A new study from scientists at Scripps Research, along with collaborators in Germany and the Netherlands, has revealed key details of how these escape mutations work.
The scientists, whose study appears in Science, used structural biology techniques to map at high resolution how important classes of neutralizing antibodies bind to the original pandemic strain of SARS-CoV-2 – and how the process is disrupted by mutations found in new variants first detected in Brazil, the United Kingdom, South Africa and India.
The research also highlights that several of these mutations are clustered in one site, known as the “receptor binding site,” on the spike protein of the virus. Other sites on the receptor binding domain are unaffected.
“An implication of this study is that, in designing next-generation vaccines and antibody therapies, we should consider increasing the focus on other vulnerable sites on the virus that tend not to be affected by the mutations found in variants of concern,” says co-lead author Meng Yuan, Ph.D.
Yuan is a postdoctoral research associate in the laboratory of senior author Ian Wilson, DPhil, Hansen Professor of Structural Biology and Chair of the Department of Integrative Structural and Computational Biology at Scripps Research.
How ‘variants of concern’ escape immune response
SARS-CoV-2 “variants of concern” include the UK’s B.1.1.7 variants, South Africa’s B.1.351 variants, Brazil’s P.1 variants and India’s B.1.617 variants. Some of these variants appear to be more infectious than the original Wuhan strain. Recent studies have found that antibody responses generated through natural infection to the original strain or via vaccination are less effective in neutralizing these variant strains.
Because of the variants’ potential to spread and cause disease—perhaps in some cases, despite vaccination—scientists consider it urgent to discover how the variants manage to escape much of the prior immune response in the body, including the antibody response.
In the study, the researchers focused mainly on three mutations in the SARS-CoV-2 spike protein: K417N, E484K and N501Y. Alone or in combination, these mutations are found in most major SARS-CoV-2 variants.
The researchers tested representative antibodies from the major classes that target the general area in and around the receptor binding site. They found that many of these antibodies lose their ability to effectively bind and neutralize the virus when the mutations are present.
Using structural imaging techniques, the team then mapped the relevant portion of the virus at atomic-scale resolution to examine how the mutations affect sites where antibodies otherwise would bind and neutralize the virus.
“This work provides a structural explanation for why antibodies elicited by COVID-19 vaccines or natural infection by the original pandemic strain are often ineffective against these variants of concern,” Wilson says.
Zeroing in on points of vulnerability
The findings suggest that while antibody responses to the SARS-CoV-2 receptor binding site can be very potent in neutralizing the original Wuhan strain, certain variants are able to escape – perhaps eventually necessitating updated vaccines.
At the same time, the study underlines the fact that the three key viral mutations, which SARS-CoV-2 seems inherently prone to develop, do not alter other vulnerable sites on the virus outside the receptor binding site.
The researchers specifically showed that virus-neutralizing antibodies targeting two other areas outside the receptor binding site were largely unaffected by these three mutations.
This suggests that future vaccines and antibody-based treatments could provide broader protection against SARS-CoV-2 and its variants by eliciting or utilizing antibodies against parts of the virus that lie outside the receptor binding site. The researchers note that broad protection against variants may be necessary if, as seems likely, the virus becomes endemic in the human population.
The Wilson lab and collaborators in this study are continuing to study human antibody responses to variants of concern and hopes to identify strategies for broad protection against not only SARS-CoV-2 and its variants but also SARS-CoV-1 and other related, emergent coronaviruses.
A novel strain of coronavirus, SARS-CoV-2, the causative agent of coronavirus disease (COVID-19) was first associated with severe acute respiratory disease in late 2019 and has triggered an ongoing pandemic since March 2020 [1–3]. The pandemic has already had a serious impact on the global economy and has resulted thus far, to over 2.7 million deaths and over 122 million infections . The rampage of the COVID-19 pandemic is ongoing.
Meanwhile, in a world effort a number of anti-SARS-CoV-2 vaccines were developed in record time by late 2020 for emergency use. The approval of vaccines in less than a year is unprecedented in human history and a triumph in medical research . The variants D614G was the first spike protein mutation of concern that spread worldwide within few months . By the end of June 2020, variants D614G were found in almost all the SARS-Cov-2 samples worldwide .
However, the detection of mutant strains of SARS-CoV-2 in Brazil (P.1), South Africa (1.351), and the United Kingdom (UK) (B.1.1.7) have triggered huge concern around the world (Table 1) . Based on available information, the highest rate of transmissibility and infection rates reported for the mutant strains of SARS-CoV-2 is the UK B.1.1.7 which has already spread to over 50 countries [8,9].
