nucleocapsid
New Clues to Delta Variant’s Spread in Studies of Virus-Like Particles
Posted on by Dr. Francis Collins
About 70,000 people in the United States are diagnosed with COVID-19 each and every day. It’s clear that these new cases are being driven by the more-infectious Delta variant of SARS-CoV-2, the novel coronavirus that causes COVID-19. But why does the Delta variant spread more easily than other viral variants from one person to the next?
Now, an NIH-funded team has discovered at least part of Delta’s secret, and it’s not all attributable to those widely studied mutations in the spike protein that links up to human cells through the ACE2 receptor. It turns out that a specific mutation found within the N protein coding region of the Delta genome also enables the virus to pack more of its RNA code into the infected host cell. As a result, there is increased production of fully functional new viral particles, which can go on to infect someone else.
This finding, published in the journal Science [1], comes from the lab of Nobel laureate Jennifer Doudna at the Howard Hughes Medical Institute, the Gladstone Institutes, San Francisco, and the Innovative Genomics Institute at the University of California, Berkeley. Co-leading the team was Melanie Ott, Gladstone Institutes.
The Doudna and Ott teams have developed an exciting new tool to study variants of the coronavirus. It’s a lab construct called a virus-like particle (VLP). These specially made VLPs have all the structural proteins of SARS-CoV-2 (shown above), but they contain no genetic material. Consequently, they are non-infectious replicas of the real virus that can be studied safely in any lab. Scientists don’t have to reserve time in labs equipped with heightened levels of biosafety, as is required when working with whole virus.
The VLPs also allow researchers to explore changes found in the coronavirus’s other essential proteins, not just the spike protein on its surface. In fact, all of the SARS-CoV-2 variants of concern, as defined by the World Health Organization (WHO), carry at least one mutation within the same stretch of seven amino acids in a viral protein known as the nucleocapsid (N protein). This protein, which hasn’t been widely studied, is required for the virus to make more of itself. It is also involved in the virus’s ability to package and release infectious RNA.
In the Science paper, Doudna and colleagues took a closer look at the N protein. They did so by developing a special system that used VLPs to package and deliver viral RNA messages into human cells.
Here’s how it works: The VLPs include all four of SARS-CoV-2’s structural proteins, including the spike and N proteins. In addition, they contain the RNA sequence that allows the virus to recognize its genetic material within the cell, so that it can be packaged into the next generation of viral particles.
Though the particles look just like SARS-CoV-2 from the outside, they lack the vast majority of the viral genome on the inside. But they do have one other key component: a snippet of RNA that makes cells invaded by VLPs glow. In fact, the more RNA messages a VLP delivers, the brighter the cells will glow. It allowed the researchers to spot successful invasions, while also quantifying the amount of RNA a particular VLP packed into a cell.
The researchers then produced SARS-CoV-2 VLPs including four mutations that are universally found within the N proteins of more transmissible variants of concern. That’s when they discovered those variants produced and delivered 10 times more RNA messages into cells.
The increased RNA also fits with what has been observed in people infected with the Delta variant. They produce about 10 times more virus in their nose and throat compared to people infected with the older variants.
But did those findings match what happens in the real virus? To find out, the researchers and their colleagues tested the N protein mutation found in the Delta variant in a high-level biosafety lab. And, indeed, their studies showed that the mutated virus within infected human lung cells produced about 50 times more infectious virus compared to the original SARS-CoV-2 variant.
The findings suggest that the N protein could be an important new target for effective COVID-19 therapeutics, and that tracking newly emerging mutations in the N protein might also be important for identifying new viral variants of concern. This new system is a powerful tool, and one that can also be used for exploring how newly arising variants in the future might affect the course of this terrible pandemic.
Reference:
[1] Rapid assessment of SARS-CoV-2 evolved variants using virus-like particles. Syed AM, Taha TY, Tabata T, Chen IP, Ciling A, Khalid MM, Sreekumar B, Chen PY, Hayashi JM, Soczek KM, Ott M, Doudna JA. Science. 2021 Nov 4:eabl6184.
