Viruses that Use Reverse Transcriptase during Replication

The retroviruses have an RNA genome that is converted to DNA by RT after infection.

The hepadnaviruses and caulimoviruses have a DNA genome that is replicated via an RNA intermediate.

The mode of replication of these various viruses is otherwise similar.

The foamy viruses are retroviruses which appear to contain the DNA phase of the replication cycle in the virion, at least in part.

DELTARETROVIRUS (formerly the BLV/HTLV group)

blood

SIMPLE RETROVIRUSES

ALPHARETROVIRUS (formerly avian type C retroviruses)

GENUS/ MEMBERS

DISEASE TRANSMISSION HOST(s)

GAMMARETROVIRUS (formerly mammalian type C retroviruses)

immunodeficiency

Vertical,including

BETARETROVIRUS (formerly mammalian type B and type D retroviruses)

Rous sarcoma

sexual transmission,

Birds

TSP, HAMc

Moloney murine leukemia

T-cell lymphoma Mice

Feline leukemia T-cell lymphoma, Cats, humans

Avian leukosis Birds

Primate T- lymphotrophic

T-cell lymphoma,

neurological disorders Vertical,including

mothers’ milk, Humans

Bovine leukemia B-cell lymphoma Cows

Mammary carcinoma, mothers’ milk

Mouse mammary tumor

T-cell lymphoma

Mason-Pfizer monkey

Mice

Monkeys Unknown

??

LENTIVIRUS

SPUMAVIRUS Chimpanzee foamy None

HIV

Visna-maedi

AIDS

Neurological disease

Worldwide

No. Europe

sexual transmission, blood

Neonatal infection, Humans

Sheep

Equine infectious anemia Current epidemic in Utah

Anemia

Human spumaretrovirus Humans Monkeys

Horses

Simian immunodeficiency Simian AIDS Africa Monkeys

EPSILONRETROVIRUS Walleye dermal sarcoma Fish Benign sarcomas

COMPLEX RETROVIRUSES

GENUS/ MEMBERS

DISEASE TRANSMISSION HOST(s) WORLD DISTRIBUTION

North America

HIV

MMTV

ASLV

Budding

Immature MatureEarly Late

Released Virions

Maturation

RetrovirusParticles

Cleavage

After

of

by

ofGag

Budding

Immature Mature

MLV

M-PMV

HTLV -1

HIV-2

Maturation of Retrovirus Virions

Maturation of virions after release from the cell occurs by cleavage of the Gag polyprotein by the viral protease

The protease is a homodimer of a polypeptide of 99 residues

The active site consists of two aspartic acid residues, one contributed by each monomer in the homodimer

The protease is active in precursor polypeptides as well as after release

Because dimerization is required for the enzyme to be active, high concentrations of the precursor polypeptides are required for cleavage to occur, which are normally present only in the assembled virion

SCHEMATIC OF A RETROVIRUS

Retroviral

Genome

is an

Dimer

RNA

Figure 5.2

LTRLTR

Capsid proteins

PolymeraseEnvelope proteins

CAP An

R U5 PB leader PP U3 R

Genome

Provirus

Virion

gag pol env

U3 U5 U3 U5

Genome Organization of the Retroviral RNA Genome and the Provirus

Terminal Regions of Retrovirus Genomes

Genus Prototype Virus Approximate Sizes in Bases of Terminal ElementsPrimer tRNA Used

U3 R U5

Alpharetrovirus RSV, ALV 230 20 80 Trpa

a Includes v-src geneb U3 contains sag gene

bBetaretrovirus MMTV 1200 Lys-315 120

Gammaretrovirus MLV 450 70 80 Pro/Gln

Deltaretrovirus HTLV-1 350 230 220 Pro

Lentivirus HIV-1 450 100 80 Lys-1,2,3

Spumavirus HRSV 910 190 160 Lys-1,2

Epsilonretrovirus 7080440WDSV His

TranslationReadthrough or frameshift translation

gag

gag pol

Splicing

Translation

env

Genome RNA(gag mRNA)(gag-pol mRNA)

Env mRNA

pro

Transcription and Translation of a Simple Retrovirus

XA AAU UUA UAG GGXXXX 5’ 3’

