Virology Introduction Student

VIROLOGY
Introduction
Dr. Ming-Han Tsai

Institution of Microbiology and Immunology
National Yang Ming Chiao Tung University
蔡明翰 (Dr. Ming-Han Tsai)
Institute of Microbiology and Immunology,
National Yang-Ming University, Taiwan
• m.tsai@nycu.edu.tw
• https://wisewind1005.wixsite.com/tsaimh-ebv
2000-2006: BS/MS: National Tsing-Hua University / Academia Sinica, Taiwan
Life Science / Immunology (Autoimmunity, Regulatory T cells, and Immune tolerance)
2007 -2010: RA: National Health Research Institute, Taiwan.
Virology (Dengue virus, Hepatitis C virus, drug screening)
2010-2015: PhD: University of Heidelberg, Germany
Virology (Epstein-Barr virus (EBV) virology)
2015-2017: Postdoc: German Cancer Research Center, Germany
Virology (EBV, tumor virology, mice model), development of EBV vaccine.
2018Feb- : Assistant Professor, IMI, NYMU/NYCU, Taiwan
Virology (EBV and human carcinoma, the viral biotechnology lab)
QUESTION 1:
• What is a virus?
• How the viruses can do?
• Why we need to learn virology?

Topics today:
• WHY YOU NEED TO STUDY VIROLOGY?
• The history of virology.
• Basic Virology
• Application of Virology
• Emerging viral issues.
Many good reasons you have to
study virology
• Viruses are ubiquitous on earth.
• Infect all forms of life (even bacteria!)
• Many viruses cause diseases
– AIDS, influenza, dengue fever, hepatitis, common cold,
herpes…
• Some viruses are useful if we know how to use
them wisely.
– Use phage to kill the specific types of bacterium
(Salmonella).
– Pesticides (insect control, rabbit control)
– Sources of enzymes (reverse transcriptase)
– Gene vectors for protein production (transduction)
– Vectors for gene therapy
– Anti-cancer agents: modified virus is used to kill cancer cells.
– Learn science form host-virus interaction.
– Good topics for Hollywood movies
Viruses kill billions
Fundamentals of Virology
Viruses kill
Application of Viruses:
Fundamental science, applications,
public health
1946-2020:
-17 Nobel prizes for virologists (also
2008 for HPV and HIV, 2020 for HCV);
-33 Nobel prizes for virology +
Immunology (“viruses as model”)
Viruses and economy
The animals or animal products derived from disease zones

are not allowed to be exported or under crazy regulations
Viruses and economy
Pork export, Taiwan FMDV case
@Before 1997: Taiwan was the 2nd largest pork exporter
@1997yr: foot and mouth disease (FMD, by virus, strain
Export
“O/Taiwan/97”), 3.8 million pigs were killed to prevent the
Import
spreading (30% of all Taiwan’s pigs).
@Lost 1.6 billions USD/year for export
*100 millions USD
Export dropped @1998yr: everything started from the beginning; all pigs
to “ZERO” were vaccinated.
@2000s: WTO: cheap pork meat were imported into TW.
@2009: stop vaccination. 7 FMD cases reported.
@2010: all pigs get vaccination again.
@2018: stop vaccination.
@2019: if no more FMD case, Taiwan will become FMD-
free zone again (22 years!!!)
Viruses and economy
African Swine Fever virus (ASFV) case
@Cause severe diseases to pigs
@ASFV is extremely stable, even can survive in the frozen
pork for months
@Consequence:
1. The price of pork will be extremely expensive in the
endemic countries;
2. The countries recognized as “ASFV ZONE” are not
allowed to export pork.
Viruses and economy
COVID-19 case (Mink)

@Important animal for the source of clothing.
@Farming in Europe (Netherlands, Danmark…etc)
Because Mink can be also infected by COVID-19

 Millions killed (for prevention).
 In case to cause human-animal transmission and to
prevent the generation of new viral mutants
植物病毒: 昆蟲、動物、花粉等造成大規模經濟損失
動物病毒: 魚蝦、雞鴨鵝、牛豬羊、貓貓狗狗
Viruses and economy
COVID-19 case HUMAN: Shops, industries all closed, no economy activities
Viruses from animals can also make
you ill!
Yellow fever
West Nile fever Rabies
Dengue fever
SARS Swine flu

Ebola FMDV
Ebola
SIV
HIV? Influenza
Always have new viruses cause
problems
A new deadly virus

originated from 4
different organisms!
Always have new viruses cause
problems
New viruses database

VIRUS HUNTER (Nature video)
Hunters of Coronavirus
(National Public Radio)
What we know about a virus now
1. Viruses are filterable agents (0.22-μm) Small
2. Viruses are obligate intracellular parasites. Depend on others
3. Viruses cannot make energy or proteins Hijack cellular machinery

independently of a host cell.
4. Viral genomes may be RNA or DNA. Inheritable
5. Viruses have a naked capsid or an envelope Simple

morphology.
6. Viral components are assembled and do not Amplify a lot
replicate by “division”, but by “multiplication”.
History: the discovery that
Pathogens cause human diseases
By God’s punishment? Louis Pasteur Robert Koch Sir Alexander Fleming

