Virology Exam 3

1983

first major breakthrough against the disease

Francoise Barre-Sinoussi and Luc Montagnier

Pasteur Instutute researches that isolated the retrovirus

Robert Gallo

described the retrovirus that he named the third of the human T-lymphotropic viruses, HTLV-III

1985

blood test for HIV developed

1987

first antiretroviral drug, aidovudine (AZT)

1994

Highly-active antiretroviral therapy (HAART)

HIV family name

Retroviridae

Group M

main/major

* worldwide pandemic

Group O

outlier

* less than 1% of HIV-1 infections, restricted to Cameroon, Gabon, and neighboring countries

Group N

non-M, non-O

* rare: fewer than 20 cases ever documented

Group P

newest group

* only 2 cases documented, both from Cameroon

HIV-1 groups

* group M
* group O
* group N
* group P

HIV-2 groups

* 8 distinct groups, A-I
* Groups A and B are most prevalent
* Groups C-I are rare
* No HIV-s subtypes exist

HIV is transmitted primarily 3 ways:

1. sexual contact that exposes a mucosal epithelium to semen, vaginal secretions, rectal secretions, or blood that contains the virus
2. from infected mother to child- transplacentally


1. through blood and blood products- injectable drug use, improperly sterilized needles or medical equipment, and through accidental exposure

T or F: mosquitoes have never been shown to transmit HIV

False

most common route of HIV infection worldwide

heterosexual transmission

the clinical course of HIV infection is divided into 3 stages:

1. acute
2. asymptomatic (clinical latency)
3. aids

Stage 1: Acute stage

* within 2-4 weeks after infection
* \
> 50% of HIV-infected individuals develop severe flu-like symptoms: fever, swollen lymph nodes, sore throat, arthralgia(joint pain), myalgia (muscle pain), headache, fatigue, weight loss, sometimes a rash
* viral loads reach very high levels
* person seroconverts (produces antibodies against the virus) as symptoms resolve
* lasts 2-8 weeks

stage 2: Asymptomatic phase (clinical latency stage)

* symptoms are absent or limited
* HIV slowly replicates, causing gradual depletion of CD4 cells
* lasts an average of 10 years without antiretroviral therapy

rapid progressors

* take 2-3 years to progress through this stage (10-15%)

long-term nonprogressors (LTNPs)

* maintain normal CD4 T cell counts and low HIV titers without ART (5%)
* a subset known as elite controllers even maintain undetectable viral loads

elite controllers

* maintain undetectable viral loads

opportunistic infections

* that infections caused by pathogens that are normally cleared by the immune system but cause disease when an individual’s immune system becomes impaired

stage 3: acquired immune deficiency syndrome (AIDS)

* a person is classified as progressed to AIDS when he/she develops one or more opportunistic infections or has a CD4 T cell count below 200 cells/µL of blood
* person diagnosed with AIDS lives around 3 years or 1 year if an opportunistic infection is acquired

Other AIDS disease complications

* kidney disease, due to:
* the infection of kidney cells by HIV
* immune complexes, antigen-antibody complexes that become lodged in the kidneys
* a side effect of antiretroviral drugs
* Neurological manifestations
* cognitive issues
* HIV- associated dementia
* Encephalitis- inflammation of the brain
* meningitis- inflammation of the meninges

molecular virology of HIV

* HIV is an enveloped retrovirus possessing a cone- or bullet-shaped capsid

molecular virology of HIV:

* capsid built from a single protein:
* two complete copies of the:

* the capsid protein (CA)
* +ssRNA genome

Molecular virology of HIV:

* within the core:

* Nucleocapsid protein (NC) that coats the viral RNA
* 3 enzymes:
* reverse transcriptase
* integrase
* protease
* Vpr- an accessory protein that is involved in the transport of cDNA into the nucleus

Molecular virology of HIV:

* the envelope surrounds the core to create a virion

* matrix protein- attaches to the inner surface of the envelope
* trimers of the envelope glycoproteins are found on the surface
* consist of gp120 (surface subunit) and gp41 (transmembrane subunit)
* gp120 and gp41 are cleaved from gp160 during replication but remain non-covalently associated with each other

why haven’t any candidate HIV vaccines been successful?