Stop

A A U A A U U AU

IUA U

I

A. Frameshifting in ALV

UUGACAAAUUUAUAGGGAGGGCCProtease

Polymerase

L T N L *RNA sequence

I G R A

L T N L I G R A

t-RNA slips on message as mRNA shifts one position to the right

B. Mechanism of (-1) Frameshifting in ALV

N LPeptide N LPeptide

3’

5’

5’ 3’

Pro-Pol fusion protein

Ribosome

X AAA UUU AUA GGG XXXX

Ribosomal Frameshift in Avian Leukosis Virus

G C G C

G G U

C

G

G U A G U

C C A G C

C G A U U A U A C U U G G C G C A U U A G C G C U G . . .CUCAGCAGGGUUUAGGAG

Slippery site

Pol ORF Gag ORF

Stem 2

Stem 1

3’ . . .

ACAUCCAAGA

G5’

Pseudoknot

nt 2025

nt 1951

nt 2005

U

nt 1983

Pseudoknot in L-A RNA that Promotes Ribosomal Frameshifting Between Gag and Pol

Reverse transcription

DNA copy of genome

Integration into host DNA

Splicing Gag

Glycoproteins

mRNAs

Translation

RNAs

RT

NUCLEUS

EUKARYOTIC HOST CELL

genomic

Maturation

Budding

RNA Synthesis

Replication of a Typical Retrovirus

Retrovirus

Replication

of a

1) Primer t-RNA anneals to PBS sequence in genome RNA

2) tRNA is extended to form DNA copy of the 5’ end of the genomic RNA

3) RNase removes hybridized RNA (R and U5)

4) First Jump. DNA hybridizes to remaining RNA R sequence at 3’ endR’U5’

An

progag pol env U3 RU5RPBS

R’U5’

PPT

An5’ 3’

3’

Strong Stop DNA

Mechanism of Retroviral DNA Synthesis (Reverse Transcription)(Steps 1-4)

R’U5’U3’

5) DNA minus strand extended and completed; most RNA removed.

6) Plus strand DNA primes at poly-purine track (PPT) downstream of env gene. 5’ end of plus strand DNA is synthesized

PPT

PPT

PPT

R’ U5’U3’

7) RNase H degrades t-RNA and PPT.

Mechanism of Retroviral DNA Synthesis (Reverse Transcription)

(Steps 5-7)

R’ U5’U3’

R U5’U3

LTR LTR

R U5U3’ progag pol envPBS PPT5’ 3’

3’ 5’

8) Second Jump Plus strand DNA binds to the primer binding sequence (PBS) near the 3’ end of minus strand DNA.

9) Both strands extended and completed to give double stranded DNA with duplicated LTRs in the same orientation at both ends.

R’ U5’U3’

PBS

Mechanism of Retroviral DNA Synthesis (Reverse Transcription)

(Steps 8-9)

Retrovirus Reverse Transcriptase

The subunit composition of active RT differs among retroviruses

MLV RT appears to function as a monomer containing pol and RNaseH

HIV-1 RT functions as a heterodimer

p66 contains both pol and RNaseH domains

p51 contains only the pol domain

ASLV RT also functions as a heterodimer

The larger subunit contains the pol, RNaseH, and IN domains

The smaller subunit contains only the pol and RNaseH domains

GT

X1234

AC

1234Y

LTRR U5U35’ 3’

LTR

ACTGGAAGGGCTAATTCACTTGACCTTCCCGATTAAGTGA

TGTGGAAAATCTCTAGCAGTACACCTTTTAGAGATCGTCA

Nucleopilic attack by water

Nucleopilic attack by water

ACTGGAAGGGCTAATTCACTACCTTCCCGATTAAGTGA

OH3’

TGTGGAAAATCTCTAGCAACACCTTTTAGAGATCGTCA

OH3’

GT

OH3’

ACACTG

OH3’

CAGTCA

X1234YX1234Y

X X4321

ACTG

AC

Y

GTCA

CA

1234YCA

R U5U3 R U5U31234YCAX1234TG

Cellular Enzymes

Integrase

IntegraseEnd processing

Joining reaction

Repair

TG

Provirus

Host DNA

Integrated provirus

AC

R U5U3

3’ 5’

Integration of Retroviral DNA into the Host Genome

B.

A.

