2. Influenza Virus Classification
Influenza virus is classified into 3 types; A, B and C.
– Avian, human, mammalian
– Human, causes epidemics disease similar to type A
– Humans, swine
– 7 segments
– lacks NA but contains esterase
– Mild infections
3. Avian Influenza Virus (AIV)
The avian influenza (AI) virus is
type A influenza isolated from
and adapted to an avian host.
4. Cont. …
Type A influenza belongs to the
orthomyxovirdae virus family, is
enveloped, and is pleiomorphic with a
size ranging from 80–120 nm.
Type A influenza strains are classified by
the serological subtypes of the primary
viral surface proteins
– Hemagglutinin (HA)
– Neuraminidase (NA)
5. Cont. …
The HA has 16 subtypes (H1–H16) and contains neutralizing
Antibodies against the NA are not neutralizing, and there are
9 neuraminidase or “N” subtypes.
6. Cont. …
The “H” and N subtypes seem to be able to be assorted into
any combination, and many of the 144 possible combinations
have been found in natural reservoir species, although some
combinations are more common than others.
7. Cont. …
All 16 HA subtypes have been
found in ducks, gulls, or
shorebirds, the natural reservoir
host species of the virus.
8. Cont. …
However, in these species certain subtypes are more common
than others; for example:
1. H3, H4, and H6 are most common in ducks in North America
2. H1 and H3 in swine
3. H3 in horses
4. H5 and H7 in chickens.
9. AIV Molecular Biology
The genome of type A influenza is
single-stranded, negative-sense RNA
and contains 8 genome segments that
encode 10 or 11 proteins depending
on the isolate.
10. Segment Name Type Function
1 PB1 Polymerase complex • Transcriptase
2 PB2 Polymerase complex • Endonuclease
3 PB3 Polymerase complex
1- RNA replication
2- proteolytic activities
4 HA Membrane glycoprotein
1. Attachment to sialyoligosacharide cell
2. Envelope fusion
3. Neutralizing AB production
5 NP Major structure RNA
1. Transport of RNP
2. Antigen target for CTL
6 NA Membrane glycoprotein
1. Cell receptor destroying enzyme (sialic
acid) that elute the virus
Matrix – 1
Non glycosylated structure
protein beneath virus envelope
Non structural – 1
RNA binding protein Inhibit processing of cellular matrix
Non structural – 2
Nuclear export protein Nuclear export viral RNA
Genome Segments Functions
11. AIV Replication Cycle
The virus replication cycle, which takes place in the nucleus,
has been well described, although details on the functions of
some proteins remain unclear.
12. Molecular Biology
In gallinaceous birds (i.e., chickens, turkeys, and quail), the HA
protein is the primary mediator of pathogenicity.
Depending on which proteolytic enzyme recognizes the HA
cleavage site, virus pathogenecity would be determined.
1. Highly pathogenic
• Requires any proteolytic (protease) enzyme.
• Cause systemic infection.
2. Low pathogenic
• Requires trypsin enzyme.
• Cause restricted to the respiratory and enteric tracts.
13. Cont. …
Additionally, relatively little is known about the molecular
determinants of pathogenicity for type A influenza in hosts
other than gallinaceous birds, although there is increasing
evidence for the importance of the NS1 protein.
14. Molecular Biology
Typical of RNA viruses, type A influenza is able to generate a
high degree of genetic diversity by mutation within genes.
In addition to a high mutation rate, reassortment (which is the
mixing of gene segments between different strains and
lineages during concomitant infection) is an additional
mechanism for generating variability in the influenza genome.
15. Cont. …
Certainly, the high genetic variability of the type A influenza
virus contributes to the high adaptability of the virus and its
ability to evade the immune system by antigenic drift
(mutation) and antigenic shift (reassortment of the
16. Host Range
Although the natural host reservoir species for the AI virus is
waterfowl, particularly ducks.
On rare occasions, the virus has been transmitted to a non
natural host species including other avian species and
numerous mammalian species.
On even rarer occasions a virus lineage may become adapted
to, and established in, the new host species (i.e., swine H1N1,
17. Cont. …
It is very important to recognize that isolation of a virus from a
particular species does not indicate that the host is a natural
host or reservoir species.
Many avian species are not natural hosts, including chickens
However, in cases where an AI virus becomes adapted to
these species, they may serve as a reservoir.
18. AIV Pathogenicity
In gallinaceous birds (i.e., chickens and turkeys), AI viruses are
classified as being:
1. Highly pathogenic AI (HPAI) virus.
2. Low pathogenic AI (LPAI) virus.
19. Cont. …
Molecular criteria have been established by the World
Organization for Animal Health (formerly the OIE) for the
identification of the HPAI virus based on the protein sequence of
the HA proteolytic cleavage site, in vivo testing is more reliable
for clinical classification.
21. Cont. …
Biologically, the difference between HPAI and LPAI is that HPAI
is a systemic infection and LPAI remains localized to the
respiratory and intestinal tracts.
For unknown reasons, all HPAI viruses have been either H5 or
H7 HA subtypes.
22. Cont. …
Cleavage site of the HA
CCT CAA AGA GAG AGA AGA AGA AAA AGA AGA GGA CTA TTT
Pro Gin Arg Glu Arg Arg Arg Lys Lys Arg Gly Leu Phe
CCT CAA AGA GAG AGA AGA --- --- --- --- GGA CTA TTT
Pro Gin Arg Glu Arg Arg --- --- --- --- Gly Leu Phe
23. Cont. …
As a result of such lowered pathogenecity,
1. Grows on chicken egg embryo and tissue culture.
2. Failed to kill chicken embryo.
3. Failed to produce plaques in tissue culture in the absence of
24. Cont. …
AI virus isolate is classified as being HPAI if it:
1. kills at least 75% of susceptible 4 to 6 week old chickens
within 10 days post inoculation by the intravenous route.
2. Some isolates will cause 100% mortality by 36–48 hours
All other isolates are considered to be LPAI viruses.
27. Cont. …
The generation of HPAI viruses appears to be a phenomenon
associated with adaptation of LPAI viruses to chickens or
28. Cont. …
AI viruses from waterfowl are LPAI for gallinaceous birds, and
some waterfowl adapted isolates will not even replicate in
However, once an H5 or H7 LPAI virus has been transmitted to
chickens or turkeys, it has the potential to become an HPAI
virus, although most strains remain low pathogenic.
29. Cont. …
In some cases, the mutation from LPAI to HPAI has occurred
within weeks of virus introduction into poultry (i.e., Chile
2002 and British Columbia 2004) and in other cases has taken
from months to years (i.e., Pennsylvania 1983 and Mexico
Shorebirds الطيور الساحلية
Shorebirds الطيور الساحلية
Reverse-transcribing RNA viruses use the enzyme to reverse-transcribe their RNA genomes into DNA
Endonucleases are enzymes that cleave the phosphodiester bond within a polynucleotide chain. Some, such as Deoxyribonuclease I, cut DNA relatively nonspecifically (without regard to sequence), while many, typically called restriction endonucleases or restriction enzymes, cleave only at very specific nucleotide sequences.