Heterogeneous infectivity of SARS-CoV-2 mutants that correlate with prevalence

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) caused a pandemic of coronavirus disease 2019 (COVID-19). Despite the rapid development of vaccines, the emergence of new variants of the virus, some with higher infectivity and some with antigenic escape, has led to continued spread of the virus.

Journal’s new paper Cell report Describes the role of mutations in the receptor binding domain (RBD) of Spike protein Generation of antibody resistance and loss of vaccine efficacy.

Preface

Given the many variants identified so far, the need to study the status of antigens in relation to viral orientation and other biological effects is clear. In the current study, a large number of RBD variants registered in the published SARS-CoV-2 genomic database, a total of 129 variants, 24 double mutant RBDs, and variants of concern or interesting variants (VOCs). Focuses on 11 variants of the virus. / VIO), respectively.

They were expressed in lentivirus pseudo-particles (LVpp) and their infectivity was measured against cells expressing the heterologous angiotensin converting enzyme 2 (ACE2) receptor from 18 animal species.The ability to neutralize these various particles has been measured using humans Convalescent plasma Polyclonal antibodies from sera from samples (HCPs), vaccines or vaccine candidates, and monoclonal antibodies (mAbs).

Scientists have also tracked the correlation between mutations in circulating RBD variants and the potential for cross-species infection and antibody avoidance.

What did the study show?

The results showed that of the 129 RBD mutants, 17 showed a 50% or greater reduction in spike expression compared to the wild-type D614G strain, whereas about 5% showed a significant reduction in spike expression. .. This was converted to a loss of more than five times the infectivity for wild-type mutants, while other mutants showed a slight increase.

SARS-CoV-2 spikes efficiently bound to 13 of the 18 ACE2 orthologs, and further analysis showed strong ACE2 spike binding. Pseudovirus infection assays have confirmed that wild-type viruses can easily infect most cell lines except for the five with insufficient ACE2 spike binding. Therefore, ACE2 spike binding correlates well with the infectivity of ACE2-expressing cells.

Most RBD mutants also showed equivalent binding to ACE2 in cells that support spike binding by wild-type virus, with the exception of 17, which reduced spike expression. Certain mutations resulted in a significant improvement or loss of infectivity. For example, in cells expressing mouse ACE2, the presence of K417N, E484K, and N501Y resulted in a sharp increase in infectivity.

In the horseshoe-shaped bat ACE2, E484K has a major influence, and among mutations such as V382L, N440K, G476S, P521R, and A522S, the infectivity has increased more than 3 times. Other mutations resulted in improved infection rates with whale ACE2 expression.

All mutants with the N501Y mutant, especially the alpha, beta, gamma, and omicron mutants, showed a 100-fold increase in infectivity against mouse ACE2-expressing cells. Other mutants containing E484K instead of N501Y showed 10-30 times higher infectivity in these cells. Certain mutations, such as L452R, appear to produce synergistic effects because they increase infectivity when present with other mutations.

Omicron showed increased infectivity in ferret ACE2-expressing cells, probably due to the N440K mutation.

Neutralizing activity was checked and 9 mAbs were used for 48 mutants with receptor binding motif (RBM) mutations. Only one of these mAbs, 4A8, binds to the N-terminal domain (NTD) of the spike and the other mAbs interact with the RBD.

Antibodies include humans, humanized mice, and mouse mAbs and belong to classes 1 to 4 depending on the recognition mode of the antigen. Antigenic escape was considered to occur when the concentration required to suppress the invasion of 50% of the particles (IC50) was reduced by more than 4-fold compared to wild-type spikes.

The findings showed that the relative neutralizing potency was reduced by up to 100-fold by E484K mutations, including those of Regeneron mAb REGEN 10933 and the human antibody COVA 2-15. With the exception of the latter antibody, similar effects were seen with the E484A mutation.

The N501Y mutation reduced the relative neutralizing ability of COVA2-15 by a factor of 14. K417N reduced the neutralizing power of REGEN10933 by more than 40 times. Mutations in the aa444-456 and aa484-494 regions reduce neutralization and promote immune avoidance. Neutralizing antibody Target RBD.

Neutralization by HCP

HCPs from the first wave of COVID-19 were found to have various cross-reactivity to viral variants. Mutations surrounding aa439-448 and aa484 appear to significantly affect neutralization by HCP antibodies, indicating that they are two essential antigenic regions.

All three HCP antibodies completely lost their neutralizing power against Omicron, while other mutants, including beta, gamma, and E484K, showed resistance to P020.

According to the author

Omicron showed the most pronounced resistance of all subspecies. “

Neutralization with vaccine serum

Vaccine-induced antisera in mice and monkeys appeared to have a cross-neutralization profile similar to human HCP antibody P020. The largest escape occurred again in Omicron, and mutants containing E484K showed neutralization resistance.

The third booster shot explains why vaccine antisera appear to have higher VOC / VIO neutralizing titers than HCP. This is due to the increased titer of nAbs, especially for most mutants except the delta mutant.

These data appeared to be consistent with the finding that triple doses of mRNA vaccination help induce human crossvariant neutralizing antibodies... “

Nevertheless, nAbs for mutants with a well-defined antigen profile remained several times lower than for wild-type.

Prevalence associated with interspecific infectivity

Interestingly, changes in infectivity with each single mutant RBD variant of other animal species compared to wild type were associated with cumulative prevalence of the mutant.

Interspecific infectivity (CSI) scores derived from the relative infectivity of ACE-carrying cells of ferrets and mice correlated with the cumulative prevalence of human-derived viral sequences. Further analysis revealed that the most common mutations in human-derived viral RBD sequences were T478K (cumulative prevalence = 59%), L452R (59%), N501Y (22%), E484K and S477N (<5% respectively). Was shown to be.

The higher the likelihood of interspecific transmission, the higher the cumulative frequency of RBD mutations, indicating that interspecific spillover may be important in maintaining transmission of the virus in humans and animals. I am.

Implications

In this fascinating study, researchers found that circulating variants of SARS-CoV-2 infect cells with different forms of ACE2 receptors in other species and become a virus for other mammals, including aquatic organisms. Showed that can be directed.

The most resistant to infection were ACE2 in ferrets, horseshoe bats, mice, tupara and brown trout, which can be overcome by RBD mutations such as K417N, E484K and N501Y, especially in the first three species and orders. .. These are found in some varieties.

In particular, the spillover to these species is an epidemiological concern, as both mice and ferrets are abundant and inhabit in the immediate vicinity of humans. These mutations increased the susceptibility of mice to alpha, beta, and gamma mutants in addition to omicrons compared to their initial resistance to ancestral mutants.

Mink susceptibility has been previously demonstrated, with pre- and post-infections between farmed mink and farmers. The Y453F mutation of SARS-CoV-2 from mink showed adaptation to the virus by these animals and increased infectivity. This study suggests that today’s VOCs / VIOs are more infectious in ferrets, and perhaps even mink.

Increased likelihood of RBD mutant infection in animals can expand the host range of SARS-CoV-2 and cause cross-species spillover.. “

These mutations often also appear to promote antigenic escape, as evidenced by a multi-fold increase in neutralization resistance with Omicron VOCs. Even after three doses of the vaccine, serum samples continued to show much lower neutralizing antibody titers against Omicron compared to other mutants. New vaccines need to leverage their current knowledge of the antigen profile of these new mutants and use mutation patches to elicit broadly neutralizing antibodies that can neutralize multiple mutants.

These findings highlight interspecific spillovers that can be caused by antigenic drift and viral genetic alterations, leading to the prediction and monitoring of SARS-CoV-2 spike mutations... “