SciMoms COVID FAQ: What you need to know about COVID variants

In this series of COVID FAQs, the SciMoms answer your frequently asked questions about the novel coronavirus or COVID-19 pandemic. In this FAQ, we focus on COVID variants, including the Delta and Omicron variants. As we learn about each new variant, we can draw on what we already know about viruses, variants, and immunity to stay informed. Most importantly, the precautions we need to take to stop the spread of COVID remain the same. Find all previous FAQs here.

This post was written by Layla Katiraee and Alison Bernstein. This post has been updated.

What are COVID variants?

Viruses are infectious agents that infect your cells and use your cells’ machinery to replicate themselves within your body (See our previous FAQ “How do viruses work?” for more details). 

Mutations are not rare events that happen only in X-Men movies. Mutations are normal in all organisms and occur randomly whenever genetic sequences are copied. They happen every time sperm or egg cells get made, every time skin cells divide, every time bacteria replicate, and every time viruses get copied. Consequently, mutations are not rare, even in humans. Anytime a virus replicates (i.e., gets copied) in a cell it infects, there is an opportunity for mutation and for a new variant to arise.

The virus that causes COVID-19 (SARS-CoV-2) contains single-stranded ribonucleic acid or RNA that serves as the template to create more copies of the virus. Every time SARS-CoV-2 replicates, there’s a chance for the virus to make a copying error in its RNA. When one of these errors (a mutation) occurs in SARS-CoV-2 RNA, it may change properties that determine how well the virus can infect and spread. These SARS-CoV-2 viruses with different properties are known as SARS-CoV-2 variants, or colloquially as COVID variants. 

Thus, with every infection, there is the potential for a new variant to spread from one person to the next. Whether a strain takes hold in a group of people depends on how well it can spread from one person to another. How easily a virus spreads depends on a combination of properties of the virus, the environment, and the host, including our own human behaviors that facilitate or prevent spread. If we allow the virus to spread, we increase the chances that it will mutate into new variants that spread to other people. Measures such as masking and physical distancing that prevent spread of the virus also prevent new variants. (See our previous FAQ “How does COVID-19 spread?”)

Scientists distinguish the variants that they are monitoring from each other by labeling each variant alphabetically by the Greek alphabet, categorizing some as “variants of interest” and others as “variants of concern” depending on their properties. A variant of interest is one that has been identified in several populations and may pose a threat to human health. A variant of concern is one where the virus’ properties have been shown to pose a threat to human health. 

For the data nerds out there, NextStrain maintains a database of all known SARS-CoV2 variants and CoVariants maintains additional information about current variants of concern.

Can COVID tests tell me if I have the Delta variant or other COVID variant?

Current COVID tests detect the presence of all COVID-19 variants, but cannot tell us which variant was detected. These test results only tell us whether the SARS-CoV-2 virus is present in the sample tested. This is true for all currently available PCR or molecular tests and rapid antigen tests (See our previous FAQ on COVID testing for explanations of these types of tests).

To identify the variant, genomic sequencing of the virus needs to be performed. Genomic sequencing is more expensive and is not used as a diagnostic test. Public health organizations worldwide are collaborating to carry out genomic surveillance to monitor the SARS-CoV-2 virus and detect and track new variants.

Do the vaccines work against COVID variants?

To date, all COVID vaccines greatly reduce the risk of severe illness, hospitalization, and death from all COVID variants, including Delta. Even with recent authorization of boosters for some groups in the US, efficacy against Delta for severe illness, hospitalization, and death in most people remains high. 

In mid-August, based on reports of waning immunity in certain populations, FDA expanded the EUA for Pfizer and Moderna vaccines to include third doses for people who are immunocompromised. Shortly after, CDC issued a recommendation for a third dose for moderately to severely immunocompromised individuals and specified who falls into these categories. 

Most recently, the FDA’s external advisory committee voted on September 17 to recommend boosters for people over 65, people with certain high-risk medical conditions, and people in high-exposure occupations (like health care workers). Data presented at this meeting suggests that the waning immunity seems to be occurring for all variants, not specifically for Delta, and is related more to the timing of shots.  (For details, we recommend this summary from Your Local Epidemiologist and this Sept 22 FDA announcement). 

Remember that both doses of the two-dose mRNA vaccines are needed for maximum efficacy against all existing variants. (We also recommend this roundup of data on Delta variant for those who have received the J&J vaccine from Your Local Epidemiologist.)

Despite vaccine efficacy against current variants, it is possible that a mutation, particularly within the spike protein, could change the virus’ properties in such a way that our immune cells and antibodies (acquired via vaccination or prior infection) no longer recognize the virus. However, a mutation in the spike protein (the antigen in all available vaccines) that evades vaccine-acquired immunity may also be less able to infect cells without a functional spike protein. We cannot predict which variants will arise, but we can stop variants in their tracks with the tools we have to slow the spread of the virus. A major concern about allowing the virus to spread without mitigation measures is that this increases the chances that a variant like Delta, or even worse, arises, as we wrote in May

(See our previous FAQ: Will mutations of the SARS-CoV2 virus make vaccines ineffective?)

Do vaccines prevent transmission of the Delta variant?

While vaccines remain strong against severe illness, hospitalization, and death, there is some evidence suggesting that current vaccines are less effective at preventing transmission for the Delta variant. However, we do not have an exact estimate yet of how much less effective or how much this is specifically driving the rise of Delta. 

