VIRO M1 | History of Virology, Nature & Origin of Viruses

T/F: Everyone is infected with viruses all the time

TRUE

Viruses are part of our microbiome

Why do we study viruses?

Primarily because they are agents of disease and could have worldwide consequences, trickling down to societal issues

T/F: There were no historical records of viral diseases before viruses were identified

FALSE

There are a lot of historical records of viral diseases before viruses were even identified

Enumerate 3 examples of historical records proving existence of viral diseases even before viruses were even identified

1. Temple Priest Sipta 1400 BC

   1. Hieroglyph portraying withered leg of Priest Sipta, most likely Poliovirus

2. Pharaoh Ramses V 1196 BC

   1. Pustules on face, resembling small pox (DNA identified)

3. Inca emperor Atahuallpa and Spaniard Francisco Pizzaro 1532

   1. Small pox lead to the downfall of many civilizations, e.g., Central and South America. When Spaniards and Portuguese went to America, they spread small pox in those civilizations that have never contracted the disease before and thus have no immunity to it, contributing to the success of the said civilization in colonizing those countries

There is _ HIV-1 genomes existing on this planet, and it is highly probably that there exists a genome which encodes resistance to each one of the antiviral drugs available

10⁶ (1 million)

Describe HIV & AIDS surveillance in Ph from Jul-Sep 2024

• Average no. of cases per day =

• No. of males infected =

• No. of females infected =

• Jan. 1984 - Sep. 2024 (total) =

  • Newly reported cases =

  • Advanced HIV cases =

• Age group with highest incidence =

• Region with highest incidence =

• Average no. of cases per day = 50

• No. of males infected = 4K

• No. of females infected = 200+

• Jan. 1984 - Sep. 2024 (total) = 139K

  • Newly reported cases = 4K

  • Advanced HIV cases = 1K

• Age group with highest incidence = 25-34 yo (47%)

• Region with highest incidence = NCR

Type of genome HIV has

RNA

T/F: DNA genomes evolve more quickly than RNA genomes

FALSE

RNA genomes evolve more quickly than DNA genomes bc there is no proofreading and editing

Vector-borne tropical diseases, e.g., Zika, Dengue, Chikungunya, are now spreading to the northern and southern hemispheres due to _

climate change (global warming)

Over the past decade, _ has made its way home at increasingly higher latitudes, partly due to climate change

Aedes albopictus (Asian tiger mosquito)

_ is the vector of chikungunya and dengue viruses and is also suspected to carry other pathogens, including Japanese encephalitis and West Nile viruses

Aedes albopictus

Explain how people tried to control viral disease earlier in history

• 2-3% of individuals receiving variolation ended up dying from from small pox

• The only reason variolation practice continued was because the chance of dying from small pox caught “naturally” from another infected person was higher, i.e., 15-20%

• Lady Mary Wortley Montagu introduced practice of variolation from Turkey to political elites back in Europe

_ is hailed one of the greatest scientific discoveries that contributed to the longevity of human life

Vaccination

_ is an early immunization method against small pox involving deliberately introducing material from small pox sores from an infected person to a healthy individual, usually by inhalation or inserting it into a small cut in the skin

Variolation

Who started a more modern protocol for vaccination in 1796?

Edward Jenner

Explain Edward Jenner’s more modern approach to vaccination in 1796

• Jenner took material from cowpox sore in milkmaid’s hand and inoculated it to an 8-yr old kid, Phipps

• After Phipps recovered from mild cowpox, Jenner then exposed the kid to smallpox, and he did not develop the disease

• Conclusion: Exposure to cowpox conferred immunity to smallpox, proving effectiveness of vaccination (“vacca” = cow)

Small pox vaccine is delivered via _

multiple punctures using special 2-pronged needle (inset) dipped in the vaccine

Describe administration of small pox vaccine

1. Drop of vaccine is held in the fork of the needle

2. Needle is held perpendicular to the arm

3. Wrist of vaccinator rests on the arm of person to be vaccinated

_ is the very first disease eradicated worldwide by vaccination in 1980

Small pox

_ are the only people left vaccinated with small pox

Military since there still stands a possibility that small pox virus may be used for bioterrorism

_ lead to the downfall of many civilizations, including Central and South Americas, because when the Spaniards and Portuguese (i.e., Inca emperor Atahuallpa, Spaniard Francisco Pizzaro 1532) went to the America, they spread small pox virus to civilizations who never contracted the disease before and thus have no immunity against it. Hence, this viruses is considered to contribute to their success in colonizing those countries.

