Published on 09/15/2022
COVID-19 Genomics and Precision Public Health Weekly Update Content
Pathogen and Human Genomics Studies
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Application of Statistical Learning to Identify Omicron Mutations in SARS-CoV-2 Viral Genome Sequence Data From Populations in Africa and the United States
LP Zhao et al, JAMA Network Open, September 8, 2022Could the SARS-CoV-2 Omicron variant have been detected earlier with existing surveillance data and a state-of-the-art statistical learning strategy? In this case series of 2698 Omicron cases in Africa and 12?141 Omicron cases in the United States, a statistical learning strategy found that Omicron was dynamically expanding in Africa and the United States with trackable expansion over time. The results indicated that Omicron could have been detected 20 days earlier in Africa; similarly, 8 Omicron cases were detected in the United States by November 25, 2021, prior to the official US Centers for Disease Control and Prevention declaration. -
Remdesivir-induced emergence of SARS-CoV2 variants in patients with prolonged infection.
Heyer Andreas et al. Cell reports. Medicine 2022 9 100735We here investigate the impact of antiviral treatments such as remdesivir on intra-host genomic diversity and emergence of SARS-CoV2 variants in patients with a prolonged course of infection. Sequencing and variant analysis performed in 112 longitudinal respiratory samples from 14 SARS-CoV2-infected patients with severe disease progression show that major frequency variants do not generally arise during prolonged infection. However, remdesivir treatment can increase intra-host genomic diversity and result in the emergence of novel major variant species harboring fixed mutations. -
Improved Robustness of SARS-CoV-2 Whole-Genome Sequencing from Wastewater with a Nonselective Virus Concentration Method
E Segelhurst et al, MEDRXIV, September 9, 2022 -
Comparing the demographics and laboratory biomarkers of the COVID-19 Omicron wave and the Alpha wave in a predominantly Afro-Caribbean patient population in New York City
HW Shin et al, Research Square, September 9, 2022 -
COVID-19 severity is associated with population-level gut microbiome variations.
Lymberopoulos Eva et al. Frontiers in cellular and infection microbiology 2022 9 963338We use an unsupervised machine learning method, Topological Data Analysis (TDA). This method analyses both the local geometry and global topology of a high-dimensional dataset, making it particularly suitable for population-level microbiome data. We report an association of distinct baseline population-level gut microbiome signatures with COVID-19 severity. This was found both with a PERMANOVA, as well as with TDA. Specifically, it suggests an association of anti-inflammatory bacteria, including Bifidobacteria species and Eubacterium rectale, with lower severity, and pro-inflammatory bacteria such as Prevotella copri with higher severity. -
The role of real-time, on-site, whole-genome sequencing of severe acute respiratory coronavirus virus 2 (SARS-CoV-2) in guiding the management of hospital outbreaks of coronavirus disease 2019 (COVID-19).
Marinelli Tina M et al. Infection control and hospital epidemiology 2022 9 1-5Real-time, on-site WGS combined with epidemiologic assessment is a useful tool to guide management of hospital SARS-CoV-2 outbreaks. WGS allowed us (1) to establish likely transmission events due to personal protective equipment (PPE) breaches; (2) to detect inadequacies in infection control infrastructure including ventilation; and (3) to confirm multiple viral introductions during periods of high community SARS-CoV-2 transmission. -
Population Normalization in SARS-CoV-2 Wastewater-Based Epidemiology: Implications from Statewide Wastewater Monitoring in Missouri
C Li et al, MEDRXIV, September 10, 2022A total of 2,624 wastewater samples (41 weeks) were collected weekly during May 2021- April 2022 from 64 wastewater facilities across Missouri, U.S. Three wastewater biomarkers, caffeine and its metabolite, paraxanthine, and pepper mild mottle virus (PMMoV), were compared for the population normalization effectiveness for wastewater SARS-CoV-2 surveillance. Paraxanthine had the lowest temporal variation and strongest relationship between population compared to caffeine and PMMoV. This result was confirmed by data from ten different Wisconsin WWTPs with gradients in population sizes, indicating paraxanthine is a promising biomarker of the real-time population across a large geographical region. -
Virological characteristics of the SARS-CoV-2 Omicron BA.2 subvariants including BA.4 and BA.5
I Kimura et al, Cell, September 13, 2022After the global spread of the SARS-CoV-2 Omicron BA.2, some BA.2 subvariants, including BA.2.9.1, BA.2.11, BA.2.12.1, BA.4 and BA.5, emerged in multiple countries. Our statistical analysis showed that the effective reproduction numbers of these BA.2 subvariants are greater than that of the original BA.2. Neutralization experiments revealed that the immunity induced by BA.1/2 infections is less effective against BA.4/5. Cell culture experiments showed that BA.2.12.1 and BA.4/5 replicate more efficiently in human alveolar epithelial cells than BA.2, and particularly, BA.4/5 is more fusogenic than BA.2. -
Heterologous vector versus homologous mRNA COVID-19 booster vaccination in non-seroconverted immunosuppressed patients: a randomized controlled trial.
