Concurrent Acquisition of a Single Nucleotide Polymorphism in Diverse Influenza
H5N1 Clade 2.2 Sub-clades
Henry L. Niman
1
, Magdi D. Saad
2
, Mona M. Aly
3
, Jeffery Tjaden
2
, Kenneth C.
Earhart
2
, Marshall R. Monteville
2
, Moustafa M. Mansour
2
, Nasr El-Sayed
5
,
Ahmed E. Nayel
5
, Ahmed S. Abdelghani
5
, Hala M. Esmat
2,5
, Emad M. E.-A.
Labib
2
, Ehab A. Ayoub
2
, Abdelattar Arafa
3
, Gregory A. Raczniak
4,6
, Mensah
Agyen-Frempong
7
, William K. Ampofo
7
, Bruce R. Boynton
2
1
Recombinomics, Inc., Pittsburgh, Pennsylvania, USA,
2
U.S. Naval Medical
Research Unit 3 (NAMRU-3), Cairo, Egypt,
3
Central Laboratory for Veterinary
Quality Control, Giza, Egypt,
4
NAMRU-3 Ghana Detachment, Accra, Ghana,
5
Ministry of Health, Arabic Republic of Egypt, Cairo, Egypt,
6
Ghana Veterinary
Services, Accra, Ghana,
7
Noguchi Memorial Institute for Medical Research,
Accra, Ghana
Department of Influenza Recombination, Recombinomics, Inc, 648 Field Club
Road, Pittsburgh, PA 15238, USA
Correspondence to Henry L Niman, E-mail:
henry_niman@recombinomics.com
617.877.0987, 412.963.1362 FAX
Text word count: 1732
3 Figures 1 Supplemental Table
Running Title: Concurrent Influenza SNP Acquisitions
Nature Precedings : hdl:10101/npre.2007.459.3 : Posted 10 Sep 2007
Highly pathogenic Influenza A H5N1 was first identified in Guangdong Province
in 1996, followed by human cases in Hong Kong in 1997
1,2
. The number of
confirmed human cases now exceeds 300 and the associated Case Fatality Rate
exceeds 60%
3
. The genetic diversity of the serotype continues to increase. Four
distinct clades or sub-clades have been linked to human cases
4-7
. The gradual
genetic changes identified in the sub-clades have been attributed to copy errors
by viral encoded polymerases that lack an editing function, thereby resulting in
antigenic drift
8
. We report here the concurrent acquisition of the same
polymorphism by multiple, genetically distinct, clade 2.2 sub-clades in Egypt,
Russia and Ghana. These changes are not easily explained by the current theory
of "random mutation" through copy error, and are more easily explained by
recombination with a common source. The recombination role is further
supported by the high fidelity replication in swine influenza
9
and aggregation of
single nucleotide polymorphisms in a human H5N1 clade 2.2 hemagglutinin
10
.
The study of influenza evolution in nature has been aided by the emergence of a
new strain (clade 2.2) first identified at Qinghai Lake in central China in the spring
of 2005. Sequencing of all eight genes
11,12
showed that isolates from migratory
waterfowl were easily distinguishable from previous isolates linked to poultry and
human infections in eastern and southeastern Asia
13,14
. The new strain was
subsequently found in outbreaks in Russia, Kazakhstan and Mongolia
15,16
. Prior
to these clade 2.2 outbreaks, the highly pathogenic Asian version of H5N1 had
never been reported west of China. The detection of H5N1 in migratory waterfowl
in the summer of 2005 in Russian and Mongolian migratory bird sanctuaries
Nature Precedings : hdl:10101/npre.2007.459.3 : Posted 10 Sep 2007
signaled the start of a major geographical expansion of H5N1. In the following 12
months, almost 50 countries west of China reported H5N1 for the first time. All
infections were clade 2.2. The geographical reach includes Europe, the Middle
East and Africa. This expansion offered a unique opportunity to study the
evolution of H5N1 as it migrated into new regions, including human cases in
Turkey, Iraq, Azerbaijan, Egypt, Djibouti in 2006 and Nigeria in 2007. Sequence
analysis indicated all cases were due to clade 2.2. The outbreaks were due to
multiple introductions and isolates had region specific polymorphisms. The
sequences also allowed for the monitoring of new acquisitions of discriminating
polymorphisms. These new acquisitions created additional sub-clades defined in
phylogenetic analysis. Moreover, close monitoring of these changes could
provide insight into the mechanisms underlying the rapid evolution of H5N1 in
general, and sub-clade 2.2 in particular.
