Researchers Dissect the Coronavirus Genome for Outbreak Answers

The early detection of SARS-CoV genetic material is crucial for improving SARS control, since patients are able to transmit the virus before it can be detected. Thirty thousand base pairs make up the (relatively tiny) SARS-CoV-2 genome. A singular genome holds limited information. But, by comparing multiple genomes from different patients, animals, places, or time periods, the DNA’s information can be unlocked. From where the virus originated to how it spilled over from animals into humans, how quickly it mutates, and how those changes affect infections—genome comparisons may provide the answers.

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The SARS-CoV genome is about 30 kb long. Differential transcription of its genes generates a gradient of subgenomic RNAs (sgRNA) with a common 3′ end. This implies that genes at the 3′ end should be transcribed at high levels and that sgRNA species produced by transcription of these genes might be the most abundant during cell infection. The genomic organization of the coronavirus, with the nonstructural genes placed at the 5′ end and structural genes placed at the 3′ end, may reflect this transcription strategy. For example, the products of nonstructural genes, such as the RNA-dependent RNA polymerase (Pol), responsible for replication and transcription of the viral genome, are needed in smaller amounts than those from structural genes, such as the nucleocapsid protein (NC), involved in assembly of the virions. Hence there may be higher levels of sgRNA from structural genes than from nonstructural genes.

The longer a virus circulates in a human populations, the more time it has to develop mutations that differentiate strains in infected people, and given that the 2019-nCoV sequences analyzed to date differ from each other by seven nucleotides at most, this suggests it jumped into humans very recently. But it remains a mystery which animal spread the virus to humans. “There’s a very large gray area between viruses detected in bats and the virus now isolated in humans.

Detection of Covid 19 can be done by  RT-PCR. Cell culture takes to patients and scientists extract the RNA in cell. Because virus use RNA for regeneration. RNA extracted with MagNA pure 96 system and use  RNA mini kit for detection of virus. It depends on the ager to detected easily in immunological cases, a young person has more leucocytes and T cells  than older age person. Than , n-CoV is not detect to easily in young patient.    In real time polymerase chain reaction 25μl master mix  using 5 μl sample and 12,5 μl 2x reaction buffer. I. This system using platinum taq polymerase containing 0.4 mM dNTP’s and 3.2 mM magnesium sulphate. Mixed with each sample and 1μl taq polymerase. In the settings the RT PCR thermal cycling 55 C° with 10 minutes for reverse transcription and 95 C° with 3 minutes than 45x cycle 95 C° with 15 seconds than 58C° with 30 seconds.

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The implication for diagnostic testing is that the current RT-PCR assays targeting the Pol gene detect SARS-CoV less efficiently and less sensitively than is possible when targeting the NC gene. The larger amount of NC sgRNA in cells observed here may mean that a stronger signal could be picked up from patient samples containing cells sooner than is currently feasible with the Pol assay, which is in widespread use due to its early introduction soon after the first SARS cases hit Europe and the Americas.

The genomes of SARS-CoV-2 holds many answers to the questions scientists are searching for at a feverish pace. It is clear that understanding the evolutionary pathway by which this novel coronavirus has transferred to humans will help us not only combat the current pandemic but assist in identifying future threats from other coronaviruses and other species.

Knowing how the coronavirus polymerase is constructed on an atomic scale opens up new possibilities to better understand and combat the pathogen. Many hopes rest on remdesivir, which directly blocks the polymerase. With the structure at hand it might be possible to optimize existing substances such as remdesivir and to improve their effect. But we also want to search for new substances that are able to stop the virus polymerase.

SARS CoV2 is a pandemic virus and recently, we don’t have any drugs, vaccine or treatment against to this virus. It may transform to different structure because viruses are easily manipulated to genetic materials, today studies are continuing. SARS CoV2 death rate is higher than influenza. Nowadays we attention to personal cleaning and we have to increase immune system to ourselves. Social distance is important to SARS CoV2. We have to isolate to everyone.

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