Researchers are racing to detect Omicron, the latest SARS-CoV-2 variant of concern, by sequencing the genomes of coronaviruses infecting people. But surveillance through genomic sequencing can be slow and patchy, complicating the picture of how and where Omicron spreads.
One positive development is that researchers are sequencing more SARS-CoV-2 genomes than ever before. This is what enabled them to notice Omicron relatively swiftly. Last April — about 16 months into the pandemic — an online database belonging to the GISAID data-science initiative contained one million SARS-CoV-2 genomic sequences. Since then, researchers have submitted another five million sequences to GISAID in about eight months — a nearly tenfold rate increase (see ‘Genome explosion’). “We are in much better shape to find Omicron or any other emerging variant now,” says Kelly Wroblewski, director of infectious diseases at the Association of Public Health Laboratories in Silver Spring, Maryland
All of these studies are evolving daily as new Omicron sequences pour in from around the world. A hint of how fast this field is moving can be seen in the rapid rise in genomes reported after the World Health Organization named Omicron a variant of concern on 26 November. Soon after the agency’s announcement, 15 countries submitted 187 genomic sequences belonging to Omicron to GISAID. By 14 December, 55 countries had shared 4,265 Omicron sequences. The figures are on course to balloon further — but Luo warns that’s not necessarily representative of how fast the variant is spreading. Many testing centres are preferentially sequencing samples after a simple, fast genotyping test picks up a possible signal for Omicron — a particular amino acid in the gene for its spike protein. As a result, Omicron might be overrepresented among SARS-CoV-2 genome sequences right now.
Genomic information is biased and messy in so many ways, Luo says. “We have to be careful about what we take away from any one source of data.”
Reference & source information: https://www.nature.com/
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