Published on 09/29/2022
COVID-19 Genomics and Precision Public Health Weekly Update Content
Pathogen and Human Genomics Studies
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Dose of approved COVID-19 vaccines is based on weak evidence: a review of early-phase, dose-finding trials
D Dunn et al, MEDRXIV, September 22, 2022 -
Evaluation of variant calling algorithms for wastewater-based epidemiology using mixed populations of SARS-CoV-2 variants in synthetic and wastewater samples
I Bassano et al, MEDRXIV, September 22, 2022 -
Estimated Effectiveness of COVID-19 Vaccines Against Omicron or Delta Symptomatic Infection and Severe Outcomes
SA Buchan et al, JAMA Network Open, September 23, 2022In this test-negative case-control study of 134?435 adults in Ontario, Canada, the estimated effectiveness of 2 doses of COVID-19 vaccine was high against symptomatic Delta infection and severe outcomes and was lower against symptomatic Omicron infection. After a third dose, estimated vaccine effectiveness against Omicron was 61% for symptomatic infection and 95% for severe outcomes. -
Deep RNA sequencing of intensive care unit patients with COVID-19.
Fredericks Alger M et al. Scientific reports 2022 9 (1) 15755We enrolled fifteen patients at a single hospital. Patients were critically ill with a mortality of 47% and 67% were on a ventilator. All the patients had the SARS-CoV-2 RNA identified in the blood in addition to RNA from other viruses, bacteria, and archaea. The expression of many immune modulating genes, including PD-L1 and PD-L2, were significantly different in patients who died from COVID-19. Some proteins were influenced by alternative transcription and splicing events, as seen in HLA-C, HLA-E, NRP1 and NRP2. -
Untargeted saliva metabolomics by liquid chromatography-Mass spectrometry reveals markers of COVID-19 severity.
Frampas Cecile F et al. PloS one 2022 9 (9) e0274967In this exploratory work, we found that saliva metabolomics and in particular amino acids can be capable of separating high severity COVID-19 patients from low severity COVID-19 patients. This expands the atlas of COVID-19 metabolic dysregulation and could in future offer the basis of a quick and non-invasive means of sampling patients, intended to supplement existing clinical tests, -
Tracking mutational semantics of SARS-CoV-2 genomes.
Singh Rohan et al. Scientific reports 2022 9 (1) 15704Here we describe how SARS-CoV-2 genomes and mutations thereof can be processed using fundamental algorithms in NLP to reveal the characteristics and evolution of the virus. We demonstrate applicability of NLP in not only probing the temporal mutational signatures through dynamic topic modelling, but also in tracing the mutation-associations through tracing of semantic drift in genomic mutation records. -
Transcriptome-wide Summary Data based Mendelian Randomization analysis reveals 38 novel genes associating with Severe COVID-19.
Krishnamoorthy Suhas et al. Journal of medical virology 2022 9We identified 309 significant gene-trait associations (FDR q-value<0.05) across 46 tissues for severe COVID-19, which mapped to 64 genes, of which 38 are novel. The top five most associated protein-coding genes were Interferon Alpha and Beta Receptor Subunit 2 (IFNAR2), 2'-5'-Oligoadenylate Synthetase 3 (OAS3), mucin 1 (MUC1), Interleukin 10 Receptor Subunit Beta (IL10RB), and Napsin A Aspartic Peptidase (NAPSA). The potential causal genes were enriched in biological processes related to type I interferons, interferon gamma inducible protein 10 production, and chemokine (C-X-C motif) ligand 2 production. -
COVID-19 Vaccine Initiation and Dose Completion During the SARS-CoV-2 Delta Variant Surge in the United States, December 2020-October 2021.
