Using pseudoviruses with single amino acid substitutions, researchers found that mutations in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reduce monoclonal antibody neutralization differently. However, convalescent sera samples did not lose neutralization potency many and were also effective against the B.1.1.7 (UK-derived) strain.
As SARS-CoV-2 continues to infect people around the world, it is also mutating. The majority of the mutations are on the virus spike protein, the key viral component that binds to host cells and the main antigenic target for vaccines and antivirals. Since many vaccines, and antibodies from a previous infection, are based on the earlier circulating strains, it is unknown how immunity will be affected by the new strains.
One way to look for potential escape mutations is to look at sites of amino acid variation and compare them to the closest virus to SARS-CoV-2, the severe acute respiratory syndrome coronavirus (SARS-CoV) – the pathogen responsible for the SARS epidemic in China from 2002-4. Although both have different disease dynamics and outcomes, they target the human angiotensin-converting enzyme 2 (ACE2) for viral entry and share about 75% of the amino acids in the spike protein.
New mutations of SARS-CoV-2 have been reported from the UK (B.1.1.7), South Africa (B.1.351), and Brazil (P.1). All have mutations in the spike protein receptor-binding domain (RBD). The mutations in the South African and Brazilian strains are believed to reduce the potency of current vaccines to neutralize the virus.
In a new study published in Cell Reports, researchers report the results of their investigation on how individual virus amino acid substitutions can help the virus to escape neutralizing antibodies.
Amino acid substitutions affect antibody neutralization
Of the 56 amino acid differences between the RBD of SARS-CoV and SARS-CoV-2, the researchers looked at 15 that had amino acid substitutions with a significant change in the biochemical character of the amino acid as well as changes that occurred in sequential positions. They mutated these positions on the SARS-CoV-2 spike protein to match those of SARS-CoV and produced 12 pseudoviruses. They tested the neutralization effect of monoclonal antibodies derived after SARS-CoV-2 infection. These antibodies were categorized into different clusters based on the regions they target.
Three of the 12 pseudoviruses had no effect on the neutralization activity of the antibodies tested. The team identified seven mutations on the spike protein that reduced the neutralization effect of at least one antibody. The most detrimental effect was seen in the TEI470-2NVP triple substitution, which reduced the potency of nearly all monoclonal antibodies.
The neutralization effect is not based only on where the antibodies bind, as antibodies binding to the same area are affected differently depending on the amino acid substitution.
The team tested the neutralization effect of sera collected from recovered patients on these mutations and found that the decrease in their potency was less than that of the individual monoclonal antibodies. Sera collected from patients with severe COVID-19 lost less of the neutralization potency compared to sera from patients with mild disease. This may likely be because of greater polyclonality from the greater antigenic stimulation during severe illness.
Virus may continue to mutate
Although the researchers investigated several amino acid substitutions, none of these have been seen frequently in the circulating SARS-CoV-2 strains. So, they added the mutations caused by the B.1.1.7 variant to their tests. They found that of the mutations, the N501Y reduced the neutralization potency of monoclonal antibodies dramatically, whereas the mutation had less effect on the neutralization potency of convalescent sera. All the sera samples neutralized the B.1.1.7 variant, and only about 10% of the sera samples lost their neutralization potency.
This suggests the different antibodies in the sera target the virus targets in slightly different ways, making them less sensitive to spike mutations. However, studies have shown that the B.1.351 (or South Africa-derived) strain is resistant to neutralization by a large fraction of convalescent sera. It is possible that a combination of mutations could lead to a greater neutralization effect than single amino acid substitutions.
Thus, the results suggest most vaccines should be effective against the B.1.1.7 strain, as the sera used in the tests were obtained in early 2020, and the circulating virus strain then is similar to those in the vaccines.
The study only analyzed RBD mutations, but other possible areas of mutations include the N-terminal domain, which should be studied further. As the population’s seropositivity increases either because of natural infection or vaccination, there could be a selection for spike mutations leading to considerable mutations and antigenic drift, which will require continued investigations and may affect vaccine efficacy.