* traditional methods (live attenuated or inactivated virus vaccines) have not been effective
* HIV is a human virus that does not infect typical animal models-testing for safety and efficacy is a challenge
* HIV mutates quickly due to low fidelity of the RT
* # of HIV subtypes make is unreasonable to create a “universal vaccine” against them all
* gp120 is highly glycosylated, preventing antibodies from easily interacting with it

“prime-boost” strategy

* “prime” vaccine- recombinant vector vaccine using canarypox to deliver and express HIV Gag, Pol, and Env peptides
* last 2 injections included the “boost” vaccine, containing the gp120 protein

Broadly neutralizing antibodies (bNAbs)

* neutralize a range of HIV isolates have been observed in rare HIV+ individuals
* requires some to have been infected for years
* antibodies have mutations that allow the antibody to pass
* through glycans to interact with conserved regions of gp120
* numerous nNAbs have been identified

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Influenza family name

* Orthomyxoviridae

characteristics of influenza viruses

Influenza A viruses accounts for…

\~ 2/3 of human infections each year

subtypes of influenza A

* codetermined by the identity of its 2 envelope glycoproteins:
* hemagglutinin (HA or H)
* neuraminidase (NA or N)

How many different HA subtypes exist?

* 18 (H1-H18)

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How many different NA subtypes exist?

* 11 (N1-N11)

Internationally accepted convention of naming Influenza viruses

* the antigenic virus type (A, B, or C)
* the species of origin, only indicated if not a human strain
* the geographic site where it was first located
* the strain number
* the year of isolation
* the HA and NA virus subtype, in parentheses

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What type of virus is Influenza?

* respiratory
* transmitted in droplets that are generated when a person coughs or sneezes
* droplets are inhaled by a susceptible person less than 3 ft away into the respiratory tract, where the virus comes into contact with cells that bear its cell surface receptor

incubation period of influenza?

* 1-4 days (average:2)

symptoms of influenza

* abrupt onset fever
* myalgia
* generalized malaise
* fatigue
* headache
* sore throat
* rhinorrha (runny nose)
* dry cough

How long do symptoms of Influenza last?

* 3-5 days

shedding Influenza virus

* occurs from the day before symptoms appear to 5 days after they begin
* children can shed the virus for longer than 10 days
* viremia is uncommon

complications of infection

* influenza A is associated with 4 times more hospitalizations than influenza B, which mostly affects children
* case fatality rate is \~ 7%
* \~ 10% of people experience myocarditis, inflammation of the heart

molecular virology of influenza virions:

* are enveloped
* contain a helical -ssRNA genome
* are pleomorphic (of varying shape)
* elongated upon initial infection, but more spherical after being propagated in cell culture
* contain a segmented genome
* influenza A and B have 8 segments
* influenza C and D have 7 segments

the 3 influenza proteins that form the RdRp and are the largest influenza proteins

1. PB2
2. PB1


1. PA

Molecular virology of influenza C:

* has one less genome segment than influenza A or B because it does not have separate HA and NA proteins
* envelope glycoprotein hemagglutinin-esterase-fusion (HEF) possess both HA and NA activity

Molecular virology of influenza virus: M1

* the matrix protein
* found immediately beneath the viral envelope
* involved in the transport of new RNPs out of the nucleus
* plays a role in the budding of the virion from the plasma membrane
* most abundant protein in the influenza virion

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Molecular virology of influenza virus: M2

* a transmembrane protein that acts as an ion channel, involved in fusion of the viral envelope with the endosomal membrane

Molecular virology of influenza virus: NS1

* interferes with the host’s production of type 1 interferon and inhibits PKR

Molecular virology of influenza virus: NS2

* known as the nuclear export protein (NEP)
* exports newly-formed RNPs from the cell nucleus

Influenza is internalized via _________

endocytosis

Generally ____________, but non-clathrin and non-caveolin pathways have also been described. \n

clathrin-mediated endocytosis

Unlike other RNA viruses, influenza viruses replicate within the ________.

nucleus

Because the influenza RdRp is error-prone, mutations occurs in the \n _________ during genome replication

vRNA

Since mutations occurs in the vRNA during genome replication, it may result in_______

* Some result in silent mutations
* Some result in missense mutations that change the amino acid sequence