France Deutschland Great Britain
Before 1850
1850s’ 1890s’ 1928
The modern science: validation of
the disease-causing pathogens
By [mike jones] - Own work, CC BY-SA 3.0,

https://commons.wikimedia.org/w/index.php?curid=24819700
Identification of the pathogens that
cause diseases
Year Diseases Pathogens Type Transmission Discovered by
1873 Leprosy Mycobacterium leprae Bacteria Human Gerhard Henrik Armauer Hansen
1880 Malaria Gensus Plasmodium Parasite Mosquito Charles Louis Alphonse Laveran
1880 Typhoid Fever Salmonella typhi Bacteria Fecal-oral route Karl Joseph Eberth
Mycobacterium
1882 Tuberculosis Bacteria aerosol droplets Robert Koch
tuberculosis
1883 Cholera Vibrio cholerae Bacteria Fecal-oral route Robert Koch
1884 Tetanus Clostridium tetani Bacteria Soil / wound Arthur Nicolaier
1887 Brucellosis Brucella species Bacteria Zoonoses David Bruce
1894 Plague Yersinia pestis Bacteria Murine, flea Alexandre Yersin, Kitasato Shibasabur
1898 Dysentery Bacillary dysentery Bacteria Fecal-oral route Kiyoshi Shiga
1905 Syphilis Treponema pallidum Bacteria Sexual, blood Fritz Schaudinn and Erich Hoffmann
1906 Pertussis B. pertussis Bacteria Zoonoses Jules Bordet and Octave Gengou
1909 Typhus Rickettsia prowazekii Bacteria Zoonoses Charles Nicolle
You are very lucky to live in this century; most of people before 1900 can’t live
longer than 35 years old
Identification of the pathogens
leads to drug development
Year Diseases Pathogens Type

1873 Leprosy Mycobacterium leprae Bacteria
1880 Malaria Gensus Plasmodium Parasite
1880 Typhoid Fever Salmonella typhi Bacteria
1882 Tuberculosis Mycobacterium tuberculosis Bacteria
1883 Cholera Vibrio cholerae Bacteria
1884 Tetanus Clostridium tetani Bacteria
1887 Brucellosis Brucella species Bacteria
1894 Plague Yersinia pestis Bacteria
1898 Dysentery Bacillary dysentery Bacteria
1905 Syphilis Treponema pallidum Bacteria
1906 Pertussis B. pertussis Bacteria
1909 Typhus Rickettsia prowazekii Bacteria
Whatever can kill these pathogens?

=> Drug development
High-throughput screening
Timeline of Antimicrobial Therapy
The year shown indicates when a given drug was released onto the pharmaceutical market. This is
not a timeline of the development of the antibiotics themselves.
Infect Chemother. 2012 Aug;44(4):263-268.

Identification of the pathogens:
etiology and epidemiology
Year Diseases Type Transmission

Quarantine works!
1873 Leprosy Bacteria Human
1880 Malaria Parasite Mosquito Improved Sanitation
1880 Typhoid Fever Bacteria Fecal-oral route
1882 Tuberculosis Bacteria aerosol droplets
Clean water
1883 Cholera Bacteria Fecal-oral route Boiled water
1884 Tetanus Bacteria Soil / wound Cooked food
1887 Brucellosis Bacteria Zoonoses
1894 Plague Bacteria Murine, flea
1898 Dysentery Bacteria Fecal-oral route
1905 Syphilis Bacteria Sexual, blood
1906 Pertussis Bacteria Zoonoses
1909 Typhus Bacteria Zoonoses
DRUG? DRUG? DRUG?

Might be not always necessary :D
To know the sources of pathogen:
1854’s London outbreak of Cholera
Sources: Wikipedia, NIH and CDC website, the history of quarantine

If it is contagious (especially by aerosol):
QUARANTINE is the best way
Sources: Wikipedia, NIH and CDC website, the history of quarantine

Thinking:
QUARANTINE in modern society?!
Nearly impossible now!!
Source: China Airlines website Source: EVA Air Corporate brochure

2022/01/03 data
Question Time
Q: What is wrong with this table?
Year Diseases Pathogens Type Transmission Discovered by
1873 Leprosy Mycobacterium leprae Bacteria Human Gerhard Henrik Armauer Hansen
1880 Malaria Gensus Plasmodium Parasite Mosquito Charles Louis Alphonse Laveran
1880 Typhoid Fever Salmonella typhi Bacteria Fecal-oral route Karl Joseph Eberth
Mycobacterium
1882 Tuberculosis Bacteria aerosol droplets Robert Koch
tuberculosis
1883 Cholera Vibrio cholerae Bacteria Fecal-oral route Robert Koch
1884 Tetanus Clostridium tetani Bacteria Soil / wound Arthur Nicolaier
1887 Brucellosis Brucella species Bacteria Zoonoses David Bruce
1894 Plague Yersinia pestis Bacteria Murine, flea Alexandre Yersin, Kitasato Shibasabur
1898 Dysentery Bacillary dysentery Bacteria Fecal-oral route Kiyoshi Shiga
1905 Syphilis Treponema pallidum Bacteria Sexual, blood Fritz Schaudinn and Erich Hoffmann
1906 Pertussis B. pertussis Bacteria Zoonoses Jules Bordet and Octave Gengou
1909 Typhus Rickettsia prowazekii Bacteria Zoonoses Charles Nicolle
Paradox: many diseases don’t
follow Koch’s Postulate
Good example: Rabies, small pox, yellow fever…etc

