Influenza: Coevolution Of Virus And Host

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Influenza Co-evolution Of Virus And Host

• Dr. Fofanovs Bioinformatics Lab
• U.H.

i
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Problem Description

• Influenza mutates and evolves rapidly
• Antigenic shift
• Antigenic drift
• Mutator mutations
• Influenza can be highly virulent
• 1918 Spanish flu (H1N1) 500,000 U.S. Deaths
• 1957 Asian flu (H2N2) 70,000 U.S. Deaths
• 1968 Hong Kong flu (H3N2) 34,000 U.S. Deaths
• 1977 Russian flu scare (H1N1) - limited mortality
• 1997 avian flu scare (H5N1) - limited mortality
• Potential for future pandemics is high
• Analysis of influenza evolution may aid design
  and development of DNA/RNA-based diagnostics

http//www.hhs.gov/nvpo/pandemics/flu3.htm
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Current State Of The Art

• CDC recognized diagnostics
• Slower, traditional laboratory culturing methods
  (e.G., Incubation within embryonic chick eggs)
• Faster, Immunilogical diagnostics
• Faster return than laboratory methods, less
  accurate and specific than DNA/RNA-based
  technology
• PCR/Microarray diagnostics
• Can be both fast and inexpensive
• Requires careful design of primers/probes
• Specificity/accuracy degraded by rapid
  mutation/evolution of target genome

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Segment Protein Assignment
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Influenza Virus Graphic - Proteins
http//www.influenzareport.com/ir/virol.htm
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Protein List

• Polymerase B2 protein (PB2)
• Polymerase B1 protein (PB1)
• Polymerase A protein (PA)
• Haemagglutinin (HA or H)
• Nucleocapsid protein (NP)
• Neuraminidase (NA or N)
• Matrix protein (M) M1 constructs the matrix And
  in influenza A viruses, only, M2 acts as an ion
  channel pump to lower or maintain the ph of the
  endosome
• Non-structural protein (NS) The function of NS2
  is hypothetical (other sources -gt facilitates
  nuclear export)

http//www.influenzareport.com/ir/virol.htm
(This Slide And Following 5)
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Haemagglutinin

• A glycoprotein containing either 2 of 3
  glycosylation sites, with a molecular weight of
  approximately 76,000
• Spans the lipid membrane so that the major part,
  which contains at least 5 antigenic domains
  presented at the outer surface
• Serves as a receptor by binding to sialic acid
  (N-acetyl-neuraminic acid) and induces
  penetration of the interior of the virus particle
  by membrane fusion
• The main influenza virus antigen the antigenic
  sites being A, B (carrying the receptor binding
  site), C, D, and E
• Body of the HA molecule contains the stalk region
  and the fusiogenic domain, which is needed for
  membrane fusion when the virus infects a new cell
• At low pH, the fusion peptide is turned to an
  interior position
• Forms trimers and several trimers form a fusion
  pore

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Neuraminidase

• A glycoprotein found as projections on the
  surface of the virus
• Forms a tetrameric structure with an average
  molecular weight of 220,000
• Presents its main part at the outer surface of
  the cell, spans the lipid layer, and has a small
  cytoplasmic tail
• Acts as an enzyme, cleaving sialic acid from the
  HA molecule, from other NA molecules and from
  glycoproteins and glycolipids at the cell surface
• Serves as an important antigenic site, and in
  addition, seems to be necessary for the
  penetration of the virus through the mucin layer
  of the respiratory epithelium

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M2 Protein

• Virus particle, taken up in the endosome,
  activity of the M2 ion channel is increased so
  that ions flood into the particle, inducing a low
  pH
• As a result, the HA-M1 linkage is disturbed, the
  particle opens, the fusion peptide within the HA
  is translocated, and the HA fuses with the inner
  layer of the endosome membrane
• Ribonucleoproteins are liberated into the
  cytoplasm of the cell and transported to the
  nucleus, where the complex is disrupted, and
  viral RNA synthesis is initiated
• Inhibited by amantadine, rimantadine and related
  substances

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NS1

• Molecular weight of 26,000
• Forms a dimer that inhibits the export of poly-A
  containing mRNA molecules from the nucleus, thus
  giving preference to viral RNA which is
  transported to the ribosome and translated
• Might also inhibit splicing of pre-mRNA
• Probably able to suppress the interferon response
  in the virus-infected cell leading to unimpaired
  virus production

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NS2

• A small molecule with a molecular weight of
  11,000
• Might be bound to M1 protein
• Function is believed to facilitate the transport
  of newly synthesised RNPs from the nucleus to the
  cytoplasm to accelerate virus production

