Home >Science >Health >How mutations have shaped the Covid-19 pandemic

The Delta variant of the Covid-19 virus is quickly becoming the dominant type of coronavirus in the U.S., making it one of most aggressive variants to take hold in the country.

Delta is the latest in a series of variants that have spread throughout the U.S. Like all viruses, coronaviruses mutate as they reproduce. Some of these genetic changes make them better at infecting human cells or evading our immune defenses. As newer, better-adapted variants emerge, they push aside earlier versions of the virus. Here is a look at how this process has played out across the U.S. since the start of the pandemic.


Descended from the ancestral version of the Covid-19 virus that was first detected in China, the A.1 lineage is associated with some of the earliest cases of Covid-19 in the U.S., including the outbreak in Washington state that was first detected in January 2020. Its numbers diminished as other variants took hold in the country.


Associated with the early 2020 outbreak in northern Italy, the virus developed a mutation called D614G, which helped make it better at infecting cells, allowing it to outcompete earlier variants. The B.1 lineage went on to become the dominant version both globally and in the U.S.


Derived from B.1, the B.1.2 variant came to account for more than 40% of U.S. samples of the new coronavirus by late last year, as it spread rapidly in the South and Southwest. Since then, its prevalence has shrunk steadily.

Regional variants: Epsilon and Iota

As U.S. Covid-19 cases were hitting new highs last winter, scientists detected the increased presence of two variants in New York and California.

The variants are now referred to as Epsilon (for California’s) and Iota (for New York’s). The World Health Organization began calling significant variants by letters of the Greek alphabet to destigmatize countries in which they were first detected.

The Epsilon variant was first identified in California in January. It has a mutation called L452R, which may make it better at infecting cells. Studies suggest Epsilon is about 20% more transmissible than early versions of the virus. By February, the variant accounted for 15% of samples nationwide.

The Iota variant began circulating in New York as early as November. It has a mutation called E484K, which may help it evade the body’s immune defenses. By April, Iota accounted for 40% of positive Covid-19 tests in New York City and 15% of samples nationally.


First detected in December in the U.K., the Alpha variant combines an arsenal of mutations that help make it about 50% more transmissible than early versions of the virus. One of these, P681H, may facilitate the virus’s entry into cells. Alpha reached the U.S. in January. By March, it had pushed aside other variants to become the dominant type nationally.

Delta variant

The variant was first detected in India last October, where it helped fuel a devastating Covid-19 surge that set records for new infections and deaths. Delta has several of the mutations found in other variants, as well as related mutations affecting the same stretches of genetic code. Researchers think it is about 60% more transmissible than the Alpha variant.

The variant has spread to more than 70 countries.

Based on genome samples, Delta is edging out Alpha in the U.S. From the last week of May to the third week of June, Delta’s prevalence increased almost six-fold as Alpha’s dropped by more than 40%.

As Delta expands its footprint in the U.S., its potential toll on public health remains uncertain. Studies suggest that the Pfizer and AstraZeneca vaccines help reduce rates of hospitalization among patients infected with the variant. But with less than half the country fully vaccinated, many could still be at risk, particularly in parts of the South where vaccination rates are low.

(This story has been published from a wire agency feed without modifications to the text)

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