virology blog

About viruses and viral disease

antibodies

Antibodies Against SARS-CoV-2 Nucleocapsid Protein May Not Be Reliable Markers for Infection in Vaccinated People

by

by Gertrud U. Rey

You are fully vaccinated against SARS-CoV-2 and have presumably never been infected with the virus. But how can you know for sure? One way to find out is by testing your blood for the presence of antibodies against the viral nucleocapsid protein, which can only be encountered during natural infection. This is because all of the SARS-CoV-2 vaccines used in the U.S. only encode the viral spike protein (none encode nucleocapsid [N] protein), and thus they only stimulate production of antibodies against spike. This approach differentiates between vaccine- and virus infection-induced antibodies and allows one to accurately determine whether a vaccinated person was naturally infected. Or so we thought until now.

Two recent letters to the editor of the Journal of Infection note that not every natural infection induces production of anti-nucleocapsid (or, “anti-N”) antibodies. The letters cast doubt on whether these antibodies are reliable markers for a prior SARS-CoV-2 infection.

The authors of the first letter measured antibody responses in 4,111 vaccinated and 974 unvaccinated Irish healthcare workers. Only 23 of the vaccinated participants, all of whom had received two doses of the Pfizer mRNA vaccine, experienced a SARS-CoV-2 infection at some time after vaccination. As expected, each of the 23 individuals had antibodies against the spike protein, but surprisingly, only six (26%) had detectable anti-N antibodies. In contrast, 82% of unvaccinated participants with a previous PCR-confirmed infection had detectable anti-N antibodies. This result suggests that anti-N antibodies may not be the most accurate indicators of a prior natural infection in vaccinated people; and it further implies that vaccinated individuals may neutralize incoming viruses early during infection, thus preventing and/or limiting their ability to develop antibodies against nucleocapsid protein.

The second letter, which was written in response to the first letter, confirmed and further substantiated these results. Citing data from serosurveys done in Japan, the authors showed that patients who were infected within two months of a third dose of the Pfizer mRNA vaccine were less likely to experience COVID-19 symptoms than patients who were infected 4-8 months after the third dose. These findings are in line with our current understanding of sterilizing immunity, a type of immunity that prevents both disease and infection, which appears to occur most often during the months following vaccination, when high levels of vaccine-induced antibodies probably sequester an incoming virus before it has a chance to infect cells. The authors also showed that participants infected within two months of their third vaccine dose had significantly lower levels of anti-N antibodies than those infected several months later. Although this result seems surprising at first, it actually further supports the notion that vaccination only induces sterilizing immunity for a short time after vaccination, when existing vaccine-induced anti-spike antibodies neutralize incoming virus before the immune system has a chance to respond to the virus and produce antibodies specific to the nucleocapsid protein.

The authors of both letters further mention that COVID-19 patients who experienced symptoms were more likely to have detectable anti-N antibodies than were patients without symptoms, an observation that is in agreement with serological surveys done before vaccines became available. This finding suggests that patients who developed symptoms did not have sterilizing immunity and were subject to a productive viral infection that led to the development of symptoms and production of antibodies to nucleocapsid and other viral proteins.

These two studies provide an interesting perspective of antibody responses to SARS-CoV-2 infection in vaccinated people, and they may inform better strategies for gauging infection after vaccination.

Heterologous Vaccine Regimens Might be Better

by

by Gertrud U. Rey

Have you ever wondered if you can “mix and match” SARS-CoV-2 vaccines? For example, would it be ok to boost a first dose of the vaccine produced by AstraZeneca with a dose of the vaccine produced by Pfizer/BioNTech? The latest science shows that such a vaccine regimen actually induces a stronger immune response than a regimen consisting of two doses of the same vaccine.

The occasional incidence of thrombosis in people under the age of 60 after receiving an adenovirus-vectored vaccine like the ones made by AstraZeneca and Johnson & Johnson has prompted several European governments to recommend the use of these vaccines only in people over 60. Because many people under 60 had already been vaccinated with a first dose of the AstraZeneca vaccine and still needed a second dose, they had to decide whether they should continue their regimen with another dose of the same vaccine (i.e., a homologous regimen), or receive an mRNA vaccine instead (i.e., a heterologous regimen).