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Preliminary Results - Measures

• To Detect Presence Of And Estimate The Rate Of
  Influenza-Host Co-Evolution, A Measure Is
  Required
• MMn MMn Sequences
• Total nMer
  Count
• Quality MM1MM2MM3MM4
• of Signature nMerSize
• Where MMn Number Of Sequences n Mismatches Away
• From Host

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Preliminary Results - Mismatches

• A mismatch sequence is
• Any clade of sequences of nMer length (16-21) not
  found in host, even when n nucleotides are
  changed to all possible nucleotide combinations
• For example, the sequence ATAGC is said to be 1MM
  away from host, if
• TTAGC, GTAGC, CTAGC are also not found in host
• AAAGC, AGAGC, ACAGC are also not found in host
• ATTGC, ATGGC, ATCGC are also not found in host
• Etc.

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Preliminary Results Method Of Comparison

• Average quality of signature
• By type (A only)
• By segment (1-8)
• By host (avian, human, others)
• By sero-type
• By time
• By locale (pending)
• Repeat with sequences blind to non-human host
  genomes
• Chicken
• Pig (pending availability of genome sequence)

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Segment 1 16mers - Mean/Std. Dev.
Human Blind Analysis Chicken Blind
Analysis
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Segment 2 16mers - Mean/Std. Dev.
Human Blind Analysis Chicken Blind
Analysis
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Segment 3 16mers - Mean/Std. Dev.
Human Blind Analysis Chicken Blind
Analysis
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Segment 4 16mers - Mean/Std. Dev.
Human Blind Analysis Chicken Blind
Analysis
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Segment 5 16mers - Mean/Std. Dev.
Human Blind Analysis Chicken Blind
Analysis
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Segment 6 16mers - Mean/Std. Dev.
Human Blind Analysis Chicken Blind
Analysis
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Segment 7 16mers - Mean/Std. Dev.
Human Blind Analysis Chicken Blind
Analysis
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Segment 8 16mers - Mean/Std. Dev.
Human Blind Analysis Chicken Blind
Analysis
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Segment 1 Human-Blind 16mers All Hosts And
Sero-Types
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Segment 1 Human-Blind 16mers Avian Host And
Sero-Types
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Segment 1 Human-Blind 16mers Human Host And
Sero-Types
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Segment 1 Human-Blind 16mers Other Hosts And
Other Host Sero-Types
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Segment 1 Human-Blind 16mers H3N2 By Host
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Segment 1 Human-Blind 16mers H5N1 By Host
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Segment 1 Human-Blind 16mers H1N1 By Host
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Segment 1 Human-Blind 16mers H9N2 By Host
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Segment 1 Human-Blind 16mers H3N2 By Year Of
Isolation
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Segment 1 Human-Blind 16mers H1N1 By Year Of
Isolation
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Segment 2 Human-Blind 16mers All Hosts And
Sero-Types
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Segment 2 Human-Blind 16mers Avian Host And
Sero-Types
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Segment 2 Human-Blind 16mers Human Host And
Sero-Types
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Segment 2 Human-Blind 16mers Other Hosts And
Other Host Sero-Types
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Segment 2 Human-Blind 16mers H3N2 By Host
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Segment 2 Human-Blind 16mers H5N1 By Host
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Segment 2 Human-Blind 16mers H1N1 By Host
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Segment 2 Human-Blind 16mers H9N2 By Host
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Segment 2 Human-Blind 16mers H3N2 By Year Of
Isolation
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Segment 3 Human-Blind 16mers All Hosts And
Sero-Types
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Segment 3 Human-Blind 16mers Avian Host And
Sero-Types
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Segment 3 Human-Blind 16mers Human Host And
Sero-Types
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Segment 3 Human-Blind 16mers Other Hosts And
Other Host Sero-Types
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Segment 3 Human-Blind 16mers H3N2 By Host
