Last Posted: May 15, 2024
Spotlight
Latest News and Publications
Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny.
Martin Hunt et al. bioRxiv 2024 5
Analytical validation of a semi-automated methodology for quantitative measurement of SARS-CoV-2 RNA in wastewater collected in northern New England.
Ashlee A Robbins et al. Microbiol Spectr 2024 5 e0112223
Prospective Validation of a Simple Risk Score to Predict Hospitalization during the Omicron Phase of COVID-19.
Ebell Mark H, et al. Journal of the American Board of Family Medicine : JABFM 2024 0 0. (2) 324-327
Relationship between HLA genetic variations, COVID-19 vaccine antibody response, and risk of breakthrough outcomes.
Xie Junqing, et al. Nature communications 2024 0 0. (1) 4031
Venous thromboembolism and severe COVID-19: a Mendelian randomization trial and transcriptomic analysis.
Chen Liang, et al. Frontiers in immunology 2024 0 0. 1363598
Data mining and machine learning in HIV infection risk research: An overview and recommendations.
Qiwei Ge et al. Artif Intell Med 2024 153102887
Improving sepsis classification performance with artificial intelligence algorithms: A comprehensive overview of healthcare applications.
Anjana G et al. J Crit Care 2024 83154815
Redefining Healthcare With Artificial Intelligence (AI): The Contributions of ChatGPT, Gemini, and Co-pilot.
Anas Alhur et al. Cureus 2024 16(4) e57795
The predictive accuracy of machine learning for the risk of death in HIV patients: a systematic review and meta-analysis.
Yuefei Li et al. BMC Infect Dis 2024 24(1) 474
Association between SARS-CoV-2 gene specific Ct values and COVID-19 associated in-hospital mortality.
Sikhosana Mpho L, et al. Frontiers in epidemiology 2024 0 0. 1375975
Continued improvement in the development of the SARS-CoV-2 whole genome sequencing proficiency testing program.
Katherine A Lau et al. Pathology 2024 5
Early Detection of the Emerging SARS-CoV-2 BA.2.86 Lineage Through Wastewater Surveillance Using a Mediator Probe PCR Assay - Shenzhen City, Guangdong Province, China, 2023.
Du Chen, et al. China CDC weekly 2024 0 0. (15) 332-338
Effectiveness of the fourth dose of COVID-19 vaccines against severe COVID-19 among adults 40 years or older in Brazil: a population-based cohort study.
Lazar Neto Felippe, et al. Lancet regional health. Americas 2024 0 0. 100755
Genomic Surveillance for SARS-CoV-2 Variants: Dominance of XBB Replacement - China, January-June 2023.
Feng Yenan, et al. China CDC weekly 2024 0 0. (15) 324-331
Incursion of SARS-CoV-2 BA.2.86.1 variant into Israel: National-scale wastewater surveillance using a novel quantitative real-time PCR assay.
Erster Oran, et al. The Science of the total environment 2024 0 0. 173164
A prospective cohort-based artificial intelligence evaluation system for the protective efficacy and immune response of SARS-CoV-2 inactivated vaccines.
Zhang Jin, et al. International immunopharmacology 2024 0 0. 112141
Molecular evolutionary characteristics of severe acute respiratory syndrome coronavirus 2 and the relatedness of epidemiological and socio-environmental factors.
Kyuyoung Shim et al. Heliyon 2024 5 (9) e30222
Predominance of A2063G mutant strains in the Mycoplasma pneumoniae epidemic in children-a clinical and epidemiological study in 2023 in Wuhan, China.
Kyi De, et al. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 2024 0 0. 107074
A systematic mutation analysis of 13 Major SARS-CoV-2 Variants.
Bai Han, et al. Virus research 2024 0 0. 199392
Country-report pattern corrections of new cases allow accurate 2-week predictions of COVID-19 evolution with the Gompertz model.
