"Two SARS-CoV-2 outbreaks occurred among intercollegiate university athletic programs during the fall 2020 semester despite mandatory directly observed daily antigen testing....We used genomic sequencing to investigate transmission dynamics in these two outbreaks."

A large volume of SARS-CoV-2 genomic data has accumulated. To timely analyze and visualize the exponentially increasing viral genomic sequences, we developed the Coronavirus GenBrowser (CGB) based on the framework of distributed genome alignments and the evolutionary tree built on an existing subtree. Among the 330,942 genomic sequences analyzed, 253,798 mutations were identified, and three prevalent European variants were found to have no mutations in three months.

Over 2500 COVID-19 cases associated with this variant have been detected in the US since December 2020, but the extent of establishment is relatively unknown. Using travel, genomic, and diagnostic data, we highlight the primary ports of entry for B.1.1.7 in the US and locations of possible underreporting of B.1.1.7 cases. Furthermore, we found evidence for many independent B.1.1.7 establishments starting in early December 2020, followed by interstate spread by the end of the month.

We formed a global network of researchers to investigate the role of human genetics in SARS-COV-2 infection and COVID-19 severity. We describe the results of three genome-wide association meta-analyses comprising 49,562 COVID-19 patients from 46 studies across 19 countries worldwide. We reported 15 genome-wide significant loci that are associated with SARS-CoV-2 infection or severe manifestations of COVID-19.

In the spike glycoprotein, we found that recurrent deletions overcome this slow substitution rate. Deletion variants arise in diverse genetic and geographic backgrounds, transmit efficiently, and are present in novel lineages, including those of current global concern. Deletions in RDRs confer resistance to neutralizing antibodies. By altering stretches of amino acids, deletions appear to accelerate SARS-CoV-2 antigenic evolution and may, more generally, drive adaptive evolution.

Wastewater-based disease surveillance is a promising approach for monitoring community outbreaks. We describe a nationwide campaign to monitor SARS-CoV-2 in the wastewater of 159 counties in 40 U.S. states. Out of 1,751 total samples analyzed, 846 samples were positive for SARS-CoV-2 RNA, with viral concentrations declining from April to May. Wastewater viral titers were consistent with, and appeared to precede, clinical COVID-19 surveillance indicators, including daily new cases.

Idiopathic pulmonary fibrosis (IPF) is a complex lung disease, characterized by progressive lung scarring. Severe COVID-19 is associated with substantial pneumonitis and has a number of shared major risk factors with IPF. Using Mendlelian randomization, this study aimed to determine the genetic correlation between IPF and severe COVID-19 and assess a potential causal role of genetically increased risk of IPF on COVID-19 severity.

Numerous variants of SARS-CoV-2 harboring mutations in spike have arisen globally. mRNA vaccines elicit potent neutralizing activity against homologous pseudovirus. Cross-neutralization of strains with receptor binding domain (RBD) mutations is poor. Both RBD and non-RBD mutations mediate escape from vaccine-induced humoral immunity.

We linked 2,245,263 positive SARS-CoV-2 community tests and 17,452 COVID-19 deaths in England. For 1,146,534 (51%) of these tests, the presence or absence of B.1.1.7 can be identified. We estimate that the hazard of death associated with S gene target failure is 55% higher after adjustment for age, sex, ethnicity, deprivation, care home residence, and local authority of residence. An absolute risk of death increased from 0.6% to 0.9% within 28 days after a positive test.

In this study of immunogenicity of the first dose of the mRNA SARS-CoV-2 vaccine among solid organ transplant recipients, the majority of participants did not mount appreciable antispike antibody responses. However, younger participants, those not receiving anti–metabolite maintenance immunosuppression, and those who received mRNA-1273 were more likely to develop antibody responses. These results contrast with the robust early immunogenicity observed in mRNA vaccine trials.

We describe the genomic epidemiology of travel-related cases in England and evaluate the effectiveness of this travel policy. Methods: Between 27/05/2020 and 13/09/2020, probable travel-related SARS-CoV-2 cases and their contacts were identified and combined with UK SARS-CoV-2 sequencing data. We found a large travel-related cluster dispersed across England identified through genomics and confirmed with contact-tracing data.