Mrak Daniel et al. Nature communications 2022 9 (1) 5362Seroconversion rates at week four are significantly higher in the mRNA (homologous vaccination, 15/24, 63%) as compared to the vector vaccine group (heterologous vaccination, 4/22, 18%). SARS-CoV-2-specific T-cell responses are reduced but could be increased after a third dose of either vector or mRNA vaccine. -
Increasing Cases of SARS-CoV-2 Omicron Reinfection Reveals Ineffective Post-COVID-19 Immunity in Denmark and Conveys the Need for Continued Next-Generation Sequencing
S Burkholtz et al, MEDRXIV, September 14, 2022 -
Non-Genomics Precision Health Studies
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Application of Statistical Learning to Identify Omicron Mutations in SARS-CoV-2 Viral Genome Sequence Data From Populations in Africa and the United States
LP Zhao et al, JAMA Network Open, September 8, 2022Could the SARS-CoV-2 Omicron variant have been detected earlier with existing surveillance data and a state-of-the-art statistical learning strategy? In this case series of 2698 Omicron cases in Africa and 12?141 Omicron cases in the United States, a statistical learning strategy found that Omicron was dynamically expanding in Africa and the United States with trackable expansion over time. The results indicated that Omicron could have been detected 20 days earlier in Africa; similarly, 8 Omicron cases were detected in the United States by November 25, 2021, prior to the official US Centers for Disease Control and Prevention declaration. -
Remdesivir-induced emergence of SARS-CoV2 variants in patients with prolonged infection.
Heyer Andreas et al. Cell reports. Medicine 2022 9 100735We here investigate the impact of antiviral treatments such as remdesivir on intra-host genomic diversity and emergence of SARS-CoV2 variants in patients with a prolonged course of infection. Sequencing and variant analysis performed in 112 longitudinal respiratory samples from 14 SARS-CoV2-infected patients with severe disease progression show that major frequency variants do not generally arise during prolonged infection. However, remdesivir treatment can increase intra-host genomic diversity and result in the emergence of novel major variant species harboring fixed mutations. -
Improved Robustness of SARS-CoV-2 Whole-Genome Sequencing from Wastewater with a Nonselective Virus Concentration Method
E Segelhurst et al, MEDRXIV, September 9, 2022 -
Comparing the demographics and laboratory biomarkers of the COVID-19 Omicron wave and the Alpha wave in a predominantly Afro-Caribbean patient population in New York City
HW Shin et al, Research Square, September 9, 2022 -
COVID-19 severity is associated with population-level gut microbiome variations.
Lymberopoulos Eva et al. Frontiers in cellular and infection microbiology 2022 9 963338We use an unsupervised machine learning method, Topological Data Analysis (TDA). This method analyses both the local geometry and global topology of a high-dimensional dataset, making it particularly suitable for population-level microbiome data. We report an association of distinct baseline population-level gut microbiome signatures with COVID-19 severity. This was found both with a PERMANOVA, as well as with TDA. Specifically, it suggests an association of anti-inflammatory bacteria, including Bifidobacteria species and Eubacterium rectale, with lower severity, and pro-inflammatory bacteria such as Prevotella copri with higher severity. -
The role of real-time, on-site, whole-genome sequencing of severe acute respiratory coronavirus virus 2 (SARS-CoV-2) in guiding the management of hospital outbreaks of coronavirus disease 2019 (COVID-19).