Single-nucleotide point mutations lead to _______, the constant \n acquisition of small changes in the influenza genome that result in the creation of new strains (NOT subtypes)

genetic drift

Other info:

* Mutations in HA and NA may result in an antigen that is no longer recognized by previous antibodies

_________ with mutations have a selective advantages because they \n are not neutralized, so they will continue infecting and replicating

Escape mutants

___________ is the basis for seasonal influenza epidemics: the strain \n circulating one year may mutate into a strain that is not recognized by previous antibodies

Antigenic drift

Other info:

* Basis for changing the strains in the yearly influenza vaccine

Antigenic shift occurs through ________,__ creating a new _______.

reassortment; subtype

Antigenic shift concerns

• Because the influenza genome is segmented, if a cell is simultaneously infected with two different subtypes of influenza, the newly-replicated vRNA segments could mix within assembling virions \n • This is a major concern to humankind, because only four influenza A subtypes have ever circulated, so the entire population has no immunity to the many subtypes that circulate in other animal reservoirs \n • Wild aquatic birds transmit avian influenza to poultry, pigs, horses, and sea mammals \n • Co-infection of one of these with an avian and human virus could lead to reassortment

In the _______, four major pandemics caused by antigenic shifts \n struck the world.

20th century

1918 Antigenic Shifts

1\. The pandemic of 1918 is the single greatest infectious disease outbreak in history, killing 20-50 million people worldwide in the course of months \n • May have begun at a U.S. Army base at Camp Funston (now Fort Riley), Kansas, in March of 1918 Figure 10.9 National Museum of Health and Medicine \n • Hundreds of soldiers were sick and 48 died from pneumonia \n • Different flu because the healthy were becoming sick, as well, not just children and the elderly \n • Virus spread to Europe with the troops of WWI

Press in Spain covered the outbreak first in Europe → _________

**“Spanish flu”**

The spread of influenza

• September 1918: soldiers began dying at Camp Devins (near Boston), and the flu spread to civilians, who also began dying of pneumonia \n \n • Moved down the eastern seaboard to New York City and Philadelphia \n • High fever, delirium, severe headache, cough, myalgia; death occurred from bacterial pneumonia or fluid in the lungs \n • Heliotrope cyanosis \n • Case fatality was 2.5% \n • Hundreds of people died every day \n • In NYC, nearly 900 people died in one day alone \n • In Philadelphia, 11,000 people died in the month of October \n • Spread South and West

Overall, the pandemic killed ________ people in the US (more than all wars of the century combined) and 20-50 million people worldwide

675,000

_________ recreated the 1918 influenza virus by artificially inserting vRNA sequences into cells to generate functional virions

Reverse genetics

Results of reverse genetics

• Infection of monkeys and mice indicated the 1918 HA and NA genes are more virulent than typical flus \n • The 1918 influenza, particularly the HA protein, induced a “cytokine storm” of inflammatory cytokines that caused tissue damage, hemorrhaging, and massive infiltration of immune cells to the lungs \n • 1918 NS1 gene downregulated the type 1 IFN response by the host

\n __Result__: a virus of increased virulence to which the human population had no immunity that inhibited the anti-viral immune response while \n overstimulating immune cells that cause damage

Reasons for why 1918 pandemic ended

After a pandemic influenza circulates through the population, it becomes unable to maintain initial transmission rates and its pandemic potential because of an newly-immune population \n →Becomes a seasonal influenza that continues undergoing antigenic drift

Look at image

• 1957 \n H1N1 → H2N2 \n “Asian influenza”

\n • 1968 \n H2N2 → H3N2 \n “Hong Kong influenza”

\n • 1977 \n H1N1 mysteriously \n reemerged \n “Russian influenza” \n Circulated alongside H3N2

\n • 2008-2009 \n Quadruple-reassortant \n H1N1

Influenza viruses of many different HA and NA subtypes circulate in \n wild bird populations, particularly _______,__ where the disease is \n ________: widespread in an animal population.

waterfowl; epizootic

Strains that have been circulated

H1N1, H1N2, H3N2

Possibility exists that more human pandemics could occur through direct infection of humans with a mutated ___________ or ____________

avian influenza; through reassortment

However in the past 20 years, we have observed that __________ viruses can be directly transmitted to humans and cause severe respiratory syndromes, pneumonia, and death

highly pathogenic avian influenza (HPAI)

Tropism of avian influenzas for ________ is a contributing factor for why the virus is so virulent in humans.

deeper in the lung

Over 600 cases of ______ since 2003; 60% of those infected have died.

