OFFLU A ian In luenza Ma ching (AIM) Technical Repo , July 2024
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OFFLU A ian In luenza Ma ching (AIM) Technical Repo , July
2024
Acknowledgemen s
This epo was p oduced by he join Wo ld O ganisa ion o Animal Heal h (WOAH) and Food and
Ag icul u al O ganisa ion (FAO) ne wo k o scien i ic expe ise on animal in luenzas, OFFLU’s A ian
In luenza Vaccina ion echnical ac i i y, Ian B own (The Pi b igh Ins i u e), Ashley Banya d, Joe
James, Joshua Lin on Jenkins (Animal Heal h and Plan Agency), F ancesco Bone an e (Is i u o
Zoop o ila ico Spe imen ale delle Venezie), E ica Spackman (US Na ional Poul y Resea ch
Cen e , USDA-ARS), F ank Wong (CSIRO Aus alian Cen e o Disease P epa edness), Nicola
Lewis (Royal Ve e ina y College), Fabien Filai e and Amelia Coggon (FAO). An igenic ca og aphy
was ca ied ou by Amelia Coggon and Nicola Lewis (Royal Ve e ina y College). Se a and
hemagglu ina ion inhibi ion (HI) da a we e gene a ed by he In e na ional Re e ence Labo a o y o
A ian In luenza eam led by Joshua Lyn on-Jenkins a he Animal Heal h and Plan Agency (Uni ed
Kingdom) and F ancesco Bon an e and Sil ia Manie o a he Is i u o Zoop o ila ico Spe imen ale
delle Venezie (I aly). Haemaglu ina ion inhibi ion (HI) da a was p o ided by E ica Spackman and
Jiho Lee a he US Na ional Poul y Resea ch Cen e , USDA-ARS (Uni ed S a es o Ame ica) and
F ank Wong and Joanne G imsey a he CSIRO Aus alian Cen e o Disease P epa edness
(Aus alia). Vi al isola es we e kindly sha ed wi h he In e na ional Re e ence Labo a o ies o A ian
In luenza om he ollowing coun ies: Bangladesh, Belgium, Bulga ia, Bu kina Faso, Cambodia,
Came oon, C oa ia, Czech Republic, Falkland Islands, Finland, Geo gia, Ghana, om he
Indonesian A chipelago, I an, I eland, Is ael, I aly, I o y Coas , Koso o, La ia, Moldo a, Nepal,
Nige , Nige ia, No way, Philippines, Poland, Romania, Slo akia, Slo enia, Spain, Swi ze land,
Sou h Geo gia and Sou h Sandwich Islands, Togo, Tu key, Uk aine, Vie Nam and he Uni ed
Kingdom. CVVs we e kindly sha ed by he GISRS ne wo k. We would like o hank all he OFFLU
ne wo k expe s, FAO and WOAH o hei suppo wi h his p ojec and Les Sims o his ex ensi e
con ibu ions o his p ojec .
OFFLU A ian In luenza Ma ching (AIM) Technical Repo , July 2024
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Disclaime : This echnical epo uses bo h published nomencla u e (widely used by many
coun ies a p esen (i.e. “GISAID clade”)
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bu no ecen ly upda ed) AND unpublished
nomencla u e p oposed by he WHO/FAO/WOAH H5 Nomencla u e Wo king G oup
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(i.e.
p o isional Nex clade/LABEL clade). Th oughou he epo , he use o he di e en nomencla u es
is disc imina ed by oo no es.
This epo p o ides he poin o iew o independen OFFLU expe s and does no necessa ily
e lec he posi ion o he pa en o ganisa ions FAO and WOAH.
Summa y
OFFLU has de eloped a sys em o p o iding in o ma ion o coun ies on he an igenic
cha ac e is ics o ci cula ing high pa hogenici y a ian in luenza (HPAI) A(H5Nx) i uses o he
Goose/Guangdong/1/96-lineage. This p ocess uses e e ence an ise a p oduced in chickens
agains ei he ep esen a i e isola es o ele an ci cula ing clades o isola es ha a e gene ic
ep esen a i es o accine seed s ains (he eina e e e ed o as su oga e accine seed s ains).
Con empo a y i uses a e es ed agains hese se a using he HI assay and an igenic ca og aphy is
applied on he HI i e s o es ablish he an igenic ela ionship be ween he i us an igens and
a ailable an ise a. This p o ides a nume ical alue o how closely ma ched he ci cula ing i uses
a e o he an igens used o aise he e e ence an ise a. G ea e an igenic dis ances be ween
su oga e accine an igens and cu en ly ci cula ing s ains indica e e olu ion o i al sequences
h ough mu a ions ha lead o inc eased an igenic dis ance o e ime, known as an igenic d i . As
poul y accines a e p ima ily designed o p o ide p o ec ion agains a speci ic an igen, his
an igenic d i can impac he abili y o accine de i ed an ibodies o bind and/o neu alise
con empo a y i uses. Consequen ly, i can become necessa y o upda e he an igens used in
accine o mula ions. Resul s he ein p o ide insigh on his need. Fu he in o ma ion on he
backg ound o he app oach aken and he me hods applied is a ailable in Module 1: Backg ound
epo and Module 2: Guidance epo . This documen p o ides he echnical esul s.