Murthy Neil et al. Public health reports (Washington, D.C. : 1974) 2022 9 333549221123584Of 51 jurisdictions, 15 reached at least 70% vaccination coverage before the Delta variant surge (ie, as of June 30, 2021), while 35 reached that goal as of October 31, 2021. Jurisdictions in the lowest quartile of vaccination coverage (44.9%-54.9%) had the greatest absolute (9.7%-17.9%) and relative (18.1%-39.8%) percentage increase in vaccination coverage during July 1-October 31, 2021. Of those who received the first dose during this period across all jurisdictions, nearly 1 in 5 missed the second dose. -
Wastewater surveillance of human influenza, metapneumovirus, parainfluenza, respiratory syncytial virus (RSV), rhinovirus, and seasonal coronaviruses during the COVID-19 pandemic
A Boehm et al, MEDRXIV, September 23, 2022 -
Higher risk of SARS-CoV-2 Omicron BA.4/5 infection than of BA.2 infection after previous BA.1 infection, the Netherlands, 2 May to 24 July 2022
SP Andeweg et al, MEDRXIV, September 23, 2022 -
Association of Primary and Booster Vaccination and Prior Infection With SARS-CoV-2 Infection and Severe COVID-19 Outcomes
DY Lin et al, JAMA, September 26, 2022In a cohort study of 10.6 million North Carolina residents from March 2020 to June 2022, receipt of a primary COVID-19 vaccine series compared with being unvaccinated, receipt of a booster compared with primary vaccination, and prior SARS-CoV-2 infection compared with no prior infection were all significantly associated with lower risk of SARS-CoV-2 infection and resulting hospitalization and death. The estimates for the associated protection decreased over time, especially for the outcome of infection, and varied by type of circulating variant. -
Incidence of Severe COVID-19 Illness Following Vaccination and Booster With BNT162b2, mRNA-1273, and Ad26.COV2.S Vaccines
JD Kelley et al, JAMA September 26, 2022This retrospective cohort study included 1?610?719 participants receiving care at Veterans Health Administration facilities, followed up for 24 weeks (July 1, 2021, to May 30, 2022) after completing a COVID-19 vaccination series and booster. Overall, the incidence of hospitalization with COVID-19 pneumonia or death was 8.9 per 10?000 persons. In a US cohort, there was a low incidence of hospitalization with COVID-19 pneumonia or death following vaccination and booster during a period of Delta and Omicron variant predominance. -
Further humoral immunity evasion of emerging SARS-CoV-2 BA.4 and BA.5 subvariants
F Jian et al, The Lancet Infectious Diseases, September 27, 2022Our findings suggest that significant humoral immune evasion, especially against convalescents from BA.4 and BA.5 breakthrough infection, contributes to the emergence and rapid spread of multiple Arg346-mutated BA.4 and BA.5 sublineages. The decreased neutralisation titres of plasma samples from BA.5 breakthrough-infection convalescents indicate worrisome potential reinfection of BA.4.6 after the recovery from BA.4 or BA.5 infection. -
Duration of viral infectiousness and correlation with symptoms and diagnostic testing in non-hospitalized adults during acute SARS-CoV-2 infection: A longitudinal cohort study
PK Drain et al, MEDRXIV, September 27, 2022During the 14 days following symptom onset, presence of N antigen (adjusted relative risk=7.66, 95% CI: 3.96-14.82), remained strongly associated with viral culture positivity, regardless of COVID-19 symptoms. Conclusions: Most adults have replication-competent SARS-CoV-2 for 10-14 after symptom onset, and N antigen testing is a strong predictor of viral infectiousness. Within two weeks from symptom onset, N antigen testing, rather than absence of symptoms or viral RNA, should be used to safely discontinue isolation. -
Interval between prior SARS-CoV-2 infection and booster vaccination impacts magnitude and quality of antibody and B cell responses
CM Buckner et al, Cell, September 26, 2022Over a two-month period, we evaluated antibody and B-cell responses to a third dose mRNA vaccine in 66 individuals with different infection histories. Uninfected and post-boost but not previously infected individuals mounted robust ancestral and variant spike-binding and neutralizing antibodies, and memory B cells. Spike-specific B-cell responses from recent infection (< 180 days) were elevated at pre-boost but comparatively less so at 60 days post-boost compared to uninfected individuals, and these differences were linked to baseline frequencies of CD27lo B cells.