Links:
COVID-19 Research (NIH)
NIH Support: National Institute of Allergy and Infectious Diseases
Study Finds People Have Short-Lived Immunity to Seasonal Coronaviruses
Posted on by Dr. Francis Collins
A key metric in seeking to end the COVID-19 pandemic is the likely duration of acquired immunity, which is how long people infected with SARS-CoV-2, the novel coronavirus that causes COVID-19, are protected against reinfection. The hope is that acquired immunity from natural infection—or from vaccines—will be long-lasting, but data to confirm that’s indeed the case won’t be in for many months or years.
In the meantime, a useful place to look for clues is in long-term data on reinfections with other seasonal coronaviruses. Could the behavior of less life-threatening members of the coronavirus family give us some insight into what to expect from SARS-CoV-2?
A new study, published in the journal Nature Medicine, has taken exactly this approach. The researchers examined blood samples collected continuously from 10 healthy individuals since the 1980s for evidence of infections—and reinfections—with four common coronaviruses. Unfortunately, it’s not particularly encouraging news. The new data show that immunity to other coronaviruses tends to be short-lived, with reinfections happening quite often about 12 months later and, in some cases, even sooner.
Prior to the discovery of SARS-CoV-2, six coronaviruses were known to infect humans. Four are responsible for relatively benign respiratory illnesses that regularly circulate to cause the condition we recognize as the common cold. The other two are more dangerous and, fortunately, less common: SARS-CoV-1, the virus responsible for outbreaks of Severe Acute Respiratory Syndrome (SARS), which ended in 2004; and MERS-CoV, the virus that causes the now rare Middle East Respiratory Syndrome (MERS).
In the new study, a team led by Lia van der Hoek, University of Amsterdam, the Netherlands, set out to get a handle on reinfections with the four common coronaviruses: HCoV-NL63, HCoV-229E, HCoV-OC43, and HCoV-HKU1. This task isn’t as straightforward as it might sound. That’s because, like SARS-CoV-2, infections with such viruses don’t always produce symptoms that are easily tracked. So, the researchers looked instead to blood samples from 10 healthy individuals enrolled for decades in the Amsterdam Cohort Studies on HIV-1 Infection and AIDS.
To detect coronavirus reinfections, they measured increases in antibodies to a particular portion of the nucleocapsid of each coronavirus. The nucleocapsid is a protein shell that encapsulates a coronavirus’ genetic material and serves as important targets for antibodies. An increase in antibodies targeting the nucleocapsid indicated that a person was fighting a new infection with one of the four coronaviruses.
All told, the researchers examined a total of 513 blood samples collected at regular intervals—every 3 to 6 months. In those samples, the team’s analyses uncovered 3 to 17 coronavirus infections per study participant over more than 35 years. Reinfections occurred every 6 to 105 months. But reinfections happened most frequently about a year after a previous infection.
Not surprisingly, they also found that blood samples collected in the Netherlands during the summer months—June, July, August, and September—had the lowest rate of infections for all four seasonal coronaviruses, indicating a higher frequency of infections in winter in temperate countries. While it remains to be seen, it’s possible that SARS-CoV-2 ultimately may share the same seasonal pattern after the pandemic.
These findings show that annual reinfections are a common occurrence for all other common coronaviruses. That’s consistent with evidence that antibodies against SARS-CoV-2 decrease within two months of infection [2]. It also suggests that similar patterns of reinfection may emerge for SARS-CoV-2 in the coming months and years.
At least three caveats ought to be kept in mind when interpreting these data. First, the researchers tracked antibody levels but didn’t have access to information about actual illness. It’s possible that a rise in antibodies to a particular coronavirus might have provided exactly the response needed to convert a significant respiratory illness to a mild case of the sniffles or no illness at all.
Second, sustained immunity to viruses will always be disrupted if the virus is undergoing mutational changes and presenting a new set of antigens to the host; the degree to which that might have contributed to reinfections is not known. And, third, the role of cell-based immunity in fighting off coronavirus infections is likely to be significant, but wasn’t studied in this retrospective analysis.
To prepare for COVID-19 this winter, it’s essential to understand how likely a person who has recovered from the illness will be re-infected and potentially spread the virus to other people. While much more study is needed, the evidence suggests it will be prudent to proceed carefully and with caution when it comes to long-term immunity, whether achieved through naturally acquired infections or vaccination.
