Chapter 6 Microbiology 2460

Viruses

Obligate intracellular and acellular pathogens.

Do not have cells but possess genetic materials.

Microscope used to observe Viruses

TEM/SEM

What part of the host cell do virus’s hijack

Cellular machinery

Why are virus’s not included in tree of life,

Because they do not have cells or ribosomes to grp genetically

Host or Cell type specificity

a particular virus can only infect certain types of cells within a specific host organism.

Where is the genetic material of virus

surrounded by capsid

T or F

Virus usually have DNA or RNA not both

TRUE

Bacteriophages

Kind of virus that can infect eukaryotes or prokaryotes

Infection of virus can be obtained: Direct contact

From infected individual

Infection of virus can be obtained: Indirect w/ fomites

Eating utensil, doorknobs, bedding, etc.

Infection can be obtained: Mechanical vector

organism carries the virus on outside of body cockroaches, flies, etc.

Infection can be obtained: Biological vector

organism carries virus inside (ticks, mosquitoes, biting flies, etc.)

Virions

Viral particles assembled in infected host cells

Range of size for virions

20-900nm

Dmiti Ivanoski

Created Chamberland filter used porcelain to filter out virus with 0.1 μm pores, now used to remove all material except viruses from cell cultures.

Component of Viruses:

capsid (capsomere-subunit),

Genomic material (rna or dna),

envelope and spikes (not all have)

What is used to classify Virus’s

Capsid Shape, Envelope and Genomic material

Type of Capsid shape this Virus exhibits?

Helical

Type of Capsid shape this Virus exhibits?

Icosehedral

Type of Capsid shape this Virus exhibits?

Complex

Where is Virus genome

Polyhedral head (USUALLY DNA)

What does the bacteriophage virus use to attach to bacterial host

Tail fibers and pins

Viral grouping: Naked Viruses

Capsid only with not envelope

Viral grouping: Viral envelope

Phospholipid membrane surrounding capsid

Viral grouping by genomic material

Single stranded DNA and RNA

Double stranded RNA and DNA

Who maintains “taxonomy” of viruses not in tree of life but still needing classification

International Committee on Taxonomy of Viruses (ICTV)

ICTV classify virus based on ?

genetics, chemistry, morphology, & mechanism for replication

With the use of binomial nomenclature with Virus’s the Family is

Virdiae

With the use of binomial nomenclature with Virus’s the genus is

Virus

Ttl Number of Orders families and genera of Virus

7 orders, 96 families & 350 genera

ID this Virus with spikes and genomic RNA

Sever acute respiratory syndrome coronavirus 2 SARS-CoV-2

ID this Virus containing Neuraminidase, no spikes, and RNA nucleoprotein.

Inflluenza Virus

Norovirus

Under caliciviridae family

is a foodborne virus causing gastroenteritis

Naked +single stranged RNA

The goal of Virus

Invade host cell, hijack machinery to make proteins and replicate

____________ have been a model for viral life cycle studies

Bacteriophages

Virulent phages

This virus life cycle phage lead to death of host cell thru lysis

Temperate (latent) phages

This virus life cycle phage become part of host genome until induced to start making viral particles

In Host #1 what phages occur

Temperate → virulent phage

In host #2 what viral phages occur

Temperate phage

Describe the Lytic cycle of virulent phages

This cycle starts by:

the phage attaches (Attachment) to host surface and viral DNA entering host cell (Penetration)→

Phage DNA then replicates (biosynthesis) making phage proteins resulting in new phage particles (maturation) →

(3) Eventually lysis releases the newly made phages (lysis)

Describe the Lysogenic virulent phages

This phage starts by:

The phage infects a cell and DNA becomes incorporated into host genome → The cell divides and prophage DNA is passed on to daughter cells → Under stressful conditions DNA is excised from bacterial chromosome and enters the lytic cycle →

Phage DNA then replicates (biosynthesis) making phage proteins resulting in new phage particles (maturation) → Eventually lysis releases the newly made phages (lysis)

What can contribute to virulence; as seen in V cholerae and C. botulinum being less virulent w/o phages due to missing toxin genese

Lysogeny

Phage Transduction

Genetical material can be transferred btw bacterial cells via this

Generalized transduction

DNA is random when transferred during lytic cycle

Specialized transduction

Occurs at end of lysogenic cycle and can transfer host DNA too.

During the excision stage of Specialized phage transduction what occurs

The phage is excised from the bacterial chromosome along with short piece of bacterial DNA, The DNA is then packaged into newly formed capsids

During the Infection stage of Specialized phage transduction what occurs

Phage containing both viral and bacterial DNA infect a new host cell.

During the recombination stage of Specialized phage transduction what occurs

The phage DNA along with attached bacterial DNA are incorporated into new cell.

The Eukaryotic viruses are like 5 stages of phage life cycle EXCEPt

mechanism of penetration, nucleic acid biosynthesis and release of viral particles (lysis or budding)

During influenza life cycle how does the cell take in the virus

Endocytosis

After the Influenza virus has successfully tricked the cell to engulf does it goes to the nucleus to be

replicated by the viral rna polymerase

What is used to make viral proteins during the life cycle of influenza virus

Viral mRNA

During the influenza life cycle where does the new viral particle go after being made

released into the extracellular fluid

How are bacteriophage life cycle different from Eukaryotic virus life cycle of influenza

The cell is not killed (lysed) but continues to make new virus

What dictates how protein and nucleic acid are replicated in Eukaryotic virus’s

The 4 types of genomes

When virus has Double stranded DNA what occurs during biosynthesis

normal flow of host cell

When virus has single stranded DNA what occurs during biosynthesis

complementary strand is synthesized and then normal flow occurs

When virus has POSITIVE single stranded RNA what occurs during biosynthesis

Acts like normal mRNA and delivers piece of mRNA that corresponds to a viral protein into a person’s cell and makes ribosomes which produce viral protein.

