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Tag: variants
February 11, 2021
Detection Of Genomic Variants Of SARS-CoV-2 Circulating In Wastewater By High-Throughput Sequencing
[Pre-print, not peer reviewed] Analysis of 40 Spanish wastewater samples obtained between April and October 2020 identified three variants with mutations in the spike protein not previously detected elsewhere and 7 non-synonymous spike protein mutations not previously detected in Spain. Three of these 7 mutations have been found at low frequencies in sequencing of genomes…
Novel SARS-CoV-2 Variant Identified in Travelers from Brazil to Japan
A novel SARS-CoV-2 strain was detected in 4 travelers flying from Brazil to Japan on January 2, 2021. Whole genome sequencing suggests the variant descends from the P.1 lineage with 12 nonsynonymous mutations in the receptor-binding domain (RBD) of the spike protein, including the K417T, E484K, and N501Y mutations also present in the B.1.1.7 and…
Emergence of a Novel SARS-CoV-2 Variant in Southern California
A novel variant of SARS-CoV-2 called “CAL.20C” was identified in Southern California and emerged contemporaneously with a local surge in cases. The authors define the variant on the basis of three mutations in the S-protein (S13I; W152C; and L452R) which differentiate the subclade from the 20C clade currently predominant in North America. The functional effect…
February 10, 2021
Neutralization of SARS-CoV-2 Spike 69/70 Deletion, E484K and N501Y Variants by BNT162b2 Vaccine-Elicited Sera
Human sera from 20 participants who received both doses of the Pfizer/BioNTech vaccine showed equivalent neutralization titers (with differences of four-fold or less) between wild type and variants strains of SARS-CoV-2 viruses that were engineered to contain spike proteins from recently emerged variants. The combinations of mutations included N501Y (present in variants emerging from the…
February 9, 2021
UK coronavirus variant detected at the UW (Message to Seattle students and employees)
[Press release, not peer-reviewed] The B.1.1.7 variant (first described in the UK) was identified in a sample obtained from a University of Washington student in late January 2021. Genetic sequencing occurred as part of the Husky Coronavirus Testing program and was performed on February 8, 2021. The student is doing well and out of their…
February 8, 2021
Infection and MRNA-1273 Vaccine Antibodies Neutralize SARS-CoV-2 UK Variant
[Pre-print, not peer-reviewed] A study using a live virus neutralization assay to compare potency of neutralization between people who had been infected with SARS-CoV-2 or had received the Moderna COVID-19 vaccine against a panel of SARS-CoV-2 variants showed that antibodies in sera from both groups were effective at neutralizing the B.1.1.7 variant. Serum neutralization titers…
Implementation of an In-House Real-Time Reverse Transcription-PCR Assay for the Rapid Detection of the SARS-CoV-2 Marseille-4 Variant
[Pre-print, not peer-reviewed] A study evaluating an in-house, real-time RT-PCR (qPCR) assay to detect a SARS-CoV-2 variant with an S477N substitution in the receptor binding domain associated with increased binding affinity to ACE2 found that the assay reliably detected this variant. All 6 cDNA samples from the variant strains tested positive using the assay, whereas…
Field Performance Evaluation of the PanBio Rapid SARS-CoV-2 Antigen Assay in an Epidemic Driven by 501Y.v2 (Lineage B.1.351) in the Eastern Cape South Africa
[Pre-print, not peer-reviewed] A prospective diagnostic evaluation of the field performance of the Abbott PanBio antigen test indicated that the assay reliably detected SARS-CoV-2 variant 501.V2 (lineage B.1.351) infections in patients presenting at mobile community testing centers in South Africa, with sensitivity strongly dependent on viral load (100% detection if cycle threshold (CT) was <20,…
Genetic Conservation of SARS-CoV-2 RNA Replication Complex in Globally Circulating Isolates and Recently Emerged Variants from Humans and Minks Suggests Minimal Pre-Existing Resistance to Remdesivir
A study analyzing the genetic diversity of the RNA replication complex that is targeted by the antiviral drug remdesivir in a large set of human SARS-CoV-2 isolates (n > 90,000), including the B.1.1.7 and 501.V2 variants and mink isolate (n>300) sequences, found that previously-identified amino acid substitutions that caused reduced susceptibility to remdesivir in-vitro were…
Genomic Epidemiology Identifies Emergence and Rapid Transmission of SARS-CoV-2 B.1.1.7 in the United States
[Pre-print, not peer-reviewed] Sequencing of 212 B.1.1.7 SARS-CoV-2 variant genomes collected from testing facilities in the U.S. between December 2020 to January 2021 found that while the proportion of B.1.1.7 variants among S gene target failure samples varied by state, detection of the variant had a doubling rate of a little over a week and…
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