Not a single virus can be isolated through
this way because viruses only grow in the
infected cells but can’t grow by themselves
Tobacco mosaic virus infected
tobacco leaf.
?????????????
The filtrates from the patients’

tissues can cause the diseases
but can’t fit Koch’s rule???
By botanist Dmitri Ivanovsky, 1892
Martinus Willem Beijerinck 1898
VIRUS
Latin word vīrus (the ī indicates a long i)

-"poison; venom", denoting the venom of a snake
Possibilities to explain:
1. Not Bacteria, but

something totally different
2. Still Bacteria, just too small

to be filtered
3. Still Bacteria, but just can’t

grow on the 1900’s medium
!!?? WHAT??
4. Not living stuffs, just “non-

living” toxins causing that
Filter can filter all the visible “bacteria”
Pioneer study showing that “virus” caused human diseases
Spanish Influenza (Killed 5% human population in 1918)
Filtrable.
Not “ordinary” bacteria

(medium remained clear)
Contagious.
Only cause disease at

correct location
Unfortunately, people still

thought flu was caused by
bacteria before 1930s
Thinking time:
Global warming and its possible effects
Successfully “rescued” the 1918 influenza virus
Nature 437, 794–795 (06 October 2005)

Milestones in Virology
• 1930s: electro microscope:

- Can eventually see virus
• 1950-60: DNA/RNA discovery
- Confirm: Viruses are genetic materials
but not toxins
• 1950s: In vitro cell culture system
- Can amplify virus in vitro and study
viral life cycle.
The identification of viruses that
cause human diseases
Diseases (mostly viruses-associated) that were
reported within one month and may cause
epidemic/pandemic outbreaks
Thinking:

Thinking: why people expanded lots of life
before antibiotics and modern virology?
1942
Commercial use of penicillin
1850 1890 1928/1942

•Reason?
• Many extremely deadly viral-associated diseases

had been solved during this golden
period ”surprisingly”; mostly due to the reason of
“vaccination”.
Edward Jenner, father of Smallpox, killed 10% up to 20% of all
population before his discovery
Immunology and vaccine
Figure: wikipedia; Janeway Immunology

Smallpox and Vaccination
1. Airborne, 30% fatality
2. Human is the only host
3. Caused 500 million death within one century
4. Wiped off 97% of American Indian in 1600s
5. Officially eradicated in 1979
Edward Jenner (1749–1823)
After 1850
Vaccination worked!
• Principle: “vaccinated” with something similar but

not so toxic can lead you “immune” from the
dangerous diseases?!
Rabies: another example
Rabies: caused by bacteria?
Can I make the “bacteria” less toxic?
Louis Pasteur
1850s’
Rabies vaccine makes rabies be eradicated from the developed countries

Attenuated vaccines (still the principle
for vaccine development now)
(note: Rabies is a “RNA” virus; not the
bacteria)
Very toxic
No Rabies
anymore
Why me?
Not so toxic
Not toxic
Louis Pasteur
Repeat 100-round of
1850s’ infection in rabbits
inactivation
Poliovirus: nearly to be eradicated
• RNA virus, only infects human and monkey
• enterovirus
• Cause paralysis in infant
• 1954: Salk developed the vaccine (chemical-inactivated vaccine)
• 1961: Sabin developed the live-attenuated vaccine
Bacteria
Vaccination / Viruses
1942
Commercial use of penicillin
Vaccination helped to
prevent huge amounts of
viral-associated diseases
1850 1890 1928/1942
during this period
VIROLOGY/VACCINATION
CANCER!!! A aging disease!!!
Facts of cancer:
1. If you live long enough, you will anyway get at least
one type of cancers.
2. Believe it or not, at least 20% cancers are caused by
infection (mostly by viruses)
Data adopted from NIH website

Virus causes tumor?
EXPERIMENT PERFORMED in 1909-1923
Francis Peyton Rous
Tumor cells Tumor juice
Culture in
vitro for N
filter
days
Tumor Nothing
grow
Tumor, why??
Virus causes tumor?
Dane Johannes Grib Fibige
1913yr: Nematode cause gastric
carcinoma in rat (NEJM)
Nominated 18 times for
Nobel prize
I found it, call it Rous
sarcoma virus (RSV)
1926yr: Nobel prize
But I was too unlucky
1928yr: die
1929yr: discovery of VitA,

and found that lack of VitA
caused the “tumor (actually
not tumor)” he discovered.
What?
1929-1950s: nobody
mentioned that pathogens
caused tumors
Yes, virus can cause tumor!
Important discovery in science
OK, I eventually can try
1930s: EM: can eventually see virus whether RSV can make Oh God, it can transform
1950s: DNA discovery normal cells into tumor or not
1950s: In vitro cell culture system
1960: RNA discovery
1964: EBV cause lymphoma
1960s: I found that this virus replicate too
slowly or even not replicated. However, the
infected cells indeed transformed, did this
virus integrate into Genome?
Oh God, I found RNA
virus and Retrovirus
Eventually other people prove my
opinion in HUMAN but not CHICKEN
1966yr: Nobel prize, I was 87 already…