It is critical to note that the higher transmissibility of Delta and the dropping of nearly all other, non-vaccine, COVID mitigation measures could be enough to account for the rise of Delta, even if vaccines do block transmission of this variant. Had we not dropped nearly all layers of protection early in the summer, we might not be in this situation, even in the face of a more transmissible variant and reduced vaccine efficacy against transmission. 

This once again underscores that a vaccine-only strategy to stop the spread is not an effective strategy. As written by Dr. Liz Marnik in a recent guest post on the latest CDC mask guidance

We are also finding out the hard way that even in highly vaccinated countries like Israel, and highly vaccinated areas within the US like San Francisco and NY, currently experiencing large surges, we still don’t have high enough vaccination rates to curb the spread without additional mitigation measures.

Why has the Delta variant spread so quickly?

The Delta variant has rapidly spread and become the dominant strain in the US, not only because it is more easily transmitted but also because we dropped our measures of protection just before the Delta variant was starting to gain ground. A perfect storm of transmissibility and lowered protections occurred over the July 4th long weekend, when thousands of people across the country met in person and without masks in the presence of a highly transmissible variant. As expected from this combination of events, a few weeks later, the Delta variant became the primary source of COVID infection in the US. 

Does the Delta variant make people sicker?

Evidence is starting to suggest that the Delta variant may cause more severe illness, in addition to spreading more easily. A large published study from Scotland and a preprint from Canada found that patients infected with Delta were more likely to be hospitalized than those infected with Alpha or the original strain. The very large majority of people hospitalized with any COVID variant are unvaccinated, serving as a strong reminder that vaccination is the single most effective way to protect yourself and your community from current and future variants of this virus.

How do we stop COVID variants? 

The only way to prevent new variants from arising is to prevent the virus from replicating, which we do by stopping the spread of the virus. The best tools we have at our disposal to fight against existing and future variants are the same tools we have now to prevent the spread of the virus: vaccination, masks, physical distancing, hand washing, and avoiding indoor gatherings. The 3Ws and the two-out-of-three rule still apply.

We haven’t been very good at that: too many in our population are not vaccinated and have not been wearing masks or physically distancing. This leads to high rates of transmission among the unvaccinated and many opportunities for new variants to arise. This is particularly bad in areas with low vaccination rates, but also in highly vaccinated areas like Israel, the UK and highly vaccinated areas of the US. As long as the virus is allowed to spread, each infection comes with the possibility of a new mutation and a new variant spreading.

It is important to recognize that vaccinations, while the most powerful tool we have, are not the only tool and are not enough on their own to end this pandemic. We can see this in highly vaccinated regions experiencing new surges. A vaccine-only strategy leaves the virus to spread through the unvaccinated population and creates opportunities for new variants of concern to arise.

In addition, until every person in every country has access to COVID vaccines, global public health efforts to contain COVID remain at risk because variants may arise with every new infection. Making vaccines available to all people and all nations is necessary to stop this pandemic. Until vaccines are in arms everywhere, other layers of protection will be needed to fight current and future variants.

Misinformation circulating online and on social media claims that vaccines are causing new SARS-CoV-2 variants to arise. This is patently false. The vaccine does not contain the virus and does not cause the virus to mutate. Viral replication is needed for mutations to occur. The vaccines do not contain the virus and do not replicate. For a detailed explanation see: Reuters Fact Check-Delta variant did not come from the COVID-19 vaccine.

In reality, the best way to prevent new variants and a variant that our vaccines do not work against is to minimize the spread of the virus. The strongest tools we have at our disposal to prevent the spread of COVID infection are masking and vaccination.

SciMoms Guide to Preventing COVID Spread, COVID Variants edition. Some variants spread more easily, but the same measures protect against new variants, including Delta. These are: get vaccinated, wear a mask, gather outside, watch your distance, and wash you hands.

Do viruses evolve to become more “gentle”?

The idea that a virus that kills its host is a virus that can no longer spread is often promoted by vaccine opponents to argue that vaccines are not needed, since COVID-19 will eventually evolve to be “gentler” and no longer harm humans. 

But, if this claim is true, it may take millions of infections for such a “gentle” virus to arise. And there is no guarantee that a virus will evolve to produce a less severe illness because mutation is random.

More importantly, even if we knew that a “gentle” SARS-CoV-2 was inevitable, if we do not take action to mitigate risk while we wait, untold numbers of people will die and suffer from preventable illness. We cannot sit back and let the virus run rampant until such a “gentler” mutation occurs if it occurs at all. 

This is clearly unethical and leaves current people to suffer for the unknown benefit of hypothetical people in an unlikely future. It is extremely problematic to allow SARS-CoV-2 to run rampant through susceptible populations, especially when we have the tools in hand to reduce risk. Those that argue in favor of this are making similar arguments as those in favor of a natural herd immunity strategy (See our previous FAQ: Is natural herd immunity a good strategy to end the COVID-19 pandemic?)

We cannot overstate how ethically problematic it is to let current people die and get sick because some future people might get somewhat less sick from the virus, especially when we have the tools to protect people now.


CDC: What You Need to Know about Variants

WHO: Tracking SARS-CoV-2 variants

​​CDC: Delta Variant: What We Know About the Science

Mayo Clinic: Do COVID-19 vaccines protect against the variants?

Yale Medicine: 5 Things to Know About The Delta Variant