Retroviruses

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Retroviruses

• TRACO
• October 5, 2009
• Frank Maldarelli

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HIV-1 PANDEMIC Total 33.2 Million cases with
1.4 M in N. America, 1.7 M in S. America, 0.7 M
in Europe, 0.9 M in Russia, 0.5 M in the Middle
East, 24.7 M in Africa, 2.5 M in asia, 0.7 M in
China and 0.08 M in Australia
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HIV/AIDSRISK 33 States, 20012004 Most males
get AIDS from homosexual relationships whereas
females get AIDS from heterosexual relationships.
MSM/IDU 5
Other 1
Other 3
Heterosexual 17
IDU 21
MSM 61
IDU 16
Heterosexual 76
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Trends in US HIV Epidemic (CDC)

• Race/ethnicity
• African Americans exceed white/not hispanic as
  most common patients living with AIDS
• Geographic spread from metropolitan areas
• 12 of cases in locations with population
  lt50,000
• Women
• comprise gt 25 of all AIDS cases
• Age
• 11 of AIDS cases are 50 years old
• By 2015, 50 of Persons living with HIV will be
  gt50 yo
• MSM most common risk group in 50 population

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• HIV
• Replication
• Origins
• Therapy and Consequences

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Retroviruses Classification by RT Sequence into
Seven Families Spumavirus exog. infection from
primates, no diseaseis closely related to MLV
endo/exo oncogene numerous mammalsand XMRV
ASSOCIATED Prostate CA. Lentiviruses HIV-1,-2,
SIV, EIAV, CAEV, VISNA is distantly
related.D-type viruses Primates-MPMV, SAIDS is
closely related to B-type viruses endog/exogen
milk-borne agent-mouse and ALV-related
endog/exogen avian oncogene. BLV-HTLV exog, no
oncogenes, neoplasms are distantly related.
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Lentivirus Relationships. HIV-2 and SIV-smm are
closely related whereas SIV-syk is distantly
related. HIV-1 and SIV-cpz are closely related
whereas SIV agm and SIV-mnd are distantly
related. VMV and CAEV are closely related
whereas FIV is distantly related. EIAV and BIV
are closely related.
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Retroviruses Conventions. Names of genes in
lower case italics, e.g., pol, envProtein gene
products are capitalized, e.g., Reverse
Transcriptase, Gp120

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Retrovirus Conventions.The viral genome is
RNA. The integrated genome is called the provirus
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Retroviruses Glossary

• gag group antigen
• pol polymerase
• env envelope
• tat Transactivator
• revRegulator of Expression of Virion proteins

• U3 unique sequence in 3 region
• U5 Unique sequence in 5 region
• R Repeat sequence
• PBS Primer binding site for initiation of RT
• Ppt polypurine tract primer for RT
• TAR Tat activating sequence
• RRE Rev responsive element
• Provirus copy of retrovirus that is integrated
  into host genome

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HIV-1 Regional Anatomy. Surface Gp120 and
transmembrane Gp41 mediate attachment and fusion.
Membrane derived by budding from infected cell. 2
identical copies of sense genomic RNA (NOT
complementary). Gag p24 is major structural
protein. RT, IN, PRO are encapsidatedl
yyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyy
yyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyy
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HIV-1 Regional Anatomy

• Virion encapsidated
• Gag
• Pol
• Env
• Nef
• Vpr
• Vif

• Cellular, Not Virion encapsidated
• Tat
• Rev
• Vpu

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HIV Replication. Reverse TranscriptionIntegrati
onTranscriptionRNA ProcessingTranslationAssemb
lyMaturation
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HIV ReplicationHIV virionAttachment/Entry
HIV virion
Attachment
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HIV Attachment and Entry

• Virus Factors
• Attachment Env glycoprotein gp120
• Entry Env glycoprotein gp41
• Host Cell Factors
• Receptor
• CD4
• Co-receptor (major)
• CXCR4
• CCR5

