Hotel quarantine for international travelers has been used to prevent coronavirus disease spread into Australia. A quarantine hotel-associated community outbreak was detected in South Australia. Real-time genomic sequencing enabled rapid confirmation tracking the outbreak to a recently returned traveler and linked 2 cases of infection in travelers at the same facility.

valuations of vaccine effectiveness (VE) are important to monitor as COVID-19 vaccines are introduced in the general population. Research staff enrolled symptomatic participants seeking outpatient medical care for COVID-19-like illness or SARS-CoV-2 testing from a multisite network. VE was evaluated using the test-negative design. Among 236 SARS-CoV-2 nucleic acid amplification test-positive and 576 test-negative participants aged =16 years, VE of mRNA vaccines against COVID-19 was 91% (95% CI: 83-95) for full vaccination and 75% (95% CI: 55-87) for partial vaccination. Vaccination was associated with prevention of most COVID-19 cases among people seeking outpatient medical care.

In this study, initial vaccine-elicited neutralizing antibody titers were negatively associated with age, resulting in a diminished ability to neutralize SARS-CoV-2 in vitro. Neutralizing titers against P.1 were reduced across all ages, although the magnitude of the age-dependent difference was smaller.

We describe an extended GWAS meta-analysis of 3,260 COVID-19 patients with respiratory failure and 12,483 population controls from Italy, Spain, Norway and Germany, as well as hypothesis-driven targeted analysis of the human leukocyte antigen (HLA) region and chromosome Y haplotypes. We include detailed stratified analyses based on age, sex and disease severity. In addition to already established risk loci, our data identify and replicate two genome-wide significant loci at 17q21.31 and 19q13.33 associated with severe COVID-19 with respiratory failure.

We used logistic regression, with variant type as the dependent variable, vaccination status as the main explanatory variable, controlling for age, sex, subpopulation, place of residence and time of sample, to estimate the odds ratio for a vaccinated case to have the B. 1.351 versus the B.1.1.7 variant, within vaccinated and unvaccinated persons who tested positive. Findings There were 19 cases of B.1.351 variant (3.2%) among those vaccinated more than 14 days before the positive sample and 88 (3.5%) among the unvaccinated. The estimated odds ratio was 1.29 [95% CI: 0.66-2.50].

We investigate the spatial invasion dynamics of lineage B.1.1.7 by jointly analyzing UK human mobility, virus genomes, and community-based PCR data. We identify a multi-stage spatial invasion process in which early B.1.1.7 growth rates were associated with mobility and asymmetric lineage export from a dominant source location....Our findings show that careful accounting of the behavioral and epidemiological context within which variants of concern emerge is necessary to interpret correctly their observed relative growth rates.

Findings Of 6775 participants in UKB who tested positive for infection with SARS-CoV-2 in the community, there were 914 (13.5%) with adverse COVID-19 outcomes. The odds ratio (OR) for adverse COVID-19 outcomes was 1·17 (95% CI 1·05–1·30; P = 0·004) per 1-SD shorter usual LTL, after adjustment for age, sex and ethnicity.

In this observational study we show that, in healthy adult individuals (n?=?96), the heterologous vaccine regimen induced spike-specific IgG, neutralizing antibodies and spike-specific CD4 T?cells, the levels of which which were significantly higher than after homologous vector vaccine boost (n?=?55) and higher or comparable in magnitude to homologous mRNA vaccine regimens (n?=?62). Moreover, spike-specific CD8 T?cell levels after heterologous vaccination were significantly higher than after both homologous regimens.

This multisite US study supports the safety of Pfizer-BioNTech or Moderna vaccine second dose administration in patients who report immediate and potentially allergic reactions after the first dose. Although mild symptoms were reported in 20% of patients with second dose administration, all patients who received a second dose safely completed their vaccination series and could use mRNA COVID-19 vaccines in the future when indicated.

We used two-sample Mendelian randomisation (MR) to assess the causal effect of vitamin D levels on SARS-CoV-2 infection risk and COVID-19 severity using publicly available data. We also carried out a genome-wide association analysis (GWA) of vitamin D deficiency in the UK Biobank. we found no evidence that vitamin D is protective against SARS-CoV-2 infection or COVID-19 severity.

