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COVID-19 GPH|Home|PHGKB Last data update: Dec 05, 2021 . (Total: 28479 Documents since 2020)

Last Posted: Dec-05-2021 05:33:54
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Omicron and Delta Variant of SARS-CoV-2: A Comparative Computational Study of Spike protein
S Kumar et al, BIORXIV December 3, 2021

We used computational studies to examine the Delta and Omicron variants in this work and found that the Omicron variant had a higher affinity for human ACE2 than the Delta variant due to a significant number of mutations in the SARS-CoV-2 receptor binding domain, indicating a higher potential for transmission. Based on docking studies, the Q493R, N501Y, S371L, S373P, S375F, Q498R, and T478K mutations contribute significantly to high binding affinity with human ACE2. In comparison to the Delta variant, both the entire spike protein and the RBD in Omicron include a high proportion of hydrophobic amino acids such as leucine and phenylalanine. These amino acids are located within the protein's core and are required for structural stability.

Severe breakthrough COVID-19 cases in the SARS-CoV-2 delta (B.1.617.2) variant era
SY Wang et al, Lancet Microbe, December 3, 2021

Despite compelling evidence that SARS-CoV-2 vaccines are highly effective in preventing COVID-19 infections, breakthrough cases have been emerging at an increasing rate. The shifting landscape of breakthrough COVID-19 cases is likely to involve multiple factors, including demonstrated waning of antibody response after full vaccination7, 8 and emergence of variant strains of SARS-CoV-2.

Baby Talk
CDC Data Tracker COVID Weekly Review

As of December 2, 2021, more than 234 million people in the United States have received at least one dose of a COVID-19 vaccine. However, vaccination among pregnant people remains low. CDC’s COVID Data Tracker shows that as of November 27, 2021, the proportion of fully vaccinated pregnant people has increased to 35%, but most pregnant people remain unprotected against COVID-19.

Inside a Sequencing Lab on the Front Lines of America’s Search for Omicron
M Smith, NY Times, December 4, 2021

In the United States, a hunt for the variant began last week when South African researchers announced Omicron’s array of worrisome mutations. The search has intensified in recent days, with at least 12 states identifying cases. Researchers are combing through wastewater samples for any sign of the variant. Contact tracers are ramping up efforts in places where cases have emerged. And at sequencing labs like the one in Nebraska, a state where case rates are already high and hospitals are already strained, scientists have sped up the screening of samples from international travelers to see if Omicron has arrived.

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Machine learning based predictive model and systems-level network of host-microbe interactions in post-COVID-19 mucormycosis.
Verma Anukriti, et al. Microbial pathogenesis 2021 0 0. 105324

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Knowledge graph analysis and visualization of AI technology applied in COVID-19.
Wu Zongsheng, et al. Environmental science and pollution research international 2021 0 0.

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Lung Ultrasound in COVID-19 and Post-COVID-19 Patients, an Evidence-Based Approach.
Demi Libertario, et al. Journal of ultrasound in medicine : official journal of the American Institute of Ultrasound in Medicine 2021 0 0.

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Comparative pathology, molecular pathogenicity, immunological features, and genetic characterization of three highly pathogenic human coronaviruses (MERS-CoV, SARS-CoV, and SARS-CoV-2).
Rabaan A A, et al. European review for medical and pharmacological sciences 2021 0 0. (22) 7162-7184

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Nucleic Acid-Based Treatments Against COVID-19: Potential Efficacy of Aptamers and siRNAs.
Khanali Javad, et al. Frontiers in microbiology 2021 0 0. 758948

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Recognition of Variants of Concern by Antibodies and T Cells Induced by a SARS-CoV-2 Inactivated Vaccine.
Melo-González Felipe, et al. Frontiers in immunology 2021 0 0. 747830

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Rapid Assessment of Binding Affinity of SARS-COV-2 Spike Protein to the Human Angiotensin-Converting Enzyme 2 Receptor and to Neutralizing Biomolecules Based on Computer Simulations.
Buratto Damiano, et al. Frontiers in immunology 2021 0 0. 730099