As o July 2024, he i uses causing he mos ou b eaks in poul y globally a e sub ype H5N1 wi hin
clade 2.3.4.4b. Howe e , ou b eaks ha e also been associa ed wi h o he H5Nx clades, including
clade 2.3.2.1a de ec ed in Sou h Asia, and clades 2.3.2.1c1/g2/e2 in Sou heas Asia. Due o he
domina ing impac o hese clades on poul y, he AIM assessmen ocused on de ining he
an igenic eac i i y be ween he sampled ield i uses in hese clades and ep esen a i e CVVs.
Following HI assessmen , an igenic ca og aphy was unde aken using eigh H5N1 clade 2.3.2.1a
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Smi h GJ, Donis RO, Wo ld Heal h O ganiza ion, Wo ld O ganisa ion o Animal Heal h, Food Ag icul u e O ganiza ion, H5 E olu ion Wo king
G oup. Nomencla u e upda es esul ing om he e olu ion o a ian in luenza A(H5) i us clades 2.1.3.2a, 2.2.1, and 2.3.4 du ing 2013-2014.
In luenza O he Respi Vi uses 2015;9(5):271-6. A ailable a : h p://onlinelib a y.wiley.com/doi/10.1111/i .12324/epd . Clade 2.3.2.1c i uses
ha e e ol ed in o di e en sublineages since hey we e las o mally classi ied in 2014. An upda ed, s anda dised clade nomencla u e o i uses
ha p e iously ell wi hin clade 2.3.2.1c is being de eloped2 bu has no ye been published.
2
P o isional nomencla u e was aken om he WHO/FAO/WOAH H5 Nomencla u e Wo king G oup who de ine "clades" using HA gene
sequences, and de ine clades as gene ically dis inc , monophyle ic g oups o i uses. This nomencla u e spli s clade 2.3.4.4 in o eigh addi ional
sub-clades, named 2.3.4.4a h ough 2.3.4.4h due o high ci cula ing di e si y wi hin he clade and. well as sub-
clades 2.3.2.1a h ough 2.3.2.1g o he 2.3.2.1 spli .
OFFLU A ian In luenza Ma ching (AIM) Technical Repo , July 2024
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i uses collec ed be ween 2021 and 2023 om Sou h Asia; one H5N1 clade 2.3.2.11 abo e1/g1
abo e i us collec ed in 2022 om Sou heas Asia; 9 H5N8 clade 2.3.4.4b i uses collec ed since
2020 om Eu ope and Asia, 74 H5N1 clade 2.3.4.4b i uses collec ed since 2020 om Asia, A ica
and Eu ope and he Ame icas; wo H5N5 clade 2.3.4.4b i us collec ed in Eu ope since 2020 and
one H5N3 i us collec ed in Eu ope in 2021. Resul s o i uses collec ed in 2023 a e ou lined and
discussed in his epo . Ou comes om he analyses unde aken wi hin his pe iod include he
ollowing poin s:
• Vaccine an igens no wi hin he clade 2.3.4.4 a e an igenically dis an om clade 2.3.4.4b
i uses and would no be expec ed o be sui able candida e an igens o inac i a ed whole
i us accines agains hese s ains ( igu e 2).
• Sub ype-speci ic he e ogenei y o e p e ious yea s was no ed in an igenic dis ances o
clade 2.3.4.4b i uses ( igu e 3).
• In geog aphically es ic ed egions, he e is e idence o an igenic d i in i uses isola ed
om poul y ( able 3).
• Vi uses es ed om wild bi ds in Eu ope did no exhibi an igenic d i ( able 3).
• Clade 2.3.2.1 and clade 2.3.4.4 i uses a e an igenically dis inc om olde i us clades
including an ise a aised agains clade 1, clade 2.2, o clade 2.3.4 i uses ( igu e 2).
This epo indica es ha , despi e ex ensi e ci cula ion in wild bi ds and global sp ead, HPAI
A(H5Nx) i uses om wild bi ds don’ appea o ha e unde gone signi ican changes in an igenic
p ope ies. Howe e , wi hin poul y popula ions in geog aphically es ic ed a eas HPAI A(H5Nx)
i uses a e e ol ing and d i ing an igenically. Con inued moni o ing o gene ic and an igenic
changes, especially in coun ies whe e he i us is enzoo ic in poul y is c ucial o ea ly de ec ion
o an igenic change and esponse o upda e accines whe e necessa y.
