The genomic SARS-CoV-2 sequencing is an important and fast-developing tool in COVID-19 diagnosis.
It also has an essential role for scientists to understand the spread and control of novel coronaviruses.
An organism’s genetic material or genome is its instruction manual. It contains much-needed information to replicate and maintain.
Humans have double-stranded DNA genomes. Human genomes have special codes of 4-letter nucleotide bases.
Thus, a human genome is made up of at least three billion base letters. In a contrast, a virus’ genome is very tiny and can be made up of either DNAs or RNAs.
The coronaviruses are the RNA type and the SARS-CoV-2 which has been newly discovered has a short RNA strand of just 30,000 base letters long.
This makes SARS-CoV-2 sequencing, a technique that can identify these letters one by one, a helpful tool.
SARS-CoV-2 Sequencing Identifies COVID-19 Virus
When a sample is taken from a person’s nose or mouth and the novel coronavirus’ RNA sequence – through the SARS-CoV-2 sequencing technique – is found, it confirms the likelihood of the COVID-19 disease as the cause of the patient’s symptoms.
A virus’ genome continually mutates; this means it changes a few letters at a time as it divides and spreads through more infections.
These changes can be taken advantage of to track the virus’ spread by SARS-CoV-2 sequencing, recording, and genome analysis.
If SARS-CoV-2 sequencing to identify genomes is taken on rapidly and on a massive scale, it can aid epidemiologists and government health authorities to understand how it is spreading.
It is also essentially helpful in evaluating how interventions have been effective so far.
SARS-CoV-2 sequencing can also determine whether new variants are associated with a set of symptom patterns or if it will bring about a more severe disease.
In the long run, it will be extremely crucial to track new SARS-CoV-2 variants through SARS-CoV-2 sequencing to ensure that COVID-19 vaccines are developed and keep up with the currently circulating COVID-19 virus strains.
SARS-CoV-2 Sequencing Identifies Local and Imported Cases
In the pandemic’s initial stages, SARS-CoV-2 sequencing can be utilized to determine which of the new cases of COVID-10 disease come from a local transmission or if they are imported cases from other foreign places.
The global databases of the genomes of the virus allow researchers to compare genomes such that a precise assessment of local transmission can be made in every country.
SARS-CoV-2 Sequencing and Epidemic Growth
Scientific models of how viruses mutate during an epidemic allow estimation of the epidemics’ growth rates, other measures of transmission and infection to be estimated using SARS-CoV-2 sequencing.
These models have been developed from the extensive study of past outbreaks.
Although these are just estimates, the data from SARS-CoV-2 sequencing of the viral genome is more useful for long-term and large-scale prediction compared to insights from other data sources.
SARS-CoV-2 sequencing significantly provides independent and validatable epidemic size and growth rate estimates.
This is especially applicable when COVID-19 cases are underreported such as when infected cases do not show symptoms.
SARS-CoV-2 Sequencing and COVID-19 Spread
Due to prevalent sampling and genome SARS-CoV-2 sequencing, reconstruction of how the virus spreads in different places or groups of people is enabled.
SARS-CoV-2 sequencing provides valuable information about what drives the spread of the SARS-CoV-2 virus in the locality and nationally.
This volume of work can be enhanced and be more accurate when SARS-CoV-2 sequencing is correlated with data on where, how, and when infected persons had traveled locally and abroad.
SARS-CoV-2 Sequencing and Transmission Chains
SARS-CoV-2 sequencing of virus genomes can identify peculiar genetic changes commonly manifested by those infected in a single transmission chain of a virus.
The picture of whether 2 clusters of cases in the same area had come up because one started infecting the other, or whether the two clusters of infections came from separate origins can be fully painted.
The latter can happen because there are 2 unique and independent chains of transmission.
The viral SARS-CoV-2 sequencing, therefore, adds to the data warranted from close contact tracing – a tool in tracking community outbreaks in communities, hospitals, and other healthcare settings.
SARS-CoV-2 Sequencing and Genetic Variations
A lot of genetic changes occurring in viral genomes do not have impactful effects on the course of infection or disease process as well as its control measures.
Nevertheless, a few changes can be important.
These changes need to be determined and tracked through SARS-CoV-2 sequencing over time.
Take for example the influenza virus, genetic changes in the virus can also change how the human immune system recognizes the virus.
It can then spell the body’s resistance to antiviral drugs and the severity of the disease. For the SARS-CoV-2 virus, these discoveries are yet amiss.
As mentioned, the rapid and large-scale SARS-CoV-2 sequencing of the viral genome will bring about a new set of data eventually contributing to the tracking of waves of infections and the development of control methodologies.
The application of genomic SARS-CoV-2 sequencing has only begun.
Setting Up a SARS-CoV-2 Sequencing Surveillance System
To detect variants of concern and develop a health response for the public requires a full-bodied genomic SARS-CoV-2 sequencing surveillance program.
This earnestly means that scientists must sample from around 5% of all COVID-19 patients.
These samples for SARS-CoV-2 sequencing of the viral genome should be selected to be population representatives as most at risk from the disease.
Without SARS-CoV-2 sequencing and genomic data, locally and abroad, new variants may wildly spread undetected.
So how do scientists determine if new variants are emerging and when should people and governments be concerned?
Researchers will look further into a variant’s genome to conclude how it overcame distancing recommendations and other interventions of public health.
As for the case of the B.1.1.7 variant, it was found that particular mutations in some spick proteins made it easier to infect the human cells.
Initial research then suggests that mutations interpreted to higher transmission rates mean they spread easily from one person to another compared to earlier strains.
This surveillance data from genomic SARS-CoV-2 sequencing can further be utilized by vaccine developers and other scientists to test whether the vaccines work well with new variants.
Finally, to be useful, working and effective genomic SARS-CoV-2 sequencing surveillance program must be fast.
Also, the data should be made publicly available at the shortest possible time to inform decision-makers in the public health sector.
This also channels valuable data to vaccine manufacturers.
Such a surveillance program will bring about control of the current pandemic.