When South African scientists announced that they had detected a new coronavirus variant with a worryingly high number of mutations, they were applauded for how quickly they were able to detect it.
The country was praised for having a robust genomic sequencing program that allowed them to identify the potentially troubling properties of the variant now known as Ômicron.
When viruses spread through populations, they mutate. Most of them don’t significantly change 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 might make it more transmissible or more dangerous in terms of the severity of the disease it causes .
The process is done in a laboratory, separate from testing for coronaviruses. It can take anywhere from 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 Ômicron variant is an example of how concerted efforts can make a big difference.
“The identification of Ômicron highlights the continuing importance and need for genomic surveillance of SARS-CoV-2, as well as access to relevant samples to do this,” said Sharon Peacock, professor of Public Health and Microbiology at Cambridge University, adding that South Africa’s Ministry of Health and its scientists “are to be applauded for their response, their science and for sounding the alarm to the world.”
In the past 30 days, during which Ômicron reached the global spotlight, less than a third of countries and territories have sequenced cases to identify how the virus has changed over time, according to analysis by CNN data reported to the global science initiative GISAID.
Nearly a third of the 241 countries and territories tracked by Gisaid failed to sequence more than 100 samples during the course of the pandemic.
Last month, when the Ômicron variant became the last variant of concern, only a dozen countries performed sequencing for more than 5% of their Covid-19 cases.
They are 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 last month, but more than 100 others that had done so previously 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 very 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 high caseload and is still able to sequence a large proportion of its samples – 13% last month and on average during the pandemic.
The United States is lagging behind, with just 2.6% of cases sequenced in the past 30 days and 4% overall, according to the database.
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, the country’s Ministry of Health and its scientists focused their efforts where it mattered. When they realized that Covid-19 cases started to grow at a much higher rate in Gauteng province compared to the rest of the country, they targeted sequenced samples in the region – and in doing so, they identified the new variant.
*This article has been translated. Read the original in English
Reference: CNN Brasil
