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Tag: variants
June 7, 2021
Early Epidemiological Signatures of Novel SARS-CoV-2 Variants Establishment of B.1.617.2 in England
[Pre-print, not peer-reviewed] A study in the UK suggested that many SARS-CoV-2 cases were S-gene positive, a pattern associated with the B.1.617.2 variant, which the authors suggest may become dominant over B.1.1.7. In early 2021, the majority of positive SARS-CoV-2 tests in England were genomically sequenced (74% in April 2021), with the sequencing subject to…
June 4, 2021
Variant-of-Concern-Attributable Health and Health System-Related Outcomes a Population-Level Propensity-Score Matched Cohort Study
[Pre-print, not peer-reviewed] A population-based propensity-score matched cohort study of all incident laboratory-confirmed COVID-19 cases in Ontario, Canada found that SARS-CoV-2 variants of concern are associated with a higher odds of hospitalization (OR=2.3), ICU admission (OR=3.3), and mortality among persons hospitalized (OR=1.6) and not hospitalized (OR=1.8) for COVID-19 relative to earlier wild-type strains. The findings…
Interim Estimates of Increased Transmissibility Growth Rate and Reproduction Number of the Covid-19 B.1.617.2 Variant of Concern in the United Kingdom
[Pre-print, not peer-reviewed] A modeling study found that the effective reproduction number of B.1.617.2 (WHO label Delta, first described in India) is almost certainly higher than that of B.1.1.7 (WHO label Alpha). The study used genomically sequenced cases from the UK diagnosed between March and May 2021 and excluded recent travelers in order to reflect…
June 3, 2021
Structural Analysis of the Novel Variants of SARS-CoV-2 and Forecasting in North America
A forecasting model incorporating North American prevalence of SARS-CoV-2 variants of concern from the genome database GISAID suggests that the B.1.1.7 variant could become dominant (>60% of sequenced strains) by summer 2021 but would sharply decrease in frequency when 75% of the population is immune through vaccination or natural infection due to its high binding…
June 2, 2021
Mechanistic Modeling of SARS-CoV-2 Immune Memory Variants and Vaccines
[Pre-print, not peer-reviewed] The COVID-19 transmission model Covasim, with updated methods accounting for trajectories in immune response, SARS-CoV-2 variants, and vaccine roll-out, found that neutralizing antibodies (NAbs) correlated strongly with infection blocking. The model suggests Nabs elicited by natural infection may provide more protection than the same level of Nabs elicited by vaccines; however, vaccines…
Emerging SARS-CoV-2 Variants of Concern Evade Humoral Immune Responses from Infection and Vaccination
[Pre-print, not peer-reviewed] Anti-SARS-CoV-2 antibody binding and neutralizing activity in sera of both convalescent individuals who had recovered from infection that occurred prior to the spread of variants of concern (VOC) (n=69) and recipients of the Pfizer-BioNTech vaccine (n=50) were reduced against the B.1.1.7, B.1.351, and P.1 VOC, according to a cohort study. The largest…
Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes
Sera collected from individuals with SARS-CoV-2 infection prior to April 2020 (n=18) neutralized pseudoviruses with the mutated spike proteins of variants of concern, including B.1.1.7, B.1.351, and B.1.1.248, with only a minor loss in neutralizing activity. Similarly, neutralizing activity among individuals fully vaccinated with the Pfizer-BioNTech vaccine (n=5) were only reduced up to 3-fold by…
Analysis of SARS-CoV-2 Mutations Reveals Three Types of Temporal Dynamics and One Is Correlated with International Travels
[Pre-print, not peer-reviewed] Analysis of over 1 million SARS-CoV-2 genomes identified 115 non-synonymous mutations estimated to be present in >3% of global COVID-19 cases. COVID-19 cases were identified from 714 country-month combinations from 98 countries. High frequency mutations were defined as frequency changes occurring between a >15% increase and <5% decrease over 2 months, including…
May 28, 2021
Reduced Sensitivity of Infectious SARS-CoV-2 Variant B.1.617.2 to Monoclonal Antibodies and Sera from Convalescent and Vaccinated Individuals
[Pre-print, not peer-reviewed] The SARS-CoV-2 B.1.617.2 variant of concern, first described in India, was experimentally shown to completely escape neutralizing activity from the monoclonal antibody (mAb) bamlanivimab (made by Eli Lilly), while neutralizing activity of etesivimab (also Eli Lilly), casirivimab and imdevimab (Regeneron) were preserved. Neutralizing activity of sera from 56 individuals recovered from critical,…
E484K as an Innovative Phylogenetic Event for Viral Evolution: Genomic Analysis of the E484K Spike Mutation in SARS-CoV-2 Lineages from Brazil
Genomic and phylogenetic analyses of SARS-CoV-2 genomes with the E484K mutation sequenced from samples in Brazil in 2020 showed that over 40% of sequenced genomes had this mutation by October 2020 across three distinct lineages (P.1, P.2, and N.9) in four different regions. Modeling of a random set of sequenced genomes suggests that the mutation…
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