8/12/2019 Lecture 01 2014

1/32

1

8/12/2019 Lecture 01 2014

2/32

1

8/12/2019 Lecture 01 2014

3/32

2

Instructor:- Dr. Eric Carstens

there is a Moodle site- read the FAQs (frequently asked questions) from 2003

and later

- post all questions to Questions About Virology link onthe Online Course Moodle page.

if you send me questions about course material byemail, other students dont get to see the responses!

ofce hours Mondays 16:00 -17:00 hr

-room 714 Botterell Hall

8/12/2019 Lecture 01 2014

4/32

3

Recommended: Microbiology 8th (7th or 6th similar)(Prescott, Harley, Klein) (on reserve in Bracken Library)

- Review Part Four chapter 12: Genes: structure, replication, expression

- Review Part Four chapter 15 and 16 Recombinant DNA technology/Genomics

- Learn Part One and Five The Viruses Part One Chapter 5

- general properties, structure, culturing, studying Part Five Chapter 25

- taxonomy and replication strategies

9thEdition is

not asgood forvirology

8/12/2019 Lecture 01 2014

5/32

Part Eight, Cha pter 37 supplemental to lecture material:- human diseases caused by viruses and prions

as menti oned in lectures (I am going to focus on theviruses and not their effects on humans or as causative

agents of disease). Learn:

- material about viruses discussed in lectures- Classication of Viruses 7th ed (on Moodle under the heading

Taxonomy of Viruses )

Excellent web sites:- ViralZone

expasy.org/viralzone- Virus Database On-line (ICTVdb) :

www.ictvonline.org/virusTaxonomy.asp?version=2011 4

http://www.ncbi.nlm.nih.gov/ICTVdb/http://expasy.org/viralzone/http://www.ncbi.nlm.nih.gov/ICTVdb/http://www.ncbi.nlm.nih.gov/ICTVdb/http://expasy.org/viralzone/http://expasy.org/viralzone/

8/12/2019 Lecture 01 2014

6/32

Fields Virology [electronic resource] / editors-in-chief,David M. Knipe, Peter M. Howley ; associate editors,

Diane E. Grifn ... [et al.].- Queen' s access only- http://g ateway.ovid.com/ovidweb.cgi?

T=JS& NEWS=N&PAGE=booktext&D=books&AN=00

139921 /5th_Edition/5&XPATH=/OVIDBOOK%5b1%5d/METADATA%5b1%5d/TBY%5b1%5d/ EDITORS%5b1%5d

