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Q&A: COVID expert on why BA.5 variant is 'substantially different'

4-year-old Max Martinez getting tested at the school district COVID-19 Testing Center in Chula Vista, Sept. 20, 2021.
Nicholas McVicker
4-year-old Max Martinez getting tested at the school district COVID-19 Testing Center in Chula Vista, Sept. 20, 2021.

Last week, San Diego County moved to the high, or orange, COVID-19 tier due to increasing disease numbers and hospitalizations. That quickly prompted an indoor mask mandate for San Diego Unified Schools District. But at the same time as another wave of infections is taking hold in the region, big public events are also returning in San Diego. The PRIDE parade and related events drew thousands last weekend, and Comic-Con returns to downtown San Diego Thursday for its first large in-person gathering since the pandemic began.

Dr. Eric Topol, director of the Scripps Research Translational Institute, joined Midday Edition Wednesday to get the latest on what is known about the now dominant BA.5 coronavirus variant. The interview below has been lightly edited for clarity.

In your most recent article on your blog, you compare our handling of COVID-19 to that of a boiling frog. Why?


Dr. Topol: Well, the issue is that BA.5, as we discussed last time we got together, was heating up throughout the country, and there's a lack of perception that it's really the worst variant ... even against severe things like hospitalizations. And so we're not feeling it because we have this immunity wall being built ... because of so many infections and vaccinations and boosters. So this lack of perception because it's gradual, all these different variants that have been occurring over the course of two and a half years, we're missing the fact that the latest variant that is now taking over the country, BA.5, and certainly in San Diego, is the worst one, and we're in a denial state. Willing it away isn't going to work.

You maintain that BA.5 is the worst version of this virus we've seen yet, despite the fact that deaths and hospitalizations are not where they once were. So why is BA.5 the worst, in your opinion?

Dr. Topol: If you look at places that didn't have lots of prior infection, like, just say, Japan, now a record number of cases throughout the whole pandemic, even exceeding BA.1, had we had this variant before BA.1, the omicron, the wave that hit us so hard in January and February, it would have been even worse. So, the point is, that the virus version is substantially different. The so-called distance of the protein or antigen distance, the genetic distance. I mean, it's basically deserves its own Greek letter it's so different than omicron, BA.1. If you look at it from every property you can think of of a virus, this one is clearly the worst since the pandemic began. But because we have so much immunity, we have this optics, this idea that it's not so bad. But actually another attribute that you are seeing is that it's lasting longer. People who are getting infected with BA.5, the time of being positive testing and having symptoms is longer than prior versions of the virus which goes along with it. You don't have to look at deaths and hospitalizations to say that that's an issue, although they're both going up throughout the country, and certainly not nearly what we saw in the worst BA.1-omicron wave. But again, that's just because we've got lots of protection out there.

Can you give us the latest on the COVID-19 situation here in San Diego? What do recent numbers tell us?


Dr. Topol: Everything's on the way up and this is not a good picture, because we don't know where the peak is going to be. We know that we have weeks to get through BA.5. And so we're starting to see the increase in hospitalizations, fortunately not at the level that in the worst times previously, but they'll continue to go up — no less the number of people infected. The critical issue that you know well is that our testing centrally is very minimal. And so the number of people who are actually infected or infectious — not even knowing that they're infected — is very high. And in the country it's gone up to about 130,000 cases a day. But it's probably at least 700,000 or a million a day. We just don't know because so many people are either not testing or doing rapid tests at home.

The Novavax vaccine was approved yesterday by the CDC. How does this vaccine differ from the Moderna or Pfizer vaccine?

Dr. Topol: This is a protein based vaccine. So instead of the Moderna or Pfizer, which is a messenger RNA, which once it gets into the cells, it encodes the protein, this is just direct to the protein. It's very similar otherwise. It's basically using the spike, the key portion of the virus to induce our immune response. And the data that was presented this week to the CDC and previously the FDA looked like it's very comparable to the mRNA vaccines. And so hopefully more people will get vaccinated. It also may have use as a booster. That is because it's somewhat different. That whole idea of mixing might have some appeal as we get more data about that.

Currently, people above 50 or those who are high risk are eligible to get the fourth shot of the COVID vaccine. Do you think it's time for eligibility to be expanded to more of the population?