While we await a COVID-19 vaccine, the best way to protect yourself, your family, and your community is to take simple steps all of us can do today: maintain social distancing, wear a mask, avoid crowded indoor gatherings, and wash your hands.
References:
[1] Seasonal coronavirus protective immunity is short-lasting. Edridge AWD, Kaczorowska J, Hoste ACR, Bakker M, Klein M, Loens K, Jebbink MF, Matser A, Kinsella CM, Rueda P, Ieven M, Goossens H, Prins M, Sastre P, Deijs M, van der Hoek L. Nat Med. 2020 Sep 14. doi: 10.1038/s41591-020-1083-1. [Published online ahead of print.]
[2] Rapid decay of anti-SARS-CoV-2 antibodies in persons with mild Covid-19. Ibarrondo FJ, Fulcher JA, Goodman-Meza D, Elliott J, Hofmann C, Hausner MA, Ferbas KG, Tobin NH, Aldrovandi GM, Yang OO. N Engl J Med. 2020 Sep 10;383(11):1085-1087.
Links:
Coronavirus (COVID-19) (NIH)
Lia van der hoek (University of Amsterdam, the Netherlands)
Discussing the Need for Reliable Antibody Testing for COVID-19
Posted on by Dr. Francis Collins
There’s been a great deal of discussion about whether people who recover from coronavirus disease 2019 (COVID-19), have neutralizing antibodies in their bloodstream to guard against another infection. Lots of interesting data continue to emerge, including a recent preprint from researchers at Sherman Abrams Laboratory, Brooklyn, NY [1]. They tested 11,092 people for antibodies in May at a local urgent care facility and found nearly half had long-lasting IgG antibodies, a sign of exposure to the novel coronavirus SARS-CoV-2, the cause of COVID-19. The researchers also found a direct correlation between the severity of a person’s symptoms and their levels of IgG antibodies.
This study and others remind us of just how essential antibody tests will be going forward to learn more about this challenging pandemic. These assays must have high sensitivity and specificity, meaning there would be few false negatives and false positives, to tell us more about a person’s exposure to SARS-CoV-2. While there are some good tests out there, not all are equally reliable.
Recently, I had a chance to discuss COVID-19 antibody tests, also called serology tests, with Dr. Norman “Ned” Sharpless, Director of NIH’s National Cancer Institute (NCI). Among his many talents, Dr. Sharpless is an expert on antibody testing for COVID-19. You might wonder how NCI got involved in COVID-19 testing. Well, you’re going to find out. Our conversation took place while videoconferencing, with him connecting from North Carolina and me linking in from my home in Maryland. Here’s a condensed transcript of our chat:
Collins: Ned, thanks for joining me. Maybe we should start with the basics. What are antibodies anyway?
Sharpless: Antibodies are proteins that your body makes as part of the learned immune system. It’s the immunity that responds to a bacterium or a virus. In general, if you draw someone’s blood after an infection and test it for the presence of these antibodies, you can often know whether they’ve been infected. Antibodies can hang around for quite a while. How long exactly is a topic of great interest, especially in terms of the COVID-19 pandemic. But we think most people infected with coronavirus will make antibodies at a reasonably high level, or titer, in their peripheral blood within a couple of weeks of the infection.
Collins: What do antibodies tell us about exposure to a virus?
Sharpless: A lot of people with coronavirus are infected without ever knowing it. You can use these antibody assays to try and tell how many people in an area have been infected, that is, you can do a so-called seroprevalence survey.
You could also potentially use these antibody assays to predict someone’s resistance to future infection. If you cleared the infection and established immunity to it, you might be resistant to future infection. That might be very useful information. Maybe you could make a decision about how to go out in the community. So, that part is of intense interest as well, although less scientifically sound at the moment.
Collins: I have a 3D-printed model of SARS-CoV-2 on my desk. It’s sort of a spherical virus that has spike proteins on its surface. Do the antibodies interact with the virus in some specific ways?
Sharpless: Yes, antibodies are shaped like the letter Y. They have two binding domains at the head of each Y that will recognize something about the virus. We find antibodies in the peripheral blood that recognize either the virus nucleocapsid, which is the structural protein on the inside; or the spikes, which stick out and give coronavirus its name. We know now that about 99 percent of people who get infected with the virus will develop antibodies eventually. Most of those antibodies that you can detect to the spike proteins will be neutralizing, which means they can kill the virus in a laboratory experiment. We know from other viruses that, generally, having neutralizing antibodies is a promising sign if you want to be immune to that virus in the future.