Villanueva I, et al. Scientific reports 2024 0 0. (1) 10775
Special Issue "Molecular and Genetic Aspects of SARS-CoV-2 Infection and COVID-19 Disease".
Cardona Fernando, et al. International journal of molecular sciences 2024 0 0. (9)
A regionally tailored epidemiological forecast and monitoring program to guide a healthcare system in the COVID-19 pandemic.
Turk Philip J, et al. Journal of infection and public health 2024 0 0. (6) 1125-1133
Implementation of AZD7442 (Tixagevimab/Cilgavimab) COVID-19 Pre-exposure Prophylaxis (PrEP) in the Largest Health Maintenance Organization in Israel: Real-world Uptake and Sociodemographic and Clinical Characteristics Across Immunocompromised Patient Groups.
Hayek Samah, et al. Infectious diseases and therapy 2024 0 0.
Mathematical assessment of the roles of age heterogeneity and vaccination on the dynamics and control of SARS-CoV-2.
Pant Binod, et al. Infectious Disease Modelling 2024 0 0. (3) 828-874
Simple mathematical model for predicting COVID-19 outbreaks in Japan based on epidemic waves with a cyclical trend.
Manabe Hiroki, et al. BMC infectious diseases 2024 0 0. (1) 465
The potential of tailed amplicons for SARS-CoV-2 detection in Nucleic Acid Lateral Flow Assays.
Vindeirinho João M, et al. PloS one 2024 0 0. (5) e0301234
Association of the C3953T (rs1143634) variant of the interleukin 1 beta gene with the features of a complicated course of COVID-19-associated pneumonia.
Pokhylko Valeriy, et al. Molecular biology reports 2024 0 0. (1) 630
Development and evaluation of a lyophilization protocol for colorimetric RT-LAMP diagnostic assay for COVID-19.
Prado Nayra Oliveira, et al. Scientific reports 2024 0 0. (1) 10612
Epidemic Features and Megagenomic Analysis of Childhood Mycoplasma Pneumoniae post COVID-19 Pandemic: A 6-year Study in Southern China.
Xu Yi, et al. Emerging microbes & infections 2024 0 0. 2353298
Genetic Polymorphism of Interleukin-6 in Asymptomatic and ICU-Admitted COVID-19 Patients in Sulaymaniyah Province, Kurdistan Region of Iraq.
Rashid Peshnyar M A, et al. Genetic testing and molecular biomarkers 2024 0 0.
Spotlight
High-resolution African HLA resource uncovers HLA-DRB1 expression effects underlying vaccine response
(Posted May 14, 2024 3PM)
From the abstract: " How human genetic variation contributes to vaccine effectiveness in infants is unclear, and data are limited on these relationships in populations with African ancestries. We undertook genetic analyses of vaccine antibody responses in infants from Uganda (n=1391), Burkina Faso (n=353) and South Africa (n=755), identifying associations between human leukocyte antigen (HLA) and antibody response for five of eight tested antigens spanning pertussis, diphtheria and hepatitis B vaccines. In addition, through HLA typing 1,702 individuals from 11 populations of African ancestry derived predominantly from the 1000 Genomes Project, we constructed an imputation resource, fine-mapping class II HLA-DR and DQ associations explaining up to 10% of antibody response variance in our infant cohorts. "
Vaccine effectiveness against emerging COVID-19 variants using digital health data
(Posted May 09, 2024 6PM)
From the abstract: " Here, we develop a methodology for identifying changes in vaccine effectiveness and COVID-19 symptomatology using the University of Maryland COVID Trends and Impact Survey data from three middle-income countries (Guatemala, Mexico, and South Africa). We implement conditional logistic regression to develop estimates of vaccine effectiveness conditioned on the prevalence of various definitions of self-reported COVID-like illness in lieu of confirmed diagnostic test results. Results: We highlight a reduction in vaccine effectiveness during Omicron-dominated waves of infections when compared to periods dominated by the Delta variant."
