we sequenced RNA directly from sewage collected by municipal utility districts in the San Francisco Bay Area to generate SARS-CoV-2 genomes. The genotypes detected in the sewage were identical to clinical genomes from the region. Observed wastewater variants were more similar to local California patient-derived genotypes than they were to those from other regions within the United States or globally.

This study demonstrates that intermittent or persistent detection of SARS-CoV-2 RNA in nursing home sewers can provide an early warning of subsequent individual cases or outbreaks in these facilities.

Two new SARS-CoV-2 lineages with the N501Y mutation in the receptor-binding domain of the spike protein spread rapidly in the United Kingdom. We estimated that the earlier 501Y lineage without amino acid deletion ?69/?70, circulating mainly between early September and mid-November, was 10% (6-13%) more transmissible than the 501N lineage, and the 501Y lineage with amino acid deletion ?69/?70, circulating since late September, was 75% (70-80%) more transmissible than 501N.

We performed a whole-blood preserving single-cell analysis protocol to integrate contributions from all major cell types including neutrophils, monocytes, platelets, lymphocytes and the contents of serum. Patients with mild COVID-19 disease display a coordinated pattern of interferon-stimulated gene (ISG) expression across every cell population and these cells are systemically absent in patients with severe disease. Severe COVID-19 patients also paradoxically produce very high anti-SARS-CoV-2 antibody titers and have lower viral load as compared to mild disease.

Severe acute respiratory syndrome coronavirus 2 has caused a pandemic in humans. Farmed mink (Neovison vison) are also susceptible. In Denmark, this virus has spread rapidly among farmed mink, resulting in some respiratory disease. Full-length virus genome sequencing revealed novel virus variants in mink. These variants subsequently appeared within the local human community.

We analyzed 91 wastewater samples from 11 states in the USA, where the majority of samples represent Maricopa County, Arizona (USA). We undertook a single-nucleotide variant (SNV) analysis on data from 52 samples with >90% SARS-CoV-2 genome coverage of sequence reads, and compared these SNVs with those detected in genomes sequenced from clinical patients. We identified 7973 SNVs, of which 5680 were novel SNVs that had not yet been identified in the global clinical-derived data.

Recent emergence of new SARS-CoV-2 variants B.1.1.7 in the UK and B.1.351 in South Africa is of concern because of their purported ease of transmission and extensive mutations in the spike protein. We now report that B.1.1.7 is refractory to neutralization by most mAbs to the N-terminal domain (NTD) of spike and relatively resistant to a number of mAbs to the receptor-binding domain (RBD).

We investigated the distribution of KLRC2 deletion and HLA-E*0101/0103 allelic variants in a study cohort of 361 patients with either mild (N = 92) or severe (N = 269) COVID-19. Both were significantly overrepresented in hospitalized patients, particularly in patients requiring intensive care (p < 0.0001 and p = 0.01), compared with patients with mild symptoms.

Summary: Generation of SARS-CoV-2 spike mutants that escape antibody neutralization. Mutant S477N is resistant to neutralization by multiple monoclonal antibodies. Mutant E484K is less sensitive to neutralization by convalescent human sera. Sequential selection identifies mutants that escape neutralization by antibody cocktails.

We map how mutations to SARS-CoV-2’s receptor-binding domain (RBD) affect binding by the antibodies in the REGN-COV2 cocktail and the antibody LY-CoV016. These complete maps uncover a single amino-acid mutation that fully escapes the REGN-COV2 cocktail. The maps also identify viral mutations that are selected in a persistently infected patient treated with REGN-COV2. The maps reveal that mutations escaping the individual antibodies are already present in circulating strains. Overall, these escape maps enable interpretation of the consequences of mutations observed during viral surveillance.

we sequenced RNA directly from sewage collected by municipal utility districts in the San Francisco Bay Area to generate SARS-CoV-2 genomes. The genotypes detected in the sewage were identical to clinical genomes from the region. Observed wastewater variants were more similar to local California patient-derived genotypes than they were to those from other regions within the United States or globally.

This study demonstrates that intermittent or persistent detection of SARS-CoV-2 RNA in nursing home sewers can provide an early warning of subsequent individual cases or outbreaks in these facilities.

Two new SARS-CoV-2 lineages with the N501Y mutation in the receptor-binding domain of the spike protein spread rapidly in the United Kingdom. We estimated that the earlier 501Y lineage without amino acid deletion ?69/?70, circulating mainly between early September and mid-November, was 10% (6-13%) more transmissible than the 501N lineage, and the 501Y lineage with amino acid deletion ?69/?70, circulating since late September, was 75% (70-80%) more transmissible than 501N.

We performed a whole-blood preserving single-cell analysis protocol to integrate contributions from all major cell types including neutrophils, monocytes, platelets, lymphocytes and the contents of serum. Patients with mild COVID-19 disease display a coordinated pattern of interferon-stimulated gene (ISG) expression across every cell population and these cells are systemically absent in patients with severe disease. Severe COVID-19 patients also paradoxically produce very high anti-SARS-CoV-2 antibody titers and have lower viral load as compared to mild disease.

Severe acute respiratory syndrome coronavirus 2 has caused a pandemic in humans. Farmed mink (Neovison vison) are also susceptible. In Denmark, this virus has spread rapidly among farmed mink, resulting in some respiratory disease. Full-length virus genome sequencing revealed novel virus variants in mink. These variants subsequently appeared within the local human community.