Collins: Are COVID-19 antibodies protective? Are there reports of people who’ve gotten better, but then were re-exposed and got sick again?
Sharpless: It’s controversial. People can shed the virus’s nucleic acid [genetic material], for weeks or even more than a month after they get better. So, if they have another nucleic acid test it could be positive, even though they feel better. Often, those people aren’t making a lot of live virus, so it may be that they never stopped shedding the virus. Or it may be that they got re-infected. It’s hard to understand what that means exactly. If you think about how many people worldwide have had COVID-19, the number of legitimate possible reinfection cases is in the order of a handful. So, it’s a pretty rare event, if it happens at all.
Collins: For somebody who does have the antibodies, who apparently was previously infected, do they need to stop worrying about getting exposed? Can they can do whatever they want and stop worrying about distancing and wearing masks?
Sharpless: No, not yet. To use antibodies to predict who’s likely to be immune, you’ve got to know two things.
First: can the tests actually measure antibodies reliably? I think there are assays available to the public that are sufficiently good for asking this question, with an important caveat. If you’re trying to detect something that’s really rare in a population, then any test is going to have limitations. But if you’re trying to detect something that’s more common, as the virus was during the recent outbreak in Manhattan, I think the tests are up to the task.
Second: does the appearance of an antibody in the peripheral blood mean that you’re actually immune or you’re just less likely to get the virus? We don’t know the answer to that yet.
Collins: Let’s be optimistic, because it sounds like there’s some evidence to support the idea that people who develop these antibodies are protected against infection. It also sounds like the tests, at least some of them, are pretty good. But if there is protection, how long would you expect it to last? Is this one of those things where you’re all set for life? Or is this going to be something where somebody’s had it and might get it again two or three years from now, because the immunity faded away?
Sharpless: Since we have no direct experience with this virus over time, it’s hard to answer. The potential for this cell-based humoral immunity to last for a while is there. For some viruses, you have a long-lasting antibody protection after infection; for other viruses, not so much.
So that’s the unknown thing. Is immunity going to last for a while? Of course, if one were to bring up the topic of vaccines, that’s very important to know, because you would want to know how often one would have to give that vaccine, even under optimal circumstances.
Collins: Yes, our conversation about immunity is really relevant to the vaccines we’re trying to develop right now. Will these vaccines be protective for long periods of time? We sure hope so, but we’ve got to look carefully at the issue. Let’s come back, though, to the actual performance of the tests. The NCI has been right in the middle of trying to do this kind of validation. How did that happen, and how did that experience go?
Sharpless: Yes, I think one might ask: why is the National Cancer Institute testing antibody kits for the FDA? It is unusual, but certainly not unheard of, for NCI to take up problems like this during a time of a national emergency. During the HIV era, NCI scientists, along with others, identified the virus and did one of the first successful compound screens to find the drug AZT, one of the first effective anti-HIV therapies.
NCI’s Frederick National Lab also has a really good serology lab that had been predominantly working on human papillomavirus (HPV). When the need arose for serologic testing a few months ago, we pivoted that lab to a coronavirus serology lab. It took us a little while, but eventually we rounded up everything you needed to create positive and negative reference panels for antibody testing.
At that time, the FDA had about 200 manufacturers making serology tests that hoped for approval to sell. The FDA wanted some performance testing of those assays by a dispassionate third party. The Frederick National Lab seemed like the ideal place, and the manufacturers started sending us kits. I think we’ve probably tested on the order of 20 so far. We give those data back to the FDA for regulatory decision making. They’re putting all the data online.
Collins: How did it look? Are these all good tests or were there some clunkers?
Sharpless: There were some clunkers. But we were pleased to see that some of the tests appear to be really good, both in our hands and those of other groups, and have been used in thousands of patients.
There are a few tests that have sensitivities that are pretty high and specificities well over 99 percent. The Roche assay has a 99.8 percent specificity claimed on thousands of patients, and for the Mt. Sinai assay developed and tested by our academic collaborators in a panel of maybe 4,000 patients, they’re not sure they’ve ever had a false positive. So, there are some assays out there that are good.
