463 hot topic(s) found with the query "Epidemiology"
Genetics of chronic respiratory disease.
Ian Sayers et al. Nat Rev Genet 2024 3
(Posted: Mar 07, 2024 8AM)
From the abstract: "Chronic respiratory diseases, such as chronic obstructive pulmonary disease (COPD), asthma and interstitial lung diseases are frequently occurring disorders with a polygenic basis that account for a large global burden of morbidity and mortality. Recent large-scale genetic epidemiology studies have identified associations between genetic variation and individual respiratory diseases and linked specific genetic variants to quantitative traits related to lung function. "
Navigating epigenetic epidemiology publications
W Yu et al, BMC Epig Comm, November 22, 2023,
(Posted: Nov 27, 2023 11AM)
From the abstract: "Since its beginning more than 75 years ago, epigenetics has been an evolving field with growing applications to the study of cancer, aging, and gene expression in response to environmental exposures. The emergence of high-throughput technology for measuring epigenetic markers has enabled population-based studies. The relatively new field of epigenetic epidemiology investigates epigenetic associations from a population perspective for insights into disease risk, prevention, and progression. "
Harnessing genomics for antimicrobial resistance surveillance
The Lancet Series, November 2023
(Posted: Nov 17, 2023 8AM)
From the article: "Historically, surveillance of bacteria harboring antimicrobial resistance (AMR) has relied on phenotypic analysis of isolates taken from infected individuals, which provides only a low-resolution view of the epidemiology behind an individual infection or wider outbreak. Recent years have seen increasing adoption of powerful new genomic technologies with the potential to revolutionize AMR surveillance by providing a high-resolution picture of the AMR profile of the bacteria causing infections and providing real-time actionable information for treating and preventing infection. "
Rapid profiling of Plasmodium parasites from genome sequences to assist malaria control.
Jody E Phelan et al. Genome Med 2023 11 (1) 96
(Posted: Nov 11, 2023 3PM)
From the abstract: "Malaria continues to be a major threat to global public health. Whole genome sequencing (WGS) of the underlying Plasmodium parasites has provided insights into the genomic epidemiology of malaria. Genome sequencing is rapidly gaining traction as a diagnostic and surveillance tool for clinical settings, where the profiling of co-infections, identification of imported malaria parasites, and detection of drug resistance are crucial for infection control and disease elimination. To support this informatically, we have developed the Malaria-Profiler tool, which rapidly (within minutes) predicts Plasmodium species, geographical source, and resistance to antimalarial drugs directly from WGS data. "
The Role of Telomeres in Human Disease.
Mary Armanios et al. Annu Rev Genomics Hum Genet 2022 5 363-381
(Posted: Jul 25, 2023 8AM)
Short telomere syndromes are the most prevalent premature aging disorders, with prominent phenotypes affecting the lung and hematopoietic system. Less understood are a newly recognized group of cancer-prone syndromes that are associated with mutations that lengthen telomeres. A large body of new data from Mendelian genetics and epidemiology now provides an opportunity to reconsider paradigms related to the role of telomeres in human aging and cancer.
Co-evolution of epidemiology and artificial intelligence: challenges and opportunities.
Joohon Sung et al. Int J Epidemiol 2023 6
(Posted: Jun 24, 2023 10AM)
Artificial intelligence (AI), also often referred to as machine learning (ML) and deep learning (DL) is an automated process whereby information is extracted from a given dataset using computing techniques to create an algorithm for making predictions and/or classifications.1 The key difference between AI and classic epidemiology is that the latter builds models based on explicit assumptions about what matters and how, so that the results can be directly interpretable, whereas AI builds algorithms in essence for predictive models discovered from the data, without necessarily understanding why.
Germline Genetic Testing After Cancer Diagnosis.
Allison W Kurian et al. JAMA 2023 6
(Posted: Jun 06, 2023 8AM)
Among patients in the Surveillance, Epidemiology, and End Results registries diagnosed with cancer between 2013 and 2019, what was the prevalence of germline genetic testing? In this observational study that included 1?369?602 patients diagnosed with cancer in California and Georgia, germline genetic testing after cancer diagnosis was low (6.8%; n?=?93?052). Testing was highest in males with breast cancer (50%) and in patients with ovarian cancer (38.6%). Compared with non-Hispanic White patients, rates of testing were lower among Asian, Black, and Hispanic patients.
Pathogen genomics in public health laboratories: successes, challenges, and lessons learned from California's SARS-CoV-2 Whole-Genome Sequencing Initiative, California COVIDNet.
