Essay on Molecular basis of corona virus

There are many reviews appeared recently which focus on a particular characteristic of the family of corona virus e.g. replication strategy and glycoproteins. Corona virus can cause infection in animals, mammals as well as in birds. Corona virus possess 3 major protein in its structure 1) nucleocapsid protein 2) small integral membrane glycoprotein 3) large spike glycoprotein. The genomic RNA of the corona virus is known to be the largest RNA virus with the size of almost 27 to 30 kb. There are almost 6 to 7 regions in organized genome of the virus with Open Reading Frame (ORF), which make themselves separate from each other by junction sequence that also include the transcription signal. In previous years, the sequenced data has been obtained, which also include the complete sequence of IBV genomic RNA. The ORFs that encode the structural protein have now been explained, even a consensus gene order 5' S-M-N 3’ can be referred through their location. The genome of corona virus serves as the template for the replication purpose. An RNA dependent polymerase activity was detected inside the infected cell. Early polymerase was involved in synthesis of negative strand RNA whereas the late polymerase synthesizes the positive strand of RNA.

The outbreak of the novel coronavirus disease COVID-19 has caused a massive increase in sales and requirements of the disinfection products. A regular practice of washing your hands and cleaning the surface of your property is one of the leading directives given by the Centre for Disease Control and Prevention. Both of these practices are the strongest defenders from the uncontrollable COVID-19, however theirs is no particular product which is promising to eradicate the bacteria of corona virus but the scientists have analyzed that coronavirus is one of the easiest types of viruses to be killed if we continue the practice of keeping our hands and environment clean. When it comes to washing hands, we talk about soap and hand sanitizers who are considered as the saving shield against the virus. The reason that soap works so well against the corona virus or other viruses is because of the reason that virus is structed as a self-organized/created nanoparticle among that the weakest area is the lipid bilayer.  Soap have the tendency to dissolve the fat membrane and restrict the virus to fall apart and die. So, soap is a better shield against the virus however we can use alcohol containing sanitizers when there is no availability of soaps.

Nucleic acid testing is the most common method for testing COVID-19. There are many reverse transcription polymerase chain reactions (RT-PCR) kits that have been made and distributed to detect SARS-CoV-2 genetically. This technique of RT-PCR includes the reverse transcription of RNA of the virus into its complementary DNA strands, then the amplification of some specific regions of the cDNA. The overall process includes 2 steps; sequence alignment and primary design and the other step is assay optimization and testing. Corman et al reported and analyzed the numbers of viral genome related to SARS in order to design a set of primers and probes. After the design of primer and probes, optimizing of assay is the next step which then followed by the PCR testing. RT-PCR can be done either by one step assay or 3 step assays. Two steps that occur simultaneously are reverse transcription and amplification so this step is difficult which lead to lower target amplicon generation. But in 2 step assay, two separate tubes are needed for assay reaction. In order to increase the number of identifies infected patients, different regions in E gene is targeted, if the test result is positive, they recommend the detection of RdRP gene which need 2 different primers and probes. If these results are also positive, then they conduct the discriminatory test with one of the two probe sequences.

The problem in the current outbreak is how to differentiate a corona virus patient from the healthy one. More tests are need to be done in order to cope with the situation. The current available tests are RT-PCR, CT imaging and some hematology parameters are used in order to diagnose the disease.  But these tests have long turn around time and are complicated in action. PCR tests require proper certified laboratories and expensive equipment and also trained technicians. There are also some numbers of false negative patients due to PCR testing. Testing for some antibodies for SARS-CoV-2 in patients’ blood is a good option to avail, as it will give rapid results. It is accepted world wide that immunoglobin M (IgM) give the first line of defense in case of viral infection. It is reported that after the attack of the virus, the immunoglobin can be detected inside the blood of the patient after 2, 3 or even 8 days. Since COVID‐19 belongs to the same large family of viruses as those that cause the MERS and SARS outbreak, we assume its antibody production process is similar and so the indication of the infection is the detection of such immunoglobin.

In-vitro assessments have proven that chloroquine is quite useful Infront of many viruses which includes critical acute respiratory syndrome corona virus Covid-19. Multiple procedural actions have been introduced for chloroquine that disrupt the initial or starting level of replication of the coronavirus. Furthermore. chloroquine brings significant changes to the immune system process via mediating a response of anti-inflammatory, which is expected to have the tendency to lessen damage cause by exaggerated inflammatory response. Chloroquine was suggested as the treatment against SARS back in 2004 however advanced studies in this regard was not done and its accurate efficiency regarding the treatment of the virus was not introduced or established.

Chloroquine is drug which is cheap and have been highly effective against treating malaria prophylaxis   and it showed excellent results in terms of safety and tolerability. Because of the reason that COVID-19 is connected to substantial morbidity and mortality and also no solution from pharma side have been developed, chloroquine and its related formulas have been included tentatively in the set of drugs which are currently being used in controlling the burden caused by COVID-19.

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