Campbell Biology, 10th, 2013

The Biology of Viruses

• 程洪强，博士，副教授，浙江大学医学院病理与病理生理学系• 研究兴趣：心血管生物学与心血管病分子病理• 电话：13735827063 电邮：hqcheng11@zju.edu.cn• 主页：http://mypage.zju.edu.cn/hqcheng• 地址：医学院科研楼A324

Ebola Virus

• 50% mortality rate

• Spread almost exclusively through bodily fluid

• The virus can survive outside of a host, but not for long

• Infected individuals will show symptoms within 3 weeks

• Only symptomatic people can spread virus

From www.realclear.com

The Origin and Evolution of Viruses (Living or nonliving is a question)

• Viruses have been found that infect every form of life, as well as other viruses.

• Originated from naked bits of cellular nucleic acids (?)

• DNA sequencing and bioinformatics analysis (most human RNA viruses emerged less than 1,000 years ago)

Concepts• General information

• Classification

• Structure

• Amplification/reproduction

• Viral disease and anti-virus therapy

• Impact on biological research

The Definition of Viruses (病毒)

• A virus is little more than DNA (or sometimes RNA)

enclosed by a protective coat, which is often

simply protein. To produce more viruses, a virus

must infect a cell and take over the cell’s

metabolic machinery. (A borrowed life) (NOT

Computer Virus)

• A virus is an infectious particle consisting of little

more than genes packaged in a protein coat.

The International Committee on Taxonomy of Viruses has

catalogued a total of 2618 known viruses or viroids (类病毒) that

either affect eukaryotes or prokaryotes in their latest list

(http://talk.ictvonline.org/files/ictv_documents/m/msl/4440.aspx).

How many are they?

烟草花叶病毒 腺病毒 噬菌体

Electron micrographs of highly purified preparations of some viruses.(a) Adenovirus. (b) Rotavirus. （轮状病毒）(c) Influenza virus (courtesy of George Leser). (d) Vesicular stomatitis virus. （水疱性口腔炎病毒）(e) Tobacco mosaic virus. (f) Alfalfa mosaic virus. （苜蓿花叶病毒）(g) T4 bacteriophage. (h) M13 bacteriophage.

Virus Structure

Virus is TinyPM2.5

Classification

• Host range (host specificity): plant, animal and phage

• They are called either a DNA or RNA virus depending on the type of nucleotide in the make-up.– Double stranded DNA– Single stranded DNA– Double stranded RNA– Single stranded RNA

• The nucleotide may be linear or circular

• The smallest have only 4 genes and largest have several hundred (giant viruses), even more (Pandoravirus).

Classification

多瘤病毒

疱疹病毒

痘病毒

细小病毒

呼吸道肠道病毒

小RNA病毒

冠状病毒

黄病毒

外衣病毒

丝状病毒

禽流感病毒

副粘液病毒莎草弹状病毒

反转录病毒

Protein synthesis----capsid

DNA replication----DNA

AmplificationA borrowed life

Amplification

Lytic or Lysogenic Cycles

• The Lytic Cycle– Culminates in the

death of the host cell– Virulent viruses

reproduce only by lytic cycle.

– Natural selection favors bacterial mutations with receptor sites that are resistant to a particular phage or that have restriction enzymes to destroy the phages.

• The Lysogenic Cycle

– Replication of the viral genome without destroying the host cell.

– A temperate virus may reproduce by either cycle.

– Lambda virus: resembles T4 but only has a single short tail fiber

• While phages have the potential to wipe out a bacterial colony in just hours, bacteria have defenses against phages.– Natural selection favors bacterial mutants with

receptors sites that are no longer recognized by a particular type of phage.

– Bacteria produce restriction nucleases that recognize and cut up foreign DNA, including certain phage DNA.

• Modifications to the bacteria’s own DNA prevent its destruction by restriction nucleases.

– But, natural selection favors resistant phage mutants

The Interactions Between Viruses and its Hosts: Evolution

RNA Virus Replication

Viral Persistence（持续性感染）

• Acute viral infection, chronic infection, latent infection

• Ability to hide from host immune systems

• Persistence is a capability acquired and strengthened in the process of evolution of many viruses that is the means of maintenance of species

Viral Persistence1. The virus may disguise itself or mimic properties of the host’s normal

cells.2. The virus may infect a small subset of cells situated in the brain,

reproductive organs, and parts of the eye and joints that are immunologically privileged, that is free from the usual scrutiny of the immune system.

