Virus Infections and Antibodies

With all the reporting on the pandemic, generalists are finding virology a steep learning curve, especially if one has been focused on climatology.  A case in point:  Recently the media reported on virus antibody testing of Major League Baseball (MLB) employees.  Various headlines and stories drew differing conclusions about the import of the findings.  Consider these few among many examples.

70% of MLB employees who had positive coronavirus antibody tests showed no symptoms-Newsday

Fewer than 1% of MLB employees test positive for COVID-19 antibodies–LA Times

MLB antibody study: 0.7% of those tested had been exposed to coronavirus–SF Chronicle

Inquiring scientific minds want to know if the large print is actually supported by what is stated in the small print.  A fourth article in the Washington Post suggested some of the places where digging for clarity is required.  Excerpts in italics with my bolds

The study reportedly involved 26 of the 30 MLB teams and based its results on 5,603 completed tests and surveys. Researchers said 60 people tested positive for covid-19 antibodies, and after controlling for an expected amount of false positives and negatives, that number was adjusted to 42. There were zero deaths among the test group.

Researchers noted that the test group was not perfectly “representative of the American population at large,” because it skewed toward subjects who mostly ranged in age from 20 to 64 and who generally were of elevated socioeconomic status.  [Note that this is a good sample of the work force, in contrast to all of the testing and cases involving elderly retirees from group homes.]

However, researchers pointed to the fact that the “overwhelming majority” of test subjects were not athletes but other types of team employees, from front-office executives to stadium vendors.

It takes about six to 10 days for 50 percent of people to develop antibodies, Bhattacharya said, and thus the snapshot provided by the study would have been from early April. MLB suspended spring training in mid-March, and it hopes to resume in June before starting to play games in July.

Bhattacharya said the 0.7 percent figure was surprising in part because players and team staffers would have been grouped together in spring training, in some cases in an environment featuring a higher than normal number of respiratory droplets, a few weeks before tests were completed April 14 and 15.

Bhattacharya said the study provided good news in the zero deaths but bad news by indicating that “the epidemic has not gotten very far.” Another positive takeaway could be gleaned from the fact that 70 percent of the subjects who tested positive described themselves as asymptomatic.

Background:  To sort out some of the interpretive variety, we can start with this helpful overview from sciencealert  Why Do Some People With COVID-19 Get Symptoms While Others Don’t? Excerpts in italics with my bolds.

What happens when coronavirus enters your body?

Like all viruses, SARS-CoV-2 needs to get inside human cells to multiply and survive. To do this, a particle on the outer shell of the virus latches onto a matching protein receptor, called ACE2, like a lock and key. ACE2 receptors are normally found in the lungs, kidneys, heart and the gut.

Once a person has been infected with the virus, it can take up to 14 days for symptoms to appear (if they do at all) – known as the incubation period.

The path from the point of infection can vary enormously. The body’s immune system is critical for determining this.

Having a strong immune response during the incubation period can prevent the infection taking hold, reduce the actual quantity of virus in the body and prevent it from getting to the lungs.

Some immune response basics

Our immune system offers us two lines of defence against viruses.

The first is the innate system and includes physical barriers such as skin and mucous membranes (the lining of the throat and nose), various proteins and molecules found in tissues, as well as some of the white blood cells that attack invading organisms. This immune response is general, non-specific and kicks in quickly.

Children have immature immune systems, but one hypothesis to explain why they don’t seem to get as sick with COVID-19 is that their innate immune response to coronavirus is greater than in adults.

This may lead to a reduced viral load – the quantity of virus particles that survive in the body – because they’re able to clear the virus more quickly.

The second line of defence is the adaptive immune response. This takes longer to initiate but once established, is much more efficient at eradicating a specific infection when encountering it again.

It’s thought that very specific genetic variations in some people might play a part in how sick they get. By generating an early adaptive immune response, the body seems to recognise the virus during the incubation period and fight it off.

A person also needs to be generally healthy to be able to mount an appropriate immune response to the infection.

After the incubation period, what determines how sick you get?

If the SARS-CoV-2 virus survives beyond the point of entry to the body (nose, eyes, throat) it might then make its way down the respiratory tract into the lungs.

