A new review of the emerging variants of concern (VOCs) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which has caused the coronavirus disease 2019 (COVID-19) pandemic, shows that there is a major need to constantly re-evaluate the utility of existing therapeutics and vaccines against the virus and to develop new ones.
The paper, published online in the journal Viruses, points to the need to exploit the power of genomic sequencing to identify crucial mutations in order to adapt preventive and therapeutic measures accordingly.
Pathogenesis of COVID-19
The novel coronavirus has four major structural proteins, the spike (S), envelope (E), membrane (M) and nucleocapsid (N). Among these, the spike mediates viral entry, binding to the host cell receptor, the angiotensin-converting enzyme 2 (ACE2), and triggering subsequent virus-cell membrane fusion for viral entry into the host cell.
The spike protein is the immunodominant antigen, with a large majority of neutralizing antibodies being directed against it, particularly the receptor-binding domain (RBD). However, it is not alone in triggering an immune response, beginning with the innate immune cells, macrophages and monocytes.
This causes the release of pro-inflammatory cytokines at the site of infection and also stimulates the adaptive immune response, mediated by CD4+ and CD8+ T cells. The cytotoxic T cells kill the infected cells and thus prevent the dissemination of the virus.
Severe or critical COVID-19 is traceable to the dysregulated immune-inflammatory response, which causes a cytokine storm, leading to tissue and organ damage. This is most notably represented by the acute respiratory distress syndrome (ARDS) or sepsis symptoms, along with collateral coagulation abnormalities and multi-organ dysfunction.
Emergence of VOCs
Several vaccines and monoclonal antibodies have been developed to deal with this threat, with many more in the pipeline. However, the VOCs show mutations of the spike antigen, allowing the virus to escape antibody-mediated recognition and destruction by the immune system. Alternatively, such mutations may improve viral transmissibility or virulence.
The D614G strain was the first VOC to be noted in January 2020. It spread with dazzling swiftness over the whole world to become the dominant strain, displacing the original Wuhan lineage due to its greater viral fitness. This is shown by the lower cycle thresholds for positive reverse transcriptase-polymerase chain reactions (RT PCR) with this VOC.
The 20I/501Y.V1 (B.1.1.7) lineage emerged almost a year later, in December 2020, with 17 mutations. It similarly spread rapidly to well over 150 countries. It is defined by the RBD N501Y mutation along with others, which changed the conformation of the spike at the interface of the two spike subunits. It is also 82% more transmissible and probably more virulent than the earlier variants, but remains as susceptible to neutralization by vaccine-elicited antibodies.
Interestingly, it has an ORF8 Q27stop mutation that splits the ORF8 gene and makes it possible for the virus to accumulate more downstream mutations. Since the ORF8 protein is implicated in immune evasion, this mutation may be responsible for the continued susceptibility of this VOC to antibodies.
The later variants 20H/501Y.V2 and 20J/501Y.V3 (B.1.351 and P.1, respectively) share the N501Y mutation with the 20I/501Y.V1. These also contain some escape mutations, particularly the E484K mutation, which allows antibody escape by structurally modifying the spike protein. The 20H/501Y.V2 is also highly transmissible.
Recently, the 20I/501Y.V1 has been reported to have acquired the E484K mutation, in a few cases, conferring immune escape capability on the strain.
Other variants of interest (VOIs) have emerged since, such as the 19B/501Y in January 2021, with the N501Y mutation as well as the H655Y found in the P.1 strain. The transmission of the virus from mink farmworkers to farmed mink also induced the Y453F mutation in the receptor-binding motif of the RBD. This is an escape mutation, also seen in the CAL20C variant. It also shows N501T mutation, which may stabilize the virus-receptor complex.
The CAL20C variant, reported in California, is better known for the L452R mutation that allows it to escape neutralization by monoclonal antibodies (mAbs). It shares the B lineage with B.1.429 and B.1.427. This mutation is also present, along with the Q677H mutation near the furin cleavage site, in the A.27 strain (19B/501Y VOI), and these may help the virus to adapt to the host and to replicate faster.
