Genomic sequencing is crucial in the battle against the coronavirus. These countries do it well

When South African scientists announced they had detected a new coronavirus variant with a worryingly high number of mutations, they were applauded for how quickly they were able to spot it.

The country was praised for having a robust genomic sequencing program, which allowed them to identify the potentially worrying properties of the variant now known as Omicron.

When viruses spread through populations, they mutate. Most mutations don’t significantly alter a virus’ behavior, but some can be concerning. Genomic sequencing involves decoding the genetic material of a virus to spot the mutations and determine what effect they might have on the virus – for example whether they could make it more transmissible or more dangerous in terms of the severity of the illness it can cause.

The process is done in a lab, separately from coronavirus testing. It can take anywhere between a few hours to several weeks – and each country has a different approach.

Sequencing efforts around the world leave much room for improvement, but South Africa’s discovery of the Omicron variant is an example of how focused efforts can make a big difference.

“[The identification of Omicron] highlights the continued importance and need for genomic surveillance of SARS-CoV-2 and access to relevant samples to do this,” Sharon Peacock, a professor of Public Health and Microbiology at the University of Cambridge, said, adding that the South African Health Ministry and its scientists “are to be applauded in their response, their science, and in sounding the alarm to the world.”

In the past 30 days – during which time Omicron came to the global spotlight – fewer than a third of countries and territories sequenced cases to identify how the virus has changed over time, according to CNN analysis of data reported to the global science initiative GISAID.

Almost a third of the 241 countries and territories tracked by Gisaid have failed to sequence more than 100 samples over the course of the pandemic.

Hundreds of protesters rallied in South Africa's capital Pretoria on June 25, 2021 calling for the country's medicines regulatory body to give the green light to China's Sinovac and Russia's Sputnik vaccines, amid a third coronavirus wave.

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In the past month, when the Omicron variant became the latest variant of concern, only a dozen countries conducted sequencing for more than 5% of their Covid-19 cases.

They were Denmark, Bahrain, Israel, Cambodia, Sweden, United Kingdom, Ghana, Luxembourg, Senegal, Aruba, New Zealand, and Botswana.

Another 63 countries sequenced a small number of cases in the past month but more than 100 others that had done so earlier in the pandemic did not report any sequences in the past month.

However, the numbers don’t tell the whole story. Some countries have been able to sequence large proportions of their cases because their overall infection levels are not too high. This was the case in Denmark, Bahrain and Israel, for example, which are not currently experiencing big spikes in cases.

The UK stands out as the only country that has a high caseload and is still able to sequence a high proportion of its samples – 13% in the past month and on average during the pandemic.

Karen Maynard, a laboratory scientist, prepares COVID-19 samples for genome sequencing at the Tennessee public health lab in Nashville, Tenn., Tuesday, Sept. 14, 2021.

Related article The Omicron variant is putting America's coronavirus sequencing efforts to the test

The US is lagging behind with just 2.6% cases sequenced in the past 30 days and 4% overall, according to the database.

Even a little sequencing can be useful though. South Africa, for example, only sequenced 0.3% of its cases last month and 0.8% of cases overall during the course of the pandemic.

However, the country’s health ministry and its scientists focused their efforts where it mattered. When they noticed that Covid-19 cases started growing at a much higher rate in Gauteng province compared to the rest of the country, they targeted sequenced samples there – and in doing so identified the new variant.