+ssRNA virus examples

SARS COv-2, HIV

When virus has NEGATIVE single stranded RNA what occurs during biosynthesis

-ssRNA is converted to +ssRNA through special RNA polymerase and then delivers piece of mRNA that corresponds to a viral protein into a person’s cell and uses ribosomes to make more viral proteins

What is the special RNA polymerase that converts -ssRNA to +ssRNA

RdRp= viral RNA-dependent RNA polymerase

T or F -ssRNA can alternate btw positive and negative using RdRP ViralRNA dependent RNA polymerase

TRUE

Example of -ssRNA virus’s

Influenza and Ebola

Retroviruses

+ssRNA viruses, single stranded RNA viruses such as HIV.

Exhibit an alternative mechanism for viral nucleic synthesis

Reverse transcriptase

+ssRNA virus such as HIV carry this special enzyme within the capsid; it synthesizes a complementary ssDNA copy using +ssRNA genome as a template.

Ultimately allowing the ssDNA to be made into dsDNA which integrates into host cell and becomes a permanent part of the host

Provirus

Integrated viral genome of a retrovirus that can remain in the host cell or a long time to establish a chronic infection and does not undergo excision after splicing into the genome.

Persistent infection

occurs when a virus is not completely cleared from the system of the host but stays in certain tissues or organs of the infected person. eg latent and chronic infection

Latent Infection

type of Persistent infection whereby virus remain hidden in host cell after initial infection eg. Herpes simplex virus

Chronic infection

Type of persistent infection that occurs when host cannot successfully eradicate virus, HIV become chronic after latency period.

T or F

Plant viruses are more similar to eukaryotic viruses than prokaryotic viruses

TRUE

Most plant viruses have what type of genetic material

+ssRNA genomes

How are most plant plant viruses transferred

Via insect or fungal mechanical vectors.

Viruses do not grow on their own but growth can still be measured; when does the number of infectious virions peak?

When host cells burst and release viral particles

When virus’s are grown in an organism either bacterial or animal cell cultures this is called ?

in vivo

When Virus’s are grown in vitro outside of an organism this is called

In vitro

Why do we grow animal virus cultures

ID pathogenic viruses, produce vaccines and for basic virology research

What animals or embryos can be used as incubators for viruses (in vivo)

eggs

When the influenza vaccine is being produced researchers infect flu strain 1 and 2 into chicken egg which produces many gene combinations, why is this important?

Can be used to predict the next influenza strain

Primary cell lines

Used for in vitro growth of viruses, whereby lines are obtained from desired tissue and cells are grown in petri dishes to allow attachment.

During In vitro growth in petri dishes mitosis is allowed to continue but is limited due to

Contact inhibition.

He La cell

Immortal cell line obtained from cervical cancer patient Henrietta lacks in 1951 these cells continued to grow and did not undergo contact inhibition.

This method of virus detection use observable cell abnormalities such as Loss of adherence, Change to cell shape, Shrinkage of nucleus, Vacuoles formed, Fusion of cytoplasmic membranes to form multiple
nuclei, Inclusion bodies and Cell lysis (death)

Cytopathic effects CPEs

Which type of virus does CPE detect faint basophilic cytoplasmic inclusion bodies

Paramyxovirus

Which type of virus does CPE detect pink eosinophilic cytoplasmic inclusion bodies arrows and cell swelling

Poxvirus

Which type of virus does CPE detect cytoplasmic stranding arrow and nuclear inclusion bodies (dashed arrow)

Herpesvirus

Which type of virus does CPE detect, cell enlargement rounding and distinctive grape-like clusters.

Adenovirus

Hemagglutination Assay

Type of Detection of virus or antibodies from patient serum, either observes clumping (agglutination) of red blood cells

Some rapid COVID tests are agglutination

What is the positive outcome of a HIA test (detection of virus)

Hemagglutination

Nucleic Acid test

Taking by a nasal swab and results in Both PCR and RT-PCR used to detect and confirm the presence of the viral nucleic acid in patient specimens.

polymerase chain reaction (PCR) for DNA

reverse transcriptase PCR for RNA

What is the gold standard for covid infection

RT-PCR

Enzyme-linked immunoassay (ELISA)

This Virus Identifier relies on the ability of antibodies to detect and attach to specific biomolecules called antigens with a high degree of specificity, colorless enzyme attached to the detecting antibody.

The enzyme acts as a tag on the detecting antibody and can interact with a colorless substrate, leading to the production of a colored end product.

Other acellular pathogens that are not viruses

Viroids, Virusoids and Prions

Viroids

Virus-like but not virus.

Circular RNA that can self replicate (No DNA conversion and no protein coating, capsid) eg. potato tuber spindle disease.

Virusoids

A second type of pathogenic RNA that can infect commercially agricultural crops. they require that the cell also be infected with a specific “helper” virus. eg. subterranean clover mottle virus

T or F

Prions have genomic material

FALSE

Prions

No genomic material; misfolded proteins that can cause others to become misfolded. eg transmissible spongiform encephalopathy (i.e.
mad cow disease)