Genetic Characterization of Avian Influenza Viruses Isolated from the Izumi Plain, Japan in 2019/20 Winter Season
Abstract
:1. Introduction
2. Results
2.1. AIV Isolation from Crane Roost Site Water on the Izumi Plain during the 2019/20 Winter Season
2.2. Phylogenetic Analyses of Our 22 AIV Isolates
2.3. Genotypes of Our 22 AIV Isolates
3. Discussion
4. Materials and Methods
4.1. Sample Collection
4.2. AIV Isolation from Water Samples
4.3. Real Time Reverse Transcription (RT)-PCR and HA and NA Subtyping
4.4. Sequence Analyses of AIV Genes
4.5. Phylogenetic Analyses for AIV Genes
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Subtype | Isolate | Collection Date | Isolate ID * |
---|---|---|---|
H1N1 | A/environment/Kagoshima/KU-G4/2020 (H1N1) | 27 January 2020 | EPI_ISL_13374949 |
H3N2 | A/environment/Kagoshima/KU-4b/2019 (H3N2) | 2 December 2019 | EPI_ISL_13374950 |
H3N8 | A/environment/Kagoshima/KU-6a/2019 (H3N8) | 18 November 2019 | EPI_ISL_13374979 |
A/environment/Kagoshima/KU-6c/2019 (H3N8) | 25 November 2019 | EPI_ISL_13375104 | |
A/environment/Kagoshima/KU-6d/2019 (H3N8) | 25 November 2019 | EPI_ISL_13375105 | |
A/environment/Kagoshima/KU-D3/2019 (H3N8) | 2 December 2019 | EPI_ISL_13375750 | |
A/environment/Kagoshima/KU-G2/2019 (H3N8) | 2 December 2019 | EPI_ISL_13375751 | |
A/environment/Kagoshima/KU-G3/2019 (H3N8) | 2 December 2019 | EPI_ISL_13417555 | |
A/environment/Kagoshima/KU-J2/2019 (H3N8) | 9 December 2019 | EPI_ISL_13418079 | |
H4N6 | A/environment/Kagoshima/KU-J1/2019 (H4N6) | 25 November 2019 | EPI_ISL_13418433 |
A/environment/Kagoshima/KU-4c/2019 (H4N6) | 23 December 2019 | EPI_ISL_13418523 | |
A/environment/Kagoshima/KU-6e/2019 (H4N6) | 23 December 2019 | EPI_ISL_13418524 | |
A/environment/Kagoshima/KU-6f/2020 (H4N6) | 20 January 2020 | EPI_ISL_13418525 | |
H6N6 | A/environment/Kagoshima/KU-3a/2019 (H6N6) | 18 November 2019 | EPI_ISL_13437619 |
A/environment/Kagoshima/KU-5a/2019 (H6N6) | 18 November 2019 | EPI_ISL_13437942 | |
A/environment/Kagoshima/KU-6b/2019 (H6N6) | 18 November 2019 | EPI_ISL_13437509 | |
A/environment/Kagoshima/KU-3b/2019 (H6N6) | 25 November 2019 | EPI_ISL_13439033 | |
A/environment/Kagoshima/KU-4a/2019 (H6N6) | 25 November 2019 | EPI_ISL_13439034 | |
A/environment/Kagoshima/KU-B1/2019 (H6N6) | 25 November 2019 | EPI_ISL_13439048 | |
A/environment/Kagoshima/KU-D1/2019 (H6N6) | 25 November 2019 | EPI_ISL_13439049 | |
A/environment/Kagoshima/KU-G1/2019 (H6N6) | 25 November 2019 | EPI_ISL_13439050 | |
H11N2 | A/environment/Kagoshima/KU-3c/2019 (H11N2) | 16 December 2019 | EPI_ISL_13439051 |
Subtype | Isolate | Genetic Clade * of the Following Gene Segment: | Genotype ** | |||||||
---|---|---|---|---|---|---|---|---|---|---|
HA | NA | PB2 | PB1 | PA | NP | M | NS | |||
H1N1 | A/environment/Kagoshima/KU-G4/2020 (H1N1) | NA | NA | PB2-I | PB1-II | PA-I | NP-II | M-I | NS-I | NA *** |
H3N2 | A/environment/Kagoshima/KU-4b/2019 (H3N2) | H3-I | N2-I | PB2-I | PB1-II | PA-II | NP-I | M-II | NS-I | NA |
H3N8 | A/environment/Kagoshima/KU-6a/2019 (H3N8) | H3-I | N8-I | PB2-I | PB1-I | PA-II | NP-I | M-II | NS-I | H3N8-I |
