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Studies have identified a Sars-CoV-2 mutant with a deletion in the genome

Geneticist Dr. Jörn Kalinowski and his team at the Center for Biotechnology use state-of-the-art nanopore sequencing to sequence the longest possible gene segment and identify genomic deletions in the Sars-CoV-2 mutant. doing.Credit: University of Bielefeld

Automated genetic analysis of SARS-CoV-2 samples consistently misses genetic segments of the viral genome that have been deleted due to mutations. This is revealed in a new study by researchers at the Biotechnology Center (CeBiTec) at the University of Bielefeld and Bethel (EvKB), one of the supporting hospitals of the OWL School of Medicine. The researchers were able to show that the samples analyzed lacked most of the ORF8 gene segment. This genetic region is thought to contribute to delaying the defense response of the human body. If it is missing, the virus can be less pathogenic. In other words, it is less likely to cause serious illness.The research team published the findings in the journal virus..

“If both hospitals and schools carry out routine tests to see if people are infected with the virus, their main purpose is to contain further infections,” said CeBiTec’s geneticist. Senior Researcher Dr. Jörn Kalinowski said. When laboratories analyze samples in widely available PCR tests, they are not just aimed at determining whether an infection is present. If they find a case of infection, they also investigate which variant of the virus is involved. “To do this, it is sufficient to identify the individual characteristic gene sections that are typical of common viral variants.” Currently, such analyzes usually yield the same results across Europe. increase. The delta variant is much more infectious than the other variants.

“Because there are only a few people Gene segment Laboratories usually just admit that they can’t identify other gene segments, “Karinovsky said. One of the reasons why the genome cannot be completely identified is, for example, poor sample preparation. In many cases, Analytical software It does not optimally recognize individual nucleotides, which are the genetic components of the viral genome. Instead of the letters A, T, G, and C used to represent the genetic components of the viral genome, the software writes the letter N to the gene sequence.

Existing software documents missing gene segments in a misleading way

According to a study by Bielefeld’s research team, this makeshift approach can lead to a wide range of problems. “Mutations can lead to variants of SARS-CoV-2 with longer gene segments removed,” said Dr. Alexander Sczyrba, a professor of bioinformatics at CeBiTec, co-author of the study. increase. “We found that commonly used standard software goes into the sequence placeholders even if the entire gene segment is not present at all.” Next, the letter N is written to the line of the gene sequence. ..

“This is a systematic error,” says Jörn Kalinowski. “Such deletion of the genome provides important clues about future exposure to the coronavirus.” Deletion of a gene segment is stored in the affected property. Genes also disappear. As the virus replicates, these properties are no longer inherited. “In addition, mutations that make the virus more dangerous to humans can no longer occur within such deletions of the genome.” According to Karinovsky, such a missing gene segment SARS-CoV. -2 may be one of the reasons for adapting to humans as a host. This makes the virus more infectious, but at the same time less dangerous. “The virus will be unique. In other words, it will appear regularly in different regions, as is the case with other anciently known coronaviruses that give only harmless colds today.”

Knowing the variant of the virus will help rebuild the infectious chain

Researchers discovered a gene deletion in the virus when analyzing virus samples from EvKB. There, medical staff and patients are continually tested for coronavirus infection. Kalinowski’s research group has been analyzing samples from hospitals since April 2020. For analysis, you will receive an extract containing the genetic material of the virus. These come from the swabs of patients who tested positive. “A detailed analysis of the sample allows us to reconstruct the infection chain when a case occurs,” said Dr. Christian Scheller, a senior physician at EvKB’s head of microbiology and co-author of the study. increase. During the peak of the second wave of infection in January and February 2021, Scheller and her team identified clusters of infection. They were able to contain them through extensive screening and contact tracing. The viral variant B.1.1.294 could not spread further to the ward.

CeBiTec analysis confirmed successful quarantine measures in the affected wards. “We were able to describe this very accurately because we discovered a special feature of the viral variant. The genetic code lacks 168 nucleotides,” reports Jörn Kalinowski. There was no gene building block in the gene region “Open Reading Frame 8” (ORF8). This genetic information is believed to be responsible for the fact that the virus has succeeded in delaying the immune response of infected individuals.

Features added to the analysis software

Scientists also applied nanopore sequencing, as opposed to standard PCR tests, to detect missing nucleotides. Compared to regular sequencing machines, these special instruments allow us to determine longer gene segments. Researchers have also added additional functionality to free-to-use gene analysis software that correctly detects and labels missing nucleotides in gene sequences. “This was the only way we could confirm that part of the ORF8 gene region had disappeared,” said Kalinowski.

“This analysis not only allowed us to identify clusters in the hospital, but also to prevent the virus mutant from reaching a dead end and infecting anyone else after it was contained,” said Christian Scheller. say. “”

The evolutionary dendrogram shows the relevant variants of the investigated viral variant.

Researchers at CeBiTec wanted to know the origin of the viral mutant from which the gene segment had been removed. To do this, they took raw data from a central database of coronavirus mutants and evaluated it using their own specially developed software. “In this way, we were able to determine where the other predecessors of the variant we were investigating appeared and where similar variants were,” explains Alexander Sczyrba. Scientists explain the results in a dendrogram of SARS-CoV-2.This indicates, for example, that it is a precursor of a virus Mutant Previously discovered in Denmark.

Researchers at CeBiTec also want to allow other scientists to pinpoint the missing gene segment of the SARS-CoV-2 mutant. To this end, they make further developments of analytical software, including source code, available for download on relevant platforms.

“If you want to clarify what an individual’s function is gene In virus It is important to be able to further search for variants with the gene segment removed, “said Jörn Kalinowski. “But this requires access to all raw data from coronavirus samples analyzed nationwide. Unfortunately, strict data protection regulations currently prevent this,” he said. say.


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For more information:
David Brandt et al, multiple occurrences of 168 nucleotide deletions in SARS-CoV-2 ORF8, unnoticed by standard amplicon sequencing and variant calling pipelines, virus (2021). DOI: 10.3390 / v13091870

Quote: Deletion from https: //medicalxpress.com/news/2021-10-sars-cov-variant-deletion-genome on October 26, 2021 (October 26, 2021) by research A Sars-CoV-2 variant has been identified. html

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Studies have identified a Sars-CoV-2 mutant with a deletion in the genome

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