The Timeline and Impact of COVID-19 Variants

Viruses replicate by making copies of their genetic material inside living hosts. Errors in this copying process can create permanent changes in the virus’s genetic code, known as mutations. All viruses change over time, including SARS-CoV-2, which causes COVID-19. While many mutations have little effect, some can alter a virus’s properties, such as how easily it spreads or the severity of the disease it causes. This evolution is a natural part of a virus’s life cycle.

How COVID-19 Variants Develop

SARS-CoV-2, the virus that causes COVID-19, is an RNA virus. RNA viruses are known to have high mutation rates because the enzymes that copy their genome are prone to errors, and they often lack a robust proofreading mechanism to fix these mistakes. This means that every time the virus replicates, there is a chance for new mutations to be introduced.

While many mutations are harmful to the virus or have no effect, some can be beneficial by offering a survival advantage. For example, a mutation might make the virus better at attaching to host cells or evading the immune system. Through selective pressure, viruses with these advantageous mutations are more likely to survive, replicate, and become more common.

When a virus accumulates a set of mutations that significantly changes its characteristics, it is classified as a new variant. This accumulation of multiple mutations, rather than a single change, can alter its transmissibility or ability to cause severe disease compared to the original virus.

A Timeline of Major Variants

The original strain of SARS-CoV-2 that emerged in late 2019 began to evolve as it spread globally. The Alpha variant (B.1.1.7), first detected in the United Kingdom in September 2020, was one of the first significant variants identified. Its mutations, particularly in the spike protein, were thought to make it between 30% and 50% more transmissible than the original virus strain.

The Delta variant (B.1.617.2) was first identified in India in late 2020 and quickly became the dominant variant by mid-2021. Delta was characterized by even higher transmissibility than Alpha. Studies also suggested that the Delta variant was associated with an increased risk of hospitalization, indicating more severe disease.

In late November 2021, the Omicron variant (B.1.1.529) was identified in South Africa and Botswana. Omicron had an exceptionally large number of mutations, many on the spike protein, which allowed it to spread rapidly and overtake Delta as the dominant strain. It also showed a capacity for immune evasion, leading to a higher number of breakthrough infections in vaccinated or previously infected individuals.

Impact on Vaccines and Treatments

The emergence of new COVID-19 variants directly impacts the effectiveness of medical countermeasures. Mutations in the spike protein can alter its shape, which is the primary target of vaccines. When these changes are significant, antibodies generated by vaccination may not recognize the new variant as effectively, a phenomenon known as immune escape. This can lead to a reduction in vaccine effectiveness against infection.

To address this challenge, vaccine manufacturers developed updated booster shots. Bivalent vaccines were introduced that targeted both the original virus strain and an early Omicron subvariant. Later, monovalent vaccines were developed to specifically target more recent Omicron lineages like XBB.1.5, providing more tailored protection against currently circulating strains.

The evolution of variants also affected certain treatments for COVID-19. Some monoclonal antibody therapies became less effective as variants emerged with mutations in their target areas. However, other treatments, such as antiviral pills like Paxlovid, have remained effective. These drugs work by interfering with the virus’s ability to replicate, a process less affected by the mutations in major variants.

Global Surveillance and Naming

A global network monitors the evolution of SARS-CoV-2 through genomic surveillance. Scientists sequence genetic material from patient samples to identify new mutations and track their spread. The World Health Organization (WHO) coordinates these efforts and, to avoid stigmatizing locations, implemented a naming system using Greek letters. This provides a simple way to refer to variants like Alpha and Omicron and helps in sharing research data.

The WHO also developed a classification system to categorize variants based on risk:

• Variant Under Monitoring (VUM): Requires tracking due to potentially concerning characteristics.
• Variant of Interest (VOI): Has genetic changes predicted to affect virus characteristics like transmissibility or immune evasion.
• Variant of Concern (VOC): Is proven to spread more easily, cause more severe disease, or reduce the effectiveness of vaccines or treatments.