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Topic: Geographic Spread
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[Pre-print, not peer-reviewed] A novel mutation (T478K) located on the SARS-CoV-2 spike protein was identified in an analysis of over 820,000 genomic sequences deposited on the global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 8, 2021
The Emergence and Ongoing Convergent Evolution of the N501Y Lineages Coincides with a Major Global Shift in the SARS-CoV-2 Selective Landscap
[Pre-print, not peer-reviewed] A study examining patterns of SARS-CoV-2 mutations via phylogenetics-based analyses found evidence for changes in the selective pressures of specific SARS-CoV-2 genes (such as N and S) that likely coincided with the emergence of the three main 501Y lineages (B.1.1.7, B.1.351, P.1). The analysis included all SARS-CoV-2 sequences in GISAID assigned to…
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[Pre-print, not peer-reviewed] Genomic sequencing of 20,453 virus specimens in Houston, Texas identified the presence of all variants of interest or concern (n=23 of B.1.1.7, n=2 of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 24, 2021
Nonmetropolitan COVID‐19 Incidence and Mortality Rates Surpassed Metropolitan Rates within the First 24 Weeks of the Pandemic Declaration: United States, March 1–October 18, 2020
The incidence and mortality trends of COVID-19 in rural counties increased and surpassed those in metropolitan areas beginning in early August 2020. Residents of nonmetropolitan counties accounted for 14% of the 8,085,214 confirmed COVID‐19 cases and 11% of the 217,510 deaths in the United States from March 1-October 18, 2020. The average daily COVID‐19 incidence rate over 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…
February 17, 2021
Early Introductions and Community Transmission of SARS-CoV-2 Variant B.1.1.7 in the United States
[Pre-print, not peer-reviewed] Using combined data from UK air travel into US airports, SARS-CoV-2 genomic sequencing, and clinical diagnostics, a study found evidence for multiple independent introductions of the SARS-CoV-2 B.1.1.7 variant (first described in the UK) into the US, many of which have led to sustained community transmission. The authors conclude that the high…
Detection of B.1.351 SARS-CoV-2 Variant Strain — Zambia, December 2020
The SARS-CoV-2 variant strain B.1.351 (first described in South Africa) was detected in Zambia in specimens collected from December 16–23, 2020. Among 23 specimens collected during this time, 22 (96%) were the B.1.351 variant, and among those 21 (95%) contained all nine B.1.351 lineage-defining mutations. Specimens with the B.1.351 variant were obtained from people across…
First Identified Cases of SARS-CoV-2 Variant B.1.1.7 in Minnesota — December 2020–January 2021
On January 9, 2021, the Minnesota Department of Health announced the identification of the B.1.1.7 SARS-CoV-2 variant (first described in the UK) in specimens from five people, and on January 25, this variant was found in samples from three additional people. The samples were collected between December 18, 2020 and January 11, 2021 from residents…
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