VIRAL PERSISTRNCES

2. Intended Learning outcomes
By the end of the session and the associated learning resources,
the student should be able to:
Highlight the typical strategies for viral persistence.
Describe mechanism of persistence in Herpes viruses and HIV

3. Patterns of viral infection
Two different approaches for infections
endured by viruses
Acute infection followed by clearance.
Acute infection followed by persistence:
The infection last for long period.
Chronic infection.
Latent infection.

4. General Principles of Viral persistence
conditions need to be met in order for the virus to avoid clearance;
Survival of
host cells
Maintenance
of the viral
genome
Evasion of the
immune
response

5. Survival of host cells
some persistent viruses establish a
non-lytic productive infection (HBV).
most persistent viruses maintain a
dynamic equilibrium with the host
(HIV, HCV).
latent viruses are maintained in a
population that is non-permissive
to viral replication

6. Evasion of immune responses
Antigenic variation
Evolution of viral variants during
persistent infection is a feature of RNA
viruses. (HCV, COVID-19)
Variation is a function of both the
generation of diversity and selective
pressure.
Variability can operate at the level of both
individual and population

7. HIV: Evasion of the immune system
integration of proviral DNA into host cell
DNA, resulting in a persistent (latent)
infection.
high mutation rate of env gene (gp120).
Down-regulation of class-I MHC
proteins impairing the recognition by
Cytotoxic T cells.

8. HIV
HIV persists in a number of compartments:
as a dynamic infection of CD4 positive T
cells.
as a low level infection of macrophages.
as partially or fully reverse transcribed,
non-integrated DNA in inactive T cells.
as an integrated but genetically silent pro-
virus in CD4 positive memory T cells

9. Evasion of immune responses
Interference with T cell functions
prevention of processing of viral proteins
(EBV EBNA1).
prevention of peptide transport to the ER
(HSV IE 110k).
down-regulation of MHC Class I expression
(adenovirus E1A and E3; HCMV)
restricted viral gene expression (true latency)

10. Maintenance of viral genome
Models:
Alpha-herpesviruses (HSV)
Gamma-herpesviruses (EBV)

11. Herpesviruses
all herpesviruses make enzymes involved
in nucleic acid metabolism and DNA
synthesis
production of progeny virus leads to
irreversible destruction of the host cell
(lytic).
all herpesviruses establish latent infection
that persists for the lifetime of the host

12. Herpesviridae: Latency
Herpes viruses nucleic acid will remain in
“quiescent” state as circular
extrachromosomal DNA known as
“Episome”.
Absence of virion production.
Primary infection  latency period 
reactivation  Recurrent infection.

13. Alpha-herpesviruses
HSV is endemic in all human
populations.
primary infection occurs by intimate
contact with an individual shedding
the virus.
HSV and all other alpha-
herpesviruses establish latent
infection in sensory neurones

14. Herpesviridae: Classification
Subfamily: Alpha Herpesvirinae:
Two Genera:
Simplex virus:
Herpes Simplex Virus – 1 (Human
herpes Virus -1 (HHV-1).
Herpes simplex Virus – 2 (Human
Herpes Virus – 2 (HHV-2).
Varicellovirus:
Varicella Zoster Virus (Human
Herpes Virus -3 (HHV-3).

15. Herpes Simplex Viruses (HSV): Transmission and
latency
HSV-1: causes infection “above waist”:
Direct contact with saliva or skin.
Latency: Trigeminal nerve ganglia.
HSV-2: causes infection “ below waist”:
Sexually.
Through infected birth canal during labour.
Latency: lumbosacral ganglia.

16. Herpes Simplex Viruses (HSV):
factors associated with reactivation
Immune suppression.
Stress.
Sunlight.
Fever.
Menstruation.
Trauma.

17. HSV and latency
HSV enters sensory neurones innervating
infected epithelium.
virus ascends to the dorsal root ganglia and is
maintained as an episome.
reactivation is induced by local and systemic
factors

18. Herpesviridae: Latency
Alpha Herpes viruses (HHV-1,2 and
3: dorsal root Sensory ganglia.
Beta Herpes viruses (HHV-5):
Monocytes.
Gamma Herpesviruses (HHV-4): B
lymphocytes.

