Result for
Topic: Geographic Spread
May 10, 2021
Travel-Driven Emergence and Spread of SARS-CoV-2 Lineage B.1.620 with Multiple VOC-like Mutations and Deletions in Europe
[Pre-print, not peer-reviewed] There is evidence from sequencing data from GISAID that the SARS-CoV-2 B.1.620 variant, which shares mutations and deletions common to variants of concern (VOCs), including E484K, S477N, HV69Δ, Y144Δ, and LLA241/243Δ, is likely contributing to ongoing transmission locally in Lithuania, France, Germany, Spain, Belgium and the Central African Republic. The authors found evidence…
May 5, 2021
Identification of and Surveillance for the SARS-CoV-2 Variants B.1.427 and B.1.429 — Colorado, January–March 2021
The SARS-CoV-2 B.1.427/B.1.429 variant (aka CAL.20C), a variant of concern/interest (VOC/VOI) first described in California, was first detected in Colorado in late January 2021, and increased from 3-4% of all sequenced infections in late January to 20-22% in early March. Cases were dispersed across nearly half of counties. Among 60 cases who completed enhanced interviews,…
Viral Genomes Reveal Patterns of the SARS-CoV-2 Outbreak in Washington State
The rapid spread of the D614G variant in Washington State was a result of multiple introductions into areas with different levels of ongoing lockdown, according to a phylogenetic analysis of 3940 SARS-CoV-2 sequences from Washington State and county-level mobility data collected between February and July 2020. Sequences derived from out-of-state introductions were unevenly distributed, with…
Emergence and Spread of SARS-CoV-2 Lineages B.1.1.7 and P.1 in Italy
Analysis of 6,515 SARS-CoV-2 sequences sampled between January 2020 to March 2021 in Italy found that the previously dominant B.1.177 variant was replaced by the B.1.1.7 variant in January 2021. By the end of the sampling period, B.1.1.7 sequences comprised 34% of all sequences whereas B.1.177 comprised only 24%. Analysis of B.1.1.7 sequences indicated multiple…
May 3, 2021
SARS-CoV-2 Worldwide Replication Drives Rapid Rise and Selection of Mutations across the Viral Genome: A Time-Course Study – Potential Challenge for Vaccines and Therapies
A summary of circulating SARS-CoV-2 mutations in 383,570 complete sequences with known sampling dates in the Global Initiative of Sharing All Influenza Data (GISAID) through April 5, 2021 showed that high incidence of COVID-19 often paralleled high numbers of new mutations and SARS-CoV-2 variant strains. The summary included data from ten countries: the United Kingdom,…
April 23, 2021
Detection and Characterization of the SARS-CoV-2 Lineage B.1.526 in New York
[Pre-print, not peer-reviewed] By February 2021, the SARS-CoV-2 B.1.526 lineage accounted for approximately 32% of 3,288 sequenced genomes from specimens collected in New York City. The lineage was first sequenced in November, 2020, when it accounted for less than 1% of sequenced genomes in the city. Using the Variant Database software, the authors noted that…
April 22, 2021
Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 Isolates from Pennsylvania
[Pre-print, not peer-reviewed] A SARS-CoV-2 B.1.1.7 sequence from Pennsylvania detected in March 2021 was found to have the E484K spike substitution, a mutation shown to confer resistance to neutralizing antibodies. Only 60 isolates with the B.1.1.7+E484K sequence profile have been detected in the US, and only 253 reported globally. Comparative genomic analysis of 235 high…
April 8, 2021
S-Gene Target Failure as a Marker of Variant B.1.1.7 Among SARS-CoV-2 Isolates in the Greater Toronto Area, December 2020 to March 2021
The B.1.1.7 SARS-CoV-2 variant (first described in the UK) rapidly became the dominant circulating strain in the greater Toronto, Canada area between December 2020 and March 2021. Based on PCR S-gene target failure, which is strongly associated with the B.1.1.7 variant, 2% of samples were inferred to be the B.1.1.7 variant in mid-December 2020, which…
April 6, 2021
A New SARS-CoV-2 Lineage That Shares Mutations with Known Variants of Concern Is Rejected by Automated Sequence Repository Quality Control
[Pre-print, not peer-reviewed] A SARS-CoV-2 variant (named B.1.x) may be an emerging lineage that has been poorly recognized due to a deletion mutation that causes the submission of its sequence to be rejected by automated sequence repository quality control in genome databases such as GISAID and Genbank. The variant, which contains a deletion in the…
Genomic Surveillance of Nevada Patients Revealed Prevalence of Unique SARS-CoV-2 Variants Bearing Mutations in the RdRp Gene
A novel SARS-CoV-2 mutation (P323 F/L) in the non-structural protein ORF was identified using a genomic surveillance sample of 200 high quality sequences obtained in Nevada from March to June 2020. Phylogenetic reconstruction of the samples cross-referenced to a subsample of sequences in the Nextstrain global genome database show that variants with the mutation P323L…
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