OFFLU A ian In luenza Ma ching (AIM) Technical Repo , July 2024
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Vaccine seed s ains
Table 1: Seed s ains o accines which a e cu en ly unde s ood o be in use o ha e been used in he pas . Whe e a ailable clade in o ma ion
and e e ences ha e been included. Clade in o ma ion is desc ibed in he li e a u e. Whe e sequences o he seed s ain a e a ailable is no ed by
* and he nomencla u e acco ding o2 included i di e en .
Seed S ain / HA Gene Sou ce
Clade1
Re e ence
Rep esen ed
A/Goose/Guangdong/96
0*
Shi e al., 2022
No
A/chicken/Vie nam/C58/04
1*
EFSA 2023
Yes
A/Vie nam/1194/2004
1*
EFSA 2023
Yes
A/Chicken/Shanxi/2/2006
7.2*
Shi e al., 2022
No
A/Chicken/Liaoning/S4092/2011
7.2
Shi e al., 2022
No
A/chicken/Legok/2003
2.1.1
EFSA 2023
Pending
A/CK/Egyp /ME1010/2016
2.2.1.1
EFSA 2023
Pending
A/Chicken/Egyp /Q1995D/2010
2.2.1.2*
EFSA 2023
Pending
A/Chicken/Egyp /RG-173 CAL/2017
2.2.1.2
EFSA 2023
Pending
A/Duck/EGYPT/M2583D/2010
2.2.1.2*
EFSA 2023
Pending
A/chicken/Wes Ja a/Pw -Wij/2006
2.3.1.2
EFSA 2023
No
A/duck/Sukoha jo/BBVW-1428- 9/2012
2.3.2.1g2*
Ind iani e al., 2014
Yes
A/Hubei/1/2010
2.3.2.1a2*
EFSA 2023
Pending
A/duck/Guangdong/S1322/2010
2.3.2.1b2*
Shi e al., 2022
Yes
A/chicken/Vie nam/NCVD-KA435/13
2.3.2.1c1/e2*
EFSA 2023
Pending
A/chicken/Tanggamus/031711076- 65/2017
2.3.2.1c
EFSA 2023
No
A/chicken/Liaoning/SD007/2017
2.3.2.1d
Shi e al., 2022
Pending
gCA2/2.3.2.1d
2.3.2.1d
Kang e al., 2022
No
A/duck/Anhui/SI246/2014
2.3.2.1
Shi e al., 2022
No
A/Duck/Anhui/1/2006
2.3.4*
Shi e al., 2022
Yes
A/chicken/Guizhou/4/2013
2.3.4.4/g2*
Shi e al., 2022
No
A/duck/Ko ea/ES2/2016
2.3.4.4/e2*
EFSA 2023
Pending
A/Wa e owl/Ko ea/S57/2016
2.3.4.4
Ku uppua achchi e al., 2022
No
A/Gy alcon/WA/41088-6/2014
2.3.4.4c2*
EFSA 2023
Yes
A/chicken/Egyp /ME-2018/2018
2.3.4.4b2*
Yes
A/g een-winged eal/Egyp /877/2016
2.3.4.4b2*
EFSA 2023
Yes
A/whoope swan/Shanxi/4–1/2020
2.3.4.4b2*
Shi e al., 2022
Yes
A/duck/Guizhou/S4184/2017
2.3.4.4h
Shi e al., 2022
Pending
A/duck/Fujian/S1424/2020
2.3.4.4h
Shi e al., 2022
Pending
gES3/2.3.4.4h
2.3.4.4h
Kang e al., 2022
No
A/duck/Guanzou/S4184/2017
2.3.4.4h
Shi e al., 2022
Pending
A/Duck/Vie Nam/QB7412
unknown
EFSA 2023
No
OFFLU A ian In luenza Ma ching (AIM) Technical Repo , July 2024
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Panel o chicken an ise a used in OFFLU AIM
Table 2: Vi uses which we e used in OFFLU aim o gene a e se a. Clade* p o isional nomencla u e was aken om he WHO/FAO/WOAH H5
Nomencla u e Wo king G oup who de ine "clades" using HA gene sequences, and de ine clades as gene ically dis inc , monophyle ic g oups o
i uses. This nomencla u e spli s clade 2.3.4.4 in o eigh addi ional sub-clades, named 2.3.4.4a h ough 2.3.4.4h due o high ci cula ing di e si y
wi hin he clade and. well as sub-clades 2.3.2.1a h ough 2.3.2.1g o he 2.3.2.1 spli .
