Japanese Study Shows Convalescent And Vaccine Sera Has No Effect On SARS-CoV-2 Variants

New alarming study findings by Japanese researchers from the University of Tokyo, Kyoto University, Chiba University and Tokai University have shown and confirmed  that convalescent and vaccine sera has little or no effect on the fast globally spreading Mu SARS-CoV-2 variants.

The study findings were published on a preprint server and are currently being peer reviewed. https://www.biorxiv.org/content/10.1101/2021.09.06.459005v1

The World Health Organization or WHO on August 30th, 2021, classified the SARS-CoV-2 Mu variant (B.1.621 lineage) as a new variant of interest (VOI).

The WHO defines “comparative assessment of virus characteristics and public health risks” as primary action in response to the emergence of new SARS-CoV-2 variants.

A VOI is not a variant of concern (VOC), which is a variant that has been proven to acquire one of those characteristics, making it more dangerous and so more consequential. However the Mu is being monitored closely to see if it should be re-designated as a VOC.

The fact that it is now fast spreading to many countries with increasing caseloads being detected, it is sending ‘warning alarms’ to many health experts and authorities.

After being detected in Colombia, Mu has since been reported in other South American countries, in Europe, USA, Japan and certain South-east Asian countries.

As of 29 August 2021, more than 4,500 sequences of Mu have been uploaded to the GISAID platform from 39 countries. However in this short time, more sequences of the MU strain are being detected across the world.

On the same 29^th of August the WHO said its global prevalence has declined to below 0.1 percent among sequenced cases but that figure is fast rising in the last 10 days. In Colombia, it is now at 39 percent and is still rising.

The Japanese study team demonstrated that the Mu variant is highly resistant to sera from COVID-19 convalescents and BNT162b2 (Pfizer–BioNTech)-vaccinated individuals.

Detailed direct comparison of different SARS-CoV-2 spike proteins revealed that the Mu spike is more resistant to serum-mediated neutralization than all other currently recognized variants of interest (VOI) and concern (VOC). This includes the Beta variant (B.1.351) that has been suggested to represent the most resistant variant to convalescent and vaccinated sera to date. https://www.nature.com/articles/s41586-021-03412-7

https://www.nature.com/articles/s41586-021-03398-2

In order to assess the sensitivity of the Mu variant to antibodies induced by SARS CoV-2 infection and vaccination, the study team generated pseudoviruses harboring the spike proteins of Mu or the other VOC/VOIs.

Alarmingly virus neutralization assays revealed that the Mu variant is 12.4-fold more resistant to sera of eight COVID-19 convalescents, who were infected during the early pandemic (April–September, 2020), than the parental virus (P=0.0078). Also, the Mu variant was 7.6-fold more resistant to sera obtained from ten BNT162b2-vaccinated individuals compared to the parental virus (P=0.0020).

Indirectly these study findings show that in reality, the convalescent and vaccine sera has little or no effect on the Mu SARS-CoV-2 variants!

Resistance to COVID-19 convalescent and vaccine recipient sera can be attributed to a variety of mutations in the viral spike protein. The majority of Mu variants harbors the following eight mutations in spike: T95I, YY144-145TSN, R346K, E484K, N501Y, D614G, 57 P681H, and D950N.

These include mutations commonly identified in VOCs: E484K (shared with Beta, Gamma), N501Y (shared with Alpha), P681H (shared with Alpha) and D950N (shared with Delta). Of those, the E484K change has been shown to reduce sensitivity towards antibodies induced by natural SARS-CoV-2 infection and vaccination.

Since breakthrough infection by newly emerging variants is a major concern during the current COVID-19 pandemic, the study team warns that that their study findings are of significant public health interest. https://www.nejm.org/doi/full/10.1056/NEJMoa2109072

The study findings will help to better assess the risk posed by the Mu variant for vaccinated, previously infected and naïve populations.

The new study findings along with new developments of the spread of the Mu variant is expected to force the WHO to upgrade the status of the MU variant to that of a VOC in a matter of weeks.

At the moment experts are still not sure as to what variants may be the next dominant player in the coming fall/winter surge, whether it’s the Lambda, the Mu or the C.1.2 variant or something new. At the same time as the Delta is also continuing to spread rapidly and also bringing forth a variety of new sub-variants, a possible scenario is that the Delta variant could become the ancestor of the new emerging dominant variant. (It should be noted that to date, more than 130 Delta sub-variants with unique mutations have been identified and experts are busy classifying them.)

A more doomsday scenario is that we have new surges where many variants are at play at once and co-infections start becoming the next pandemic trend!

For more on the fun times ahead for the coming fall and winter, keep on logging to Thailand Medical News, the only site rooting for the virus.

