COVID-19 and genomic sequencing: Tracking variants and lessons for future pandemics

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As COVID-19 continues to affect us all, it has become evident that our fight against the virus is not just about developing vaccines and therapeutics. Equally crucial is our ability to track the virus’s mutations and adaptations. Enter genomic sequencing – a technology that has taken centre stage in our ongoing battle against the pandemic. Here, we explore how genomic sequencing has been instrumental in tracking SARS-CoV-2 variants and its implications for future pandemics.

What is genomic sequencing?

Genomic sequencing is the process of determining the DNA or RNA sequence of an organism. This provides a detailed map of its genetic composition. For viruses like SARS-CoV-2, this knowledge is important because by comparing sequences, we can identify changes or mutations in the virus over time.

How has SARS-CoV-2 changed over time? 

The SARS-CoV-2 virus, responsible for COVID-19, has undergone numerous genetic changes since its emergence. These genetic variations have led to the identification of multiple strains or variants of the virus. Here's an overview of some of the most notable variants and their genetic variations:

Alpha variant (B.1.1.7): First detected in the UK in September 2020, the SARS-CoV-2 Alpha variant is an early mutated strain, characterised by significant mutations such as N501Y, P681H, and NTD deletions at positions 69–70 and 144, along with various non-spike mutations, classifying it as a variant of concern.

Beta variant (B.1.351): Identified in South Africa in May 2020, the Beta variant has key mutations, notably N501Y, E484K, and K417N in the spike protein and NTD deletions at positions 242–244, leading to its classification as a variant of concern. Multiple studies have highlighted this variant's potential for partial or complete viral evasion from monoclonal antibodies.

Gamma variant (P.1): First identified in Brazil in January 2021, the Gamma variant has over 22 mutations, with 12 on the spike protein, including key RBD mutations like L18F, N501Y, E484K, and K417T. This variant is associated with a 3 to 4-fold increase in hospitalisation and morbidity rates compared to earlier variants.

Delta variant (B.1.617.2): The Delta variant, first identified in India in late 2020, quickly became the predominant strain worldwide due to its heightened transmissibility, as highlighted by the WHO. This variant, characterised by key mutations such as E484Q, L452R, and P681R in the spike protein and mutations in ORF3 and ORF7, has shown increased infectiousness, with studies indicating a higher prevalence among the young.

Omicron variant (B.1.1.529): First reported by South Africa in November 2021, this variant possesses numerous mutations, with over 50 believed to enhance transmissibility or facilitate immune escape, and it presents over 30 genetic changes in the spike protein, distinguishing it from previous variants. Researchers have yet to establish a link between this variant and its predecessors.

While these are some of the most discussed variants, viruses, by nature, mutate over time. Many mutations are inconsequential, while others can confer advantages to the virus, like increased transmissibility or evasion from the immune response. Continuous genomic surveillance and research are important to monitor these changes and adapt our public health response accordingly.

How genomic sequencing helps track SARS-CoV-2 variants

From the beginning of the pandemic, scientists worldwide began sequencing the genome of the SARS-CoV-2 virus. As samples from various regions and patients were sequenced, databases began to amass genetic blueprints of the virus. The collaboration across countries continues to make it possible to quickly identify any significant genetic variations or emerging variants.

This information is shared via WHO technical briefings on variants and through country-specific government variant surveillance mechanisms. Organisations such as GISAID (Global Initiative on Sharing All Influenza Data) provide open access to genomic data of influenza viruses and the coronavirus responsible for the COVID-19 pandemic. All of this data has proven crucial for several reasons:

Monitoring spread: Identifying a variant allows health agencies to monitor its spread, guiding containment measures and public health strategies.

Vaccine efficacy: Variants can potentially impact the efficacy of existing vaccines. By understanding these variants at a genetic level, researchers can modify vaccines accordingly, ensuring they remain effective.

Understanding virus behaviour: Some mutations make the virus more contagious or cause more severe disease. By keeping an eye on these changes, health officials can adapt their responses and warnings.

Implications for future pandemics

The role of genomic sequencing in the COVID-19 pandemic has been a clear demonstration of the technology's value. As we consider future pandemics, several lessons emerge:

Early and wide-scale sequencing: The earlier we can sequence a new pathogen, the better we can understand its behaviour and transmission dynamics. Coupled with wide-scale sequencing, it can provide a real-time overview of a pathogen's evolution.

Global collaboration: The global databases and collaborative spirit seen during COVID-19 will be critical for future success. Shared knowledge will enable quicker responses to emerging threats.

Preparedness for vaccine modification: As seen with COVID-19, no vaccine is a one-size-fits-all solution forever. Sequencing allows us to keep vaccines updated with changing pathogens.

Predictive analysis: With more data, we can potentially predict how a virus might evolve, giving us a heads-up on possible challenges.

Infrastructure development: Investment in genomic sequencing infrastructure globally, especially in low and middle-income countries, will be crucial. Early detection of emerging diseases can change the course of pandemics.


The COVID-19 pandemic highlighted the significance of genomic sequencing. This invaluable tool has not only been instrumental in tracking SARS-CoV-2 variants but also offers us a blueprint for managing future pandemics. As we continue learning to live with COVID-19, the lessons learned will pave the way for a more prepared and proactive global response in the future.

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