US falters in testing to detect dangerous Covid mutations

First known US case of variant from Brazil was detected while California is investigating possible new American strain

Long Beach Airport (LGB), offers COVID-19 testing to travelers going to any destination, in Long Beach, Calif., on Monday, Jan. 18, 2021. EMT Karly Morrow swabs a client at the testing site. (Brittany Murray /The Orange County Register via AP)
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The US faces a steep uphill struggle in monitoring Covid-19 variants, dangerous mutations that might spread quickly, evade vaccines or kill more infected people.

Other countries, such as the UK, have established robust, nationwide surveillance programmes to identify new Covid genomes and track the spread of existing ones.

But the US has not. It ranks 32nd in the world in number of sequences completed for every 1,000 Covid cases, says Gisaid, a global database where researchers share new genomes.

While the Biden administration is promising to boost the country's sequencing efforts, it will not be easy.

The US system now in place includes a scattered collection of academic, commercial and public health laboratories that are typically underfunded and under-resourced.

This amounts to a gaping hole in national security at a time when at least three dangerous global variants have already been identified and others may yet be discovered.

“The problem is that this was never a public health lab priority,” said Michael Osterholm, director of the Centre for Infectious Disease Research and Policy at the University of Minnesota and an adviser to US President Joe Biden.

"Most of the sequencing was going on in private labs.”

Mr Osterholm said it must be made a priority.

Over the past week, federal health officials promised to increase the US ability to track variants.

“We are now scaling up both our surveillance of these and our study of these,” Rochelle Walensky, the new director of the US Centres for Disease Control and Prevention, told Fox News on Sunday.

But the administration has yet to outline concrete steps to turn the current effort into a cohesive and efficient national programme.

In the US, about 200,000 Americans test positive for Covid-19 weekly, but only about 3,000 of those tests are sequenced to hunt for mutations, according to the centre.

The US is behind nations known for their genomic processing expertise, such as the UK and Iceland, and behind Gambia, Senegal and Latvia, the Gisaid listings show.

Creating a viral surveillance network “is a public health need, but also a defence need", said Francis deSouza, chief executive of the sequencing company Illumina, which has been working with partners to help monitor the evolution of the virus.

“Understanding how the virus is mutating will tell you whether the tools you’re using to combat the virus will continue to be effective,” Mr deSouza said.

The three variants that have raised concerns among scientists and public health experts were identified in the UK, South Africa and, most recently, Brazil.

The Brazil variant was found in a Minnesota resident who had travelled to that country, the state's Department of Health said.

This suggests the variant may not yet be widely circulating in the US.

The highly transmissible UK variant has already been found in more than 20 US states.

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We see case rates go up and we don't know if that's because people aren't doing the right things in terms of staying home and masking and social distancing, or whether it's a variant. We're in the dark.

The California Department of Public Health said this month that scientists had identified a variant of the coronavirus, known as L452R, in many parts of the state.

Officials said they were not yet sure whether the variant was more transmissible, but noted that it had been found among patients in large outbreaks in Santa Clara County, which health officer Dr Sara Cody called a “red flag.”

Moderna on Monday expressed concern that the South Africa variant may cause vaccination immunity to decrease more quickly.

The company said it was planning human studies for a vaccine booster to address this concern.

"When you have something that maybe is twice as readily transmitted as something else, that alone is going to cause a problem because the more people that get infected, the more people are going to get hospitalised," said Anthony Fauci, the top US infectious disease doctor, referring to the UK variant.

Sars-CoV-2, the coronavirus that causes Covid-19, mutates frequently, although not as often as the virus that causes influenza, scientists have said.

While most mutations will have no significant effect on Covid-19's ability to infect, the UK and South Africa variants appear to have the ability to infiltrate the bodies' cells better than the original form of the virus, which could make them more contagious.

The B117 variant that was detected in south-eastern England in September contributed to a surge in cases that in January sent the UK back into lockdown.

By early January, cases caused by this variant had also been identified in about 50 countries and territories, including the US, Australia, Canada, Germany, Italy, Japan, Lebanon, the Netherlands, Singapore and South Korea.

The effort to advance US sequencing began in May, when the Centres for Disease Control established a consortium of sequencing labs known as the Sars-CoV-2 Sequencing for Public Health Emergency Response, Epidemiology and Surveillance, or Spheres.

But US sequencing efforts have been spotty at best. The UK sequences about 10 per cent of its positive Covid-19 cases, while the US sequences about 0.3 per cent, Mr deSouza said.

As of January, California, with three million Covid-19 cases, sequenced more than 9,000 cases.

Texas, with more than a million cases, sequenced about 15,000.

But Virginia, where cases are approaching half a million and rising, has sequenced only seven viral genomes.

“We see case rates go up and we don’t know if that’s because people aren’t doing the right things in terms of staying home and masking and social distancing, or whether it’s a variant,” said Eric Topol, director of Scripps Research Translational Institute.

“We’re in the dark.”

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