We isolated H5N1 from patients and poultry in Egypt. The first poultry isolates
were collected February 2006, and the first human cases developed symptoms in
March 2006. Analysis of the H5N1 isolates collected between February and May
2006 defined a series of HA and NA regional markers. These markers from
Egypt were also found in the human case from Djibouti, as well as in poultry
isolates from Israel and Gaza. These isolates are listed in table S1.
After a lull in reported infections over the summer, H5N1 re-emerged in Egypt in
September 2006. The more recent isolates had the same regional markers seen
in the previous season. However, both poultry and human isolates had acquired
Nature Precedings : hdl:10101/npre.2007.459.3 : Posted 10 Sep 2007
a series of new polymorphisms. Non-synonymous polymorphisms were identified
in samples collected from a cluster of three family members from the Gharbiya
governorate in the Nile Delta. HA gene polymorphisms were identified in or near
the receptor binding domain, including V223I and M230I, as well as the
oseltamivir resistance polymorphism, N294S, in the NA gene. The patients first
developed symptoms in December 2006 and all three infections were fatal (a
detailed report on patients and polymorphism tracing will be described
elsewhere).
Additional cases in early 2007 included HA sequences with a 3 BP deletion of the
nucleotides encoding Ser at position 133 (H3 numbering), as well as a case with
a novel HA cleavage site, REGRRRKR. The changes were found in multiple
patients in central and southern Egypt. The above non-synonymous changes
were associated with additional synonymous and non-synonymous changes in
the HA and NA sequences that created additional sub-clades of sub-clade
2.2. However, the isolates from the 2006/2007 season maintained the regional
markers seen in early 2006 in isolates from Egypt, Djibouti, Israel and Gaza.
Chicken isolates from Gharbiya samples collected on February 15, 2007 included
one sequence that was closely related to the sequences from the human
Gharbiya cluster. The sequence from this isolate, A/chicken/1892N3-HK49/2007
(HK49), had the regional markers previously seen in the 2006 and 2007 isolates,
as well as HA non-synonymous changes, V223I and M230I. Additionally, it also
had an NA synonymous polymorphism, G743A, appended onto the genetic
Nature Precedings : hdl:10101/npre.2007.459.3 : Posted 10 Sep 2007
background of the human Gharbiya cluster, as seen in the NA cladogram in
figure 1. The location of the isolate on the tip of the branch indicated it was a
recent acquisition.
This polymorphism was also found in two additional chicken isolates,
A/chicken/1890N3-HK45/2007 and A/chicken/1891N3-CLEVB/2007, collected
the same week in the Gharbiya governorate, but these two isolates fell onto a
separate branch of the tree, indicating the same polymorphism had been
appended onto two distinct sub-clades. Moreover, plaque-purified sub-clones of
HK49 were isolated because the original sequence had mixed signals in the NA
and HA sequences. These HK49 sub-clones fell into two major groups. The NA
consensus sequences for the two groups had 11 differences that matched the 11
differences between the two sets of chicken sequences. The major species were
closely related to the sequences from the human cluster, while the minor species
were closely related to the two additional chicken sequences. However, all
sequenced, plaque-purified clones had G743A (data not shown).
The G743A was subsequently found in human isolates from patients who
developed symptoms in April 2007. Included were siblings with HA sequences
that had the 3 BP deletion seen in earlier patients from central Egypt. Like the
chicken sequences above, the G743A polymorphism was appended onto
sequences identified earlier in Egypt. Similarly, distinct sequences from another
patient, A/Egypt/2630-NAMRU3/2007, that acquired G743A, also fell onto a
separate branch.
Nature Precedings : hdl:10101/npre.2007.459.3 : Posted 10 Sep 2007
The distinct branches displayed in the NA cladogram were also seen in the HA
cladogram in figure 1B. The isolates with G743A are also located at the tips of
the branches, supporting a recent acquisition of the polymorphism.
In February 2007, an H5N1 clade 2.2 outbreak occurred near Moscow,
Russia. Isolates from infected chickens were most closely related to 2006
sequences from Azerbaijan. Figure 2A is an expanded cladogram with isolates
from Europe, the Middle East and western Africa. Like the acquisitions in Egypt,
the isolates with G743A, mapped onto the tip of a branch composed of earlier
isolates that did not have the acquisition.