Dr. Topol: Yes, both that we don't have enough people who are 50 and older getting a four shot. We're at about 27%. That should be 100%. The reason being is the risk of death and hospitalization in people over age 50 is substantially lowered by a four shot. We have four studies to prove that. But then people less than 50, there's many people there, such as health care workers or essential workers who have lots of risk. And that would be great to use those shots because otherwise they're going to get thrown away because they're about to expire. Tens of millions of doses to be thrown away. So we don't have the green light to get these out there, but we should we should have gotten them going some time ago. But the people who have a considerable risk because of their work or because of their medical status with lots of different coexisting conditions, even less than age 50, should give this a consideration.

What is the data telling us about these newer variants? BA.4.and BA.5 and long COVID?

Dr. Topol: Yeah, well, let's put aside BA.4 because that really got completely outcompeted by BA.5, which is taking over the country in terms of soon to be all the cases. BA.5, it's about 80% right now. So this variant, as I mentioned earlier, is quite problematic. I don't think we're giving you enough respect as to the fact that it's showing attrition of our vaccines, even against severe protection to some extent. So this decoy to our immune system, that is this escape artist, it's a real problem. And the fact is, we may not be done at BA.5. We could see BA.X or even a whole other family like omicron. Hopefully not, but what's in store, unfortunately, is that the virus evolution is accelerated. As we've seen, we've gone from BA.1 to 5 in a matter of months, whereas in the first year of the pandemic, there was no substantive evolution of the virus to change its properties. So we really should plan. That's why we need much better vaccines ... because we may be seeing over the months ahead that the Paxlovid, which is keeping hospitalizations down, and that's important to emphasize, we could develop resistance to it, the mutations in the critical portion of the virus to Paxlovid. So we should get more backup drugs out there and that's something that's not enough effort, along with these better vaccines is not happening right now.

On the subject of drugs like Paxlovid, how are coronavirus treatments such as that doing against the BA.5 variant? Are they proving to be effective against these newer variants?

Dr. Topol: Yes. The good thing about Paxlovid is that it really hasn't been a variant specific pill. The problem, however, even though it has a very good track record for reducing hospitalizations and deaths, there is this issue of rebound that's occurred commonly, whereby after five days of treatment of the Blister pack, a couple of days later, symptoms come back and the person does testing and they're still infectious and that can go on for several more days. So rebound is a problem. People are not winding up in the hospital. It's rare after Paxlovid, but the prolonged symptoms and infectiousness is not good. And what we're studying is whether a prolonged course instead of five days rather than ten days to deal with these omicron variants like BA.5 might be better to help avoid the rebound phenomena. The problem is the pills cause a lot of side effects. The taste is really altered and also a lot of gastrointestinal side effects. So you don't want to take it for ten days, but that may wind up being the way to deal with rebound. But it is working well in terms of reducing hospitalizations. And that's another part of this illusion that things aren't too bad when a lot of those people that might have wound up in the hospital were preventing it.

Is anyone eligible to get Paxlovid, or is it being reserved for people who are high risk?

Dr. Topol: Well, it's supposed to be for high risk, but it's a doctor's prescription, so anybody who is symptomatic, has other conditions that might be in the department of worry that just progressed, they could wind up in the hospital. It's not hard to access Paxlovid. There's a very good supply right now. My biggest concern besides rebound, is it's working well, but how long? And we don't have a backup pill. We really need that. And there's a bunch of candidates, just like with the vaccines that are pan-coronavirus and nasal vaccines, a bunch of candidates for all these things, but we're not doing anything about that yet.

San Diego County reentered the high COVID-19 tier last week. Are you satisfied with the local public health officials' response since that change?

Dr. Topol: It's disappointing because, as you mentioned, it's only the San Diego Unified School District that has asked for indoor masks to be used routinely. But we don't have that from anyone else. And we know masks help if they're KN95s or N95s, and we're just not using them. People are tired and fed up, and they don't want to mask, but it's a help. It's not a guarantee to avoid BA.5. But the problem is the virus is so hyper-infectious, and we're just playing into its properties by not masking up, particularly indoors, but possibly even outdoors, by not using our tools of ventilation, filtration, and distancing. These things help while we're waiting for better ways to get on top or ahead of the virus with the three biggies: the pan-coronavirus, the nasal vaccines, and better drugs. So we need something to bridge that, and we're ignoring it, largely, and that's unfortunate.

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  • San Diego county is now in the high COVID-19 tier due to increasing case numbers and hospitalizations. Everything’s on the way up and this is not a good picture because we don’t know where the peak is going to be, Dr. Eric Topol tells Midday Edition.