In the lungs, it latches onto ACE2 receptors and continues replicating itself, triggering further immune responses to clean out infected cells. The amount of virus that gets deep into the lungs may be another important factor determining how sick you get.

As the battle between virus and immune responses proceeds, infected airway linings produce large amounts of fluid that fill the air sacs, leaving less room for transferring oxygen into the bloodstream and removing carbon dioxide. Symptoms of pneumonia appear, such as fever, cough with sputum (phlegm) and shortness of breath.

For some people, the immune response is excessive or prolonged and causes what’s known as a “cytokine storm”. Cytokines are a group of proteins that send signals to cells in the immune system, helping direct the response. A cytokine storm is a catastrophic overreaction that causes so much inflammation and organ damage, it can be fatal.

In people with COVID-19, as well as the previous SARS and MERS coronaviruses, this causes acute respiratory distress syndrome (ARDS), when fluid builds up in the lungs. This is the most common cause of death from SARS-CoV-2.

Elderly people and those with chronic lung disorders are more likely to develop ARDS and therefore to die. This is currently thought to be due to these groups of people having fewer ACE2 receptors in their lungs.  This seems counter-intuitive, because the virus attaches itself to these receptors. However, ACE2 receptors have an important role in regulating the immune response, particularly in managing the degree of inflammation.  So the reduced levels of ACE2 receptors in the elderly may actually make them more at risk of a cytokine storm and severe lung disease.

Conversely, children have more ACE2 receptors in their lungs which might explain why they do not get as sick.

In some cases, medications that work to suppress the immune system have successfully treated this excessive immune response in people with COVID-19.

Can people without symptoms pass it on?

Some studies have indicated people with COVID-19 tend to have a high viral load just before and shortly after they start getting symptoms.  This suggests they can transmit it when they first get sick and up to 48 hours before, while they’re pre-symptomatic.

However, there is no good evidence that asymptomatic people who never develop symptoms are able to pass it on.

Researchers and clinicians are working around the clock to understand the complex relationship between humans’ immune systems and SARS-CoV-2 but it remains very much a work in progress.

Source:  The Conversation Abela Mahimbo, Lecturer in Public Health, University of Technology Sydney; David Isaacs, Professor of Pediatric Infectious Diseases, University of Sydney; Melanie Wong, Head of Diagnostic Immunology Laboratory, Kids Research, and Melissa Kang, Associate professor, University of Technology Sydney.

An article at Clinical Chemistry discusses issues around the role of generic versus specfic coronavirus antibodies. SARS-CoV-2 Serology: Much Hype, Little Data.  Excerpt in italics with my bolds.

What could be the reason for these false positive results?

Given the homology of SARS-CoV-2 to other coronaviruses, it is likely that antigens used as targets in poorly designed assays will cross react. This risk is exaggerated in older populations who are likely to have been exposed to a wider variety of coronaviruses (12). Many serologic assays also cross-react in patients with EBV, rheumatoid factor, and heterophile antibodies. Careful antigen selection in COVID-19 serological assays is required to avoid cross reactivity of anti-seasonal coronavirus antibodies. If validation studies are not designed appropriately (ie. if only young, asymptomatic pre-pandemic patients are used as the negative population), then these limitations may not be thoroughly vetted and specificity of the assay may be grossly overestimated. [Note the authors are concerned with overestimating cases with SARS CoV-2 specific antibodies by counting presence of other coronavirus antibodies.  They do not consider the possibility that other generic antibodies act against SARS CoV-2 infection.]

An article at The Scientist delves more deeply into these issues. What Do Antibody Tests For SARS-CoV-2 Tell Us About Immunity? Excerpts in italics with my bolds.

It’s months into the coronavirus pandemic and public health officials still don’t know how many people have actually contracted the culprit, SARS-CoV-2. In many countries testing capacity has lagged behind the spread of the virus. Large numbers of people have developed COVID-19 symptoms but have not been tested, and the vast majority of people who had the virus but never developed symptoms and therefore were not tested, are not reflected in official statistics.