In an effort to evaluate the efficacy of a heterologous SARS-CoV-2 vaccine regimen, the authors of this Brief Communication engaged the participants of an ongoing clinical trial, which aims to monitor the immune responses to SARS-CoV-2 in health care professionals and individuals with potential exposure to SARS-CoV-2. All study participants had already received a first dose of the AstraZeneca vaccine (referred to as “ChAd” in the study) and were given the option of receiving a second dose of the same vaccine or a dose of Pfizer/BioNTech’s mRNA vaccine (referred to as “BNT”). Although both of these vaccines encode the gene for the full-length SARS-CoV-2 spike protein, it is housed slightly differently. In the ChAd vaccine, the spike protein is encoded in an adenovirus vector of chimpanzee origin, while in the BNT vaccine it is surrounded by a lipid nanoparticle.

Out of the 87 individuals who participated in the study, 32 chose a second dose of ChAd and 55 chose to be vaccinated with BNT instead. Participants who chose a homologous ChAd/ChAd regimen received their second dose of ChAd on day 73 after the initial dose and donated a blood sample for analysis 16 days later. Participants who chose a heterologous ChAd/BNT regimen received their dose of BNT 74 days after their initial ChAd dose and donated a blood sample 17 days later. All results obtained from the analyses of the blood samples from these two groups were compared to results obtained from a group of 46 health care professionals who had been vaccinated with two doses of BNT (i.e., a homologous BNT/BNT regimen).

Briefly, the findings were as follows. Relative to the antibody levels induced by the first dose, homologous boosting with ChAd led to a 2.9-fold increase in IgG antibodies against the SARS-CoV-2 spike protein. IgG antibodies are mostly present in the blood and provide the majority of antibody-based immunity against invading pathogens. In contrast, heterologous boosting with BNT led to an 11.5-fold increase in anti-spike IgG, within the range observed in BNT/BNT-vaccinated individuals. A similar pattern was observed with anti-spike IgA antibodies, which are predominantly found in mucus membranes and their fluids. Boosting with BNT induced significantly higher increases in anti-spike IgA than did boosting with ChAd, suggesting that a heterologous boosting regimen induces better antibody responses. Interestingly, although the booster immunization induced an increase in neutralizing (i.e., virus-inactivating) antibodies in both vaccination groups, only heterologous ChAd/BNT vaccination induced antibodies that neutralized all three tested variants (Alpha, Beta, and Gamma), similar to what was observed in BNT/BNT vaccine recipients.

The authors also analyzed the effect of the two different boosting regimens on spike-specific memory B cells, which circulate quiescently in the blood stream and can quickly produce spike-specific antibodies upon a subsequent exposure to SARS-CoV-2. All vaccinees from both the ChAd/ChAd and ChAd/BNT groups produced increased levels of spike-specific memory B cells after receiving their booster shot, with no significant differences observed between the two groups. These results emphasize the importance of booster vaccination for full protection from SARS-CoV-2 infection.

ChAd/BNT recipients also had significantly higher levels of spike-specific CD4+– and CD8+ T cells compared to ChAd/ChAd recipients. CD4+ T cells are a central element of the adaptive immune response, because they activate both antibody-secreting B cells and CD8+ T cells that kill infected target cells. Compared to the ChAd/ChAd regimen, ChAd/BNT vaccination also induced significantly increased levels of T cells that produce spike-specific interferon gamma – a cytokine that inhibits viral replication and activates macrophages, which engulf and digest pathogens. Overall, these results suggest that a heterologous ChAd/BNT regimen induces significantly stronger immune responses than a homologous ChAd/ChAd regimen.

The study did have several limitations. First, it was not a randomized, placebo-controlled trial where each participant was randomly assigned to an experimental group or a control group. Randomizing trial participants eliminates unwanted effects that have nothing to do with the variables being analyzed, so that the only expected differences between the experimental and control groups are the outcome variable studied (efficacy in this case). Subjects in a control group receive a placebo – a substance that has no therapeutic effect, so that one can be sure that the effects observed in the experimental group are real and result from the experimental drug. Second, the authors were unable to test the antibodies for their ability to neutralize the Delta variant, which has recently become the predominantly circulating variant in many parts of the world. Third, the study mostly included young and healthy people, making it difficult to extrapolate the data to other specific patient groups outside of this category. Fourth, the data only show the results of assays performed in vitro, which may not necessarily manifest a clinical significance. Extended studies aimed at determining the practical importance of the observed immune responses are needed to validate the relevance of these responses. 

