Virologie

Susceptibility: The cell expresses a receptor for viral entry. The virus can enter the cell

Permissivity: The cell can multiply the virus and release new viruses

envelope: viral membrane

Envelope protein: viral protein embedded into viral membrane

capsid: viral protein core

nucleocapsid: capsid that directly interacts with the viral genome

pfu: plaque forming units

moi: multiplicity of infection

CPE: cytopathic effect

+ssRNA, -ssRNA, dsRNA, +ssDNA, -ssDNA, dsDNA: positive- or negative-oriented single stranded or double stranded RNA/DNA

ID50: infectious dose that infectes 50%

ccID50: ID50 in cell culture (cell culture infectious dose 50%)

LD50: lethal dose 50%; dose at which 50% of animals die

budding: release of viral particles through a cellular membrane and the acquisition of a viral envelope through this process

Virus-like particle: empty capsids that spontanously form from capsid monomers; used for vaccines

in vitro: - experiments with enzyme mix (e.g. in an Eppi),

- experiments in cell culture

in vivo: experiments in living organisms. E.g. animal experiments, treatment of patients

tropism: which cell type can become infected?

-> the presence of binding receptors on a cell determines the tropism of a virus: the virus can only enter cells that express this molecule. Cells that don‘t express this molecule cannot become infected

host range (Wirtsspektrum): which species can become infected?

RBD: receptor binding domain

FP: fusion peptide

Viral attachment: lose binding to attachment factors

Viral binding: binding to entry receptor

Affinity: binding strength between ligand and receptor

Avidity: sum of all affinities if multiple binding sites exist

adeno viruses

hepadna viruses

herpes viruses

orthomyxo viruses

picorna viruses

retro viruses

nido viruses

The replication cycle e.g.: Poliovirus

1. Attachment and Entry

2. Release of Genome (Uncoating)

3. Translation of viral proteins

4. Genome replication

5. Assembly

6. Release

7. (sometimes: maturation)

= fusion of cells (fusion of the viral envelope membrane with the cell membrane), mediated by viral envelope proteins, often seen as CPE in cell cutures infected with enveloped viruses

physical titer: measurement of viral particles (protein or genome; by ELISA or PCR)

biological titer: determined from infection experiments; physical titer is usually higher than biological titer

-> biological titer measures only intact/infectious particles and is also dependent on the type of cell culture being used

PCR with 2 primers and a probe

- Probe carries fluorochrome and quencher

- Taq Pol has exonuclease activity and digests probe if it binds to PCR product

- Fluorochrome gets released from quencher and fluorescence is measured in a light cycler

receptor: viral entry

coreceptor: assists in viral entry, a second binding receptor that is needed to allow viral entry

attachment factor: lose attachment of virus to cell

•…endemic: normal/usual occurrence of a certain infectious disease in a certain population

• …epidemic: Unusually strong and temporally limited occurrence (accumulation) of a certain infectious disease in a certain area

• …pandemic: An epidemic of a new pathogen that spans continents/the whole world

• … prevalence: total number of infections in a population

• …incidence: number of new infections in a given time period

• …morbidity: number of disease cases in an entire population caused by a virus

• …mortality: number of deaths in an entire population caused by a virus

• …CFR: case fatality rate, number of deaths among infected individuals

• …prevalence: 504 infections/100.000 inhabitants

• …mortality: 27 deaths/100.000 inhabitants

• …CRF: 27 deaths/504 infections

4-field analysis: control treatment without disease, control treatment with disease, active treatment without disease, active treatment with disease (example 90%, 10%versus 98% versus 2%)

Calculations from 4-field analysis:

• …RRR: (10%-2%)/10% = treatment reduces risk by 80%

• …ARR: 10%-2% = treatment reduces risk by 8%-points

• …NNT: 1/ARR = 1/0.08 = 12.5

• …NNV: 1/ARR = 1/0.08 = 12.5

Weekly incidence: the number of new infections per week is given

- If the number of infections increase over time, weekly incidence increases

- If the number of infections over time declines, weekly incidence decreases

• Cumulative incidence: the number of new infections in each week is added to the number of infections in the past.

