Study population and setting
This study described the recent emergence of a new SARS-CoV-2 variant of concern, B.1.526, in New York. Other variants of concern (B.1.1.7, B1.351, and P.1) carry mutations in spike protein (E484K and N501Y) that may lead to increased levels of transmission or immune escape. In order to better monitor the prevalence of these SARS-CoV-2 variants, researchers developed a PCR-based genotyping assay (targeting the E484K and N501Y mutations) that was used to screen a randomly-selected subset of SARS-CoV-2 positive samples (n=1,142) collected at Columbia University Irving Medical Center (New York City) between November 2020 and February 2021. Patient metadata were extracted from electronic health records stored in Columbia’s COVID-Care database. Whole genome sequencing was completed for all samples with cycle threshold [Ct] values <35 that had positive genotyping results and for a random subset of those with negative results. Sequences that were positive for either mutation (n=65, 5.7%) were used for phylogenetic analyses, along with a diverse set of SARS-CoV-2 global background sequences (n=140). Mutational profiling was completed by aligning variant spike sequences to the Wuhan-Hu-1 reference genome (NC_045512). A pseudovirus-based assay was used to quantify the effect of the E484K mutation on viral neutralization with monoclonal antibodies, convalescent plasma, and sera from vaccinated persons.
Summary of Main Findings
The genotyping assay identified 83 (9.0%) samples with the E484K mutation and 17 (1.8%) samples with the N501Y mutation; one sample had both mutations. The prevalence of cases that were positive for the E484K mutation increased over time from 1.3% in November to 12.3% in February. The results of the genotyping assay were successfully confirmed by whole genome sequencing for all samples tested. Patients infected with E484K variants vs. wildtype SARS-CoV-2 were older (58.1 vs 52.4 years) and were more likely to visit the emergency room or require hospital admission (85.9% vs 70.8%), but E484K status did not appear to impact overall rates of ICU admission. Phylogenetic analysis revealed that most samples with the E484K mutation (n=49) clustered together in a single, newly-identified lineage (B.1.526) with several mutations in spike protein (L5F, T95I, D253G, E484K, D614G, and A701V). Public SARS-CoV-2 sequence databases contained an additional ~140 genomes (from the Northeastern US) that were highly similar to the B.1.526 lineage, suggesting that it may be spreading throughout the region. Neutralizing antibody activity against a SARS-CoV-2 pseudovirus modified to contain the E484K mutation was significantly reduced for monoclonal antibody treatments (REGN10933, CB6, and LY-CoV555), convalescent plasma, and sera from persons vaccinated with either the Pfizer or Moderna vaccines. These results imply that spread of containing the E484K mutation (including B.1.526) could have significant clinical consequences, as this mutation may negatively impact the efficacy of antibody-based treatment and prevention modalities.
Positive genotyping results for both mutations of interest (E484K and N501Y) were verified using whole genome sequencing. Further, functional impact of the E484K mutation on neutralization was quantified using an in vitro assay.
Samples were collected at a single tertiary care center. Although B.1526 samples originated from diverse neighborhoods, the majority came from two distinct communities. A broader sample would provide more information about the spread of this new variant. Functional relevance of lineage-defining mutations was assessed based on the impact of a single mutation (E484K) in the context of an in vitro pseudovirus assay. Impact of all lineage-defining mutations in combination was not assessed, and no clinical data is presented confirming viral immune escape for patients infected with E484K variants.
This study describes the use of genomic surveillance to identify a newly-emergent SARS-CoV-2 variant of concern, B.1.526, in New York City between November 2020 and February 2021. This study also presents in vitro data suggesting that the E484K mutation (found in B.1.526 and other variants of concern) contributes to a loss of neutralizing antibody activity against viruses carrying the mutation.
This review was posted on: 9 April 2021