After 50 years of my first discovery, people eventually believe me
RSV and Nobel prizes
2nd Nobel prize (1975 Howard Temin)
Q: If RSV is integrated into genome as DNA, but it’s a RNA virus How?
Hypothesis: this virus must have something to make RNA into DNA
Result: he found reverse transcriptase (enzyme you use for RT-PCR).
3rd Nobel prize (1989; Varmus and Bishop)

Q: How RSV transform the infected cells?
Hypothesis: (1) retrovirus cause tumor? Or (2) something in RSV cause tumor
Result: the discovery of oncoprotein (or you can say proto-oncoprotein)
At least 20% human cancers are
caused by infection
% of total human
Pathogens Cancers
cancer
HBV Liver cancer 3%
HCV Liver cancer 3%

Cervical cancer,
HPV 5%
carcinomas
HTLV lymphoma 0.03%
H. Pylori (BACTERIA) Gastric carcinoma 5%
KSHV Kaposi’s sarcoma 0.70%
Nasopharyngeal
carcinoma, B, T, NK
lymphoma, gastric
EBV 3-up to 8%
carcinoma, lung
cancer, colon
cancer
Understand basic virology can help us
to eradicate the diseases
Let’s go back to the BASIC VIROLOGY!!

1. Concept
2. Classification
3. Genome
4. Life cycle
5. Transmission
6. Other important
knowledge of viruses
1. Concept of the Virus:
very different from the other two bros
Life style:
Only virus can’t survive by itself but has to live
inside the infected host cells, bacteria and fungi can
live alone
Microbiology For the treatment:

-Bacteria/Fungi Antibiotics are available for nearly all the
pathogenic Bacteria and Fungi.
-Viruses For virus: NO antibiotics! Even for drugs, usually
one drug can only treat one virus.
For immune response:

B/F: Mostly depended on innate immunity
V: Mostly depended on adaptive immunity
Virus: different way to amplify
Human: Bacteria: Virus:

(WILLING) (DIVISION) (REPLICATION)
From 2-> 1.125 (Taiwan…) From 1->2->4 From 1->103-6
From 2-> 6.6 (Some African -Depended on -Depended on killing cells or
countries) outside nutrition infecting more cells
limitation: limitation: limitation:
…$……$…house…?….. No nutrition No cells “to be killed”
Lumen.com
1+1<2??
2. Classification of the viruses
It helps us to understand how to deal with a pathogenic
virus quickly according to the classification.
Method 1: by their genome Method 2: with or without envelope
dsDNA Linear
Enveloped
DNA dsDNA circular
Non-enveloped
ssDNA Linear
dsRNA
RNA +ssRNA
-ssRNA
Segmented virus
There are two kinds of viruses: DNA virus or RNA virus
Principles of virology Fig.1.9

Principles of virology Fig.1.9
Enveloped vs non-enveloped virus
Envelope Viruses Non-Enveloped Viruses
Outer lipid layer, surrounding
Most outer layer capsid
the capsid
Not so aggressive, not always
To the host cell accompany with cell lysis of Very aggressive, cause cell lysis
the hosts
Expose to outside environment,

Protected by bio-lipids; usually
Transmission transmitted through oral or feces (so
through blood or body fluids
usually infect through respiratory/oral)
Unstable, sensitive to heating,

drying, detergent (anything Stable. After drying out still highly
Stability
breaks lipid layers cause non- infectious.
infectious)
HIV, HCV, Influenza, HSV, EBV,

Good example Adenovirus, Norovirus
HPV
Kalpesh Zunjarrao, slideshare.net

3. Genome: highly compacted with
viral-coding transcripts
HPV: 8kb dsDNA virus EBV: 170kb dsDNA virus
Small molecule inhibitors of human papillomavirus

protein - protein interactions.
D'Abramo CM, Archambault J - Open Virol J (2011)
“Courtesy of the National Library of Medicine."
4. Life cycle in an infected cell
 Receptor: define the tropism
 Entry: endocytosis or fusion
 Replication,
transcription, translation:
virus-specific enzymes
 Proteases: virus-
specific enzymes
 Assembly
 Release: lysis, exocytosis,
budding
 Re-initiation of the Peakman M. et al, Basic and clinical Immunology
replication: extracellular,
cell-to-cell fusion (syncytia).
https://www.youtube.com/watch?v=7aEL0EQtyGA
Binding / Enter
 Replication,
specific enzymes
 Assembly
budding
https://www.youtube.com/watch?v=7aEL0EQtyGA
A virus infects the cells only if this
virus can recognize this cell
A virus infects the cells only if this
virus can recognize this cell
• Receptor-ligand need to match
• Sometimes requires co-receptor
• Then either directly fusion or endocytosis
https://jvi.asm.org/content/91/4/e01906-16
Replication and assembly
 Replication,
specific enzymes
 Assembly
budding
Viruses need to produce viral proteins to
perform transcription, translation,
replications, and assembly
II VII
VI
I
+RNA
III
IV
V
For easy understanding, you can read this first

