The very recent identification of a new strain of SARS-CoV-2 leading to COVID-19 disease has caused worldwide concern with particularly significant health and socio-economic implications.
The Doctors of the Therapeutic Clinic of the Medical School of the National and Kapodistrian University of Athens Theodora Psaltopoulou, Giannis Danasis, Panos Malandrakis and Thanos Dimopoulos (Rector of EKPA) summarize the latest data.
The new strain was first identified in samples of COVID-19 patients collected on November 11, 2021 in Botswana, and was soon identified in South Africa as well as in a vaccinated traveler who had returned to Hong Kong after a trip to South Africa during the period October 22 to November 11, 2021.
The B.1.1.529 strain was detected in another person in the hotel where the traveler with whom he came in contact was staying in quarantine. Subsequently, new cases of COVID-19 due to the new strain were recorded in Israel and Belgium. It is worth noting that the case found in Belgium had not been vaccinated or previously infected with COVID-19 and had traveled only to Egypt and Turkey, while it showed symptoms 11 days after the trip to Egypt via Turkey in early November 2021.
The fact raises concerns about the spread of the new strain in more countries not only in Africa but also on other continents. COVID-19 cases due to the new strain have also been reported in the United Kingdom, Germany and Italy. To date, there is no evidence to suggest that infection with the new strain leads to more severe symptoms.
The World Health Organization named the new strain B.1.1.529 “Omicron” and described it as a “strain of concern”. The new strain B.1.1.529 displays a particularly alarming profile of 32 mutations in the S-protein of the S gene that the virus uses to invade human cells. The number and type of mutations are causing concern in the international scientific community.
Virologist Tom Peacock of Imperial College London notes that he is the first strain of SARS-CoV-2 with two mutations encoding the furin cleavage site in protein S, P681H and N679K. These mutations, along with H655Y, are associated with improved ability of the virus to enter human cells and increased transmission potential, and it is worth noting that the P681H mutation is also detected in the Delta strain. In addition, deletion of nsp6 (Δ105-107) may be associated with the escape of natural human immunity, as it leads to antagonism of the action of interferons that have antiviral activity, and may also be associated with increased transmissibility. This mutation has also been detected in Alpha, Beta, Gamma and Lambda strains. In addition to S protein mutations, there are other disturbing mutations in the Omicron strain such as nucleocapsid R203K and G204R, which are associated with increased virulence and have also been detected in Alpha, Gamma and Lambda strains. Mutations detected in the new Omicron strain may also increase the risk of re-infection, escape of the protection offered by the vaccine, and reduced effectiveness of monoclonal antibody therapies against SARS-CoV-2. However, further research is needed to determine the exact level of risk.
Particularly worrying are the epidemiological data from the SARS-CoV-2 genome sequencing data in South African cases, where it appears that the new strain B.1.1.529 predominates over the delta strain. Recent COVID-19 outbreaks in South Africa have been attributed almost entirely to the new Omicron strain. Taking all of the above into account, epidemiological risk assessment models predict that the Omicron strain has a clear rapid dominance advantage over the Delta strain.
Regarding the diagnosis of the new Omicron strain, it is possible to rapidly detect with existing polymerase chain reaction (PCR) technology and the S-gene dropout test before confirmation by sequencing the virus genome, which requires more time. Early data based on PCR S-gene dropout tests on samples from new COVID-19 cases in different South African provinces suggest that the new Omicron strain has probably already spread across the country.
Both Europe and the United Kingdom and the United States have already imposed travel restrictions on African countries where a new outbreak of Omicron has been reported. 600 travelers who returned to the Netherlands from South Africa are in quarantine and are being examined for possible detection of the new strain as at least 61 of them have confirmed COVID-19 infection.
Pfizer, Moderna and Novavax have already announced that they are working hard to verify the effectiveness of their vaccines against the new Omicron strain and to adapt them appropriately to offer strong protection against the new strain.
In conclusion, the new SARS-CoV-2 Omicron strain raises serious concerns about the potential for transmission, re-infection and escape of vaccine protection. Clear data in relation to the above will be available within the next four weeks. In this context, it is even more necessary to vaccinate with the third booster dose to achieve maximum protection against the serious disease COVID-19, as well as the constant vigilance for the early detection and isolation of cases in order to stop the transmission chain. In addition, increasing vaccinations in developing countries must be a priority for developed countries and international organizations. The majority of Experts note that even in the possibility of confirming the most unfavorable scenarios, we will not return to the original state of the pandemic.
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