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Conquering the Pandemic with SARS-CoV-2 Sequencing

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The SARS-CoV-2 sequencing is an important and rapidly developing technology that is being used to diagnose COVID-19, as well as to better understand its spread and to better control it.

The genetic code of an organism is referred to as its genome, and it serves as the organism’s ‘instruction manual’ in that it contains all of the information required to construct and maintain the organism. Human genomes are formed from double-stranded DNA and are transcribed through a one-of-a-kind code that consists of four nucleotide base ‘letters’. There are three billion base letters in the human genome, and the genetic material that is making up a viral genome is either DNA or its close relative, RNA, and it is incredibly compact. Considering that coronaviruses are classified as RNA viruses, the newly detected SARS-CoV-2 virus comprises a single short strand of RNA that is just 30,000 letters long. The sequential reading of these letters is referred to as sequencing.

Using genomes as a method of virus classification

If the novel coronavirus sequence is detected in a sample normally collected from the nose or mouth, this supports the premise that a patient has COVID-19.

The genomes of viruses are constantly changing, usually by changing one or two letters at a time as they replicate and spread from infection to infection. However, by sequencing, documenting, and analyzing genomes, it is possible to use these mutations to track the progression of a virus’s transmission.

The sequencing of the viral genome can help epidemiologists and other public health professionals determine how the virus spreads and evaluate how successful their therapies are if it is done quickly and on a large scale. In addition, it can be of use in evaluating whether unique polymorphisms are associated with specific patterns of symptoms or the severity of the condition. In the long term, it is anticipated that monitoring new variations will be of crucial importance in order to guarantee that immunizations developed in the future will remain current with the virus strains that are now circulating.

Comparing community transmission from imported COVID-19 cases

In the early stages of an epidemic, sequencing may be used to assess the number of newly imported or locally transmitted cases of the disease.

Global databases of viral genomes enable scientists to compare genomes in order to obtain an accurate calculation of local transmission in each nation.

Progression of the COVID-19 pandemic

Through comprehensive investigation of prior outbreaks, mathematical models of virus development during an epidemic have been established, allowing for the estimate of epidemic growth rates and other metrics of transmission, such as transmission from virus genome sequences. Compared to other data sources, insights derived from viral genomes are superior for forecasting long-term, widespread changes. Notably, they facilitate impartial validation of estimates of an epidemic’s size and growth rate. This is especially important when cases are underreported since many infected individuals do not display symptoms.

Distributed in several places or clusters

The extensive sampling and genome sequencing of the new coronavirus make it possible to recreate the virus’s dispersal across multiple locales or populations. This provides insight into the local and national aspects that contribute to the virus’s propagation. This work might be improved by integrating viral genomes with information on where, when, and how individuals migrate locally and worldwide.

COVID-19 transmission chain

In addition, viral genome sequencing can show specific genetic alterations shared by all infected people within a certain virus transmission chain. This can be used to identify if two clusters of cases in the same place were caused by infection moving from one to the other, or by two different and independent pathways of transmission with discrete, earlier beginnings. Consequently, data may now be complemented with the usage of viral genomes obtained by patient contact tracing, which is vital for monitoring epidemics in communities, hospitals, and other care settings.

Differences in genetic material

Numerous mutations in the genome of the virus have no detectable effect on the progression of infection or illness or the efficacy of control attempts. However, there may be necessary adjustments that must be identified and implemented over time since these findings have not yet been made about the newly identified coronavirus.

Rapid, large-scale viral genome sequencing produces new data that may be utilized to track epidemics and develop innovative management methods. Its application to the recently identified coronavirus has just begun.

How essential is SARS-COV-2 sequencing to the COVID-19 response?

The sequencing of the COVID-19 genome had a crucial role in the reaction. Since the beginning of the pandemic, genetic data have supported governments in making timely and informed decisions on public health, since new variants appear every day. For example, the Ministry of Health and President Cyril Ramaphosa were immediately notified upon detecting the Beta strain in South Africa during our second wave. In less than a day, new legislation was drafted to place the nation under a stricter lockdown in order to avoid infection and save lives. After learning about the new kind, this occurred within 48 hours. same, the Delta variation for the third wave was identical.

The significance of sequencing for public health action goes beyond identifying when to initiate lockdown protocols. As these strains are more transmissible, they can aid counties in preparing for future outbreaks and implementing crucial measures, such as improving oxygen supply, extending hospital beds, and increasing testing. In addition, it was crucial to aid African governments in determining the most appropriate vaccinations for usage in the continent. Vaccine reluctance is a big concern, and we must ensure that the vaccines administered are as effective as possible from the start. South Africa’s decision to use COVID-19 immunizations from Johnson & Johnson and Pfizer was based on genetic data.

Furthermore, governments can respond to new mutations without access to their genetic information. Angola is an outstanding example of how basic public health interventions may effectively prevent the introduction of new diseases. Without adopting a travel ban, the government has isolated the bulk of positive cases and decreased the spread of these more lethal strains of concern. Financially, travel restrictions are too costly, but an efficient triage system and entry-point screening are almost as effective.

James Wallace did his degree in psychology at the University of Hertfordshire. He is interested in psychology, mental health, and wellness.

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