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Segment 3 Human-Blind 16mers H5N1 By Host
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Segment 3 Human-Blind 16mers H1N1 By Host
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Segment 3 Human-Blind 16mers H9N2 By Host
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Segment 3 Human-Blind 16mers H3N2 By Year Of
Isolation
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Segment 4 Human-Blind 16mers All Hosts And
Sero-Types
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Segment 4 Human-Blind 16mers Avian Host And
Sero-Types
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Segment 4 Human-Blind 16mers Human Host And
Sero-Types
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Segment 4 Human-Blind 16mers Other Hosts And
Other Host Sero-Types
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Segment 4 Human-Blind 16mers H3N2 By Host
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Segment 4 Human-Blind 16mers H5N1 By Host
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Segment 4 Human-Blind 16mers H1N1 By Host
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Segment 4 Human-Blind 16mers H9N2 By Host
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Segment 4 Human-Blind 16mers H3N2 By Year Of
Isolation
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Segment 5 Human-Blind 16mers All Hosts And
Sero-Types
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Segment 5 Human-Blind 16mers Avian Host And
Sero-Types
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Segment 5 Human-Blind 16mers Human Host And
Sero-Types
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Segment 5 Human-Blind 16mers Other Hosts And
Other Host Sero-Types
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Segment 5 Human-Blind 16mers H3N2 By Host
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Segment 5 Human-Blind 16mers H5N1 By Host
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Segment 5 Human-Blind 16mers H1N1 By Host
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Segment 5 Human-Blind 16mers H9N2 By Host
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Segment 5 Human-Blind 16mers H3N2 By Year Of
Isolation
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Segment 6 Human-Blind 16mers All Hosts And
Sero-Types
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Segment 6 Human-Blind 16mers Avian Host And
Sero-Types
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Segment 6 Human-Blind 16mers Human Host And
Sero-Types
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Segment 6 Human-Blind 16mers Other Hosts And
Other Host Sero-Types
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Segment 6 Human-Blind 16mers H3N2 By Host
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Segment 6 Human-Blind 16mers H5N1 By Host
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Segment 6 Human-Blind 16mers H1N1 By Host
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Segment 6 Human-Blind 16mers H3N2 By Year Of
Isolation
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Segment 7 Human-Blind 16mers All Hosts And
Sero-Types
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Segment 7 Human-Blind 16mers Avian Host And
Sero-Types
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Segment 7 Human-Blind 16mers Human Host And
Sero-Types
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Segment 7 Human-Blind 16mers Other Hosts And
Other Host Sero-Types
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Segment 7 Human-Blind 16mers H3N2 By Host
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Segment 7 Human-Blind 16mers H5N1 By Host
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Segment 7 Human-Blind 16mers H1N1 By Host
84
Segment 7 Human-Blind 16mers H9N2 By Host
85
Segment 7 Human-Blind 16mers H3N2 By Year Of
Isolation
86
Segment 8 Human-Blind 16mers All Hosts And
Sero-Types
87
Segment 8 Human-Blind 16mers Avian Host And
Sero-Types
88
Segment 8 Human-Blind 16mers Human Host And
Sero-Types
89
Segment 8 Human-Blind 16mers Other Hosts And
Other Host Sero-Types
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Segment 8 Human-Blind 16mers H3N2 By Host
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Segment 8 Human-Blind 16mers H5N1 By Host
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Segment 8 Human-Blind 16mers H1N1 By Host
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Segment 8 Human-Blind 16mers H9N2 By Host
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Segment 8 Human-Blind 16mers H3N2 By Year Of
Isolation