Non-Genomics Precision Health Studies
-
Dose of approved COVID-19 vaccines is based on weak evidence: a review of early-phase, dose-finding trials
D Dunn et al, MEDRXIV, September 22, 2022 -
Evaluation of variant calling algorithms for wastewater-based epidemiology using mixed populations of SARS-CoV-2 variants in synthetic and wastewater samples
I Bassano et al, MEDRXIV, September 22, 2022 -
Estimated Effectiveness of COVID-19 Vaccines Against Omicron or Delta Symptomatic Infection and Severe Outcomes
SA Buchan et al, JAMA Network Open, September 23, 2022In this test-negative case-control study of 134?435 adults in Ontario, Canada, the estimated effectiveness of 2 doses of COVID-19 vaccine was high against symptomatic Delta infection and severe outcomes and was lower against symptomatic Omicron infection. After a third dose, estimated vaccine effectiveness against Omicron was 61% for symptomatic infection and 95% for severe outcomes. -
Deep RNA sequencing of intensive care unit patients with COVID-19.
Fredericks Alger M et al. Scientific reports 2022 9 (1) 15755We enrolled fifteen patients at a single hospital. Patients were critically ill with a mortality of 47% and 67% were on a ventilator. All the patients had the SARS-CoV-2 RNA identified in the blood in addition to RNA from other viruses, bacteria, and archaea. The expression of many immune modulating genes, including PD-L1 and PD-L2, were significantly different in patients who died from COVID-19. Some proteins were influenced by alternative transcription and splicing events, as seen in HLA-C, HLA-E, NRP1 and NRP2. -
Untargeted saliva metabolomics by liquid chromatography-Mass spectrometry reveals markers of COVID-19 severity.
Frampas Cecile F et al. PloS one 2022 9 (9) e0274967In this exploratory work, we found that saliva metabolomics and in particular amino acids can be capable of separating high severity COVID-19 patients from low severity COVID-19 patients. This expands the atlas of COVID-19 metabolic dysregulation and could in future offer the basis of a quick and non-invasive means of sampling patients, intended to supplement existing clinical tests, -
Tracking mutational semantics of SARS-CoV-2 genomes.
Singh Rohan et al. Scientific reports 2022 9 (1) 15704Here we describe how SARS-CoV-2 genomes and mutations thereof can be processed using fundamental algorithms in NLP to reveal the characteristics and evolution of the virus. We demonstrate applicability of NLP in not only probing the temporal mutational signatures through dynamic topic modelling, but also in tracing the mutation-associations through tracing of semantic drift in genomic mutation records. -
Transcriptome-wide Summary Data based Mendelian Randomization analysis reveals 38 novel genes associating with Severe COVID-19.
Krishnamoorthy Suhas et al. Journal of medical virology 2022 9We identified 309 significant gene-trait associations (FDR q-value<0.05) across 46 tissues for severe COVID-19, which mapped to 64 genes, of which 38 are novel. The top five most associated protein-coding genes were Interferon Alpha and Beta Receptor Subunit 2 (IFNAR2), 2'-5'-Oligoadenylate Synthetase 3 (OAS3), mucin 1 (MUC1), Interleukin 10 Receptor Subunit Beta (IL10RB), and Napsin A Aspartic Peptidase (NAPSA). The potential causal genes were enriched in biological processes related to type I interferons, interferon gamma inducible protein 10 production, and chemokine (C-X-C motif) ligand 2 production. -
COVID-19 Vaccine Initiation and Dose Completion During the SARS-CoV-2 Delta Variant Surge in the United States, December 2020-October 2021.