Emily A Smith et al. Microb Genom 2023 6 (6)
(Posted: Jun 04, 2023 2PM)
The California Department of Public Health, in partnership with Theiagen Genomics, was an early adopter of cloud-based resources for bioinformatics and genomic epidemiology, resulting in the creation of a SARS-CoV-2 genomic surveillance system that combined the efforts of more than 40 sequencing laboratories across government, academia and industry to form California COVIDNet, California's SARS-CoV-2 Whole-Genome Sequencing Initiative. Open-source bioinformatics workflows, ongoing training sessions for the public health workforce, and automated data transfer to visualization tools all contributed to the success of California COVIDNet.
3-year anniversary of national viral genomics consortium to better map SARS-CoV-2 transmission
CDC, May 2023
(Posted: May 07, 2023 7AM)
In early 2020, CDCs Office of Advanced Molecular Detection (OAMD) launched the Sequencing for Public Health Emergency Response, Epidemiology and Surveillance (SPHERES) consortium?to coordinate SARS-CoV-2 sequencing and help accelerate the use of pathogen sequence data and molecular epidemiology for the pandemic response. Today, the SPHERES collaboration includes 1,800 scientists from clinical and public health laboratories, academic institutions, and non-profit organizations.
Evaluation of polygenic risk scores to differentiate between type 1 and type 2 diabetes.
Muhammad Shoaib et al. Genetic epidemiology 2023 2
(Posted: Mar 04, 2023 9AM)
We evaluated PRS models for T1D and T2D in European genetic ancestry participants from the UK Biobank (UKB) and then in the Michigan Genomics Initiative (MGI). Specifically, we investigated the utility of T1D and T2D PRS to discriminate between T1D, T2D, and controls in unrelated UKB individuals of European ancestry. We derived PRS models using external non-UKB GWAS. The T1D PRS model with the best discrimination between T1D cases and controls (area under the receiver operator curve [AUC]?=?0.805) also yielded the best discrimination of T1D from T2D cases in the UKB (AUC?=?0.792) and separation in MGI (AUC?=?0.686).
Detection of the Omicron BA.1 Variant of SARS-CoV-2 in Wastewater From a Las Vegas Tourist Area.
Van Vo et al. JAMA network open 2023 2 (2) e230550
(Posted: Feb 25, 2023 6AM)
In this cross-sectional study, the rapid onset of the Omicron BA.1 variant of concern in Las Vegas Strip wastewater was leveraged to quantify relative SARS-CoV-2 contributions from visitors (>60%) and estimate Omicron prevalence in this subpopulation in late 2021 (40%-60% on December 13 and 80%-100% on December 20). These findings suggest that mobile populations (eg, tourists and commuters) may disproportionately affect wastewater surveillance data, leading to overestimates of infection burden with wastewater-based epidemiology.
Increasing serum iron levels and their role in the risk of infectious diseases: a Mendelian randomization approach.
Guillaume Butler-Laporte et al. International journal of epidemiology 2023 2
(Posted: Feb 20, 2023 6AM)
Using MR, we did not observe an increase in risk of most infectious diseases with increases in iron stores. However for bacterial infections, higher iron stores may increase odds of infections. Hence, using genetic variation in iron pathways as a proxy for iron supplementation, iron supplements are likely safe on a population level, but we should continue the current practice of conservative iron supplementation during bacterial infections or in those at high risk of developing them.
Design and Implementation of the All of Us Research Program COVID-19 Participant Experience (COPE) Survey.
Claire E Schulkey et al. American journal of epidemiology 2023 2
(Posted: Feb 20, 2023 6AM)
In response to the rapidly evolving COVID-19 pandemic, the All of Us Research Program longitudinal cohort study developed the COVID-19 Participant Experience (COPE) survey to better understand the pandemic experiences and health impacts of COVID-19 on diverse populations within the United States. Six survey versions were deployed between May 2020 and March 2021 covering mental health, loneliness, activity, substance use, and discrimination, as well as COVID-19 symptoms, testing, treatment, and vaccination. A total of 104,910 All of Us Research Program participants, of whom over 73% were from communities traditionally underrepresented in biomedical research, completed 275,201 surveys; 9,693 completed all six surveys
The role of wastewater-based epidemiology for SARS-CoV-2 in developing countries: cumulative evidence from South Africa supports sentinel site surveillance to guide public health decision-making
SJI Jaja et al, MEDRXIV, February 15, 2023
(Posted: Feb 17, 2023 6AM)
Seven laboratories using different test methodology, quantified influent wastewater collected from 87 wastewater treatment plants (WWTPs) located in all nine South African provinces for SARS-CoV-2 from 01 June 2021 to 31 May 2022 inclusive, during the 3rd and 4th waves of COVID-19. Variation in the strength of correlation across testing laboratories, and redundancy of findings across co-located testing plants, suggests that test methodology should be standardised and that surveillance networks may utilize a sentinel site model without compromising the value of WBE findings for public health decision-making.
