Micro chapter 6

•AstraZeneca/Oxford University clinical trials in the United Kingdom include children and the elderly

-A genetically modified adenovirus that cannot replicate in humans has been engineered to produce the SARS-CoV-2 spike protein

•Middle Eastern Respiratory Syndrome (MERS) appeared in 2012 •First patient from Jeddah, Saudi Arabia •Zoonosis - Camels to People •Nosocomial "Hospital" infections Present with severe )______ _____ diseases

Respiratory, kidney

•Types of diagnostic tests available: 1 diag test •PCR test - this was the first available test; it amplifies and detects ___ ______ _____ (RNA) if present in a person's secretions collected with a swab -Advantages: accurate if sample is taken approximately 3+ days post-exposure, option of at-home saliva test limits need for healthcare provider wearing PPE -Disadvantages: may not catch early infections, takes several days for results, rapid tests (results in less than an hour) lack accuracy

Viral genetic material

1 Diag test Antigen test - this is a newer test that detects ____ ______(those that act as antigens) vs. _____ ______ -Advantages: results in a few minutes, good screening tool -Disadvantages: not as accurate as PCR test

Viral proetins Genetic material

Entry to host: •Once transmitted, _________ bind to host cells via angiotensin-converting enzyme 2 (ACE2) (viral tropism). •The physiological functions of ______ include ______ ______ _______, controlling fluid balance, and regulating the inflammatory response. •ACE2 proteins are present in many tissues, including lungs, kidneys, heart, arteries, and the gastrointestinal tract. •Multicellular tropism accounts for the high rate of infectivity. •S-proteins embedded in viral envelope bind to ACE2 on host cells, which triggers either viral endocytosis, or membrane fusion and viral genome entry.

Viral-S protein ACE2 Lowering blood pressure

•Most DNA viruses use the ________as their genome but some may have ssDNA genomes •Few RNA viruses have ______ genomes -Polio, TMV, SARS, rabies, mumps, measels, influenza, HIV, are all ssRNA viruses

dsDNA dsRNA

•A 61 year old man presents to the hospital in Wuhan China on December 27th. •Reports _____,_____ beginning on Dec 20th. •_________ __________ increased over previous 2 days. •Patient was placed on a .

fever,cough Respiratory distress Mechanical ventilator

Capsids are

helical •Shaped like hollow tubes with protein walls •Protomers self assemble •Size of capsid is a function of nucleic acid Example: Tobacco mosaic virus Can have enveloped helical struc, example influenza icosahedral •An icosahedron is a regular polyhedron with 20 equilateral faces and 12 vertices complex -do not fit into the category of having helical or icosahedral capsids -large bacteriophages - binal symmetry •head resembles icosahedral, tail is helical

All virions contain a nucleocapsid which is composed of

nucleic acid (DNA or RNA) and a protein coat (capsid) -some viruses consist only of a nucleocapsid, others have additional components need electron micro to see this

Virion Genome

•Diverse nature of genomes •A virus may have single or double stranded DNA or RNA •The length of the nucleic acid also varies from virus to virus •Genomes can be segmented(more than one piece of linear RNA)/unsegmented or circular Size is gonna vary from virus to virus (genome to genome)

Role of viral envelope protein:

•Envelope proteins, which are viral encoded, may project from the envelope surface as spikes or peplomers -involved in viral attachment to host cell •e.g., hemagglutinin of influenza virus -used for identification of virus -may have enzymatic or other activity •e.g., neuraminidase of influenza virus may play a role in nucleic acid replication

•Viral Life Cycle (Simplified)

-Adsorption (aka attachment to host) -Entry into Host •Enveloped viruses will fuse their envelope with the host PM •Nonenveloped viruses can trigger receptor mediated endocytosis -Synthesis of Viral Genome •Can be done by host polymerases (DNA viruses) or by viral polymerases (RNA viruses) -Assembly of Viral proteins •Late proteins (aka the capsid proteins) are transcribed and translated to build the virions -Release •Occurs by budding or lysis

•Novavax Inc. has a vaccine in clinical trials in Australia

-Harmless copies of the spike protein are synthesized and extracted from insect cells, then packaged into nanoparticles for delivery via vaccine

•Moderna Therapeutics began clinical trials in the United States in March 2020

-Injects mRNA enclosed in a lipid nanoparticle, rather than a protein product, allowing the host cells to make the viral protein for recognition by the immune system

•Types of viral genomes

-dsDNA -ssDNA -ssRNA -dsRNA

•Most are eukaryotic viruses? •Classified into families based on?

-plants, animals, protists, and fungi -genome structure, life cycle, morphology, genetic relatedness, function

Virion size range

10-400 nm

SARS-CoV-2 belongs to the genus _______, family ________

B-Corona virus, Coronaviridae

•Extensive _______of virus particles leads to apoptosis and death of alveolar cells. •Non-specific immune cells release _________that stimulate a targeted attack on the infected cells, crippling normal cell function (stage 3). •In critical cases, a "______ _______" an overreaction by the immune system, causes immune cells to attack healthy tissues. •As of May 2020, the link between the virus and the occurrence of multisystem inflammatory syndrome in children (MIS-C) has not been elucidated.