Similarly, in April, 2007, an H5N1 clade 2.2 outbreak occurred near Tema,
Ghana. Sequences from three chickens were most closely related to turkey
isolates collected in December 2006 in the Ivory Coast. Like the Egypt and
Moscow isolates above, the recent isolates with G743A mapped to the tip of a
branch containing earlier isolates that did not have the G743A polymorphism.
Additional HA polymorphisms are noted in the HA phylogram in figure 2B.
Isolates that had the NA polymorphism, G743A, also had a synonymous HA
polymorphism, C689T. This polymorphism was also in human and bird isolates
from the Nile Delta (see table S1). Another polymorphism, G754A, that encodes
M230I is in one of the German isolates
15
, A/eagle owl/Germany/R166/2006, and
maps to another branch with Egyptian human and poultry isolates from the Nile
Delta. A third polymorphism, C1614T, that encodes T517I, is in another German
isolate, A/mute swan/Germany/R797/2006, and another branch with human
Nature Precedings : hdl:10101/npre.2007.459.3 : Posted 10 Sep 2007
isolates from southern Egypt. The isolates also have the novel HA cleavage site
initially found in whooper swan isolates in Mongolia in 2005. The polymorphisms
found in German isolates in 2006 were in Russian clade 2.2 isolates in 2005.
The NA G743A polymorphism can be traced through public H5N1 sequences.
Isolates with full NA sequences are listed in the NA phylogram in figure 3. The
polymorphism was identified in the first reported sequences linked to the spread
of H5N1 in Asia in 2003/2004 in South Korea
18
and Japan
19
. The polymorphism
was subsequently identified in clade 1 isolates in southeast Asia, as well as clade
2.1 isolates in Indonesia and clade 2.3 isolates in China. The first reported clade
2.2 isolates were in wild birds in Germany (see figure 2) collected in February
2006. The isolates in Germany formed distinct HA and NA branches due to a
series of regional markers in these isolates.
The concurrent acquisition of the same polymorphism by multiple sub-clades
challenges the current theory of influenza evolution that invokes random
mutations as a mechanism for the generation of antigenic drift. The isolates with
the newly acquired polymorphisms map to the tips of the branches of the
phylogenetic trees, indicating the acquisitions were recent. All discussed isolates
on the tips of the branches were collected over a short time frame between
February and April 2007, and in three geographically distinct regions. These data
do not support a common progenitor sequence because the most closely related
sequences to each of the respective recent isolates do not have this
change. Similarly, concurrent mutation / selection by eleven isolates that map to
Nature Precedings : hdl:10101/npre.2007.459.3 : Posted 10 Sep 2007
six branches in three countries and were collected over a short time frame is also
unlikely.
An alternative explanation for the appending of these sequences is through
homologous recombination between closely related sequences. The newly
acquired polymorphisms in the recent isolates in Egypt are readily found in
recent H5N1 isolates, as noted in the three HA examples previously described
above. Moreover, the G743A polymorphism is found in these genetically distinct
sequences collected over a short time frame.
Polymorphism tracing demonstrates that most of the newly acquired
polymorphisms can be traced to the same serotype identified recently at
locations that are linked together by migratory bird flyways, raising the possibility
that the distribution and acquisition of the polymorphism is linked to
recombination between H5N1 sequences transmitted and transported by
migratory birds. This explanation is further supported by the aggregation of clade
2.2 polymorphisms from Germany, Egypt, and sub-Sahara Africa into a single
human hemaglutinnin sequence
10
.
The individual polymorphisms recombine, generating sequences that create
antigenic drift. Mapping of these pathways and associations may be used to
develop novel vaccine targets representing rapidly evolving genomes.
Figure 1 NA and HA Phylograms of Egyptian Isolates
Nature Precedings : hdl:10101/npre.2007.459.3 : Posted 10 Sep 2007
A. NA phylogram of positions 43-1337. Isolates with G743A marked with red
arrows. NA regional markers are C150T, C236T, A703G, A740G, T1088C and
G1280A.
Accession numbers and additional isolates with G743A listed in Table
S1.
B. HA phylogram of positions 93-1688. Isolates with G743A marked with red
arrows. HA regional markers are G467A, C661T, C727T, A880G, T937C, and
G1018T.
Egyptian isolates, accession numbers, collection date and governorate in Table
S1. Trees generated using neighbor joining with 100 bootstrap repetitions.