Despite its limitations, the study provides information that could have some valuable practical implications. Most of the currently approved SARS-CoV-2 vaccine regimens involve two doses of the same vaccine. However, access to two doses of the same vaccine may be limited or absent under some circumstances, thus necessitating the use of a different type of vaccine to boost the first dose.

[For a more in-depth discussion of this study, I recommend TWiV 782.]

Are the SARS-CoV-2 Vaccines Safe for Pregnant and Lactating People?

by

by Gertrud U. Rey

Vaccination is the gold standard for preventing infectious diseases and reducing the impact of emerging pathogens. As more and more people are becoming immunized against SARS-CoV-2, a prominent question continues to arise: are the vaccines safe for pregnant and breast-feeding people?

(Image credit: Shutterstock)

None of the clinical trials for SARS-CoV-2 vaccines included pregnant or lactating subjects. Pregnant people in particular are a historically difficult group to study in the context of drug safety because of concerns of liability over potential adverse effects of a new product on a fetus. This lack of safety data further complicates treatment of SARS-CoV-2 infection in pregnant people, who already have an increased risk for premature birth and miscarriage if they become infected. Based on these risk factors, the currently available data, and interim recommendations by the Advisory Committee on Immunization Practices for people over the age of 16, the American College of Obstetricians and Gynecologists recommends that pregnant and lactating people should have access to SARS-CoV-2 vaccines. Fortunately, many pregnant and lactating people have opted to be vaccinated, and the data on the safety and efficacy of vaccination in these two cohorts are beginning to emerge.

A recent publication in the American Journal of Obstetrics and Gynecology describes the safety and immunogenicity of SARS-CoV-2 vaccines in pregnant and lactating women compared to non-pregnant controls and women who had been naturally infected with SARS-CoV-2 during pregnancy. The researchers collected blood and breast milk from 131 women of reproductive age, including 84 pregnant, 31 lactating, and 16 non-pregnant participants who had received two doses of either the Pfizer/BioNTech or Moderna mRNA COVID-19 vaccine; and analyzed the samples for the presence of IgG and IgA antibodies. IgG antibodies are mostly present in the blood and provide the majority of antibody-based immunity against invading pathogens. IgA antibodies are predominantly found in mucus membranes and the fluids secreted by these membranes, including saliva, tears, and breast milk. IgA antibodies are particularly suitable for protecting against pathogens like SARS-CoV-2, which invade the body through these membranes.

Samples were collected at the time of the first and second vaccination, 2 to 6 weeks after the second dose, and at delivery. The researchers also collected umbilical cord blood from 10 infants born during the study period.

The main findings were as follows. Side effects resulting from vaccination were rare and occurred with similar frequency in all participants. These findings are consistent with post-vaccination data tracked by the CDC via the V-safe application, suggesting that post-vaccination reactions in pregnant people are not significantly different from those in non-pregnant people.

Pregnant, lactating, and non-pregnant vaccine recipients produced significantly higher levels of SARS-CoV-2-specific IgG than pregnant women who had been naturally infected. Interestingly, the second vaccine dose led to increased concentrations of coronavirus-specific IgG but not IgA, in both maternal blood and breast milk. The authors speculate that this lack of IgA boosting may have to do with the intramuscular route of immunization, which usually does not induce very high levels of serum IgA. The role of IgA in the serum is mostly secondary to IgG, in that IgA mediates elimination of pathogens that have breached the mucosal surface. In contrast, natural infection induces higher levels of mucosal (IgA) antibodies because SARS-CoV-2 enters the body through the mucosal surfaces. Nevertheless, studies have shown that IgG in breast milk is critical for protecting newborns from other pathogens like HIV, RSV, and influenza. It is possible that this type of antibody is equally important for protecting infants from SARS-CoV-2.