Using multivariate modelling, we found that the course of the SARS-COV-2 pandemic in the UK seems highly predicted by an earlier model based on the lockdown stringency, humidity and temperature and unaltered by the emergence of newer viral genotype.

We conducted a multicenter, double-blind, randomized, controlled trial to assess the safety and efficacy The two-dose regimen of the ChAdOx1 nCoV-19 vaccine did not show protection against mild-to-moderate Covid-19 due to the B.1.351 variant. of the ChAdOx1 nCoV-19 vaccine (AZD1222) in people not infected with the human immunodeficiency virus (HIV) in South Africa.

We found a significant reduction in neutralizing titers when the E484K mutation was present. Using both rVSV and lentiviral neutralization assays, we observed a similar trend in serum samples obtained from macaque monkeys. Protection conferred by the mRNA-1273 vaccine against the P.1, B.1.427/B.1.429, and B.1.351 variants remains to be determined. Our findings underscore the importance of continued viral surveillance and evaluation of vaccine efficacy against new variants.

Of 143,994 samples obtained from staff and residents of long-term care facilities throughout England, 4442 (3.1%) were positive for at least one gene target on PCR assay. Overall, the total number and proportion of positive samples with S gene target failure increased from 70 of 582 (12.0%) to 491 of 813 (60.4%) between November 16 and December 13.

"Two SARS-CoV-2 outbreaks occurred among intercollegiate university athletic programs during the fall 2020 semester despite mandatory directly observed daily antigen testing....We used genomic sequencing to investigate transmission dynamics in these two outbreaks."

A large volume of SARS-CoV-2 genomic data has accumulated. To timely analyze and visualize the exponentially increasing viral genomic sequences, we developed the Coronavirus GenBrowser (CGB) based on the framework of distributed genome alignments and the evolutionary tree built on an existing subtree. Among the 330,942 genomic sequences analyzed, 253,798 mutations were identified, and three prevalent European variants were found to have no mutations in three months.

Over 2500 COVID-19 cases associated with this variant have been detected in the US since December 2020, but the extent of establishment is relatively unknown. Using travel, genomic, and diagnostic data, we highlight the primary ports of entry for B.1.1.7 in the US and locations of possible underreporting of B.1.1.7 cases. Furthermore, we found evidence for many independent B.1.1.7 establishments starting in early December 2020, followed by interstate spread by the end of the month.

We formed a global network of researchers to investigate the role of human genetics in SARS-COV-2 infection and COVID-19 severity. We describe the results of three genome-wide association meta-analyses comprising 49,562 COVID-19 patients from 46 studies across 19 countries worldwide. We reported 15 genome-wide significant loci that are associated with SARS-CoV-2 infection or severe manifestations of COVID-19.

In the spike glycoprotein, we found that recurrent deletions overcome this slow substitution rate. Deletion variants arise in diverse genetic and geographic backgrounds, transmit efficiently, and are present in novel lineages, including those of current global concern. Deletions in RDRs confer resistance to neutralizing antibodies. By altering stretches of amino acids, deletions appear to accelerate SARS-CoV-2 antigenic evolution and may, more generally, drive adaptive evolution.

Wastewater-based disease surveillance is a promising approach for monitoring community outbreaks. We describe a nationwide campaign to monitor SARS-CoV-2 in the wastewater of 159 counties in 40 U.S. states. Out of 1,751 total samples analyzed, 846 samples were positive for SARS-CoV-2 RNA, with viral concentrations declining from April to May. Wastewater viral titers were consistent with, and appeared to precede, clinical COVID-19 surveillance indicators, including daily new cases.

Idiopathic pulmonary fibrosis (IPF) is a complex lung disease, characterized by progressive lung scarring. Severe COVID-19 is associated with substantial pneumonitis and has a number of shared major risk factors with IPF. Using Mendlelian randomization, this study aimed to determine the genetic correlation between IPF and severe COVID-19 and assess a potential causal role of genetically increased risk of IPF on COVID-19 severity.