Sequences generated as described previously
20
.
Figure 2 NA and HA phylogram of Clade 2.2 isolates.
A. NA phylogram of positions 43-1337. Isolates with G743A marked with red
arrows.
Accession numbers and additional isolates with G743A listed in Table
S1.
Nature Precedings : hdl:10101/npre.2007.459.3 : Posted 10 Sep 2007
B. HA phylogram of positions 93-1688. Isolates with C628T marked with blue
arrows / bars. Isolates with G754A marked with green arrows / bars. Isolates
with C1614T marked with orange arrows / bars.
Accession numbers and additional isolates with HA polymorphisms listed in
Table S1
Figure 3 NA Phylogram of H5N1 isolates with G743A
Accession numbers and additional isolates with G743A listed in Table S1.
Table S1 Isolates and Accession Numbers
Names and accession numbers of HA and NA sequences used in figures 1-3.
Partial sequences
21-28
with polymorphisms in figures 1-3 are listed.
Acknowledgements
We thank Cecilia DeMattos from US NAMRU-3 for plaque purification of avian
isolates; Evelyn Yayra Bonney, Ivy Asante, Ken-Edwin Aryee, Kofi Bonney,
Jacob Barnor and Professor Alexander Nyarko from Noguchi Memorial Institute
Nature Precedings : hdl:10101/npre.2007.459.3 : Posted 10 Sep 2007
for Medical Research; Mr. Jerry Odoi, Drs. Joseph Gaari-Kweku, Joseph
Adongo Awuni, John Niendow Karimu and Bashiru Kikimoto from the Ghana
Veterinary Services; Mr. Michael Adjabeng, Drs. Edward Antwi and Lawson
Ahadzie from the Ghana Health Service; for the collection, screening and testing
of avian and human samples for H5NI in Ghana.
References
1.
Subbarao, K. et al. Characterization of an Avian Influenza A (H5N1) Virus
Isolated from a Child with a Fatal Respiratory Illness Science 279, 393-
396 (1998).
2.
Claas, E. C. et al. Human influenza A H5N1 virus related to a highly
pathogenic avian influenza virus. Lancet 351, 472-477 (1998).
3.
Cumulative number of confirmed cases of human influenza A/(H5N1)
reported to WHO. Available from
http://www.who.int/csr/disease/avian_influenza/country/cases_table_2007
_05_16/en/index.html
4.
Peiris, J. S. et al. Re-emergence of fatal human influenza A subtype H5N1
disease. Lancet 363, 617-619 (2004).
Nature Precedings : hdl:10101/npre.2007.459.3 : Posted 10 Sep 2007
5.
Fouchier, R., Kuiken, T., Rimmelzwaan, G., & Osterhaus, A. Global task
force for influenza. Nature 435, 419-420 (2005).
6.
Osterholm, M. T. Preparing for the next pandemic. N. Engl. J. Med. 352,
1839-1842 (2005).
7.
Monto, A. S. The threat of an avian influenza pandemic. N. Engl. J. Med.
352, 323-325 (2005).
8.
Webster, R. G., Bean, W. J., Gorman, O. T., Chambers, T. M. & Kawaoka,
Y. Evolution and ecology of influenza A viruses Microbiol. Rev. 56, 152-
179 (1992).
9.
Niman, H. L. Swine Influenza A Evolution via Recombination - Genetic
Drift Reservoir. Available from Nature Precedings
http://hdl.nature.com/10101/npre.2007.385.1
(2007).
10.
Niman, H.L. et al. Aggregation of Single Nucleotide Polymorphisms in a
Human H5N1 Clade 2.2 Hemagglutinin. Available from Nature Precedings
http://hdl.nature.com/10101/npre.2007.743.2
(2007).
11.
Chen, H. et al. Avian flu: H5N1 virus outbreak in migratory waterfowl.
Nature 436, 191-192 (2005).
Nature Precedings : hdl:10101/npre.2007.459.3 : Posted 10 Sep 2007
12.
Liu, J. et al. Highly Pathogenic H5N1 Influenza Virus Infection in Migratory
Birds Science, 309, 1266-1267 (2005).
13.
Li, K. S. et al. Genesis of a highly pathogenic and potentially pandemic
H5N1 influenza virus in eastern Asia. Nature 430, 209-213 (2004).
14.