We investigate the spatial invasion dynamics of lineage B.1.1.7 by jointly analyzing UK human mobility, virus genomes, and community-based PCR data. We identify a multi-stage spatial invasion process in which early B.1.1.7 growth rates were associated with mobility and asymmetric lineage export from a dominant source location, enhancing the effects of B.1.1.7's increased intrinsic transmissibility. We further explore how B.1.1.7 spread was shaped by non-pharmaceutical interventions and spatial variation in previous attack rates. Our findings show that careful accounting of the behavioral and epidemiological context within which variants of concern emerge is necessary to interpret correctly their observed relative growth rates.

Prevalence of the B.1.1.7 (Alpha) variant increased rapidly and caused 63%-90% of new cases in the latter half of May. Eleven B.1.1.7 genomes had an E484K replacement in spike protein, a change also identified in other SARS-CoV-2 lineages. Compared with non-B.1.1.7-infected patients, individuals with B.1.1.7 had a significantly lower cycle threshold (a proxy for higher virus load) and significantly higher hospitalization rate. Other variants (e.g., B.1.429 and B.1.427 (Epsilon), P.1 (Gamma), P.2 (Zeta), and R.1) also increased rapidly, although the magnitude was less than B.1.1.7. We identified 22 patients infected with B.1.617.1 (Kappa) or B.1.617.2 (Delta) variants; these patients had a high rate of hospitalization. Breakthrough cases (n=207) in fully vaccinated patients were caused by a heterogeneous array of virus genotypes, including many that are not currently designated variants of interest or concern

Our study explores evolution of SARS-CoV-2 in a representative cohort of sequences covering the entire genome in the United States, through all of 2020 and early 2021. Strikingly, we detected many accumulating Single Nucleotide Variations (SNVs) encoding amino acid changes in the SARS-CoV-2 genome, with a pattern indicative of RNA editing enzymes as major mutators of SARS-CoV-2 genomes. We report three major variants through October of 2020. These revealed 14 key mutations that were found in various combinations among 14 distinct predominant signatures. These signatures likely represent evolutionary lineages of SARS-CoV-2 in the U.S. and reveal clues to its evolution such as a mutational burst in the summer of 2020 likely leading to a homegrown new variant, and a trend towards higher mutational load among viral isolates.

It is important to note that this surveillance was designed to determine exposure of deer to SARS-CoV-2 in their natural environment. It was not designed to determine whether the deer were replicating and shedding SARS-CoV-2. APHIS supports a One Health approach to addressing animal diseases, including SARS-CoV-2. Widespread human infections with SARS-CoV-2 combined with human-wildlife interactions create the potential for spillover between people and animals. Studying the susceptibility of certain mammals, such as deer, to SARS-CoV-2 helps to identify species that may serve as reservoirs or hosts for the virus, as well as understand the origin of the virus, and predict its impacts on wildlife and the risks of cross-species transmission.

Hotel quarantine for international travelers has been used to prevent coronavirus disease spread into Australia. A quarantine hotel-associated community outbreak was detected in South Australia. Real-time genomic sequencing enabled rapid confirmation tracking the outbreak to a recently returned traveler and linked 2 cases of infection in travelers at the same facility.

valuations of vaccine effectiveness (VE) are important to monitor as COVID-19 vaccines are introduced in the general population. Research staff enrolled symptomatic participants seeking outpatient medical care for COVID-19-like illness or SARS-CoV-2 testing from a multisite network. VE was evaluated using the test-negative design. Among 236 SARS-CoV-2 nucleic acid amplification test-positive and 576 test-negative participants aged =16 years, VE of mRNA vaccines against COVID-19 was 91% (95% CI: 83-95) for full vaccination and 75% (95% CI: 55-87) for partial vaccination. Vaccination was associated with prevention of most COVID-19 cases among people seeking outpatient medical care.

In this study, initial vaccine-elicited neutralizing antibody titers were negatively associated with age, resulting in a diminished ability to neutralize SARS-CoV-2 in vitro. Neutralizing titers against P.1 were reduced across all ages, although the magnitude of the age-dependent difference was smaller.