Exocytosis Chemokines (Signal) Cytokine storm

•Progeny are released from cells through _________, and infect nearby cells. •Immune system triggers inflammatory response (stage 2). If not blocked by the immune system, virions migrate to the ______ ______ ______where they infect _______ _______ ______ _______ (gas exchange units) that are rich in ________ proteins

Exocytosis Lower respiratory tract Alveoli type 2 cells ACE2

•Stage 3 - Lower airway •Around 20% of patients progress to ____ ______ •Virus infects alveolar type 2 cells preferentially over type 1 •Viral infection leads to aleveolar cell apoptosis •Alveolar cell death triggers dysregulated wound healing marked by fibrin rich regions and formation of occasional multinucleated cell masses •Patient develops _____ ______ ______ _____ _____ (ARDS)

LRT infection Acute resp distress syndrome

•Once inside the host cell, the virus takes over the replicative ________ _____ ________ within the cell (stage 1). •Direct damage to the infected cell includes _______, detachment, degeneration, and ______ ______.

Machinery and multiplies Rounding, Syncytium formation

•______________ originated from a _____ ______ with direct transfer to humans.

Mers-COV Camel Reservoir

Bacterial viruses called

bacteriophages

Both SARS-CoV and SARS-CoV-2 likely originated from _______ as the reservoir, with _____ ________as intermediate hosts between bat and human

bats, small mammals

•Basic Reproductive Number (R0)

capacity to spread can be quantified - it is given an R0 ("R naught") value, which represents the number of individuals that can be infected from one single person. R0 is not a constant number, it can vary depending on the environment (for example, population density) •R0 of less than 1 suggests a disease will ultimately die out in a population.

SARS COV2 Reservoir: •Human coronaviruses are _________ and the natural host for many are bats

zoonotic •Chinese Rhinolophid bats •Chinese horseshoe bats

The World Health Organization (WHO) named the novel coronavirus that causes the disease COVID-19"_________ _________ _______ _________" (SARS-COV2)

severe acute respiratory syndrome coronavirus 2

Virion enzymes:

some are associated with the envelope or capsid but most are within the capsid

•Organs/systems affected in critical care patients

•Eyes - conjunctivitis more common in critical patients •Nose - patients lose their sense of smell from viral damage of nerve cells in the nasal passage •Lungs - inflammation and breakdown of alveolar walls restrict oxygen uptake and delivery •Liver - overactive immune system and therapeutic drugs affect liver enzymes •Kidneys - damage is common in severe cases either from direct viral attack or multisystem organ failure •Cardiovascular system - virus directly infects cells that have ACE2 receptors leading to clots, inflammation, and heart attacks •Brain - some patients experience confusion, seizures, inflammation, strokes •Intestines - GI tract is rich in ACE2 receptors; 20% of patients experience diarrhea

•1965 Tyrell and Bynoe isolated the first coronavirus •Tyrell, McIntosh struggled to grow virus in cell culture (in the lab) and progress was slow.

•Isolated from URT of young boy. •Grown and studied by infecting volunteers •Eventually they grew the viruses in the brains of still nursing baby mice. •Finally the virus adapted to lab cell culture.

Capsid role

•Large macromolecular structures which serve as protein coat of virus •Protect viral genetic material and aids in its transfer between host cells •Made of protein subunits called protomers

Viral Envelopes and Enzymes

•Many viruses are bound by an outer, flexible, membranous layer called the envelope •Animal virus envelopes (lipids and carbohydrates) usually arise from host cell plasma or nuclear membranes -Few proteins embedded on envelope to help with attachment -Protein spike, helps attach to host cell. examples: rabies and Herpesvirus

Entry into the Host:

•Portals of entry include: •Nasal and oral passages of the respiratory tract •Conjunctiva of the eyes passing through nasolacrimal duct •Oral cavity and esophagus

Coronaviridae History: •Originally, only two human coronaviruses discovered, but dozens of animal coronaviruses were soon described

•Rats, mice, chickens, turkeys, cats, rabbits, pigs, bats... •Though Coronavirus was highly infectious, the severity of the disease was low.

•Direct transmission of bat SARS-like CoVs to humans is difficult unless they are adapted in another animal host

•SARS - Civet cat •MERS - Camel Bats=animals=human

•SARS-CoV-2 Charc

•The S proteins protrude from the viral surface resembling a crown, or corona •It is comprised of four main structural proteins: •spike (S) glycoproteins •envelope (E) glycoproteins •membrane (M) glycoproteins •nucleocapsid (N) proteins

The genome also codes (SARVS-COV2)

•for 16 nonstructural proteins that are involved in viral replication, maturation, and release.