Hunting for variants requires a concentrated effort. South Africa and the United Kingdom were the first major countries to implement national genomic surveillance efforts for SARS-CoV-2 as early as April 2020. The scientists in South Africa are sequencing the virus and studying its danger
By: Prof. Wolfgang Freiser, Head of Medical Virology Division, Stellenbosch University; Catherine Schippers, Senior Medical Scientist, University of the Witwatersrand; Jinal Bhiman, Chief Medical Scientist at the National Institute of Communicable Diseases (NICD); Marity Venter, Zoonotic, Arbo and Respiratory Virus Programme, Professor in the Department of Medical Virology, University of Pretoria; Tulio de Oliveira leads KRISP – KwaZulu-Natal Research and Innovation Platform, University of KwaZulu-Natal
Since the beginning of the corona epidemic, the network for genomic surveillance in South Africa has been monitoring changes in SARS-CoV-2. This was a valuable tool to better understand how the virus spread. At the end of 2020, the network identified a new virus lineage, 501Y.V2, which later became known as the beta version. Now a new version of SARS-CoV-2 - B.1.1.529 has been identified. The World Health Organization has declared it of concern, giving it the name Omicron. To help us understand more, THE CONVERSATION South Africa asked scientists to share what they know.
What is the science behind the search?
Hunting for variants requires a concentrated effort. South Africa and the United Kingdom were the first major countries to implement national genomic surveillance efforts for COVID-2 Already in April 2020.
Variant hunting, as exciting as it sounds, is done by whole-genome sequencing of samples that have tested positive for the virus. This process involves checking each sequence received and finding differences compared to what we know is circulating in South Africa and the world. When we see multiple differences, this immediately raises a red flag and we investigate further to confirm our hypotheses.
Fortunately South Africa is well prepared for this. This is thanks to a central database of laboratory results in the public sector in National Health Laboratory Service, (NGS-SA), good links to private laboratories, the Western Cape Health Information Center and advanced sampling expertise.
In addition, in South Africa there are a number of laboratories that can grow and study the virus in practice and find out to what extent antibodies, created in response to vaccination or previous illness, are able to neutralize the new virus. These data will allow us to characterize the new virus.
The beta version spread much more efficiently between people compared to the "wild type" or "protovirus" of COVID-2 and caused the second epidemic wave in South Africa. It is therefore classified as a concern variant. During 2021, another variant causing concern called Delta spread almost all over the world, including South Africa, where it caused a third epidemic wave.
Recently, it was detected in routine sequencing by my friends labs Network for Genomics Surveillance A new virus lineage, called B.1.1.529 , in South Africa. It was detected in 77 samples collected in mid-November 2021 in Gauteng province. It has also been reported in small numbers from neighboring Botswana as well as Hong Kong. According to the reports, the infected person found in Hong Kong is a traveler from South Africa.
The World Health Organization awarded B.1.1.529 Are you there Omicron and classified it as a version of worry, like beta and delta.
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Why are variants that cause concern discovered in South Africa?
We don't know for sure. It certainly seems to be more than just a result of concerted efforts to monitor the virus that is circulating. One theory is that people with severely compromised immune systems, who experience prolonged active infection because they cannot clear the virus, may be the source of new viral variants.
It is assumed that a certain amount of "immune pressure" (meaning an immune response that is not strong enough to eliminate the virus but exerts a certain amount of selective pressure that "forces" the virus to evolve) creates the conditions for the emergence of new variants.
Despite an advanced antiretroviral treatment program for people living with HIV, many people in South Africa suffer from a disease HIV progressive and are not treated with effective treatment. Several clinical cases have been studied to support this hypothesis, but much remains to be learned.
Why is this version worrying?
The short answer is we don't know. The long answer is, B.1.1.529 carries certain mutations that are worrisome. They have not been seen in this combination before, and the spike protein alone has more than 30 mutations. This is important, because the spike protein is the protein that makes up most vaccines and which the body is supposed to recognize and create antibodies against.
We can also say thatB.1.1.529 has a very different genetic profile than other variants in the cycle of interest and concern. He does not appear to be a "son of Delta" or "grandson of Beta" but represents a new lineage of COVID-2.
Some of the genetic changes in B are known from other variants and we know that they can affect transmission or allow evasion of the vaccine, but many of them are new and have not yet been studied. While we can make some predictions, we are still investigating how much the mutations will affect her behavior.
We want to know about the infectivity, the severity of the disease and the ability of the virus to "escape" the immune response in vaccinated people or those who have recovered. We learn it in two ways.
First, we perform careful epidemiological studies to find out whether the new lineage shows changes in the rate of spread, in the ability to infect vaccinated or previously infected people, and so on.
At the same time, laboratory studies are testing the properties of the virus. Its viral growth characteristics are compared to those of other variants of the virus and it is determined to what extent the virus can be neutralized by antibodies found in the blood of vaccinated or recovered individuals.
Ultimately, the full significance of the genetic changes observed inB.1.1.529 It will become clear when the results from all these different types of studies come. It is a complex, demanding and expensive task that will take months, but is necessary to better understand the virus and devise the best strategies to fight it.
Are there early indications that this variant causes different symptoms or a more severe disease?
There is no evidence yet of any clinical differences. What is known is that the number of cases of infection B.1.1.529 Growing rapidly in Gauteng, where the country's fourth wave of the epidemic appears to be starting. We can't really tell yet if B.1.1.529 More efficiently delivered than the popular version of concern, Delta.
more likely toCOVID-19 In the Omicron version, it will manifest as a serious disease, often life-threatening, in the elderly and chronically ill. But the population groups most often first exposed to a new virus are younger, mobile and generally healthy people. If Omicron spreads further, it will take time to assess its effects, in terms of disease severity.
Fortunately, all the diagnostic tests done so far seem to be able to detect the new virus.
Even better, some widely used commercial assays seem to show a specific pattern: two of the three genome sequences are positive, but the third is not. It's as if the new version responds consistently to two out of three boxes in the existing test. This may be used as a marker for Omicron, meaning we can quickly estimate the rate of positive cases due to Omicron contamination per day and per region. This is very useful for monitoring the spread of the virus in near real time.
Are the current vaccines likely to protect against the new version?
Again, we don't know. Known cases include people who have been vaccinated. However, we have learned that the immune protection provided by the vaccine wanes over time and does not protect so much against infection as against serious illness and death. One of the epidemiological analyzes that have begun is looking at how many vaccinated people become infected with Omicron.
The possibility that Omicron might evade the immune response is troubling. The hopeful expectation is that the vaccination and recovery rates will provide a degree of "natural immunity" at least for a certain period.
Ultimately, everything that is known about Omicron so far emphasizes that a universal vaccine is still our best bet against severe COVID-19 and, together with non-drug interventions, will help the healthcare system cope during the next wave.
to mamr on The Conversation website
More of the topic in Hayadan:
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And if you meant to teach her - the one who eliminated him was the delta species...
The species you spoke of has not disappeared. This is the delta variety. The omicron contains some of these mutations as well as many others.
The timing really has nothing to do with any holidays, but to reach established information that enables decision-making.
So, it's interesting that a new low-corona variety that has 30 mutations is much more dangerous compared to a variety that has 20 mutations and has disappeared in the meantime, and it's interesting that just before the pre-Christmas shopping frenzy this is published when it was known since October, and it's interesting that this will end in a moment of silence (at least I hope that Today it is no longer possible to know what is real and what is fake) what will the experts say, we will hope for a Hanukkah miracle