Understanding of Host-Pathogen Interaction & Applications (SARS-CoV-2)

SARS-CoV-2 origin and transmission

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ﬁrst identiﬁed in December 2019, is the etiological agent of coronavirus disease (COVID-19).
SARS-CoV-2 has zoonotic origin and shares genomic similarity with other zoonotic viruses responsible for SARS (SARS-CoV-1) and MERS (MERS CoV EMC/2012).
The discovery that its closest identified viral relatives are enzootic in horseshoe (Rhinolophus) bat indicates that SARS-CoV-2 probably emerged from an as-yet-unidentified bat reservoir either directly or after infection of an intermediate host such as a pangolin (Morens et al. 2020).
SARS-CoV-2 has a receptor binding domain (RBD) in the spike (S) protein consisting of 6 amino acids which not only differentiates it from SARS- CoV-1 but also confers it with ability to bind human or human-like Angiotensin Converting Enzyme-2 (ACE2) with high aﬃnity (Figure. 1).
SARS-CoV-2 also has a polybasic furin cleavage site on the highly variable spike protein which is also unique to SARS-CoV-2. This site allows cleavage by proteases and determines viral host range and is potentially associated with increased transmission of SARS-CoV-2 in humans.
SARS-CoV-2 is airborne, thus wearing a mask remains one of the most effective precautionary measures for preventing acquisition of the virus

Figure 1: The virus binds to ACE 2 cell receptor in synergy with the transmembrane serine protease 2 (cell surface protein), which is principally expressed in the airway epithelial cells and vascular endothelial cells. This leads to membrane fusion and releases the viral genome into the host cytoplasm (2). Stages (3-7) show the remaining steps of viral replication, leading to viral assembly, maturation, and virus release. [Source: Cevik et al., 2020]

SARS-COV-2 Pathogenesis

SARS-CoV-2 causes a broad-spectrum of diseases ranging from asymptomatic infection to severe symptomatic disease (Figure 2). Most individuals infected with SARS-CoV-2 are asymptomatic or develop mild symptoms as fever, cough, myalgia, headache, and taste and smell disturbance.
Severe COVID-19 is associated with excessive levels of pro-inflammatory cytokines due to unregulated immune response defining a cytokine storm syndrome which leads to more tissue damage even when viral load is low. IL-6 and TNFα serum levels have been shown to be significant predictors of disease severity and death (Del Valle et al. 2020).
Additionally, individuals with severe COVID-19 can also develop complications such as thrombosis, sepsis and multi-organ dysfunction.
Robust virus replication accompanied by delayed type I interferon (IFN-I) signalling orchestrates inflammatory responses and lung immunopathology with diminished survival (Figure. 3). This delayed IFN-I signalling promote the accumulation of pathogenic inflammatory monocyte macrophages resulting in elevated lung cytokine/chemokine levels, vascular leakage, and impaired virus-specific T cell responses.
Infection induces robust antibody and T cell responses, which in most cases likely controls viremia before COVID-19 pathogenesis progressors.
Studies have shown that although circulating SARS-CoV-2-speciﬁc Ab and T cell responses may wane quickly, natural infection (and potentially vaccination) induces long-lasting memory B cell immunity which persists despite a decline in circulating SARS-CoV-2-antibodies.

Figure 2: After the initial exposure, patients typically develop symptoms within 5-6 days. SARS-CoV-2 generates diverse clinical manifestations, ranging from mild infection to severe disease accompanied by high mortality. In patients with mild infection, initial immune response can control the infection. In severe disease, excessive immune response leads to organ damage, intensive care admission, or death. The viral load peaks in the ﬁrst week of infection, declines thereafter gradually, while the antibody response gradually increases and is often detectable by day 14. [Source: Cevik et al., 2020]

Figure 3: Robust SARS-CoV replication and delayed IFN-I signaling promote SARS disease while disease severity is ameliorated in the absence of IFN signaling [Source: Channappanavar et al., 2016]

