South Africa, which found omicron variant first, sequences less than 1% of coronavirus samples

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Passengers undergo coronavirus testing at Rome’s Leonardo da Vinci International Airport on Nov. 28. Italy imposed a travel ban on several African nations after a new coronavirus variant was discovered late last week in South Africa. (Telenews/EPA-EFE/REX/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.

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 and 1 percent in April but is still below the rate thatscientists say is needed to stay on top of major changes to the virus