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Identification of Intercellular Signaling Changes Across Conditions and Their Influence on Intracellular Signaling Response From Multiple Single-Cell Datasets.
Hao Mengqian, et al. Frontiers in genetics 2021 0 0. 751158

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Evolutionary and Antigenic Profiling of the Tendentious D614G Mutation of SARS-CoV-2 in Gujarat, India.
Nimavat Jay, et al. Frontiers in genetics 2021 0 0. 764927

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Antibody titers against the Alpha, Beta, Gamma, and Delta variants of SARS-CoV-2 induced by BNT162b2 vaccination measured using automated chemiluminescent enzyme immunoassay.
Kato Hideaki, et al. Journal of infection and chemotherapy : official journal of the Japan Society of Chemotherapy 2021 0 0.

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About COVID-19 GPH

COVID-19 GPH is an online, continuously updated, searchable database of published scientific literature, CDC and NIH resources, and other materials that captures emerging discoveries and applications of genomics, molecular and other precision medicine and precision public health tools in the investigation and control of COVID-19. Contents include PubMed records via an automated pubmed search algorithm, preprint records from NIH iCite, the relevant information from many media sources picked by experts, and linkages to contents from our curated PHGKB databases.
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All Records28479
Genomics Precision Health20203
Non-Genomics Precision Health8276

Publication Categories Brand

Mechanism 5689
Treatment 5247
Vaccines 5141
Variants 4835
Diagnosis 3841
Prevention 3446
Forecasting 2298
Surveillance 2149
Transmission 1190
Health Equity 725

Publication Types

PubMed Records20696
Online News/Reports/Publications557

Genomics Precision Health (GPH): The use of pathogen and human genomics and advanced molecular detection methods in discovery, clinical and public health investigations and response to COVID-19.
Non Genomics Precision Health (non-GPH): The use of big data, data science, digital health, machine learning and predictive analytic methods (not involving genomics) in discovery, clinical and public health investigations and response to COVID-19

Following categories are annotated by LitCovid from NCBI NIH.
MechanismUnderlying cause(s) of covid-19 infections and transmission & possible drug mechanism of action
Transmission Characteristics and modes of covid-19 transmissions, such as human-to-human
DiagnosisDisease assessment through symptoms, test results, and radiological features
PreventionPrevention, control, response and management strategies
Case ReportDescriptions of specific patient cases
ForecastingModelling and estimating the trend of covid-19 spread

Following categories are annotated by the text mining tool from CDC PHGKB
Health EquityRelevant to health equity. Search terms are derived from a list provided by the Association for Territorial Health Officials which include terms such as diversity, health disparities, and others.
VaccineRelevant to vaccine development, evaluation, implementation and impact. For additional information on vaccines and COVID-19. Check out general CDC Information pages
VariantRelevant to SARS-CoV-2 variants and their impact on public health. For additional information on variants COVID-19. Check out CDC New Variants of the Virus that Causes COVID-19 page
SurveillanceRelevant to SARS-CoV-2 public health surveillance and tracking. For additional information on COVID-19 surveillance, check out CDC COVID-19 Data Tracker

Disclaimer: Articles listed in the Public Health Genomics and Precision Health Knowledge Base are selected by the CDC Office of Public Health Genomics to provide current awareness of the literature and news. Inclusion in the update does not necessarily represent the views of the Centers for Disease Control and Prevention nor does it imply endorsement of the article's methods or findings. CDC and DHHS assume no responsibility for the factual accuracy of the items presented. The selection, omission, or content of items does not imply any endorsement or other position taken by CDC or DHHS. Opinion, findings and conclusions expressed by the original authors of items included in the update, or persons quoted therein, are strictly their own and are in no way meant to represent the opinion or views of CDC or DHHS. References to publications, news sources, and non-CDC Websites are provided solely for informational purposes and do not imply endorsement by CDC or DHHS.