COVID-19 vaccines

There have been multiple COVID-19 vaccine candidates with a variety of platforms that have been tested in pre-clinical and clinical trial settings, some of which are highlighted in Table 1.
Approved vaccines have been through randomized clinical trials to test their quality, safety and efficacy. To be approved, vaccines are required to have a high efficacy rate of 50% or above.
mRNA vaccines (mRNA-1273, BNT162b2) and Sputnik V (viral vector; Gamaleya) demonstrated over 90% eﬃcacy against SARS-CoV2 infection, while other viral vector vaccines (Ad26.COV2.S and AZD1222) didn’t perform as well with eﬃcacies above 70%. The first protein subunit COVID-19 vaccine to become available Novavax showed a 89% efficacy.
The duration of vaccine protection is still being studied. A gradually declining trend in vaccine protection against infection have been suggested. For BNT162b2, the 95% efficacy number down to 84% after 6 months. The effectiveness of vaccines against infection after 6 months decreases in a variable way depending on the variants, for example for the delta: the effectiveness of Pfizer falls to 42% while that of Moderna is 76% (Puranik et al, 2021)
Single-shot booster doses of BNT162b2 vaccine are recommended by CDC at least six months after completion of the primary doses for those over 65, people with underlying medical conditions and healthcare professionals. Booster shots for other vaccines are suggested.

Table 1. COVID-19 Vaccines

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* Vaccine candidates in phase 3 clinical trials and not yet approved for use by WHO.

Interested in learning more about COVID-19 vaccines? Read the following news summaries:

Viral genomic analysis of breakthrough infections (infection in fully vaccinated individuals) highlighted the emergence of SARS-CoV-2 variants (discussed in detail below) which signiﬁcantly lowered eﬃcacy signal of Ad26.COV2.S (Johnson & Johnson) and AZD1222 (Oxford/Astra-Zeneca), while other vaccine mRNA-1273 (Moderna), BNT162b2 (Pﬁzer/BioNTech) and Sputnik V (Gamaleya) were tested when the original SARS-CoV-2 variant was still the most prevalent.
Approved vaccines have been shown to induce robust vaccine induced humoral and cellular immunity and are very eﬃcacious against severe COVID-19 which may require hospitalization or even lead to mortality.

Heterologous prime-boost vaccination

Due to limited global access to COVID-19 vaccines, largely resulting in vaccine inequity in Asia and Africa. Researchers are investigating novel vaccination strategies, such as heterologous prime-boost strategies to facilitate mass COVID-19 vaccinations.
As the different platforms differ in efficacy, duration of protection, and side effects, heterologous prime-boost vaccination can maximize the benefits of vaccination.
In light of concerns regarding thrombotic thrombocytopenia after the first dose of AZD1222, several countries are now advising that individuals previously primed with this vaccine should receive an alternative vaccine as their second dose, most commonly mRNA vaccines such as the BNT162b2.
In a phase 2 trial testing, Borobia et al. demonstrated that BNT162b2 given as a second dose in individuals vaccinated with AZD1222 induced a robust immune response, with an acceptable and manageable reactogenicity proﬁle. Additionally immune responses in the heterologous vaccination arm had signiﬁcantly higher levels than control vaccination arm (Figure. 4)

Figure 4: Humoral and cellular immune responses (A) Neutralising antibodies measured in both intervention and control groups on days 0 and 14. (B) IFN-γ concentrations measured in both intervention and control groups on days 0 and 14. *p<0·0001. [Source: Borobia et al., 2021]