Murthy Neil et al. Public health reports (Washington, D.C. : 1974) 2022 9 333549221123584Of 51 jurisdictions, 15 reached at least 70% vaccination coverage before the Delta variant surge (ie, as of June 30, 2021), while 35 reached that goal as of October 31, 2021. Jurisdictions in the lowest quartile of vaccination coverage (44.9%-54.9%) had the greatest absolute (9.7%-17.9%) and relative (18.1%-39.8%) percentage increase in vaccination coverage during July 1-October 31, 2021. Of those who received the first dose during this period across all jurisdictions, nearly 1 in 5 missed the second dose. -
Wastewater surveillance of human influenza, metapneumovirus, parainfluenza, respiratory syncytial virus (RSV), rhinovirus, and seasonal coronaviruses during the COVID-19 pandemic
A Boehm et al, MEDRXIV, September 23, 2022 -
Higher risk of SARS-CoV-2 Omicron BA.4/5 infection than of BA.2 infection after previous BA.1 infection, the Netherlands, 2 May to 24 July 2022
SP Andeweg et al, MEDRXIV, September 23, 2022 -
Association of Primary and Booster Vaccination and Prior Infection With SARS-CoV-2 Infection and Severe COVID-19 Outcomes
DY Lin et al, JAMA, September 26, 2022In a cohort study of 10.6 million North Carolina residents from March 2020 to June 2022, receipt of a primary COVID-19 vaccine series compared with being unvaccinated, receipt of a booster compared with primary vaccination, and prior SARS-CoV-2 infection compared with no prior infection were all significantly associated with lower risk of SARS-CoV-2 infection and resulting hospitalization and death. The estimates for the associated protection decreased over time, especially for the outcome of infection, and varied by type of circulating variant. -
Incidence of Severe COVID-19 Illness Following Vaccination and Booster With BNT162b2, mRNA-1273, and Ad26.COV2.S Vaccines
JD Kelley et al, JAMA September 26, 2022This retrospective cohort study included 1?610?719 participants receiving care at Veterans Health Administration facilities, followed up for 24 weeks (July 1, 2021, to May 30, 2022) after completing a COVID-19 vaccination series and booster. Overall, the incidence of hospitalization with COVID-19 pneumonia or death was 8.9 per 10?000 persons. In a US cohort, there was a low incidence of hospitalization with COVID-19 pneumonia or death following vaccination and booster during a period of Delta and Omicron variant predominance. -
Further humoral immunity evasion of emerging SARS-CoV-2 BA.4 and BA.5 subvariants
F Jian et al, The Lancet Infectious Diseases, September 27, 2022Our findings suggest that significant humoral immune evasion, especially against convalescents from BA.4 and BA.5 breakthrough infection, contributes to the emergence and rapid spread of multiple Arg346-mutated BA.4 and BA.5 sublineages. The decreased neutralisation titres of plasma samples from BA.5 breakthrough-infection convalescents indicate worrisome potential reinfection of BA.4.6 after the recovery from BA.4 or BA.5 infection. -
Duration of viral infectiousness and correlation with symptoms and diagnostic testing in non-hospitalized adults during acute SARS-CoV-2 infection: A longitudinal cohort study
PK Drain et al, MEDRXIV, September 27, 2022During the 14 days following symptom onset, presence of N antigen (adjusted relative risk=7.66, 95% CI: 3.96-14.82), remained strongly associated with viral culture positivity, regardless of COVID-19 symptoms. Conclusions: Most adults have replication-competent SARS-CoV-2 for 10-14 after symptom onset, and N antigen testing is a strong predictor of viral infectiousness. Within two weeks from symptom onset, N antigen testing, rather than absence of symptoms or viral RNA, should be used to safely discontinue isolation. -
Interval between prior SARS-CoV-2 infection and booster vaccination impacts magnitude and quality of antibody and B cell responses
CM Buckner et al, Cell, September 26, 2022Over a two-month period, we evaluated antibody and B-cell responses to a third dose mRNA vaccine in 66 individuals with different infection histories. Uninfected and post-boost but not previously infected individuals mounted robust ancestral and variant spike-binding and neutralizing antibodies, and memory B cells. Spike-specific B-cell responses from recent infection (< 180 days) were elevated at pre-boost but comparatively less so at 60 days post-boost compared to uninfected individuals, and these differences were linked to baseline frequencies of CD27lo B cells.
