Dr. Benjamin Pinsky is a clinician and professor of pathology and infectious diseases at Stanford, and the editor-in-chief of the international Journal of Clinical Virology. He directs Stanford Medicine’s Clinical Virology Laboratory, which in January launched an ambitious project to identify and track variants of the Covid-19 virus in order to provide crucial information to vaccine researchers and public health officials. Earlier this month, his lab detected the first two cases of the South African Covid-19 variant in California.
Pinsky spoke with J. from his office in Palo Alto.
Tell me about the lab’s project to find Covid variants. What are you doing?
We’re screening all positive samples that come through the Stanford lab for mutations that are associated with known variants. Those include the UK variant, the South Africa variant, there’s two different Brazil variants, and more recently the California — or now called West Coast — variant. And those have specific mutation patterns that we can detect by basically the same technology we use for diagnosis.
When we get a screen positive, we then sequence the whole genome to make sure that it’s really that variant, for confirmation. And additionally we take a subset of the samples that don’t have one of these known mutations and sequence the whole genome of those, so we can identify new mutations and new variants.
Why is keeping an eye on the spread of variants so important?
This monitoring is important for a number of reasons. These variants, first of all, may be more transmissible — that’s already been shown for the UK and South African variants. Secondly, there’s the possibility that the variants may cause more severe disease. That’s still uncertain for these variants, but definitely if that were the case we’d want to be out in front of that. Thirdly, the variants may have an impact on vaccine efficacy. That has certainly been shown for the South African variant.
How many samples have been tested that way so far at the Stanford lab?
We started doing this on a larger scale a little over three weeks ago, so we’ve now screened over 1,700 samples and sequenced several hundred. We’re trying to do this for all of the positive samples that come through the Stanford lab. We serve Stanford Health Care, Stanford Children’s Health and also Valley Care, so we’re getting samples from across the Bay Area counties.
What has your research found so far?
Right now, the most common variant in our area is this California variant, which has a specific mutation in encoding the spike protein. This California variant right now is in about a third of the samples that we’re evaluating, and that has rapidly increased over the last, I’d say, about six weeks or so. It was first identified in Southern California at Cedars-Sinai and then identified in a large outbreak in San Jose. Since then it’s been seen in increasing prevalence in samples in the Bay Area and across California.
The other variants are much less common. We’ve identified four UK variants, we just reported two South African variants, which I believe are the first two in California, and then I believe we’ve confirmed two of the Brazil P2 variants.
Which variant is the one to keep an eye on?
That remains to be seen, which variants may take over in our population here. For example, early on in the pandemic one particular mutation sort of took over basically the entire globe; it’s found now in basically every sample. More recently the UK variant is now in 80 different countries and appears to be more transmissible. So we’ll see what variant takes over, or whether any of these variants become the predominant strain here in California or in the United States.
The one to really keep an eye on that may be the most challenging one, particularly for vaccine efficacy and also the effectiveness of antibody therapies, is the South African strain. The vaccine trials in South Africa with high prevalence of that particular variant have performed less well than in other parts of the world. Most recently, the Oxford-AstraZeneca vaccine trial in South Africa was put on hold; that was due to apparently poor efficacy in South Africa due to the variant. I think that’s the one to keep an eye on.
And then also the Brazil P1 has a very similar constellation of mutations. That one doesn’t seem to have spread as widely, but that’s another one to keep an eye out for. And of course the California one just because it’s in our area and it’s becoming quite highly prevalent.
What should the public keep in mind about mutations? And what does the data you’re collecting mean for public health?
I would say a lot of the reporting has been quite good on the variants, but there is a tendency to make it more alarmist than perhaps is necessary. I think it is reasonable to monitor and make sure we are aware of the spread of these variants, and also to find new variants. What I think is important is that all of the public health interventions like masking, social distancing and handwashing are still effective, so that should continue. And perhaps the emergence of these variants will encourage people to continue to do these things.
In addition, this should not discourage folks from getting vaccinated. It’s still very important that folks get vaccinated. In the U.S., the vast majority of strains are completely susceptible to vaccines, so efficacy would not be expected to be reduced.
Even in places where the South African variant is highly prevalent, even though the vaccines are less efficacious they still appear to be effective at preventing severe disease. So vaccination is still critically important. Folks shouldn’t be waiting to get vaccinated, for any reason.