H5N1

Other info:

• Primarily direct bird-to-human transmission \n • Virus continues to circulation throughout the world in both wild birds and poultry populations \n • Can also infect pigs, dogs, ferrets, housecats, and wild cats

_________ is inflammation of the liver

Hepatitis

Other info:

• Caused by excessive alcohol consumption, drugs, toxins, metabolic disorders \n • Several viruses are also a major cause of hepatitis

Major Hepatitis Viruses:

• Hepatitis A virus (HAV) \n • Hepatitis B virus (HBV) \n • Hepatitis C virus (HCV) \n • Hepatitis D virus (HDV) \n • Hepatitis E virus (HEV)

Hepatitis __*___*__*and hepatitis* ______cause 80% of global cases of liver cancer

B; C

Hepatitis viruses are Classified ________ based upon the similar clinical condition they cause, although they are all found in different viral families and possess different molecular properties

together

Acute infection:

1\. Incubation period of 1-3 months, depending upon the virus.

2\. Prodromal period (non-specific symptoms) \n • Malaise \n • Loss of appetite \n • Nausea \n • Vomiting \n • Low-grade fever \n • Occasionally, myalgia and arthralgia

\n 3. Illness period (specific symptoms) begins 3-10 days later \n • Abdominal pain in liver area \n • Dark but clear urine \n • Jaundice due to build up of bilirubin in the blood \n • Gray-colored stools \n • Increased serum aspartate transaminase (AST) and alanine transaminase (ALT) \n • Symptoms peak within 1-2 weeks \n • Jaundice fades during convalescence period \n Clinical Course of Hepatitis Virus Infections \n

_______ that are cleared from the host provide ________ immunity.

Acute infections; lifelong

________,__ ______do not generally lead to chronic infections

HAV; HEV

What are some hepatitis virus infections that cause chronic infections in which the virus continues replicating within the liver, causing damage?

\-HBV \n • >90% of infants \n • 25-50% of children between 1-5 years of age \n • 6-10% of older children and adults

\n -HCV \n • 70% of those infected

\n -HDV \n •

Because each hepatitis virus is a ______ virus, they exhibit _______ \n modes of transmission and portals of entry

distinct; differing

Hepatitis D virus is a defective virus, unable to replicate without _____.

HBV

Other info:

no approved serological test that are approved by the FDA, for HEV.

Hepatitis A Virus

• Transmitted through fecal-oral route \n • Drinking contaminated drinking water \n • Eating shellfish from sewage-contaminated water \n • Consuming raw or undercooked foods that have come in contact with virus \n • Non-enveloped \n • Can survive for prolonged periods at low pH, in fresh water, in \n seawater, and in freezing to moderate temperatures \n • Humans are the only known reservoir

After ingestion, the virus is absorbed by the gastrointestinal tract \n and travels via the hepatic portal vein to the liver, where it infects \n and replicates within _______.

hepatocytes

Be familiar for hepatitis A virus

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• After 10-12 days (2 weeks before symptoms appear), virus is \\n present in bloodstream and in feces \\n • Most transmissible at this point, although it is shed for up to 3 weeks after symptoms appear \\n • Children can shed virus for up to 6 months following infection \\n • Incubation period is 28 days (range: 15-50 days) \\n • Jaundice occurs 70% of the time in older children and adults \\n • 70% of infections are asymptomatic in children

After HAV, _____ is the second most common cause of acute viral \n hepatitis.

