The Journey of a Nose Swab: How Genomic Sequencing Tracks COVID-19 Variants

Summary

Genomic sequencing is an essential tool used to analyze the genetic makeup of the SARS-CoV-2 virus and track its variants. Nose swabs collected for PCR testing are sent to laboratories that conduct genomic sequencing, where researchers use bioinformatic pipelines and algorithms to piece together the viral genome. By analyzing the genome of the virus, scientists can track emerging variants that may threaten public health, monitor how evolving variants impact existing treatment, and assess the effectiveness of vaccines and therapeutics.

What is genomic sequencing?
How is genomic sequencing used to track COVID-19 variants?
What is the process of genomic sequencing?
How are variants classified?
What is Omicron?
How are variants named?
What is the importance of genomic sequencing in pandemic response?

What is genomic sequencing?

Genomic sequencing is a process used to analyze the genetic makeup of viruses. By sequencing the genome of a virus, researchers can analyze the genetic code of the virus and identify any mutations.

How is genomic sequencing used to track COVID-19 variants?

Genomic sequencing is used to track COVID-19 variants by analyzing the genome of the virus to identify mutations. Variants are classified by the Centers for Disease Control and Prevention (CDC) into four categories: variant being monitored, variant of interest, variant of concern, and variant of high consequence. Researchers use genomic sequencing to monitor how evolving variants might impact existing treatment and assess the effectiveness of vaccines and therapeutics.

What is the process of genomic sequencing?

In the case of SARS-CoV-2, most labs use an approach called amplicon sequencing, where small overlapping pieces of the genome are amplified by PCR. The sequencing is then done by a mix of academic and clinical laboratories, along with local, state, and federal agencies. Within two weeks of the sample being taken, the sequence is available in public databases. Bioinformatic pipelines and algorithms are used to piece together the genome from the small overlapping pieces amplified by PCR.

How are variants classified?

Variants of concern are classified by the CDC into four categories: variant being monitored, variant of interest, variant of concern, and variant of high consequence. Variants of concern, the next category after a variant being monitored or a variant of interest, may be less responsive to existing therapeutics, vaccines, and treatments. A variant of high consequence is the most serious, and there has not yet been a variant classified as such.

What is Omicron?

Omicron is a variant of concern that emerged in late 2021. It has an accumulation of 32 documented mutations in the spike protein, leading to the SGT, or SG in target failure marker, frequently used to understand where and how it is transmitted. Omicron is much more transmissible than other reported variants and shows evidence of immune invasion even among vaccinated individuals. It is classified as a variant of concern.

How are variants named?

The WHO brought together a group to help name and designate variants of interest and variants of concern, devising a consistent nomenclature system for the variants. The names have to be specific, distinctive, and easy to pronounce and search for in multiple languages. The WHO decided on Greek letters, as association with specific places or people may have negative connotations.

What is the importance of genomic sequencing in pandemic response?

Genomic sequencing is an important tool in pandemic response. Open data and rapid data sharing are incredibly useful tools for public health and pandemic response, but there are still many barriers researchers have to overcome, including pulling together different types of data and collecting timely samples. By contributing a nose swab for PCR testing, individuals can help researchers understand transmission dynamics and track the variants of the virus circulating in their community, state, and country.

Conclusion

Genomic sequencing is an essential tool in the fight against COVID-19. It allows researchers to analyze the genetic makeup of the virus, track the emergence of variants that pose threats to public health, monitor the effectiveness of existing treatments, and assess the efficacy of vaccines and other therapeutics. By contributing a nose swab for PCR testing, individuals can help researchers understand transmission dynamics and track the variants of the virus circulating in their community, state, and country. The potential for global public health is exciting, but there are still many barriers that researchers have to overcome to fully realize the benefits of genomic sequencing for pandemic response.