News, Reviews and Commentaries
-
Dose of approved COVID-19 vaccines is based on weak evidence: a review of early-phase, dose-finding trials
D Dunn et al, MEDRXIV, September 22, 2022 -
Evaluation of variant calling algorithms for wastewater-based epidemiology using mixed populations of SARS-CoV-2 variants in synthetic and wastewater samples
I Bassano et al, MEDRXIV, September 22, 2022 -
Estimated Effectiveness of COVID-19 Vaccines Against Omicron or Delta Symptomatic Infection and Severe Outcomes
SA Buchan et al, JAMA Network Open, September 23, 2022In this test-negative case-control study of 134?435 adults in Ontario, Canada, the estimated effectiveness of 2 doses of COVID-19 vaccine was high against symptomatic Delta infection and severe outcomes and was lower against symptomatic Omicron infection. After a third dose, estimated vaccine effectiveness against Omicron was 61% for symptomatic infection and 95% for severe outcomes. -
Deep RNA sequencing of intensive care unit patients with COVID-19.
Fredericks Alger M et al. Scientific reports 2022 9 (1) 15755We enrolled fifteen patients at a single hospital. Patients were critically ill with a mortality of 47% and 67% were on a ventilator. All the patients had the SARS-CoV-2 RNA identified in the blood in addition to RNA from other viruses, bacteria, and archaea. The expression of many immune modulating genes, including PD-L1 and PD-L2, were significantly different in patients who died from COVID-19. Some proteins were influenced by alternative transcription and splicing events, as seen in HLA-C, HLA-E, NRP1 and NRP2. -
Untargeted saliva metabolomics by liquid chromatography-Mass spectrometry reveals markers of COVID-19 severity.
Frampas Cecile F et al. PloS one 2022 9 (9) e0274967In this exploratory work, we found that saliva metabolomics and in particular amino acids can be capable of separating high severity COVID-19 patients from low severity COVID-19 patients. This expands the atlas of COVID-19 metabolic dysregulation and could in future offer the basis of a quick and non-invasive means of sampling patients, intended to supplement existing clinical tests, -
Tracking mutational semantics of SARS-CoV-2 genomes.
Singh Rohan et al. Scientific reports 2022 9 (1) 15704Here we describe how SARS-CoV-2 genomes and mutations thereof can be processed using fundamental algorithms in NLP to reveal the characteristics and evolution of the virus. We demonstrate applicability of NLP in not only probing the temporal mutational signatures through dynamic topic modelling, but also in tracing the mutation-associations through tracing of semantic drift in genomic mutation records. -
Transcriptome-wide Summary Data based Mendelian Randomization analysis reveals 38 novel genes associating with Severe COVID-19.
Krishnamoorthy Suhas et al. Journal of medical virology 2022 9We identified 309 significant gene-trait associations (FDR q-value<0.05) across 46 tissues for severe COVID-19, which mapped to 64 genes, of which 38 are novel. The top five most associated protein-coding genes were Interferon Alpha and Beta Receptor Subunit 2 (IFNAR2), 2'-5'-Oligoadenylate Synthetase 3 (OAS3), mucin 1 (MUC1), Interleukin 10 Receptor Subunit Beta (IL10RB), and Napsin A Aspartic Peptidase (NAPSA). The potential causal genes were enriched in biological processes related to type I interferons, interferon gamma inducible protein 10 production, and chemokine (C-X-C motif) ligand 2 production. -
COVID-19 Vaccine Initiation and Dose Completion During the SARS-CoV-2 Delta Variant Surge in the United States, December 2020-October 2021.
