What are different variants of SARS- CoV-2 (COVID-19) detected so far?
Sai Krishna Muthyanolla
April 22, 2021
The SARS- CoV-2, the coronavirus that causes COVID-19 has undergone mutations and given rise to multiple variants. Many variants of the virus are being detected in various parts of the world. Some of these are popularly known as the UK variant, South African variant, etc. A new double mutant variant has recently been discovered in India. Here is a review of all these variants.
The total number of confirmed cases of COVID-19 has crossed 142 million and over 3 million deaths have been reported worldwide, as of 20 April 2021. Recently, India surpassed Brazil as the country with the second-highest number of confirmed cases in the world, after the USA. India has so far reported more than 15.6 million cases and 1.82 lakh deaths. Since 16 April 2021, India has been reporting more than 2 lakh new cases every day. States have begun imposing curfews and localized lockdowns to curb the rapid spread during the current wave. India’s surge in cases has raised alarm with the discovery of new variants of the virus. The rapid spread during the current wave means that countries like the UK have included India in the red list of countries from which travel to the UK is banned for those who are not UK or Irish residents or a British citizen if they’ve been in India in the previous 10 days.
With time, variants of the virus emerge through mutations
Viruses are constantly changing. Genetic variations occur with time which results in the emergence of new variants with varying characteristics. SARS- CoV-2, the coronavirus behind the ongoing pandemic is no exception to it. Each coronavirus contains a sequence of around 30,000 letters of RNA. When the virus infects a living cell, it makes copies of itself and while doing so, there can be small copying errors known as mutations which result in a new ‘lineage’ of the virus as the mutation gets passed down. A variant is a virus with one or more new mutations as compared to the original virus. That is, with the mutations, the variant virus is genetically different from the main strain but is not different enough to be considered a new strain.
CDC has classified variants into 3 broad categories
It has been more than a year since the pandemic began. Multiple variants of SARS- CoV-2 are being detected globally. The Centers for Disease Control and Prevention (CDC), USA has classified all the variants into three- Variants of Interest (VoI), Variants of Concern (VoC), and Variants of High Consequence (VoHC).
VoI and VoC have D614G mutation which increases Virus’ transmissibility
Those variants which show an increase in transmissibility, more infectious and causing more severe disease resulting in increased hospitalizations or deaths, reduced response to treatments and vaccines, a significant reduction in neutralization by antibodies generated during previous infection or vaccination, or failure in diagnostic detection are treated as Variants of Concern, VOC. Currently, there are five VOCs according to CDC. All the five variants share one specific mutation called D614G which makes the virus more transmissible than its original form.
3 variants have been categorized as Variants of Interest (VoI)
Variants with specific genetic markers that have been associated with changes to receptor binding, reduced neutralization by antibodies generated against previous infection or vaccination, reduced efficacy of treatments, potential diagnostic impact, or predicted increase in transmissibility or disease severity are VOIs. That is, the mutations may help the virus to dodge antibodies and treatment but is not as infectious as VOCs. CDC has classified three variants as VOIs. All three, share a specific mutation, D614G, and have the potential to evade antibodies.
VoHCs are variants with evidence that prevention measures or medical countermeasures have significantly reduced effectiveness as compared to other variants. So far, no SARS-CoV-2 variant falls under this category.
INSACOG detected UK and South African variants in India in March 2021
The Indian SARS-CoV-2 Genomics Consortium (INSACOG) is a network of ten laboratories established in December 2020 for continuously monitoring the genomic changes of SARS-CoV-2 in India. INSACOG has detected 771 VoCs in a total of 10787 positive samples shared by States since it began the work. These include 736 samples positive for viruses of the UK (B.1.1.7) lineage. 34 samples were found positive for viruses of the South African (B.1.351) lineage.  One sample was found positive for viruses of the Brazilian (P.1) lineage, across 18 states in the country as of March 2021.
New variant with two mutations was discovered by INSACOG in India
INSACOG also discovered the double mutant variant in India upon analysing samples from Maharashtra which revealed an increase in the fraction of samples with E484Q and L452R mutations. The E484Q mutation is similar to that found in the B.1.1.7 lineage identified in UK and B.1.351 variants identified in South Africa which gives the virus the ability to evade antibodies and the L452R mutation is like that in the Californian B.1.427 and B.1.429 variants, which is infectious. Both the mutants are present in the B.1.617 variant of SARS-CoV-2 found in India. Research about the virus is still ongoing, and this virus has still not been classified by the CDC.
B.1.617 has spread to USA, UK, and other countries
The new double mutant has spread to the USA, Germany, UK, Australia, and Germany.  It also has been found in Belgium, Ireland, Namibia, and New Zealand. Higher transmissibility of this variant is not established as yet, according to the Health Ministry’s recent press release.  It also added that RT PCR tests used in India do not miss these mutations and that the sensitivity and specificity of the RTPCR tests remain the same as earlier.
Sequences of B.1.618 lineage has been discovered in West Bengal
Initial sequences in B.1.618 lineage have been identified in West Bengal, according to a tweet by Vinod Scaria, who is a researcher at the Council of Scientific and Industrial Research’s Institute of Genomic and Integrative Biology (CSIR-IGIB). Members in this lineage have also been reported from the USA, Germany, Switzerland, and Singapore. However, it is predominantly found in India. The variant is characterized by the deletion of two amino acids in the spike protein —H146del and Y145del, which are both linked to immune escape or in other words evade antibodies. In addition, the variant also carries the D614G mutation in the spike protein and the E484K mutations, which are associated with increased infectivity and immune escape, respectively. It has also been noticed that the proportion of SARS-CoV-2 samples of the B.1.618 lineage has been increasing in West Bengal in recent months. However, there is no conclusive data as yet to ascertain that the new lineage is driving the epidemic in West Bengal.
Efficacy of vaccine may be lowered but may not be completely ineffective according to WHO
With the identification of new variants, a major concern is the effectiveness of vaccines that are being administered across the world. As seen previously, the efficacy of the AstraZeneca vaccine against the B.1.351 variant from South Africa was low. Studies also suggest that the efficacy of the Pfizer-BioNTech vaccine and Moderna vaccine substantially decreased in the presence of the E484K mutation. An ICMR study claims to have found that Covaxin was effective against multiple variants of the coronavirus including the variants that originated in the UK, Brazil, and South Africa. It was also stated that the vaccine was effective against the double mutant strain as well. But detailed knowledge & information about vaccine efficacy against emerging variants is still not available. However, the vaccines which are under development and approved are expected to provide some form of protection against the new variants. Changes or mutations in the virus need not make vaccines completely ineffective, according to WHO. Moreover, since the mutations and variants are related to the original strain, the changing composition of vaccines may also help if they prove to less effective.
Taking precautions is a must
With the increasing number of mutants and variants being detected around the world, emphasis must be on using public health interventions to slow the spread of viruses which can also slow down the emergence of variants as more mutations and variants are formed through infections. For this, one must continue to follow the precautions of respiratory hygiene, social distancing, wearing masks, and getting vaccinated.