It was previously unclear whether vaccine-induced SARS-CoV-2 antibodies are transferred across the placenta to the fetus. However, the authors also found vaccine-induced IgG in cord blood, suggesting that these antibodies do cross the placenta, as has been previously observed after vaccination of pregnant people against influenza virus, Bordetella pertussis, and other pathogens. Whether these antibodies protect the baby from SARS-CoV-2 infection after birth, remains to be determined.

This study provides the first set of clinical data suggesting that vaccination of pregnant and lactating people against SARS-CoV-2 is both safe and beneficial. Some people have expressed concern over the possible incidence of fever following the second vaccine dose in pregnant people; however, the potential risk to the fetus from a 24-hour fever must be weighed against the possibility of chronic, severe COVID-19 in the mother. Accumulating data suggest that the benefits of vaccination during pregnancy and lactation outweigh the risks of adverse effects to the fetus or infant and align with the abundance of clinical data showing the beneficial effects of vaccinating these groups of people against influenza virus. Analyses of cord blood from infants whose mothers were naturally infected with SARS-CoV-2 during pregnancy indicate that the potential for transfer of antibodies is greater early during gestation, suggesting that immunization during the earlier stages of pregnancy might be preferable. However, more studies are needed to assess the optimal timing of maternal vaccination to achieve enhanced neonatal immunity. In the meantime, these preliminary data allow pregnant and lactating people to make more informed decisions, and also aid physicians in providing evidence-based recommendations.

The Route Matters

by

by Gertrud U. Rey

There are currently 315 therapeutic drugs and 210 vaccine candidates in development to treat or prevent SARS-CoV-2 infection. Many of these vaccines are designed to be administered by injection into the muscle. 

Intramuscular injection of a vaccine antigen typically induces a systemic (serum) immune response that involves the action of IgM and IgG antibodies. IgM antibodies appear first and typically bind very strongly to antigens, to the extent that they often cross-react with other, non-specific antigens. IgG antibodies arise later, are a lot more specific than IgM, and provide the majority of antibody-based immunity against invading pathogens. Intramuscular immunization usually does not induce very high levels of serum IgA, a type of antibody that is more prevalent in mucosal surfaces and represents a first line of defense against invasion by inhaled and ingested pathogens. The role of IgA in the serum is mostly secondary to IgG, in that IgA mediates elimination of pathogens that have breached the mucosal surface.    

Several of the SARS-CoV-2 vaccine candidates currently in clinical trials consist of a replication-deficient adenovirus with an inserted gene that encodes a SARS-CoV-2 antigen. The suitability of adenoviruses as vectors for delivering foreign genes into cells was discussed in a previous post, which summarized preliminary phase I/II clinical trials assessing the safety and efficacy of a chimpanzee adenovirus-vectored replication-deficient SARS-CoV-2 vaccine candidate encoding the full-length SARS-CoV-2 spike protein (AZD1222). The spike protein has been the primary antigenic choice for a number of SARS-CoV-2 vaccine candidates because it mediates binding of the virus to the ACE2 host cell receptor via its receptor-binding domain (RBD), and it also mediates fusion of the viral particle with the host cell membrane via its fusion domain. Both of these spike domains are highly immunogenic and are targeted by neutralizing antibodies, which bind viral antigens, inactivating virus and preventing infection of new cells. However, preliminary results suggest that AZD1222 only protects against SARS-CoV-2 lung infection and pneumonia but doesn’t appear to prevent upper respiratory tract infection and viral shedding.

To mediate fusion of the virus particle to the host cell membrane, the SARS-CoV-2 spike protein undergoes a structural rearrangement from its pre-fusion conformation. Because the pre-fusion form is more immunogenic, vaccines encoding the spike protein often contain a mutation that locks the translated spike protein into this pre-fusion structure. In a recent publication, virologist Michael Diamond and colleagues analyzed the efficacy of an adenovirus-vectored SARS-CoV-2 vaccine candidate and compared its protective effects after intramuscular injection to those after administration by the intranasal route. The vaccine, named ChAd-SARS-CoV-2-S, is similar to AZD1222 except that its spike gene encodes the pre-fusion stabilized spike protein. To assess the antibody responses induced by intramuscular vaccination with ChAd-SARS-CoV-2-S, the authors injected mice with 10 billion viral particles of either ChAd-SARS-CoV-2-S or a control vaccine consisting of the same adenovirus shell, but lacking the spike protein gene insert. They found that one dose of ChAd-SARS-CoV-2-S induced strong serum IgG responses against both the entire spike protein and the RBD, but no IgA responses in the serum or in mucosal lung cells.

