagated from the same samples following isolation in specific-pathogen-free embryonated chicken eggs. The data were analyzed using population genetic approaches including evaluation of single nucleotide polymorphism (SNP) frequencies and divergence with pooled-sequencing analyses, consensus sequence placement in neighbor-joining trees, and haplotype reconstruction and networks. We found that propagation of virus in eggs leads to skewed SNP mutation spectra with some SNPs going to fixation. Both synonymous and nonsynonmous SNP frequencies shifted. We found multiple consensus sequences that differed between the swabs and the isolates, with some sequences from the same sample falling into divergent genetic clusters. Twenty of 23 coinfections detected had different dominant subtypes following virus isolation, thus sequences from both the swab and isolate were needed to obtain full subtype data. Haplotype networks revealed haplotype frequency shifts and the appearance or loss of low-frequency haplotypes following isolation. The results from this study revealed that isolation of wild bird avian influenza viruses in chicken eggs leads to skewed populations that are different than the input populations. Consensus sequence changes from virus isolation can lead to flawed phylogenetic inferences, and subtype detection is biased. These results suggest that for genomic studies of wild bird influenza viruses the biological field should move away from chicken egg isolation towards directly sequencing the virus from host samples.
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Affiliation(s)
- Matthew W Hopken
- Department of Microbiology, Immunology, and Pathology, College of Veterinary and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA; United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, Fort Collins, CO 80521, USA.
| | - Antoinette J Piaggio
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, Fort Collins, CO 80521, USA
| | - Kristy L Pabilonia
- Department of Microbiology, Immunology, and Pathology, College of Veterinary and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA; Veterinary Diagnostics Laboratories, College of Veterinary and Biomedical Sciences, Colorado State University, Fort Collins, CO 80526, USA
| | - James Pierce
- Department of Microbiology, Immunology, and Pathology, College of Veterinary and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Theodore Anderson
- Veterinary Diagnostics Laboratories, College of Veterinary and Biomedical Sciences, Colorado State University, Fort Collins, CO 80526, USA
| | - Courtney Pierce
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, Fort Collins, CO 80521, USA
| | - Zaid Abdo
- Department of Microbiology, Immunology, and Pathology, College of Veterinary and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
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14
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Williams T, Athrey G. Cloacal Swabs Are Unreliable Sources for Estimating Lower Gastro-Intestinal Tract Microbiota Membership and Structure in Broiler Chickens. Microorganisms 2020; 8:E718. [PMID: 32408567 PMCID: PMC7285018 DOI: 10.3390/microorganisms8050718] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 04/22/2020] [Accepted: 05/09/2020] [Indexed: 01/04/2023] Open
Abstract
The gastrointestinal microbiota of chickens plays a central role in health and performance. Cloacal swabs, due to their proximity to the ceca (a vital site of functional activity), are an alternative, non-invasive method used for assaying microbial communities and might be a viable option for longitudinal studies. In this study, the microbiota of twenty paired cecal content and cloacal swab samples representing two dietary treatments was assessed using 16S rRNA V4 hypervariable region sequencing and was analyzed using the MOTHUR pipeline, Phyloseq, and Vegan packages. Paired t-test and Wilcoxon signed-rank tests showed significant differences in the Chao1 index (p-value <0.0001 and p-value <0.0001, respectively) but not in the Inverse Simpson species diversity estimator (p-value = 0.06763 and p-value = 0.06021, respectively) between the cecal content and cloacal swabs. β-diversity between the cloacal swabs and cecal microbiota also showed significant differences using PERMANOVA, HOMOVA, and weighted UniFrac testing (p-values < 0.001). Based on a paired sample analysis, this study provided evidence of the high inter-individual variation and randomness of cloacal microbiota, in contrast to cecal microbiota. Our findings indicated that cloacal swabs do not approximate the α or β diversity of cecal samples and are not suitable for longitudinal studies of gut microbiota.