Many other variants have been reported in smaller clusters, but remain stable at low frequencies or die out in a few months. However, the 0A/484Q Variant (Lineage B.1.617) has the L452R common to the CAL.20C variant and E484Q, similar to the E484K mutation in biological effects. The presence of the so-called double mutant could make it more transmissible, and resistant to neutralization by antibodies. This variant is now spreading rapidly over much of the world.
Not only do these mutations change the biology of the virus with regard to its immune response, but they lead to the emergence of multiple different strains within a single individual. This is called viral quasi-species and could affect tissue tropism.
Broad tissue tropism
Though SARS-CoV-2 is primarily a respiratory virus, it also affects many other organs such as the kidney (which expresses ACE2 a hundred-fold higher relative to lung tissue), heart, blood vessels, liver, brain and digestive tract. Other receptors suspected of allowing the virus to enter the host cells include neuropilin-1 (NRP-1) and the widespread CD147 molecules.
Some mutations may shape the tissue tropism of the virus as well, modulating the interaction of the virus with cell receptors specific to certain tissues. Involvement of the digestive tract could enhance its spread via feces, though this remains to be proved by rigorous experiments.
Impact of mutations on vaccine and antibody efficacy
Current vaccines largely rely on the spike antigen of the Wuhan strain. These include the messenger ribonucleic acid (mRNA) vaccines encoding the spike protein, the adenovirus-vectored spike vaccines, and inactivated virus vaccines.
Newer vaccines could incorporate the N protein as well, which is reported to be highly immunogenic. The non-structural protein NSP3 is another potential vaccine antigen as it is conserved between coronaviruses and may also trigger CD4+mediated responses.
Monoclonal antibodies have been used to prevent or treat COVID-19, including those who have weakened immunity or are otherwise unprotected. Two anti-RBD mAbs were approved by the Food and Drug Administration, namely, Bamlanivimab (LY-CoV555 or LY3819253), and the combination of Casirivimab (REGN10933) + Imdevimab (REGN10987), by Eli-Lilly and Regeneron, respectively.
Combinations of mAbs have been found to be capable of compensating for antibody resistance by SARS-CoV-2 VOCs, since at least one of the cocktail components is always active against the virus even when one is reduced in neutralization efficacy. For instance, the REGN 10933 + REGN 10987, CoV2-2196 + CoV2-2130, and the combination LY-CoV 555 + CB6 combinations all show this pattern, though the last shows decreased efficacy against 20H/501Y.V2.
The presence of a K417N compensatory mutation prevents this resistance, however, in the case of the Wash SA-B.1351 strain.
Convalescent plasma also remains effective against most variants, though the S982A mutation in the S2 spike subunit increases neutralization resistance slightly. Again, the 20H/501Y.V2 variant differs in its significant resistance to antibodies in convalescent plasma and antisera from vaccine recipients. This is linked to the E484K mutation that affects an immunodominant epitope.
This may be the case with the 20J/501Y.V3 variant and others containing this mutation.
What are the implications?
Studies have shown that B.1.351, P.1 lines, and B.1.1.7 with the E484K mutation are a source of concern in terms of vaccination, because of their potential resistance to sera from convalescents, immune sera from animals, and human sera from vaccinated patients.”
While vaccine antigens must be selected so as to trigger both innate and adaptive immunity, the vaccine must not stimulate abnormal Th2-skewed responses, which may be associated with antibody-dependent enhancement (ADE) of disease.
To counter emerging VOCs, vaccines must be updated periodically, as is in development with most major vaccines now available. A number of manufacturers have announced that they are planning to release booster vaccines based on neutralization-resistant strains such as 20H/501Y.V2.
Antibody cocktails should also exploit more epitopes, especially highly conserved ones, to prevent mutational escape. Animal reservoirs must be identified, and potential spread back into humans must be prevented.
Genomic sequencing efforts have been key in the fight against the virus, and must be promoted further to identify such VOCs and execute appropriate strategies to contain the pandemic and allow recovery of global health and economic activity.