In comparison, the South African strain has spread to 20 countries , and the Brazilian mutant strain has spread to Japan, Germany, and some other countries . The detection of the new mutant strains in many countries prompted border closures, lockdowns, and new restrictions and ultimately massive economic loss and further deaths.
The UK B.1.1.7 strain is linked to higher number (>60%) of infections in the UK since its detection and is considered to be at least 50–70% more contagious than the original Wuhan strain. A recent study conducted by Imperial College London (Preprint), reported that the reproduction number (R) of B.1.1.7 is 1.45 compared to 0.92 for the original non-mutated SARS-CoV-2 virus . To control a pandemic the R-value should be below 1.
Very recently, there are reports for the emergence of further new variants, primarily, the New York variant (B.1.526) and the California variant (B.1.427/B.1.429) which are spreading rapidly. By mid-February 2021, B.1.526 cases had risen to 27% of viral sequences in the database. By January 2021, the California variant accounted to 53% of cases sampled.
A snapshot on the emerging new mutant strains of SARS-CoV-2 virus
|Source country||Detection time||Strain/variant name||Key mutations in spike protein||Transmission rate||References|
|UK||Late September 2020||B.1.1.7||N501Y, P681H, deleted 69–70||Very high, linked to 60% of local cases in UK since detection, spread to over 50 countries.|||
|P.1 or B.1.1.248||N501Y & K417T. There is also an escape mutant known as ‘escape mutation’ or E484K||Very high with high transmission rate and has been detected in Japan, Germany, and some other countries|||
|South Africa||Early October|
|1.351||N501Y & K417N|
There is also an escape mutant known as ‘escape mutation’ or E484K
|Increased transmissibility and has already spread to 20 countries|||
|Ney York, USA||Late 2020||B.1.526||E484K and S477N||Has not been reported in any other country. However, the numbers are increasing in New York, USA|||
|California, USA||Late November 2020||B.1.427/B.1.429||L452R||By January 2021, the variant accounted for 53% of cases sampled.|||
Genetic mutations of viruses is a common phenomenon, and currently, 4000 mutations in the spike protein of SARS-CoV-2 have already been identified and most of them do not have any effect on the virus in regard to its ability to spread or cause disease . However, the Brazilian P.1, UK B.1.1.7, and South African 1.351 mutations are dangerous as they possess features such as, escape from the immune system, bind strongly with ACE2 receptor and may cause more harm [10,14].
More specifically the UK B.1.1.7 strain has received considerable attention due to its high transmissibility rate and has been identified by a unique number and combination of mutations. Currently 17 unique mutations with the UK variant have been identified .
It is unclear whether mutations or combination of mutations are responsible for increased transmissibility of the UK B1.1.7 strain. In addition, it is speculated that the South African 1.351 mutant strain, has mutations located on the spike protein which helps strong binding to angiotensin-converting enzyme 2 (ACE2) and eventually contributes to higher transmission .
Furthermore, mutations are known to help the virus to escape the immune system or replicate more efficiently once in the host. The Brazilin (P.1) strain also contains an escape mutant known as E484K where the negatively charged (E, glutamic acid) is substituted with a positively charged amino acid (K, lysine), resulting in a new and stronger binding site of ACE and also aids the virus to escape the immune system, making it more infectious (Figure 1).
Can anti-SARS-CoV-2 vaccines currently in roll-out in many countries, protect against the new SARS-CoV-2 mutants?
The emergence of these new mutant strains could have a great impact on the efficacy of the anti-SARS-CoV-2 vaccines . Most of the vaccines have been designed to target the spike protein to stop its binding with ACE2 receptor. Due to the mutation in the spike protein of the coronavirus, the antibodies produced by the vaccines may not be able to recognize the mutant and hence will fail to neutralize the coronavirus .
The spike region of the SARS-CoV-2 virus has several immunogenic regions. When a person gets infected with the SARS-CoV-2 virus their antibody responses are to specific immunogenic regions in the majority of the population. The vaccines developed thus far, were developed and approved before the emergence of the new highly contagious strains and assumed that current vaccines may not be effective against the new strains .
This notion was further supported in a study where the South African 1.351 variant which has mutations in the immunogenic region of the spike protein and exposed to monoclonal antibodies raised against non-mutant SARS-CoV-2; South African 1.351 strain completely escaped the binding of the monoclonal antibodies .
