Geno ype di e en ia ion o highly pa hogenic a ian in luenza
i uses (HPAIV) o he goose/Guangdong lineage in Ge many -
De i a ion and deploymen o e e ence sequences.
Summa y
Highly pa hogenic a ian in luenza i uses (HPAIV) o he H5 goose/Guangdong (gs/GD)
lineage ha e epea edly eme ged in Ge many since 2006. Roo ed in he espec i e gs/GD
lineages, HPAI i uses in Ge many ha e gene ically di e si ied in o a ple ho a o clades and
subclades and e ol ed in o an asso men o sub- and geno ypes. This echnical no e
summa izes he geno ype di e en ia ion p ocedu e, lis s he success ully assigned
geno ypes and supplies co esponding e e ence sequences.
Me hodology
Geno ype di e en ia ion and de i a ion o e e ence sequence we e es ablished wi h a
combined phylogene ic and simila i y-based me hod. Full genome sequences om clinical
samples and i us isola es we e con inuously sc eened o new geno ypes and compa ed wi h
he de i a ed e e ence sequences. Fo geno ype assignmen segmen -speci ic mul iple
alignmen s we e gene a ed using MAFFT (Ka oh & S andley, 2013). In addi ion, alignmen s
o conca ena ed genomes we e gene a ed and included in he analysis. Subsequen
maximum likelihood (ML) ees we e calcula ed sepa a ely o all segmen s and o he
conca ena ed genome alignmen wi h RAxML (S ama akis, 2014) u ilizing model GTR GAMMA
wi h apid boo s apping and sea ch o he bes sco ing ML ee suppo ed wi h 1000
boo s ap eplica es. Geno ypes we e assigned, and new geno ypes we e di e en ia ed i
hey clus e ed sepa a ely as a monophyle ic g oup wi h obus boo s apping alues (>80)
and i di e ences in no malized pa is ic dis ances we e obse ed a segmen le el. The i s
comple e genome sequence o a newly de ec ed geno ype is used as a e e ence sequence,
and addi ional e e ences o new geno ypes we e de i ed as needed. Geno ype designa ion
he e is iled o include locali y (ISO 3166-1 alpha-2), da e o i s disco e y (yea -mon h),
and NA sub ype. When mul iple geno ypes o he same sub ype we e assigned wi hin he
same locali y and da e, he names we e numbe ed consecu i ely. Re e ence sequences we e
deployed along HA clades and HPAIV season and a e a ailable he e. The nomencla u e sys em
cu en ly in use he e is di e en om ha p oposed by he Eu opean Re e ence Labo a o y
(EURL) o A ian In luenza, Pado a, I aly; he co esponding EURL designa ion is shown in
he las column o he able p o ided i applicable.
2
O e iew o geno ypes
season
yea
clade
sub ype
geno ype
EURL
US
2006
2.2.1
H5N1
DE-06-03-N1
2.2.2
H5N1
DE-06-02-N1
2007
2.2
H5N1
DE-07-06-N1
2008
2.2.1
H5N1
DE-08-10-N1
2014/2015
2014
2.3.4.4a
H5N8
DE-14-11-N8
2016/2017
2016
2.3.4.4b
H5N5
DE-16-12-N5.1
DE-16-12-N5.2
H5N8
DE-16-11-N8
DE-16-12-N8.1
DE-16-12-N8.2
2016/2017
2017
2.3.4.4b
H5N6
DE-17-12-N6
2019/2020
2020
2.3.4.4b
H5N8
DE-20-01-N8
Enzoo ic pe iod
2.3.4.4b
H5N8
DE-20-10-N8
A
DE-20-10-N8.1
DE-20-10-N8.2
H5N5
DE-20-10-N5
2.3.4.4b
H5N3
DE-20-12-N3
2021
2.3.4.4b
H5N1
DE-21-02-N1
C
DE-21-07-N1
C
DE-21-10-N1.1
C
A1A2
DE-21-10-N1.2
C
A5
DE-21-10-N1.3
C
DE-21-10-N1.4
DE-21-10-N1.5
AB
DE-21-11-N1.1
DE-21-11-N1.2
DE-21-11-N1.3
DE-21-11-N1.4
A3
DE-21-11-N1.5
DE-21-11-N1.6
DE-21-12-N1.1
A4
DE-21-12-N1.2
DE-21-12-N1.3
DE-21-12-N1.4
DE-21-12-N1.5
DE-21-12-N1.6
H5N4
DE-21-02-N4
H5N8
DE-21-02-N8
DE-21-03-N8
DE-21-08-N8.1
DE-21-08-N8.2
2022
2.3.4.4b
H5N1
DE-22-01-N1.1
3
DE-22-01-N1.2
DE-22-04-N1.1
CA
DE-22-09-N1.1
CC
DE-22-11-N1.1
CH
DE-22-12-N1.1
CH
H5N2
DE-22-01-N2.1
AU
2023
2.3.4.4b
H5N1
DE-23-02-N1.1
BB
H5N1
DE-23-11-N1.1
DB
H5N1
DE-23-11-N1.2
AB
H5N1
DE-23-11-N1.3
DG
H5N1
DE-23-11-N1.4
DA
2024
2.3.4.4b
H5N1
DE-24-01-N1.1
DJ
H5N1
DE-24-01-N1.2
DO
H5N1
DE-24-02-N1.1
DQ
H5N1
DE-24-02-N1.2
DR
H5N8
DE-24-03-N8.1
DS
H5N1
DE-24-03-N1.1
DI.1
H5N1
DE-24-10-N1.1
DI.2
H5N5
DE-24-02-N5.1
I
A6
H5N1
DE-24-11-N1.1
EF
2025
2.3.4.4b
H5N1
DE-25-01-N1.1
EE
H5N1
DE-25-02-N1.1
EJ
H5N1
DE-25-04-N1.1
EK
2025
2.3.4.4.b
H5N1
DE-25-10-N1.1
DI.2.1
Re e ences
Ka oh K & S andley DM (2013) MAFFT mul iple sequence alignmen so wa e e sion
7: imp o emen s in pe o mance and usabili y. Mol Biol E ol 30(4):772-780.
S ama akis A (2014) RAxML e sion 8: a ool o phylogene ic analysis and pos -
analysis o la ge phylogenies. Bioin o ma ics 30(9):1312-1313.
Pohlmann, A. (2023) HPAIV Geno ypes in Ge many. Zenodo.
doi.o g/10.5281/zenodo.8135769
