Does last year’s cold protect against this year’s COVID? – Lessons from preclinical models on sequential coronavirus infections

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When Severe Acute Respiratory Syndrome Coronavirus 2, or SARS-CoV-2, first emerged, it was clear that its disease COVID-19 (Coronavirus Disease 2019) can range from mild to severe and even lead to death. Why SARS-CoV-2 causes mild disease in some and lethal disease in others was an immediate question. Children, in particular, are perplexing as they seem less susceptible to severe disease. Importantly, understanding the factors leading to disease severity may be the key to protecting people from dying. Even for centuries before the COVID-19 pandemic, people have dealt with the family of coronaviruses. Specifically, the pestering common cold with mild respiratory symptoms can be caused by infection with one of several human seasonal coronaviruses. Since both colds and COVID-19 are caused by coronaviruses, clinicians, public health officials, and scientists wondered if a recent cold caused by a seasonal coronavirus could protect from severe COVID-19 following SARS-CoV-2 infection. These questions arise from the fact that our immune systems are designed to learn and remember pathogens, such as viruses. Then when we encounter that same virus again our immune memory can be recalled to either completely or partially block that virus thereby decreasing disease. However, if the second virus is slightly different than the first virus, there might not be a robust recall of immune memory to be protective. Very little is known about immune memory and coronaviruses.  Here, for the first time, we used a preclinical model to investigate the direct effects of a previous seasonal coronavirus infection on the outcomes of a secondary SARS-CoV-2 infection.  Although both viruses are members of the coronavirus family, they are distantly related, and we found seasonal coronaviruses were not able to protect against SARS-CoV-2. Conversely, our results showed significant immune memory recall and protection from disease when the first infection was SARS-CoV-2 and the second was a more related SARS-CoV-2 variant of concern.

Below we provide details of our work and discuss how the findings provide important insight into the factors affecting COVID-19 disease severity as well as the immune mechanisms regulating cross-protection throughout the family of coronaviruses. This information will guide the design of improved vaccines against coronaviruses such as a pan-coronavirus vaccine. Next generation vaccines are an essential tool for protecting public health against both the currently circulating coronaviruses as well as the next spillover coronavirus with pandemic potential.

Coronaviruses: Virus spillover from animals causes colds, MERS, and COVID-19

Coronaviruses are a large family of diverse viruses which consist of four genera: alphacoronaviruses, betacoronaviruses, gammacoronaviruses and deltacoronaviruses (Figure 1A)1,2. Bats are considered the reservoir host or in other words, bats are the animal able to be infected with all four genera of these viruses3-5. Humans on the other hand are only susceptible to alphacoronaviruses and betacoronaviruses. Importantly, prior to 2003, human coronaviruses (HCoVs) were thought to only cause a mild cold-like disease6,7. Therefore, it was quite surprising when a new coronavirus called SARS-CoV (Severe Acute Respiratory Syndrome coronavirus) spilled over from animals into humans causing severe disease with a 10% case fatality rate. The subsequent spillover of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) in 2012 confirmed that coronaviruses can cause severe disease8,9. Since this time, coronaviruses have been considered a significant pandemic threat as a new severe coronavirus could spillover from animals into humans at anytime3-7. As anticipated, in late 2019 the world was presented again with another coronavirus spillover. This virus, SARS-CoV-2, led to the worst pandemic seen for 100 years. Prior to emergence of SARS-CoV-2, HCoV-NL63 (NL63), HCoV-OC43 (OC43), HCoV-229E (229E), and HCoV-HKU1 (HKU1) viruses of the coronavirus family circulated in humans causing up to 30% of common colds associated with mild disease2,10-15. Therefore, most people would have previously had a cold caused by a coronavirus suggesting the presence of some kind of pre-exiting immunity or immunological memory to at least one of the coronaviruses in most people prior to the COVID-19 pandemic (Figure 1B). However, significant sequence diversity exists within the coronavirus family. The seasonal coronaviruses only share ~30% sequence identity with SARS-CoV-2. Comparatively, there is less diversity within the SARS-CoV-2 clade as SARS-CoV-2 and its variants share over 95% sequence identity.

