- New Coronavirus Variant Discovered in Humboldt’s Granada Care Home Outbreak, Public Health Office Says
Are we confident that the new coronavirus variant linked to December’s outbreak in Eureka’s Granada assisted living facility has been contained? How was it discovered? Did the mutation that apparently developed there make that outbreak particularly large? Did it make people sicker?
Dr. Ian Hoffman, Humboldt’s public health officer, fielded these questions and more in an emergency media availability earlier this morning. Video above, rough transcript below.
Thank you for joining us for the February 18th media availability with County Health Officer Dr. Ian Hoffman, who would like to begin by providing a brief statement on the new COVID-19 variant that was recently identified in Humboldt County. Dr. Hoffman?
Thank you. This came out of an incredible partnership with many, many folks who work both here within Public Health, at a research lab in San Francisco, the CZ Biohub, folks from the CDPH - California Department of Public Health and our partners here at Granada. The findings of this really highlight how well all of these different groups have worked together and I think Humboldt County should be really proud of the work that’s been done to allow this finding. So thank you to everyone who’s participated in this. We really feel that although the outcome within Granada is devastating, the larger implications for how this turned out for the community are really a wonderful story to tell, so, thank you.
From the Times-Standard: How many variants, and how many cases of each, have been detected in Humboldt County to date?
So far the sequencing that we’ve done here for Humboldt County has identified only one of the variants of concern or the variants that are being monitored, which is the L452r. That is widely being called the ‘California variant’. So we found one of those back in November through some of the sequencing that was done and the information that came a few weeks ago. In this latest round there were another 13 of those that were found. So we’ve had 14 of those L452r variants found to date in Humboldt County, which is not a surprising number considering that statewide this is now becoming the dominant variant that they’re finding in genetic sequencing. As many as 40% in some of the sampling to date. This other - the N501y mutation that we found and identified that was specific only to the Granada outbreak, is not a variant of concern. It is a single point mutation that is also contained in some of the variants of concern from the U.K., South Africa and Brazil, but in and of itself that single mutation is not considered a variant of concern. So far these are the only major findings in our sequencing that have been found to date.
From the Times-Standard: Is the county going to invest more in genomic sequencing to keep track of new variants?
We do a lot of genomic sequencing. Of our positive samples in the county, we’ve sequenced nearly 22%, which is much higher than the recommended. Within our lab, which are the ones that get sequenced, so the Humboldt County Public Health lab has had about 50% of all of our positives have been sent to CZ Biohub for sequencing. Now, that’s nearly all of this possible sequenceable specimens because not every single positive specimen can be sequenced. There has to be enough of enough virus in there to sequence it. So, we really are doing a lot more sequencing than most in both in California and in the country. There is a new national initiative from the Biden administration to increase funding for sequencing. So if there’s a possibility of doing more we’ll certainly look into that, but we’re doing quite a bit already.
From the Times-Standard: With multiple variants on the rise, can you explain how they would interact if they were spreading in the community at the same time? Would the more virulent and vaccine-resistant strains become more dominant?
There’s a lot going into the factors that would determine if a variant became more dominant or not. Things like the investigations and the tracing, the ability to stop strains if they do enter our community or if mutations like this come up; the amount of testing goes into it; additionally how the public is acting. If we’re following the guidance, if we’re masking and distancing, we have less virus transmission in our community. We’re not traveling bringing in new viruses from the outside - those are all things that will determine whether or not a variant of concern comes into our county and spreads easily. Or, if we have something like this like a de novo mutation, would it be able to take a hold and become more widespread.
From the Redwood News: Can you tell us everything that Public Health knows about the characteristics of the new mutation identified in Humboldt County? Is it more transmissible? Does it make people sicker? How is it different from other strains of the virus seen here locally?
This one particular mutation, the N501y, as I mentioned, is part of the three variants of concern, but those have other mutations as well. So we don’t know whether this one would behave exactly the same as those other ones, in terms of its transmissibility or infectiousness. Given some of the laboratory studies that have been done around 501y mutations, it is highly suggested that it is stickier and can bind more to the receptors that allow the virus to enter the cells. So based on that and the fact of what we saw in Granada, it could be one of the reasons that we saw such wide transmissibility and fast transmission in that setting.
From the Redwood News: The press release says that cases of the variant have been linked to Granada Rehabilitation and Wellness Center and that it doesn’t appear to have spread to the broader community. Can you explain how Public Health came to this conclusion? Is this variant still present in our community? Is there any chance it could potentially spread to the broader community in the future?
Through our investigations and contact tracing, we can really feel confident that there were no lines of transmission from the case at Granada. All of the contacts of anyone who was there were contacted, put on quarantine and there is no evidence that any of those folks either transmitted to other settings outside of Granada. Additionally, the sequencing that we’ve done to date has not shown any spread of that particular - we haven’t seen the 501y mutation - in any other samples. We’ll continue to monitor for that through ongoing genetic sequencing, but I do think that given the time period that’s passed since Granada, that if this were something that was going to be much more widespread we very likely would have seen it by now.