Neutralizing Antibodies

Monoclonal antibodies (mAbs) antagonizing the interleukin-6 (IL-6) receptor have been utilized as anti-inflammatory agents to combat the cytokine storm characteristic of severe COVID-19. In this context, the mAbs studied include tocilizumab, sarilumab, and siltuximab [5]. However, the results from such investigations were inconclusive. More efficacious results were observed with the administration of convalescent sera of recovering COVID-19 patients, which improved the overall clinical status of critically ill COVID patients upon administration due to their high titers of neutralizing antibodies (nAbs) [6,7].

The entry of SARS-CoV-2 into human cells is mediated by the interaction of surface spike (S) proteins and angiotensin-converting enzymes (ACE2), after which the S protein is primed by transmembrane serine protease 2 (TMPRSS2) [8]. The S protein has two subunits (S1 and S2), which facilitate viral entry. S1 contains the receptor-binding domain (RBD) and interacts with ACE2, while S2 allows subsequent membrane fusion and cell entry [9,10].

Several neutralizing antibodies targeting the RBD of S protein are being analyzed and evaluated clinically [11,12]. The N terminal-domain (NTD) of S protein also contains immunoprotective epitopes, the most immunodominant of which elicits the production of antibody 4A8, a mAb with high neutralizing potency against the NTD of SARS-CoV-2 [13,14].

Bamlanivimab and Etesevimab, codenamed LY-CoV555 and LY-CoV016, respectively, were granted emergency use authorization (EUA) by the US Food and Drug Administration (FDA) on 10 November 2020, specifically for nonhospitalized COVID-19 patients with mild to moderate infection but with a high risk of progressing to severe disease or hospitalization [15]. Bamlanivimab, approved as a mAb monotherapy by the FBA, is a human neutralizing IgG1 that targets the RBD of the SARS-CoV-2 S protein to block attachment to ACE2. Etesevimab is a mAb that targets an epitope of the S protein distinct from that of Bamlanivimab and was developed for synergistic effect with Bamlanivimab [16].

A BLAZE-1 study evaluating the efficacy of both bamlanivimab monotherapy and combination therapy (bamlanivimab/etesevimab) compared to a placebo revealed significant reductions in SARS-CoV-2 load with the cocktail [16]. Another phase 2 clinical trial assessing the impact of 700 mg, 2800 mg, and 7000 mg doses of bamlanivimab monotherapy on quantitative viral load revealed significant decreases in viral load in patients receiving the 2800 mg dose, whereas the other two doses did not accelerate the decrease in viral load [17].

Similarly, REGN-COV2 is an antibody cocktail comprised of two non-competing neutralizing mAbs named imdevimab (REGN10987) and casirivimab (REGN10933). It was approved for EUA by the FDA for use in the same setting as Bamlanivimab and Etesevimab. Imdevimab and casirivimab both target the S protein RBD, preventing virus–host cell interaction, thus leading to neutralization. The binding site of imdevimab overlaps significantly with that of ACE2, whereas the engagement of casirivimab to its receptor does not obstruct ACE2 binding.

The REGN-COV2 antibody cocktail was shown to reduce viral load in the respiratory tract and, consequently, COVID-19 severity and complications in both rhesus macaques and golden hamsters [18]. Provisional results and analysis of data involving 275 nonhospitalized COVID-19 patients in an ongoing double-blind, phase 1–3 trial evaluating the efficacy and safety of REGN-COV2 against placebo showed significant reductions in viral loads in REGN-COV2 receivers [19,20]. Furthermore, no mutant strains arose secondary to combination therapy with imdevimab and casirivimab. Cocktail therapy is therefore preferred over monotherapy [21].

Antibodies targeting the viral nucleocapsid (N) protein—which may mediate viral genome expression and assembly—have been isolated from convalescent sera of COVID-19 patients in the early recovery phase; in contrast, anti-S protein antibodies dominate late-phase sera [14,22,23]. A recent study highlighted a particular anti-N-protein nAb, nCoV396, which inhibited N-protein–MASP-2 interaction [14], thus blocking N-protein-mediated complement hyperactivation and combatting the pro-inflammatory state characterizing COVID-19 [14]. Further work is required to elucidate the full prophylactic and therapeutic potential of these Abs.

Types of COVID-19 Vaccines

Vaccines aim to trigger the adaptive arm of host immunity—comprising both cell-mediated and humoral responses—leading to the generation of neutralizing, or virus-blocking, antibodies. Vaccines contain an antigen of the virus whose introduction triggers antibody production, which confers protective immunity. In the context of SARS-CoV-2, the antigen administered is the surface S protein. Different types of COVID vaccines introduce the S protein in different ways to initiate host immune defense without causing disease. On this basis, there are currently four types of COVID vaccines in use: viral vector vaccines, genetic vaccines using nucleic acids, virus vaccines, and protein vaccines.