Use of incorrect and correct methods to account for age in studies on epigenetic accelerated aging: implications and recommendations for best practices.
Nancy Krieger et al. American journal of epidemiology 2023 2
(Posted: Feb 05, 2023 11AM)
Motivated by our conduct of a literature review on social exposures and accelerated aging as measured by a growing number of epigenetic “clocks” (which estimate age via DNA methylation patterns (DNAm)), we report on three different approaches – 1 incorrect and 2 correct – in the epidemiologic literature on treatment of age in these and other studies using other common exposures (i.e., body mass index and alcohol consumption).
Cohort-guided insights into gene-environment interactions in autism spectrum disorders.
W Ian Lipkin et al. Nature reviews. Neurology 2023 1 1-8
(Posted: Feb 02, 2023 6AM)
Prospective birth cohorts offer unprecedented opportunities to investigate the pathogenesis of complex disorders such as autism, in which gene–environment interactions must be appreciated in a temporal context. This Perspective article considers the history of autism research, including missteps that reflected an incomplete understanding of the epidemiology of autistic spectrum disorders, the effects of advocacy and philanthropy on the trajectory of scientific inquiry, and the current and future roles of prospective birth cohort research.
15 years of GWAS discovery: Realizing the promise.
Abdellaoui Abdel et al. American journal of human genetics 2023 1
(Posted: Jan 20, 2023 6AM)
It has been 15 years since the advent of the genome-wide association study (GWAS) era. Here, we review how this experimental design has realized its promise by facilitating an impressive range of discoveries with remarkable impact on multiple fields, including population genetics, complex trait genetics, epidemiology, social science, and medicine.
Estimating the transmission dynamics of SARS-CoV-2 Omicron BF.7 in Beijing after the adjustment of zero-COVID policy in November - December 2022.
Leung Kathy et al. Nature medicine 2023 1
(Posted: Jan 16, 2023 6AM)
After China’s announcement of ‘20 measures’ to transition from zero-COVID, we estimated that Rt increased to 3.44 (95% CrI: 2.82–4.14) on November 18 and the infection incidence peaked on December 11. We estimated that the cumulative infection attack rate (that is the proportion of population who have been infected since November 1) in Beijing was 75.7% (95% CrI: 60.7–84.4) on December 22, 2022, and 92.3% (95% CrI: 91.4–93.1) on January 31, 2023. Surveillance programmes should be rapidly set up to monitor the evolving epidemiology and evolution of SARS-CoV-2 across China.
A one-year genomic investigation of Escherichia coli epidemiology and nosocomial spread at a large US healthcare network
EG Mills et al, Genome Medicine, December 30, 2022
(Posted: Dec 31, 2022 7AM)
Whole-genome sequencing (WGS), phylogenetic analysis, and antibiotic susceptibility testing were performed for a complete set of 2075 E. coli clinical isolates collected from 1776 patients at a large tertiary healthcare network in the USA between October 2019 and September 2020. The study provides a rare and contemporary survey on the epidemiology and spread of E. coli in a large US healthcare network. While surveillance and infection control efforts often focus on ESBL and MDR lineages, our findings reveal that non-MDR isolates represent a large burden of infections, including those of predicted nosocomial origins.
Improved two-step testing of genome-wide gene–environment interactions
ES Kawagushi et al, Genetic Epidemiology, December 26, 2022
(Posted: Dec 26, 2022 11AM)
We introduce a new significance-based allocation into bins for Step-2 testing that overcomes the displacement issue and propose a computationally efficient approach to account for multiple testing within bins. Simulation results demonstrate that these simple improvements can provide substantially greater power than current methods under several scenarios. An application to a multistudy collaboration for understanding colorectal cancer reveals a G?×?Sex interaction located near the SMAD7 gene.
Effectiveness of fourth dose of COVID-19 vaccine against the Omicron variant compared with no vaccination.
Zeng Jessie et al. International journal of epidemiology 2022 12
(Posted: Dec 17, 2022 9AM)
A fourth dose of the BNT162b2 vaccine appears to restore, if not boost even more (although uncertainty intervals overlap), the protection conferred by a third dose at an equivalent time post-vaccination. Our estimates are likely to be of interest to the public and policy makers weighing up the benefits and costs of a fourth dose in the context of waning immunity derived from triple vaccination who are asking the question: ‘Does a fourth dose return one to the same, or even higher, protection that one had shortly after a third dose?
