The Washington PostDemocracy Dies in Darkness

South Africa, which found the omicron variant first, leads Africa in coronavirus sequencing

Passengers undergo coronavirus testing at a Rome airport Nov. 28. (Telenews/EPA-EFE/Shutterstock)

South Africa’s announcement Thursday that it had identified a new, possibly highly contagious coronavirus variant sent shock waves worldwide. Stock markets fell as the United States, among other countries, imposed a travel ban on southern Africa.

Much remains unknown about the mutations that make up the new omicron variant. But what scientists do know is that 20 months and several variants into the coronavirus pandemic, one tool to stem the spread of infection — sequencing the virus to catch significant genetic changes — remains used only patchily.

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The United States is sequencing and sharing 3.6 percent of its coronavirus samples, according to a Washington Post analysis of data from the GISAID tracking initiative, which provides a global database of coronavirus genomes. That means the United States ranks 20th among countries sequencing 5,000 or more samples. It’s a sizable rise from 0.3 percent in December 2020 and 1 percent in April but is still below the rate that scientists say is needed to stay on top of major changes to the virus.

Coronavirus variants like omicron, delta and mu are an expected part of the virus's life cycle, but vaccines can prevent more infectious variants from forming. (Video: John Farrell, Hadley Green/The Washington Post)

South Africa, in contrast, is sequencing 0.8 percent of its virus samples and ranks 37th worldwide. About 35 percent of its population is vaccinated, according to the country’s Department of Health. (Other trackers have lower numbers.) No other country in Africa has surpassed the threshold of sequencing 5,000 samples. Kenya, however, is close to doing so and is one of several African countries with an overall higher percentage of sequencing than South Africa.

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India, which this spring was the center of a devastating outbreak, is sequencing 0.2 percent of samples, up from 0.06 percent in April.

The countries with the highest sequencing rates are largely European ones with comparatively high vaccination rates. Iceland tops the chart, with 56.2 percent of its virus samples sequenced and more than 88 percent of its population fully vaccinated, according to a Reuters tracker.

Since the vaccine rollout began nearly one year ago, scientists have warned rich, mainly Western countries against monopolizing vaccine stocks at the expense of a more equitable global distribution. The longer the virus circulates among unvaccinated populations, the more chances there are for highly transmissible variants to develop.

Just 6 percent of Africa’s 1.2 billion people are vaccinated, compared with about 59 percent of people in the United States. While the United States and some countries in Europe are providing their populations with booster shots, only around 3 percent of people in low-income countries are fully vaccinated, according to Gordon Brown, the World Health Organization’s ambassador for global health financing and a former British prime minister.

“Until we vaccinate enough people, we’re going to have this happen over and over again,” Glenda Gray, head of the South African Medical Research Council, told The Washington Post.

South African officials have criticized the travel bans imposed on their country over the weekend after the new variant was announced, saying that such moves could deter other nations from reporting new variants. For weeks, Europe has been battling a surge in coronavirus cases.

The travel restrictions are “akin to punishing South Africa for its advanced genomic sequencing and the ability to detect new variants quicker,” South Africa’s Ministry of International Relations and Cooperation said in a statement. “Excellent science should be applauded and not punished.”

Chiqui Esteban contributed to this report, which has been updated.

Read more:

Here’s just how unequal the global coronavirus vaccine rollout has been

Why America is ‘flying blind’ to the coronavirus mutations racing across the globe

Why Africa is perilously far behind on coronavirus vaccinations