S ain
Sub ype
Clade1
Clade2
Simila accine seed s ain
A/Vie nam/1194/2004/1
H5N1
1
1
A/chicken/Vie nam/C58/04
A/Tu key/ u key/2005
H5N1
2.2
2.2.1
A/swan/Hunga y/4999/2006
A/Anhui/1/2005
H5N1
2.3.4
2.3.4
A/Duck/Anhui/1/2006
A/mynah/Indonesia/13064792-010/2013
H5N1
2.3.2.1c
2.3.2.1g
A/duck/Sukoha jo/BBVW-1428- 9/2012
A/chicken/Nepal/T360/2014
H5N1
2.3.2.1a
2.3.2.1a
A/duck/Guangdong/S1322/2010
A/Mu e_Swan/C oa ia/102/2016
H5N8
2.3.4.4b
2.3.4.4b
A/g een-winged eal/Egyp /877/2016
A/malla d/Geo gia/DT09382/2017
H5N8
2.3.4.4b
2.3.4.4b
A/chicken/ME-2018
A/chicken/Czech Republic/1175-1/2020
H5N8
2.3.4.4b
2.3.4.4b
A/chicken/Bulga ia/722-1_22VIR778-1/2021
H5N1
2.3.4.4b
2.3.4.4b
A/duck/Cambodia/ 4k241D3/2021
H5N8
2.3.4.4b
2.3.4.4b
A/whoope swan/Shanxi/4–1/2020
A/g ea _skua/Sco land/B07779/2021
H5N1
2.3.4.4b
2.3.4.4b
A/gy alcon/Washing on/41088/6/2014
H5N8
2.3.4.4c
2.3.4.4c
A/Gy alcon/WA/41088-6/2014

OFFLU A ian In luenza Ma ching (AIM) Technical Repo , July 2024
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Phylogene ic ela ionships o i uses included in he OFFLU AIM s udy
Figu e 1: A maximum likelihood phylogene ic ee o he HA1 o Gs/Gd lineage H5 i uses included in his p ojec and accine seed s ains whe e sequences we e a ailable. Lea es a e colou ed by es
an igens in his s udy, accine seed s ains, an ise a used in his s udy and an ise a and accine seed s ains used in his s udy. Majo clades a e anno a ed along he b anches acco ding o
nomencla u e, mino clade a e no anno a ed2. This image was gene a ed in Auspice using Nex clade.
OFFLU A ian In luenza Ma ching (AIM) Technical Repo , July 2024
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An igenic ca og aphy
An igenic ca og aphy was unde aken o quan i y and isualise he an igenic dis ances be ween
i uses ep esen a i e o accine seed s ains and con empo a y ci cula ing i uses as desc ibed in
he AIM pilo p ojec . Maps we e analysed and isualised using R S udio e sion 2023.03.1+446 and
he Racmacs package e sion 1.2.9 buil unde R e sion 4.3.1 as desc ibed by Smi h e al., (2004)
and p e iously used in Lewis e al., (2021). Fo in o ma ion ega ding map gene a ion and
in e p e a ion please con ac an app op ia e e e ence labo a o y. Complemen a y gene ic
analysis was ca ied ou o map es ing using manually cu a ed da ase s wi h me hods desc ibed
as in he OFFLU a ian da a package o zoono ic in luenza componen o he VCM. Amino acid
changes in he HA1 we e isualised by econs uc ing ances y using ee ime e sion 0.11.1
(Sagulenko e al., 2018) and we e compa ed be ween wi hin-clade and wi hin-sub ype es
an igens. An igenic maps we e colo ed acco ding o unpublished i al clade nomencla u e and
sub ype using he H5Nx da ase in Nex clade (Aksamen o e al., 2021).
OFFLU A ian In luenza Ma ching (AIM) Technical Repo , July 2024
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Figu e 2: A 3-dimensional an igenic map showing he e olu iona y ela ionships o H5 HPAI Gs/Gd lineage i uses. Each an ise um is ep esen ed by a ed cube, o accine seed s ains o su oga es and
black cube o o he . An igens a e ep esen ed as balls and a e colou ed by clade 1 o 2 acco ding o he key. Each squa e ep esen s one an igenic uni . One an igenic uni is ep esen a i e o a 2- old
di e ence in HA assay i e . The co esponding able o an igenic dis ances can be ound in able 3.
OFFLU A ian In luenza Ma ching (AIM) Technical Repo , July 2024
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Figu e 3: A 3-dimensional an igenic map showing he e olu iona y ela ionships o H5 HPAI Gs/Gd lineage i uses o he clade 2.3.4.4. Each an ise um is ep esen ed by a ed cube, o accine seed
s ains o su oga es and black cube o o he . An igens a e ep esen ed as balls and a e colou ed by clade 1 o 2 acco ding o he key. Each squa e ep esen s one an igenic uni . One an igenic uni is
ep esen a i e o a 2- old di e ence in HA assay i e . The co esponding able o an igenic dis ances can be ound in able 3.