Virology & Infectious Diseases

Coronavirus Variants

Understanding the history of prior coronaviruses and tracking the major mutations of SARS-CoV-2.

1. Prior Coronaviruses

At the beginning of 2003, the first severe coronavirus with true pandemic potential emerged from China and spread to several other countries.

Severe Acute Respiratory Syndrome (SARS) had a case fatality rate of an estimated 3%, but fortunately, transmission networks were effectively interrupted, and the aggressive spread of the virus was largely halted. Nine years later, Saudi Arabia officially reported their first case of an even deadlier severe coronavirus, named the Middle Eastern Respiratory Syndrome Coronavirus (MERS-CoV), which tragically claimed the lives of 30-40% of all individuals infected with the virus. While the active transmission of MERS-CoV has not completely halted, the level of baseline transmissibility of MERS-CoV remains low and relatively contained to particular geographic regions.

The Common Cold Coronaviruses

While SARS-CoV-1 and MERS-CoV produce severe systemic disease and high mortality, the broader coronavirus family actively contributes several endemic strains to the more mild-to-moderate common cold globally. Hundreds of coronaviruses continuously circulate between animal and human hosts, but the four most common human coronaviruses (HCoVs) are referred to as HCoV-NL63, HCoV-OC43, HCoV-HKU1, and HCoV-229E. These four coronaviruses circulate on a predictable seasonal cycle that differs between regions, and most individuals typically contract at least one of these four seasonal coronaviruses by the age of 5.

2. Major SARS-CoV-2 Variants

Just seven years after the first MERS-CoV case was reported in Saudi Arabia, China reported a novel severe coronavirus, officially named SARS-CoV-2, that was actively causing severe respiratory disease, now known as Coronavirus Disease 2019 (COVID-19). This initial strain is considered the “wild-type” foundational variant. Since then, continuous global circulation has driven the rapid emergence of several major variants of concern.

SARS-CoV-2 Alpha / B.1.1.7

In the fall of 2020, several distinct genetic mutations were reported in critical regions of the SARS-CoV-2 viral proteins, and these novel variants began circulating globally, prompting the creation of a formal classification system. One particular variant, originally reported in the United Kingdom, rapidly emerged with a large number of targeted mutations in the spike surface protein that appeared to significantly alter both transmissibility and overall mortality. This variant was deemed the Alpha variant, or B.1.1.7 lineage.

SARS-CoV-2 Beta / B.1.351

Independent of the B.1.1.7 lineage, another aggressive viral strain emerged with a totally different set of spike mutations and was first reported in South Africa. The Beta strain was quickly detected in multiple countries worldwide, heavily suggesting widespread transmission similar to that seen in prior variants. Crucially, some reports suggested the mutations documented in B.1.351 may significantly affect monoclonal or polyclonal antibody neutralization.

SARS-CoV-2 Gamma / P.1

First identified in Brazilian travelers arriving in Japan, the Brazilian P.1 lineage was also reported in the fall of 2020. This unique lineage harbors 17 unique mutations, notably including three directly within the receptor binding domain (RBD) region of the crucial spike protein. Some of these point mutations are genetically identical across the alpha and beta lineages. The Gamma variant was reported to have fundamentally altered transmissibility and neutralization profiling, heavily resulting in decreased systemic protection acquired by natural prior infection or standard vaccination.

SARS-CoV-2 Delta / B.1.617.2

A massive variant of concern, the Delta variant was universally reported to possess incredibly increased transmissibility and vastly reduced antibody neutralization by post-vaccination sera. This strain, first identified in India, rapidly dominated new global infections due to its highly altered transmission profile and the relaxing of public protection measures in some regions. The functional mutations acquired in the Delta variant resulted in greater than two-fold overall transmissibility compared to the wild-type virus.

SARS-CoV-2 Omicron / B.1.1.529 (BA.1+)

Another major structural variant of concern, named the Omicron variant, was also first reported out of South Africa. The raw number of mutations actively acquired in the Omicron variant increased exponentially when compared directly with the concurrently-circulating Delta variant. These extreme mutations were shown to increase transmissibility immensely and severely reduce the effectiveness of clinical antibody therapies and neutralization by post-vaccination sera. Of special note, the Omicron variant is structurally considered a family of variants, composed of various BA lineages. Initially, BA.1 dominated viral sequences globally. A newer, highly adapted sublineage, BA.2, eventually overtook the BA.1 lineage in several countries due to being significantly more transmissible.

Need Reagents for Variant Research?

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