Small pox virus

Poliovirus was also on its way on being eradicated, but there was a reemergence around _ (year)

2017-2019

Poliovirus outbreak in 2017-2019 were preceded by early childhood diseases, including _

mmr

• Measles

• Mumps

• Rubella

• The largest outbreak in the WHO Western Pacific region occurred in the Philippines, where _ in 2018

• Reported cases of measles from

  • 2017 =

  • 2018 =

  • 2019 =

• first-dose measle-containing virus (MVC1) coverage had reduced to 75%

• Reported cases of measles from

  • 2017 = 2K

  • 2018 = 20K

  • 2019 = 48K

There was a dramatic drop in public confidence after the Philippine dengue vaccine controversy in 2018, with _% people strong agreeing that vaccines are important in 2015 to only _% by 2018

• 93% strongly agree in 2015

• 32% strongly agree in 2018 (drop due to dengvaxia crisis)

In Feb. 2018, DOH reported that only around _% of children across the country got their scheduled vaccines, lower than their 85% target

60%

From Jan. 1 to Aug. 25, 2018, MMR cases were _% higher than the number of cases reported during the same period in 2017

419%

_ % of individuals receiving variolation ended up dying from small pox, but variolation practice continued because the chances of dying from small pox caught “naturally” from another person was higher, i.e., _ %

• 2-3 %

• 15-20%

_ introduced practice of variolation from Turkey to political elites back in Europe

Lady Mary Wortley Montagu

A series of nationwide surveys shows that Filipinos are hesitant to receive COVID19 vaccines, with almost _ of Filipinos not willing or unsure whether they should be vaccinates.

*The level of hesitancy is higher in Ph compared w/ other countries in the region

half

Enumerate factors cited as reasons for hesitancy on getting vaccinated (2015-2019)

• Lack of information about vaccines

• Misinformation about their efficacy / side effects

• Mistrust

• Underestimation of their benefits and overestimation of their risks

• Survey results show that highlighting _ of vaccination had a signficant impact on reducing vaccine hesitancy and increasing vaccine acceptance by almost 15%

• This suggests that communication campaigns highlighting the potential benefits of _ by emphasizing the prospect of holding family gatherings again and protecting families can significantly reduce vaccine hesitancy in the country

• personal and social benefits

• herd immunity and vaccines

• Although African swine fever (ASF) doesn’t harm humans, outbreaks have caused significant economic losses in various countries, including the Philippines, where a 2019 outbreak lead to the culling of _

• Pork production decreased by _ in 2021, leading to higher pork prices and affecting livelihoods of many consumers

• 300,000 pigs

• 20.8%

_ is very important when it comes to viral diseases such as avian influenza

Surveillance in areas where there’s congregation of migratory birds in close contact to domesticated animals, e.g., duck farms

Example of viral disease affecting both domesticated animals and humans

Foot and mouth disease

How did Avian flu enter Philippines?

Through smuggled poultry

Over 60% of all emerging infectious diseases worldwide are of _ origin

zoonotic (spread by animals)

T/F: Over time, the broken tulips virus causes bulb to weaken and thus inhibits proper reproduction

TRUE

With each new generation, the bulb grows weaker and weaker, until it has no strength left to flower and withers away

T/F: All viruses cause disease

FALSE

Not all viruses cause disease, though it is easier to study disease-causing viruses bc there is an outward signal of infection

T/F: Viruses are everywhere and infect all cellular life forms

TRUE

_ are by far the most abundant biological entities in the ocean, comprising approximately 94% of the nucleic-acid-containing particles, but because of their small size, they only comprise ~5% of the biomass

