How Viruses Spread, Mutate and Turn Into New Variants

A virus needs a host cell to make copies of itself. Every time that copying happens, there is a chance the new copy differs slightly from the original — a change called a mutation. Enough mutations accumulated in one lineage, and health agencies start calling it a variant. Repeated across millions of infections, this process is how respiratory viruses such as influenza or SARS-CoV-2 keep changing over time.

How a virus moves from person to person

The World Health Organization groups the ways respiratory viruses move between people into contact, droplet and airborne transmission. Contact transmission happens when virus-laden secretions pass directly between people or indirectly through a contaminated surface. Droplet transmission involves larger respiratory particles — over 5 to 10 micrometres across — that fall to the ground or land on another person's mouth, nose or eyes within roughly one metre. Airborne transmission involves smaller particles that stay suspended in the air and can travel farther; WHO says this route is most clearly documented during medical procedures that generate aerosols.

In its commentary on SARS-CoV-2, WHO notes that clusters of cases have been reported in crowded, poorly ventilated indoor spaces — restaurants, gyms, places of worship — especially after close contact lasting roughly an hour or longer. Ventilation, physical distance and time spent together all influence how easily a respiratory virus moves through a group.

Measuring spread: the reproduction number

Epidemiologists summarize how fast an infection spreads with the basic reproduction number, R0 — the expected number of new infections caused by one infected person in a fully susceptible population, according to a review published on the US National Institutes of Health's PubMed Central (PMC) platform. If R0 is above 1, a typical infected person passes the virus to more than one other person on average and the outbreak grows; if it stays below 1, the outbreak shrinks. The review notes R0 depends on the contact rate between people, the chance of transmission per contact, and how long someone stays infectious — not on the pathogen alone.

From copying error to mutation

Mutations are not something a virus does deliberately. According to the WHO, mutations are simply the changes that occur when a virus's genetic material is copied; the agency notes that the more a virus spreads and replicates, the more chances it has to pick up such changes. RNA viruses such as coronaviruses and influenza tend to accumulate these copying errors especially often, according to an explainer published by Science News Explores, a publication of the Society for Science.

The US Centers for Disease Control and Prevention (CDC) states that SARS-CoV-2 keeps accumulating mutations in its genetic sequence as it continues to circulate. Most of these changes make no noticeable difference to how the virus behaves.

When a mutation becomes a variant — and maybe a strain

WHO defines a variant as a virus with one or more new mutations compared with the version it descended from. Science News Explores draws a further distinction: a variant only becomes a strain once researchers can show it has a genuinely new biological capability, such as spreading more easily, causing more severe disease, or partially evading immunity built up from earlier infection or vaccination. By that logic, every strain is a variant, but not every variant qualifies as a strain.

Whether a new variant spreads depends on natural selection. Changes that make a virus copy of itself less able to infect cells tend to disappear quickly, while changes that make the virus fitter in its current environment — more transmissible, better at evading immune defenses, or both — tend to become more common over time, according to Science News Explores. Because large outbreaks generate more infections, and therefore more replication events, sustained high transmission gives a virus more chances to generate the kind of mutation that turns into a successful new variant.

How agencies track new variants

To keep up with viral change, the CDC runs genomic surveillance: laboratories sequence the genetic code of virus samples from patients and upload the sequences to shared databases so researchers can compare them. The agency groups related sequences into lineages using the Pango nomenclature system, a naming framework used internationally by public-health bodies and researchers to track how lineages relate to one another and spread over time, according to the CDC.

Surveillance combines this genetic data with phenotypic data — direct laboratory or clinical observations of how a variant actually behaves — to assess whether existing tests, treatments and vaccines still work against it, the CDC says. WHO adds that COVID-19 vaccines were designed to trigger a broad immune response involving multiple types of antibodies and immune cells, which is why individual mutations are unlikely on their own to make a vaccine completely ineffective; if a variant does meaningfully reduce protection, WHO says vaccine composition can be updated in response.