Bacteria, Viruses and the Cells of Immunity - Microbiology and Immunology

Lung Disease - Tuberculosis (TB) Key points.

Tuberculosis is caused by the pathogenic bacteria: Mycobacterium tuberculosis.

TB infection: Step 1 - Step 6.

TB common symptoms.

How does TB affect Ventilation Rate?

TB is a common, secondary infectious disease.

Viruses are the smallest and simplest of the microorganisms, 

they are acellular - which means "they are not made of cells!"

Since viruses are acellular and cannot reproduce (in fact, viruses don't actually fulfil any of the seven characteristics of life on their own)... viruses are classified as NON-LIVING.

So, viruses are non-living (consider them more like complex chemical packages than simple living organisms), and think about their definition: -

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"Viruses are obligate parasites which are only able reproduce (replicate) inside host cells"

...and what is a parasite?

​Parasites are organisms that "live" inside or on other species and cause harm to the host species. 

​Well as we now know, viruses are not alive, but they do require a host cell to replicate - and when they do replicate, they cause damage to the host, Hence viruses are [intracellular] parasites.

Viruses (Virions) are tiny! On average they range in size from about 10nm to 400nmso it stands to reason that viruses cannot be seen with a light microscope. Thus, viruses were first observed in the 1930s using more powerful electron microscopy. 

Viruses are defined as “obligate intracellular parasites” which exist either extracellularly or intracellularly. 

Extracellular, i.e. outside of a host cell viruses are “inactive” or “dormant” because they do not have the necessary cellular machinery (e.g. DNA or RNA, Enzymes, Ribosomes, Golgi, ER etc.) which would allow them to replicate, or multiply (outside of the host). 

Intracellular. Viruses are known to infect all cells, from all classifications of life. There are viruses that infect prokaryotes (bacteria), the so called bacteriophages, but mostly viruses infect eukaryotic organisms, such as plants, algae, fungi, protists and of course, viruses that infect animals.

​A complete virus particle is known as a virion.

​The terms virus and virion are often used synonymously. However, for clarity just be aware that a “virion” is the “dormant” yet, complete form of a virus which is transmitted between host cells. 

Whilst a “virus” is the “active infectious agent". Once inside a host cell, the virus dismantles into its separate parts, and can now be reproduced (replicated) by using the host cells “machinery” (DNA or RNA, Ribosomes, Enzymes, etc).

There is always an exception! Biology is the study of life, all the fascinating forms of life, interactions, cycles and biochemistry that make life possible… Biology is vast, complicated and multidisciplinary - to say the least. And, there are always exceptions. Viruses for example are so tiny they cannot be seen without an electron microscope… that is unless the virus is the comparatively massive mimi virus! Mimi viruses are from the family of mimiviridae (commonly called the giant viruses) and these large viruses (average size 400nm) infect amoebas. Now 400nm is massive if you’re a virus, so 600nm would be considered gigantic! So when Megavirus chilensis was first discovered in 2010 it became the new big boy in town measuring in at (on average) 600nm and some measuring 750nm! large enough to be observed with a light microscope!

In 2013 another new ‘giant’ virus was discovered - the pandoravirus. This giant virus is not only impressive because of its size (500nm) but also its genome. Described as “evolutionary innovators” these giant viruses have muddied the waters of what was once the clear distinction between the viral world and that of the cellular world, due to their genomes being as complex as some simple eukaryotic cells. 

To throw another spanner in the works, there are also the Acidionus Two-Tailed Viruses (from the family Bicaudaviridae. These hyperthermophilic archaeal viruses have shown extracellular activity - that is to say they have shown to be “active” outside of their host cells. Now, the Acidionus Two-Tailed Viruses still require the host cell to replicate, but following host cell lysis, two “protein tails” composed of 800 amino acids begin to project out and continue to assemble from each end of the virion until they reach a length at least equal to that of the capsid. But what is more perplexing is that the protein tails are only produced if the virions are exposed to high temperatures (hence the viruses being classified as hyperthermophilic). The natural environment of the Acidionus Two-Tailed Viruses are acidic hot springs with a pH of around 1.5, and temperatures of 85 - 93°C.

• Nucleic acid. The nucleic acid in a virus can be either DNA or RNA (never both) and may be single or double-stranded. Viruses are classified according to the type of nucleic acid they contain,(e.g. HIV is an RNA virus whilst the Epstein–Barr virus is a DNA virus).

• A capsid (protein coat called made of subunits called capsomeres). If the capsid proteins are closely bound to the nucleic acid, then the combination is called a nucleocapsid. Capsids are composed of many repeating subunits and typically have simple geometrical shapes, i.e. helix viruses such as the tobacco mosaic virus or icosahedral viruses (An icosahedron is a regular polyhedron with 20 equilateral triangular faces). Examples of icosahedral viruses are adenovirus, poliovirus and rhinovirus.

• A lipid envelope. Viral envelopes derive from the plasma (cell membrane) or nuclear membranes of host cells.

• Proteins which attach the capsid to the envelope (called matrix proteins).

• Glycoproteins which allow the virus to attach to host cells.

• Enzymes, (e.g. Reverse transcriptase) which are required to replicate the viral nucleic acid or incorporate it into a host cell.

Tobacco mosaic virus (TMV) has a very simple structure: just a coil of RNA surrounded by a helical capsid.

Adenovirus contains single stranded DNA surrounded by an icosahedral capsid.

Bacteriophages: e.g. T2 virus have complex structures that combine icosahedral and helical capsids.