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Segment 1 Chicken-Blind 16mers All Hosts And
Sero-Types
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Segment 1 Chicken-Blind 16mers Avian Host And
Sero-Types
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Segment 1 Chicken-Blind 16mers Human Host And
Sero-Types
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Segment 1 Chicken-Blind 16mers Other Hosts And
Other Host Sero-Types
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Segment 1 Chicken-Blind 16mers H3N2 By Host
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Segment 1 Chicken-Blind 16mers H5N1 By Host
101
Segment 1 Chicken-Blind 16mers H9N2 By Host
102
Segment 1 Chicken-Blind 16mers H3N2 By Year Of
Isolation
103
Segment 1 Chicken-Blind 16mers H1N1 By Year Of
Isolation
104
Segment 2 Chicken-Blind 16mers All Hosts And
Sero-Types
105
Segment 2 Chicken-Blind 16mers Avian Host And
Sero-Types
106
Segment 2 Chicken-Blind 16mers Human Host And
Sero-Types
107
Segment 2 Chicken-Blind 16mers Other Hosts And
Other Host Sero-Types
108
Segment 2 Chicken-Blind 16mers H3N2 By Host
109
Segment 2 Chicken-Blind 16mers H5N1 By Host
110
Segment 2 Chicken-Blind 16mers H9N2 By Host
111
Segment 2 Chicken-Blind 16mers H3N2 By Year Of
Isolation
112
Segment 3 Chicken-Blind 16mers All Hosts And
Sero-Types
113
Segment 3 Chicken-Blind 16mers Avian Host And
Sero-Types
114
Segment 3 Chicken-Blind 16mers Human Host And
Sero-Types
115
Segment 3 Chicken-Blind 16mers Other Hosts And
Other Host Sero-Types
116
Segment 3 Chicken-Blind 16mers H3N2 By Host
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Segment 3 Chicken-Blind 16mers H5N1 By Host
118
Segment 3 Chicken-Blind 16mers H9N2 By Host
119
Segment 3 Chicken-Blind 16mers H3N2 By Year Of
Isolation
120
Segment 4 Chicken-Blind 16mers All Hosts And
Sero-Types
121
Segment 4 Chicken-Blind 16mers Avian Host And
Sero-Types
122
Segment 4 Chicken-Blind 16mers Human Host And
Sero-Types
123
Segment 4 Chicken-Blind 16mers Other Hosts And
Other Host Sero-Types
124
Segment 4 Chicken-Blind 16mers H3N2 By Host
125
Segment 4 Chicken-Blind 16mers H5N1 By Host
126
Segment 4 Chicken-Blind 16mers H9N2 By Host
127
Segment 4 Chicken-Blind 16mers H1N1 By Year Of
Isolation
128
Segment 4 Chicken-Blind 16mers H3N2 By Year Of
Isolation
129
Segment 4 Chicken-Blind 16mers H1N1 By Year Of
Isolation
130
Segment 5 Chicken-Blind 16mers All Hosts And
Sero-Types
131
Segment 5 Chicken-Blind 16mers Avian Host And
Sero-Types
132
Segment 5 Chicken -Blind 16mers Human Host And
Sero-Types
133
Segment 5 Chicken-Blind 16mers Other Hosts And
Other Host Sero-Types
134
Segment 5 Chicken-Blind 16mers H3N2 By Host
135
Segment 5 Chicken-Blind 16mers H5N1 By Host
136
Segment 5 Chicken-Blind 16mers H9N2 By Host
137
Segment 5 Chicken-Blind 16mers H3N2 By Year Of
Isolation
138
Segment 5 Chicken-Blind 16mers H1N1 By Year Of
Isolation
139
Segment 6 Chicken-Blind 16mers All Hosts And
Sero-Types
140
Segment 6 Chicken-Blind 16mers Avian Host And
Sero-Types
141
Segment 6 Chicken-Blind 16mers Human Host And
Sero-Types
142
Segment 6 Chicken-Blind 16mers Other Hosts And
Other Host Sero-Types
143
Segment 6 Chicken-Blind 16mers H3N2 By Host
144
Segment 6 Chicken-Blind 16mers H5N1 By Host
145
Segment 6 Chicken-Blind 16mers H9N2 By Host
146
Segment 6 Chicken-Blind 16mers H1N1 By Host
147
Segment 6 Chicken-Blind 16mers H3N2 By Year Of
Isolation
148
Segment 6 Chicken-Blind 16mers H1N1 By Year Of
Isolation
149
Segment 7 Chicken-Blind 16mers All Hosts And
Sero-Types
150
Segment 7 Chicken-Blind 16mers Avian Host And
Sero-Types
151
Segment 7 Chicken-Blind 16mers Human Host And
Sero-Types
152
Segment 7 Chicken-Blind 16mers Other Hosts And
Other Host Sero-Types
153
Segment 7 Chicken-Blind 16mers H3N2 By Host
154
Segment 7 Chicken-Blind 16mers H5N1 By Host
155
Segment 7 Chicken-Blind 16mers H9N2 By Host
156
Segment 7 Chicken-Blind 16mers H1N1 By Host
157
Segment 7 Chicken-Blind 16mers H3N2 By Year Of
Isolation
158
Segment 8 Chicken-Blind 16mers All Hosts And
Sero-Types
159
Segment 8 Chicken-Blind 16mers Avian Host And
Sero-Types
160
Segment 8 Chicken-Blind 16mers Human Host And
Sero-Types
161
Segment 8 Chicken-Blind 16mers Other Hosts And
Other Host Sero-Types
162
Segment 8 Chicken-Blind 16mers H3N2 By Host
163
Segment 8 Chicken-Blind 16mers H5N1 By Host
164
Segment 8 Chicken-Blind 16mers H9N2 By Host
165
Segment 8 Chicken-Blind 16mers H1N1 By Host
166
Segment 8 Chicken-Blind 16mers H3N2 By Year Of
Isolation
167
Segment 8 Chicken-Blind 16mers H1N1 By Year Of
Isolation
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Research Plan

• Analysis using sequence distant from other hosts
  (preliminary data are human-blind)
• Avian-blind
• Swine-blind
• Mouse-blind