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The Hunt for COVID Variants: How the New Omicron Variant Was Discovered and What We Have Learned Thus Far




The South African Network for Genomics Surveillance has been monitoring changes in SARS-CoV-2 since the outbreak of the COVID pandemic began in 2003. When it came to getting a better grasp on how the virus spread, this was a tremendously useful tool. A new virus lineage, 501Y.V2, was discovered by the network in late 2020, and it was dubbed the "beta variant." SARS-CoV-2 variant B.1.1.529 has now been identified as a new SARS-CoV-2 variant. The World Health Organization has classified it as a variant of concern and given it the designation Omicron. The Conversation Africa's Ozayr Patel asked scientists to share their knowledge in order to aid in our understanding.


On what scientific foundation is this investigation based?


An organized effort is required for variant hunting. A nationwide genomic surveillance program for SARS-CoV-2 began in April 2020 in South Africa and the United Kingdom.


As thrilling as it may sound, variant hunting is accomplished by sequencing the entire genomes of samples that have tested positive for the virus in the first instance. As part of this process, we will compare each sequence obtained to what we believe to be in circulation in South Africa and throughout the world. When we notice multiple differences, it immediately raises a red flag, prompting us to conduct additional research to confirm our findings.


In this regard, South Africa is fortunate in that it is well prepared. There are several factors contributing to this, including the National Health Laboratory Service's (NGS-SA) central repository of public sector laboratory results, strong links with private laboratories, the Western Cape Province's Provincial Health Data Centre, and state of the art modeling expertise.


Apart from that, South Africa is home to several laboratories that are capable of growing and studying the actual virus, allowing researchers to determine whether or not antibodies developed in response to vaccination or previous infection are effective against the new virus. We will be able to characterize the newly discovered virus with the assistance of this information.


Because the beta variant spread much more quickly between people than the "wild type" or "ancestral" SARS-CoV-2, the beta variant was responsible for the second pandemic wave in South Africa. Because of this, it has been labeled as a subtype of problem. After spreading throughout much of the world, including South Africa, in 2021, a new strain of the virus known as delta was discovered, resulting in a third pandemic wave worldwide.


An outbreak of a new virus lineage, designated B.1.1.529, in South Africa was discovered through routine sequencing by member laboratories of the Network for Genomics Surveillance. This virus was found in 77 samples collected in the province of Gauteng in the middle of November 2021. Minor outbreaks of the virus have also been reported in nearby Botswana and Hong Kong. According to reports, the traveler from South Africa is the subject of the Hong Kong case..


A variant of concern, B.1.1.529, has been designated by the World Health Organization as Omicron and is included in the same category as beta and delta.


Why is South Africa presenting variants of concern?


There is no way for us to know for sure. In any case, it does not appear to be the result of concerted efforts to keep track of the virus that is currently circulating. An alternative theory proposes that individuals with severely compromised immune systems who are infected for an extended period of time due to their inability to clear the virus may serve as a source of new viral variants.


The assumption is that some degree of "immune pressure" (defined as an immune response that is insufficiently strong to eliminate the virus but exerts sufficient selective pressure to "force" the virus to evolve) creates the conditions for the emergence of new variants of the virus to emerge.


A sophisticated antiretroviral treatment program for HIV-positive individuals is in place in South Africa, but many people are suffering from advanced HIV disease and are not receiving effective care. This hypothesis has been supported by a large number of clinical cases, but there is still much more to learn.


Why is this variant cause for concern?


Short answer: we have no idea what you are talking about. There are several concerning mutations in B.1.1.529, which is the long answer. This is the first time they have been observed together, and the spike protein alone contains more than 30 mutations! Having this information is essential because the spike protein is the primary component in the vast majority of vaccines.


As an added bonus, we can say that the genetic profile of B.1.1.529 differs significantly from that of other circulating variants of interest or concern. This virus appears to be a novel SARS-CoV-2 lineage, rather than a "daughter of delta" or "grandson of beta."


While some of its genetic changes are known from other variants and have been shown to affect transmissibility or allow immune evasion, the majority of them are novel and have not been studied in any previous research. The extent to which the mutations will affect the organism's behavior is still being investigated, despite our ability to make some predictions.


Specifically, we're interested in learning more about the virus' transmissibility, disease severity, and ability to "escape" the immune response in individuals who have been vaccinated or who have recovered from a previous infection. A two-pronged approach is being taken to investigate this.


As a starting point, meticulous epidemiological studies are being carried out to determine whether the new lineage demonstrates changes in transmissibility, the ability to infect people who have been vaccinated or previously infected, and so on.


Laboratory studies are being conducted at the same time to determine the virus's characteristics. A comparison is made between the characteristics of its viral growth and those of other virus variants, and the virus's ability to be neutralized by antibodies found in the blood of people who have been vaccinated or who have recovered is assessed.


Last but not least, when the results of all of these various types of studies are taken into consideration, the full significance of the genetic changes observed in B.1.1.529 will become apparent. However, even though it will take months to complete this laborious, time-consuming, and expensive endeavor to gain a better understanding of the virus and develop the most effective strategies for combating it, it is necessary.


Do early indications point to this variant causing different symptoms or more severe disease?


Clinical differences are not currently supported by any evidence. What is known is that the number of B.1.1.529 infection cases has increased significantly in Gauteng, which appears to be the province where the country's fourth pandemic wave is beginning to manifest itself. Even though non-pharmaceutical interventions are much more relaxed and the number of cases is low, this indicates that transmission is simple. Consequently, we are unable to determine conclusively whether B.1.1.529 is more efficiently transmitted than the previously prevalent variant of concern, beta.


COVID-19 is more likely to manifest as a severe, sometimes fatal disease in the elderly and chronically ill people. The population groups that are most frequently the first to be infected by a new virus, on the other hand, are younger, more mobile, and generally healthier individuals. The severity of the disease will not be known for a long time if B.1.1.529 spreads throughout the population.


All diagnostic tests performed thus far, it appears, are capable of identifying the new virus. This is encouraging news.


Even better, it appears as though several widely used commercial assays follow a consistent pattern: two of the three target genome sequences are positive, but the third is negative, which is consistent with the findings. For all intents and purposes, it appears as though the new variant consistently checks two out of three of the three boxes on the existing test.. On a daily and per-area basis, this could serve as a biomarker for B.1.1.529 infection, allowing us to estimate the proportion of positive cases due to B.1.1.529 infection in a timely manner. Because of its near real-time nature, this is extremely useful for tracking the spread of the virus.


Are there any indications that the current vaccines will provide protection against the newly discovered variant?


We have no idea what is going on once again! There are known cases of individuals who have received a vaccination. The immune protection provided by vaccination, on the other hand, has been found to diminish over time and to be more effective against severe disease and death rather than infection. Vaccinated individuals who contract B.1.1.529 is one of the epidemiological analyses that has begun, and it is being investigated.


That B.1.1.529 is capable of evading the immune response is a source of concern. Many studies have discovered high seroprevalence rates, or the number of people who have already been infected, and the optimistic expectation is that this will provide some measure of "natural immunity" for at least a short period of time.


Finally, everything we know about B.1.1.529 so far indicates that universal vaccination remains our best defense against severe COVID-19 and that, when combined with non-pharmacological interventions, will significantly aid the healthcare system in coping with the upcoming wave of infections and diseases.

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