Biobanking as a Tool for Genomic Research: From Allele Frequencies to Cross-Ancestry Association Studies
TE Lazavera et al, J Per Med, December 9, 2022
(Posted: Dec 10, 2022 7AM)
We summarize the main directions in which biobanks aid medical genetics and genomic research, from providing reference allele frequency information to allowing large-scale cross-ancestry meta-analyses. The largest biobanks greatly vary in the size of the collection, and the amount of available phenotype and genotype data. Nevertheless, all of them are extensively used in genomics, providing a rich resource for genome-wide association analysis, genetic epidemiology, and statistical research into the structure, function, and evolution of the human genome.
How to estimate heritability: a guide for genetic epidemiologists.
Barry Ciarrah-Jane S et al. International journal of epidemiology 2022 11
(Posted: Dec 10, 2022 7AM)
We provide an overview of common methods applied in genetic epidemiology to estimate heritability, i.e. the proportion of phenotypic variation explained by genetic variation. We provide a guide to key genetic concepts required to understand heritability estimation methods from family-based designs (twin and family studies), genomic designs based on unrelated individuals [linkage disequilibrium score regression, genomic relatedness restricted maximum-likelihood (GREML) estimation] and family-based genomic designs.
Sepsis as a Challenge for Personalized Medicine
R Zahorek et al, J Per Med, December 1, 2022
(Posted: Dec 01, 2022 3PM)
The remarkable progress in clinical medicine in the field of Sepsis can be attributed to basic research, genomics and proteomics, together with a better understanding of the immunopathology, biology and epidemiology of sepsis syndrome. The aim of this Special Issue is to provide research evidence and potential uses for personalized medicine in Sepsis, highlighting eight papers focused on research achievements in animal and human studies.
Equitable and Informed Consent in Genetic Studies.
Navar Ann Marie et al. JAMA cardiology 2022 11
(Posted: Nov 18, 2022 6AM)
As costs of genetic sequencing have declined and access to testing has become more widespread, genetic epidemiology studies are increasingly conducted to identify new pathogenic variants and understand the prevalence and implications of known pathogenic variants. Ensuring diversity in these studies is critical to ensure the generalizability of their results. Unfortunately, people of African and Latin American ancestry and Indigenous populations are underrepresented in clinical research and even more so in genetic studies. This is a particular concern in nonischemic dilated cardiomyopathy (DCM), a disease that disproportionately affects Black persons in the United States.
Development of a Molecular Blood-Based Immune Signature Classifier as Biomarker for Risks Assessment in Lung Cancer Screening.
Fortunato Orazio et al. Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology 2022 9 (11) 2020-2029
(Posted: Nov 13, 2022 6AM)
Monocytic myeloid-derived suppressor cell (MDSC), polymorphonuclear MDSC, intermediate monocytes and CD8+PD-1+ T cells distinguished patients with lung cancer from controls with AUCs values of 0.94/0.72/0.88 in the training, validation, and lung cancer specificity set, respectively. AUCs raised up to 1.00/0.84/0.92 in subgroup analysis considering only MSC-negative subjects. A 14-immune genes expression signature distinguished patients from controls with AUC values of 0.76 in the validation set and 0.83 in MSC-negative subjects.
Genomic epidemiology of SARS-CoV-2 within households in coastal Kenya: a case ascertained cohort study
CN Agoti et al, MEDRXIV, October 30, 2022
(Posted: Oct 31, 2022 9AM)
Combining pathogen and host metagenomics for a better sepsis diagnostic.
Gant Vanya et al. Nature microbiology 2022 10 (11) 1713-1714
(Posted: Oct 29, 2022 11AM)
Sepsis is defined in the clinic as an assemblage of various failing physiology and laboratory markers of organ function triggered by infection. Efforts have been made to provide tighter definitions and criteria for sepsis to achieve better and more focused clinical care, research and epidemiology. A recent study shows that combining simultaneous host and pathogen metagenomic profiles in a cohort of hospitalized and critically ill patients allows for more accurate diagnosis of sepsis.
The genomic epidemiology of SARS-CoV-2 variants of concern in Kenya
G Githinji et al, MEDRXIV, October 27, 2022
(Posted: Oct 28, 2022 8AM)
Impact of sample clarification by size exclusion on virus detection and diversity in wastewater-based epidemiology
TOC Faleye et al, MEDRXIV, October 26, 2022
(Posted: Oct 26, 2022 1PM)
Epidemiology and prevention of venous thromboembolism.
