Four years ago, on December 12, 2019, the first case of the disease that would be known as COVID-19 was reported. Since then, many strains of the pathogen that causes it, SARS-COV-2, have been discovered and labeled. Sometime during the pandemic, many of us may have received news of the nefarious Omicron variant, or something concerning called B.1.1.7–but what are these things, and where did they come from? How are they related to the “original” COVID virus, and what’s different about them? 

Although the origin of SARS-COV-2 has been subject to much debate (and conspiracy), it seems that now we have concrete genomic evidence of its “birth”. Research presents strong evidence that the virus arose from a “recombination event” (where two viral genomes exchange DNA segments) between a pangolin coronavirus and a bat coronavirus, when they co-infected the same pangolin (a small scaly mammal). The recombined virus then spread from the pangolin to humans. This spreading of a virus from animals to humans is known as zoonosis. 

In order to identify the original genome, researchers compared viral genomes collected from patients at the beginning of the pandemic to bat and pangolin coronavirus strains. The ancestral coronavirus they found was labeled type “A” and the derived ones type “B” in the West. The B-type mutated into further types, one of which (B.1) is the ancestor of the major global variants of concern (VOC). The VOC were labeled alpha, beta, gamma, delta, and omicron by the World Health Organization. 

Alpha (B.1.1.7) 

This strain was first widely noticed in the UK in December 2020. It is believed to be 30 to 50% more contagious than the ancestral strain of SARS-CoV-2. Illnesses caused by the Alpha strain comprised 66% of total cases of COVID in the US in mid-April 2021. 

Beta (B.1.351)

This strain was first identified in South Africa in December 2020. It was said to be about 50% more contagious than the original strain. However, this strain was not common in the US. 

Gamma (P.1) 

This strain was first identified in Japan in January 2021. It was described to be “not anywhere as transmissible as Alpha or Delta”. 

Delta (B.1.617.2) 

This name probably rings a bell. The Delta strain was first identified in India in October 2020. By June 2021, Delta had become the global dominant strain. In the United Kingdom, it was found that Delta infections carried a higher risk of hospitalization than Alpha ones. 

Omicron (BA.1) 

This strain was first reported in South Africa in November 2021. Sub-variants of Omicron are considered to be “especially efficient spreaders” of the disease. In fact, the current dominant strain in the US is one dubbed XEC, which is a recombinant strain from two other Omicron sub-variants, K.P.3.3 and KS.1.1. As of February 2025, infections by this strain constituted 37% of total cases. Although it was discovered in late 2021, the closest match to Omicron’s genome was a strain that was circulating in mid-2020. How has this strain leaped forward in time? One hypothesis is that it had been “incubating” in an immunocompromised person–someone with a weakened immune system. Over the span of nearly a year, the individual’s immune system was unable to vanquish the virus, but suppressed it enough to keep them alive. Throughout this time, the virus had been replicating and accumulating mutations, until it became so infectious that it caused an outbreak which epidemiologists caught onto. 

Phew, that was a lot of information! Unfortunately, descriptive paragraphs probably don’t do the relationships between the strains of this complex virus justice. For any reader that may be interested in taking a closer look, this link will take you to the SARS-CoV-2 virus’ phylogenetic tree–a visual tool scientists use to depict the genetic relatedness of analyzed genomes. In the graph, we can see the relationship between each strain clearly, including how distantly related to all of the other VOCs Omicron was!