The human influenza A virus is enveloped virus. It contains 8 single- stranded RNA segments

combined with capsomeres to form helical nucleocapsids surrounded by a sphere of matrix proteins attached to a lipid envelope.

Viruses can only reproduce (or Replicate!) inside host cells.

The general strategy of viral replication is broadly speaking "the same" in the sense that a virus uses the host cell enzymes to replicate and translate viral RNA or DNA. which consequently use host cell machinery (Ribosomes, ER, Golgi etc.) to making more virus particles. upon completion, newly synthesised viruses then either burst out of the cell (the lytic cycle) or for viruses such as influenza and HIV which have lipid envelopes, their strategy is to 'bud' out of the host cell acquiring their lipid envelope!

There are two methods of viral replication: -

Lysis (The lytic cycle) and The "budding" cycle. 

Lysis (the lytic cycle) results in the death of an infected host cell. A common example of a human virus which replicates this way is variola major (the virus that causes smallpox). 

Alternatively, viruses such as influenza A, which have a “ lipid envelope” are typically released from the host cell by “budding” (budding is exocytosis). It is through the budding process that results in the acquisition of the viral lipid envelope upon on release of the virus from the host cell. 

As outlined above, the two commonly assessed viral diseases in a-level biology are Influenza and HIV/AIDS which both replicate via ‘budding’ since both these viruses possess a lipid envelope. However, remember HIV is a retrovirus so exhibits a slightly different mechanisms of replication when compared to influenza.

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Firstly we'll learn the lytic cycle (for an unspecified viral infection). (The second method "the budding cycle will be covered in HIV replication)

Infectious diseases caused by viruses:

The Diseases often examined are HIV/AIDS and  Influenza which you need to know more about and are considered below.

How is HIV/AIDS transmitted?

Through infected semen or vaginal secretions during sexual activity, or through infected blood in transfusions or contaminated needles. Infected mothers can also pass the virus on to their children through the placenta or milk. Before 1985 many hospital patients, especially haemophiliacs, became infected through blood transfusions, but since 1985 all blood donations in the UK are tested for HIV. Many drug addicts have been infected through sharing needles. By far the most important method of transmission of HIV world-wide is unprotected sexual intercourse. HIV cannot survive in air and therefore cannot be transmitted by skin contact or kissing.

HIV in the blood attaches to cells that carry the "CD4" antigen, including the T lymphocyte and macrophage white blood cells. After entering these cells it becomes a provirus in the nuclear DNA, remaining dormant but being replicated for a long latency period of 8-10 years. Eventually the virus particles are re-assembled and emerge into the blood, rupturing and killing the T cells in the process. The lack of T cells leaves the immune system severely compromised.

What are the signs and symptoms of HIV/AIDS?

Like other retroviruses, HIV has a long latency of 8-10 years, during which time there are no symptoms, but the individual is infectious. After this period the person starts to shows mild symptoms of the AID-related complex (ARC), such as tiredness, fever, weight loss and diarrhoea. This is followed by the more serious symptoms of full-blown AIDS. Since the immune system no longer functions the patient has no defence against a variety of opportunistic infections. The most common of these are Kaposi's sarcoma (a skin cancer), TB and pneumonia, which is usually fatal.

Can HIV/ADIS be Treated?

There is as yet no cure or vaccination for AIDS, though drugs like AZT can delay its onset for many years. Vaccinations are difficult because the HIV genome is highly variable (probably because reverse transcriptase make many base copying errors). Prevention of AIDS has concentrated on "safe sex" education (using condoms and reducing promiscuity), not sharing needles, and screening blood transfusions.

Defence Against Infectious Disease:

We are surrounded by microbes in the air, on the ground and all other surfaces, and in our food and water. The only reason we are still alive is because humans (and all other animals) have a very powerful defence mechanism – The Immune System.

In your A Level Biology it is essential that you know the structure of the HIV Virus and that HIV infects T-cells. You MUST be able to interpret a graph detailing the course of HIV/AIDS infection.

How is influenza transmitted?

Influenza Transmission is through airborne droplet infection from the coughs and sneezes of infected individuals. Infected people are infectious from a day before symptoms show themselves until a week afterwards. The virus invades the epithelial cells lining the upper respiratory tract (nose, mouth, throat, trachea and bronchi) and reproduces inside them, killing many cells in the process. These dead cells increase the amount and thickness of mucus produced during an infection, which irritates the throat, causing coughing.

What are the signs and symptoms of influenza?

The onset is sudden after an incubation period of 1-4 days, and the symptoms include fever, shivering, headache, muscular pain, coughing of excess mucus and a loss of appetite. Recovery normally takes about 4 days, unless there are secondary infections, which can be fatal if untreated. The influenza pandemic of 1918 killed 22 million people world-wide, making it the greatest killer disease ever.

How can Influenza be treated?

Treatment is by bed rest with plenty of fluids and analgesic drugs like asprin or paracetamol. Since this is a viral infection, antibiotics are useless.

Can influenza be prevented?

Vaccination is difficult because of genetic changes in the influenza virus, but vaccinations based on a variety of antigens are now used to protect at-risk groups (infants and elderly). Prevention would require the quarantine (isolation) of influenza flu victims.

Links to (practical microbiology) Can Virus be Cultured in a Lab?

Yes, But Because viruses are parasites, they cannot be cultured in the lab like other microbes. Instead they must be grown inside their specific living host cells. In the past this meant infecting whole animals or plants, but with improvements in tissue culture techniques almost any host cell can now be grown in the lab and infected with a virus. Bacteriophages are perhaps the most-studied of all viruses, simply because their hosts, bacteria, are so easy to grow in the lab.