19. Herpes simplex virus latency-associated
transcript (LATs)
establishment of latency does not require viral
functions.
a set of nuclear transcripts (LATs) are
expressed in infected neurones during latency.
During latency, only (LATs) are produced
the major LATs are ‘intron’ sequences spliced
from an 8.3 kb transcript.
the function of LATs remains controversial

20. Epstein-Barr Virus (EBV): Conditions
Infections: “Infectious Mononucleosis”
(Glandular fever).
Tumours: Burkitt's Lymphoma,
Nasopharyngeal carcinoma.
Infections & Tumours in
immunocompromised

21. Gamma-herpesviruses
EBV establishes productive infection in
the oropharyngeal mucosa
EBV infects cells latently, its circularized
chromosome is replicated only once per
cell cycle
EBV can then establish three forms of
latent infection, designated I to III
all require the presence of a viral origin
of replication and expression of EBNA-1.

22. OriP
OriP contains two essential elements
DS: contains 4 low affinity binding
sites for EBNA-1 and is the origin of
replication (kid).
FR: contains 20 copies of a 30 bp
sequence, each containing a high
affinity site for EBNA-1

23. EBNA-1
is expressed in latently infected B
lymphocytes that persist for life in healthy
virus carriers and is the only viral protein
EBNA-1 is the only EBV encoded protein
to bind OriP.
the NH2 terminus of EBNA1 has a Gly-
Gly-Ala repeat that inhibits ubiquitinisation.

24. EBV latency I
Expression of EBV EBNA-1 (and
LMP-2A) only.
B cells supporting this type of
infection are a major reservoir of
EBV in healthy individuals.
latency I is the pattern found in
EBV positive Burkitt’s lymphoma,
NK-cell lymphoma and gastric
cancer

25. EBV latency II
expression of EBNA-1, LMP-1
and LMP-2.
this form of latency is found in
Hodgkin’s disease and
nasopharyngeal carcinoma

26. EBV latency III
expression of 9 EBV genes:
nuclear antigens EBNA-1, -2, -3A,
-3B, -3C and -LP and membrane
proteins LMP-1, LMP2A and -2B.
latency III is the second major
form of EBV persistence and also
occurs in post-transplant
lymphomas

27. gene/antigen Stage Description
EBNA-1 latent+lytic
EBNA-1 protein binds to a replication origin (oriP) within the viral genome and
mediates replication and partitioning of the episome during division of the host
cell. It is the only viral protein expressed during group I latency.
EBNA-2 latent+lytic EBNA-2 is the main viral transactivator.
EBNA-3 latent+lytic These genes also bind the host RBP-Jκ protein.
LMP-1 latent LMP-1 is a six-span transmembrane protein that is also essential for EBV-
mediated growth transformation.
LMP-2 latent LMP-2A/LMP-2B are transmembrane proteins that act to block tyrosine kinase
signaling.
EBER latent
EBER-1/EBER-2 are small nuclear RNAs, which bind to certain nucleoprotein
particles, enabling binding to PKR (dsRNA dependent serin/threonin protein
kinase) thus inhibiting its function. EBER-particles also induce the production of
IL-10 which enhances growth and inhibits cytotoxic T-cells.
EBV-EA lytic early antigen
EBV-MA lytic membrane antigen
EBV-VCA lytic viral capsid antigen
EBV-AN lytic alkaline nuclease

28. Further Reading
Notes on Medical Virology. 11th Edition. Morag Timbury. Churchill
Livingstone. ISBN 0-443-05845-8.
The Biology of Viruses. Bruce Voyles.Mosby Publishers. ISBN 0-
8016-6391-1. 1993.
https://www.ncbi.nlm.nih.gov/books/NBK8174/
Bashaw JM, Yates JL. Replication from oriP of Epstein-Barr virus
requires exact spacing of two bound dimers of EBNA1 which bend
DNA. J Virol. 2001 Nov;75(22):10603-11. doi:
10.1128/JVI.75.22.10603-10611.2001. PMID: 11602702; PMCID:
PMC114642.