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HIV Receptors

• HIV receptor is CD4
• Lymphocytes
• Macrophages
• Microglial
• CD4 Receptor alone is NOT SUFFICIENT!
• A Coreceptor is essential
• Chemokine receptor family members are integral
  membrane proteins which serve as coreceptors

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HIV Coreceptor Blockade

• CCR5 is essentially absolutely necessary for
  infection
• Individuals with a deletion in BOTH copies of
  CCR5 mutants are poorly if ever infected
• Suggests that CCR5 tropic viruses are important
  in the transmission of HIV-1
• CCR5 is in linkage disequilibrium in certain
  human populations, including northern Europe
• CCR5 involved in susceptibility to plague? Cool
  story that might explain linkage disequilibrium
  but perhaps not so likely

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HIV Coreceptor BlockadeMultiple binding domains
predictedBinding disrupts structure
generallyDoes not require blocking CCR5-gp120
interactionPotential for simultaneous
inhibitionResistance emerges by reducing
affinity for drug
Maeda, JBC,2006
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HIV Fusion-Gp41. A spring - loaded mechanism that
drives the membranes together to overcome a high
energy barrier to fusion
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HIV gp41Coiled coil in a hydrophobic cavity
Spring-loaded mechanismT-20 D amino acid
interacting (PS Kim)
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HIV ReplicationUncoating
Uncoating
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HIV Post Entry Events

• Uncoating is a fundamental step in virus
  replication
• Restricts replication
• Source of host range restriction
• Requires interactions between viral and cellular
  factors
• Virus
• Gag
• Cell
• Trim 5 alpha

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HIV Post Entry EventsHost Trim 5 AlphaHIV
infects the human and chimp but not the
monkey.SIV Chimp infects the human and chimp but
not the monkey.SIV monkey infects the human and
monkey but not the chimp.
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HIV Replication Reverse transcription
Reverse Transcription
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Reverse TranscriptionBind tRNA primeranneal to
RNA templateExtend primer to synthesize(-)
strong stop DNAJump, anneal via R region To
RNA, extend and Complete round 1 RNA-Dependent
DNA synthesisRNA removed by RNase H, Maybe role
for NC

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Reverse Transcription Dual PPT anneal and
synthesize strand strong stop DNAJump 2 and
extend 5-3DNA-dependent DNA Synthesis, likely
cell ligationFinal is ds DNA with complete LTR

4 5 6
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HIV-1 Reverse Transcriptase has a thumb, palm,
fingers, p66 subunit, catalytic site and p51
subunit.
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NNRTI bind in a hydrophobic pocket at the base of
the thumb. Mutations change the nature of the
binding pocket. NNRTI binding is prevented.
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Reverse TranscriptaseEnzymatic Activities

• RNA-dependent DNA Polymerase
• RNase H
• DNA-dependent DNA Polymerase
• Error rate on order of 1-4 / 100,000 bases
  synthesized
• Recombination occurs during reverse transcription
  permitting reassortment of sequences
• Replication rapid and error prone

MUTANTS ARE LIKELY TO EXIST PRIOR TO THE THERAPY
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Error-Prone HIV Replication is a Pathogenic
Determinant. Each round of HIV replication
generates numerous mutants.The ability of the
mutants to replicate (viral fitness) may vary
greatly.The virus population can respond rapidly
to a selective pressure
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HIV Replication.Integration
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Integration
Bushman , TIG
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HIV ReplicationTranslation, Assembly, Maturation
Maturation
Assembly
Translation

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Translation of HIV gag/pol and env Paradigm
Process Polyprotein Precursors
env
Gp120 Gp41
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HIV Particle MaturationImmature particle and
mature particle

