Genomic sequencing has been quite an essential part in the Covid-19 response around the world. New variants are always appearing, but genomic data has provided countries with information they need to make quick and educated public health decisions since the beginning of the pandemic. For instance, countries draft new legislations to impose lockdowns once they discover new data on the virus. It takes less than 48 hours of knowing about a new Covid-19 variant to understand how it works and what steps must be done to prevent it. SARS-sCoV-2 sequencing is necessary for detection and surveillance of new Covid-19 variants and other mutations.
The value of SARS-CoV-2 sequencing for public health response goes beyond simply knowing when to impose a lockdown. It can be helpful in preparing countries for potential increase in infections and to take important measures such as opening more hospital beds, increasing oxygen supply, or to increase texting because these variants are transmissible. Genomic sequencing has also helped counties in choosing the right type of vaccines to be used. Vaccine hesitancy exists and it is a huge problem affecting vaccination rates across the world. So, we must get it right the first time and make sure that the vaccines rolled out are the most effective one on the market.
There are also methods that countries can use in response to new variants, without their genomic data. Angola, in the African continent, has done a great job of using simple public health responses to prevent new variants from entering the country. Thanks to point of entry testing of all travelers, Angola was able to isolate most positive cases and slowed down the spread of more dangerous variants without having to impose a travel ban. Travel bans can lead to a negative economic impact, but a good triage system and testing at point of entry is more or less as effective.
Virus Genome Sequencing and Covid-19
Virus genome sequencing is an important and fast-growing tool that aids in the diagnosis of Covid-19 and in understanding its spread and control.
A genome basically acts as an organism’s instruction manual—it carries all the information you need to make and maintain it. Human genomes are made of double-stranded DNA and are written in its special code of four nucleotide base ‘letters’.
Human genomes are made up of more than 3 billion base letters long. A virus genome, on the other hand, can be made from DNA or it’s close cousin RNA. A virus genome is tiny as well. Coronaviruses are RNA viruses that contains a single short RNA strand made up of 30,000 letters long. These letters can be ‘read’ through genome sequencing.
Genomes Can Identify Viruses
If a new coronavirus sequence is found in a sample (taken from the nose or mouth), it confirms the likelihood that a patient’s symptoms are those of Covid-19.
Viral genomes always alter or mutate, changing a few letters at a time as they divide. As a result, more and more people get infected. You can make use of these changes to monitor the spread of the virus by sequencing, analyzing and recording genomes.
If we rapidly undertake SARS-CoV-2 sequencing or any virus genome sequencing and on a large-scale, then it can help public health officials and epidemiologists in understanding how the virus spreads. It can also help in evaluating whether interventions taken towards it have been effective so far.
Genome sequencing also helps determine whether new variants are linked to specific patterns of symptoms or strength of disease. Tracking new variants will be very important in the long run, as it guarantees that vaccines, when developed, can be updated with the strains of virus currently circulating.
Local transmission vs. imported cases
In the early stages of the epidemic, sequencing can be utilized to determine how many new cases of disease are locally transmitted or imported. Global information on virus genomes allow researchers to compare genomes so they can accurately assess local transmissions in each country.
Growth of the Epidemic
Mathematical models showing how viruses grow and evolve during an epidemic (created from large-scale analysis of past outbreaks) allow experts to estimate epidemic growth rates, transmissions, infections from virus genome sequences.
Unlike estimates from other sources of data, information from virus genetics are quite useful in the prediction of long-term, large-scale trends. Most importantly, genome sequencing validates the estimates of the size and growth rate of an epidemic. This can be quite useful when cases are under-reported, perhaps due to people not showing any symptoms.
Transmission in Different Groups or Places
Large-scale sampling and sequencing of the new coronavirus strains enable the reconstruction of virus spreads in various places or groups of people. Through this, experts learn what is causing the spread of the virus locally and nationally. This work can be performed with precision if virus genomes are combined with information on where, how, and when people travel locally and/or internationally.
Transmission Chains and Genetic Variations
Virus genome sequences are also used to identify distinct genetic changes shared by everyone infected in a single virus transmission chain. This information can be used to determine whether two clusters of cases in the same area happened because one started the infection in another, or because there were two unique and independent series of transmissions with different/separate, earlier origins. This means that virus genomes can add to the information provided by contract tracing patients, a method deemed necessary for monitoring outbreaks in hospitals, communities, and other care settings.
A number of genetic changes take place in the virus genome will have no significant impact on the course of infection or disease, or the impact of control measures. But a few changes may be important. These changes must be identified and monitored through time. In the case of viruses such as influenza, we all know that genetic changes can modify how our immune system recognizes viruses, severity of the disease, and resistance to antiviral drugs. For the new coronavirus, however, such discoveries have yet to be made.
Quick and large-scale genome SARS-CoV-2 sequencing is a new stream of information that can help in monitoring epidemics and developing new control methods. Its application to the new coronavirus is only the beginning.
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