BREs

AP1

200bp TATA

TATA200bpNRE HREME

MAFNF-1 NF-1Oct 1GRNBP

U3 R U5

100bpTATAenhancer

EFII EFI

EFIII

100bpTATA

(+)enhancer promoter

(-)PBS

(+)(-)(-)

GR MCREF

bHLHCBF

ETsNF-1 ETsELPUCRBP C/EBP

Factor A

100bpTATAETs NF-1

Sp-1

Myb

Myb

21 bp TREs

ETs

100bpTATA

Sp-1 LBP-1TAR

ETsAP2TCF-1

GR

NFAT-1

NRE (+/-)

NF-BUSF-1COUPTF

enhancer

(+)

U3 R U5

Transcription Signals in Retroviral LTRs

RSV

MLV

PTLV-1

HIV-1

HSRV

MMTV

Myristylate Acetate

p10 p19 p27 p12 ALV

p15 p12 p30 p10MLV

p17 p24 p6p7p24HIV-1

p10 p21 p3p8? p27 p14MMTV

p19 p24 p15PTLV-1

(MA) (CA) (NC)HSRV

MA (matrix) CA (capsid)NC (nucleocapsid)“Minimum”

GAG

p10 p20 (p10) p25 p14WDSV

Organization of the Gag Proteins in Retroviruses Representative of each of the Seven Genera

SU protein

TM protein Transmembrane anchor

Fusion domain Signalase

Furin CHO

Pro (viral protease)

N-linked carbohydrate

ALV L gp85 gp37

L gp52 gp36MMTV

MLV p15E/12Egp70L

L gp41gp120HIV

gp21L gp46PTLV-1

gp80L gp48HSRV

SUL gp90WDSV

Envelope Proteins of Representative Members of Each of the Seven Genera of Retroviruses

POLENVPRO

GAGLTR

U3RU5

0 2 4 6 8 10kb

ALVAlpharetrovirus

vif

tat

rev

vprnef

LentivirusHIV

vpu

BetaretrovirusMMTV orf

tax

DeltaretrovirusPTLV

rex

MLVGammaretrovirus

SpumavirusHSRV

bel3bel1

betbel2

c ba

EpsilonretrovirusWDSV

Coding Regions of Representative Members of Each of the Seven Genera of Retroviruses

Genome

Organization

of

Retroviruses

Virus GenusMLVFeLVHERV-CWDSV

HSRV

HIV-1HIV-2EIAVVMV

MPMV

MMTVHERV-KIAP

RSV

BLVPTLV-1PTLV-2

Gammaretrovirus

Epsilonretrovirus

Spumavirus

Lentivirus

Betaretrovirus

Alpharetrovirus

Deltaretrovirus

new env

new env

orfA, orfB, orfC

bel1, bel2

tat, rev

dut

sag

tax, rex

Phylogenetic Tree of the Retroviridae

Lentivirus (HIV-1)

Spumavirus (HRSV)

Deltaretrovirus (HTLV/BLV)

Accessory Genes in Retroviruses

GENE FUNCTIONS

tatrevvifvpr/vpxnefvpu

dut

See Table of HIV Proteins

dUTPase (in nonprimate lentiviruses) Facilitates replication in certain cell types.

sag Superantigendut dUTPase

taxrex

Transcription activator (like tat)

Splicing/RNA transport regulator (like rev)

bel 1bel 2bet

Activates transcription??

Betaretrovirus (MMTV)

Epsilonretrovirus (WDSV)Orf AOrf BOrf C

???

Transcription activator (like tax)

Splicing/RNA transport regulator (like rex)

Transcriptional Activators

Tax protein of PTLV/BLV activates transcription

Transcription factors bind to TRE in U3 region

Tax interacts with these to increase their activity

Tat protein of lentiviruses activates transcription

Tat of visna interacts with transcription factors

Requires sequence element in U3

Tat of HIV binds to TAR element at 5’ end of RNA

This increases transcription by an unknown mechanism

. . . 5’

G

GG

G

GG

G

GG

GGG

G

G

AC

C

U

U

GU

U

U

U

UUU

UU

U

U

A

A

A

AAA

A

A

CC

AC

C

CC

C

C

C

C

C

C CUUU AA G

U ACGCGCG

•

•

1

10

40

20

50

60

30

1

10

20

30

40

50

60

70

90100

130

80

120

110

GG G

G

GGG G GG

GGG

G

G

GGG

GG

G G G

GGG

U

UU

U

U

U

UU

U

U

U

U

UU UU UU

G

A

A

A

A

AA A

A

A

A CCCCCCCC

CC

C

C

CC C

C C

CCCC

U

C

G

GU

U

A

AC

C

C

G

GUC

AC

GC

C

•

•

GG

UUCG

GA

CC

5’

C

G•G

UA

UG

CGC

GC

AU

C

GG

CA

UU

AC

G

AU

GC

AU

GC

. . .