3. The virus may paralyze or destroy certain immune functions directly responsible for its elimination.

4. It may integrate itself into the genetic make-up of the cell, thereby insuring itself subsistence as long as the normal cell is not eliminated.

5. The virus may have genetic controlling elements that regulate and limit its expression.

6. The virus may have an ability to continually change itself on a regular basis such that the immune system is never able to “catch up.”

7. More

Surprisingly, it appears that not just retroviruses but almost all types of viruses can become endogenous.

Viroids and prions

Viroid（类病毒）: An infectious particle, similar to but smaller than a virus, that consists solely of a strand of RNA and is capable of causing disease in plants.

Prion（朊病毒）: A prion in the Scrapie form (PrPSc) is an infectious agent composed of protein in a misfolded form.

The Evolution of Viruses is a Myth

• Plasmids, transposons and viruses share an important feature: they are mobile genetic elements.

• Read information from viral genomes

• Mimivirus (400 nm, 1000 genes) and Pandoravirus (0.7 um, 2556 genes)

Emerging Viruses

HIV (human immunodeficiency virus)

• ssRNA, retrovirus, reverse transcriptase

• Discovered at 1980s, AIDS (acquired immunodeficiency syndrome)

• Treatments: vaccines, antiviral drugs (ATZ and cocktails)

• Vaccines are successful in fighting to smallpox virus（天花）, hepatitis B, rubella（麻疹）, mumps（流行性腮腺炎）……but, not for HIV now.

Life Cycleof HIV

Adapted from WHO

HIV Researches and Medicines

Demberg T, 2012, controlling HIV/AIDS epidemics: Current status and global challenges

SUMMARY AND CONCLUSION

As briefly summarized by this review the substantial progress made in AIDS treatment has stimulated the concept of “treatment as prevention.” Additionally, vaccine development has picked up momentum due to new discoveries and the modest success of the RV144 clinical trial in Thailand. However, to achieve global control of HIV/AIDS infection in the absence of a highly efficacious vaccine or cure, a combination of multiple preventive measures will need to be continuously applied. Further investigation of all elements of the host immune system, both innate and adaptive, as well as development of novel treatment strategies should proceed in order to insure strong control of the AIDS pandemic and eventual eradication of the disease.

Demberg T, 2012, controlling HIV/AIDS epidemics: Current status and global challenges

HIV Researches and Medicines

Nuno R. Faria et al. Science 2014

1953

1920

1946

1937

1939

1937

HIV Evolution

金沙萨

黑角市

卢本巴希

基桑加尼

Antiviral Drugs and Vaccine（疫苗）

• A vaccine is a harmless variant or derivative of a pathogen that stimulates the immune system to mount defenses against the harmful pathogen

Viruses as Bioresearch Tools

1. Biological researches 2. Powerful toolslViral proteins (retrotranscriptase, RT-PCR and

Cre recombinase, homologous recombination and genetic modification)lDelivery tools: Transfection and overexpression

(viral vectors, adenovirus, lentivirus) and viruses mediated therapy

Example: RetrovirusReverse transcriptionReverse transcriptase

G U A A U C C U CAAAAAAAAAAAAAAAReverse

transcriptase

mRNA

cDNATTTTTTTTTTTTTTT

逆转录polyT引物

Retrotranscription in Tubes

RTase

RT-PCR

Example: Cre-Loxp and Gene Modification

• Cre recombinase: a DNA recombinase from bacteriophage P1• Loxp site: a 34-bp DNA sequence

5' - ATAACTTCGTATA - ATGTATGC - TATACGAAGTTAT - 3'

3' - TATTGAAGCATAT - TACATACG - ATATGCTTCAATA - 5'• Genetic manipulation

Example:Gene Therapy

There are an estimated 1031 viruses on Earth. That is to say: there

may be a hundred million times more viruses on Earth than there

are stars in the universe. The majority of these viruses infect

microbes, including bacteria, archaea, and microeukaryotes, all of

which are vital players in the global fixation and cycling of key

elements such as carbon, nitrogen, and phosphorus. These two facts

combined—the sheer number of viruses and their intimate

relationship with microbial life—suggest that viruses, too, play a

critical role in the planet’s biosphere.