- If the number of infections increase over time, cumulative incidence increases

- If the number of infections over time declines, cumulative incidence still increases

- If the number of infections over time is 0, cumulative incidence stays on a plateau

R0: basic reproduction number: average number of infections that are caused by 1 infected individual

herd immunity: is reached if a high-enough amount of people in a population is immune so that the virus can no longer spread in the population with a positive R

calculate herd immunity from R0? R0-1/R0

=> there is a seasonal variation of R0 and herd immunity for respiratory infections

SIR-model: Mathematical model to predict numbers of infections in a population: 3 key parameters. S = number of susceptible, I = numbers of infected, R: numbers of resistant/immune people

• SEIR-model: better mathematical model to predict numbers of infections in a population: 4 key parameters. S = number of susceptible, E= exposed but not yet infectious, I = numbers of infected, R: numbers of resistant/Immune people

• Excess deaths: more deaths than usually expected

how to calculate excess deaths: example: (deaths per week of this year)-(averagenumber of deaths of the same week of the last 4 years)

• RRR: relative response rate, good parameter for treatment

• ARR: absolute response rate, good parameter for prophylaxis

• NNT: number needed to treat in order to prevent 1 disease case

• NNV: number needed to vaccinate in order to prevent 1 infection

• Serial interval: describes the average time between the infection of a patient and the transmission to the next patient

• “flatten the curve”: Attempt to slow down infection spread in a population, e.g by wearing masks etc. Total number of deaths/illness until herd immunity is reached is not changed, but peak numbers are lower. Concept to protect hospitals from overcrowding

HAV, HBV, HCV, HDV, HEV

chronic disease —> HBV, (HDV),HCV

transmission:

—> Sex: HBV, HDV, HCV

—> smear infection/oral: HAV,HEV

—> drug abuse: HBV, HCV

prevented by vaccination: HAV, HBV, (HDV)

—> virus contains partly dsDNA,

—> DNA is completed in the cell,

—> cccDNA persists as episome in nucleus,

—> genomic RNA transcription from cccDNA,

—> reverse transcription of DNA genome from genomic RNA,

—> DNA incorporation into newparticles,

—> ds-DNA synthesis stops in virus particle if all nucleotides are being used up

• Comparison early and late RT (retroviruses, HBV):

HIV: RT immediately acer infection: gemonic RNA -> cDNA (early)

HBV: RT late in replication prior to exit: genomic RNA -> genomic DNA (late)

• How can HBV infection be treated? Nucleoside analogs (RT-inhibitors)

-> +ssRNA genome, gets directly translated at ribosome after infection

-> dsRNA, new +ssRNA genomes transcribed from the dsRNA, incorporation into new particles, nucleus not involved

treatment: Nucleoside analogs, protease inhibitors, NS5B-inhibitors

=> HCV has no mechanism of persistence. If replication is blocked, the virus is gone. HBV has a mechanism of persistence: ccc-DNA persists lifelong in nuclei of hepatocytes

similarities: +ssRNA

differences: no cap but IRES, no poly A but UTR

IRES: Initiation of translation; mimics the function of the 5’ cap of mRNAs

in molecular biology: IRES allows expression of 2 different proteins (not a fusionprotein) under control of one promotor: promotor-geneX-IRES-geneY

Retrovirus (RT): Virus with RNA genome, integrates into host genome

Endogenous Retrovirus: Retrovirus that has entered the germline. Some Endogenous Retroviruses have lost their ability to replicate

PBS: primer binding site

LTR: long terminal repeat

Provirus: retroviral genome integrated into host-genome

retroviral replication cycle: virus particle with RNA, entry into cell, release of RNA, RT of RNA into cDNA, integration of cDNA into host genome (provirus), transcription of provirus: translation of viral proteins and transcription of genomic RNA, assembly andpackaging, budding at cell membrane

