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Tag: geographic spread
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[Pre-print, not peer-reviewed] By February 2021, the SARS-CoV-2 B.1.526 lineage accounted for approximately 32% of 3,288 sequenced genomes from specimens collected in New York City.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 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[Pre-print, not peer-reviewed] A SARS-CoV-2 variant (named B.1.x) may be an emerging lineage that has been poorly recognized due to a deletion mutation that causes the submission of its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…
March 30, 2021
Preliminary Report on SARS-CoV-2 Spike Mutation T478K
[Pre-print, not peer-reviewed] A novel mutation (T478K) located on the SARS-CoV-2 spike protein was identified in an analysis of over 820,000 genomic sequences deposited on the global genome database GISAID up to March 26, 2021. Since its identification in the beginning of 2021, T478K is present in almost 2% of all sequenced genomes. Among the…
March 25, 2021
Emergence of the E484K Mutation in SARS-CoV-2 Lineage B.1.1.220 in Upstate New York
[Pre-print, not peer-reviewed] A novel SARS-CoV-2 variant (assigned name B.1.1.220) was detected by ongoing surveillance in samples collected in early February in four patients in upstate New York. B.1.1.220 was characterized with the E484K substitution in the spike protein, also present in the B.1.351 variant that was first described in South Africa and the P.1…
March 3, 2021
Sequence Analysis of 20453 SARS-CoV-2 Genomes from the Houston Metropolitan Area Identifies the Emergence and Widespread Distribution of Multiple Isolates of All Major Variants of Concern
[Pre-print, not peer-reviewed] Genomic sequencing of 20,453 virus specimens in Houston, Texas identified the presence of all variants of interest or concern (n=23 of B.1.1.7, n=2 of B.1.351, n=4 of P.1, and n=143 of B.1.429 and n=19 of B.1.427). None of the affected patients were from a common household or reported recent international travel, suggesting…
Travel from the United Kingdom to the United States by a Symptomatic Patient Infected with the SARS-CoV-2 B.1.1.7 Variant — Texas, January 2021
On January 10, 2021, an individual infected with the SARS-CoV-2 B.1.1.7 variant was identified in Texas. No secondary cases with epidemiologic links to the patient have been identified to date. A case investigation revealed that the individual had traveled to the United Kingdom during November 13–December 30, 2020, and reported having been exposed to a…
First Identified Cases of SARS-CoV-2 Variant P.1 in the United States — Minnesota, January 2021
On January 25, 2021, the Minnesota Department of Health identified the first US cases of infection with the SARS-CoV-2 variant of concern P.1 (first identified in persons from Brazil) in two individuals, one of whom had a recent travel history to Brazil. Whole genome sequencing revealed identical sequences from both individuals, who lived in the…
February 23, 2021
Characterizing SARS-CoV-2 Genome Diversity Circulating in South American Countries: Signatures of Potentially Emergent Lineages?
Analysis of nearly 6,000 publicly available SARS-CoV-2 genome assemblies in South America identified a total of 169 circulating lineages across 16 South American countries, with the B lineage the predominantly circulating lineage. Lineages of concern that were identified include the P.1 variant (94 genomes) and the B.1.1.7 variant (28 genomes), with both variants displaying 33…
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