COVID19 testing explainer 1: What is a virus?

virus

This post is intended as an explainer for the general public

To understand how the testing works we first need to understand what a virus is and how each species of virus differs.

Viruses can infect all types of life, not just humans. There are viruses that infect animals, plants, and even ones that infect bacteria. Viruses infect life forms, but they’re not considered to be either alive or dead themselves. They’re really quite clever little hijackers. They gain entry to a host cell and then use the cell’s own molecular machinery to make more copies of the virus using a genetic blueprint of instructions contained inside the virus. The cell then becomes a microscopic virus factory which ultimately bursts and releases all the new viruses it just made. The new viruses then go on to infect other cells as the infection progresses. The ultimate aim of a virus is to make as many copies of themselves as possible, and often cause chaos along the way which we call disease.

We classify organisms by splitting them into groups – a taxonomy – based on their characteristics. The groups get split into smaller and more specific sub-groups until all the similar organisms are grouped together. Virus taxonomy splits viruses by how they look (morphology), how they copy themselves, what kind of genetic material they have, which organisms they infect and even the type of disease they cause.

The first big split in virus taxonomy is whether the virus genetic material is DNA or RNA. You’ve probably heard of DNA because it’s the same language our own genetics are written in. It’s made of four letters: A, C, T and G. RNA is a similar molecule but the T is replaced with a U. DNA and RNA can be both double stranded or single stranded.

dna_vs_rna

SARS-CoV-2 (the proper name for the virus causing COVID-19 disease) is a single stranded RNA (ssRNA) virus. This type of virus tends to mutate quite quickly and rather than “strains” they tend to form something we call a quasispecies. The mutations accumulate over time as the virus infects more people and this means that we can track the infections using genomic epidemiology techniques by comparing the full genome sequence of the virus (the A, C, U and G letters) of all the different isolates. If you’d like to see more info on this have a look at the Next Strain website, it’s where the scientists are putting the genome data during the outbreak. I’ll put a post about genomic epidemiology on my to-do list.

The letters in the SARS-CoV-2 genome code for the instructions to make the proteins of the virus. This is comparable to having the blueprints to build a house. The virus hijacks the host cell and uses it’s molecular machinery to make more copies of itself. As an aside, this is why computer viruses got their name as they’re malicious code which likes to replicate itself. The RNA inside SARS-CoV-2 codes for a number of proteins which sit on the membrane of the virus as well as for enzymes which do the copying of the instructions themselves (the RNA-dependent RNA polymerase, or RdRp).

SARS-CoV-2

Once we know the sequence of letters in the viral genome we can start to design tests to detect it using those letters to our advantage.

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