Guan, Y. et al. H5N1 influenza: A protean pandemic threat. Proc. Natl.
Acad. Sci. U.S.A. 101, 81568161 (2004).
15.
Shestopalov, A. M. et al.
H5N1 Influenza virus, domestic birds, western
Siberia, Russia. Emerg. Infect. Dis. 12, 1167-1169 (2006).
16.
Lipatov, A. S. et al. Influenza (H5N1) viruses in poultry, Russian
Federation, 20052006. Emerg. Infect. Dis. 13, 539-546 (2007).
17.
Weber, S. et al. Molecular analysis of highly pathogenic avian influenza
virus of subtype H5N1 isolated from wild birds and mammals in northern
Germany. J. Gen. Virol. 88, 554-558 (2007).
18.
Lee, C. W. et al. Characterization of highly pathogenic H5N1 avian
influenza A viruses isolated from South Korea. J. Virol. 79, 3692-3702
(2005).
19.
Mase, M. et al. Characterization of H5N1 influenza A viruses isolated
during the 2003-2004 influenza outbreaks in Japan. Emerg. Infect. Dis.
11, 699-701 (2005).
Nature Precedings : hdl:10101/npre.2007.459.3 : Posted 10 Sep 2007
20.
Yingst, S. L., Saad, M. D., & Felt, S. A. Qinghai-like H5N1 from
domestic cats, Northern Iraq. Emerg. Infect. Dis. 12, 1295-1297 (2006).
21.
Ducatez, M. F. et al. Avian flu: multiple introductions of H5N1 in Nigeria.
Nature 442, 37 (2006).
22.
Salzberg, S. L. et al
.
Genome analysis linking recent European and
African influenza (H5N1) viruses. Emerg. Infect. Dis.13, 713-718 (2007).
23.
Ducatez, M. F. et al. Genetic characterization of HPAI (H5N1) viruses from
poultry and wild vultures, Burkina Faso. Emerg. Infect. Dis. 13, 611-613
(2007).
24.
Thanawongnuwech, R. et al. Probable tiger-to-tiger transmission of avian
influenza H5N1. Emerg. Infect. Dis. 11, 699-701 (2005).
25.
Smith, G. J. et al. Evolution and adaptation of H5N1 influenza virus in
avian and human hosts in Indonesia and Vietnam. Virology 350, 258-268
(2006).
26.
Chen, H. et al. Establishment of multiple sublineages of H5N1 influenza
virus in Asia: implications for pandemic control. Proc. Natl. Acad. Sci. U S
A. 103, 2845-2850 (2006).
Nature Precedings : hdl:10101/npre.2007.459.3 : Posted 10 Sep 2007
27.
Smith, G. J. et al Emergence and predominance of an H5N1 influenza
variant in China. Proc. Natl. Acad. Sci. U S A. 103, 16936-16941 (2006).
28.
Payungporn, S, et al. Single step multiplex real-time RT-PCR for H5N1
influenza A virus detection. J. Virol. Methods 131, 143-147 (2006).
Nature Precedings : hdl:10101/npre.2007.459.3 : Posted 10 Sep 2007
Figure 1A NA Egypt G743A
Nature Precedings : hdl:10101/npre.2007.459.3 : Posted 10 Sep 2007
Figure 1B HA Egypt G743A