Viruses

In contrast, while _ only represent less than 10% of nucleic-acid-containing particles in the ocean, they represent more than 90% of the biomass

Prokaryotes

T/F: There is no living organism not infected by viruses

TRUE

There are even viruses infecting other viruses, i.e., virophages

Describe human body in terms of cell composition

• 1 trillion human cells in our body

• 10 trillion bacterial cells

• 100 trillion viral particles, which make us

• 0.01% human, 0.1% bacterial, 99.89% viral

T/F: Viruses are by far the most abundant biological entities in the ocean, comprising 94% of the biomass

FALSE

Viruses are by far the most abundant biological entities in the ocean, comprising 94% of the nucleic-acid-containing particles, only ~5% of biomass because of their small size

Describe human body in terms of genome composition

• 4% eukaryotic

• 10% bacterial

• 68% viral (virome)

• 15% unknown

• 4% other sequences

Explain the nucleotide sequence content of the human genome

Even in human genome, we carry fossils of viral DNA segments

• Repeated sequences

  • Segmental duplications

  • Simple sequence repeats (SSRs)

  • Transposons

    • DNA-only transposon fossils ~42%

      • Nonfunctional DNA remnants that were once capable of moving but now are inactive

    • Retroviral-like elements

    • SINEs (Short Interspersed Nuclear Elements) 30%

      • Cannot encode proteins but propagate using enzymes produced by LINEs

    • LINEs (Long Interspersed Nuclear Elements) 20%

      • Can copy and insert themselves elsewhere in the genome

• Unique sequences

  • Non-repetitive DNA (neither in introns or codons) 60%

  • Genes

  • Introns 98%

  • Protein-coding regions (exons) 100%

Viruses are becoming more widely recognized as _, with metagenomic studies suggesting that _

• shuttles of genetic material

• the billions of viruses on Earth harbor more genetic information than the rest of the living world combined

Explain Hershey-Chase experiment (1952) using bacteriophages

Hershey & Chase, using bacteriophages, established that DNA is the genetic material

• Bacteriophages (bacteria-infecting viruses) have 2 components:

  • DNA inside

  • Protein coat outside

• They labeled DNA with 32P (phosphorus) and protein coat with 35S (sulfur), then infected bacteria with bacteriophages

• After infection, they blended and centrifuged mixture to separate viral particles from DNA

• Results: They found the 32P (phosphorus) label inside bacterial cell, while 35S (sulfur) stayed outside, suggesting that DNA is the genetic material

Enumerate major discoveries/breakthroughs we’ve had using viruses

• Hershey-chase experiment using bacteriophages to establish DNA as the genetic material

• Used viruses to study eukaryotic gene expression, specifically introns, exons, splicing discovery

• Used viruses to study prokaryotic gene expression, transcription factors, roles of enhancers, 5’ cap, internal ribosomal elements

Enumerate 5 utility of viruses (elaborate on the first one)

• Vectors for recombinant protein production; biopharmaceuticals

  • General steps to recombinant protein production

    • Harvest cells from a patient

    • In lab, alter virus to prevent it from reproducing

    • Then insert gene of interest into the altered virus

    • Mix altered virus + harvested patient cells, altering harvested patient cells in lab

    • Inject altered cells into patient’s body, so that altered cells produce the desired protein

• Vectors for treatment of genetic disease

• Source of enzymes, e.g., reverse transcriptase, RNA polymerases

• Phage typing of bacteria

• Pesticides (Baculovirus, Myxoma virus)

Describe the Global Virome Project and their targeting strategy

• Global Virome Project (GVP) is an international initiative aiming to understand the diversity of viruses in the animal kingdom, particularly those with potential to cause pandemics

  • Its goal is to predict and prevent future viral outbreaks by studying viruses circulating in wildlife and their likelihood of spilling over into human populations

• Targeting strategy

  • GVP will capitalize on economies of scale in viral testing, systematically sampling mammals and birds to identify currently unknown, potentially zoonotic viruses they carry