Correlates of protection: Neutralizing antibodies

Correlates of protection define the immune responses that are statistically associated with protection against disease.
Due to limited knowledge of what protective immune responses are associated with prevention of COVID-19, majority of COVID-19 vaccines were tested without knowledge of the correlates of protection of SARS-CoV-2 infection.
Neutralizing antibodies are often considered potential correlates of protection against viruses; thus majority of natural SARS-CoV-2 infection and COVID-19 vaccine immunogenicity studies measure the induction of neutralizing antibodies (nAbs) as one of the trial endpoints. However, are Abs truly correlate of SARS-CoV-2 protection?
A large number of NAbs have been identified, and some have been shown to reduce the viral load in patients with COVID-19. The level of IgG against the S protein RBD was demonstrated to be correlated with SARS-CoV2-neutralizing activities in the sera from COVID-19 patients.
Results from non-human primates suggest mRNA-1273 vaccine induced Abs detectable in serum and localized at mucosal sites can restrict SARS-CoV-2 replication and confer protection against SARS-CoV-2 infection (Corbett et al., 2021). Further passive transfer of vaccine-induces IgG in naïve hamsters was sufficient for protection (Figure 5).
High levels of protection were noted after vaccination with one dose of BNT162b2 mRNA vaccine, despite modest levels of neutralizing antibody, strongly supporting the concept that other mechanisms are at play as co-correlates of protection.

Figure 5: Passive transfer of mRNA-1273 immune non-human primates (NHP) IgG into Syrian hamsters. (A) Sera were pooled from all NHP in a primary vaccination series. (B) immune NHP IgG or pre-immune NHP IgG was passively transferred to Syrian hamsters 24 hours prior to SARS- CoV-2 challenge. 23 hours post-immunization, hamsters were bled to quantify circulating S-speciﬁc IgG (C) and SARS-CoV-2 pseudovirus neutralizing antibodies (D). Following challenge, hamsters were monitored for weight loss (E). (C-D) Circles represent individual NHP. Bars and error bars represent GMT and geometric SD, respectively. Asterisks at the axis represent animals that did not receive adequate IgG via passive transfer and were thus excluded from weight loss analyses. (D) The dotted line indicates the neutralization assay limit of detection. (E) Circle and error bars represent mean and SEM, respectively. [Source: Corbett et al., 2021]

Correlates of protection: Cellular response

Following natural SARS-CoV-2 infection, T-cell responses are rapidly activated (Figure 6).
Virus-specific T-cell responses have been shown to be associated with milder disease in COVID-19 patients. The involvement of T cells is also critical for B-cell maturation and the induction of strong and durable antibody responses. Therefore, the generation of a robust cellular immune response is a desirable attribute for a vaccine against SARS-CoV-2.
It is considered advantageous if a COVID-19 vaccine activates type 1 helper T-cell (Th1)-skewed T-cell responses or balanced T-cell responses. Th2-skewed responses have raised safety concerns about the potential for vaccine-associated enhanced respiratory disease (ERD) in previous experience with coronavirus vaccines.
mRNA vaccines elicited Th1-biased T-cell responses were induced and were characterized by expression of IFNγ, TNFα and IL-2 but very low levels of IL-4 with minimal Th2 cytokine expression (IL-4 and IL-13).
In addition, S-specific IFNγ +CD8+ T cells were also robustly induced by BNT162b2. Another mRNA vaccine, mRNA-1273, elicited low levels of SARS-CoV-2 S-specific CD8+ T-cell responses.
Humoral and cellular responses were induced by DNA and all viral vectored vaccines for which data have been published.
Inactive virus vaccines show lower cellular responses. Zhang et al. showed that boosting with either recombinant subunit, adenovirus vectored or mRNA vaccine after two-doses of inactivated vaccine further improved both neutralizing antibody and Spike-specific Th1-type T cell responses compared to boosting with a third dose of inactivated vaccine.

A summary of data published on humoral and cellular responses of COVID-19 vaccines can be found in this article by Xu et al.