We describe an extended GWAS meta-analysis of 3,260 COVID-19 patients with respiratory failure and 12,483 population controls from Italy, Spain, Norway and Germany, as well as hypothesis-driven targeted analysis of the human leukocyte antigen (HLA) region and chromosome Y haplotypes. We include detailed stratified analyses based on age, sex and disease severity. In addition to already established risk loci, our data identify and replicate two genome-wide significant loci at 17q21.31 and 19q13.33 associated with severe COVID-19 with respiratory failure.

We used logistic regression, with variant type as the dependent variable, vaccination status as the main explanatory variable, controlling for age, sex, subpopulation, place of residence and time of sample, to estimate the odds ratio for a vaccinated case to have the B. 1.351 versus the B.1.1.7 variant, within vaccinated and unvaccinated persons who tested positive. Findings There were 19 cases of B.1.351 variant (3.2%) among those vaccinated more than 14 days before the positive sample and 88 (3.5%) among the unvaccinated. The estimated odds ratio was 1.29 [95% CI: 0.66-2.50].

We investigate the spatial invasion dynamics of lineage B.1.1.7 by jointly analyzing UK human mobility, virus genomes, and community-based PCR data. We identify a multi-stage spatial invasion process in which early B.1.1.7 growth rates were associated with mobility and asymmetric lineage export from a dominant source location....Our findings show that careful accounting of the behavioral and epidemiological context within which variants of concern emerge is necessary to interpret correctly their observed relative growth rates.

Findings Of 6775 participants in UKB who tested positive for infection with SARS-CoV-2 in the community, there were 914 (13.5%) with adverse COVID-19 outcomes. The odds ratio (OR) for adverse COVID-19 outcomes was 1·17 (95% CI 1·05–1·30; P = 0·004) per 1-SD shorter usual LTL, after adjustment for age, sex and ethnicity.

In this observational study we show that, in healthy adult individuals (n?=?96), the heterologous vaccine regimen induced spike-specific IgG, neutralizing antibodies and spike-specific CD4 T?cells, the levels of which which were significantly higher than after homologous vector vaccine boost (n?=?55) and higher or comparable in magnitude to homologous mRNA vaccine regimens (n?=?62). Moreover, spike-specific CD8 T?cell levels after heterologous vaccination were significantly higher than after both homologous regimens.

This multisite US study supports the safety of Pfizer-BioNTech or Moderna vaccine second dose administration in patients who report immediate and potentially allergic reactions after the first dose. Although mild symptoms were reported in 20% of patients with second dose administration, all patients who received a second dose safely completed their vaccination series and could use mRNA COVID-19 vaccines in the future when indicated.

We used two-sample Mendelian randomisation (MR) to assess the causal effect of vitamin D levels on SARS-CoV-2 infection risk and COVID-19 severity using publicly available data. We also carried out a genome-wide association analysis (GWA) of vitamin D deficiency in the UK Biobank. we found no evidence that vitamin D is protective against SARS-CoV-2 infection or COVID-19 severity.

We investigate the spatial invasion dynamics of lineage B.1.1.7 by jointly analyzing UK human mobility, virus genomes, and community-based PCR data. We identify a multi-stage spatial invasion process in which early B.1.1.7 growth rates were associated with mobility and asymmetric lineage export from a dominant source location, enhancing the effects of B.1.1.7's increased intrinsic transmissibility. We further explore how B.1.1.7 spread was shaped by non-pharmaceutical interventions and spatial variation in previous attack rates. Our findings show that careful accounting of the behavioral and epidemiological context within which variants of concern emerge is necessary to interpret correctly their observed relative growth rates.

Prevalence of the B.1.1.7 (Alpha) variant increased rapidly and caused 63%-90% of new cases in the latter half of May. Eleven B.1.1.7 genomes had an E484K replacement in spike protein, a change also identified in other SARS-CoV-2 lineages. Compared with non-B.1.1.7-infected patients, individuals with B.1.1.7 had a significantly lower cycle threshold (a proxy for higher virus load) and significantly higher hospitalization rate. Other variants (e.g., B.1.429 and B.1.427 (Epsilon), P.1 (Gamma), P.2 (Zeta), and R.1) also increased rapidly, although the magnitude was less than B.1.1.7. We identified 22 patients infected with B.1.617.1 (Kappa) or B.1.617.2 (Delta) variants; these patients had a high rate of hospitalization. Breakthrough cases (n=207) in fully vaccinated patients were caused by a heterogeneous array of virus genotypes, including many that are not currently designated variants of interest or concern

