Of the hundreds of SARS-CoV-2 mutations detected during the pandemic, the attention of health authorities falls on four variants of concern – Alpha, Beta, Gamma and Delta – present in Portugal with community transmission.
Alpha, associated with the United Kingdom, was the first of these variants to have a high prevalence in Portugal, and it is estimated that, in May, it was responsible for almost 90% of the cases of infection by the new coronavirus in the country.
More recently, attention has turned to the Delta variant, initially detected in India, considered more transmissible, and which, according to national health authorities, could surpass Alpha and become prevalent in Portugal within a few weeks.
According to the European Center for Disease Prevention and Control (ECDC), the Delta variant of SARS-CoV-2 will account for 90% of new infections in Europe by the end of August and an increase in hospital admissions and deaths.
Variants considered of concern by the World Health Organization
Currently, the World Health Organization (WHO) has classified four “variants of concern” (VOC), having assigned, in late May, the designation of letters of the Greek alphabet to facilitate understanding.
In the VOC category are, therefore, Alpha, initially detected in the United Kingdom in December 2020, Beta, associated with South Africa since December 2020, Gamma, identified in Brazil in January 2021, and Delta, originating India and classified as of concern in May this year.
A variant is considered to be of concern when one or more of the following conditions occur: increased virus transmissibility, increased virulence or clinical change in the disease, and decreased effectiveness of social and public health measures, diagnoses, vaccines and available treatments .
In addition to VOCs, WHO has classified seven other alterations of the SARS-CoV2 virus as “variants of interest” (VOI), the last of which is Lambda, associated with Peru.
The other six VOI are Epsilon (United States, initially detected in March 2020), Zeta (Brazil, April 2020), Eta (several countries since December 2020), Theta (Philippines, January 2021), Iota (United States, November 2020) and Kappa (India, October 2020).
A variant is considered of interest when it has been identified as a cause of community transmission and detected in several countries.
Variants with community transmission in Portugal
The four variants classified by WHO as being of concern – Alpha, Beta, Gamma and Delta – are present in Portugal and present community transmission, that is, when there are cases where it is not possible to trace the origin of the infection.
According to preliminary June data from the Doctor Ricardo Jorge National Health Institute (INSA), the prevalence of the Delta variant (B.1.617.2, associated with India) is over 60% in the Lisbon and Vale do Tejo region, being, however, still less than 15% in the North.
The INSA estimates that the Delta variant has a degree of transmissibility about 60% higher than the Alpha variant, associated with the United Kingdom and which was predominant in Portugal during May.
However, the institute predicts that Delta, which has multiple mutations in the `spike’ protein that makes it more capable of transmitting and evading the immune system, could overtake Alpha in the coming weeks.
Regarding Beta, associated with South Africa, and Gamma, identified in Manaus, Brazil, until June 16, 133 cases and 146 cases had been identified, respectively, with these two variants also having community transmission in the country.
Impact of variants on vaccine efficacy
The Delta variant of the new SARS-CoV-2 coronavirus is already circulating in 92 countries, indicated the WHO, safeguarding that vaccines remain effective against this strain, preventing cases of serious illness and death.
According to the technical leader in response to covid-19 at the WHO, Maria Van Kerkhove, on Monday, the Delta variant “is spreading rapidly” and “has greater transmissibility than the Alpha variant”, initially diagnosed in the United Kingdom .
Maria Van Kerkhove said the vaccines “work against the Delta variant” because, as with other strains of the virus, they prevent severe covid-19 and death if the vaccination cycle is complete.
Virologist Pedro Simas also considers that, so far, there has not been a variant of the SARS-CoV-2 coronavirus that “breaks the protective effect” of vaccines against covid-19, stressing that they are all efficient in preventing serious illness and death .
It doesn’t mean that very rare cases don’t appear, but we can’t focus on the rare and now we have to look for the common good, which is to deconfine”, said the specialist to Lusa.
Recently, the Directorate-General of Health (DGS) decided to reduce the interval for taking the second dose of Astrazeneca vaccine from 12 to eight weeks to ensure “faster protection” against the transmission of new “concern variants” of the SARS-virus. CoV-2.
According to the DGS, the vaccination schedule of the VAXZEVRIA vaccine (formerly called Astrazeneca) is two doses with an interval of eight to 12 weeks, “the interval of eight weeks being currently recommended in order to ensure the quickest protection” provided by the vaccination completes “on the transmission of new SARS-CoV-2 Concern (VoC) variants” such as the Delta variant.
The day before, the European Commissioner for Health, Stella Kyriakides, said that evidence was emerging to show that the Delta variant of the SARS-CoV-2 coronavirus “decreases the strength of the protective shield” created by vaccines, urging the acceleration of full vaccination of the population.
“Evidence has emerged that the variants – namely the Delta variant – diminish the strength of the protective shield provided by vaccines, especially when vaccination is not yet complete. It is therefore crucial that as many citizens as possible be vaccinated against covid -19, and that it is fully vaccinated as soon as possible,” said Stella Kyriakides.
How variants of the original virus arise
All viruses, including the SARS-CoV-2 that causes covid-19, tend to change with time and circulation, although most changes have little or no impact on their properties.
When a virus makes copies of itself, these changes are considered mutations. A virus with one or several new mutations is considered to be a variant of the original.
Some mutations can lead to changes in the characteristics of a virus, such as its greater or lesser transmission capacity and the level or severity of a disease it can cause.
According to the WHO, SARS-CoV-2, which causes covid-19, tends to change more slowly than other known viruses, such as the Influenza that causes the flu.
To date, hundreds of variations of SARS-CoV-2 have been identified in various parts of the world, with the vast majority having little impact on the properties of the original coronavirus.
Worldwide concert to understand SARS-CoV-2 variants
Since the beginning of the pandemic, WHO has been working with a global network of specialized research and testing laboratories to better understand the behavior of SARS-CoV-2.
These research groups sequence SARS-CoV-2 and share the results in public databases, including GISAID, a research organization recognized by the European Commission and partner of PREDEMICS, a project on the prediction and prevention of zoonotic viruses (with transmission from animals to humans) with pandemic potential.
This global collaboration allows scientists from around the world to track the virus and its mutations more efficiently and quickly.
The WHO global laboratory network also includes a working group on the evolution of SARS-CoV-2 specifically dedicated to detecting new mutations and assessing their predictable impact.
How is this monitoring done in Portugal
The INSA is coordinating the monitoring of the dissemination of the new coronavirus in Portugal, through the genome analysis of this pandemic virus.
This study involves collaboration with the Gulbenkian Science Institute (IGC), the Institute of Biomedicine (iBiMED, University of Aveiro), the BioSystems & Integrative Sciences Institute (BioISI, University of Lisbon), the Institute for Research and Innovation in Health ( i3S) and the Research Center on Biodiversity and Genetic Resources (CIBIO, University of Porto), for sample processing purposes, and with a network of more than 60 hospitals and laboratories across the country to send positive samples to INSA.
The “Study of the genetic diversity of the new SARS-CoV-2 coronavirus (COVID-19) in Portugal” aims to determine the mutational profiles of SARS-CoV-2 for the identification and monitoring of transmission chains of the new coronavirus, as well as the identification of new ones introductions of the virus in Portugal.