HIV-1 TAR HIV-2 TAR

HIV-1 and HIV-2 TAR RNA Elements

NUCLEUS

EUKARYOTIC HOST CELL

Early events(minus REV)

Late events(plus REV)

multiply-spliced mRNAs

Translation

Rev, Nef, Tat

Export ofnon- and singly-spliced mRNAs

Export of

TranslationGag, Pro, Pol, Env, and other proteins

AnAnAn

An

An

An

Spliceosome

An

An

An

+ Rev oligomer+RAB

Further splicing

RRE

Integrated provirus of complex retrovirus

C

AB

An

Rev oligomer RAB (similar to nucleoporins)

REV response element (RRE) Components of spliceosome

Model for the Regulation of Retroviral Gene Expression by Rev

Regulationof

Splicingand

Exportof

mRNAsBy

REV

Leukemia-Sarcoma Viruses

The simple retroviruses can cause leukemia, neurological disease, and other diseases

Leukemia takes many years to develop and the mechanisms are complex

They can also cause sarcomas and other tumors upon incorporation of a cellular oncogene

The incorporated oncogene is usually mutant so that it no longer responds to regulatory signals

Oncogenes are of many types and function to regulate the cell cycle

Avian Leukosis virus Rous sarcoma virus (nondefective)

Retrovirus v-onc- containing Retroviral Genome

gag-pro pol env gag-pro pol env src

p60 src

gag-pro pol envv-myb

myb-env

Avian myeloblastosis virus (defective)

Murine leukemia virus

gag-pro-pol env

Abelson murine leukemia virus (defective)

envgag v-abl

gag-abl

gag v-mosmos

Moloney murine sarcoma virus (defective)

Alpharetrovirus

Gammaretrovirus

Two Retroviruses and Examples of v-onc-containing Retroviral Genomes Derived from Them

Selected Retroviral Oncogenes

Oncogene/ functional class Retrovirus Viral oncoprotein

Growth factorssis Simian sarcoma virus p28 env-sis

Tyrosine kinase growth factor receptorserbB Avian erythroblastosis virus gp65 erbB

fms McDonough feline sarcoma virus gp180gag-fmssea S13 Avian erythroblastosis virus gp160env-sea

kit Harvey-Zuckerman-4 feline sarcoma virusgp80gag-kit

ros UR2 avian sarcoma virus p68gag-ros

mpl Mouse myeloproligerative leukemia virus

p68gag-ros

eyk Avian retrovirus RPL30 gp37eyk

G Proteins (GTPases)H-ras Harvey murine sarcoma virus p21ras

K-ras Kirsten murine sarcoma virus p21ras

Nonreceptor tyrosine kinases/ signal transduction factorssrc Rous sarcoma virus pp60src

abl Abelson murine leukemia virus p460gag-abl

fgr Gardner-Rasheed feline sarcoma virusp770gag-actin-fgr

yes Y73 avian sarcoma virus p90gag-yes

Serine-threonine kinases/signal transduction factors

fps Fujinami avian sarcoma virus p130gag-fpsc

fes Snyder-Theilen feline sarcoma virus p85gag-fesc

mos Moloney murine sarcoma virus p37env-mos draf 3611 murine sarcoma virus p75gag-raf d

mil MH2 avian myelocytoma virus p100gag-mil

b

Hormone receptor (thyroid hormone receptor)erbA Avian erythroblastosis virusb p75gag-erbA

Transcription factorsjun Avian sarcoma virus 17 p65gag-jun

fos Finkel-Biskis-Jenkins murine sarcoma virus

p55fos

myc OK10 avian leukemia virus p200gag-pol-myc

myb Avian myeloblastosis virusb p45myb

ets Avian myeloblastosis virusb p135gag-myb-ets

rel Avian reticuloendotheliosis virus p64rel

maf Avian retrovirus AS42 p100gag-maf

Primate T-Cell Leukemia Viruses (PTLV)