Numerous variants of SARS-CoV-2 harboring mutations in spike have arisen globally. mRNA vaccines elicit potent neutralizing activity against homologous pseudovirus. Cross-neutralization of strains with receptor binding domain (RBD) mutations is poor. Both RBD and non-RBD mutations mediate escape from vaccine-induced humoral immunity.

We linked 2,245,263 positive SARS-CoV-2 community tests and 17,452 COVID-19 deaths in England. For 1,146,534 (51%) of these tests, the presence or absence of B.1.1.7 can be identified. We estimate that the hazard of death associated with S gene target failure is 55% higher after adjustment for age, sex, ethnicity, deprivation, care home residence, and local authority of residence. An absolute risk of death increased from 0.6% to 0.9% within 28 days after a positive test.

In this study of immunogenicity of the first dose of the mRNA SARS-CoV-2 vaccine among solid organ transplant recipients, the majority of participants did not mount appreciable antispike antibody responses. However, younger participants, those not receiving anti–metabolite maintenance immunosuppression, and those who received mRNA-1273 were more likely to develop antibody responses. These results contrast with the robust early immunogenicity observed in mRNA vaccine trials.

We describe the genomic epidemiology of travel-related cases in England and evaluate the effectiveness of this travel policy. Methods: Between 27/05/2020 and 13/09/2020, probable travel-related SARS-CoV-2 cases and their contacts were identified and combined with UK SARS-CoV-2 sequencing data. We found a large travel-related cluster dispersed across England identified through genomics and confirmed with contact-tracing data.

Using multivariate modelling, we found that the course of the SARS-COV-2 pandemic in the UK seems highly predicted by an earlier model based on the lockdown stringency, humidity and temperature and unaltered by the emergence of newer viral genotype.

We conducted a multicenter, double-blind, randomized, controlled trial to assess the safety and efficacy The two-dose regimen of the ChAdOx1 nCoV-19 vaccine did not show protection against mild-to-moderate Covid-19 due to the B.1.351 variant. of the ChAdOx1 nCoV-19 vaccine (AZD1222) in people not infected with the human immunodeficiency virus (HIV) in South Africa.

We found a significant reduction in neutralizing titers when the E484K mutation was present. Using both rVSV and lentiviral neutralization assays, we observed a similar trend in serum samples obtained from macaque monkeys. Protection conferred by the mRNA-1273 vaccine against the P.1, B.1.427/B.1.429, and B.1.351 variants remains to be determined. Our findings underscore the importance of continued viral surveillance and evaluation of vaccine efficacy against new variants.

Of 143,994 samples obtained from staff and residents of long-term care facilities throughout England, 4442 (3.1%) were positive for at least one gene target on PCR assay. Overall, the total number and proportion of positive samples with S gene target failure increased from 70 of 582 (12.0%) to 491 of 813 (60.4%) between November 16 and December 13.

"Two SARS-CoV-2 outbreaks occurred among intercollegiate university athletic programs during the fall 2020 semester despite mandatory directly observed daily antigen testing....We used genomic sequencing to investigate transmission dynamics in these two outbreaks."

A large volume of SARS-CoV-2 genomic data has accumulated. To timely analyze and visualize the exponentially increasing viral genomic sequences, we developed the Coronavirus GenBrowser (CGB) based on the framework of distributed genome alignments and the evolutionary tree built on an existing subtree. Among the 330,942 genomic sequences analyzed, 253,798 mutations were identified, and three prevalent European variants were found to have no mutations in three months.

Over 2500 COVID-19 cases associated with this variant have been detected in the US since December 2020, but the extent of establishment is relatively unknown. Using travel, genomic, and diagnostic data, we highlight the primary ports of entry for B.1.1.7 in the US and locations of possible underreporting of B.1.1.7 cases. Furthermore, we found evidence for many independent B.1.1.7 establishments starting in early December 2020, followed by interstate spread by the end of the month.

We formed a global network of researchers to investigate the role of human genetics in SARS-COV-2 infection and COVID-19 severity. We describe the results of three genome-wide association meta-analyses comprising 49,562 COVID-19 patients from 46 studies across 19 countries worldwide. We reported 15 genome-wide significant loci that are associated with SARS-CoV-2 infection or severe manifestations of COVID-19.