Nature Precedings : hdl:10101/npre.2007.459.3 : Posted 10 Sep 2007
Figure 2A NA Phylogenetic Tree
G743A
G743A
Nature Precedings : hdl:10101/npre.2007.459.3 : Posted 10 Sep 2007
Figure 2B HA Phylogenetic Tree
C689T
C689T
C1614T
G754A
C689T
C1614T
Nature Precedings : hdl:10101/npre.2007.459.3 : Posted 10 Sep 2007
Figure 3 NA G743A
Nature Precedings : hdl:10101/npre.2007.459.3 : Posted 10 Sep 2007
Table S1 H5N1 Isolates and Accession Numbers
Accession
Name
Year Goverate
Sero
Figure
EF624253
A/chicken/Ghana/3158-NAMRU3/2007
2007 Tema
H5N1 HA
2B
EF624254
A/chicken/Ghana/3159-NAMRU3/2007
2007 Tema
H5N1 HA
2B
EF624255
A/chicken/Ghana/3160-NAMRU3/2007
2007 Tema
H5N1 HA
2B
EF441277
A/chicken/Egypt/1079-NAMRU3/2007
2007 Beni Suef
H5N1 HA
1B, 2B
EF469650
A/chicken/Egypt/1129N3-HK9/2007
2007 Fayoum
H5N1 HA
1B, 2B
EF441280
A/chicken/Egypt/1300-NAMRU3/2007
2007 Gharbiya
H5N1 HA
1B, 2B
EF469653
A/chicken/Egypt/1889N3-SM26/2007
2007 Giza
H5N1 HA
1B, 2B
EF469654
A/chicken/Egypt/1890N3-HK45/2007
2007 Gharbiya
H5N1 HA
1B, 2B
EF469659
A/chicken/Egypt/1891N3-CLEVB/2007
2007 Gharbiya
H5N1 HA
1B, 2B
EF469660
A/chicken/Egypt/1892N3-HK49/2007
2007 Gharbiya
H5N1 HA
1B, 2B
EF441281
A/duck/Egypt/1301-NAMRU3/2007
2007 Gharbiya
H5N1 HA
1B, 2B
EF469657
A/duck/Egypt/1888N3-SM25/2007
2007 Giza
H5N1 HA
1B, 2B
EF382359
A/Egypt/0636-NAMRU3/2007
2007 Beni Suef
H5N1 HA
1B, 2B
EF535817
A/Egypt/1394-NAMRU3/2007
2007 Fayoum
H5N1 HA
1B, 2B
EF535818
A/Egypt/1604-NAMRU3/2007
2007 Fayoum
H5N1 HA
1B, 2B
EF535819
A/Egypt/1731-NAMRU3/2007
2007 Sharkia
H5N1 HA
1B, 2B
EF535820
A/Egypt/1902-NAMRU3/2007
2007 Dakahlia
H5N1 HA
1B, 2B
EF535821
A/Egypt/2256-NAMRU3/2007
2007 Dakahlia
H5N1 HA
1B, 2B
EF535822
A/Egypt/2321-NAMRU3/2007
2007 Aswan
H5N1 HA
1B, 2B
EF535823
A/Egypt/2331-NAMRU3/2007
2007 Aswan
H5N1 HA
1B, 2B
EF535824
A/Egypt/2616-NAMRU3/2007
2007 Aswan
H5N1 HA
1B, 2B
EF535825
A/Egypt/2620-NAMRU3/2007
2007 Menia
H5N1 HA
1B, 2B
EF535826
A/Egypt/2621-NAMRU3/2007
2007 Qena
H5N1 HA
1B, 2B
EU095025
A/Egypt/2629-NAMRU3/2007
2007 Qena
H5N1 HA
1B, 2B
EU095026
A/Egypt/2630-NAMRU3/2007
2007 Sohag
H5N1 HA
1B, 2B
EU095027
A/Egypt/2631-NAMRU3/2007
2007 Qalubiea
H5N1 HA
1B, 2B
EU095028
A/Egypt/2750-NAMRU3/2007
2007 Menia
H5N1 HA
1B, 2B
EU095029
A/Egypt/2651-NAMRU3/2007
2007 Shoubra
H5N1 HA
1B, 2B
EF441276
A/chicken/Egypt/1078-NAMRU3/2006
2006 Menoufiya
H5N1 HA
2B
EF441278
A/chicken/Egypt/1080-NAMRU3/2006
2006 Damietta
H5N1 HA
2B
EF441279
A/chicken/Egypt/1081-NAMRU3/2006
2006 Gharbiya
H5N1 HA
2B
EF042622