Formerly called human T-cell leukemia (or lymphotropic) viruses (HTLV)

PTLV-1 causes T-cell leukemia in ~1% of infected humans after a very long latent period (20-30 years)

ATL (adult T-cell leukemia) is rapidly fatal once it arises

PTLV-1 can also cause a neurological disease called HAM (HTLV-1-associated myelopathy)

HAM develops in ~1% of infected humans and is characterized by demyelination of the spinal cord

accompanied by an inflammatory response

Equator

Global Distribution of PTLV-1 and PTLV-2

Areas in which PTLV-2 is endemic

Areas in which PTLV-1 is endemic Location of PTLV-1 isolates

Location of PTLV-2 isolates

Patient

with

Adult

Acute

T-cell

Leukemia

Human Immunodeficiency Virus

There are two HIVs, called HIV-1 and HIV-2.

By the end of 2000, 22 million people had died of AIDS and 36 million were living with HIV infection.

Acute immunodeficiency syndrome is characterized by a decline in CD4 T-cells, destruction of lymph nodes, and progressive loss of immune function.

Neurological disease is also a common feature of AIDS.

HIV requires CD4 as a receptor as well as a chemokine coreceptor.

Virus responsible for primary infection usually requires CCR5 as a coreceptor (M-tropic virus).

In late stage disease virus requiring CXCR4 usually arises (T-tropic virus).

The immune system, especially CTLs, are important in controlling the virus during the long latent period. With decline in immune function, virus replication accelerates and AIDS develops.

Genomic RNA(gag mRNA)

(gag-pro-pol mRNA)AnCAP

CAPvif mRNA An

CAPvpr mRNA An

CAPtat mRNA An

kb1 2 3 4 5 6 7 8 9

CAPrev mRNA An

CAPvpu, env mRNA AnCAPnef mRNA An

RRE

Proviral DNA

ORFsgag

propol env

vif

Frame 3Frame 2Frame 1

nef

rev

revtat

tat

vpuvpr

LTR LTR

Other mRNAs

TAR

Genome organization of HIV (Lentivirus)

The HIV Proteins

PROTEIN mRNA SIZE kD FUNCTIONS POST-TRANSLATIONAL MODIFICATIONS

p17 (MA) myristylated at 2Gly Matrix protein

p7 ? RNA-binding protein

p2 ? RNA binding protein

gag p25(CA) none Capsid structural proteingenomic RNA

pro genome RNA frameshifted

p10 (PR) Viral protease, processes gag proteins

pol genome RNA frameshifted

p66/p51 RT Heterodimer, p51 lacks RNase H domain present in p66

Reverse transcriptase

env vpu/env mRNA gp 120 (SU) 24 sites for N-linked glycosylationSurface glycoprotein, mediates cellular attachment

gp 41(TM) 7 sites of N-linked glycosylationTransmembrane glycoprotein

nef nef mRNA p27 myristylated at Gly-2, phosphorylated at Tyr-15

Homodimer, causes pleiotropic effects, including downregulation of CD4

tat tat mRNA p14 Required for replication transactivates RNA synthesis, binds to TAR RNA

rev rev mRNA p19 Regulates splicing/RNA transport; binds RRE element and facilitates env translation

vif vif mRNA p23 viral infectivity factor, essential for spread in macrophages

vpr vpr mRNA p15 associates with p7 Augments replication

vpu vpu/env mRNA p16 phosphorylated on Ser Helps in virion assembly and release, dissociates gp160/CD4 complex

AIDS HIV

RN

A (

Cop

ies/

ml

pla

sma)

CD

4+ T

-cell

s (c

ell

s/µ

l)

107

106

105

104

103

102

1200

1000

800

600

400

200

03 6 9 12 2 4 6 8 10 12

YearsTime after infection

Weeks

Primary Infection

Acute HIV Infection

Clinical Latency

Onset of Symptoms

Opportunistic Infections

Death

Anti-HIV immune responses

Typical Time Course of HIV Infection and Progression to Disease (AIDS)

