The more infectious ‘super-covid’ variant from the UK is in at least seven states, a CDC official told DailyMail.com Tuesday, but refused to reveal which remaining two states beyond Colorado, California, Florida New York and Georgia have cases.
Dr Greg Armstrong, director of the Office of Advanced Molecular Detection at the CDC’s National Center for Emerging and Zoonotic Infectious Diseases said that the new variant accounts for ‘fewer than one in 200’ samples run by US labs.
‘It’s up to the states’ to disclose when they have discovered a case of the new variant, Dr Armstrong said. ‘Almost all regulatory authority is at the state level.’
Georgia on Tuesday announced its first case of the ‘mutant’ COVID-19 strain.
The new variant is between 50% and 70% more transmissible, scientists say.
Georgians cast high-stakes final votes Tuesday in elections to determine the balance of power in the new Congress, deciding Senate runoff elections sure to shape President-elect Joe Biden’s ability to enact what could be the most progressive governing agenda in generations.
The first US case of the strand was reported in a remote nursing home in Colorado last week. It has since also been discovered elsewhere in the state, as well as in New York, Florida and California.
San Diego on Tuesday was reporting 32 cases of the variant, bringing to the total cases across the US to 37. Wilma Wooten, county public health officer, said: ‘The fact that these cases have been identified in multiple parts of the region shows that this strain of the virus could be rapidly spreading.’
The ‘mutant’ variant of the virus that began ravaging across the UK towards the end of last year, causing cases to surge and forcing Prime Minister Boris Johnson to announce a third nationwide lockdown Monday.
The first US case of the strand was reported in a remote nursing home in Colorado last week. It has since also been discovered elsewhere in the state, as well as in New York, Georgia, Florida and California, with at least 37 people now infected
The mutant strain was picked up on the same day voters went to the polls in Georgia. Voters are pictured at Sara Smith Elementary polling station, in the Buckhead district, on January 5, 2021 in Atlanta during the Georgia runoff elections
Georgia DPH Commissioner Kathleen E. Toomey said: ‘The emergence of this variant in our state should be a wake-up call for all Georgians.’
Dr Armstrong told DailyMail.com that a hallmark of the variant that’s sent the UK into lockdown is seen in about half of a percent of all samples seen in the US, according to testing data from Helix.
THE US IS CATCHING ON TO BETTER WAYS TO LOOK FOR NEW CORONAVIRUS VARIANTS – BUT IT STILL LAGS BEHIND THE UK
Helix uses a kind of test that just happens to detect an certain gene deletion that is found in the UK variant, B117, as well as others.
The UK has been using this trait to monitor trends in the more infectious variant more efficiently because sequencing virus’s whole genome can take 48 hours for large batches but could be run in six hours in smaller batches.
The CDC is testing in large batches and says they have several hundred samples suspected to be the B117 to run. Yet the agency is running the lengthy type of genome sequencing because it considers this ‘less urgent sequencing,’ because since learning of the new variant last month, officials ‘assumed it was already here in the US, given the strong economic ties [between the UK and the US],’ Dr Armstrong said.
Regular coronavirus testing can’t detect which particular variant someone has been infected by. These diagnostics aren’t designed to.
Standard diagnostic tests search samples of human saliva or mucus for bits of virus genome that are are distinctive to coronavirus, but would be shared across many variants.
Some diagnostic tests can detect the presence of the ‘S dropout’ mutation in a coronavirus sample. B117 has this mutation, and although other strains do too, monitoring how often this comes up helps the UK monitor likely upticks in the more infectious variant, geneticist Theo Sanderson of the Francis Crick Institute explained on Twitter
It’s important that they detect these relatively general traits of SARS-CoV-2 because it and all viruses change fairly frequently, but usually in small meaningless ways.
The new UK variant has more significant changes that make it more infectious.
In order to know for sure that a sample contains the new variant, the whole genome needs to be sequenced.
The genome is a very long chain, in molecular terms, consisting of nearly 30,000 nucleotides – chemical letters. Sequencing an entire coronavirus genome takes at least a couple hours.
And as the central health authority for a country of nearly 331 million people, the CDC receives massive numbers of samples to sequence.