https://en.wikipedia.org/wiki/Baltimore_classification
Concept: +mRNA is the template for producing proteins
(it’s also the template for RNA viral replication!!)
Able to enter
the nucleus II VII
VI
I
+RNA
III
IV
V
II VII
VI
MUST have
Reverse I
Transcriptase +RNA
within the
virion and
may require III
“integrase”
enter the
nucleus IV
V
II VII
VI
I
+RNA
III
IV
V
Must have RNA-depend-RNA polymerase (RdRp)

II VII
VI
I
+RNA
III
IV
V
May need to have RNA-depend-RNA

polymerase (RdRp) within the virion!
II VII
VI
I
+RNA
III
III
IVIV V
Exception: HBV (dsDNA-RT virus), a very special virus

(has DNA polymerase within its virion)
(can transcript RT since it’s replication require RNA as template….)
Release (amount, killing hosts or not)
• Choice 1: Have millions of babies and kill the hosts;
few of these babies may survive and find new hosts.
Mostly viruses cause acute diseases, accompany with cell lysis
• Choice 2: making babies slowly and steadily

without killing the hosts immediately.
HIV is a good example (with latency)
• Choice 3: Depend on whether you have money and

time and change the strategies….
Usually the complicated viruses: EBV and HSV are good examples
Remember: virus is a genetic material that have a way to sustain its genome in
the world efficiently. All these 3 choices make it possible.
5. Transmission
Viruses can spread through the air in two ways: inside large droplets that fall quickly to the ground (red),
or inside tiny droplets that float in the air (gray). In the first route, called droplet transmission, the virus
can spread only about 3 to 6 feet from an infected person. In the second route, called airborne
transmission, the virus can travel 30 feet or more.
Adam Cole/NPR
Transmission routes
1. Oral Fecal or saliva: Enteroviruses, Noro, Polio, HAV

2. Air-borne: Influenza, Measles, SARS…etc
3. Urine (rare): Lassa fever (rodent urine/feces)
4. Blood (HIV, HBV, HCV, HSV, HPV)
5. Sexual (HIV, HBV, HSV, HPV)
6. Vertical (cross placenta) HBV, CMV, HSV, Zika,
Rubella virus
7. Milk/Saliva at birth: CMV, EBV, HSV, HIV
8. Mosquito-borne: JEV, DENV, Zika, YEV
9. Animal-borne: (biting): Rabies
For ladies and future mothers:
-> It‘s very important to take vaccines against the viruses that
might cause the abnormal babies
(Please contact your doctor before or immediately after
knowing you are at pregnancy)
@CMV (before 20th week of pregnancy, cause minimal 1/750 child with defect in
the DEVELOPED COUNTRIES
Cause 10-15% children with congenital abnormalities
@Rubella virus:
Cause 25% to 52% chance for the children with congenital problems
@Chickenpox (VSV):
Cause birth defects, including leg deformities
@Coxsackievirus
Cause death of baby
@Zika
Small-head child
@Some others might be transmitted to child at birth (blood contact: HIV, HBV..etc)
EBV: the most successful virus that
!
(Pavlova et al., 2013). The space between envelope and nucleocapsid is filled with
protein tegument complexes composed of many different proteins that originate from
the virus and its host (Penkert and Kalejta, 2011). These viral tegument proteins might
infects human population

facilitate EBV infection, as an EBV with deletion of major tegument proteins BNRF1
infects B-cells 20-fold less efficiently (Feederle et al., 2006). The protein composition
of an EBV virion and an electron micrograph of an EBV particle are depicted in
figure 1.
Figure 1. An EBV virion

The left panel shows a schematic that depicts the general composition of an EBV virion. The size of
the characters reflects the relative amount of the protein in the virus. This figure is adapted and
reorganized from results of the paper published by Johannsen et al, PNAS 2004. These authors did a
mass spectrometry analysis on the purified EBV virions derived from B95-8 strain. The right panel
shows an electron micrograph EBV virion of the B95-8 strain. The diameter of an EBV virion is
usually between 120-180 nm.
Genome structure: EBV, as well as the other members of Herpesviridae family,
consists of a complex linear double-strand DNA genome that is around 180 kb in size.
10!
6. Other important knowledge of virology:
A. Pseudotyped of the viruses
Outcome: change the cell tropism of a virus.
Curr Gene Ther. Author manuscript;

available in PMC 2006 Feb 15.
Published in final edited form as:
Curr Gene Ther. 2005 Aug; 5(4): 387–
398.
B. Error-prone replication (RNA virus)
Error rate: 1 mutation
type in/base
Reverse Transcriptase Retrovirus RNA 3*10^4
RNA-dependent RNA Polymerase RNA virus RNA 10^4
DNA polymerase II human DNA 10^9
T4 DNA polymerase phage DNA 10^8
Vaccination !!?
Today? My computer is bad can’t
run out the result
C. Virus also infects prokaryotic cells
Virus kills bacteria -phage (Bacteriophage)
??????? Why Indian people don’t
get the outbreak of Cholera????
????
Ganges
Ernest Hanbury Hankin
DNA virus, 40-50kb