Pathology and Opportunistic Infections of Patients with HIV/AIDS

STAGE OF HIV/AIDS

SYNDROME/ SYMPTOMS

TYPE OF INFECTIOUS AGENT

ORGANISM

CD4+ T-Cell count 200-500 cells/µl

Skin lesions Viral Molluscum contagiosum

Oral lesionsThrush Fungal Candida albicans

Basal cell carcinomas of skin

Lung disease (Tuberculosis)Bacterial Reactivation of Mycobacterium tuberculosis

Hairy Leukoplakia Viral Epstein-Barr virus

CD4+ T-cell count <200 cells/µl

Microbial InfectionsProtozoan Pneumocystis cariniiPneumonia

Toxoplasma gondiiDisseminated toxoplasma ProtozoanIsospora belliProtozoanSevere diarrheaCryptosporidiaProtozoanChronic diarrhea

Tuberculosis Bacteria Mycobacterium tuberculosisBacteria Salmonella, Streptococcus,

Hemophilus, Cryptococcus CNS disease Cryptococcus neoformansFungal

PML Viral JC polyomavirusDisseminated disease of lungs,brain, etc.

Viral Genital herpes, cytomegalovirus

B-cell lymphoma Viral Epstein Barr virus, HHV-8

Viral Infections and Malignancies

Kaposi’s sarcoma Viral HHV-8Anogenital carcinoma Viral Human papilloma virus

Other SyndromesWasting disease ?? ??Aseptic meningitisAIDS dementia complex Viral HIV encephalopathy

Generalised lymphadenopathy

Shingles Viral Reactivation of herpes zoster

Headache, fever, malaiseGneralized weight loss

Lymph Node Germinal Centers in HIV Disease

The follicular dendritic cell network within the germinal center of a lymph node is stained pink with an antibody. This network degenerates over time following HIV infection.

Monotherapy

Multidrug therapieswith protease inhibitors

AIDS casesDeaths

1993 AIDS case definition

85 86 87 88 89 90 91 92 93 94 95 96 97 98

Nu

mb

er

of

Case

s/D

eath

s in

Th

ou

san

ds

25

20

15

10

5

0

Year of Diagnosis/Death

99

Primarily nucleoside inhibitors

Incidence of AIDS and Deaths due to AIDS among Adults in the United States 1985-1999

Pneumonia and Influenza

Injuries

Cancer

Homicide

Suicide

Liver Disease

200019961992198819841980

5

10

15

20

25

30

Unintentional InjuryCancer

Homicide Suicide

Stroke Diabetes

HIV/AIDS

An

nu

al

Death

s in

Th

ou

san

ds

Heart Disease

Heart Disease

Liver Disease

HIV/AIDS

Year

Annual Deaths in Persons 25-44 years old in the United States

due to the Ten Leading Causes of Death (1980-1998)

Characteristics of the Global HIV/AIDS Epidemic through December 1999

Geographical Region

Number of people with HIV/AIDS

Women %

Adult prevalence rate, 1999

PrimaryMode of Transmission

1996 1999 % Change96-99

1996 1999

Deaths from HIV/AIDS

% Change96-99

North America

750,000

20% 0.58% 1) MSM 2) IDU and hetero

900,000 20% 61,300 20,000 -67%

South America 1.3 million 25% 0.49% 1) MSM 2) IDU and hetero

70,9001.3 million0% 48000 -32%

Caribbean 270,000 35% 2.11% Hetero14,500360,000 33% 30000 107%

Sub-Saharan Africa

14 million >50% 8.57% Hetero783,70024.5 million75% 2.2 million181%

North Africa and Middle East

200,000 20% 0.12% 1) IDU 2) Hetero

10,800220,000 10% 13,000 20%

W. Europe 510,000 25% 0.23% 1) MSM 2) IDU and hetero

21,000520,000 2% 6800 -68%

C. and E. Europe and Central Asia

50,000 20% 0.14% 1) IDU 2) MSM

1,000420,000 740% 8500 750%

South and Southeast Asia

5.2 million 35% 0.54% Hetero143,7005.6 million8% 460,000 220%

East Asia and Pacific

100,000 13% 0.06% 1) IDU and hetero 2) MSM

1,200530,000430% 18,000 1500%

Australia and New Zealand

13,000 10% 0.13% 1) MSM 2) IDU and hetero

1,00015,000 15% <200 -80%

87 2043

461454

586107

1861525

<5

5 to 9.9

10 to 14.9

15 to 47.9838

District of ColumbiaPuerto Rico

1247

Virgin Islands

39

3181854 421 476 1678

5468

15

100

5445

880 93

242155 319

360

22525

13

1516

67

171

959

794759

277

5473631557

531

152649

190

69943

20 80

194148

1967

7703

Rate: Cases/100,000 population

7

AIDs in the United States in 1999

AIDS in Africa

In a number of subSaharan African countries, 24-36% of adults aged 15-49 are infected with HIV.

