What SARS-CoV-2 Sequencing Is and How It Influences COVID-19 Response

All viruses mutate or change as they try to replicate and spread in people. Viruses that have RNA genetic materials, such as SARS-CoV-2 detected in SARS-CoV-2 sequencing and influenza viruses, mutate much quicker than viruses with DNA in them. Each time SARS-CoV-2 multiples, the ability of the virus to change is also there. A lot of mutations do not affect the ability of the virus to cause disease or spread as they do not modify the main proteins involved in transmission and infection.

When one of these mutations eventually affects the ability of the virus to cause disease or spread, there can be a viable higher advantage over the other existing lineages of SARS-CoV-2. Over time, some lineages of the SARS-CoV-2 with certain advantages become more prevalent and later circulate throughout the population. When a SARS-CoV-2 lineage or group of it has features that impact public health, the CDC then classify or labels them as a variant of interest (VOI) or variant of concern (VOC).


How Scientists Track Variants Through SARS-CoV-2 Sequencing


Scientists make use of genomic SARS-CoV-2 sequencing to determine which variant of SARS-CoV-2 is in the sample. Scientists are continually collecting sequences for SARS-CoV-2 sequencing. They analyze similarities as well as differences among the SARS-CoV-2 sequences and call this process the genomic surveillance. Using genomic surveillance, scientists record and track the spread of variants and monitor all the changes in the SARS-CoV-2 variants’ genetic codes. As a whole, this data is used to get a better understanding of how variants may affect public health.

CDC and their public health partners gather more genomes through SARS-CoV-2 sequencing. This has greatly improved the understanding of which variants are circulating in the US. Massive SARS-CoV-2 sequencing and genomic surveillance have also made it possible to identify how quickly variants emerge and which one is most important to study and monitor.

SARS-CoV-2 sequencing has also helped scientists identify the spread of variants to new regions. Take for example, upon the receipt of the SARS-CoV-2 sample from the first carrier of the Omicron variant it took only 5 hours to detect that it was Omicron and characterize the entire genomic SARS-CoV-2 sequence in 8 hours. It has prevented widespread community transmissions.

The rapid detection of the Omicron variant of the COVID-19 worldwide has further emphasized the power of a well-rounded genomic SARS-CoV-2 sequencing and surveillance. This has also stressed the value of sharing genomic SARS-CoV-2 data across the globe.



Where Data for SARS-CoV-2 Sequencing and Genomic Surveillance Comes From


Scientists employ the process called genomic SARS-CoV-2 sequencing to determine its variants. Scientists and laboratories collect viral specimens from a portion of the population who test positive for COVID-19 and do SARS-CoV-2 sequencing.

After a positive test is determined, additional time is taken to prepare and do SARS-CoV-2 sequencing on the viral specimen, and analyze the data thereafter. Genomic SARS-CoV-2 sequencing may take a few days to weeks.



Why SARS-CoV-2 Sequencing is Vital


These sequences as a result of SARS-CoV-2 sequencing offer scientists valuable information to be used to:


  • Characterize the SARS-CoV-2 virus
  • Estimate the prevalence of a particular variant in a population
  • Estimate the effectiveness of medical treatments (like monoclonal antibodies) against particular variants
  • Study the spread of SARS-CoV-2 virus outbreaks



How Genomic SARS-CoV-2 Sequencing Works


Genomic SARS-CoV-2 sequencing goes beyond just testing for SARS-CoV-2. It allows scientists to form a classification of the virus as a variant and identify its lineage. SARS-CoV-2 sequencing and genomic surveillance have been key in the government’s public health efforts to mitigate the COVID-19 pandemic.


Here’s a summary of steps taken in SARS-CoV-2 sequencing:


  • Extraction: The stands of RNA are extracted from the virus


  • Library Preparation: The SARS-CoV-2 RNA must be prepared before it can be put into the SARS-CoV-2 sequencing machine. The procedure in this step may vary depending on the type of sample and the equipment specifically used.


  • Sequencing Proper: The library is loaded into the sequencing machine. This machine will identify the nucleotide bases in the RNA.


  • Analysis: The SARS-CoV-2 sequencing machine produces data. The data are millions of long strings of letters. These letters are taken together or aligned with a top-quality reference sequence. Certain analytical programs compare newly sequenced data to the reference. Analytical programs also identify variations in the sample. These identifications allow scientists to form solid inferences on the ancestral relationship or lineage, much like a family tree.



How Crucial SARS-CoV-2 Sequencing is to COVID-19 Response


Genomic SARS-CoV-2 sequencing has played a very important role in the COVID-19 response formation. Newer COVID-19 variants are forming continually. Data from genomic surveillance has guided countries to perform quicker and more informed decisions for public health since the start of the COVID-19 pandemic.

The value and importance of genomic SARS-CoV-2 sequencing for the government’s response to public health and safety go beyond knowing when to enforce lockdowns. Genomic SARS-CoV-2 sequencing has helped countries prepare for potential spikes in cases. It has also allowed governments to take important steps like securing oxygen supply, setting up more hospital beds, or upping testing procedure frequencies by looking into more transmissible COVID-19 variants. Vaccine decisions remain to be crucial amidst the huge vaccine hesitancy among a lot of populations. Governments therefore should make informed choices regarding this through genomic SARS-CoV-2 sequencing. Therefore, with the genomic SARS-CoV-2 sequencing data, countries can take early steps to respond to new variants.

Beyond this pandemic, genomic surveillance is not new at all. Scientists have been utilizing genomic sequencing and surveillance to gain more understanding of the transmission and drug resistance of pathogens. Among these pathogens studied through genomic sequencing and surveillance are HIV and tuberculosis. Great examples of how genomic identification has helped nations select the best possible response, diagnostics, vaccines, and treatments are the Dengue, Yellow Fever Virus, and Chikungunya. This field of study and practice has also been proven to be important in identifying not only viral transmissions such as that obtained through the SARS-CoV-2 sequencing but for new zoonotic diseases as well like Ebola and Lassa Fever.

There is so much value in genomic SARS-CoV-2 sequencing and genomic surveillance as a whole not only in first-world countries like the U.S. but in developing countries and regions such as Africa. These evolving regions should continue to invest in laboratories for genomic sequencing. The spotlight now is on COVID-19 and genomic SARS-CoV-2 sequencing, but it cannot be more emphasized that an opportunity presents itself to figure out sustainable infrastructure for the future.

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