Doss J et al., Viruses 2017, 9(3), 50; doi:10.3390/v9030050
Phage is everywhere!!!
Phage is everywhere!!!
Thinking time:
1. Why there are so many phage?
2. If no phage, what will happen!!?
D. Virus help evolution
Why these non-coding retroviral relics help evolution?

1. They insert randomly
2. LTRs of retroviruses are “promoter”
3. Might alter the gene function.
4. Might cause gene duplication
……many possibilities
?????
If there was a pandemic viral infection of monkeys that targeting neurons….
human Dead island movie

D. Virus help evolution; still ongoing
E. Virus can escape from immune system at
certain extend (viral evolution)
E. Virus can escape from immune system at
certain extend (viral evolution)
You are a virologist now! we can
discuss: Application of Virology
• 1. How to treat viral-associated diseases through

the knowledge of basic virology?
• 2. How to use viruses to benefit our researches or

life?
I think today you know how to make the
attenuated viruses for vaccine purpose
(note: Rabies is a “RNA” virus; not the
bacteria)
Very toxic
No Rabies
anymore
Why me?
Not so toxic
Not toxic
Louis Pasteur
Repeat 100-round of
1850s’ infection in rabbits
inactivation
Thinking time:
If Vaccine is sooooo good, why not all the
viruses have vaccines?
Thinking time: why not all the viruses
have vaccines?
1. Low chance to infect human population (Ebola for example..develop
the vaccine needs money….)
2. Some diseases are really bad but can be predicted. (Rabies, still
incidence problem; passive immunity is enough)
3. The degree of diseases. Even if many people infected but too mild,
nobody care. (Herpes) Even with vaccine, will you pay?
4. Virus mutation rate is too high (HIV, HCV, influenza)
5. Too many virus variations (or variants, subtypes)
6. No attenuated virus available (not safe). The heat-killed virus have no
effect. (Question: why??)
7. Some cases vaccination even makes disease worse. (especially when
the virus can infect the cells with Fc-receptor).
8. Vertical transmission (from placenta, mother)
9. Infect too many people but only parts of them will get diseases. (EBV).
IE: Nasopharyngeal carcinoma: 0.1-100 / 100,000 population
10. Cause diseases under immunodeficiency cases. (KSHV)
11. Side effects are significant.
12. Any other possibility? (QUESTION)
If there‘s no vaccine, you can
consider how to block the viral life
cycle properly
• Binding (VACCINE)
• Enter the cell (there’s nothing you can do)
• Perhaps enter the “latency” and escape from
immune system (drug blocks this effect)
• Start to replicate crazily, kill the hosts (block
replication)
• Transmit to the other cells
• Question: any other step?
High-throughput screening
Issue for drug screening against viruses (most
of cases):
 You can “easily” find plenty of drugs against
the virus you study
 But most of these “drugs” also kill, or make
the cell sick
 Even if the cells are OK during screening,
most of time meet problems in animal
experiment
 Reason: The viruses “hijack” the cell
machinery; so most of these drugs
targeting essential host proteins.
Best solution:
 Fundamental virology, understand the

roles of each viral protein and the
physiological meaning of a virus
 Screen the drug by targeting viral
proteins
If there’s no vaccine: consider how to
block the viral life cycle properly?
TRANSMISSION THROUGH? • Proper receptors/viral
attachment proteins
• All the requirements
(enzymes, proteins)
• Particular stage of the cell
cycle (eg. retrovirus,
parvovirus)
• Evade host defense
Fundamentals of Virology, Fig. 1.6
mechanism
Application of Virology: anti-viral
• Binding drugs
• Perhaps enter the “latency” and escape from immune system (drug blocks this effect)
• Start to replicate crazily, kill the hosts (block replication)
Virology of HSV-1/2 (Herpes, painful! But not lethal!)