In the spike glycoprotein, we found that recurrent deletions overcome this slow substitution rate. Deletion variants arise in diverse genetic and geographic backgrounds, transmit efficiently, and are present in novel lineages, including those of current global concern. Deletions in RDRs confer resistance to neutralizing antibodies. By altering stretches of amino acids, deletions appear to accelerate SARS-CoV-2 antigenic evolution and may, more generally, drive adaptive evolution.

Wastewater-based disease surveillance is a promising approach for monitoring community outbreaks. We describe a nationwide campaign to monitor SARS-CoV-2 in the wastewater of 159 counties in 40 U.S. states. Out of 1,751 total samples analyzed, 846 samples were positive for SARS-CoV-2 RNA, with viral concentrations declining from April to May. Wastewater viral titers were consistent with, and appeared to precede, clinical COVID-19 surveillance indicators, including daily new cases.

Idiopathic pulmonary fibrosis (IPF) is a complex lung disease, characterized by progressive lung scarring. Severe COVID-19 is associated with substantial pneumonitis and has a number of shared major risk factors with IPF. Using Mendlelian randomization, this study aimed to determine the genetic correlation between IPF and severe COVID-19 and assess a potential causal role of genetically increased risk of IPF on COVID-19 severity.

Numerous variants of SARS-CoV-2 harboring mutations in spike have arisen globally. mRNA vaccines elicit potent neutralizing activity against homologous pseudovirus. Cross-neutralization of strains with receptor binding domain (RBD) mutations is poor. Both RBD and non-RBD mutations mediate escape from vaccine-induced humoral immunity.

We linked 2,245,263 positive SARS-CoV-2 community tests and 17,452 COVID-19 deaths in England. For 1,146,534 (51%) of these tests, the presence or absence of B.1.1.7 can be identified. We estimate that the hazard of death associated with S gene target failure is 55% higher after adjustment for age, sex, ethnicity, deprivation, care home residence, and local authority of residence. An absolute risk of death increased from 0.6% to 0.9% within 28 days after a positive test.

In this study of immunogenicity of the first dose of the mRNA SARS-CoV-2 vaccine among solid organ transplant recipients, the majority of participants did not mount appreciable antispike antibody responses. However, younger participants, those not receiving anti–metabolite maintenance immunosuppression, and those who received mRNA-1273 were more likely to develop antibody responses. These results contrast with the robust early immunogenicity observed in mRNA vaccine trials.

We describe the genomic epidemiology of travel-related cases in England and evaluate the effectiveness of this travel policy. Methods: Between 27/05/2020 and 13/09/2020, probable travel-related SARS-CoV-2 cases and their contacts were identified and combined with UK SARS-CoV-2 sequencing data. We found a large travel-related cluster dispersed across England identified through genomics and confirmed with contact-tracing data.

Using multivariate modelling, we found that the course of the SARS-COV-2 pandemic in the UK seems highly predicted by an earlier model based on the lockdown stringency, humidity and temperature and unaltered by the emergence of newer viral genotype.

We conducted a multicenter, double-blind, randomized, controlled trial to assess the safety and efficacy The two-dose regimen of the ChAdOx1 nCoV-19 vaccine did not show protection against mild-to-moderate Covid-19 due to the B.1.351 variant. of the ChAdOx1 nCoV-19 vaccine (AZD1222) in people not infected with the human immunodeficiency virus (HIV) in South Africa.

We found a significant reduction in neutralizing titers when the E484K mutation was present. Using both rVSV and lentiviral neutralization assays, we observed a similar trend in serum samples obtained from macaque monkeys. Protection conferred by the mRNA-1273 vaccine against the P.1, B.1.427/B.1.429, and B.1.351 variants remains to be determined. Our findings underscore the importance of continued viral surveillance and evaluation of vaccine efficacy against new variants.

Of 143,994 samples obtained from staff and residents of long-term care facilities throughout England, 4442 (3.1%) were positive for at least one gene target on PCR assay. Overall, the total number and proportion of positive samples with S gene target failure increased from 70 of 582 (12.0%) to 491 of 813 (60.4%) between November 16 and December 13.