While antibodies are an important part of the adaptive immune response, cell-mediated immunity is just as important and at the very least results in activation of white blood cells that destroy ingested microbes and also produces cytotoxic T cells that directly kill infected target cells. During a first exposure to a pathogen, T helper cells typically sense the presence of antigens on the surface of the invading pathogen and release a variety of signals that ultimately stimulate B cells to secrete antibodies to those antigens and also stimulate cytotoxic T cells to kill infected target cells. Analysis of these T cells in mice immunized with one or two doses of intramuscularly administered ChAd-SARS-CoV-2-S revealed that two vaccine doses induced both T helper and cytotoxic T cell responses against the whole spike protein. Collectively, these results suggest that although intramuscular vaccination produces strong systemic adaptive immune responses against SARS-CoV-2, it induces little, if any, mucosal immunity.

To determine whether intramuscular immunization with ChAd-SARS-CoV-2-S protects mice from infection, the authors intentionally infected (“challenged”) immunized mice with SARS-CoV-2. Although a single vaccine dose protected the mice from SARS-CoV-2 infection and lung inflammation, the mice still had high levels of viral RNA in the lung after infection, suggesting that intramuscular administration of the vaccine does not lead to complete protection from infection.  

In an effort to see whether vaccination by the intranasal route provides more complete protection, the authors inoculated mice with a single dose of ChAd-SARS-CoV-2-S or control vaccine through the nose. Analysis of serum samples and mucosal lung cells four weeks after vaccination revealed that recipients of ChAd-SARS-CoV-2-S had high spike- and RBD-specific levels of neutralizing IgG and IgA in both the serum and the lung mucosa, and that the number of B cells producing IgA was about five-fold higher than that of B cells producing IgG. Interestingly, the neutralizing antibodies were also able to inactivate SARS-CoV-2 viruses containing a D614G change in the spike protein, suggesting that ChAd-SARS-CoV-2-S can effectively protect against other circulating SARS-CoV-2 viruses. Intranasal vaccination also induced SARS-CoV-2-specific cytotoxic T cells in the lung mucosa, specifically T cells that produce interferon gamma, an important activator of macrophages and inhibitor of viral replication.

The ideal immune response is “sterilizing” – meaning that it completely protects against a new infection and does not allow the virus to replicate at all. To evaluate the ability of a single intranasal dose of ChAd-SARS-CoV-2-S to induce sterilizing immunity, the authors analyzed immunized and infected mice for serum antibodies produced against the viral NP protein. Because the vaccine does not encode the NP protein, any antibodies produced against this protein would be induced by translation of the NP gene from the challenge virus and active replication of the virus. All of the mice immunized with a single dose of intranasally administered ChAd-SARS-CoV-2-S had very low levels of anti-NP antibodies compared to recipients of the control vaccine, suggesting that ChAd-SARS-CoV-2-S induced strong mucosal immunity that prevented SARS-CoV-2 infection in both the upper and lower respiratory tract. This means that if intranasally immunized mice were to be exposed to SARS-CoV-2, they would not be able to replicate the virus or transmit it to others. 

The study has some notable limitations. First, it is well known that mice can be poor predictors of human disease outcomes. Second, because the mouse ACE2 receptor doesn’t easily bind SARS-CoV-2, the mice were engineered to express the human ACE2 receptor, which added a further artificial variable to an already imperfect model system. Third, it is presently unknown how long the observed immune responses would last. That being said, studies with influenza virus have shown that mucosal immunization through the nose can elicit strong local protective IgA-mediated immune responses. Further, there are clear advantages to intranasal vaccine administration: inoculation is simple, painless, and does not require trained professionals. The adequacy of a single dose would also lead to more widespread compliance. Lastly, a vaccine that prevents viral shedding would be ideal, because in addition to preventing disease in the exposed individual, it would prevent transmission to others. 

