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Noh EB, Heo GB, Lee KN, Kang YM, An SH, Kim N, Lee YJ. Subtype specific virus enrichment with immunomagnetic separation method followed by NGS unravels the mixture of H5 and H9 avian influenza virus. J Virol Methods 2023; 320:114773. [PMID: 37467847 DOI: 10.1016/j.jviromet.2023.114773] [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: 04/26/2023] [Revised: 07/12/2023] [Accepted: 07/13/2023] [Indexed: 07/21/2023]
Abstract
Wild bird avian influenza type A virus (AIV) surveillance is important for the early detection of highly pathogenic AIVs and for providing early warnings to the poultry industry and veterinary services to implement more effective control measures against these viruses. Some field samples are often found to contain more than two kinds of AIV. Correct determination of the HA/NA subtype and complete nucleotide sequences of the component viruses in those samples are often critical for timely and accurate understanding of the field situation, but it is not easy to define the genomic structure of the constituent viruses unambiguously because AIV has eight segmented genomes. In this study, with immunomagnetic beads incorporating polyclonal antibodies of chicken for subtype-specific viral enrichment, we could selectively decrease the density of one of the two constituent viruses in a sample of different subtypes, H5 and H9, artificially generated; this was represented in the changes of Ct values with subtype specific real-time RT-PCR. Following this, with NGS, we could recover nearly complete genomic sequences and arrange the consensus sequences of gene segments of the constituent viruses confidently with the quantitative variable like genome coverage, linked along the gene segments and associated with the number of viral copies in a sample.
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Affiliation(s)
- Eun Bi Noh
- Avian Influenza Research and Diagnostic Division, Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon-si, Gyeongsangbuk-do, Republic of Korea.
| | - Gyeong-Beom Heo
- Avian Influenza Research and Diagnostic Division, Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon-si, Gyeongsangbuk-do, Republic of Korea.
| | - Kwang-Nyeong Lee
- Avian Influenza Research and Diagnostic Division, Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon-si, Gyeongsangbuk-do, Republic of Korea.
| | - Yong-Myung Kang
- Avian Influenza Research and Diagnostic Division, Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon-si, Gyeongsangbuk-do, Republic of Korea.
| | - Se-Hee An
- Avian Influenza Research and Diagnostic Division, Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon-si, Gyeongsangbuk-do, Republic of Korea.
| | - Nayeong Kim
- Avian Influenza Research and Diagnostic Division, Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon-si, Gyeongsangbuk-do, Republic of Korea.
| | - Youn-Jeong Lee
- Avian Influenza Research and Diagnostic Division, Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon-si, Gyeongsangbuk-do, Republic of Korea.
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Chrzastek K, Lee DH, Smith D, Sharma P, Suarez DL, Pantin-Jackwood M, Kapczynski DR. Use of Sequence-Independent, Single-Primer-Amplification (SISPA) for rapid detection, identification, and characterization of avian RNA viruses. Virology 2017. [PMID: 28646651 PMCID: PMC7111618 DOI: 10.1016/j.virol.2017.06.019] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Current technologies with next generation sequencing have revolutionized metagenomics analysis of clinical samples. To achieve the non-selective amplification and recovery of low abundance genetic sequences, a simplified Sequence-Independent, Single-Primer Amplification (SISPA) technique in combination with MiSeq platform was applied to target negative- and positive-sense single-stranded RNA viral sequences. This method allowed successful sequence assembly of full or near full length avian influenza virus (AIV), infectious bronchitis virus (IBV), and Newcastle disease virus (NDV) viral genome. Moreover, SISPA analysis applied to unknown clinical cases of mixed viral infections produced genome assemblies comprising 98% NDV and 99% of IBV genomes. Complete or near complete virus genome sequence was obtained with titers at or above 104.5 EID50/ml (50% embryo infectious dose), and virus identification could be detected with titers at or above 103 EID50/ml. Taken together, these studies demonstrate a simple template enrichment protocol for rapid detection and accurate characterization of avian RNA viruses. A simple, random priming technique was optimized to target viral RNA genomes. This technique allows characterization of multiple viruses in single reaction. Complete or near complete genome sequence with titers at or above 104.5 EID50/ml. The detection limit with viral titers at or above 103 EID50/ml.