Collins: There’s been talk about how there will soon be monoclonal antibodies directed against SARS-CoV-2. How are those derived?
Sharpless: They’re picked, generally, for appearing to have neutralizing activity. When a person makes antibodies, they don’t make one antibody to a pathogen. They make a whole family of them. And those can be individually isolated, so you can know which antibodies made by a convalescent individual really have virus-neutralizing capacity. That portion of the antibody that recognizes the virus can be engineered into a manufacturing platform to make monoclonal antibodies. Monoclonal means one kind of antibody. That approach has worked for other infectious diseases and is an interesting idea here too.
Collins: I can say a bit about that, because we are engaged in a partnership with industry and FDA called Accelerating COVID-19 Therapeutic Interventions and Vaccines (ACTIV). One of the hottest ideas right now is monoclonal antibodies, and we’re in the process of devising a master protocol, one for outpatients and one for inpatients.
Janet Woodcock of Operation Warp Speed tells me 21 companies are developing monoclonal antibodies. While doing these trials, we’d love to do comparisons, which is why it’s good to have an organization like ACTIV to bring everybody together, making sure you’re using the same endpoints and the same laboratory measures. I think that, maybe even by late summer, we might have some results. For people who are looking at what’s the next most-hopeful therapeutic option for people who are really sick with COVID-19, so far we have remdesivir. It helps, but it’s not a home run. Maybe monoclonal antibodies will be the next thing that really gives a big boost in survival. That would be the hope.
Ned, let me ask you one final question about herd, or group, immunity. One hears a bit about that in terms of how we are all going to get past this COVID-19 pandemic. What’s that all about?
Sharpless: Herd immunity is when a significant portion of the population is immune to a pathogen, then that pathogen will die out in the population. There just aren’t enough susceptible people left to infect. What the threshold is for herd immunity depends on how infectious the virus is. For a highly infectious virus, like measles, maybe up to 90 percent of the population must be immune to get herd immunity. Whereas for other less-infectious viruses, it may only be 50 percent of the population that needs to be immune to get herd immunity. It’s a theoretical thing that makes some assumptions, such as that everybody’s health status is the same and the population mixes perfectly every day. Neither of those are true.
How well that actual predictive number will work for coronavirus is unknown. The other thing that’s interesting is a lot of that work has been based on vaccines, such as what percentage do you have to vaccinate to get herd immunity? But if you get to herd immunity by having people get infected, so-called natural herd immunity, that may be different. You would imagine the most susceptible people get infected soonest, and so the heterogeneity of the population might change the threshold calculation.
The short answer is nobody wants to find out. No one wants to get to herd immunity for COVID-19 through natural herd immunity. The way you’d like to get there is with a vaccine that you then could apply to a large portion of the population, and have them acquire immunity in a more safe and controlled manner. Should we have an efficacious vaccine, this question will loom large: how many people do we need to vaccinate to really try and protect vulnerable populations?
Collins: That’s going to be a really critical question for the coming months, as the first large-scale vaccine trials get underway in July, and we start to see how they work and how successful and safe they are. But I’m also worried seeing some reports that 1 out of 5 Americans say they wouldn’t take a vaccine. It would be truly a tragedy if we have a safe and effective vaccine, but we don’t get enough uptake to achieve herd immunity. So, we’ve got some work to do on all fronts, that’s for sure.
Ned, I want to thank you for sharing all this information about antibodies and serologies and other things, as well as thank you for your hard work with all your amazing NCI colleagues.
Sharpless: Thanks for having me.
Reference:
[1] SARS-CoV-2 IgG Antibody Responses in New York City. Reifer J, Hayum N, Heszkel B, Klagsbald I, Streva VA. medRxiv. Preprint posted May 26, 2020.
Links:
Coronavirus (COVID-19) (NIH)
At NCI, A Robust and Rapid Response to the COVID-19 Pandemic. Norman E. Sharpless. Cancer Currents Blog. April 17, 2020 (National Cancer Institute/NIH)
Serological Testing for SARS-CoV-2 Antibodies (American Medical Association, Chicago)
COVID-19 Antibody Testing Primer (Infectious Diseases Society of America, Arlington, VA)
Accelerating COVID-19 Therapeutic Interventions and Vaccines (NIH)
