Genomic Sequencing and the Emergence of SARS-CoV-2 Variants

Summary

In this article, we explore how genomic sequencing is used to track the emergence of SARS-CoV-2 variants. We discuss the process of genomic sequencing and how it allows scientists to analyze the genetic makeup of viruses, including SARS-CoV-2. We also examine the importance of naming new variants and how the World Health Organization is using Greek letters to avoid negative associations with specific places or people. Finally, we highlight the barriers to collecting timely and diverse data and the role of testing and sharing data openly in understanding transmission dynamics and trends in local regions, states, and countries.

The Process of Genomic Sequencing
Amplicon Sequencing
Omicron Variant and Variants of Concern
Naming New Variants
Barriers to Overcome
Conclusion

The Process of Genomic Sequencing

Genomic sequencing is a process that analyzes the genetic makeup of viruses, creating and assembling a large puzzle. The SARS-CoV-2 genome is about 30,000 bases long, and all viruses continually evolve through mutations. Labs analyze the genome of SARS-CoV-2 to keep track of variants that pose threats to public health. Laboratories conducting genomic sequencing receive around 5-10% of PCR test nose swabs.

Amplicon Sequencing

Most labs use an approach called amplicon sequencing, where small overlapping pieces of the genome are amplified by PCR and sequenced. The sequencing is done by a mix of academic and clinical laboratories, along with local, state, and federal agencies. Within two weeks, the sequence is available in public databases. While lab results may not tell you what variant you have, genetic sequencing often focuses on the spike protein, allowing scientists to assess how evolving variants might impact existing treatments.

Omicron Variant and Variants of Concern

Omicron is a variant of concern and looks different from Delta and many viruses that went before it. Omicron was first identified in Botswana and South Africa and has an accumulation of 32 documented mutations in the spike protein. With variants of concern, existing therapeutics, vaccines, and treatments still work to stop the virus’s spread, but they may not be as effective. The most serious category of variants is the variants of high consequence, but there hasn’t been one identified yet. The Omicron variant is highly transmissible and can invade the immune system even in vaccinated individuals, causing strain on communities and healthcare systems.

Naming New Variants

Naming new variants is important, and the World Health Organization (WHO) decided on using Greek letters to avoid negative associations with specific places or people. The WHO also encourages the use of scientific names, but these are often difficult to remember and pronounce. The use of Greek letters has been criticized by some, but it provides a standardized way to refer to new variants and avoids stigmatizing specific regions or populations.

Barriers to Overcome

Genomic sequencing plays a crucial role in monitoring and adapting to the pandemic, but there are barriers to overcome, such as collecting timely and diverse data. Testing and sharing data openly can help understand transmission dynamics and trends in local regions, states, and countries. The lack of resources and infrastructure in some areas can also hinder the ability to conduct genomic sequencing. Addressing these barriers is crucial to effectively track and respond to emerging variants of SARS-CoV-2.

Conclusion

Genomic sequencing is a powerful tool for monitoring and adapting to the pandemic. It allows scientists to track the emergence of new variants and assess their potential impact on existing treatments. Naming new variants is important to avoid stigmatizing specific regions or populations. However, there are barriers to collecting timely and diverse data, and addressing these barriers is crucial to effectively track and respond to emerging variants of SARS-CoV-2.