5

http://gateway.ovid.com/ovidweb.cgi?T=JS&NEWS=N&PAGE=booktext&D=books&AN=00139921/5th_Edition/5&XPATH=/OVIDBOOK%5b1%5d/METADATA%5b1%5d/TBY%5b1%5d/EDITORS%5b1%5dhttp://gateway.ovid.com/ovidweb.cgi?T=JS&NEWS=N&PAGE=booktext&D=books&AN=00139921/5th_Edition/5&XPATH=/OVIDBOOK%5b1%5d/METADATA%5b1%5d/TBY%5b1%5d/EDITORS%5b1%5dhttp://gateway.ovid.com/ovidweb.cgi?T=JS&NEWS=N&PAGE=booktext&D=books&AN=00139921/5th_Edition/5&XPATH=/OVIDBOOK%5b1%5d/METADATA%5b1%5d/TBY%5b1%5d/EDITORS%5b1%5dhttp://gateway.ovid.com/ovidweb.cgi?T=JS&NEWS=N&PAGE=booktext&D=books&AN=00139921/5th_Edition/5&XPATH=/OVIDBOOK%5b1%5d/METADATA%5b1%5d/TBY%5b1%5d/EDITORS%5b1%5dhttp://gateway.ovid.com/ovidweb.cgi?T=JS&NEWS=N&PAGE=booktext&D=books&AN=00139921/5th_Edition/5&XPATH=/OVIDBOOK%5b1%5d/METADATA%5b1%5d/TBY%5b1%5d/EDITORS%5b1%5dhttp://gateway.ovid.com/ovidweb.cgi?T=JS&NEWS=N&PAGE=booktext&D=books&AN=00139921/5th_Edition/5&XPATH=/OVIDBOOK%5b1%5d/METADATA%5b1%5d/TBY%5b1%5d/EDITORS%5b1%5dhttp://gateway.ovid.com/ovidweb.cgi?T=JS&NEWS=N&PAGE=booktext&D=books&AN=00139921/5th_Edition/5&XPATH=/OVIDBOOK%5b1%5d/METADATA%5b1%5d/TBY%5b1%5d/EDITORS%5b1%5dhttp://gateway.ovid.com/ovidweb.cgi?T=JS&NEWS=N&PAGE=booktext&D=books&AN=00139921/5th_Edition/5&XPATH=/OVIDBOOK%5b1%5d/METADATA%5b1%5d/TBY%5b1%5d/EDITORS%5b1%5dhttp://gateway.ovid.com/ovidweb.cgi?T=JS&NEWS=N&PAGE=booktext&D=books&AN=00139921/5th_Edition/5&XPATH=/OVIDBOOK%5b1%5d/METADATA%5b1%5d/TBY%5b1%5d/EDITORS%5b1%5dhttp://gateway.ovid.com/ovidweb.cgi?T=JS&NEWS=N&PAGE=booktext&D=books&AN=00139921/5th_Edition/5&XPATH=/OVIDBOOK%5b1%5d/METADATA%5b1%5d/TBY%5b1%5d/EDITORS%5b1%5dhttp://gateway.ovid.com/ovidweb.cgi?T=JS&NEWS=N&PAGE=booktext&D=books&AN=00139921/5th_Edition/5&XPATH=/OVIDBOOK%5b1%5d/METADATA%5b1%5d/TBY%5b1%5d/EDITORS%5b1%5dhttp://gateway.ovid.com/ovidweb.cgi?T=JS&NEWS=N&PAGE=booktext&D=books&AN=00139921/5th_Edition/5&XPATH=/OVIDBOOK%5b1%5d/METADATA%5b1%5d/TBY%5b1%5d/EDITORS%5b1%5dhttp://gateway.ovid.com/ovidweb.cgi?T=JS&NEWS=N&PAGE=booktext&D=books&AN=00139921/5th_Edition/5&XPATH=/OVIDBOOK%5b1%5d/METADATA%5b1%5d/TBY%5b1%5d/EDITORS%5b1%5dhttp://gateway.ovid.com/ovidweb.cgi?T=JS&NEWS=N&PAGE=booktext&D=books&AN=00139921/5th_Edition/5&XPATH=/OVIDBOOK%5b1%5d/METADATA%5b1%5d/TBY%5b1%5d/EDITORS%5b1%5dhttp://gateway.ovid.com/ovidweb.cgi?T=JS&NEWS=N&PAGE=booktext&D=books&AN=00139921/5th_Edition/5&XPATH=/OVIDBOOK%5b1%5d/METADATA%5b1%5d/TBY%5b1%5d/EDITORS%5b1%5d

8/12/2019 Lecture 01 2014

7/326

Topical slide to start each lecture History

- Discovery and isolation of viruses- What is a virus?

Virus structure and taxonomy

Principles of virus replication - steps in the replicationcycle Classes of viruses and their modes of replication Viruses as tools in molecular virology - expression

vectors, virus-host interactions

8/12/2019 Lecture 01 2014

8/327

HOPEFULLY, WHAT I SAY IS IMPORTANT TO YOURLEARNING!

Slide Title will usually provide essential information

You are responsible for:- material discussed in class- material in text book related to what is discussed in

class- knowing characteristics of major families of viruses

discussed during the lectures

lecture slides are available on Moodle as PDFs (if youwant a different format, let me know)

8/12/2019 Lecture 01 2014

9/32

identify major virus families and understand theirstructure and replication strategies

know how information about viruses is derived recognize the role viruses play in life sciences

(knowledge generation) in addition to their potential aspathogens

go out into the world and critically analyze articles andreports about viruses

8

8/12/2019 Lecture 01 2014

10/32

Louis Pasteur: 1822-1895

Robert Koch: 1843-1910

Joseph Lister: 1827-1912

Their discoveries leadto a new experimental

approach for medicalscience, deningwhether an organismwas the causative agentof a disease

9

8/12/2019 Lecture 01 2014

11/3210

1. The same pathogen must be present in every case ofthe disease

2. The pathogen must be isolated from the diseased hostand grown in pure culture

3. The pathogen from the pure culture must cause thedisease when inoculated into a healthy, susceptible

laboratory animal4. The pathogen must be isolated from the inoculated

animal and must be shown to be the original organism

The Germ Theory as proposed by Pasteur and articulated by Koch(and his postulates) did not recognize the existence of viruses.

8/12/2019 Lecture 01 2014

12/32

In the beginning ...