-We learn that the symptoms are accompanied with viral lytic replication
Actually there’s a super good drug to

cure Herpes (by blocking viral
replication)
Application of Virology: anti-viral
drugs block HIV binding
Approved by FDA in 2018

Application of Virology: safe vaccine
• Binding
• Perhaps enter the “latency” and escape from immune system (drug
blocks this effect)
• Start to replicate crazily, kill the hosts (block replication)
Harald zur Hausen
(German Cancer Research Center)
Nobel prize 2008
1. Prove HPV cause cervical cancer

2. Find out the mechanisms
3. Use basic virology to develop vaccine
Current and future applications:

Basic research: 1. Virus-like particle and vaccine
E6, E7 are the main viral 2. Therapeutic vaccine against E6/E7
proteins cause tumor 3. Drug screening of E6/E7 inhibitor
Virus-like particle (VLP):
A good vaccine candidate of the viruses that are too bad,
too oncogenic (so live-attenuated virus is impossible), and
can’t create vaccines through heat-inactivated viruses.
VLP of EBV had been created in my previous

lab, German Cancer Research Center
Application of Virology: anti-viral drugs
expel HCV from human body
(basic virology is so important)
• Binding
• Perhaps enter the “latency” and escape from immune system (drug blocks this effect)
• Start to replicate (block replication)
Ralf F.W. Bartenschlager

German Cancer Research Center /
University of Heidelberg
Basic virology He eradicates 3% of human cancer
Replicon system
Drug screening
•Scientific Reports volume 7, Article number: 14421(2017)

Now 16% of human cancers may be
protected or cured
% of total human
Pathogens (病原體) Cancers Reason Prevent Treatment
cancer
Chronic Vaccine:
HBV Liver cancer 2-3%
inflammation 1980s
Chronic Antiviral drug:

HCV Liver cancer 2%
inflammation 2016
Cervical cancer, Vaccine:

HPV Viral oncoproteins 5%
carcinomas 2000s
HTLV lymphoma Viral oncoproteins No No 0.03%
Itself not cause
Can be prevented
cancer but
HIV Immunodeficiency Safe sex through many N/A
immunodeficiency
available drugs
does
Chronic
H. Pylori (BACTERIA) Gastric carcinoma Antibiotics 5%
inflammation
KSHV Kaposi’s sarcoma Viral oncoproteins As HIV 0.70%
Nasopharyngeal
3 up to 8% (more
carcinoma, B, T, NK
EBV Viral oncoproteins No No and more being
lymphoma, gastric
identified)
carcinoma
Application of Virology: Take advantages
of the viruses for our usages
1. Genome modification. (Retrovirus, Adenovirus)
2. Cancer treatment. (depend on their tropisms)
3. Oncolytic viruses. (train the virus)
4. Molecular biology of mammalian cells (CAP of mRNA,
IRES, enhancer, transcription elements, NLS, intron,
promoter elements….).
5. Enzymes (RT, RdRp, integrase..etc)
6. Unlimited Cell source (cell lines established by viruses)
7. Plasmids
8. Immunotherapy
9. Any other? (question)
Application of retroviruses:
transgene / gene therapy
DANGEROUS!
Virology:
1. Each viral gene’s functions
2. Minimal parts of genome required for packaging
3. Packaging elements
SAFE!
www.abmgood.com
You can alter the

tropism by modifying
the envelope
Only this part can be packaged into viral particle and integrate
into host genome
-no further viral replication
-Can be used as gene delivery system
How CAR-T is used, often in conjunction with other

chemotherapies (Source: Klebanoff et al. (2014) Nature
Reviews Clinical Oncology 11, 685–686
doi:10.1038/nrclinonc.2014.190)
Application of Adenovirus
transgene / gene therapy / Oncolytic
• Not integrate into the host genome
• Kill the infected cells
• Usually cause only mild disease in immuno-
competent individuals
You can see that it’s a non-envelope virus.
-Highly infectious
-Strongly replicating
-Huge amount of viral particle 10^5-7 times
more than lentivirus
-Cause the infected cell die
Addgene
Coxsackie virus and

adenovirus receptor Replication-incompetent Adenovirus
Recognize human CAR -Gene-deliver system
protein
You can modify its capsid by random mutations
or adaptive selection, to pick up the one that
can infect the cell you want “specifically”
1. Select or make a viral capsid that only recognize the
cancer cell!
2. Through gene regulation elements
-Transcription factor-regulated E1
-Post-transcriptional regulation of E1 (ie: miRNAs)
-Gene deletion (remove E1A that bind to p53 to
suppress immune responses). Then this mutant can
only replicate happily in tumors that usually have
problem of P53.
-P53-Adenovirus: like previous one, send a functional
P53 gene back to tumor
Application of Parvovirus
Oncolytic
Application of Bacteriophages
Gene delivery / killing bacteria
DNA virus, 40-50kb

Doss J et al., Viruses 2017, 9(3), 50; doi:10.3390/v9030050
Appl. Environ. Microbiol.November 2011 vol. 77no. 21 7868-7872

killing antibiotics resistant bacteria
Appl. Sci. 2020, 10(21),

7654; https://doi.org/10.3390/app10217654
Perhaps we can use specific phages to kill
the bad bacteria and ameliorate our gut
microbiota?
Fundamental science
Advantage: simple, easy to modify
Discovery basic through using virology:
-DNA replication mechanisms (promoter, regulator, transcription factors….etc)