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Affiliation(s)
- Klaudia Chrzastek
- US National Poultry Research Center, Agricultural Research Service, US Department of Agriculture, 934 College Station Road, Athens, GA 30605, USA
| | - Dong-Hun Lee
- US National Poultry Research Center, Agricultural Research Service, US Department of Agriculture, 934 College Station Road, Athens, GA 30605, USA
| | - Diane Smith
- US National Poultry Research Center, Agricultural Research Service, US Department of Agriculture, 934 College Station Road, Athens, GA 30605, USA
| | - Poonam Sharma
- US National Poultry Research Center, Agricultural Research Service, US Department of Agriculture, 934 College Station Road, Athens, GA 30605, USA
| | - David L Suarez
- US National Poultry Research Center, Agricultural Research Service, US Department of Agriculture, 934 College Station Road, Athens, GA 30605, USA
| | - Mary Pantin-Jackwood
- US National Poultry Research Center, Agricultural Research Service, US Department of Agriculture, 934 College Station Road, Athens, GA 30605, USA
| | - Darrell R Kapczynski
- US National Poultry Research Center, Agricultural Research Service, US Department of Agriculture, 934 College Station Road, Athens, GA 30605, USA.
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Miller PJ, Afonso CL, Spackman E, Scott MA, Pedersen JC, Senne DA, Brown JD, Fuller CM, Uhart MM, Karesh WB, Brown IH, Alexander DJ, Swayne DE. Evidence for a new avian paramyxovirus serotype 10 detected in rockhopper penguins from the Falkland Islands. J Virol 2010; 84:11496-504. [PMID: 20702635 PMCID: PMC2953191 DOI: 10.1128/jvi.00822-10] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2010] [Accepted: 07/16/2010] [Indexed: 11/20/2022] Open
Abstract
The biological, serological, and genomic characterization of a paramyxovirus recently isolated from rockhopper penguins (Eudyptes chrysocome) suggested that this virus represented a new avian paramyxovirus (APMV) group, APMV10. This penguin virus resembled other APMVs by electron microscopy; however, its viral hemagglutination (HA) activity was not inhibited by antisera against any of the nine defined APMV serotypes. In addition, antiserum generated against this penguin virus did not inhibit the HA of representative viruses of the other APMV serotypes. Sequence data produced using random priming methods revealed a genomic structure typical of APMV. Phylogenetic evaluation of coding regions revealed that amino acid sequences of all six proteins were most closely related to APMV2 and APMV8. The calculation of evolutionary distances among proteins and distances at the nucleotide level confirmed that APMV2, APMV8, and the penguin virus all were sufficiently divergent from each other to be considered different serotypes. We propose that this isolate, named APMV10/penguin/Falkland Islands/324/2007, be the prototype virus for APMV10. Because of the known problems associated with serology, such as antiserum cross-reactivity and one-way immunogenicity, in addition to the reliance on the immune response to a single protein, the hemagglutinin-neuraminidase, as the sole base for viral classification, we suggest the need for new classification guidelines that incorporate genome sequence comparisons.
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Affiliation(s)
- Patti J. Miller
- Southeast Poultry Research Laboratory, Agricultural Research Service, United States Department of Agriculture, Athens, Georgia, Diagnostic Virology Laboratory, National Veterinary Services Laboratory, United States Department of Agriculture, Ames, Iowa, Southeastern Cooperative Wildlife Disease Study, University of Georgia, Athens, Georgia, Veterinary Laboratories Agency, Weybridge, Surrey, United Kingdom, Wildlife Conservation Society, Bronx, New York
| | - Claudio L. Afonso
- Southeast Poultry Research Laboratory, Agricultural Research Service, United States Department of Agriculture, Athens, Georgia, Diagnostic Virology Laboratory, National Veterinary Services Laboratory, United States Department of Agriculture, Ames, Iowa, Southeastern Cooperative Wildlife Disease Study, University of Georgia, Athens, Georgia, Veterinary Laboratories Agency, Weybridge, Surrey, United Kingdom, Wildlife Conservation Society, Bronx, New York
| | - Erica Spackman
- Southeast Poultry Research Laboratory, Agricultural Research Service, United States Department of Agriculture, Athens, Georgia, Diagnostic Virology Laboratory, National Veterinary Services Laboratory, United States Department of Agriculture, Ames, Iowa, Southeastern Cooperative Wildlife Disease Study, University of Georgia, Athens, Georgia, Veterinary Laboratories Agency, Weybridge, Surrey, United Kingdom, Wildlife Conservation Society, Bronx, New York
| | - Melissa A. Scott