Our study explores evolution of SARS-CoV-2 in a representative cohort of sequences covering the entire genome in the United States, through all of 2020 and early 2021. Strikingly, we detected many accumulating Single Nucleotide Variations (SNVs) encoding amino acid changes in the SARS-CoV-2 genome, with a pattern indicative of RNA editing enzymes as major mutators of SARS-CoV-2 genomes. We report three major variants through October of 2020. These revealed 14 key mutations that were found in various combinations among 14 distinct predominant signatures. These signatures likely represent evolutionary lineages of SARS-CoV-2 in the U.S. and reveal clues to its evolution such as a mutational burst in the summer of 2020 likely leading to a homegrown new variant, and a trend towards higher mutational load among viral isolates.

It is important to note that this surveillance was designed to determine exposure of deer to SARS-CoV-2 in their natural environment. It was not designed to determine whether the deer were replicating and shedding SARS-CoV-2. APHIS supports a One Health approach to addressing animal diseases, including SARS-CoV-2. Widespread human infections with SARS-CoV-2 combined with human-wildlife interactions create the potential for spillover between people and animals. Studying the susceptibility of certain mammals, such as deer, to SARS-CoV-2 helps to identify species that may serve as reservoirs or hosts for the virus, as well as understand the origin of the virus, and predict its impacts on wildlife and the risks of cross-species transmission.

Hotel quarantine for international travelers has been used to prevent coronavirus disease spread into Australia. A quarantine hotel-associated community outbreak was detected in South Australia. Real-time genomic sequencing enabled rapid confirmation tracking the outbreak to a recently returned traveler and linked 2 cases of infection in travelers at the same facility.

valuations of vaccine effectiveness (VE) are important to monitor as COVID-19 vaccines are introduced in the general population. Research staff enrolled symptomatic participants seeking outpatient medical care for COVID-19-like illness or SARS-CoV-2 testing from a multisite network. VE was evaluated using the test-negative design. Among 236 SARS-CoV-2 nucleic acid amplification test-positive and 576 test-negative participants aged =16 years, VE of mRNA vaccines against COVID-19 was 91% (95% CI: 83-95) for full vaccination and 75% (95% CI: 55-87) for partial vaccination. Vaccination was associated with prevention of most COVID-19 cases among people seeking outpatient medical care.

In this study, initial vaccine-elicited neutralizing antibody titers were negatively associated with age, resulting in a diminished ability to neutralize SARS-CoV-2 in vitro. Neutralizing titers against P.1 were reduced across all ages, although the magnitude of the age-dependent difference was smaller.

We describe an extended GWAS meta-analysis of 3,260 COVID-19 patients with respiratory failure and 12,483 population controls from Italy, Spain, Norway and Germany, as well as hypothesis-driven targeted analysis of the human leukocyte antigen (HLA) region and chromosome Y haplotypes. We include detailed stratified analyses based on age, sex and disease severity. In addition to already established risk loci, our data identify and replicate two genome-wide significant loci at 17q21.31 and 19q13.33 associated with severe COVID-19 with respiratory failure.

We used logistic regression, with variant type as the dependent variable, vaccination status as the main explanatory variable, controlling for age, sex, subpopulation, place of residence and time of sample, to estimate the odds ratio for a vaccinated case to have the B. 1.351 versus the B.1.1.7 variant, within vaccinated and unvaccinated persons who tested positive. Findings There were 19 cases of B.1.351 variant (3.2%) among those vaccinated more than 14 days before the positive sample and 88 (3.5%) among the unvaccinated. The estimated odds ratio was 1.29 [95% CI: 0.66-2.50].

We investigate the spatial invasion dynamics of lineage B.1.1.7 by jointly analyzing UK human mobility, virus genomes, and community-based PCR data. We identify a multi-stage spatial invasion process in which early B.1.1.7 growth rates were associated with mobility and asymmetric lineage export from a dominant source location....Our findings show that careful accounting of the behavioral and epidemiological context within which variants of concern emerge is necessary to interpret correctly their observed relative growth rates.