A/chicken/Egypt/10845-NAMRU3/2006
2006
H5N1 HA
2B
EF469651
A/chicken/Egypt/12378N3-CLEVB/2006
2006 Gharbiya
H5N1 HA
2B
EF469652
A/chicken/Egypt/12379N3-CLEVB/2006
2006 Sharqiya
H5N1 HA
2B
DQ837587
A/chicken/Egypt/5610NAMRU3-F3/2006
2006 Fayoum
H5N1 HA
2B
DQ837588
A/chicken/Egypt/5611NAMRU3-AN/2006
2006 Cairo
H5N1 HA
2B
DQ837589
A/chicken/Egypt/5612NAMRU3-S/2006
2006 Giza
H5N1 HA
2B
DQ447199
A/chicken/Egypt/960N3-004/2006
2006
H5N1 HA
2B
DQ666146
A/Djibouti/5691NAMRU3/2006
2006 Djibouti
H5N1 HA
2B
EF469655
A/duck/Egypt/12380N3-CLEVB/2006
2006 Gharbiya
H5N1 HA
2B
EF469656
A/duck/Egypt/13010N3-CLEVB/2006
2006 Menoufiya
H5N1 HA
1B, 2B
EF061116
A/Egypt/12374-NAMRU3/2006
2006 Gharbiya
H5N1 HA
1B, 2B
EF200512
A/Egypt/14724-NAMRU3/2006
2006 Gharbiya
H5N1 HA
1B, 2B
EF200513
A/Egypt/14725-NAMRU3/2006
2006 Gharbiya
H5N1 HA
1B, 2B
EF042614
A/Egypt/2763-NAMRU3/2006
2006 Qaliubiya
H5N1 HA
2B
DQ464377
A/Egypt/2782-NAMRU3/2006
2006 Qaliubiya
H5N1 HA
2B
EF042615
A/Egypt/2783-NAMRU3/2006
2006 Qaliubiya
H5N1 HA
2B
EF042616
A/Egypt/2786-NAMRU3/2006
2006 Gharbiya
H5N1 HA
2B
EF042617
A/Egypt/2947-NAMRU3/2006
2006 Kafr El-Sheikh H5N1 HA
2B
EF042618
A/Egypt/3105-NAMRU3/2006
2006 Sohaj
H5N1 HA
2B
EF042619
A/Egypt/3458-NAMRU3/2006
2006 Minufiyah
H5N1 HA
2B
EF042620
A/Egypt/5494-NAMRU3/2006
2006 Sharabeya
H5N1 HA
2B
EF042621
A/Egypt/5614-NAMRU3/2006
2006 Al Minya
H5N1 HA
2B
EF469658
A/goose/Egypt/13009N3-SM2/2006
2006 Menoufiya
H5N1 HA
2B
DQ837590
A/turkey/Egypt/5613NAMRU3-T/2006
2006 Menoufiya
H5N1 HA
2B
EF042624
A/teal/Egypt/14051-NAMRU3/2005
2005 Damietta
H5N1 HA
2B
EF624250
A/chicken/Ghana/3158-NAMRU3/2007
2007 Tema
H5N1 NA
2A, 3
EF624251
A/chicken/Ghana/3159-NAMRU3/2007
2007 Tema
H5N1 NA
2A, 3
EF624252
A/chicken/Ghana/3160-NAMRU3/2007
2007 Tema
H5N1 NA
2A, 3
A/chicken/Egypt/1079-NAMRU3/2007
2007 Beni Suef
H5N1 NA
1A, 2A
EF486240
A/chicken/Egypt/1129N3-HK9/2007
2007 Fayoum
H5N1 NA
1A, 2A
A/chicken/Egypt/1300-NAMRU3/2007
2007 Gharbiya
H5N1 NA
1A, 2A
EF486243
A/chicken/Egypt/1889N3-SM26/2007
2007 Giza
H5N1 NA
1A, 2A
EF486244
A/chicken/Egypt/1890N3-HK45/2007
2007 Gharbiya
H5N1 NA 1A, 2A, 3
EF486245
A/chicken/Egypt/1891N3-CLEVB/2007
2007 Gharbiya
H5N1 NA 1A, 2A, 3
EF486246
A/chicken/Egypt/1892N3-HK49/2007
2007 Gharbiya
H5N1 NA 1A, 2A, 3
A/duck/Egypt/1301-NAMRU3/2007
2007 Gharbiya
H5N1 NA
1A, 2A
EF486249
A/duck/Egypt/1888N3-SM25/2007
2007 Giza
H5N1 NA
1A, 2A
EF382360
A/Egypt/0636-NAMRU3/2007
2007 Beni Suef
H5N1 NA
1A, 2A
A/Egypt/1394-NAMRU3/2007
2007 Fayoum
H5N1 NA
1A, 2A
