immunity

by Gertrud U. Rey

A recent preprint by Kizzmekia Corbett and others describes experiments done to assess the efficacy of Moderna’s SARS-CoV-2 “Spikevax” vaccine in rhesus macaques one year after vaccination. The authors immunized eight animals with two doses of Spikevax at four-week intervals and then collected blood samples, nasal swabs, and lung wash samples at various time points over the course of the following year. The macaques were then challenged with the SARS-CoV-2 delta variant virus at 49 weeks, and more samples were collected at different time points after challenge.

Blood samples collected at 6, 24, and 48 weeks post-vaccination were used to analyze the ability of IgG antibodies in these samples to bind the receptor-binding domains of three different viruses: 1) “ancestral” SARS-CoV-2, which had the exact spike protein antigen encoded in the vaccine, 2) the delta variant, and 3) the beta variant. These latter two had variant spike proteins. IgG antibodies are mostly blood-resident and provide the majority of antibody-based immunity against invading pathogens. IgG levels were highest at 6 weeks after vaccination for all three viruses; they then declined rapidly between 6 weeks and 24 weeks, and more slowly between 24 weeks and 48 weeks. Most IgG detected at 6 weeks bound ancestral virus, with 5.4-fold and 8-fold fewer IgG molecules binding the delta and beta variants, respectively. However, when delta and beta variant-specific IgG antibodies were tested for their ability to block binding between SARS-CoV-2 and its cognate ACE2 receptor, they inhibited almost 100% of binding of both delta and beta variant viruses, suggesting that the antibodies were still functional in preventing infection, in spite of their diminished quantity.

The ability of blood-resident IgG antibodies to neutralize the three respective viruses followed a similar trend, with a gradual decline in neutralizing activity against all viruses by 48 weeks post-vaccination. Interestingly, even though the quantity of total binding and neutralizing antibodies targeting the delta variant decreased over time, the number of antibodies targeting regions associated with neutralization increased. In addition, the binding avidity of antibodies to ancestral virus increased significantly between week 6 and 24 and remained steady through week 48 post-vaccination. In contrast to affinity, which measures the strength of the binding interaction between antigen and antibody at a single binding site, avidity measures the total binding strength of an antibody at every binding site. These two shifts – the increase in the number of antibodies binding targets associated with neutralization and the increase in antibody avidity over time in spite of a decrease in total antibody levels – are suggestive of a maturing immune response that is more focused on viral regions of high immunological relevance. It is noteworthy to mention that the regions associated with neutralization are outside of areas where the variant viruses have accumulated changes in the spike protein, further implying that Spikevax and other SARS-CoV-2 vaccines are just as effective against viral variants as they are against ancestral virus.

Next, the authors analyzed lung wash samples and nasal swabs for delta-binding IgG and IgA antibodies. IgA antibodies are predominantly found in mucus membranes and their fluids, where they protect against invasion by inhaled and ingested pathogens. IgG kinetics in the lung were similar to those observed in the blood – both binding and neutralizing IgG to all three viruses were highest at 6 weeks after vaccination and decreased steadily over time until they were indistinguishable to those observed in unvaccinated animals. In contrast, IgG levels in the nose increased through week 25, plateaued, and remained stable through week 42 post-vaccination. IgA levels in the lung were highest at week 6 post-vaccination, but decreased to levels similar to those observed in unvaccinated animals by week 24. IgA levels in the nose were similar to those in unvaccinated animals at all time points. These results suggest that although SARS-CoV-2 vaccination may not induce a detectable mucosal immune response in the nose, it does induce good initial mucosal immunity in the lung, which is typically the site of severe COVID-19. This immunological difference between the lung and the nose might also explain why SARS-CoV-2 vaccines are more effective at preventing severe disease than at preventing infection.

The authors also analyzed blood samples from vaccinated animals for the presence of SARS-CoV-2-specific memory B cells, which can quickly produce spike-specific antibodies upon subsequent exposure to SARS-CoV-2. At week 6 post-vaccination, about 0.14% of all memory B cells were specific for the ancestral virus, and about 0.09% were specific for the delta variant. In comparison, about 2.5% of all memory B cells were specific for both the ancestral virus and the delta variant, and this high proportion of dual-binding to single-binding cells remained constant through week 42 post-vaccination.

To see whether these vaccine-induced immune parameters are protective after viral challenge, the authors infected the animals with delta variant virus at 49 weeks after the initial immunization. Lung washes and nasal swabs were collected on days 2, 4, 7, and 14 after challenge to monitor viral replication. On day 2 after challenge, vaccinated animals had about 11-fold fewer viral RNA copies per milliliter in their lungs than unvaccinated animals, and these RNA levels declined rapidly over the following days. In contrast, viral RNA levels in unvaccinated animals remained significantly elevated through day 7 post-infection. Viral RNA levels in the nose followed a similar trend; however, their decline in vaccinated animals was not as dramatic as that observed in the lung.

Antibodies to all three viruses in the lungs of vaccinated animals were significantly higher on day 4 after challenge than at week 42 after immunization, suggesting that memory B cell responses to infection were quick and robust. Viral challenge after vaccination also induced both T helper cells, which stimulate B cells to make antibodies, and cytotoxic T cells, which kill virus-infected cells. Analysis of lung tissue also revealed that vaccination prevented lung pathology and protected the lower respiratory tract from severe inflammation after infection.

Perhaps the most interesting observation in the study relates to whether vaccinated individuals who become infected replicate and transmit virus to others. When the authors analyzed lung wash samples for T cells specific for the SARS-CoV-2 N protein, which is not encoded in the Spikevax vaccine, they only found these cells in unvaccinated animals. This suggests that even though it had been one year since vaccination, immunized animals that were then infected did not replicate the challenge virus to a sufficient extent to produce T cells specific for the SARS-CoV-2 N protein – a response that would only be elicited by actual infection with whole virus. In other words, the memory response to the SARS-CoV-2 spike protein induced by the vaccine eliminated incoming virus so quickly that the immune system had no chance to mount a response to the viral N protein encoded in the challenge virus, presumably because the virus was cleared quickly.

In summary, vaccinated animals appear to be better protected from severe disease and to clear virus faster than unvaccinated animals. This result aligns with data published in a previous preprint, which showed that viral RNA levels in delta variant-infected people who had been vaccinated prior to infection declined more rapidly than in people who were not vaccinated. And although monkeys are not human, previous studies assessing the protective efficacy of Spikevax have shown that rhesus macaques are reliably predictive of outcomes in humans, making them a great model for determining the effects of waning antibody levels on long-term protection against SARS-CoV-2 infection.

[Kizzmekia Corbett, a viral immunologist at Harvard who was central to the development of the Moderna mRNA vaccine, was previously a guest on TWiV 670. The preprint described in this post was also discussed on TWiV 824.]