Murthy Neil et al. Public health reports (Washington, D.C. : 1974) 2022 9 333549221123584Of 51 jurisdictions, 15 reached at least 70% vaccination coverage before the Delta variant surge (ie, as of June 30, 2021), while 35 reached that goal as of October 31, 2021. Jurisdictions in the lowest quartile of vaccination coverage (44.9%-54.9%) had the greatest absolute (9.7%-17.9%) and relative (18.1%-39.8%) percentage increase in vaccination coverage during July 1-October 31, 2021. Of those who received the first dose during this period across all jurisdictions, nearly 1 in 5 missed the second dose. -
Wastewater surveillance of human influenza, metapneumovirus, parainfluenza, respiratory syncytial virus (RSV), rhinovirus, and seasonal coronaviruses during the COVID-19 pandemic
A Boehm et al, MEDRXIV, September 23, 2022 -
Higher risk of SARS-CoV-2 Omicron BA.4/5 infection than of BA.2 infection after previous BA.1 infection, the Netherlands, 2 May to 24 July 2022
SP Andeweg et al, MEDRXIV, September 23, 2022 -
Association of Primary and Booster Vaccination and Prior Infection With SARS-CoV-2 Infection and Severe COVID-19 Outcomes
DY Lin et al, JAMA, September 26, 2022In a cohort study of 10.6 million North Carolina residents from March 2020 to June 2022, receipt of a primary COVID-19 vaccine series compared with being unvaccinated, receipt of a booster compared with primary vaccination, and prior SARS-CoV-2 infection compared with no prior infection were all significantly associated with lower risk of SARS-CoV-2 infection and resulting hospitalization and death. The estimates for the associated protection decreased over time, especially for the outcome of infection, and varied by type of circulating variant. -
Incidence of Severe COVID-19 Illness Following Vaccination and Booster With BNT162b2, mRNA-1273, and Ad26.COV2.S Vaccines
JD Kelley et al, JAMA September 26, 2022This retrospective cohort study included 1?610?719 participants receiving care at Veterans Health Administration facilities, followed up for 24 weeks (July 1, 2021, to May 30, 2022) after completing a COVID-19 vaccination series and booster. Overall, the incidence of hospitalization with COVID-19 pneumonia or death was 8.9 per 10?000 persons. In a US cohort, there was a low incidence of hospitalization with COVID-19 pneumonia or death following vaccination and booster during a period of Delta and Omicron variant predominance. -
Further humoral immunity evasion of emerging SARS-CoV-2 BA.4 and BA.5 subvariants
F Jian et al, The Lancet Infectious Diseases, September 27, 2022Our findings suggest that significant humoral immune evasion, especially against convalescents from BA.4 and BA.5 breakthrough infection, contributes to the emergence and rapid spread of multiple Arg346-mutated BA.4 and BA.5 sublineages. The decreased neutralisation titres of plasma samples from BA.5 breakthrough-infection convalescents indicate worrisome potential reinfection of BA.4.6 after the recovery from BA.4 or BA.5 infection. -
Duration of viral infectiousness and correlation with symptoms and diagnostic testing in non-hospitalized adults during acute SARS-CoV-2 infection: A longitudinal cohort study
PK Drain et al, MEDRXIV, September 27, 2022During the 14 days following symptom onset, presence of N antigen (adjusted relative risk=7.66, 95% CI: 3.96-14.82), remained strongly associated with viral culture positivity, regardless of COVID-19 symptoms. Conclusions: Most adults have replication-competent SARS-CoV-2 for 10-14 after symptom onset, and N antigen testing is a strong predictor of viral infectiousness. Within two weeks from symptom onset, N antigen testing, rather than absence of symptoms or viral RNA, should be used to safely discontinue isolation. -
Interval between prior SARS-CoV-2 infection and booster vaccination impacts magnitude and quality of antibody and B cell responses
CM Buckner et al, Cell, September 26, 2022Over a two-month period, we evaluated antibody and B-cell responses to a third dose mRNA vaccine in 66 individuals with different infection histories. Uninfected and post-boost but not previously infected individuals mounted robust ancestral and variant spike-binding and neutralizing antibodies, and memory B cells. Spike-specific B-cell responses from recent infection (< 180 days) were elevated at pre-boost but comparatively less so at 60 days post-boost compared to uninfected individuals, and these differences were linked to baseline frequencies of CD27lo B cells.
- Page last reviewed:Feb 1, 2024
- Page last updated:Apr 25, 2024
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