- Southeast Poultry Research Laboratory, Agricultural Research Service, United States Department of Agriculture, Athens, Georgia, Diagnostic Virology Laboratory, National Veterinary Services Laboratory, United States Department of Agriculture, Ames, Iowa, Southeastern Cooperative Wildlife Disease Study, University of Georgia, Athens, Georgia, Veterinary Laboratories Agency, Weybridge, Surrey, United Kingdom, Wildlife Conservation Society, Bronx, New York
| | - Janice C. Pedersen
- Southeast Poultry Research Laboratory, Agricultural Research Service, United States Department of Agriculture, Athens, Georgia, Diagnostic Virology Laboratory, National Veterinary Services Laboratory, United States Department of Agriculture, Ames, Iowa, Southeastern Cooperative Wildlife Disease Study, University of Georgia, Athens, Georgia, Veterinary Laboratories Agency, Weybridge, Surrey, United Kingdom, Wildlife Conservation Society, Bronx, New York
| | - Dennis A. Senne
- Southeast Poultry Research Laboratory, Agricultural Research Service, United States Department of Agriculture, Athens, Georgia, Diagnostic Virology Laboratory, National Veterinary Services Laboratory, United States Department of Agriculture, Ames, Iowa, Southeastern Cooperative Wildlife Disease Study, University of Georgia, Athens, Georgia, Veterinary Laboratories Agency, Weybridge, Surrey, United Kingdom, Wildlife Conservation Society, Bronx, New York
| | - Justin D. Brown
- Southeast Poultry Research Laboratory, Agricultural Research Service, United States Department of Agriculture, Athens, Georgia, Diagnostic Virology Laboratory, National Veterinary Services Laboratory, United States Department of Agriculture, Ames, Iowa, Southeastern Cooperative Wildlife Disease Study, University of Georgia, Athens, Georgia, Veterinary Laboratories Agency, Weybridge, Surrey, United Kingdom, Wildlife Conservation Society, Bronx, New York
| | - Chad M. Fuller
- Southeast Poultry Research Laboratory, Agricultural Research Service, United States Department of Agriculture, Athens, Georgia, Diagnostic Virology Laboratory, National Veterinary Services Laboratory, United States Department of Agriculture, Ames, Iowa, Southeastern Cooperative Wildlife Disease Study, University of Georgia, Athens, Georgia, Veterinary Laboratories Agency, Weybridge, Surrey, United Kingdom, Wildlife Conservation Society, Bronx, New York
| | - Marcela M. Uhart
- Southeast Poultry Research Laboratory, Agricultural Research Service, United States Department of Agriculture, Athens, Georgia, Diagnostic Virology Laboratory, National Veterinary Services Laboratory, United States Department of Agriculture, Ames, Iowa, Southeastern Cooperative Wildlife Disease Study, University of Georgia, Athens, Georgia, Veterinary Laboratories Agency, Weybridge, Surrey, United Kingdom, Wildlife Conservation Society, Bronx, New York
| | - William B. Karesh
- Southeast Poultry Research Laboratory, Agricultural Research Service, United States Department of Agriculture, Athens, Georgia, Diagnostic Virology Laboratory, National Veterinary Services Laboratory, United States Department of Agriculture, Ames, Iowa, Southeastern Cooperative Wildlife Disease Study, University of Georgia, Athens, Georgia, Veterinary Laboratories Agency, Weybridge, Surrey, United Kingdom, Wildlife Conservation Society, Bronx, New York
| | - Ian H. Brown
- Southeast Poultry Research Laboratory, Agricultural Research Service, United States Department of Agriculture, Athens, Georgia, Diagnostic Virology Laboratory, National Veterinary Services Laboratory, United States Department of Agriculture, Ames, Iowa, Southeastern Cooperative Wildlife Disease Study, University of Georgia, Athens, Georgia, Veterinary Laboratories Agency, Weybridge, Surrey, United Kingdom, Wildlife Conservation Society, Bronx, New York
| | - Dennis J. Alexander
- Southeast Poultry Research Laboratory, Agricultural Research Service, United States Department of Agriculture, Athens, Georgia, Diagnostic Virology Laboratory, National Veterinary Services Laboratory, United States Department of Agriculture, Ames, Iowa, Southeastern Cooperative Wildlife Disease Study, University of Georgia, Athens, Georgia, Veterinary Laboratories Agency, Weybridge, Surrey, United Kingdom, Wildlife Conservation Society, Bronx, New York
| | - David E. Swayne
- Southeast Poultry Research Laboratory, Agricultural Research Service, United States Department of Agriculture, Athens, Georgia, Diagnostic Virology Laboratory, National Veterinary Services Laboratory, United States Department of Agriculture, Ames, Iowa, Southeastern Cooperative Wildlife Disease Study, University of Georgia, Athens, Georgia, Veterinary Laboratories Agency, Weybridge, Surrey, United Kingdom, Wildlife Conservation Society, Bronx, New York
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