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HIV Particle Maturation by HIV proteaseImmature
particle and mature particle
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Protease with flap domain, substrate and
catalytic center
Protease RT Int
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HIV Origins
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HIV-1 PANDEMIC Total 33.2 Million cases with
1.4 M in N. America, 1.7 M in S. America, 0.7 M
in Europe, 0.9 M in Russia, 0.5 M in the Middle
East, 24.7 M in Africa, 2.5 M in asia, 0.7 M in
China and 0.08 M in Australia
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HIV Distribution, 1996 Group M Worldwide,
Subtypes A-JGroup O Africa
F
B
D
B
B
B
B
B
E
A
B
A
D
E
C
A
G
C
D
F
H
B
F
HIV-2
C
A
A
C
B
C

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HIV Origins HIV-2
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Lentivirus RelationshipsHIV-2 is closely related
to SIV-smm, whereas SIV-syk is distantly
relatedHIV-1 and SIV-cpz are closely related
whereas SIV agm and SIV-mnd are distantly
relatedVMV and CAEV are closely relatedEIAV and
BIV are closely related whereas FIV is distantly
related
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Geographic Distribution of HIV-2 Infection.Cases
are reported in Protugal, Spain, Mauritania,
Mali, Niger, Senegal, Guinea, Leone, Liberia,
Ghana, Nigeria, Cameroon, Angola, Mozambique and
India.
HIV-2 W. Africa Portugal India US -67 cs ( 97)
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HIV-1vpu present in HIV-1 but NOT in HIV-2vpu
not present in most SIVUseful tool to study the
origins of HIV-1Are there ANY SIV with vpu?
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LB1 molecular characterization of SIV with vpu
from Greater spot Nosed Monkey

• Seroprevalence study identified 19 Spot Nosed
  Monkeys with ab to HIV
• Highly divergent from other SIVs closest
  relative looks like Sykes monkey isolate

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Greater Spot Nosed Monkey
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Higher Primate Origins of HIV-1
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Bushmeat Trade in Central and West Africa
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HIV evolutionM originated in 1930, H originated
in 1935, B originated in 1941, C originated in
1949, D originated in 1950, J originated in 1951
and F originted in 1966.
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Spread of Non B Subtypes 2003Group M Worldwide,
Subtypes A-JGroup O AfricaGroup N lt10 cases,
Cameroon
F
B
CADG
D
B
B
A
B
C
Non-B Subtypes 2.1 HIVpositive donors -5
Military (USA stationed)
G
B
C
F
B
E
A
B
CRF 01 AE/B
A
D
E
C
CRF01AE
A
G
C
D
F
H
B
CRF02AG
F
C
A
CRF BF
D
A
C
B
C
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HIV Spread

• Biologic
• Blood and body fluid
• Iatrogenic
• Blood transfusion
• Vaccination needles not vaccine
• Mother to Child

• Non-Biologic
• Political
• Economic
• Multiple Epidemics

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HIV Spread

• Modes of Transmission. Consequences of large
  political upheaval are population movement and
  potential for malnutrition and immunodeficiency

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HIV Spread

• Modes of Transmission
• Trans Africa Highway

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Cumulative U.S. AIDs cases as of 2/83 N 1000
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Cumulative U.S. AIDs cases as of 5/85 N 10000
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Cumulative AIDs cases as of 7/89 N 100000
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Cumulative AIDs cases as of 12/95 N 500000
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Improvements in Pediatric HIV-1
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AIDS DRUGSNRTI drugs were developed in
1987NNRTI drugs were developed in 1996Protease
inhibitors were developed in 1995Fusion
inhibitors were developed in 2003CoReceptor
inhibitors were developed in 2007Integrase
inhibitors were developed in 2007
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Estimated incidence of AODS and deaths of adults
and adolescents with AIDS, 1985-2001, United
States
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XMRV - The Next BIG Thing (Singh 2009)
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Lessons

• Epidemics
• Are stubborn things
• Multifactorial causes and strategies
• Partial success is endemicity
• Resistance
• Is resistance really futile?
• If yes, for whom?