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A 101 on Covid-19 variants

Updated: Sep 8, 2021

A background on variants and and why they matter.


1. What is a variant of Covid 19?


The development of new “variants”, or “strains” happens to all viruses naturally - including SARS-CoV-2, the virus that causes COVID-19. Viruses constantly change over time. As a virus spreads they replicate, making copies of themselves. When a virus replicates, occasionally its genetic information is copied incorrectly, causing it to change. This process of change is called “mutation”. A virus that develops one or more mutations is called a variant of the original virus. New variants of the virus that cause COVID-19 are expected to occur[1][2].


Mutations are usually nothing to be concerned about as most changes to a virus’s genetic information are small and have little impact on the virus. But every so often a mutation occurs that affects how a virus behaves. Sometimes mutations make a virus weaker, these variants tend to die out. Occasionally, mutations make a virus a bit stronger. For example, it may make them better at transmitting (spread more easily), or become more resistant to the body’s immune system. These variants can thrive, creating new strains of a virus that spread throughout the population[3][4].


When a virus is circulating throughout a population and transmission is high, causing many new infections, the chances of variants developing increases. The more a virus spreads, the more it replicates - giving the virus more opportunities to mutate. It is not surprising that new variants of the virus that caused COVID-19 are emerging globally because there is a lot of transmission of the disease going on[5].



2. How are variants classified?


As mutations in the SARS-CoV-2 virus are natural, and to be expected of a virus circulating among the global population, there have been several recorded instances of slight changes in the virus globally[6]. Most of these variants are not much to be concerned about, because the changes are so small that they don’t affect how the virus behaves. Variants become a cause for concern when they behave differently to the initial strain of the SARS-CoV-2 virus in ways that affect its ability to transmit, disease severity and/or disease presentation/symptoms. Changes in the behaviour of the virus is also concerning if measures to control the pandemic, including, testing/diagnosing cases, treatments and vaccines become less effective against new variants, as well as being able to re-infect people who have already had COVID-19[7][8][9][10].


How variants of the SARS-CoV-2 virus that behave differently are classified as something to be concerned about varies a bit depending on where you are in the world. If you look for information online about COVID-19 variants you might find different terminology is used depending on where the information was published. For example, in the US they used a three tiered system classification system (in order of concern, from lowest to highest): 1.) “Variant of Interest”; 2.) “Variant of Concern”; 3.) “Variant of High Consequence”. The World Health Organisation (WHO) also refers to variants of the virus as “Variants of Interest” and “Variants of Concern”[11]. The UK classifies variants as “Variants Under Investigation” and “Variants of Concern”[12]. The names used are similar, but the criteria used to classify variants that are of concern can vary from place to place.


The WHOs classification of COVID-19 variants is the most commonly used.


The WHO classifies “variants of interest” (VOI) if a variant that has been identified has:

  1. caused an increase in cases

  2. changes in its genetic code that are predicted to affect transmission, testing, treatment, vaccines or immunity is identified.


Variants of interest then undergo further investigation and may be upgraded to a “variant of concern” (VOC) if there is evidence that the variant causes:

  1. an increase in transmission

  2. an increase in disease severity

  3. a decrease in the treatment, testing or vaccines efficacy

  4. a decrease in immunity developed from previous COVID-19 infections[13]


Overall, a “variant of concern” usually refers to a detected variant of SARS-CoV-2 for which there is evidence of there is evidence of either an increase in the ability of the virus to spread, more severe disease (e.g. increased hospitalisations or deaths), reduced efficacy of treatments, testing, vaccines, or the ability to re-infect people who have already had COVID-19.


3. How are variants identified


Because variants are created out of mutations in the virus’s genetic information, variants can be identified by looking at the virus’s genetic makeup - known as genomic sequencing. Using genomic sequencing scientists can identify and monitor how the virus that causes COVID-19 changes over time and develops into new variants[14].


Lots of places across the world have research facilities that have the capability to conduct genomic sequencing of the virus that causes COVID-19[15][16][17]. Currently countries that are focussing on identifying new variants and their genetic information include the UK[18], USA[19] and Mainland China[20]. Global organisations like the WHO are working to develop global surveillance systems to detect new variants of the virus, and track their spread around the world[21][22]. The capability to identify variants varies from country to country and not all samples of the virus will be tested for new variants so we might not yet have a completely accurate picture of the variants of the SARS-CoV-2 virus, where they are in the world and how prevalent they are[23].


Work to track variants is also happening in Hong Kong. The Hong Kong Polytechnic University has developed a comprehensive viral test that can detect existing variants of COVID-19[24].


4. What is the impact of variants?


Where mutations are located in a virus’s genetic information affects how the virus’s behaviour may change. The virus that causes COVID-19 is part of a family of viruses, called coronaviruses - named after the crown-like spike on its surface. The virus uses these spike proteins to attach to cells, causing infections. worries about variants of the virus that causes COVID-19 are related to mutations of the S protein. Variants of concern have changes in the spike protein that might cause an increase in the virus’s ability to transmit, cause more severe disease, or that they could be more resistant to the effects of vaccines.


Are these variants transmitted more easily?


There is evidence that most variants of concern that are currently circulating around the world do seem to spread more easily and quickly than the original SARS-CoV-2 strain. Variants that transmit more easily could cause increased cases of COVID-19[25][26].


Do these variants cause more severe disease?


It is currently suggested that the two of the four existing variants of concern, Alpha and Delta variant, may potentially cause more severe disease and illness than other variants or the original strain. [27] It seems that the Delta variant is more dangerous than the Alpha variant as a large national study showed that people infected by the Delta variant were almost twice as likely to be hospitalised than those infected by the Alpha variant. The risk of going to the hospital with the Delta variant was similar for patients in the study who were vaccinated and those who were not[58].