Marinelli Tina M et al. Infection control and hospital epidemiology 2022 9 1-5Real-time, on-site WGS combined with epidemiologic assessment is a useful tool to guide management of hospital SARS-CoV-2 outbreaks. WGS allowed us (1) to establish likely transmission events due to personal protective equipment (PPE) breaches; (2) to detect inadequacies in infection control infrastructure including ventilation; and (3) to confirm multiple viral introductions during periods of high community SARS-CoV-2 transmission. -
Population Normalization in SARS-CoV-2 Wastewater-Based Epidemiology: Implications from Statewide Wastewater Monitoring in Missouri
C Li et al, MEDRXIV, September 10, 2022A total of 2,624 wastewater samples (41 weeks) were collected weekly during May 2021- April 2022 from 64 wastewater facilities across Missouri, U.S. Three wastewater biomarkers, caffeine and its metabolite, paraxanthine, and pepper mild mottle virus (PMMoV), were compared for the population normalization effectiveness for wastewater SARS-CoV-2 surveillance. Paraxanthine had the lowest temporal variation and strongest relationship between population compared to caffeine and PMMoV. This result was confirmed by data from ten different Wisconsin WWTPs with gradients in population sizes, indicating paraxanthine is a promising biomarker of the real-time population across a large geographical region. -
Virological characteristics of the SARS-CoV-2 Omicron BA.2 subvariants including BA.4 and BA.5
I Kimura et al, Cell, September 13, 2022After the global spread of the SARS-CoV-2 Omicron BA.2, some BA.2 subvariants, including BA.2.9.1, BA.2.11, BA.2.12.1, BA.4 and BA.5, emerged in multiple countries. Our statistical analysis showed that the effective reproduction numbers of these BA.2 subvariants are greater than that of the original BA.2. Neutralization experiments revealed that the immunity induced by BA.1/2 infections is less effective against BA.4/5. Cell culture experiments showed that BA.2.12.1 and BA.4/5 replicate more efficiently in human alveolar epithelial cells than BA.2, and particularly, BA.4/5 is more fusogenic than BA.2. -
Heterologous vector versus homologous mRNA COVID-19 booster vaccination in non-seroconverted immunosuppressed patients: a randomized controlled trial.
Mrak Daniel et al. Nature communications 2022 9 (1) 5362Seroconversion rates at week four are significantly higher in the mRNA (homologous vaccination, 15/24, 63%) as compared to the vector vaccine group (heterologous vaccination, 4/22, 18%). SARS-CoV-2-specific T-cell responses are reduced but could be increased after a third dose of either vector or mRNA vaccine. -
Increasing Cases of SARS-CoV-2 Omicron Reinfection Reveals Ineffective Post-COVID-19 Immunity in Denmark and Conveys the Need for Continued Next-Generation Sequencing
S Burkholtz et al, MEDRXIV, September 14, 2022 -
News, Reviews and Commentaries
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Application of Statistical Learning to Identify Omicron Mutations in SARS-CoV-2 Viral Genome Sequence Data From Populations in Africa and the United States
LP Zhao et al, JAMA Network Open, September 8, 2022Could the SARS-CoV-2 Omicron variant have been detected earlier with existing surveillance data and a state-of-the-art statistical learning strategy? In this case series of 2698 Omicron cases in Africa and 12?141 Omicron cases in the United States, a statistical learning strategy found that Omicron was dynamically expanding in Africa and the United States with trackable expansion over time. The results indicated that Omicron could have been detected 20 days earlier in Africa; similarly, 8 Omicron cases were detected in the United States by November 25, 2021, prior to the official US Centers for Disease Control and Prevention declaration. -
Remdesivir-induced emergence of SARS-CoV2 variants in patients with prolonged infection.
Heyer Andreas et al. Cell reports. Medicine 2022 9 100735We here investigate the impact of antiviral treatments such as remdesivir on intra-host genomic diversity and emergence of SARS-CoV2 variants in patients with a prolonged course of infection. Sequencing and variant analysis performed in 112 longitudinal respiratory samples from 14 SARS-CoV2-infected patients with severe disease progression show that major frequency variants do not generally arise during prolonged infection. However, remdesivir treatment can increase intra-host genomic diversity and result in the emergence of novel major variant species harboring fixed mutations. -
Improved Robustness of SARS-CoV-2 Whole-Genome Sequencing from Wastewater with a Nonselective Virus Concentration Method
E Segelhurst et al, MEDRXIV, September 9, 2022 -
Comparing the demographics and laboratory biomarkers of the COVID-19 Omicron wave and the Alpha wave in a predominantly Afro-Caribbean patient population in New York City
HW Shin et al, Research Square, September 9, 2022 -
COVID-19 severity is associated with population-level gut microbiome variations.
