Biological Perspective

Viruses are the smallest of all the microbes and are unique because they are only alive and able to multiply inside the cells of other living things. The cell they multiply in is called the host cell.

A virus is made up of a core of genetic material which is either DNA or RNA (the viral genome) and is surrounded by a protective protein shell called a capsid. The viral genome is the blueprint for all the components of that particular virus and can either be made up of DNA (as it is with most creatures) or RNA which is similar but more flexible and much less stable.

The capsid keeps the viral genome safe and helps the virus latch onto cells and get inside. It is made of proteins and the properties of these protein subunits will decide what the capsids structure and function is. Some viruses also have a lipid membrane envelope which is why soap and water works against them as it disrupts the greasy membrane.

For a virus to spread it must infect a cell. This usually happens when part of the capsid binds with a protein on the host cell.

RNA virus

Each coronavirus has at the core a strand of RNA which carries all of the virus's genes and tells the cell how to build protein. Around this is a protein shell which is surrounded by 2 layers of molecules called lipids. On this outer membrane are proteins, some that stick out like a spike which are an anchor for the virus when it attaches to a protein on the outside of a cell.

A coronavirus particle viral envelope consists of a lipid bilayer on which of 4 structural proteins are attached:

SARS COV-2 Genome

Coronaviruses contain a positive sense, single stranded RNA genome.

Viruses invade a host cell and use it to make copies of themselves, but RNA replication typically lacks the error-correction mechanisms that cells use when copying DNA. This makes RNA less stable and means that RNA viruses have higher mutation rates making eradication more difficult as they change and evolve faster.

However, the SARS COV-2 genome is a strand of RNA that is about 29,900 bases long, near the limit of RNA viruses, (Influenza has about 13,500, cold Rhinoviruses about 8,000) and is able to proof read and correct copies. This ablity to correct is common in human cells and in DNA viruses but not in RNA viruses.

Its length gives it the ability to code a lot of information which in turn allows it to create more proteins and maybe carry out more sophisticated replication than other viruses. One of these proteins is an enzyme called exonuclease (ExoN) which helps it proofread and correct copies as they are made. Only viruses with genomes longer than 20,000 bases are able to make this enzyme.

Mutations

However, replication mistakes will happen many times in the body of an individual who is infected with COVID-19 and some genomes may pick up a change that is beneficial for the survival of the virus. Within the infected patient there are hundreds of millions of virus particles and the mutations or variants that are better than the original virus are the ones that will become successful during the pandemic.

The variants of concern have changes that may affect the vaccine rollout.

The variant first identified in South Africa (B.1.351) has been seen to have multiple changes in the spike protein which help the virus evade and antibody response.

The variant first identified in the UK (B.1.1.7) has changes which seem to allow the virus to attach more tightly to the ACE2 receptor and enter the human cells more easily.

The variant first identified in traveller from Brazil P.1 has three mutations to the spike protein. One the E484K mutation is the most worrying and is also the mutation in the South African variant.This is the mutation thought to give the variants some ability to escape the vaccines.

In order to prevent these variants becoming widespread genomic sequencing followed by contract tracing is required. The UK does more genomic sequencing of viral samples than any other country, but others are stepping up their gnomic sequencing capability as controlling the spread of variants which may be able to evade the vaccines becomes even more important

Influenza and Coronavirus

COVID-19 is often mistakenly called a flu, but flu and COVID-19 come from different viruses which have some similarities, but are genetically different.

Both Influenza A and SARS COV-2 are RNA viruses spread though droplets, both can cause fever, cough, respiratory symptoms (including pneumonia) body aches, fatigue and other symptoms. Both have a single strand of RNA as the genetic material.

However, SARS COV-2 is "positive sense" which means that the infected cell can use it as is, recognising the viral RNA as its own messenger RNA and being fooled into making viral proteins. An influenza virus is "negative" sense which means that a cell first has to copy it into a complementary form, as RNA is normally transcribed from DNA.

The genome of Influenza consists of 8 RNA segments that encode12 proteins. The viral surface sports two types of glycoproteins. Whereas SARS COV-2's genome encodes 16 enzymes required to make the viral parts plus the 4 structural proteins.

They use different receptors to get into the host cell so they can replicate. The influenza A glycoprotein attaches to sugars on respiratory cell surfaces, the doorway for the virus. Whereas SARS COV-2 binds to ACE2 (angiotensin-converting enzyme 2) protein which is found on human cells of the lower lungs, in the respiratory passages and in some blood vessel linings.