A/Egypt/1604-NAMRU3/2007
2007 Fayoum
H5N1 NA
1A, 2A
A/Egypt/1731-NAMRU3/2007
2007 Sharkia
H5N1 NA
1A, 2A
A/Egypt/1902-NAMRU3/2007
2007 Dakahlia
H5N1 NA
1A, 2A
A/Egypt/2256-NAMRU3/2007
2007 Dakahlia
H5N1 NA
1A, 2A
A/Egypt/2321-NAMRU3/2007
2007 Aswan
H5N1 NA
1A, 2A
A/Egypt/2331-NAMRU3/2007
2007 Aswan
H5N1 NA
1A, 2A
A/Egypt/2616-NAMRU3/2007
2007 Aswan
H5N1 NA
1A, 2A
A/Egypt/2620-NAMRU3/2007
2007 Menia
H5N1 NA
1A, 2A
A/Egypt/2621-NAMRU3/2007
2007 Qena
H5N1 NA 1A, 2A, 3
A/Egypt/2629-NAMRU3/2007
2007 Qena
H5N1 NA 1A, 2A, 3
A/Egypt/2630-NAMRU3/2007
2007 Sohag
H5N1 NA 1A, 2A, 3
A/Egypt/2631-NAMRU3/2007
2007 Qalubiea
H5N1 NA
1A, 2A
A/Egypt/2750-NAMRU3/2007
2007 Menia
H5N1 NA
1A, 2A
A/Egypt/2651-NAMRU3/2007
2007 Shoubra
H5N1 NA
1A, 2A
EF486241
A/chicken/Egypt/12378N3-CLEVB/2006
2006 Gharbiya
H5N1 NA
1A, 2A
EF486242
A/chicken/Egypt/12379N3-CLEVB/2006
2006 Sharqiya
H5N1 NA
1A, 2A
EF486247
A/duck/Egypt/12380N3-CLEVB/2006
2006 Gharbiya
H5N1 NA
1A, 2A
EF486248
A/duck/Egypt/13010N3-CLEVB/2006
2006 Menoufiya
H5N1 NA
1A, 2A
EF222324
A/Egypt/12374-NAMRU3/2006
2006 Gharbiya
H5N1 NA
1A, 2A
EF222323
A/Egypt/14724-NAMRU3/2006
2006 Gharbiya
H5N1 NA
1A, 2A
A/Egypt/14724a-NAMRU3/2006
2006 Gharbiya
H5N1 NA
1A, 2A
EF222322
A/Egypt/14725-NAMRU3/2006
2006 Gharbiya
H5N1 NA
1A, 2A
A/Egypt/14725a-NAMRU3/2006
2006 Gharbiya
H5N1 NA
1A, 2A
A/Egypt/2991-NAMRU3/2006
2006 Kafr El-Sheikh H5N1 NA
1A, 2A
EF486250
A/goose/Egypt/13009N3-SM2/2006
2006 Menoufiya
H5N1 NA
1A, 2A
EF474450
A/chicken/Moscow/2/2007
2007
H5N1 HA
2B
I
SDN230945 A/Nigeria/6e/07
2007
H5N1 HA
2B
I
SDN140057 A/Azerbaijan/001-161/2006
2006
H5N1 HA
2B
I
SDN140058 A/Azerbaijan/002-115/2006
2006
H5N1 HA
2B
I
SDN140054 A/Azerbaijan/006-207/2006
2006
H5N1 HA
2B
I
SDN140055 A/Azerbaijan/008-208/2006
2006
H5N1 HA
2B
I
SDN140056 A/Azerbaijan/011-162/2006
2006
H5N1 HA
2B
EF165057
A/buzzard/Bavaria/13/2006
2006
H5N1 HA
2B
EF165049
A/buzzard/Bavaria/5/2006
2006
H5N1 HA
2B
AM403474
A/Canada goose/Germany/R1207/06
2006
H5N1 HA
2B
AM403461
A/Canada goose/Germany/R71/06
2006
H5N1 HA
2B
EF395844
A/cat/Austria/649/2006
2006
H5N1 HA
2B
DQ864720
A/cat/Dagestan/87/06
2006
H5N1 HA
2B
DQ643982
A/cat/Germany/606/2006
2006
H5N1 HA
2B
AM403468
A/cat/Germany/R606/06
2006
H5N1 HA
2B
DQ864715
A/chicken/Adygea/203/06
2006
H5N1 HA
2B
AM400974
A/chicken/Burkina Faso/01.03/2006
2006
H5N1 HA
2B
AM400973
A/chicken/Burkina Faso/13.1/2006
2006
H5N1 HA
2B
CY016811
A/chicken/Cote d'Ivoire/1787-34/2006
2006
H5N1 HA
2B
EF532628
A/chicken/Gaza/450/2006
2006
H5N1 HA
1B, 2B