Since variants are more easily transmitted, it could cause a surge in cases and in turns, an increase in the number of people needing to go to hospital. Hospitals overburdened by high number of COVID-19 cases unfortunately may not have the resources to effectively treat everyone which could cause more severe illness or deaths[28].


Surges in cases of COVID-19 have led to some disagreement about whether variants are more severe or deadly. For example, the UK variant was claimed to potentially be more deadly because some researchers found that more people that died with COVID-19 were infected with the variant[29]. Other researchers disagree because new evidence shows that out of the people admitted to hospital with COVID-19 those infected with the variant were not anymore likely to die compared to people infected with other strains. As the variants spread more easily, it likely infected more people so an increase in the number of deaths might be a reflection of increased cases and overburdened hospital resources rather than of a more severe disease[30].


Are COVID-19 vaccines effective against these variants?


Given how important the spike protein is to the virus, the vaccines available in Hong Kong have been designed around spike protein. The Fosun Pharma/BioNTech Comirnaty vaccine[31] gives instructions to our immune system to make our own version of the spike protein, which starts the production of antibodies and T cells that protect us when we come into contact with the virus. Sinovac’s CoronaVac vaccine uses inactivated coronaviruses, with the spike proteins still attached, to teach the immune system to make antibodies that are the right shape to stick to live coronaviruses’ spike proteins[32]. These vaccines were developed using spike proteins from the beginning of the outbreak so people are worried that vaccines won’t be effective against new variants. The concern is that if mutations have changed the spike protein too much the virus will no longer be recognised by the immune response that the vaccines taught our bodies[33].


Current COVID-19 vaccines are expected to provide at least some protection against new virus variants because they produce a broad immune response in our bodies that involve a range of antibodies and T cells. Mutations in the coronavirus spike proteins shouldn’t make current vaccines ineffective[34].


The WHO held a global meeting to assess the risks of COVID-19, laying groundwork for the detecting, monitoring and assessing variants of the virus, as well as evaluating the impact of variants on vaccines. Existing vaccines have been deemed to be effective against known variants of concern. However, scientists have stated that it is very likely that some mutations of the virus will escape the protection offered by existing vaccines[35]. If any vaccines prove to be less effective against any variants in the future, the WHO and its partner organisations are preparing so that they will be able to recommend any changes to the vaccines that might be needed[36].


It is entirely possible to change the composition of vaccines so that they are effective against new variants. This is not a new process in vaccine development. New flu vaccines are developed each year because the flu-virus mutates quickly, creating new strains that have to be vaccinated against. Some places, like Hong Kong where vaccine uptake is low, will be slow to vaccinate their populations. The longer it takes to vaccinate the population the greater the risk of existing vaccines becoming ineffective against future variants, because the virus has more time to spread and mutate. COVID-19 vaccines are likely to be around for a long time - just like flu vaccines - they will have to be updated if very different variants emerge and people might have to be vaccinated regularly to stay immune to new strains[37][38].


Detecting as assessing variants is really important to find out if vaccines are becoming any less effective so that vaccine development can adapt quickly. Global surveillance systems tracking changes in the virus that causes COVID-19 are being developed. The ability to identify and track variants of viruses already exists globally, infrastructure used to track changes in the flu virus, such as the GISAID genomic database, have been taken advantage of to quickly create systems that are able to track COVID-19 variants[39]. Vaccines are also undergoing efficacy testing. Around the world, clinical trials are actively investigating the efficacy of existing vaccines against variants[40]. As efficacy testing proceeds and new variants are detected, the ability of existing vaccines to immunise people against emerging strains will continue to be evaluated by scientific communities worldwide. Insights from these evaluations will allow vaccine developers to alter the structure of the vaccines, keeping them effective into the future.



What do we know about the effectiveness of the vaccines available in Hong Kong against existing variants


Fosun Pharma/BioNTech Comirnaty vaccine

Evidence shows the vaccine is just as effective against some mutations of the virus[41] but may not be as effective against all variants[42].

  • The Comirnaty vaccine is very effective against the Alpha variant. Studies show it is around 95% effective at protecting against the Alpha variant[43] and also 88% effective at protecting against the Delta variant after two doses of vaccine[58][60].

  • The Cominarity vaccine does provides protection against the South Africa variant, the protection is less effective[44].


Sinovac CoronaVac vaccine

  • The Sinovac vaccine has been shown to be 50% effective against the Gamma variant[45], 59% effective against the Delta variant [59]


This evidence only tells us that the vaccines available in Hong Kong are still effective against some of the existing variants. There have not yet been studies that test the efficacy of the available vaccines against all variants, so we still don’t know if they protect against all existing variants or if they will remain effective against any variants that might emerge in the future. More testing is needed to understand how effective vaccines are against new variants.


5. What variants of the virus that causes COVID-19 exist?


There are currently 5 variants of concern that have been detected and are circulating globally.

[47] [48] [49] [50] [51] [52] [53] [54] [55]


6. Do vaccines stop new variants from developing?


Viruses mutate more when lots of people are transmitting the virus, stopping the spread of the virus that causes COVID-19 is the best way to avoid new variants developing. Current measures to reduce transmission - frequent hand washing, wearing a mask, social distancing etc - all help. Vaccinations are critical in reducing transmission. Vaccinating as many people as quickly and efficiently as possible will limit transmission of the virus, reducing opportunities for the virus to mutate and generate new variants[56][57].




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