  • 111 viral families have been discovered to date

  • Of 111, GVP plans to target 25 viral families containing viruses known to or have the substantial risk to infect people

  • Of 25 families, 1.67M unknown viruses exist in mammals and birds, which are hosts with 99% risk for viral emergence

  • Of 1.67M, an estimate of 600,000 - 800,000 likely have capacity to infect people

• Site: 5-hectare land in New Clark City

• Site development and construction of facilities to be financed by DOST

• Project to be completed in 6 yrs

• What’s inside: Administration building, lecture hall, manufacturing product building, human and animal virology lab, plant virology lab, animal isolation, BSL 3 and 4 lab building, plant cultivation area, dormitory, power station, sewage treatment plant

Virology Institute of the Philippines (VIP)

Explain why virus discovery is no longer just driven by disease

• The advent of metagenomics using high throughput sequencing has revolutionized not only the rate of virus discovery but also the nature of the discoveries.

• For example, vnd

  • viral ecology and etiology of human diseases are being characterized,

  • nonpathogenic viral commensals are ubiquitous, and

  • description of environmental viromes is making progress.

Ongoing projects in Virology Institute of the Philippines (VIP)

• Detection of food- and waterborne bacterial pathogens using phage-based diagnostics

• Combination therapy: Lytic bacteriophages and plant extracts against multi-drug resistant bacteria

• Isolation and purification of Philippine common viruses with medical importance and pandemic potential for antigen-antibody studies

Enumerate and explain 3 significant people in microbiology and their contributions

• Antonie Van Leeuwenhoek (1632 - 1723)

  • First to describe cells “animalcules” with microscope

• Louis Pasteur (1822 - 1895)

  • Disproved spontaneous generation using swan-necked flask

  • Pasteurization to get rid of undesirable microbes in milk

• Robert Koch (1843 - 1910)

  • Koch’s postulates for linking disease to microbes

Explain Koch’s postulates (1890)

1. The microorganism should be found in abundance in all organisms suffering from the disease but should not be found in healthy organisms

2. The microorganism should be isolated from the diseased organism and grown in pure culture

3. The cultured microorganism should cause the same disease when inoculated into a healthy organism

4. The microorganism should be re-isolated from the diseased experimental host and identified as identical to the original specific causative agent
   

*While Koch’s postulates were essential for defining many agents of disease, not all pathogenic viruses fulfilled these criteria

Explain how not all pathogenic viruses fulfill Koch’s postulate

1. The microorganism should be found in abundance in all organisms suffering from the disease but should not be found in healthy organisms

   1. Not observed when HIV has already integrated its genome into host

   2. Chicken pox virus can cause shingles when you’re older

2. The microorganism should be isolated from the diseased organism and grown in pure culture

   1. Can’t be grown in pure culture, needs a host!

3. The cultured microorganism should cause the same disease when inoculated into a healthy organism

   1. Not all the time

4. The microorganism should be re-isolated from the diseased experimental host and identified as identical to the original specific causative agent

• Common definition of virus

• “Virus” acc to Louis Pasteur means

• Obligate intracellular parasites

• “Virus” = poison or venom

What was the first virus (and viral disease) identified? Explain.

• Ivanovski & Beijerinck (1950s) identified “filterable infectious agents” that caused tobacco mosaic disease, now known as Tobacco Mosaic Virus (TMV)

• How they discovered

  • Crushed the diseased tobacco leaf

  • Filtered it through a 0.22 um filter

  • Had 2 setups

    • Inoculated leaf w/ cell debris = leaf remained healthy

    • Inoculated w/ filtrate (whtvr that passed thru the filter) = leaf died but when cultured, nothing grew from filtrate bc viruses need host to live

3 other milestones in early history of virology

• Loeffler and Frosch (1898) discovered the first animal-infecting viral disease → Foot and Mouth Disease

• Reed (1901) discovered the first insect-borne viral disease → Yellow Fever Virus