Viral vector vaccines use an unrelated virus that infects cells and subsequently expresses the SARS-CoV-2 S protein gene to activate the immune response. The Oxford AstraZeneca (ChAdOx1) and Johnson & Johnson’s (J&J) Janssen (Ad26.COV2.S) vaccines are examples of viral vector vaccines that are currently in use. COVID-19 nucleic acid vaccines contain DNA/RNA encoding the surface S protein.

After administration, through transcription and translation, host cells present S protein in the context of major histocompatibility complexes (MGC) to helper and cytotoxic T cells to provide immunity. Examples of this vaccine group are the Pfizer BioNTech (BNT162b2) and Moderna (mRNA-1273) vaccines, which contain RNA encoding the S protein. The third set of vaccines involves injecting a killed/inactivated or weakened form of SARS-CoV-2 to elicit an immune response without causing COVID-19. The Sinopharm and Sinovac vaccines are examples of inactivated vaccines. Currently, the Pfizer-BioNTech, Moderna, and J&J vaccines have gained approval by the FDA for use in the United States of America.

Protein vaccines inject viral proteins, such as the S protein of SARS-CoV-2, into the body to elicit an immune challenge. One such vaccine under development is the Novavax vaccine, codenamed NVX-CoV2373. Comprising a full-length S protein on a nanoparticle platform that is administered intramuscularly with a matrix-M adjuvant, it can trigger a protective Th1-dominant B and T cell response in mice and baboons [24].

A placebo-controlled phase 1–2 trial involving 131 healthy adults compared the reactogenicity and safety of anti-S protein IgG titers generated from the administration of NVX-CoV2373 to convalescent serum from symptomatic COVID-19 patients. The adjuvanted two-dose regimen triggers a Th1 dominant immune response that demonstrated a four times higher efficacy compared to convalescent sera, reaching levels comparable with those observed in hospitalized COVID-patients [25]. Thus, nanovaccines, such as virus-like particles (VLPs), may also represent a viable and rapid approach, serving as ideal scaffolds for antigen display due to their emulation of naturally occurring viruses in size and geometry [26,27,28,29]. This results in an enhanced clustering of B cell receptors and resultant immunogenicity [30]. Indeed, the S protein displayed on nanoscale scaffolds seems more immunogenic in mice compared to S protein administered alone [31]. In Syrian hamsters and mice with SARS-CoV-2, this approach generated high neutralizing antibody titers following a single dose, with no infectious virus detected in the lungs [29,32].

Efficacy of Vaccines, Convalescent Sera, and Neutralizing Antibodies on SARS-CoV-2 Variants

SARS-CoV-2 acquires mutations that lead to genetic drift due to changes in infectivity and virulence, antigenicity, and the ability to evade pre-existing host antibodies acquired either through infection, antibody therapy, or vaccination. Initially, SARS-CoV-2 underwent genetic evolution, giving rise to the D614G variant that subsequently became the dominant variant during the pandemic owing to its increased transmissibility [25,33]. However, subsequent studies have revealed that the D614G mutation might confer increased susceptibility to neutralization by antibodies and, therefore, does not pose a threat to vaccine development [33].

Since then, many variants have arisen, some of which have been classified by the CDC and WHO as variants of concern (VOCs) and variants of interest (VOIs) (Figure 1). This categorization was based on variants possessing increased transmissibility and virulence, the ability to evade detection, and the ability to curb prophylactic and therapeutic countermeasures such as vaccines, neutralizing mAbs, and the administration of convalescent sera.

The currently designated VOCs include four variants, including strains first detected in the UK (B.1.1.7 lineage or alpha), South Africa (B.1.351 lineage or beta), Brazil (P.1 lineage or gamma), and India (B.1.617.2 lineage or delta) [34,35]. The alpha, beta, and gamma variants exhibit a higher transmissibility, which is attributed to the N501Y mutation common to all three strains, as it improves the affinity of S protein to host cell receptors [36,37].

However, the N501Y mutation does not affect neutralization by protective host antibodies and, therefore, does not interfere with the potency of vaccines, convalescent sera, or mAbs. The delta variant (B.1.617 lineage—with 3 subsets) was first described in India in October 2020 and is believed to account for the recent increase in COVID-19 cases. It exhibits characteristic mutations in the S protein, including D11D, G142D, L45R, and E484q. L452R and E484Q are located in the RBD and, along with the P681R mutation in the furin cleavage site at the junction between S1 and S2, are thought to confer increased transmissibility to the delta variant [38,39].

