Ômicron variant: what is known about the new strain of SARS-CoV-2

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The B.1.1.529 variant of the new coronavirus was named as Ômicron and classified as a variant of concern by the World Health Organization (WHO) on Friday (26).

The WHO Technical Advisory Group’s decision on the evolution of the SARS-CoV-2 virus was based on the evidence presented that indicates harmful changes in the epidemiology of Covid-19 due to the strain.

Currently, WHO considers as variants of concern five strains of the new coronavirus: Alpha (B.1.1.7), from the United Kingdom, Beta (B.1.351), from South Africa, and Delta (B.1.617.2) ), from India, the Gama (P.1), from Brazil, and the Ômicron (B.1.1.529), from different countries, according to the WHO.

The strain was first reported to WHO by South Africa on 24 November. The epidemiological situation in the country showed three distinct peaks of Covid-19 cases, the last being predominantly due to the Delta variant.

In recent weeks, infections have increased abruptly, coinciding with the detection of the new variant. According to the WHO, the first known confirmed case of Covid-19 was from a sample collected on November 9, 2021.

“This variant has a large number of mutations, some of which are of concern. Preliminary evidence suggests an increased risk of reinfection with this variant compared to other variants of concern,” WHO said in a statement.

WHO recommends strengthening genomic surveillance by countries

WHO advised that countries should improve surveillance and efforts to carry out genomic sequencing of the virus, which allows for a better understanding of circulating variants. Scientists must submit the complete genome sequences and associated data about the variant to a publicly available database such as GISAID.

In addition, cases associated with the variant of concern must be reported to WHO through the International Health Regulations (IHR) mechanism. In countries where there is capacity, and in coordination with the international community, field investigations and laboratory evaluations should be carried out.

The objective of the measure, according to the WHO, is to improve the understanding of the potential impacts of the Ômicron variant on epidemiology, disease severity, for public health, in addition to possible repercussions of the strain for diagnostic methods, immunological responses, neutralizing antibodies and efficacy of vaccines.

For the population in general, WHO reinforced the need to take measures to reduce the risk of Covid-19 infection, including the use of well-fitting masks, hand hygiene, physical distance, improved ventilation of indoor spaces, avoidance crowded spaces and adherence to vaccination.

How do they detect the ômicron variant?

The number of cases of the variant has increased in almost all provinces of South Africa. According to WHO, current molecular diagnostic tests (RT-PCR) are able to detect the strain. From these tests, the variant was detected at faster rates than previous outbreaks, suggesting that the strain may have a spread advantage.

The micron variant has scientists worried because it has many mutations that could confer advantages to the virus. The strain has also been found in Botswana, Hong Kong, Israel and Belgium. So far, there are no records of the variant in Brazil.

From the identification, carried out through the genomic sequencing of the virus, scientists seek to answer different questions such as transmission capacity, increased lethality and whether there is any kind of reduction in the effectiveness of the vaccines developed against Covid-19.

“The whole process of what these mutations mean, in terms of increased transmissibility, potential cases of reinfection and how the vaccine’s response will be is still being studied. We still do not have robust and concrete data to show about this new variant, which was predominantly discovered in South Africa”, said researcher Marilda Siqueira, from the Oswaldo Cruz Institute (IOC/Fiocruz) in an interview with CNN.

“What you see there is the increase in the number of cases. However, the impact of the variant on hospitalizations and people who have already been vaccinated is not yet determined”, completed Marilda.

So far, scientists have detected that the Ômicron variant has several mutations, which may indicate advantages to the virus, such as a potential for greater transmissibility and the escape of antibodies.

However, further studies are needed to answer whether the new variant could have any impact on the effectiveness of the Covid-19 vaccines in use in the world.

Ômiceron ten grabde number of mutations

The Ômicron variant has a wide range of mutations. In isolation, these mutations can both bring advantages to the virus, such as a greater ability to transmit or escape from the immune system, or not represent any kind of gain for the microorganism.

“What is most striking is that the variant has a large number of mutations, there are at least 32. It has several mutations that we have already seen in other variants that were important over time, such as the Alpha variant”, explains the virologist Fernando Spilki, researcher at the Feevale University, in Rio Grande do Sul.

According to the researcher, in addition to mutations, the new variant has a characteristic technically called deletion. Because they are very simple structures, viruses have a great capacity for modification. Among these genetic changes, deletions arise, which are characterized by the removal of one or more nucleotides (which are the building blocks that make up RNA or DNA) from a gene.

The virologist explains that the variant has at least three deletions in the genetic material of the Spike protein, which is used by the virus to invade human cells, a fundamental part of the Covid-19 infection process.

“One deletion that caught my attention was the height of amino acids 69 and 70, which was found in the Alpha variant, identified in the UK. The variant also has the N501Y mutation, very characteristic of the Gamma variant, which also occurred in the Beta variant strains. It also has the E484A mutation, which demonstrates that the strain is ‘mutating’ in several ‘sites’ that we had already mapped over time”, he explains.

What is known about transferability

One of the main concerns of scientists with the emergence of a new variant is to find out if there is greater transmissibility, which could lead to Covid-19 outbreaks.

According to the virologist at the University Feevale, Fernando Spilki, in-depth studies that can answer the question regarding the Ômicron variant are still needed. However, the specialist points out that the strain has been widely disseminated in the places where it has been detected so far.

“In places where the variant occurred, in the last two weeks, it has evolved to 90% of detections, including places where the highly transmissible Delta variant had already spread and was causing an increase in cases. The Ômicron variant, even so, today predominates with 90% of detections”, explains Fernando.

Impact on vaccine efficacy remains unknown

The researcher Fernando Spilki considers that understanding the impacts of mutations on characteristics such as transmissibility, lethality and effectiveness of vaccines against Covid-19 depends on additional studies.

“These mutations do not mean that we are in a critical situation. We need to test, both in vitro and in vivo, which are the effects of this accumulation of mutations, it is something that needs to be investigated”, he adds.

According to the virologist, South Africa has an efficient genomic sequencing program for the new coronavirus samples, which allowed the identification of the new variant even with a low number of cases.

However, the rapid increase in the number of cases throughout November in Gauteng province, where Johannesburg is located, has drawn the attention of local health authorities.

Genome sequencing revealed that the variant was responsible for all 77 virus samples analyzed in Gauteng, collected between 12 and 20 November. Hundreds of other samples are currently being analyzed.

Repercussions of the new variant

On Friday, the Ministry of Health issued a warning to state and municipal departments about the risk of the new variant of the coronavirus.

The National Health Surveillance Agency (Anvisa) recommended restrictive measures for flights and travelers from South Africa, Botswana, Swatini, Lesotho, Namibia and Zimbabwe. Second survey (see list here) made by CNN this Friday afternoon, at least 17 nations had announced total or partial blockades to travelers from southern African countries.

The WHO, however, warned that it does not advise imposing travel restrictions related to the new variant, but that countries should strengthen genomic surveillance strategies.

Belgium was the first country in Europe to report a case of the new Covid-19 variant. The information was released by virologist Marc Van Ranst, whose laboratory works in conjunction with the Belgian public health department. The case was identified in a traveler returning from Egypt to Belgium on 11 November.

The Ômicron variant was also detected in Israel this Friday. According to the local Ministry of Health, the case was identified in a person who came from Malawi. In addition to this already confirmed case, there are suspicions of two more cases coming from abroad awaiting test results.

With information from Giovanna Galvani, Carolina Figueiredo, Rafaela Lara, Giovanna Inoue, Layane Serrano, Vinícius Bernardes, João de Mari and Kenzô Machida, from CNN.

Reference: CNN Brasil

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