The UK’s new variant of the virus is not more deadly but is around 50 percent more infectious. This chart from different regions from the UK shows how much more infectious the new super-COVID strain is in comparison to other virus variants
So the agency tends to run large batches of hundreds of samples at a time. Running such large quantities stretches out the process even longer. Getting the full sequence of the genomes of hundreds of virus samples might take four up to four days to run end-to-end.
In the lab, that includes two time-consuming stages.
‘It takes about 3 days to make the library’ – of all the bases in a strand of viral genetic material, called RNA – ‘and the sequencer takes about a day at a time,’ Dr Jasmine Plummer, a research scientist at the Cedars-Sinai Center for Bioinformatics and Functional Genomics in Los Angeles told DailyMail.com.
Dr Howard Zucker, Commissioner of the New York State Department of Health, said the department’s Wadsworth Lab has that process down to about 44 hours.
That’s about as fast as the process can go, Dr Plummer said.
Meanwhile, Dr Zucker said he had ‘heard reports it can take several weeks to get results back [from the CDC].’
Although CDC’s Dr Armstrong said this is largely due to the volume of samples the CDC runs at a time, Dr Plummer said there are more mundane reasons.
‘We’re in a hospital, we get samples directly and sequence them in-house,’ she said of the Cedars-Sinai lab.
‘There are transport issues getting to the CDC, quality control issues – they’re hindered by delivery.’
Samples also get contaminated by the people providing them, collecting them and transporting. Dr Plummer says cleaning those up sufficiently for a diagnostic test to work is easy enough, but getting them in shape for accurate sequencing is a much taller order.
Still, the US an the CDC have not been sequencing the same volume of viral genomes per capita that other nations have.
Dr Armstrong says that the CDC is ramping up the number of samples that get the full work up from 3,500 a week in December to some 6,500 a week.
THE NEW UK STRAIN HAS TRIGGERED A CALIFORNIA CLUSTER AND IS IN ‘SEVERAL STATES’
Already the variant is ‘present in low numbers but present in several states,’ with at least seven confirmed to the CDC, but not to the American public.
He explained that state health departments have only confirmed the presence of cases to the CDC, but have not revealed any further details to the agency.
CDC does not yet know which county in each of the remaining two mystery states has a case, nor any identifying details of the infected individuals.
States need to investigate and contact these cases and confirm as many details as possible before publicly reporting them, Dr Armstrong said.
For the time being, ‘this is a variant with a low prevalence and it its not going to impact what non-pharmacological interventions [states implement],’ he said.
But in the UK, a handful of cases, first announced on December 14, have exploded. The new variant now accounts for an estimated 62 percent of cases in London and is all over England.
In San Diego 24 newly confirmed people with virus are said have no travel history and to have come from 19 different homes.
New York Gov. Andrew Cuomo on Tuesday identified the New York patient Monday as a male jewelry store worker in Saratoga Springs, who is in his 60s. The man did have COVID-19 symptoms but is ‘on the mend.’
He said the state is testing three more possible cases of the strain in Saratoga with it taking up to 44 hours to do the genome sequencing to detect the variant.
Much like the first US case of the variant in Colorado, the man had no recent travel history, suggesting a community spread.
The CDC believes the strain first emerged in Britain in September and said last week it suspects it has been circulating in the US for some time.
The strain is thought to be 50 to 70 percent more transmissible but not more deadly.
The Empire State had earlier become the fourth in the nation to detect the ‘mutant’ variant of the virus.
Cuomo on Tuesday appeared to push back against NYC Mayor Bill de Blasio’s calls to ban all flights from the UK to the US.
The governor called on the federal government to begin enforcing mandatory testing on all international passengers arriving in the US, like they are already doing with travelers from the UK.
De-Blasio had urged the Trump administration to ‘stop the madness’ and block all travel to and from the Britain to help stop any further spread of the new super-infectious UK variant of the virus.
It’s now reported in the UK that around one of every 50 residents – or roughly one million people – now has the coronavirus.
In light of the surge, as of December 28, the CDC began requiring all airline passengers arriving from Britain – including U.S. citizens – to test negative for COVID-19 within 72 hours of departure. Unless a dual-citizen or travelling for essential purposes, the majority of Brits are currently banned from entering the US.
The UK is also currently grappling with a second mutant strain of the virus, said to originate from South Africa, which experts fear may be resistant to vaccines and potentially more deadly.
That strain has not yet been detected in the US.