Rapid pathogen surveillance: field-ready sequencing solutions
(Posted May 03, 2024 5PM)
From the article: "Genetic sequencing of pathogens has revolutionized the surveillance of infectious diseases, empowering scientists and health officials to anticipate and respond effectively to outbreaks. Despite their transformative potential, next-generation sequencing technologies have traditionally been inaccessible to many in the global scientific community, particularly in the Global South. This is primarily due to the prohibitively high capital costs and a widespread deficiency in laboratory infrastructure and genomics expertise. Ironically, it is in these regions where genomic surveillance could yield the most crucial insights, underscoring the urgent need for equitable access to such transformative technologies. "
Bird flu virus has been spreading in US cows for months, RNA reveals Genomic analysis suggests that the outbreak probably began in December or January, but a shortage of data is hampering efforts to pin down the source.
(Posted Apr 29, 2024 11AM)
From the article: "A strain of highly pathogenic avian influenza has been silently spreading in US cattle for months, according to preliminary analysis of genomic data. The outbreak is likely to have begun when the virus jumped from an infected bird into a cow, probably around late December or early January. This implies a protracted, undetected spread of the virus — suggesting that more cattle across the United States, and even in neighbouring regions, could have been infected with avian influenza than currently reported. These conclusions are based on swift and summary analyses by researchers, following a dump of genomic data by the US Department of Agriculture (USDA) into a public repository earlier this week. "
Latest News and Publications
Martin Hunt et al. bioRxiv 2024 5
Analytical validation of a semi-automated methodology for quantitative measurement of SARS-CoV-2 RNA in wastewater collected in northern New England.
Ashlee A Robbins et al. Microbiol Spectr 2024 5 e0112223
Prospective Validation of a Simple Risk Score to Predict Hospitalization during the Omicron Phase of COVID-19.
Ebell Mark H, et al. Journal of the American Board of Family Medicine : JABFM 2024 0 0. (2) 324-327
Relationship between HLA genetic variations, COVID-19 vaccine antibody response, and risk of breakthrough outcomes.
Xie Junqing, et al. Nature communications 2024 0 0. (1) 4031
Venous thromboembolism and severe COVID-19: a Mendelian randomization trial and transcriptomic analysis.
Chen Liang, et al. Frontiers in immunology 2024 0 0. 1363598
Data mining and machine learning in HIV infection risk research: An overview and recommendations.
Qiwei Ge et al. Artif Intell Med 2024 153102887
Improving sepsis classification performance with artificial intelligence algorithms: A comprehensive overview of healthcare applications.
Anjana G et al. J Crit Care 2024 83154815
Redefining Healthcare With Artificial Intelligence (AI): The Contributions of ChatGPT, Gemini, and Co-pilot.
Anas Alhur et al. Cureus 2024 16(4) e57795
The predictive accuracy of machine learning for the risk of death in HIV patients: a systematic review and meta-analysis.
Yuefei Li et al. BMC Infect Dis 2024 24(1) 474
Association between SARS-CoV-2 gene specific Ct values and COVID-19 associated in-hospital mortality.
Sikhosana Mpho L, et al. Frontiers in epidemiology 2024 0 0. 1375975
Continued improvement in the development of the SARS-CoV-2 whole genome sequencing proficiency testing program.
Katherine A Lau et al. Pathology 2024 5
Early Detection of the Emerging SARS-CoV-2 BA.2.86 Lineage Through Wastewater Surveillance Using a Mediator Probe PCR Assay - Shenzhen City, Guangdong Province, China, 2023.
Du Chen, et al. China CDC weekly 2024 0 0. (15) 332-338
Effectiveness of the fourth dose of COVID-19 vaccines against severe COVID-19 among adults 40 years or older in Brazil: a population-based cohort study.