Figure 6: Schematic representation of the induced immune response following SARS-CoV-2 infection. The gray, blue, green and brown lines indicate upper respiratory tract (URT) virus load, T-cell responses, IgM level and IgG level, respectively. [Source: Xu et al. 2021]

Natural VS Vaccinal protection:

A recent CDC study found that 36% of COVID-19 cases didn’t result in development of SARS-CoV-2 antibodies. These people presented with different levels of illness from asymptomatic infection to severe COVID-19. Subsequently, a third of people who get COVID-19 don’t develop appropriate protection from reinfection.
Natural immunity seems to fade more quickly than vaccine immunity as a CDC study reported that 94% of previously infected people experienced a decline in SARS-CoV-2 antibodies after 60 days and 28% among them seroreverted to below the threshold of positivity. mRNA vaccine protection seems to last longer, up to at least six months.
Gazit et al. demonstrated that natural immunity confers longer lasting and stronger protection against infection, symptomatic disease and hospitalization caused by the Delta variant of SARS-CoV-2, compared to the BNT162b2 two-dose vaccine-induced immunity.
Natural immunity alone is weak. After a SARS CoV-2 infection, unvaccinated people are 2.34 times likelier to get COVID-19 again, compared to fully vaccinated people. So after infection, vaccinated people have half the risk of reinfection than people relying on natural immunity alone. Thus, the vaccine gives a booster response to the natural infection.

SARS-CoV-2 Immune escape: Effect of SARS-CoV-2 variants on pre-existing immune responses

Viruses are known to naturally mutate without impacting the ability of the virus to cause infection nor diseases. However, if mutations occur cumulatively in proteins that are required for viral entry or in epitopes targeted by immune responses this may impact transmissibility or diseases severity of the mutated virus.
SARS-CoV-2 has evolved more rapidly than researchers anticipated, resulting in the evolution of multiple variants (viruses with one or multiple mutations distinct from the initial detected SARS-CoV-2 strain). These variants have been designated as variants of concern (VOC) and variants of interest (VOI).
VOI present with genetic changes that are predicted to affect virus characteristics such as transmissibility, disease severity, immune escape, diagnostic or therapeutic escape. VOI have an epidemiological impact as they cause significant community transmission or multiple COVID-19 clusters.
VOC are VOI that has been demonstrated to be associated with an Increase in transmissibility or in virulence, a change in clinical disease presentation, or a decrease in effectiveness of social measures or available diagnostics, vaccines, therapeutics.
Recently a new class of variants was added designated as Variants Being Monitored (VBM). A previously designated VOI or VOC that has conclusively demonstrated to no longer pose a major added risk to global public health, can be reclassified as VBM.
As of 6^th October 2021, 4 VOCs were identified by the WHO (Table 2).

Table 2: SARS-CoV-2 Variants of interest

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Source: https://www.who.int/en/activities/tracking-SARS-CoV-2-variants/

New SARS-CoV-2 variants, emerged in the UK (501Y.V1, B.1.1.7 lineage), South Africa (501Y.V2, B.1.351 lineage) and Brazil (501Y.V3, P.1 lineage), were spreading globally and were found to escape neutralization induced by virus infection and vaccination.
It was demonstrated that S protein E484K found in B.1.1.7, B.1.351 and P.1 variants, was a key mutation that resulted in variant virus resistance to the neutralizing activity of most NAb engaging the RBD, convalescent sera and mRNA vaccine-induced immune sera.
Plasma from persons infected with the original variant showed substantially lower neutralization of the B.1.351 variant than of the original variant. Interestingly, the reverse experiment showed immune responses induced by the B.1.351 variant conferred cross-reactive immunity against both the original variant and P.1 (Moyo-Gwete et al., 2021). This cross reactivity suggests that developing vaccines that include known mutations in the VOC may increase the eﬃcacy of vaccines.
T cells in infected or vaccinated individuals can also elicit robust and cross-reactive immune responses against VOCs. Tarke et al. demonstrated that T cells of exposed donors or vaccinees effectively recognize SARS-CoV-2 variants and 93% and 97% of CD4 and CD8 epitopes are 100% conserved across variants.