8/12/2019 Lecture 01 2014

13/32

12

Adolf Mayer (1843-1942),German working in Holland

tobacco mosaic disease -light and dark spots on leaves

juice from infected leavesinoculated into healthy plants

caused disease transmission

agent was unknown,speculated it was caused byan unknown infectious form

8/12/2019 Lecture 01 2014

14/32

Dimitri Ivanofsky (1864-1920) commissioned by Russian Department of Agriculture -

tobacco disease

repeated Mayers experiments, with additional step- passed infected sap through a lter known to blockbacteria

- 1892 - the sap of leaves infected with tobaccomosaic disease retains its infectious properties evenafter ltration through Chamberland lter candles

provided operational denition of viruses- The concept of lterable infectious agent was against all accepted scientic concepts at

that time, so it was not widely accepted and Iwanowski himself even suspected thedisease was a result of a toxin.

13

8/12/2019 Lecture 01 2014

15/3214

The Berlin Inquiry of 1886 gave greatprominence to the filtration of water

for domestic purposes, and thatmade for the German War Office in1895 by Dr. Plagge drew particular

attention to the PasteurChamberland

The Pasteur Chamberland filter ismade of a porous porcelain tube

through which the water is forcedunder pressure. The residue left onthe outside of the tubes can easily

be removed, and the tubesthemselves should be sterilized

periodically by boiling.

At Darjeeling 9500 of these tubes arein use in the municipal water-works,

and the supply given is 150,000gallons a day.

8/12/2019 Lecture 01 2014

16/3215

Martinus Beijerinck (1851-1931), collaborated with Mayer ltered sap c ould be diluted and then regain its strength

(virulence) after transfer through living, growing plant tissue

- contagium vivum uidum (soluble living germ) agent remained infective through several transfers so was

not a toxin

explained failure to culture the pathogen outside its host

- 1998 centenary celebration of virology (Tobacco mosaicvirus) (TMV)

- http://www.sciencedirect.com/science/article/pii/ S0966842X98013754

http://www.sciencedirect.com/science/article/pii/S0966842X98013754http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TD0-3VCVF42-4&_user=2281995&_coverDate=12%252F01%252F1998&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_searchStrId=1638502723&_rerunOrigin=google&_acct=C000050549&_version=1&_urlVersion=0&_userid=2281995&md5=717ef5ce9dc5be5f15b755afc505bf75&searchtype=ahttp://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TD0-3VCVF42-4&_user=2281995&_coverDate=12%252F01%252F1998&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_searchStrId=1638502723&_rerunOrigin=google&_acct=C000050549&_version=1&_urlVersion=0&_userid=2281995&md5=717ef5ce9dc5be5f15b755afc505bf75&searchtype=ahttp://www.sciencedirect.com/science/article/pii/S0966842X98013754http://www.sciencedirect.com/science/article/pii/S0966842X98013754http://www.sciencedirect.com/science/article/pii/S0966842X98013754http://www.sciencedirect.com/science/article/pii/S0966842X98013754http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TD0-3VCVF42-4&_user=2281995&_coverDate=12%252F01%252F1998&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_searchStrId=1638502723&_rerunOrigin=google&_acct=C000050549&_version=1&_urlVersion=0&_userid=2281995&md5=717ef5ce9dc5be5f15b755afc505bf75&searchtype=ahttp://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TD0-3VCVF42-4&_user=2281995&_coverDate=12%252F01%252F1998&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_searchStrId=1638502723&_rerunOrigin=google&_acct=C000050549&_version=1&_urlVersion=0&_userid=2281995&md5=717ef5ce9dc5be5f15b755afc505bf75&searchtype=a

8/12/2019 Lecture 01 2014

17/3216

http ://www.tnw.tudelft.nl/live/pagina.jsp?id=8e07d591-c3c7-4801-94c2-82302a62be90&lan =en

http://www.tnw.tudelft.nl/live/pagina.jsp?id=8e07d591-c3c7-4801-94c2-82302a62be90&lang=enhttp://www.tnw.tudelft.nl/live/pagina.jsp?id=8e07d591-c3c7-4801-94c2-82302a62be90&lang=enhttp://www.tnw.tudelft.nl/live/pagina.jsp?id=8e07d591-c3c7-4801-94c2-82302a62be90&lang=enhttp://www.tnw.tudelft.nl/live/pagina.jsp?id=8e07d591-c3c7-4801-94c2-82302a62be90&lang=enhttp://www.tnw.tudelft.nl/live/pagina.jsp?id=8e07d591-c3c7-4801-94c2-82302a62be90&lang=enhttp://www.tnw.tudelft.nl/live/pagina.jsp?id=8e07d591-c3c7-4801-94c2-82302a62be90&lang=en

8/12/2019 Lecture 01 2014

18/3217

new Concept for the turn of the 20th century:- a lterable agent too small to observe in the light

microscope but able to cause disease by multiplyingin living cells

Loefer and Frosch (1898) isolated rst lterable agentfrom animals ( Foot-and-mouth disease virus - familyPicornaviridae )

Reed et al. (1900) recognized rst human lterableagent ( Yellow fever virus - family Flaviviridae ) and alsoshowed mosquito transmission of agent

8/12/2019 Lecture 01 2014

19/3218

methods to purify proteins (precipitation) also puriedTobacco mosaic virus (TMV)

-how did they detect the agent?

assayed by infectivity (in host plants!) TMV, like proteins, migrated in an electric eld rabbit antibodies directed against TMV neutralized

infectivity Led to the question:

- Are viruses proteins?