Lazar Neto Felippe, et al. Lancet regional health. Americas 2024 0 0. 100755
Genomic Surveillance for SARS-CoV-2 Variants: Dominance of XBB Replacement - China, January-June 2023.
Feng Yenan, et al. China CDC weekly 2024 0 0. (15) 324-331
Incursion of SARS-CoV-2 BA.2.86.1 variant into Israel: National-scale wastewater surveillance using a novel quantitative real-time PCR assay.
Erster Oran, et al. The Science of the total environment 2024 0 0. 173164
A prospective cohort-based artificial intelligence evaluation system for the protective efficacy and immune response of SARS-CoV-2 inactivated vaccines.
Zhang Jin, et al. International immunopharmacology 2024 0 0. 112141
Molecular evolutionary characteristics of severe acute respiratory syndrome coronavirus 2 and the relatedness of epidemiological and socio-environmental factors.
Kyuyoung Shim et al. Heliyon 2024 5 (9) e30222
Predominance of A2063G mutant strains in the Mycoplasma pneumoniae epidemic in children-a clinical and epidemiological study in 2023 in Wuhan, China.
Kyi De, et al. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 2024 0 0. 107074
A systematic mutation analysis of 13 Major SARS-CoV-2 Variants.
Bai Han, et al. Virus research 2024 0 0. 199392
Country-report pattern corrections of new cases allow accurate 2-week predictions of COVID-19 evolution with the Gompertz model.
Villanueva I, et al. Scientific reports 2024 0 0. (1) 10775
Special Issue "Molecular and Genetic Aspects of SARS-CoV-2 Infection and COVID-19 Disease".
Cardona Fernando, et al. International journal of molecular sciences 2024 0 0. (9)
A regionally tailored epidemiological forecast and monitoring program to guide a healthcare system in the COVID-19 pandemic.
Turk Philip J, et al. Journal of infection and public health 2024 0 0. (6) 1125-1133
Implementation of AZD7442 (Tixagevimab/Cilgavimab) COVID-19 Pre-exposure Prophylaxis (PrEP) in the Largest Health Maintenance Organization in Israel: Real-world Uptake and Sociodemographic and Clinical Characteristics Across Immunocompromised Patient Groups.
Hayek Samah, et al. Infectious diseases and therapy 2024 0 0.
Mathematical assessment of the roles of age heterogeneity and vaccination on the dynamics and control of SARS-CoV-2.
Pant Binod, et al. Infectious Disease Modelling 2024 0 0. (3) 828-874
Simple mathematical model for predicting COVID-19 outbreaks in Japan based on epidemic waves with a cyclical trend.
Manabe Hiroki, et al. BMC infectious diseases 2024 0 0. (1) 465
The potential of tailed amplicons for SARS-CoV-2 detection in Nucleic Acid Lateral Flow Assays.
Vindeirinho João M, et al. PloS one 2024 0 0. (5) e0301234
Association of the C3953T (rs1143634) variant of the interleukin 1 beta gene with the features of a complicated course of COVID-19-associated pneumonia.
Pokhylko Valeriy, et al. Molecular biology reports 2024 0 0. (1) 630
Development and evaluation of a lyophilization protocol for colorimetric RT-LAMP diagnostic assay for COVID-19.
Prado Nayra Oliveira, et al. Scientific reports 2024 0 0. (1) 10612
Epidemic Features and Megagenomic Analysis of Childhood Mycoplasma Pneumoniae post COVID-19 Pandemic: A 6-year Study in Southern China.
Xu Yi, et al. Emerging microbes & infections 2024 0 0. 2353298
Genetic Polymorphism of Interleukin-6 in Asymptomatic and ICU-Admitted COVID-19 Patients in Sulaymaniyah Province, Kurdistan Region of Iraq.
Rashid Peshnyar M A, et al. Genetic testing and molecular biomarkers 2024 0 0.
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Disclaimer: Articles listed in the Public Health Knowledge Base are selected by Public Health Genomics Branch 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.