A/environment/Kagoshima/KU-6c/2019 (H3N8) | H3-I | N8-I | PB2-I | PB1-II | PA-II | NP-I | M-II | NS-I | H3N8-II | |
A/environment/Kagoshima/KU-6d/2019 (H3N8) | H3-I | N8-I | PB2-I | PB1-II | PA-II | NP-I | M-II | NS-I | H3N8-II | |
A/environment/Kagoshima/KU-D3/2019 (H3N8) | H3-II | N8-I | PB2-II | PB1-I | PA-III | NP-IV | M-II | NS-I | H3N8-III | |
A/environment/Kagoshima/KU-G2/2019 (H3N8) | H3-I | N8-I | PB2-I | PB1-II | PA-II | NP-I | M-II | NS-I | H3N8-II | |
A/environment/Kagoshima/KU-G3/2019 (H3N8) | H3-I | N8-I | PB2-I | PB1-I | PA-IV | NP-II | M-I | NS-I | H3N8-IV | |
A/environment/Kagoshima/KU-J2/2019 (H3N8) | H3-I | N8-I | PB2-I | PB1-III | PA-II | NP-IV | M-I | NS-I | H3N8-V | |
H4N6 | A/environment/Kagoshima/KU-J1/2019 (H4N6) | NA | N6-II | PB2-I | PB1-II | PA-IV | NP-I | M-I | NS-I | H4N6-I |
A/environment/Kagoshima/KU-4c/2019 (H4N6) | N6-II | PB2-IV | PB1-II | PA-I | NP-IV | M-I | NS-I | H4N6-II | ||
A/environment/Kagoshima/KU-6e/2019 (H4N6) | N6-II | PB2-I | PB1-II | PA-II | NP-IV | M-I | NS-I | H4N6-III | ||
A/environment/Kagoshima/KU-6f/2020 (H4N6) | N6-II | PB2-IV | PB1-II | PA-I | NP-IV | M-I | NS-I | H4N6-II | ||
H6N6 | A/environment/Kagoshima/KU-3a/2019 (H6N6) | NA | N6-I | PB2-III | PB1-IV | PA-V | NP-III | M-III | NS-III | H6N6-I |
A/environment/Kagoshima/KU-5a/2019 (H6N6) | N6-I | PB2-III | PB1-IV | PA-V | NP-III | M-III | NS-III | H6N6-I | ||
A/environment/Kagoshima/KU-6b/2019 (H6N6) | N6-I | PB2-III | PB1-IV | PA-V | NP-III | M-III | NS-III | H6N6-I | ||
A/environment/Kagoshima/KU-3b/2019 (H6N6) | N6-I | PB2-III | PB1-IV | PA-V | NP-III | M-III | NS-III | H6N6-I | ||
A/environment/Kagoshima/KU-4a/2019 (H6N6) | N6-I | PB2-III | PB1-IV | PA-V | NP-III | M-III | NS-III | H6N6-I | ||
A/environment/Kagoshima/KU-B1/2019 (H6N6) | N6-I | PB2-III | PB1-IV | PA-V | NP-III | M-III | NS-III | H6N6-I | ||
A/environment/Kagoshima/KU-D1/2019 (H6N6) | N6-I | PB2-I | PB1-I | PA-II | NP-II | M-I | NS-II | H6N6-II | ||
A/environment/Kagoshima/KU-G1/2019 (H6N6) | N6-I | PB2-III | PB1-IV | PA-V | NP-III | M-III | NS-III | H6N6-I | ||
H11N2 | A/environment/Kagoshima/KU-3c/2019 (H11N2) | NA | N2-I | PB2-I | PB1-II | PA-III | NP-I | M-I | NS-I | NA |
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Okuya, K.; Khalil, A.M.; Esaki, M.; Kojima, I.; Nishi, N.; Koyamada, D.; Matsui, T.; Yoshida, Y.; Ozawa, M. Genetic Characterization of Avian Influenza Viruses Isolated from the Izumi Plain, Japan in 2019/20 Winter Season. Pathogens 2022, 11, 1013. https://doi.org/10.3390/pathogens11091013
Okuya K, Khalil AM, Esaki M, Kojima I, Nishi N, Koyamada D, Matsui T, Yoshida Y, Ozawa M. Genetic Characterization of Avian Influenza Viruses Isolated from the Izumi Plain, Japan in 2019/20 Winter Season. Pathogens. 2022; 11(9):1013. https://doi.org/10.3390/pathogens11091013
Chicago/Turabian StyleOkuya, Kosuke, Ahmed Magdy Khalil, Mana Esaki, Isshu Kojima, Natsuko Nishi, Donna Koyamada, Tsutomu Matsui, Yuuhei Yoshida, and Makoto Ozawa. 2022. "Genetic Characterization of Avian Influenza Viruses Isolated from the Izumi Plain, Japan in 2019/20 Winter Season" Pathogens 11, no. 9: 1013. https://doi.org/10.3390/pathogens11091013