Federal and state governments, companies, and research groups are now racing to develop antibody tests to shine a light on the true spread of SARS-CoV-2. While PCR tests currently used to diagnose cases detect the virus’s genetic material, antibody tests can screen for virus-attacking antibodies that are formed shortly after an initial infection. Those antibodies usually linger in the blood long after the virus is gone. One such antibody, or serological, test was given emergency use authorization by the Food and Drug Administration in early April, and a number of other groups are making more tests, and in some cases even deploying them.

The National Institutes of Health has launched a study to detect antibodies in order to gather data for epidemiological models. And a recent survey of residents in a German town was one of the first to use an antibody test among the public, reporting that 14 percent of people there were likely to have been infected with SARS-CoV-2 due to the presence of antibodies.

It’s not clear yet whether milder or asymptomatic cases will develop antibodies.

Policymakers have another reason to scramble to deploy antibody tests: they could indicate whether someone is immune to SARS-CoV-2. With around 3 billion people globally under lockdown, pressure is mounting to re-open national economies. In recent weeks, several politicians have proposed the idea of “immunity passports” or “immunity certificates” to identify people who have had the virus and therefore gained immunity to it and could re-enter the workforce again. Officials in Germany, the UK, Italy, and the US are already discussing such proposals.

The success of such a program hinges on:

  • whether everyone who has contracted SARS-CoV-2 actually develops antibodies,
  • whether those antibodies protect against secondary infections, and if so,
  • how long the antibodies hang around in the body.

So far, scientists don’t have firm answers to any of these questions. Although antibody surveys of communities around the world could yield information that is crucial to understanding the spread of the pathogen, some consider the idea of “immunity passports” premature.

“People understand that [it] would be very powerful, if we could say, ‘you’re immune now, and you can return to work,’ or, ‘you could safely return to your family if you’re a healthcare worker,’” notes Stanford University and Chan Zuckerberg Biohub immunologist Taia Wang. But there are a lot of unknowns, she cautions. “To get to that point where we’ll know with some certainty what the antibody response means, we just have to collect [more] data.”

The antibody response to SARS-CoV-2

There is solid evidence emerging that COVID-19 patients are developing antibodies to the virus, as the human body does for most infectious pathogens. Kara Lynch, a clinical chemist at the University of California, San Francisco, and her colleagues have been testing around 500 serum samples from roughly 100 COVID-19 patients who were treated at the Zuckerberg San Francisco General Hospital, where Lynch co-directs a clinical chemistry laboratory. The team is using an assay that was applied to samples from patients in China and picks out antibodies that target a protein-binding site of the virus’s spike protein.

“What we’re seeing is that patients are [developing antibodies] anywhere from two to about fifteen days” after developing symptoms, Lynch says. In most patients, the antibody response is broadly reminiscent of the typical reaction to many other pathogens: first, a flush of IgM, a generic type of antibody, followed later by the longer-lasting and more-specific IgG antibodies. Other studies have yielded similar results and suggest that antibodies circulate in the blood of COVID-19 patients for at least two weeks.

The data are skewed toward severe cases, however, as most of the subjects that Lynch’s group tested had been hospitalized, and it’s not clear yet whether milder or asymptomatic cases will develop antibodies, Lynch notes. “I’m optimistic [but] I’m still a little bit cautious.”

Recently, researchers at Fudan University in Shanghai examined the plasma from 175 COVID-19 patients who recovered after mild symptoms. The vast majority of patients developed antibodies that targeted the spike protein around 10 to 15 days after symptom onset, the scientists reported in preprint. The report generated some concern on social media because the researchers couldn’t detect antibodies in 10 of the patients. That could have been a fluke, notes Shane Crotty, an immunologist at the La Jolla Institute for Immunology. It’s possible that that the PCR test for SARS-CoV-2 was a false positive, and those people in fact had a different respiratory infection.

It’s also possible that some patients simply don’t develop antibodies.

While years ago, “pretty much everybody infected with SARS made an antibody response,” Crotty says, that did not hold true for MERS. Some studies on MERS have found that PCR-positive mild or asymptomatic infections can cause varied immune responses that are undetectable in antibody assays. Lynch points out that in her cohort, there are three patients who have not yet developed antibodies even though it’s been 17 days or more since their symptoms started. Some of those patients were immunocompromised, “but there are examples of healthy individuals that did not generate antibodies,” she writes in an email to The Scientist.

