Skip to Main Content


Information and resources on SARS-CoV-2 (the virus that causes COVID-19)

What are SARS-CoV-2 Variants?

In microbiology and virology, the term variant (or genetic variant) is used to describe a subtype of a microorganism that is genetically distinct from a main strain, but not sufficiently different to be termed a distinct strain.

SARS-CoV-2 Virus

The earliest sequence of SARS-CoV-2 was a sample from December 24, 2019. This sequence was known as Wuhan-Hu-1. Another early sequence, hCoV-19/Wuhan/WIV04/2019 was taken from a symptomatic patient on December 30, 2019. This sequence became known as the "reference sequence". 

These two sequences are  considered the two original haplotypes or lineages of SARS-CoV-2. Wuhan-Hu-1 became known as Lineage B and WIV04/2019 became known as Lineage A. It is unclear when, where, or how the progenitor virus that gave rise to these two lineages appeared. 

As the pandemic evolved, SARS-CoV-2 mutated and created distinct variants, often with mutations that allowed it to become more transmissible or virulent, or to evade immunity. These SARS-CoV-2 variants are grouped according to their lineage and mutations.

SARS-CoV-2 Virus Classification

While there are many thousands of variants of SARS-CoV-2, subtypes of the virus can be put into larger groupings such as lineages or clades.

There are three primary nomenclatures being used to describe SARS-CoV-2 variants:
  • NextStrain

See Lineages Explained for more information on these classification systems.

Early SARS-CoV-2 Viral Lineages

The two original haplotypes (A and B) discovered in December 2019 were Wuhan-Hu-1 and WIV04/2019. They were assigned the initial classification nomenclature for NextStrain and PANGO.


The first sequence identified, Wuhan-Hu-1 became known as haplotype B with the following nomenclature:

  • NextStrain: 19A
  • PANGO: B.3 - B.6
The Wuhan-Hu-1 sample and it's lineage, haplotype B was much less common of an early lineage and quickly petered out.



The reference sequence, WIV04/2019 became known as haplotype A with the following nomenclature:

  • NextStrain: 19B
  • PANGO: A.1 - A.6

All SARS-CoV-2 lineages today descend from the reference sequence lineage known as haplotype A.

A pandemic is Seeded

By the time the virus spread to Europe (mainly Northern Italy), it had already mutated enough to be designated by a new name:

  • NextStrain: 20A
  • PANGO: B.1

Variant B.1 seeded the pandemic as it is today, and nearly all extant variants descended from it, including all of the WHO Variants of Concern (VOC) and Variants of Interest (VOI) - the Greek letter variants, including:

  • Alpha (B.1.1.7)
  • Beta (B.1.351)
  • Gamma (B.1.1.28)
  • Delta (B.1.617.2)
  • Omicron (B.1.1.529)

SARS-CoV-2 Variant Resources