Lymberopoulos Eva et al. Frontiers in cellular and infection microbiology 2022 9 963338We use an unsupervised machine learning method, Topological Data Analysis (TDA). This method analyses both the local geometry and global topology of a high-dimensional dataset, making it particularly suitable for population-level microbiome data. We report an association of distinct baseline population-level gut microbiome signatures with COVID-19 severity. This was found both with a PERMANOVA, as well as with TDA. Specifically, it suggests an association of anti-inflammatory bacteria, including Bifidobacteria species and Eubacterium rectale, with lower severity, and pro-inflammatory bacteria such as Prevotella copri with higher severity. -
The role of real-time, on-site, whole-genome sequencing of severe acute respiratory coronavirus virus 2 (SARS-CoV-2) in guiding the management of hospital outbreaks of coronavirus disease 2019 (COVID-19).
Marinelli Tina M et al. Infection control and hospital epidemiology 2022 9 1-5Real-time, on-site WGS combined with epidemiologic assessment is a useful tool to guide management of hospital SARS-CoV-2 outbreaks. WGS allowed us (1) to establish likely transmission events due to personal protective equipment (PPE) breaches; (2) to detect inadequacies in infection control infrastructure including ventilation; and (3) to confirm multiple viral introductions during periods of high community SARS-CoV-2 transmission. -
Population Normalization in SARS-CoV-2 Wastewater-Based Epidemiology: Implications from Statewide Wastewater Monitoring in Missouri
C Li et al, MEDRXIV, September 10, 2022A total of 2,624 wastewater samples (41 weeks) were collected weekly during May 2021- April 2022 from 64 wastewater facilities across Missouri, U.S. Three wastewater biomarkers, caffeine and its metabolite, paraxanthine, and pepper mild mottle virus (PMMoV), were compared for the population normalization effectiveness for wastewater SARS-CoV-2 surveillance. Paraxanthine had the lowest temporal variation and strongest relationship between population compared to caffeine and PMMoV. This result was confirmed by data from ten different Wisconsin WWTPs with gradients in population sizes, indicating paraxanthine is a promising biomarker of the real-time population across a large geographical region. -
Virological characteristics of the SARS-CoV-2 Omicron BA.2 subvariants including BA.4 and BA.5
I Kimura et al, Cell, September 13, 2022After the global spread of the SARS-CoV-2 Omicron BA.2, some BA.2 subvariants, including BA.2.9.1, BA.2.11, BA.2.12.1, BA.4 and BA.5, emerged in multiple countries. Our statistical analysis showed that the effective reproduction numbers of these BA.2 subvariants are greater than that of the original BA.2. Neutralization experiments revealed that the immunity induced by BA.1/2 infections is less effective against BA.4/5. Cell culture experiments showed that BA.2.12.1 and BA.4/5 replicate more efficiently in human alveolar epithelial cells than BA.2, and particularly, BA.4/5 is more fusogenic than BA.2. -
Heterologous vector versus homologous mRNA COVID-19 booster vaccination in non-seroconverted immunosuppressed patients: a randomized controlled trial.
Mrak Daniel et al. Nature communications 2022 9 (1) 5362Seroconversion rates at week four are significantly higher in the mRNA (homologous vaccination, 15/24, 63%) as compared to the vector vaccine group (heterologous vaccination, 4/22, 18%). SARS-CoV-2-specific T-cell responses are reduced but could be increased after a third dose of either vector or mRNA vaccine. -
Increasing Cases of SARS-CoV-2 Omicron Reinfection Reveals Ineffective Post-COVID-19 Immunity in Denmark and Conveys the Need for Continued Next-Generation Sequencing
S Burkholtz et al, MEDRXIV, September 14, 2022 -
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- Page last updated:May 03, 2024
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