In many viral infections, “the magnitude of an antibody response correlates well with how big the infection was,” Crotty notes. In other words, severe infections are more memorable to the immune system. Interestingly, the preprint on COVID-19 patients in China also reported a positive correlation between the patients’ antibody levels and their age, which in turn, is known to correlate with the severity of COVID-19 symptoms. If it were the case that milder SARS-CoV-2 infections are less likely to produce a detectable antibody response, that may reduce the usefulness of antibody tests in detecting asymptomatic or mild cases.

Are the antibodies actually protective?

Overall, Crotty says he finds the data from the Chinese study robust and encouraging, noting that the researchers had extracted the patients’ antibodies and conducted in vitro experiments to see if they prevented SARS-CoV-2 from entering human host cells. “They tested 175 people and almost all of them had really nice antibody responses and really nice neutralizing responses,” he says. This is consistent with a recent study in macaques, and some other studies that have extracted antibodies from COVID-19 survivors and also found those antibodies were neutralizing, that is, capable of binding to the virus and its blocking entry into host cells.

Those experiments are important, and the results encouraging, but it’s still a mystery whether neutralizing activity in vitro correlates with protection in vivo for SARS-CoV-2, Wang notes. And even if antibodies aren’t neutralizing—and don’t physically stop the virus from entering host cells—they can still play important roles in immunity by recruiting other components of the immune system. “In vivo, there are many more cells that come into play to clear virus, to clear infected cells,” says Wang. It may well be that other components of the immune system—such as helper T cells or killer T cells—also play important roles in protecting against SARS-CoV-2.

On the whole, Wang finds it too early to say what the role of antibodies is for SARS-CoV-2. “We have no idea if production of antibodies during a primary infection, for example, has any role in clearing virus during that infection, or for that matter, we don’t have any good data on whether antibodies produced during an infection are protective against a second infection,” she says. And even if they were protective, they may not be protective for everyone. “Antibody responses can vary tremendously from person to person.”

How long will antibody levels last?

Ideally, the human antibody response to SARS-CoV-2 would mirror that to measles. A single exposure is enough to generate robust, neutralizing IgG antibodies that circulate in the blood throughout life and provide lifelong protection, Crotty notes.

But immune responses to coronaviruses appear to differ. Studies of survivors of the 2003 SARS epidemic suggest that concentrations of neutralizing antibodies lasted for up to three years. Although, a recent yet-to-be-peer-reviewed preprint reports to have found neutralizing antibodies in SARS survivors 17 years after the epidemic.

In MERS, the levels of neutralizing antibodies have been observed to fade after three years. For the less deadly, cold-causing coronaviruses, neutralizing antibody levels also fall off in that two-to-three-year range. One 1990 study of fewer than a dozen volunteers found that people exposed twice to the coronavirus 229E developed much milder symptoms compared with people getting exposed the first time, suggesting that re-infection could occur, but with reduced symptoms.

However, how long those cells or the antibodies they produce persist in the blood is not a surefast indicator of how long someone is immune to secondary infection, he stresses.

That’s because an initial encounter with a pathogen not only prompts the antibody-supplying cells, called plasmablasts, in the blood to turn into plasma cells that generate specific antibodies. It also stimulates memory B cells. These memory B cells can last decades, hiding out in lymph nodes, the spleen, bone marrow, and the lung, while some circulate in the blood. Upon re-infection by the same pathogen, they swing back into action, taking two-to-four days to differentiate into cells that secrete neutralizing antibodies, Menachery explains. He speculates that one might be able to acquire a second SARS-CoV-2 infection once the initial burst of neutralizing antibodies fades—which he reckons might be after one or two years—but the second infection will be milder thanks to immune memory.

It helps matters that SARS-CoV-2’s RNA genome appears to be relatively stable, meaning that the immune system may have a better chance of developing longer-lasting immunity compared to frequently-mutating influenza viruses, for instance, which require researchers to design new vaccines every year.

Summary:  There are a lot of moving parts in this puzzle, and the observational record is short.  The presence of SARS CoV-2 antibodies can estimate the minimum extent of people whose adaptive immune system fought off this virus.  We are still in the dark about how many have been exposed to the virus but did not come down with the disease Covid-19 due to innate immunity.

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