In another study , blood samples of 20 volunteers who were either vaccinated with Moderna (mRNA1273) or PfizerBioNTech (BNT162b2) vaccines were analyzed to determine the level of anti-SARS-CoV-2 viral antibodies. Eight weeks after the second vaccination, all volunteers demonstrated a high level of IgM and IgG. However, K417N, or E484K, or N501Y mutations had reduced or abolished the neutralization efficiency of 14 out of 17 most potent monoclonal antibodies investigated.
In another study, it was noted that the UK B.1.1.7 strain did not reduce the effectiveness of the vaccine, and, the South African 1.351 strain had slightly reduced effectiveness . In a another study, the efficacy of PfizerBioNTech (BNT162b2) vaccine against UK B.1.1.7 mutated strain was examined .
The neutralizing antibody responses were measured after a single immunization using pseudoviruses expressing the wild-type spike protein or the 8 mutations found in the UK B.1.1.7 strain. The vaccine sera showed a wide range of neutralizing titers of < 1:4 and up to 1:3449 to the wild-type spike protein, and, significantly reduced titers (by 3.85-fold) against UK B.1.1.7 variant .
Likewise, decreased neutralization to UK B.1.1.7 was also noted with 9 out 10 monoclonal antibodies targeting the N-terminal domain and 5 out of 29 targeting the receptor-binding motif of the spike protein. When E484K mutation was introduced there was further loss of neutralization.
Further research is required to determine the impact of these findings on protective vaccine efficacy with the various vaccines in use as the evolving UK B.1.1.7 lineage strain will likely acquire the E484K mutation .
In an another study conducted by University of Texas and Pfizer-BioNTech, three SARS-CoV-2 virus mutants were engineered, namely N501Y, Δ69/70+ N501Y+D614G, and E484K+N501Y+D614G. Neutralization titers of twenty human sera from Pfizer/BioNTech vaccine (BTN162b2) which cross reacted with three engineered mutant virus were 0.81 to 1.46fold compared to the wild type strain titers.
This shows that there may be minimal effect on the vaccine efficacy with viruses bearing these mutations. Further, it was recently announced (February 8, 2021), by the South African authority announced that the AstraZeneca vaccine failed to provide protection against the South African 1.351 mutant strain.
This strain accounts for 90% of new COVID-19 cases in South Africa. As a result, the South African authority decided to hold off the roll-out of AstraZeneca vaccine . Likewise, most of the approved vaccine has demonstrated similar effectiveness trend. A summary of the effectiveness of approved vaccines against mutated strains are presented in Table 2.
Table 2. – Summary of the effectiveness of some approved vaccines against new variants 
|Vaccine||Neutralizing antibody against variants|
|BioNTech-Pfizer (BNT162b2)||Slightly less effective against the UK and South African strain, effective against Brazil strains. Its effectiveness against New York and California strains have not been reported yet|
|Astra Zeneca- University of Oxford (AZD1222)||Effective against UK, Brazil but not against South African strains. Its effectiveness against New York and California strains has not been reported yet|
|Moderna vaccine (mRNA-1273)||Its effectiveness against UK strain has been reported. However, no effectiveness data against Brazil, South African, New York, and California strain has been reported yet.|
|Johnson & Johnson Vaccine (Ad26.COV2.S)||Effective against UK, Brazil, and South African variants. No specific data is available against New York and California strain|
|Russian vaccine (Sputnik V)||No specific data is available on its effectiveness against new variants.|
|SinoVac Vaccine (Coronavac)||Effective against UK and South African strain. No specific data is available against Brazil, New York, and California strain|
|Indian vaccine (Covaxin)||Effective against UK strain. No specific data is available against Brazil, South African, New York, and California strain|
|CanSinoBio (Convidecia)||Not reported.|
|SinoPharma (BBIBP-CorV)||Effective against South African strain. No specific data is available against UK, Brazil, New York, and California strain|
It is clear that some of the current vaccines may not be as effective against the new emerging mutant strains and further studies are required to ascertain this. If they are not effective, new vaccines may be required to be developed. This is not uncommon and as seen with the influenza virus, vaccines are needed to be updated regularly in order to increase the protection capacity against new mutated strains.
Moderna, USA recently reported that they are developing booster doses to cover the new strains . PfizerBioNTech are also moving forward to include mutated South African 1.351 strain into their vaccine. It is likely that there will be another long wait to get the new vaccine, causing further international travel bans, local lockdowns, restrictions, and an increase in the number of infections, deaths, and economic loss .
reference link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8074646/
More information: Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants, Science (2021). DOI: 10.1126/science.abh1139 , science.sciencemag.org/content … 5/19/science.abh1139