Houston, Texas, is the first city in the US to identify all of the major coronavirus variants spreading in the US, according to a soon-to-be-posted pre-print.
Meanwhile, scientists in Florida identified the state’s first case of the South African variant over the weekend, meaning it has all three of the imported variants.
Florida already had more cases of the UK B117 variant than any other state. Its number of UK ‘super-covid’ infections stood at 599 as of Monday, in addition to its first case of South Africa’s B1351 variant, and five cases of the Brazilian P1 variant.
Scientists at Houston Methodist found 28 cases of variants, including positive for variants from the UK, South Africa, Brazil, New York and California, in the latest batch of samples it performed genome sequencing for.
Their lab alone has identified more than 200 cases of these variants altogether, study co-author Dr James Musser, chair of the department of pathology and genomic medicine, told DailyMail.com.
Dr Musser is both concerned over the presence of variants, and cool-headed about what they mean.
Houston, Texas, is the first city in the US to identify all of the major coronavirus variants spreading in the US, according to a soon-to-be-posted pre-print. The US has reported 2,463 confirmed cases of ‘super-covid’ in the US, but Florida has nearly 600 of those
He notes that Houston Methodist is sequencing the viral up to 1,700 a week, and has already sequenced more than 20,000 genomes in total.
That’s a very high volume for a lab of that size, considering the US as a whole has submitted fewer than 140,000 viral genome sequences to the international GISAID database since the beginning of the pandemic.
So Dr Musser suspects that menagerie of mutants identified in Houston may be as much a reflection of testing volume, as anything out of the ordinary – for the COVID-19 pandemic – happening in the city of 2.3 million people.
Houston Methodist has identified the following in the city, Dr Musser says:
- UK variant B117: 23
- South African variant B1351: 2
- Brazilian variant P1: 4
- Brazilian variant P2: 39
- California variant B1329: 143
- California variant 1427: 19
- New York variant B1526: 5
But with considerable evidence that some of these variants spread more easily than earlier forms of coronavirus, and that some may evade vaccines, he also sees the need to not only sequence genomes but to follow the people who are infected with them, as dire.
And the US needs to be completing this process much faster, he says.
‘We in the US need to get to a point where we’re doing a much better job than we are right now,’ Dr Musser said.
‘We need to do [genome sequencing and follow-up] in as close to real time as we can.’
He said a major US diagnostic company told him that their turnaround time between a sample being swabbed from a patient and getting the genome of that sample sequenced is about two weeks.
‘We’ve got to condense that because, in my opinion, one wants to be able to do things as rapidly as possible if you want to have any opportunity to play what I call whack-a-mutant,’ said Dr Musser.
‘Having the genome sequence alone can be important, but the crucial thing is going to to be to mate that genome sequence up with the patient information. Only in that fashion are we going to be able to get a relationship between the genotype and phenotype of variants.’
The genotype is the genetic profile of a virus (or animal, plant or person) and the phenotype id the physical manifestation of those genes.
So in the case of coronavirus variants, Dr Musser says that the most critical information will come from finding out how infection with a variant affects how sick someone gets, how at-risk of dying of the infection they are, and how likely they are to spread the virus, compared to those infected with earlier forms.
The US has finally stepped up its efforts to detect coronavirus variants, sequencing about 7,000 samples last week, compared to fewer than 1,000 the last week of December 2020, according to the Centers for Disease Control and Prevention (CDC).
But it still lags sorely behind countries like the UK, which is sequencing about 20,000 samples a week.
And beyond the slow sequencing, the ability of the US to track the spread and effects of variants has been hamstrung by red tape.
Labs, including Dr Musser’s, can’t inform patients if they are infected with a variant.
That’s due to two bureaucratic factors. For one, viral genomic sequencing is not approved as a diagnostic tool by the FDA, so whatever information comes out of sequencing is barred from being used as clinical information.
Instead, genome sequencing performed by most labs – especially advanced university-affiliated ones like Houston Methodist’s – is performed as ‘research.’
And researchers are not permitted to tell participants in their ‘studies’ the results of these tests.
Instead, Dr Musser says his lab must pass the information on to state health departments, which then pass the information along to state health departments.
So state health departments might know nothing more than what county the patient in question lives in.
And if they do identify who tested positive for the variant, they can track that person down and do the typical contact tracing – but the genomic sequencing results that showed they were positive for a variant are still off-limits, because they’re not considered diagnostic.
The patient would be told they had COVID-19, but not that they have a potentially more infectious or vaccine-evading form of the virus.
And the time lag between all these steps is considerable.
Even the findings of Dr Musser’s study, which hasn’t even been posted as a pre-print, are about 10 days old – ‘ancient history,’ in coronavirus time, he says.
Sequencing remains too spotty and too slow to really give scientists useful information to tell patients, even if they could notify them that they are infected with a variant.
‘The jury is still out’ on whether the UK’s B117 variant causes more severe disease, and just about everything about the California and New York variants is mysterious at this point, though the evidence that both of Brazil’s variants (P1 and P2) and the one that emerged in South Africa have some resistance to antibodies from both prior infection and vaccines.
It’s tempting to look at Houston, with its menagerie of mutants, or Florida, which has more variant cases than any other state in the country, and now has all three imported ones, as a crystal ball into what the future may hold as variants become common in the US.
But Dr Musser cautions against that. To his mind, each location is more like a tide pool than a crystal ball: there are common elements and dynamics, but each is a little world unto its own.
‘There very well may be different stories to each of those locations,’ he says.
‘If one could choose one particular city and know everything about the rest of the country, that would be great, but I just don’t think it’s true.’