Figure 1. The Life and Times of Coronaviruses. Structure of coronaviruses depicting the four coronavirus genera (A). Prior to 2019, seasonal coronaviruses were circulating in people causing the common cold. Since December 2019, SARS-CoV-2 has emerged and spread rapidly throughout the world but the interaction within the host with previous immunity to seasonal coronaviruses is unclear.

Seasonal coronaviruses do not protect against SARS-CoV-2

Recent research has investigated the role of a previous cold in COVID-19 severity; however, since these studies focused on humans, the results are not straight forward due to the complex immune background and pre-existing health conditions of people16-19. In our study we used the Syrian hamster model to investigate pre-existing immunity and COVID-19. Using this strategy, we controlled both the animals’ seasonal cold coronavirus and SARS-CoV-2 infections as well as the animals’ general health before infection. Syrian hamsters were an ideal model for studying the pathology of coronaviruses as they have been the gold standard for investigating COVID-19 and they are susceptible to other coronaviruses such as SARS-CoV20-23. Although used for the study of some coronaviruses, hamsters had not previously been used to study seasonal coronavirus infection. Therefore, our initial experiments tackled this knowledge gap. Our results showed that hamsters can be infected with the seasonal coronaviruses NL63 and OC43. Following infection with these viruses, hamsters develop mild disease in the upper respiratory tract ‘nare’, or nose, similar to a human cold. 

Now that we had a model of common cold coronavirus infection, we were able to determine what would happen if a hamster was first infected with a seasonal virus, then came into contact with SARS-CoV-2. Leveraging an infection-challenge study design, hamsters were first infected through the nare with a common cold coronavirus (NL63 or OC43) and then were infected, or ‘challenged’, with SARS-CoV-2 (Figure 2A). Similar studies were then performed with SARS-CoV-2 and its variants. These infection-challenge combinations represent real-world scenarios where a person who had a cold prior to the pandemic was then exposed to SARS-CoV-2 or had SARS-CoV-2 and then was exposed to a new variant. 

Looking first at the distant coronavirus combinations, we found that Syrian hamsters first infected with the seasonal coronaviruses NL63 or OC43 were not protected from SARS-CoV-2 infection. To understand why the animals were not protected, we dug deeper into the regulation of the immune system during the second virus exposure or challenge by investigating the dynamics of antibody production and markers of T cell activation. Although we found no evidence of cross-reactive antibodies between OC43 and SARS-CoV-2, there was increased T cell activity in these animals. Animals who were exposed to NL63 developed neutralizing antibodies to this virus which were then increased or ‘back-boosted’ during the SARS-CoV-2 infection. This result suggested that B cells had cross-recognition between NL63 to SARS-CoV-2 which was surprising since there was no protection provided by the NL63 infection on the development of COVID-19. However, there was little evidence of induction of secondary germinal centers which are essential to antibody refinement.

Figure 2. Study Schematic. Syrian hamsters undergoing a distant infection-challenge combination were first infected with a seasonal (common cold coronavirus) followed by challenge with the ancestral SARS-CoV-2 (A). Syrian hamsters undergoing a more similar infection-challenge combination were first exposed to ancestral SARS-CoV-2 and then challenged with a SARS-CoV-2 variant (Beta or Omicron) (B

Since distant seasonal coronaviruses were not able to induce cross-protection against SARS-CoV-2, we were next interested if cross-protection could be conferred by more similar coronaviruses. Infection-challenge studies with SARS-CoV-2 and its closely related SARS-CoV-2 variants were then performed. For these studies, we recapitulated the common scenario experienced by people of first being infected with ancestral SARS-CoV-2 and then being challenged with variants Beta or Omicron (Figure 2B). Importantly, these more similar infection-challenge combinations WERE protective. Supporting this protection and the reactivation of immune memory, we found that cross-protective antibodies were recalled. Further examination of the immune mechanisms driving recall and protection from disease indicated that a more productive germinal center response regulating antibody specificity was initiated in the mediastinal lymph node.