In 9 subSaharan countries, 20-30% of children less than 15 years old are AIDS orphans.

The prospects for a vaccine remain remote, and developing countries cannot afford the drug regimes that are successful in the U.S., nor could compliance with the strict demands of >20 pills per day and close observation by medical professionals be expected even if the drugs were available.

25 million people in subSaharan Africa are infected with HIV.

19991984

20 - 36%10 - 20%5 - 10%

0 - 1%no data

Percentage of Adults (15-49 yrs) Infected with HIV

1 - 5%

HIV/AIDS Infection in Africa, 1984 - 1999

Lif

e e

xpecta

ncy

at

bir

th

Malawi

ZambiaUganda

Zimbabwe

Botswana

1960 1970 1980 1990 2000

65

60

55

45

40

35

50

Year

Life expectancy in Selected African Countries with High HIV Prevalence, 1955 - 2000

Viral RNA copies/ml

Š4500

4500-13000

13000-36000

>36000

0 2 4 6 8 10

Time (Years)

Perc

en

t S

urv

ivin

g

100

75

50

25

00 2 4 6 8 10

Perc

en

t S

urv

ivin

g

100

75

50

25

0

<300

>800500-800300-500

CD4+ cells / µl

Time (Years)

Extent of HIV Replication as a Predictor of Disease Progression in AIDS

Inhibitors of HIV Replication

The first inhibitors used were nucleoside analogues that inhibited HIV RT

Therapy with a single analogue soon failed because mutations in RT arose within a few months that made it resistant to the analogue

Using two analogues was more successful but ultimately failed because resistant mutants arose

The development of protease inhibitors that better inhibit virus replication has led very successful therapy in about half of of HIV patients

Protease inhibitors are used in combination therapy with two nucleoside analogues to inhibit RT

Such therapy reduces virus to undetectable levels but does not eradicate the infection

It is unknown if such triple therapy will ultimately fail because of the appearance of resistant variants

SIV mac

SIV stm

SIV mnd

SIV l’hoest

SIV agm

SIV syk

SIV smm

SIV cpz US

SIV cpz gab

SIVsyk

SIVsmm,

SIVmac,

HIV-2

SIVmnd

SIVagm

SIVcpz,

HIV-1

0.02 substitutions per site

HIV-2 ROD

HIV-2 EOH

HIV-1 ANT70C (0)

HIV-1 YBF30HIV-1 U455 (A)

Phylogenetic Tree of the Primate Lentiviruses

HEPADNAVIRIDAE

GENUS/ MEMBERS

DISEASETRANSMISSIONNATURALHOST(S)

Orthohepadnavirus

Avihepadnavirus

Duck hepatitis B virus

DucksGeese

ACS, hepatitisPredominantly vertical

Heron hepatitis B virus

Herons Predominantly vertical

Woodchuck hepatitis B virus

Woodchucks Horizontal, sexual, blood

ACS, hepatitis, HCC

Ground squirrel hepatitis B virus

Ground squirrels, woodchucks, chipmunks

ACS, hepatitis, HCC

Horizontal, sexual, blood

Hepatitis B virus Humans,chimpanzees, gibbons, wooly monkeys

Horizontal, IDU, sexual, infected blood vertical

ACS, hepatitis, cirrhosis, HCC

Figure 5.25

0 500 1000 1500 2000 2500 3000

DR1 An Eco RI DR2(-) DNA(+) DNA

TP (spacer) POLYMERASE RNAse HFrame 2Frame 3

Protein XPre COREFrame 1 PreS1PreS2 S

Open reading frames

cccDNA

Transcription and translation of m RNAsAnpreS1 RNA

An

S1

S2preS2 RNA

S2S RNA

XAn

AnX RNA CpreC RNAC RNA

C An

An

AnC

S1

S2

X

Eco RI

DRs

PromotersProtein on 5’end of minus strand

ds DNA

A. Genome organization

B.