The analysis of these variants revealed that the alpha variant discovered in the UK was resistant to neutralization by most mAbs targeting the NTD of the S protein and relatively resistant to a few mAbs against the RBD. However, responses to convalescent sera or vaccine sera were unchanged compared to ancestral strains [40,41]. By contrast, the beta variant, in addition to displaying E484K and K417N spike mutations, is resistant to neutralization by mAb therapy, convalescent sera, and vaccinee sera from individuals vaccinated with the Pfizer-BioNTech and Moderna mRNA vaccines. The alpha and gamma variants exhibit normal neutralization—relative to the parent strain—with these mRNA vaccines [40,42,43,44].

Therefore, an increase in the prevalence of the beta variant poses a threat to the efficacy of the current mRNA vaccines. In addition, the results from a clinical trial revealed that the Oxford AstraZeneca vaccine fails to confer protection from the beta variant, with an overall efficacy of 22% [45]. Furthermore, the clinical efficacy of the vaccine against the beta variant was reduced relative to ancestral strains [46]. Encouragingly, however, the REGN-COV2 and bamlanivimab/etesevimab antibody cocktails retained their activity in vitro against the alpha and beta VOCs.

A phase 3 trial conducted in South Africa evaluating the efficacy of the J&J vaccine involving 6576 participants revealed efficacies of 52% and 64% at days 14 and 28, respectively [47]. The efficacy of the two-dose adjuvanted regimen of NVX-CoV2373 Novavax is currently being assessed in an ongoing randomized, observer-blinded, placebo-controlled 2a-b trial involving 6324 participants in South Africa.

Preliminary safety results were acceptable, with headache (20–25%), muscle pain (17–20%), and fatigue (12–16%) being the most common [48]. Early results estimated a vaccine efficacy of 52.2%. Additionally, this trial showed that infection with the prototypical, wildtype (WT) SARS-CoV-2 Wuhan strain does not protect against reinfection by the beta variant [48]. Therefore, the J&J and Novavax vaccines afford modest protection against beta and gamma VOCs.

The resistance of the B.1.617.1 lineage (a subset of the delta variant) to convalescent sera and nAbs induced by the Pfizer and Moderna vaccines was assessed. Neutralization titers were found to be lower in all relative to the WT; B.1.617.1 was 6.8 times less susceptible to neutralization by convalescent and vaccinee sera [49].

Another study evaluating the degree of inhibition of S protein–ACE 2 interaction and subsequent cell entry by convalescent sera from intensive care unit patients revealed a twofold reduction in inhibition relative to the WT; by comparison, the delta variant showed a sixfold decrease [50]. Additionally, delta showed a threefold reduction in inhibition by sera obtained from individuals who received the Pfizer-BioNTech vaccine compared to WT.

In contrast, beta exhibited an elevenfold reduction [50]. Monotherapy with either mAb failed to inhibit virus-host cell interactions [43,50]. However, bamlanivimab/etesevimab cocktail therapy has recently been reported to resolve symptoms in a severely ill patient infected with the delta variant [51]. Furthermore, studies testing the efficacy of the Pfizer-BioNTech and Oxford AstraZeneca vaccines against the delta variant relative to alpha revealed only small differences with two-dose regimens; indeed, one dose barely induced nAbs [52,53]. This suggests that greater public emphasis be placed on two-dose vaccinations in susceptible populations for protection against the delta (B.1.617.2) variant [53].

It is important to note that these studies have not yet been formally peer-reviewed and, consequently, are not definitive. Therefore, the results of these preliminary studies should be interpreted with caution because all vaccines did show efficacy, albeit to varying success, and an objective cut-off value for a protective antibody response is currently not known. Furthermore, COVID-19 vaccines elicit antibody production against various, unrelated S protein epitopes, allowing for the possibility of some nAbs retaining neutralizing capacity against the VOCs. Lastly, other components of adaptive host defense, such as T cell-mediated immunity, may constitute important mechanisms unaffected by the VOCs.

Rather encouragingly, concerns underlying variants that could be partially resistant to vaccine-induced antibody responses may exhibit other immune responses that protect against viruses. Of particular interest is T cell-mediated immunity, which targets and eliminates virus-infected cells. Indeed, data are increasingly suggesting that such responses could provide enhanced immunity against COVID-19 despite decreased effectiveness of humoral responses [54,55,56].

While T cells do not prevent infections, they exert a role in clearing them, potentially meaning the difference between a mild or severe infection, and also potentially reducing community transmission [54,56]. Furthermore, T cells could also be more resistant to the genetic drift of emerging variants compared to antibodies [54]. Indeed, T cell responses to coronavirus vaccination or previous infection did not target mutation-susceptible regions of SARS-CoV-2, conferring a type of ‘resistance’ against such mutations [54,56].

While most antibody-based vaccines target the mutation-prone S region, T cells target very stable viral proteins inside infected cells, potentially indicating powerful avenues of vaccination research incorporating targets from multiple proteins into one vaccine.

reference link : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8402590/