Findings Of 6775 participants in UKB who tested positive for infection with SARS-CoV-2 in the community, there were 914 (13.5%) with adverse COVID-19 outcomes. The odds ratio (OR) for adverse COVID-19 outcomes was 1·17 (95% CI 1·05–1·30; P = 0·004) per 1-SD shorter usual LTL, after adjustment for age, sex and ethnicity.

In this observational study we show that, in healthy adult individuals (n?=?96), the heterologous vaccine regimen induced spike-specific IgG, neutralizing antibodies and spike-specific CD4 T?cells, the levels of which which were significantly higher than after homologous vector vaccine boost (n?=?55) and higher or comparable in magnitude to homologous mRNA vaccine regimens (n?=?62). Moreover, spike-specific CD8 T?cell levels after heterologous vaccination were significantly higher than after both homologous regimens.

This multisite US study supports the safety of Pfizer-BioNTech or Moderna vaccine second dose administration in patients who report immediate and potentially allergic reactions after the first dose. Although mild symptoms were reported in 20% of patients with second dose administration, all patients who received a second dose safely completed their vaccination series and could use mRNA COVID-19 vaccines in the future when indicated.

We used two-sample Mendelian randomisation (MR) to assess the causal effect of vitamin D levels on SARS-CoV-2 infection risk and COVID-19 severity using publicly available data. We also carried out a genome-wide association analysis (GWA) of vitamin D deficiency in the UK Biobank. we found no evidence that vitamin D is protective against SARS-CoV-2 infection or COVID-19 severity.

We investigate the spatial invasion dynamics of lineage B.1.1.7 by jointly analyzing UK human mobility, virus genomes, and community-based PCR data. We identify a multi-stage spatial invasion process in which early B.1.1.7 growth rates were associated with mobility and asymmetric lineage export from a dominant source location, enhancing the effects of B.1.1.7's increased intrinsic transmissibility. We further explore how B.1.1.7 spread was shaped by non-pharmaceutical interventions and spatial variation in previous attack rates. Our findings show that careful accounting of the behavioral and epidemiological context within which variants of concern emerge is necessary to interpret correctly their observed relative growth rates.

Prevalence of the B.1.1.7 (Alpha) variant increased rapidly and caused 63%-90% of new cases in the latter half of May. Eleven B.1.1.7 genomes had an E484K replacement in spike protein, a change also identified in other SARS-CoV-2 lineages. Compared with non-B.1.1.7-infected patients, individuals with B.1.1.7 had a significantly lower cycle threshold (a proxy for higher virus load) and significantly higher hospitalization rate. Other variants (e.g., B.1.429 and B.1.427 (Epsilon), P.1 (Gamma), P.2 (Zeta), and R.1) also increased rapidly, although the magnitude was less than B.1.1.7. We identified 22 patients infected with B.1.617.1 (Kappa) or B.1.617.2 (Delta) variants; these patients had a high rate of hospitalization. Breakthrough cases (n=207) in fully vaccinated patients were caused by a heterogeneous array of virus genotypes, including many that are not currently designated variants of interest or concern

Our study explores evolution of SARS-CoV-2 in a representative cohort of sequences covering the entire genome in the United States, through all of 2020 and early 2021. Strikingly, we detected many accumulating Single Nucleotide Variations (SNVs) encoding amino acid changes in the SARS-CoV-2 genome, with a pattern indicative of RNA editing enzymes as major mutators of SARS-CoV-2 genomes. We report three major variants through October of 2020. These revealed 14 key mutations that were found in various combinations among 14 distinct predominant signatures. These signatures likely represent evolutionary lineages of SARS-CoV-2 in the U.S. and reveal clues to its evolution such as a mutational burst in the summer of 2020 likely leading to a homegrown new variant, and a trend towards higher mutational load among viral isolates.

It is important to note that this surveillance was designed to determine exposure of deer to SARS-CoV-2 in their natural environment. It was not designed to determine whether the deer were replicating and shedding SARS-CoV-2. APHIS supports a One Health approach to addressing animal diseases, including SARS-CoV-2. Widespread human infections with SARS-CoV-2 combined with human-wildlife interactions create the potential for spillover between people and animals. Studying the susceptibility of certain mammals, such as deer, to SARS-CoV-2 helps to identify species that may serve as reservoirs or hosts for the virus, as well as understand the origin of the virus, and predict its impacts on wildlife and the risks of cross-species transmission.