Researchers at the Center for Epidemic Response and Innovation (CERI) in Cape Town, South Africa, have identified a new variant of the coronavirus SARS-CoV-2 characterized by a high number of mutations. Named BA.2.87.1 by experts, this variant has over 100 mutations, of which more than 30 are located on the S or Spike protein. The latter is essential for the virus as it acts as a “biological lock pick”, allowing the virus to bind to the ACE2 receptor on human cells.
Mutations on the Spike favor the virus’s ability to penetrate human cells, cross the cell wall, introduce viral RNA inside, and start the replication process. This mechanism contributes to the spread of infection and the onset of the disease known as COVID-19.
What is known about the new variant and symptoms
Professor Tulio de Oliveira, a leading geneticist in the field of the Covid pandemic, presented the new variant of the virus on X (formerly Twitter). The professor is known to lead the team that identified the Omicron variant in November 2021, which subsequently supplanted the other variants and became predominant with several descendant lineages.
The new variant, called BA.2.87.1, was discovered between September and November last year and initially classified as Ba.2.X. At the moment, its characteristics are not completely known, but according to Professor Raj Rajnarayanan of Arkansas State University, who analyzed the genomic sequences deposited in international databases, does not appear to cause particular concern in terms of immunoevasiveness. The latter refers to the ability of the virus to evade the neutralizing antibodies of the immune system, both those induced by the anti-Covid vaccination and by previous natural infections.
Even if it does not cause concern, it still needs to be kept under control as the specific symptoms still need to be identified, for now we can intercept them in the list of the most common circulating Covid variants, starting from Omicron, such as cough, sore throat and fever . The cough is dry, the nose is congested, you suffer from headaches, continuous sneezing and a sense of fatigue.
How dangerous it is
The epidemiological data presented on X by Tulio de Oliveira highlight that the BA.2.87.1 variant has already been present in South Africa for several weeks. The geneticist clarified that at the moment there are no signs of a wide spread of the variant and above all there has not been a significant rise to supplant the two predominant variants in the country, namely JN.1 and BA.2.86.
Data from public hospitals involved in pandemic surveillance, especially regarding pneumonia, they do not indicate an increase in the rate of cases since the new variant was identified. This suggests that BA.2.87.1 may currently be less immunoevasive and not of particular concern in terms of severity of infection and ability to spread.
However, the presence of multiple mutations is the main reason to maintain tight control over the variant. According to Professor de Oliveira, compared to the BA.2 variant (also part of the Omicron family) from which it appears to derive, BA.2.87.1 presents over 30 non-synonymous substitutions on the Spike protein and 7 deletions, of which 3 are concentrated on the Spike. Two of these deletions, 15-26del and 136-146del, are located in the “antigenic supersite of the N-terminal domain”, while there are multiple mutations in important antigenic sites in the receptor binding domain.
The number and characteristics of the mutations present in the BA.2.87.1 variant require careful monitoring, but at the moment there are no indications of greater danger or diffusivity of the virus. Regarding the origins, it is hypothesized that the variant could derive directly from the BA.2 lineage of Omicron, also known as the “invisible variant”.
This evolution may have occurred in a patient with a chronic infection, since in people with immunodeficiency the infection can persist for months, allowing the virus to evolve significantly through mutations. It will only be through careful monitoring of cases in the coming weeks that it will be possible to understand whether the BA.2.87.1 variant actually has the characteristics to become a new variant of concern in the pandemic, which is about to enter its fourth year.
The JN.1 variant still predominant in Italy
Despite the arrival of the South African variant, JN.1. is still predominant in Italy, reaching one prevalence equal to 77%. All this information is based on data collected in the survey conducted on samples notified from 15 to 21 January, compared to 38.1% in the previous flash survey carried out from 11 to 17 December. The Istituto Superiore di Sanità (ISS) has announced that the spread of the variant of interest, deriving from BA.2.86, is increasing globally and currently represents the dominant variant. According to currently available evidence, the JN.1 variant does not appear to pose additional risks to public health compared to other co-circulating lineages.
Furthermore, according to what was reported by the Istituto Superiore di Sanità (ISS), one can note co-circulation of other viral variants, albeit with clearly decreasing prevalence values, attributable to XBB, in particular to the variant of interest EG.5. Its estimated national prevalence is now 7.3%, compared to 30.6% in the previous survey.
In this current scenario, the ISS recommends continuing to monitor the spread of viral variants very carefully, in line with national and international recommendations and ministerial indications. Particular attention is paid to variants with greater transmissibility and/or mutations related to potential evasion of the immune response.
Covid bulletin: decline in hospitalizations in the last week
Good news regarding the Covid epidemic: according to the data of the latest weekly monitoring conducted by the Ministry of Health and the ISS, all indicators are decreasing. In the period from 25 to 31 January, there were 3,858 infections recorded, with 115 deaths, but there is also a decline in incidence and hospitalizations both in the medical area and in intensive care. Contrary to what happened during the Christmas period, where a peak in hospitalizations and sick people was reported.
The virologist and medical director of the IRCCS Galeazzi Hospital – Sant’Ambrogio, Fabrizio Pregliasco, commented on the situation, calling it “a season of respiratory viruses that we could define as the heaviest in the last 15 years, with the presence of a cocktail of viruses in which Covid was predominant especially in the first period of winter.”
According to official data from the last week, there has been a decline in incidence, which stood at 7 cases per 100,000 inhabitants in the week from 25 to 31 January, compared to 10 cases per 100,000 the previous week. The weekly incidence of diagnosed and reported cases is decreasing in almost all Regions/Autonomous Provinces compared to the previous week. The Veneto Region reports the highest incidence (13 cases per 100,000 inhabitants), while Basilicata, Sardinia and Sicily record the lowest incidence (1 case per 100,000 inhabitants).
The Rt transmissibility index, based on cases with hospitalization as of January 23, is also decreasing, equal to 0.57, slightly lower than the previous week when it was at 0.60. Regarding the variants, the JN.1 variant confirms its predominant role, representing 75.2% of the sequenced samples.