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Tag: geographic spread
June 15, 2021
Rapidly Emerging SARS-CoV-2 B.1.1.7 Sub-Lineage in the United States of America with Spike Protein D178H and Membrane Protein V70L Mutations
Genomic surveillance of SARS-CoV-2 cases identified an expanding US-specific sub-lineage of the B.1.1.7 (Alpha) variant. This sub-lineage is characterized with sequential acquisition of a membrane protein mutation, V20L, in November 2020 and a spike mutation, D178H, in early February 2021. The proportion of B.1.1.7 (Alpha) isolates in the US belonging to this sub-lineage increased from…
June 10, 2021
Genomic Surveillance for SARS-CoV-2 Variants Circulating in the United States, December 2020–May 2021
During April 11-24, 2021, the SARS-CoV-2 B.1.1.7 (Alpha) variant accounted for an estimated 66% of US infections and the P.1 (Gamma) variant accounted for 5% of US infections, according to the CDC. Estimates are based on sequencing of 25,000 SARS-CoV-2-positive specimens, representing 3% of all reported positive tests and weighted to the general population. Estimated…
June 7, 2021
2020 SARS-CoV-2 Diversification in the United States Establishing a Pre-Vaccination Baseline
[Pre-print, not peer-reviewed] A study investigating SARS-CoV-2 genetic diversity in the US using sequences publicly available prior to December 15th, 2020, when vaccination was initiated in the U.S., found that the regional distribution of COVID-19 cases varied by pandemic phase and was not always correlated with the level of viral sequencing in different regions. In…
June 2, 2021
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[Pre-print, not peer-reviewed] Analysis of over 1 million SARS-CoV-2 genomes identified 115 non-synonymous mutations estimated to be present in 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 27, 2021
Emergence of a New SARS-CoV-2 Variant from GR Clade with a Novel S Glycoprotein Mutation V1230L in West Bengal India
[Pre-print, not peer-reviewed] Genomic surveillance detected a potential new variant emerging in West Bengal, India from an analysis of over 2,000 sequenced samples collected from January to March 2021. The new variant, identified in 70 of 412 sequences submitted from West Bengal, is characterized by 11 mutations including V1230L and P681H, also found in the…
May 21, 2021
Emergence and Spread of the Potential Variant of Interest (VOI) B.1.1.519 Predominantly Present in Mexico
[Pre-print, not peer-reviewed] Investigators described the emergence and spread of a novel SARS-CoV-2 variant of interest (B.1.1.519) in Mexico with mutations T478L, P681H, and T732A in the spike protein. Out of 2,692 SARS-CoV-2 samples analyzed for genomic sequence between March 1, 2020 and March 21, 2021, 37.8% were B.1.1.519. The variant was not detected prior…
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…
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