HBV

familiar with HBV

• HBV is transmitted through blood, semen, vaginal fluid, and other \n bodily fluids \n • Highest concentrations of virus are found in blood \n • Percutaneous transmission (through the skin) can occur through sharing of contaminated needles during injection-drug use, unsafe reuse of needles or medical devices in health care settings, or accidental needle pricks with infected human blood \n • Sexual and perinatal transmission are the most common routes of \n transmission \n • In endemic areas, perinatal transmission -- primarily during birth -- is the most important factor in maintaining high HBV prevalence \n • HBV virions can remain infectious for 7+ days at room temperature \n • Humans are the only known natural host of HBV

Additional info of HBV

• Chronic infection varies with age: \n • >90% of infants \n • 25-50% of children between 1-5 years of age \n • 6-10% of older children and adults \n • Chronic infection can lead to chronic liver disease, cirrhosis, or liver \n failure \n • Up to 50% of the cases of hepatocellular carcinoma (HCC) are \n attributable to HBV

Prevalence geography

• Prevalence is low in U.S., Western Europe, and Australia \n • Still, 1.6 million people are chronically infected in the U.S. \n • 3,000 new acute cases reported each year (more likely 19,000-20,000) \n • Infection in U.S. associated with certain high-risk behaviors:

Hepatitis C virus

• is almost exclusively associated with exposure to contaminated \n blood \n • Most frequently transmitted through sharing of contaminated needles or \n paraphernalia by injection-drug users \n • People that received blood transfusions or organ transplants before 1992 \n (when the blood supply began being screened for HCV) are also at risk \n • Less frequent modes: \n • Sexual contact \n • Perinatal transmission \n • HCV only naturally infects humans

Incubation of HCV

• Incubation period is 45 days (range: 14-180 days) \n • 80% of people are asymptomatic

\n • 70% of people infected develop persistent infections \n • Most common symptom of chronic infection is fatigue \n • Chronic infection can progress to chronic liver disease, cirrhosis (10-25% of \n those with chronic infection), and death from HCC or cirrhosis (20% of those \n developing cirrhosis)

HCV treatment

• No vaccine exists for HCV \n • Over 14,000 people die each year of HCV-related liver diseases \n • HCV is the #1 cause of liver transplants \n • Half of those with chronic HCV infection are not aware of it

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\-New direct acting antiviral (DAA) medications are effective: \n • Composed of two or three compounds that include protease inhibitors and/or nucleoside analogs that inhibit HCV polymerase \n • Current drug combinations result in >95% sustained viral response: viral load is undetectable after treatment is stopped.

Hepatitis D virus

• Hepatitis D virus (HDV) is also known as “hepatitis delta virus”. \n • HDV is a defective virus: it is unable to replicate on its own. \n • HDV requires a helper virus -- in this case, HBV -- that contributes HBsAg that HDV uses for virion assembly \n • Infection with HDV and HBV can occur through: \n • __Coinfection__: HDV and HBV are contracted at the same time \n • Incubation period of 90 days \n • __Superinfection__: HBV+ individual becomes later infected with HDV \n • Incubation period is 14-56 days \n • HDV is transmitted through contact with infectious blood or \n contaminated injection devices \n • HDV infection can be acute or chronic; if HBV is cleared from the \n host, then HDV is unable to replicate

HDV treatment

• Geographical prevalence of HDV mirrors that of HBV \n • Worldwide, 15-20 million people are infected with HDV \n • 5% of those infected with HBV \n • Chronic coinfection with HBV and HDV leads to more severe liver \n disease than HBV infection alone \n • NRTIs used to treat HBV do not prevent HDV replication, since HDV \n does not possess a RT \n • Vaccination against HBV protects against HDV infection

Hepatitis E Virus

• __Like HAV, HEV is transmitted through the fecal-oral route__ \n • HEV is the #1 cause of waterborne jaundice outbreaks, primarily \n transmitted by fecal contamination of drinking water \n • Due to poor sanitation or inadequate sewage treatment \n • Shellfish can also concentrate the virus if living in waters polluted with sewage \n • HEV is unique among hepatitis viruses because some genotypes \n infect animals \n • HEV-1 through HEV-4 and HEV-7 infect humans \n • HEV-1 and HEV-2 infect only humans (fecal-oral transmission) \n • HEV-3 and HEV-4 infect humans and animals \n • Pigs (main reservoir), boars, deer, and rabbits \n • Can be transmitted through zoonotic transmission or through \n consumption of inadequately cooked meat from these animals \n • High titers of virus in liver and intestines (and sausages using them \n • HEV is relatively resistant to heat; foods must be cooked completely