Table 1. DNA sequence homologies between highly pathogenic avian influenza A(H5N1) clade 2.3.4.4b viruses isolated from domestic ducks in Indonesia, 2022, and those from Banjarbaru and East Asia*.
| Virus name | GISAID no.† | Collection date | % Nucleic acid similarity for each gene segment |
|||||||
|---|---|---|---|---|---|---|---|---|---|---|
| PB2 | PB1 | PA | HA | NP | NA | MP | NS | |||
| Viruses from first outbreak in Hulu Sungai Utara |
EPI_ISL_17371282, EPI_ISL_17371283, EPI_ISL_17371284 |
2022 Apr |
100 |
100 |
99.8–99.9 |
99.9–100 |
100 |
100 |
100 |
99.8–100 |
| A/Muscovy duck/Banjarbaru/A0523532-9/2023 |
EPI_ISL_18438033 |
2023 Jul 7 |
99.4 |
99.3–99.4 |
99.1–99.2 |
98.9–99.0 |
99.1 |
98.8 |
99.8 |
98.7 |
| A/mandarin duck/Korea/WA585/2021 |
EPI_ISL_6959592 |
2021 Oct 26 |
99.6 |
99.5–99.6 |
99.6–99.7 |
99.2–99.3 |
99.6 |
99.8 |
99.6 |
99.4 |
| A/quail/Korea/H526/2021 |
EPI_ISL_6959593 |
2021 Nov 8 |
99.4 |
99.2 |
99.2–99.3 |
99.0–99.1 |
99.3 |
99.6 |
99.3 |
99.2 |
| A/duck/Guangdong/S4525/2021 |
EPI_ISL_12572655 |
2021 Dec 8 |
99.6 |
99.6 |
99.3–99.4 |
99.2–99.3 |
99.5 |
99.7 |
99.7 |
99.2 |
| A/duck/Hubei/SE220/2022 |
EPI_ISL_12572659 |
2022 Jan 10 |
99.6 |
99.5 |
99.3–99.4 |
99.0–99.2 |
99.5 |
99.5 |
99.6 |
99.2 |
| A/duck/Guizhou/S1321/2022 |
EPI_ISL_12572656 |
2022 Feb 22 |
99.6 |
99.6 |
99.5–99.6 |
97.2–97.3 |
99.5 |
99.4 |
99.8 |
99.2 |
| A/chicken/Kagoshima/21A6T/2021 |
EPI_ISL_6829533 |
2021 Nov 12 |
99.6 |
99.6 |
99.6–99.7 |
99.1–99.2 |
99.6 |
99.7 |
99.8 |
99.4 |
| A/chicken/Saitama/TU7-34,36/2021 |
EPI_ISL_15063425 |
2021 Dec 7 |
99.6 |
99.3–99.4 |
99.1–99.2 |
98.4–98.6 |
99.1 |
99.6 |
99.3 |
99.0 |
| A/chicken/Ehime/TU11-2-24 25/2022 |
EPI_ISL_15063431 |
2022 Jan 4 |
99.8 |
92.0 |
99.5–99.6 |
99.2–99.3 |
99.3 |
99.6 |
99.7 |
99.3 |
| A/common buzzard/Japan/2601B013/2022 |
EPI_ISL_16831015 |
2022 Jan 27 |
99.6 |
99.2–99.3 |
99.3–99.4 |
98.6–98.7 |
99.3 |
99.6 |
99.3 |
99.2 |
| A/teal/Miyazaki/211109-32/2021 | EPI_ISL_15613494 | 2021 Nov 9 | 99.4 | 99.2–99.3 | 99.3 | 98.7–98.8 | 99.1 | 99.6 | 99.2 | 99.2 |
*H5N1 clade 2.3.4.4b viruses isolated from the initial poultry outbreak in Hulu Sungai Utara in April 2022 were compared with those isolated later from Banjarbaru, Indonesia, in July 2023 and H5N1 clade 2.3.4.b viruses from East Asia isolated during October 2021–February 2022. HA, hemagglutinin; MP, matrix protein; NA, neuraminidase; NP, nucleoprotein; NS, nonstructural; PA, polymerase acidic; PB1, polymerase basic 1; PB2, polymerase basic 2. †GISAID database (https://www.gisaid.org).