  • Setup

    • In 1 room, they allowed insects to feed on soldier infected with YF and kept a group of soldiers on the next room

    • Opened the door, causing insects to infect those soldiers from another room, resulting in death of most from YF

• Rous (1911) discovered that viruses contribute to formation of solid tumors or sarcoma

  • Obtained tumors from chicken’s breast muscle and broke those down into smaller chunks of tissue

  • Then ground up the tumor tissues with sand and filtered it through 0.22 um filter

  • Collected and inoculated filtrate to young chicken, which later on developed sarcoma

French scientists who studied bacteriophages (bacteria-infecting viruses)

Twort (1915) & d’Herelle (1917)

Explain how Twort and d’Herelle studied bacteriophages

1. Created bacterial lawn

2. Spread appropriate dilution of virus sample into lawn to enumerate viruses by counting the clearings called “plaques,” which represent 1 viral particle that replicated and when bacteria burst, new parasites infected neighboring cells

_ refers to inanimate vectors

Fomites

2 types of vectors

• Living vectors (e.g., arthropods)

• Fomites (non-living vectors)

Basic components of a cell vs. of a virus

Cell

1. DNA

2. Plasma membrane

3. Cytoplasm + ribosomes

Virus

1. Genetic material (DNA/RNA)

2. Protein coat (capsid)

T/F: It is possible for infectious agents to just have nucleic acids or proteins

TRUE

T/F: All viruses are smaller than all known bacterial cells

FALSE

There are giant viruses larger than bacterial cells

_ represent 1 viral particle in bacterial lawn that replicated and when bacteria burts, its new parasites infected the neighboring bacterial cells

Plaques

_ is the first insect-borne viral disease discovered by Reed (1901)

Yellow fever virus

Who discovered that viruses can contribute to formation of solid tumors (sarcoma) in chicken?

Rous (1911)

_ is the first animal-infecting viral disease discovered by Loeffler and Frosch (1898)

Foot and mouth disease (FMD)

T/F: Humans carry exogenous retrovirus elements in their genome, including LINEs and SINEs

FALSE

Humans carry endogenous retrovirus elements in their genome, including LINEs and SINEs

T/F: Some viruses have envelope consisting of lipid bilayer derived from host cell, e.g., HIV, coronaviruses

TRUE

T/F: Herpesviruses are smaller than Polioviruses

FALSE

Herpesviruses are larger (200 nm) than Polioviruses (30 nm)

T/F: Virions are always present and detectable in the host cell

FALSE

It’s possible they have not been assembled yet

Virus vs. Virions

• Virus = infectious particle that takes over host machinery; obligate intracellular parasites

• Virions = detectable infectious particles outside the host cell; only a transport/delivery form

T/F: Virions can be considered a specific physical form of a virus designed for protection and transmission outside the host

TRUE

T/F: The term 'virus' refers exclusively to the infectious particle outside the host cell

FALSE

The term "virus" refers to the infectious entity in all stages, whether inside or outside the host cell. "Virion" specifically refers to the virus outside the host.

In 2003, giant viruses, also known as _, were discovered, e.g., Mimivirus

Nucleocytoplasmic large DNA viruses (NCLDV)

T/F: Giant viruses or nucleocytoplasmic large DNA viruses (NCLDV) have identified ribosomal genes

FALSE

Giant viruses or nucleocytoplasmic large DNA viruses (NCLDV) don’t have identified ribosomal genes

T/F: Size of E. coli genome in terms of base pair is smaller than that of Mimivirus

FALSE

• Humans = 6,000,000,000 bp

• Yeasts (fungi) = 10,600,000 bp

• E. coli (bacteria) = 4,700,000 bp

• Mimivirus (viruses) = 800,000 bp

• MS2 (bacteriophage) = 3,200 bp

Explain 5 characteristics defining a virus

ocdpv

1. Viruses are infectious, obligate intracellular parasites

2. Viral genome comprises DNA or RNA

3. Viral genome directs the synthesis of viral components by cellular systems within an appropriate host cell

4. Infectious progeny virus particles called virions form via de novo self assembly from newly synthesized components

5. Progeny virion assembled during infection cycle is vehicle for transmission of viral genome to the next host cell or organism, where it’s disassembly initiates the next infectious cycle