3 enzyms of reverse transcriptase

• RNA-dependent DNA polymerase

• DNA-dependent DNA polymerase

• RNaseH

in vivo: RNA template, RT, tRNA as primer, nucleotides

in vitro: RNA template, RT, DNA primers, nucleotides

-> RNA genome, tRNA primer bind at PBS,

-> synthesis of first cDNA strand by RT,

-> degradation of RNA in DNA/RNA heteroduplex by RT,

-> synthesis of second cDNA strand using parts of the original RNA template as primer and removal of RNA primer by RT

HIV protease: Cleavage of Gag proteins to allow maturation of viral particles

HIV integrase:Integration of HIV cDNA into host genome

HIV: RT immediately after infection: gemonic RNA -> cDNA (early)

HBV: RT late in replication prior to exit: genomic RNA-> genomic DNA (late)

productive infection: provirus is transcriptionally active so that new viral particles are being produced

latent infection: provirus is transcriptionally inactive and no viral particles are being produced

reactivation: switch from latent to productive infection

HIV pathogenesis: HIV infects CD4+ T cells, depletion of CD4-T cells over time, after 10 years (on average) AIDS

therapy: combination therapy of different antiviral substances (RT inhibitors, Integrase inhibitors, protease inhibitors)

SARS-CoV-2: Covid19

Rhinoviruses: common cold

HAV: hepatitis

HCV: hepatitis

-> RNA genome is infectious because it can directly be translated at the ribosome

-> replication involves dsRNA because +RNA replication requires a -RNA template strand

-> homologous recombination: template switching after coinfection

(+) RNA: can directly be translated at the ribosome into proteins

• mRNA: cap, UTR, ORF, UTR, poly A

• viral +ssRNA: often no cap, but: VPg/FAD and IRES, sometimes no poly A

• function of VPg or FAD: Substitute for mRNA-cap, examples for viruses that require VPg (picornaviridae, caliciviridae) or FAD (flaviviridae)

• function of the furin cleavage site in SARS-CoV-2: Cellular furin proteases cleave S2 protein

• +ssRNA-viruses need RdRp: RNA-dependent RNA polymerase for replication, but it’s not part of the virion particle (in contrast to -ssRNA viruses) because it can be directly translated from +ssRNA genome

• SARS-CoV2 receptor: ACE2

-> Mononegavirales= -ssRNA viruses with nonsegmented genome

-> RSV (lower respiratory tract disease)

-> parainfluenzavirus (respiratory disease)

-> measles virus (measles)

-> mumps virus (mumps)

• virions require: RNA-dependent RNA Polymerase

• isolated -ssRNA genomes are non-infectious after transfection

• RSV is the most common cause of LRTI in children <2years

• important ARI (acute respiratory infections) viruses: influenza, Corona, RSV, Adeno,HMPV, PIV, rhino, coxsackie

• symptoms: respiratory tract symptoms include rhinitis, pharyngitis, bronchitis, pneumonia

• seasonality of viruses

-> winter: influenza, Corona, RSV

-> summer: coxsackie virus

-> all year: all others (Adeno, HMPV, PIV, rhino)

A: aquatic birds

B: humans are the only host

influenza antigen dric and shic:

-> point mutations in the genome are called antigendric

-> reassorting is called antigen shic

• mechanism of reassertion: influenza genome is segmented;

-> infection of one cell with 2 different strains;

-> Segmented influenza genome gets reassorted (e.g the new virus contains 3 segments of strain X and 5 segments of strain Y)

• influenza clinic: cause of severe respiratory infections and hospitalization in old people

• natural reservoir of influenza A: poultry, pig as “mixing vessel”, spread into human population

• natural reservoir of influenza B: humans are the only hosts

• influenza: what does H1N1 or H5N1 mean? Serotypes are determined by H and N antigens. Different antigen-families exist that can be combined. HxNy indicates which antigen families are present in a particular strain