What is a variant?
A variant is a virus that displays genetic changes compared to an "original" version of the virus. When it comes to COVID-19, the original version is the one that showed up in China at the end of 2019. The SARS-CoV-2 chromosome, which contains the genetic material, can be described as 30,000 words, letters long, and the 4 letters A, U, G, and C. The exact order of these letters specifies the structure of the 15 genes responsible for manufacturing the virus's proteins. Therefore, any change, however small, to this long sequence of letters is likely to make changes to any of these proteins.
When the virus reproduces, a copy of the original chromosome is incorporated into the new virus particles, but each copy is likely to contain one or more errors that will distinguish it from the original version. These are the differences called mutations. Some of these latters will be "lethal" and prevent new virus particles from forming. Further mutations will be passed on to complete generations of new viruses, called "variants."
The vast majority of variants behave quite identically to the classic virus and are therefore of no clinical concern. Others, such as the British, South African, Brazilian, and Indian variants, are of great concern as they modify the famous S (spike) protein, which is responsible for much of the infectivity of SARS-CoV-2. The problem is that vaccines are based on the S protein of the original chromosome (without mutations) and might not protect us against these variants that have different S protein.
VOC or VOI: how are variants classified?
The World Health Organization (WHO) has classified the variants into two categories:
The "variants of concern" (VOC)
are characterized by an "increase in transmissibility or detrimental evolution of the epidemiology of COVID-19", an "increase in virulence or modification of the clinical picture," or a "decrease the effectiveness of public health and social measures or diagnostic tools, vaccines and treatments available. " For the moment, these are the Alpha (English), Beta (South African), Gamma (Brazilian), and Delta (Indian) variants.
The "variants of interest" (VOI)
"to be followed if, compared to a reference isolate, [their] genome presents mutations with established or presumed phenotypic implications," and "if it is known to be at the 'origin of community transmission / of several cases / of a group of cases of COVID-19, or that it has been detected in several countries ", or" if it is considered, for other reasons, to be a variant to be monitored by WHO, in consultation with the WHO SARS-CoV-2 Virus Evolution Working Group ". For now, these are the variants Epsilon (American), Zeta (another Brazilian variant), Eta (several countries), Theta (Philippines), Iota (another American variant), Kappa (another Indian variant), and Lambda (Peruvian).
What is the characteristic of the Covid-19 variants?
The worrying variants of Covid-19 are often more contagious than the original strain. The mutations mainly affect the protein responsible for attaching the virus to the respiratory tract (S protein, such as Spike or Spicule).
There is also a risk of immune escape, which means that antibodies produced after infection or vaccination are less protective against these strains of variants of concern.
The Indian variant was first isolated in the Indian state of Maharashtra, where Bombay is located. "Its current prevalence is difficult to quantify, and the lack of epidemiological data correlated with virological results of molecular sequencing on a large scale calls for a certain caution," notes the Covid-19 Scientific Council in a press release dated April 23. Nevertheless, it has been considered by the WHO as a variant of concern since May 11, 2021.
It is different from other viruses. As stated by the Scientific Council, the Indian variant is different from the British, South African, Brazilian, and Californian variants. It contains 15 divergent mutations except 2 common to other viruses on the Spike protein: one identical to the Californian variant and another also present on the variants qualified as VOC.
British or alpha variant
First appearing in September 2020 in the UK, the UK variant, also known as VOC 202012/01 or B.1.1.7, was stated by the UK authorities on December 14, 2020, and has since caused a sharp rise cases on the island.
According to a study posted on March 10 in the medical journal BMJ (British Medical Journal), the English variant is more contagious and 64% more deadly than the classic coronavirus. For 1,000 cases identified, the British variant causes 4.1 deaths, against 2.5 for the classic coronavirus, conclude the writers of this work. "There is a high probability that the death risk is increased by an infection" with the British variant, write these researchers from the universities of Exeter and Bristol.
By the end of January, NERVTAG, the group that advises the British government on respiratory viruses, said a "realistic possibility" that infection with this variant was linked to a higher risk of death. According to several studies, this group predicted that the mortality of the variant (risk of dying of those infected) could be 30 to 40% higher.
South African variant or Beta
On December 18, 2020, the South African Department of Health announced the emergence of a variant on national territory. Several days later, the number of cases augmented strongly throughout the country.
Although it is not more mortal than SARS-COV-2, it is 1.5 times more contagious, depending on South African experts. Called 501Y.V2, this mutation "is 50% more contagious", but "there is nothing to indicate that the new variant is more serious," said Prof. Salim Abdool Karim, an epidemiologist.
In addition, several studies meet to say that the South African variant seems to reduce the vaccines' effectiveness, mainly because of the E484K mutation. The latter two were posted on February 17 in the medical journal "NEJM" and were produced by scientists from Pfizer / BioNTech and Moderna, the makers of the two main vaccines.
They show that the quantity of protective antibodies produced after the injection of these two vaccines is less important when we are in the presence of the South African variant (compared to the English variant or the classic coronavirus). This, therefore, suggests that the protection is weaker. Prof. Schwartz's team, responsible of the Viruses and Immunity unit at the Pasteur Institut, achieved the same study, according to which "it is much more difficult to protect against the South African variant over time."
However, a preparatory study carried out in early March by the South African scientific team that discovered the South African variant 501Y.V2 shows that people infected with the South African variant of the new coronavirus have good immunity to other mutations the virus.
South African researchers have said that plasma from individuals infected with the variant had "good neutralizing activity" against "first wave" viruses and potentially alarming other variants. "501Y.V2 can generate a high level of antibody able of neutralizing it," virologist Tulio de Oliveira explained in a video conference, reporting an immune response that exceeds that of other variants.
The Brazilian variants
Two Brazilian variants originating from the Amazon, P1 alias Gamma listed as "alarming" by the WHO.
The first variant, B1.1.248, was identified in early January in Japan in a family from Brazil and, more specifically, from the Amazon. It became dominant in Manaus, the Amazonas capital: "In December it was found in 51% of sequenced samples from coronavirus patients, and between the beginning and January 13 it was 91 % ", clarifies Felipe Naveca.
The contagiousness of the variant was also quickly noticed: "All the indications already indicate that (this variant) is more contagious because it has mutations which have been linked to the greater transmission of the virus observed in the variants from the United Kingdom and South Africa, "the researcher said.
At the end of January, another second variant appeared, called P.1. It is "one of the 18 coronavirus variants that have outspread in the Amazonas since the start of the pandemic," 10 months ago, explains the researcher.
The variants result in greater transmissibility of Covid-19, but tests performed at Cerballiance detect all forms of Covid-19. In addition, thanks to the specialized laboratory Cerba, we can identify, if necessary, the presence or not of the variant form in a sample thanks to the mastery of complex techniques for sequencing the complete genome of the virus.