_ directs synthesis of viral components by cellular systems within an appropriate host cell

Viral genome

Progeny virions are formed from _ using newly synthesized components

de novo self assembly

_ are vehicles for transmission of viral genome to the next host cell or organism, where its disassembly initiates the next infectious cycle

Progeny virion

Viruses are capable of _ when inside the host

grhme

• Growth and reproduction

• Response to stimuli

• Homeostasis

• Metabolism

• Evolution

In 1935, Stanley proved that viruses are non-living because _

even after crystallizing them, the virus still maintained its biological properties and infected cells of the tobacco leaf

Explain virus life cycle

• Extracellular phase

  • Virions are metabolically inert and do not reproduce outside host cell; have few enzymes but are not active

• Intracellular phase

  • These then enter host cell, attaching and entering host cell, so whatever nucleic acid they have will be replicated, genes and structural proteins will be expressed, then assembled into virions, which exit then the cell

T/F: Despite viruses having 1 phase in their life cycle where they can be considered “living,” they are not reflected in the tree of life

TRUE

Bc the basis of the tree were genes encoding 16S rRNA and viruses do not have ribosomal elements

_ used 16S rRNA gene sequences to create Tree of Life (Domain Bacteria, Archaea, Eukarya)

Carl Woese

Where do eukaryotes get their 16S rRNA?

Mitochondria

How did they resolve the issue with (reconcile the phylogeny of) viruses not being included in the Tree of life, especially with some biologists arguing that they should be included in it?

All organisms should be divided into:

• Ribosome-encoding organisms (REOs), which include Bacteria, Archaea, Eukarya, and;

• Capsid-encoding organisms (CEOs), which are the viruses of BAE

• For _, through the REOs, CEOs division, giant viruses should take their place among microbes and, more importantly, among the living as the 4th branch of life

• Whether viruses should be classified as a new domain, superkingdom, or TRUC (Things Resisting Uncomplete Classification) (which means “stuff” in French) is still up to debate

Didier Raoult

Raoult suggested the existence of a 4th domain for viruses, but the domains so far have been defined based on _, which are absent from these viruses

ribosomes

_ is the author of the study that promoted the use of hydroxychloroquine as cure for COVID-19 (didn’t undergo clinical trials; paper retracted last year)

Didier Raoult

T/F: Viruses are monophyletic in origin

FALSE

Viruses are polyphyletic in origin

Explain 5 major monophyletic virus classes + support for monophyly

Classes prstn	Lineages	Hosts	Support for monophyly
Positive strand RNA viruses	Superfamily I (picona-like), II (alpha), III (flavi), RNA bac	Animals, Plants, Protists, Bacteria appb	Conserved RdRp, JRC in most SI, SSII, SSII
Retroid viruses & elements	Retroviruses, Hepadnaviruses	APPB + Fungi, Archaea	Conserved RT
Small DNA viruses, plasmids, & transposons w/ rolling circle replication	Gemini-, Circo-, Parvo-, archaeal & bacterial plasmids, euk helitron transposons	Animals, Plants, Bacteria, Archaea	Conserved RCRE, JRC, S3H
Tailed bacteriophages (Caudovirales)	Myo (T4), Podo (T7), Sipho (Lambda)	Bacteria, Euryarchaea	Complex, overlapping array of genes
Nucleocytoplasmic large DNA viruses (NCLDVs)	Poxviruses, Mimiviruses, Asfarviruses, Iridoviruses	Animals, protists, algae	Core set of 11 conserved genes, including JRC, S3H

Describe general timeline of life on Earth

• 4 bya = Prokaryotes (Bacteria, Archaea)

• 2 bya = Eukaryotes

• <1 bya = Insects, mammals, humans

T/F: It is possible for viruses to have originated prior to cells (its hosts), after it, or across

TRUE