From the Redwood News: What does the presence of this new variant mean for Humboldt County moving forward? How can residents best protect themselves against this new variant?
I don’t think there’s any concern for Humboldt with this new variant. I think it’s really important for us to recognize that this is not a variant of concern and it’s different than say the U.K. variant, the South African variant, the Brazilian variants and other variants that we are monitoring. It’s a single mutation and it very much seems to be contained to this one outbreak and did not spread from there. As far as all variants go, the best thing we can do is to continue to do everything that we’ve been doing. We have to wear masks, distance avoid gatherings, and wash our hands. And those things will prevent the variants of concern and if this were circulating in our community, that would be the same exact thing that would stop that from circulating broadly here.
From KMUD News: Can you describe how Covid variants occur in general and how this local variant may have developed?
The coronavirus reproduces inside of our body and makes millions of new viruses every time it makes a copy of itself, there’s a potential that it can make a mistake in that replication of the genetic code. Those sorts of mistakes can sometimes confer advantages to the genetics of the virus. This is not the first time this has been seen. This mutation has come up in other places, obviously in those variants of concern, but also as a single point mutation it has shown up in other places around the United States and around the world. The way it can propagate is if it’s able to continue to spread beyond the original outbreak and if it’s not contained. So I think that’s the important piece that we’re really focusing on with this particular situation with Granada that it really based on all of our evidence today it appears to be contained and did not spread and so was not able to become a variant of concern.
From KMUD News: Will this variant be added to the CDC’s “Emerging Variant Cases in the United States” map?
No. The CDC map is only for variants of concern. So those are ones that again have been identified as circulating broadly. This is a different kind of situation with a single point mutation that seems to be contained to one local outbreak.
From KMUD News: Have other samples been sent to CZ Biohub since January? Will there be continued genomic surveillance locally?
Absolutely. We continue to send samples as frequently as we possibly can.
From KMUD News: How does the genetic sequences from this variant differ from others and why was it more contagious?
I believe we already addressed that.
From the North Coast Journal: How many samples from Humboldt County have been sent to CZ Biohub for testing since the beginning of the Granada outbreak in November? Do you believe it is a comprehensive enough sample to say with confidence that this variant did not spread beyond the facility?
I don’t have exact numbers on for that, but we do send 100% really of what is sequenceable with the regularity. So yes, there have been more sent since this time and we continue to get that information back from CZ Biohub and we’ll continue to let anyone know immediately if there’s a variant of concern. In this case with a mutation, we want to really kind of study it and see and understand it before we make any determinations about talking more broadly about it so that we can do it in a thoughtful way.
From the North Coast Journal: Is there evidence to suggest whether this new variant is linked to a higher rate of critical outcomes from the disease?
I don’t believe there’s enough evidence to suggest that right now.
From the North Coast Journal: How is this variant similar/dissimilar to others discovered in other parts of the state, country and world?
This shares only that one mutation at the in 501y. So that is with those three variants, but also has been seen in other locations as single mutations that haven’t tended to spread. From the North Coast Journal: Does discovery of this variant change anything about how samples will be sent for genomic testing moving forward? No. We continue to send samples on a regular basis and as many as we can, we’ll continue to do that.
From the North Coast Journal: What are the next steps to study this new variant and monitor for its spread?
We’ll continue to do our ongoing epidemiological and investigations which could potentially link any cases to each other. We’ll continue to monitor through genetic sequencing and I think really this just reinforces again the need for more testing in our community, so that we can find these types of things if they are out there. And for really following distancing, masking and gathering guidance.
From Reporter Daniel Mintz: A quote from today’s news release indicated that it isn’t unexpected to see variants occasionally emerge from outbreaks. But this is one of many variants around the world that have adopted mutations useful to the virus. What are the implications of this level of viral diversity and how likely is it to be a continuing trend?
I think it really shows that this virus, every chance it gets to reproduce it is a chance for it to show a mutation. Some mutations like this one likely confer some sort of advantage to the virus. So, again going back to the basics of the more we can stop the spread of this the less chance this virus has to mutate. We will continue to do everything we can here at Humboldt County Public Health and the Humboldt County Public Health lab to try to stop this disease from spreading and we ask everyone to do our part with masking, distancing, avoiding gatherings, hand washing.
From the Times-Standard: Should people be concerned about reinfection after they’ve been vaccinated?
There are rare cases that have been reported so far and it’s being very closely monitored. I would just encourage everyone once you’re vaccinated, really important we gotta continue to do all the same things: distancing, wearing a mask, avoiding gathering, keeping and just keeping in your household and hopefully as there’s more data out there, we’ll know more and can update folks on whether there is a risk for reinfection or what the risk is.
From the Times-Standard: Is it likely COVID-19 is here to stay and may require a yearly booster shot like the flu once everyone is vaccinated?
Again, time will tell and studies will tell, but I think that’s probably likely.