8/12/2019 Lecture 01 2014

20/3219

by 1929, concluded that viruses consisted of protein

but, in 1934, Max Schlesinger in Germany showed thatbacteriophages contained both protein anddeoxyribonucleic acid (DNA)

- rst suggestion that viruses were composed ofnucleoprotein (nucleic acid plus protein)

8/12/2019 Lecture 01 2014

21/32

in 1935, Wendell Stanley crystallized TMV- these infectious crystals contained protein and 5%

RNA

in 1940, Hoagland at the Rockefeller Institute showedthat vaccinia virus contained DNA but no RNA

Concept:- Virus genetic material is DNA or RNA but not both!

20TMV crystals

8/12/2019 Lecture 01 2014

22/32

in 1935, Wendell Stanley crystallized TMV- these infectious crystals contained protein and 5%

RNA

in 1940, Hoagland at the Rockefeller Institute showedthat vaccinia virus contained DNA but no RNA

Concept:- Virus genetic material is DNA or RNA but not both!

20TMV crystals

8/12/2019 Lecture 01 2014

23/32

21

in 1939, the rst electronmicrographs showed TMV wasrod shaped while x-raydiffraction suggested TMV wasbuilt up from repeating subunits.

Concept:

most simple viruses consistof one or a few identicalprotein subunits

Helmut Ruska (c 1969)

8/12/2019 Lecture 01 2014

24/32

21

in 1939, the rst electronmicrographs showed TMV wasrod shaped while x-raydiffraction suggested TMV wasbuilt up from repeating subunits.

Concept:

most simple viruses consistof one or a few identicalprotein subunits

Helmut Ruska (c 1969)

8/12/2019 Lecture 01 2014

25/32

22

Adenovirus Rhabdovirus

Coronavirus Papillomavirus

Herpesvirus

Tobacco mosaic virus

8/12/2019 Lecture 01 2014

26/32

a virus is an infectious, obligate intracellular parasite the genetic material of a virus enters a host cell and

directs the production of the building blocks of new virusparticles (called virions )

new virions are made in the host cell by assembly ofthese building blocks

the new virions produced in a host cell then transportthe viral genetic material to another host cell ororganism to carry out another round of infection

23

8/12/2019 Lecture 01 2014

27/32

24

viruses differ from bacteria in size, their inability to growin lifeless media and that they contain only one kind of

nucleic acid, either DNA or RNA

lterable, disease-causing agent, completely dependentupon living cell (intracellular parasite)

- self replicating in host cell- inert (dormant) outside a living cell

contrasts with dynamic growth of bacteria

8/12/2019 Lecture 01 2014

28/32

viruses are easy to understand when we reduce theirproperties to simple descriptions such as those listedabove. The confounding issues lie in the details, andwith viruses, there are many, many details.

knowledge comes from understanding the details

25

8/12/2019 Lecture 01 2014

29/32

8/12/2019 Lecture 01 2014

30/32

Best estimates range from ~3 x 10 6 viruses/ml in the deepsea to ~10 8/ml in productive coastal waters.

The oceans contain a total of ~4 x 10 30 viruses equal to 200Megatonnes (200 x 10 9 kg) of carbon, roughly the amountof carbon in 75 million blue whales!

If aligned end to end they would span ~10 million lightyears, or ~100 times the distance across our galaxy!

Every second ~10 23 viral infections occur in the ocean.

Viruses are the most abundant biological entity in theoceans and the second largest component of biomass afterprokaryotes.

27

Sources: C. A. Suttle. Nature Reviews Microbiology. 2007. 5:801.C. A.Suttle (2005).Viruses in the sea. Nature 437:356.

8/12/2019 Lecture 01 2014

31/32

There is more biological diversity within viruses than inall the rest of bacterial, plant and animal kingdoms puttogether!

Virus/host interactions are molecular negotiations offundamental and practical signicance that must beunderstood if we are to defend ourselves againstviruses.

However, the very things that make viruses insidiousand lethal can be exploited for practical use through thedevelopment of viruses as productive tools andtherapeutic agents.

28

8/12/2019 Lecture 01 2014

32/32