Key Points

1. Definition (living or nonliving is a question)

2. Structure

3. Amplification/life cycle

4. Illness and treatments, anti-viral drugs and vaccines

5. Contributions to biological research

References:

1. Must read: Campbell Biology: P427-441

2. May read: • Takashi Yamada, Giant viruses in the environment: their origins and

evolution, Curr Opin Virol. 2011 Jul;1(1):58-62.

• Thorsten Demberg and Marjorie Robert-Guroff, Controlling the HIV/AIDSepidemic: current status and global challenges, Front Immunol. 2012;3:250.

• Philippe N, Legendre M, Pandoraviruses: amoeba viruses with genomes up to 2.5 Mb reaching that of parasitic eukaryotes. Science. 2013, 341:281-6.

• Legendre M, et al. Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology. PANS, 2014

• http://www.nature.com/news/giant-virus-resurrected-from-30-000-year-old-ice-1.14801

References:• Viruses, chapter19

• How many mammalian viruses? (http://www.the-scientist.com/?articles.view/articleNo/37327/title/How-Many-Mammalian-Viruses-/)

“In my life time, we might be able to find every mammalian virus that might infect us,” said Daszak. “And once you know your enemies, you can start to do something about them.”

• Mark Woolhouse, Fiona Scott, Zoe Hudson, Richard Howeyand Margo Chase-Topping. Human viruses: discovery and emergence. Phil. Trans. R. Soc. B, vol. 367 :2864-2871

(There are 219 virus species that are known to be able to infect humans. )

References:

Going ViralFrom therapeutics to gene transfer, bacteriophages offer a sustainable and powerful method of controlling microbes. (http://www.the-scientist.com/?articles.view/articleNo/37208/title/Going-Viral/)

Ebola Virus

• SSRNA

• Envelop, matrix nuclecapsid

• Replication

• First break in 1976

• Symptoms resemble malaria, hemorrhagic fever

Poliovirus（脊髓灰质炎病毒）

• ssRNA, serves as mRNA

• Isolated at 1909 and sequenced at 1981

• Poliomyelitis or infantile paralysis

• Poliovirus receptor (CD155), endocytosis

• One long polypeptide for 10 proteins

• Each dying cell can release up to 10,000 polio virions.

Polio Vaccines

• 1948, John Enders and Thomas Weller

（1954 Nobel，病毒学研究）

• 1952, Salk vaccine, inactivated

（沙克疫苗）

• 1950s-60s, Oral vaccine, worldwide

（沙滨疫苗）

Countries

Year-to-date 2012 Year-to-date 2011

Total in2011*

Date of mostrecent caseWPV1 WPV3 W1W

3 Total WPV1 WPV3 W1W3 Total

Nigeria 67 16 83 19 7 26 62 15-Aug-12

Pakistan 26 2 1 29 76 1 77 198 21-Jul-12

Afghanistan 17 17 18 18 80 21-Jul-12

India 1 1 1 13-Jan-11

Chad 5 5 106 3 109 132 14-Jun-12

DR Congo 76 76 93 20-Dec-11

Angola 4 4 5 07-Jul-11

Niger 1 1 2 5 22-Dec-11

CAR 4 08-Dec-11

China 4 4 21 09-Oct-11

Guinea 2 2 3 03-Aug-11

Kenya 1 1 1 30-Jul-11

Côte d'Ivoire 35 35 36 24-Jul-11

Mali 7 7 7 23-Jun-11

Congo 1 1 1 22-Jan-11

Gabon 1 1 1 15-Jan-11

Total 115 18 1 134 308 56 0 364 650Total in endemic countries 110 18 1 129 114 8 0 122 341

Total

Data in WHO as of 06 Sep 2011 for 2011 data and 04 Sep 2012 for 2012 data.

Case breakdown by country

1988, 350000 cases