We analyzed 91 wastewater samples from 11 states in the USA, where the majority of samples represent Maricopa County, Arizona (USA). We undertook a single-nucleotide variant (SNV) analysis on data from 52 samples with >90% SARS-CoV-2 genome coverage of sequence reads, and compared these SNVs with those detected in genomes sequenced from clinical patients. We identified 7973 SNVs, of which 5680 were novel SNVs that had not yet been identified in the global clinical-derived data.

Recent emergence of new SARS-CoV-2 variants B.1.1.7 in the UK and B.1.351 in South Africa is of concern because of their purported ease of transmission and extensive mutations in the spike protein. We now report that B.1.1.7 is refractory to neutralization by most mAbs to the N-terminal domain (NTD) of spike and relatively resistant to a number of mAbs to the receptor-binding domain (RBD).

We investigated the distribution of KLRC2 deletion and HLA-E*0101/0103 allelic variants in a study cohort of 361 patients with either mild (N = 92) or severe (N = 269) COVID-19. Both were significantly overrepresented in hospitalized patients, particularly in patients requiring intensive care (p < 0.0001 and p = 0.01), compared with patients with mild symptoms.

Summary: Generation of SARS-CoV-2 spike mutants that escape antibody neutralization. Mutant S477N is resistant to neutralization by multiple monoclonal antibodies. Mutant E484K is less sensitive to neutralization by convalescent human sera. Sequential selection identifies mutants that escape neutralization by antibody cocktails.

We map how mutations to SARS-CoV-2’s receptor-binding domain (RBD) affect binding by the antibodies in the REGN-COV2 cocktail and the antibody LY-CoV016. These complete maps uncover a single amino-acid mutation that fully escapes the REGN-COV2 cocktail. The maps also identify viral mutations that are selected in a persistently infected patient treated with REGN-COV2. The maps reveal that mutations escaping the individual antibodies are already present in circulating strains. Overall, these escape maps enable interpretation of the consequences of mutations observed during viral surveillance.

we sequenced RNA directly from sewage collected by municipal utility districts in the San Francisco Bay Area to generate SARS-CoV-2 genomes. The genotypes detected in the sewage were identical to clinical genomes from the region. Observed wastewater variants were more similar to local California patient-derived genotypes than they were to those from other regions within the United States or globally.

This study demonstrates that intermittent or persistent detection of SARS-CoV-2 RNA in nursing home sewers can provide an early warning of subsequent individual cases or outbreaks in these facilities.

Two new SARS-CoV-2 lineages with the N501Y mutation in the receptor-binding domain of the spike protein spread rapidly in the United Kingdom. We estimated that the earlier 501Y lineage without amino acid deletion ?69/?70, circulating mainly between early September and mid-November, was 10% (6-13%) more transmissible than the 501N lineage, and the 501Y lineage with amino acid deletion ?69/?70, circulating since late September, was 75% (70-80%) more transmissible than 501N.

We performed a whole-blood preserving single-cell analysis protocol to integrate contributions from all major cell types including neutrophils, monocytes, platelets, lymphocytes and the contents of serum. Patients with mild COVID-19 disease display a coordinated pattern of interferon-stimulated gene (ISG) expression across every cell population and these cells are systemically absent in patients with severe disease. Severe COVID-19 patients also paradoxically produce very high anti-SARS-CoV-2 antibody titers and have lower viral load as compared to mild disease.

Severe acute respiratory syndrome coronavirus 2 has caused a pandemic in humans. Farmed mink (Neovison vison) are also susceptible. In Denmark, this virus has spread rapidly among farmed mink, resulting in some respiratory disease. Full-length virus genome sequencing revealed novel virus variants in mink. These variants subsequently appeared within the local human community.

We analyzed 91 wastewater samples from 11 states in the USA, where the majority of samples represent Maricopa County, Arizona (USA). We undertook a single-nucleotide variant (SNV) analysis on data from 52 samples with >90% SARS-CoV-2 genome coverage of sequence reads, and compared these SNVs with those detected in genomes sequenced from clinical patients. We identified 7973 SNVs, of which 5680 were novel SNVs that had not yet been identified in the global clinical-derived data.

Recent emergence of new SARS-CoV-2 variants B.1.1.7 in the UK and B.1.351 in South Africa is of concern because of their purported ease of transmission and extensive mutations in the spike protein. We now report that B.1.1.7 is refractory to neutralization by most mAbs to the N-terminal domain (NTD) of spike and relatively resistant to a number of mAbs to the receptor-binding domain (RBD).

We investigated the distribution of KLRC2 deletion and HLA-E*0101/0103 allelic variants in a study cohort of 361 patients with either mild (N = 92) or severe (N = 269) COVID-19. Both were significantly overrepresented in hospitalized patients, particularly in patients requiring intensive care (p < 0.0001 and p = 0.01), compared with patients with mild symptoms.

Summary: Generation of SARS-CoV-2 spike mutants that escape antibody neutralization. Mutant S477N is resistant to neutralization by multiple monoclonal antibodies. Mutant E484K is less sensitive to neutralization by convalescent human sera. Sequential selection identifies mutants that escape neutralization by antibody cocktails.

We map how mutations to SARS-CoV-2’s receptor-binding domain (RBD) affect binding by the antibodies in the REGN-COV2 cocktail and the antibody LY-CoV016. These complete maps uncover a single amino-acid mutation that fully escapes the REGN-COV2 cocktail. The maps also identify viral mutations that are selected in a persistently infected patient treated with REGN-COV2. The maps reveal that mutations escaping the individual antibodies are already present in circulating strains. Overall, these escape maps enable interpretation of the consequences of mutations observed during viral surveillance.