Tracking the coronavirus’s evolution, letter by letter, is revolutionizing pandemic science.
The teams in Africa who detected the new Covid genome moved quickly. Their actions should not result in economic loss.
Every week across the U.K., a fleet of courier trucks ferries chilled waste material from half a million Covid-19 tests to a genome-sequencing facility in Cambridgeshire, eastern England.
The daily operation is part of a Covid-19 surveillance system that has made the U.K. the world’s leading sequencer of the coronavirus genome and helped it to spot a more contagious, and possibly more deadly, variant of the virus that in most countries would have long gone unnoticed.
The US’s genome sequencing system has improved, but surveillance is dangerously inadequate in much of the world.
One of the most powerful ways of fighting a pandemic caused by a never-before-seen virus is by decoding the microbial culprit’s genome.
“You can’t fix what you don’t measure” is a maxim in the business world. And it holds true in the world of public health as well.
Public and private health labs sequence more COVID-19 samples in Minnesota than almost any other state.
With current massive genomic sequencing efforts, virological epidemiological surveillance is being performed near to real time. Mutations in the viral genome are also detected and shared near to real time, leaving the interpretation of their relevance for future work.
The current coronavirus disease 2019 (COVID-19) pandemic is the first to apply whole-genome sequencing near to real time, with over 2 million severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) whole-genome sequences generated and shared through the GISAID platform.
It makes it all the more difficult to stop new infections.
For the Covid-19 pandemic to stay on a downward trend, the U.S. must optimize a national viral sequencing network that is scalable and based on regional capabilities for sequencing and public health intervention. Without such efforts, Covid-19 infections could again move through communities without adequate public health knowledge of what is happening, and why. This places society at great risk of going back to square one in the battle against this pandemic.
"There's a reason we haven't heard of something called the United States variant, and it's not because it doesn't exist. It's because we just don't detect these things early," says Dr. Kavita Patel, a non-resident fellow at the Brookings Institution and physician practicing in Washington, D.C. "They're picked up in other places that tend to have better surveillance systems."
Genomic surveillance has improved enormously in recent months, but the system has built-in delays, and blind spots remain.
The US lags behind on yet another tool to end the pandemic: viral genetic sequencing.
Continual genetic monitoring of viruses and mutations can help overcome the covid-19 crisis and prevent the next pandemic.
Sequencing SARS-CoV-2 in the Americas.
The California SARS-CoV-2 Whole Genome Sequencing Initiative called COVIDNet is an unprecedented public-private partnership to provide California with genomic sequencing data for epidemiological efforts to control the spread of COVID-19.
As CDC and public health partners sequence more SARS-CoV-2 genomes, we will improve our understanding of which variants are circulating in the US, how quickly variants emerge, and which variants are the most important to characterize and track in terms of health.
There’s a golden opportunity to track deadly new variants of the virus in the sewers.