None of the SARS-CoV-2 vaccine candidates currently in clinical trials are delivered by the intranasal route. If the results observed in these mouse experiments can be duplicated in humans, ChAd-SARS-CoV-2-S would clearly be superior to other SARS-CoV-2 vaccine candidates. 

TWiV 638: Do, there is no try

by

Daniel Griffin provides a clinical update on COVID-19, then Viviana Simon joins to review serological assays developed at Mt. Sinai for SARS-CoV-2 infection, tracking the outbreak in NYC, and listener questions.

Click arrow to play
Download TWiV 638 (99 MB .mp3, 164 min)
Subscribe (free): iTunes, Google Podcasts, RSS, email

Become a patron of TWiV!

Intro music is by Ronald Jenkees

Send your virology questions and comments to twiv@microbe.tv

Show notes at microbe.tv/twiv

Enterovirus D68 and childhood paralysis

by

EV-D68The Centers for Disease Control and Prevention thinks that viruses play a role in the childhood paralysis called acute flaccid myelitis (AFM). The finding of antibodies to enterovirus D68 (EV-D68) in the cerebrospinal fluid of patients with AFM strengthens the link between infection with this virus and AFM.

Acute flaccid myelitis (AFM), which mainly occurs in children, involves weakness of the arms and legs and may include other symptoms such as inability to breathe or swallow. There have been outbreaks of AFM in the US in 2014, 2016, and 2018, mainly in the late summer and early fall. The outbreaks of AFM are associated with infection with enteroviruses.

AFM was first defined in 2014 after reports of limb weakness in children across the US during an outbreak of respiratory disease caused by EV-D68 (pictured). AFM may also be associated with infections caused by other viruses, such as enterovirus A71, Coxsackievirus A16, West Nile virus and adenovirus.

Of the 233 patients with confirmed AFM in 2018, EV-D68 was the most frequently detected virus, mainly in respiratory samples. Confirming a viral etiological agent of AFM would be greatly strengthened by finding virus in the cerebrospinal fluid (CSF). However in 2018 only two samples of cerebrospinal fluid from AFM patients were found to be positive for viral RNA: one for EV-D68 and one for EV-A71. There may be multiple reasons for the failure to detect viral RNA in CSF, including clearance of virus by the time AFM is diagnosed, or very low levels of viral genomes.

An alternative to searching for viral genomes in CSF is to identify anti-viral antibodies, which may be produced during infection of the brain and spinal cord. Peptide microarrays were used to detect antibodies against enteroviruses in CSF of AFM patients. In this method, 160,000 unique peptides from the capsid proteins of all known human enteroviruses were spotted on slides. CSF samples were incubated with the slides and binding of antibodies to peptides was quantified. The results revealed antibodies to an 18 amino acid peptide of capsid protein VP1 in serum and CSF of 11/14 AFM patients and 3/26 controls. This amino acid sequence is known to be conserved among diverse human enteroviruses.

More importantly, antibodies to a 22 amino acid sequence in VP1 of EV-D68 were identified in CSF of 6/14 AFM, and in 8/11 serum samples. No immunoreactivity to this peptide was detected in samples from 26 controls.

Detection of antibodies in the CSF is not diagnostic of CNS infection because antibodies are known to pass from blood to CSF. The normal ratio of antibodies in blood to CSF is 250:1. Consequently, for diagnostic purposes, both serum and CSF should be analyzed for the presence of antibodies.

The authors of the study acknowledge this issue, noting that they do not have sufficient simultaneously collected serum and CSF samples to exclude that antibodies they detected in the CSF simply came from the blood. They note that of the 16 control patients with serum antibodies to enteroviruses, only 3 also had such antibodies in CSF. Furthermore, in a study of unexplained encephalitis in India, of 77 children with serum antibodies to enteroviruses, only 3 also had EV antibodies in CSF. For these reasons the authors do not believe that the anti-EV-D68 antibodies they have detected in CSF have come from the blood.

How can it be definitively proven that EV-D68 causes AFM? With an outbreak of AFM expected in the late summer of 2020, there should be ample opportunity to obtain numerous clinical samples – nasopharyngeal wash, serum and CSF – to examine for the presence of EV-D68 antibodies and viral genomes.