nucleotides

(or pg RNA)

nt 1nt 3221

Genome Organization of Hepatitis B Virus

RT

RT

RT(-) DNA

CAP12

1

AnCAP 21 122

RT(-) DNApg RNA

CAP12RT (-) DNA

(+) DNACAP 121

1 (-) DNA5’

AnCAP 1 2 1 pg RNA

5’

1)

2)

3)

4)

5)

6)

TP

TP

TP

TP

2

5’CAP1

5’

1

(-) DNA

TP

111

(+) DNA

5’

5’

7)

5’

3’

(-) DNA

P

Mechanism of HBV DNA Synthesis

CAUGCAACUUUUUCACCUCUGC CUAAUCAUCUCUU

CORE

G

UU

CAGGUACG

UAC

UU GC GC GU G

PRECORE

5’ DR1

GAACC

CU

CGAA

CUUGGG

GGCUU

CUG UGC

A

CUUGUC

AUUG3’

50

40

302010

60

70

80

U

Packaging Signal in Hepatitis B RNA

Kuwait

Equator

Endemicity

High (7-15% carriers, 50-95% seropositive)

Medium (2-5% carriers, 30-50% seropositive)

Low (<2% carriers, few seropositives)

Worldwide Hepatitis B Prevalence as of June, 1998

Equator

10

7 6

9

8 21

22

17

13

13 1211

15

17

16

14

18

20

19

3

2

5

4

1Incidence

Cases/100,000

0 - 5.0

5.1-10.0

10.1-15.0

15.1-20.0

>20.1

No Data

Incidence of Liver Cancer in Various Geographic Regions in 1990

Kuwait

Equator

Worldwide Hepatitis B Infant Immunization Policy as of March, 2000

No Routine Immunization

Routine Infant immunization

Retroelements and Their Distribution in Nature

CLASS DISTRIBUTION

Retroviruses

Eukaryotic Retroelements Vertebrates

Hepadnaviruses Mammals, Birds Pararetroviruses

Caulimoviruses Plants

Retrotransposons LTR retrotransposons Animals, Plants, Fungi, Protozoa

Non-LTR Retrotransposons Animals, Plants, Fungi, Protozoa

Mitochondrial Elements Group II Introns (retrointrons) Mitochondria of Fungi and plants, plastids of algae

Mauriceville Plasmid Mitochondria of Neurospora

RTL gene Mitochondria of Chlamydomonas

Prokayotic Retroelements

msDNA = multi-copy single-stranded DNA

msDNA-associated RT Myxococcus xanthus, E. coli, other bacteria

l kb

LTR Gag-related sequencesProteaseEnv-related sequences

Polymerase motifsReverse transcriptaseRNase HIntegrase

LTRLTR

Exon 1 Exon 2

D. Group II intron

RT

A. Retroviruses

B. LTR Retrotransposons

C. Non-LTR Retrotransposons

LTR LTR

ORF 2ORF 3

AAAAA

(TAA)n

Gypsy

LTRLTR

ORF Copia

I Factor

R2

ORF 1

ORF 1 ORF 2

ORF RT

Gag Env Pol

ORF

(Drosophila)

(Drosophila)

Genome Organizations of Retroelements

RNA dependent RNA polymerases

Yeast Human

L1R2I Factor

TadJockeyR1

Poly A transposons

Retrointrons

Retroplasmids

Retrons

al1al2

Mito

Ec67Mx65

Yeast

Neurospora

Bacteria

Human

Neurospora

Telomerases

Yeast

MMTVMPMVRSVPTLVHIVMLVHSRV

RetrovirusesVert.

Plant

D.m.

D.m.D.m.

WHBVHBVDHBV

Ted

CaMVCoYMV

PararetrovirusesVert.

Plants

17.6 D.m.Gypsy D.m., yeastTy3 D.m.412 D.m.

Name Host Family

Tnt1 Plant

Copia D.m.173 D.m.

D.m.

LTR Retrotransposons(Invertebrate)

LTR Retrotransposons(Invertebrate)

Ty1

Phylogenetic Tree of the Retroelements