-Transcription (DNA-> RNA)
-Immunology (Vaccine, Inteferon, cytokines, adaptive immunity, antibodies)
-Cancer biology (definition of “oncoproteins”; discovery of oncovirus)
-Reverse transcription; reverse transcriptase (from retrovirus, for cDNA synthesis)
-CRISPR-Cas9 (a system bacteria applied for fighting phage)
-T4 DNA ligase, T4 DNA polymerase (from phage)
-RNA-dependent RNA polymerase (from RNA virus)
-Restriction enzyme (bacteria uses it to digest phage)
…….more
Fundamental science
1951-2011:
-16 Nobel prizes for virologists;
-33 Nobel prizes for virology +
Immunology (using viruses as
model)
Genome-modified organisms (GMO)
• Better food, anti-pests plants

• Healthy animals
• Beautiful flowers and fishes
• .....many
Front plant Sci. 2017

The modified viruses for tumor vaccines
• Vaccine against the virus itself
• Viruses encoding tumor-antigens, to stimulate

immunity against cancer cells (remember, the
viruses themselves are strongly immunogenic).
Final section:
Emerging viral issues
• Globalization issue for viral spreading
• Global Warming
• Bio-terrorism
• New viruses inter-species
• New viruses from wild animals
• ….endless story
Thinking:
(most of the virus-associating diseases have the “incubation time” for several days)
Thinking:
International viral disease map
(yesterday reported in Europe, perhaps
tomorrow in your country)
Thinking:
Global warming may make some ancient
viruses reappear? Possibly.
Nature 437, 794–795 (06 October 2005)
Who knows when the smallpox might be appeared again from the
frozen soil and at the time nobody has immunity
Thinking:
Bio-terrorism become much easier now.
• Smallpox is always concerned as the possible bioweapon by crazy
government or people, it can easily killed billions of people today.
• We stop vaccinated Smallpox vaccine from 1980 due to this disease is
entirely eradicated from the world.
• Issue: still 2 places reserve smallpox virus (Russia and USA).
• Issue2: advanced genome synthesis (it’s a DNA virus)
• Issue3: global warming.
• People are discussing whether we should get vaccines against smallpox
again.
• Other viruses, such as SARS or 1918 flu may have the same issues.
Thinking:
Viruses from animals or wild animals may cause
human diseases but we live so close to them
Carrier, no symptom
1. Dense human population

2. Human evading the
environment where the wild
animals are living.
3. Viruses in animals as carrier
without diseases, but very bad
in human.
4. Human transmit to each other.
5. End of the world?
Reservoir Mammals Human
Nothing happen many die plenty die
Thanks for your attention

Virology Introduction Student

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VIROLOGY

Dr. Ming-Han Tsai

• How the viruses can do?

• Why we need to learn virology?

The animals or animal products derived from disease zones

COVID-19 case (Mink)

Because Mink can be also infected by COVID-19

SARS Swine flu

A new deadly virus

New viruses database

1. Viruses are filterable agents (0.22-μm) Small

2. Viruses are obligate intracellular parasites. Depend on others

3. Viruses cannot make energy or proteins Hijack cellular machinery

5. Viruses have a naked capsid or an envelope Simple

By God’s punishment? Louis Pasteur Robert Koch Sir Alexander Fleming

By [mike jones] - Own work, CC BY-SA 3.0,

Year Diseases Pathogens Type

Whatever can kill these pathogens?

Infect Chemother. 2012 Aug;44(4):263-268.

Year Diseases Type Transmission

DRUG? DRUG? DRUG?

Sources: Wikipedia, NIH and CDC website, the history of quarantine

Sources: Wikipedia, NIH and CDC website, the history of quarantine

Source: China Airlines website Source: EVA Air Corporate brochure

Good example: Rabies, small pox, yellow fever…etc

The filtrates from the patients’

Latin word vīrus (the ī indicates a long i)

1. Not Bacteria, but

2. Still Bacteria, just too small

3. Still Bacteria, but just can’t

4. Not living stuffs, just “non-

Not “ordinary” bacteria

Only cause disease at

Unfortunately, people still

Successfully “rescued” the 1918 influenza virus

Nature 437, 794–795 (06 October 2005)

• 1930s: electro microscope:

Source: China Airlines website Source: EVA Air Corporate brochure

1850 1890 1928/1942

• Many extremely deadly viral-associated diseases

Figure: wikipedia; Janeway Immunology

Edward Jenner (1749–1823)

• Principle: “vaccinated” with something similar but

Rabies vaccine makes rabies be eradicated from the developed countries

Data adopted from NIH website

Francis Peyton Rous

Tumor cells Tumor juice

1929yr: discovery of VitA,

1966yr: Nobel prize, I was 87 already…

3rd Nobel prize (1989; Varmus and Bishop)

HCV Liver cancer 3%

Let’s go back to the BASIC VIROLOGY!!

Microbiology For the treatment:

For immune response:

Human: Bacteria: Virus:

Principles of virology Fig.1.9

Expose to outside environment,

Unstable, sensitive to heating,

HIV, HCV, Influenza, HSV, EBV,

Kalpesh Zunjarrao, slideshare.net

HPV: 8kb dsDNA virus EBV: 170kb dsDNA virus

Small molecule inhibitors of human papillomavirus

For easy understanding, you can read this first