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Affiliation(s)
- Travis Williams
- Department of Poultry Science, Texas A&M University, 101 Kleberg Center, 2472 TAMU, College Station, TX 77843-2472, USA;
| | - Giridhar Athrey
- Department of Poultry Science, Texas A&M University, 101 Kleberg Center, 2472 TAMU, College Station, TX 77843-2472, USA;
- Faculty of Ecology and Evolutionary Biology, Texas A&M University, 101 Kleberg Center, 2472 TAMU, College Station, TX 77843-2472, USA
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15
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Ferreri LM, Ortiz L, Geiger G, Barriga GP, Poulson R, Gonzalez-Reiche AS, Crum JA, Stallknecht D, Moran D, Cordon-Rosales C, Rajao D, Perez DR. Improved detection of influenza A virus from blue-winged teals by sequencing directly from swab material. Ecol Evol 2019; 9:6534-6546. [PMID: 31236242 PMCID: PMC6580304 DOI: 10.1002/ece3.5232] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 04/10/2019] [Accepted: 04/12/2019] [Indexed: 12/22/2022] Open
Abstract
Abstract The greatest diversity of influenza A virus (IAV) is found in wild aquatic birds of the orders Anseriformes and Charadriiformes. In these birds, IAV replication occurs mostly in the intestinal tract. Fecal, cloacal, and/or tracheal swabs are typically collected and tested by real-time RT-PCR (rRT-PCR) and/or by virus isolation in embryonated chicken eggs in order to determine the presence of IAV. Virus isolation may impose bottlenecks that select variant populations that are different from those circulating in nature, and such bottlenecks may result in artifactual representation of subtype diversity and/or underrepresented mixed infections. The advent of next-generation sequencing (NGS) technologies provides an opportunity to explore to what extent IAV subtype diversity is affected by virus isolation in eggs. In the present work, we evaluated the advantage of sequencing by NGS directly from swab material of IAV rRT-PCR-positive swabs collected during the 2013-14 surveillance season in Guatemala and compared to results from NGS after virus isolation. The results highlight the benefit of sequencing IAV genomes directly from swabs to better understand subtype diversity and detection of alternative amino acid motifs that could otherwise escape detection using traditional methods of virus isolation. In addition, NGS sequencing data from swabs revealed reduced presence of defective interfering particles compared to virus isolates. We propose an alternative workflow in which original swab samples positive for IAV by rRT-PCR are first subjected to NGS before attempting viral isolation. This approach should speed the processing of samples and better capture natural IAV diversity. OPEN RESEARCH BADGES This article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. The data is available at https://doi.org/10.5061/dryad.3h2n106.
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Affiliation(s)
- Lucas M Ferreri
- Poultry Diagnostic and Research Center, Department of Population Health, College of Veterinary Medicine University of Georgia Athens Georgia
| | - Lucia Ortiz
- Poultry Diagnostic and Research Center, Department of Population Health, College of Veterinary Medicine University of Georgia Athens Georgia.,Centro de Estudios en Salud Universidad del Valle de Guatemala Guatemala City Guatemala
| | - Ginger Geiger
- Poultry Diagnostic and Research Center, Department of Population Health, College of Veterinary Medicine University of Georgia Athens Georgia
| | - Gonzalo P Barriga
- Laboratory of Emerging Viruses, Virology Program Institute of Biomedical Sciences, Faculty of Medicine Universidad de Chile Santiago Chile
| | - Rebecca Poulson
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine University of Georgia Athens Georgia
| | | | - Jo Anne Crum
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine University of Georgia Athens Georgia
| | - David Stallknecht
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine University of Georgia Athens Georgia
| | - David Moran
- Centro de Estudios en Salud Universidad del Valle de Guatemala Guatemala City Guatemala
| | - Celia Cordon-Rosales
- Centro de Estudios en Salud Universidad del Valle de Guatemala Guatemala City Guatemala
| | - Daniela Rajao
- Poultry Diagnostic and Research Center, Department of Population Health, College of Veterinary Medicine University of Georgia Athens Georgia
| | - Daniel R Perez
- Poultry Diagnostic and Research Center, Department of Population Health, College of Veterinary Medicine University of Georgia Athens Georgia
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