The germinal center response is an important aspect of immunity as it is responsible for producing improved, matured antibodies. The lack of a robust germinal centre response and cross-protective antibody responses after initial seasonal common cold coronavirus infection and SARS-CoV-2 challenge in our studies could explain why people were susceptible to a robust SARS-CoV-2 infection despite being previously exposed to cold viruses. The clinical findings of this work are summarized in relation to viral load and the induction of immune responses and immune mechanisms (Figure 3).

 Figure 3. Protection against secondary exposure to a SARS-CoV-2 virus or variant depends on the antigenic distance from the primary infection. Antigenically distant infection-challenge combinations led to increased viral load and decreased antiviral response compared to antigenically similar infection-challenge combinations. The similar infection-challenges had decreased inflammation and an improved antibody response accompanied with signs of an improved germinal center response.

A lasting solution: Universal coronavirus vaccines

Universal vaccines, pan-virus vaccines, and broadly protective vaccines, are vaccines designed to provide protection against a wide range of related pathogens for example against all viruses or a branch of viruses within an entire virus family24. Unlike traditional vaccines that target one specific strain or variant of a pathogen, universal vaccines aim to stimulate an immune response that can defend against multiple viruses at the same time with a single dose or vaccine regime25,26. The concept of universal vaccines is particularly appealing in the context of rapidly evolving pathogens, such as influenza viruses or SARS-CoV-2 where new strains or variants can emerge frequently25. Traditional vaccines for such pathogens often need to be updated regularly to match the current circulating strains, which can be challenging and time-consuming. Given the rapidly evolving nature of SARS-CoV-2 variants and the continual threat that a new coronavirus could spillover from the animal reservoir at any time, the development of a pan-coronavirus vaccine is a key research priority for protecting global health27-29. From our current work we have learned that there is minimal cross-protection amongst the most distant coronaviruses that are currently capable of infecting people, the seasonal coronaviruses and SARS-CoV-2. This finding may suggest that pan-coronavirus vaccines should consider the inclusion of a wide range of viral antigens to be broadly protective as one representative antigen may not induce immunity across all genera and strains. Additionally, our results of infection-challenges with SARS-CoV-2 and variants illustrated that the broadness of protection provided from the various combinations was dictated by how related the first and second coronaviruses were to each other. Specifically, a primary infection to the ancestral SARS-CoV-2 followed by exposure challenge to the Beta variant led to greater antibody cross-neutralizing abilities against more variants compared to the challenge with Omicron. We hypothesize that the greater antigenic distance between Omicron and SARS-CoV-2 compared to Beta and SARS-CoV-2 decreased the potential for cross-reactivity. Taken together, these results demonstrate the protective range which one variant can cover in relation to the spectrum of the other variants, as well as the increase of antibody breadth provided after a challenge. Understanding the limits of cross-reactivity and protection from one virus family member to another is essential for developing broadly protective vaccines.

Conclusions

            In conclusion, our present findings offer important insights into what the public will require to be protected against SARS-CoV-2 or the next virus that spills over from the animal reservoir. We have shown that common cold coronaviruses that have been circulating seasonally will not protect against COVID-19. While this may seem to be a negative result, these findings offer important information about what needs to be included in a vaccine to initiate broad protection against a wide array of coronaviruses including the next coronavirus with pandemic potential. This essential knowledge is not only important for understanding virus evolution and the susceptibility of human subpopulations but will also provide a foundation for the development of universal coronaviruses so that we are better prepared for the next virus with pandemic potential (Figure 4).

Figure 4. Pan-coronavirus vaccine development for addressing future coronavirus spillovers.  

 

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