We entered the laboratory in South Africa that studies the omicron variant 3:03
(CNN) -
When South African scientists announced that they detected a new variant of the new coronavirus with a worryingly high number of mutations, they were applauded for how quickly they were able to detect it, thanks to genomic sequencing.
The country was praised for having a robust genomic sequencing program, which allowed it to identify the potentially worrisome properties of the variant now known as omicron.
When viruses spread through populations, they mutate.
Most mutations do not significantly alter the behavior of a virus, but some can be worrisome.
Genomic sequencing involves decoding the genetic material of a virus to detect 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 disease it can cause.
The process is done in a laboratory, separate from coronavirus testing.
It can take anywhere from a few hours to several weeks, and each country has a different approach.
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Sequencing efforts around the world leave much room for improvement, but South Africa's discovery of the omicron variant is an example of how concentrated efforts can make a big difference.
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"[The identification of the omicron variant] highlights the continued importance and need for SARS-CoV-2 genomic surveillance and access to relevant samples to do this," said Sharon Peacock, professor of Public Health and Microbiology at the University of Cambridge.
He added that the South African Ministry of Health and its scientists "should be applauded for their response, their science and for raising the alarm to the world."
Countries that have achieved genomic sequencing
In the past 30 days, during which the omicron variant became the center of global attention, less than a third of countries and territories sequenced cases to identify how the virus has changed over time, according to CNN's analysis of the 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 during the course of the pandemic.
In the last month, when the omicron variant became the last worrying variant, only a dozen countries carried out sequencing of more than 5% of their covid-19 cases.
These are Denmark, Bahrain, Israel, Cambodia, Sweden, the United Kingdom, Ghana, Luxembourg, Senegal, Aruba, New Zealand, and Botswana.
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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 reported no sequence 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 large spikes in cases.
The UK stands out as the only country that has a large number of cases and is still able to sequence a high proportion of its samples: 13% in the last month and on average during the pandemic.
The United States is lagging behind with only 2.6% of cases sequenced in the past 30 days and 4% overall, according to the database.
However, even a little sequencing can be helpful.
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, that country's Ministry of Health and its scientists focused their efforts where it mattered.
When they noticed that COVID-19 cases started to grow at a much higher rate in Gauteng province, compared to the rest of the country, they targeted samples sequenced there and, in doing so, identified the new variant.
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