Lutsey Pamela L et al. Nature reviews. Cardiology 2022 10
(Posted: Oct 20, 2022 6AM)
Venous thromboembolism (VTE) surveillance systems are lacking, but VTE is estimated to affect one to two individuals per 1,000 person-years in Europe and the USA, with lower rates in other regions. Risk factors for VTE are varied, and include triggers (acute and subacute), basal risk factors (demographic, behavioural, anthropometric and genetic) and acquired clinical risk factors. Numerous complications can occur after a VTE event, and quality of life can decrease.
Wastewater Surveillance for Infectious Disease: A Systematic Review.
Kilaru Pruthvi et al. American journal of epidemiology 2022 10
(Posted: Oct 16, 2022 7AM)
Herein we identify what infectious diseases have been previously studied via wastewater surveillance prior to the COVID-19 pandemic. Infectious diseases and pathogens were identified in 100 studies of wastewater surveillance across 38 countries, as well as themes of how wastewater surveillance and other measures of disease transmission were linked. Twenty-five separate pathogen families were identified in the included studies.
The Impact of COVID-19 on the All of Us Research Program.
Hedden Sarra L et al. American journal of epidemiology 2022 10
(Posted: Oct 09, 2022 10AM)
Before the pandemic, the program was enrolling approximately 12,500 participants per month at more than 400 clinic sites. In March 2020, all in-person activity at sites and by engagement partners was paused to develop processes and procedures for in-person activities that incorporate strict safety protocols because of the pandemic. In addition, the program adopted new data collection methodologies to reduce the need for in-person activities. Through February 2022, 224 clinic sites have reactivated in-person activity, and all enrollment and engagement partners have adopted new data collection methodologies that can be completed remotely.
Microbiome epidemiology and association studies in human health
H VanEvery et al, Nature Rev Genetics, October 5, 2022
(Posted: Oct 06, 2022 7AM)
Recent advances, including next-generation sequencing and the proliferation of multi-omic data types, have enabled the exploration of the mechanisms that connect microbial communities to human health. Here, we review the ways in which features of the microbiome at various body sites can influence health outcomes, and we describe emerging opportunities and future directions for advanced microbiome epidemiology.
Racial Disparities in Pulse Oximeter Device Inaccuracy and Estimated Clinical Impact on COVID-19 Treatment Course.
Sudat Sylvia E K et al. American journal of epidemiology 2022 9
(Posted: Oct 02, 2022 8AM)
Pulse oximetry systematically overestimated blood oxygenation by 1% more in NHB individuals than in NHW individuals. For people with COVID-19, this was associated with lower admission probability (-3.1 percentage-points), dexamethasone treatment (-3.1 percentage-points), and supplemental oxygen treatment (-4.5 percentage-points), as well as increased time-to-treatment: +37.2 minutes before dexamethasone initiation and +278.5 minutes before initiation of supplemental oxygen.
Impact of sample clarification by size exclusion on virus detection and diversity in wastewater-based epidemiology
OC Temitope et al, MEDRXIV, September 26, 2022
(Posted: Sep 27, 2022 8AM)
Somatic loss of the Y chromosome is associated with arsenic exposure among Bangladeshi men.
Demanelis Kathryn et al. International journal of epidemiology 2022 9
(Posted: Sep 26, 2022 6AM)
Ten percent of genotyped men had LoY in at least 5% of cells and % LoY increased with age. Among men randomly selected for genotyping (n?=?778), higher arsenic in drinking water, arsenic consumed and urinary arsenic were associated with increased % LoY (P?=?0.006, P?=?0.06 and P?=?0.13, respectively). LoY was associated with increased risk of incident skin lesions (P?=?0.008).
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
(Posted: Sep 23, 2022 7AM)
CDC announces $90M funding to support new Pathogen Genomics Centers of Excellence network
CDC, September 20, 2022
(Posted: Sep 21, 2022 7AM)
The PGCoE network is meant to foster and improve innovation and technical capacity in pathogen genomics, molecular epidemiology, and bioinformatics to better prevent, control, and respond to microbial threats of public health importance. The network also represents an unprecedented opportunity to expand and deepen collaboration between U.S. public health agencies and academic institutions to form a national resource to better prevent, control and respond to microbial threats of public health importance.
Wastewater based epidemiology beyond SARS-CoV-2: Spanish wastewater reveals the current spread of Monkeypox virus
G Guzman et al, MEDRXIV, September 19, 2022
(Posted: Sep 20, 2022 6AM)
This study shows that MPXV DNA can be reproducibly detected by qPCR in longitudinal samples collected from different Spanish wastewater treatment plants. According to data from the National Epidemiological Surveillance Network (RENAVE) in Spain a total of 6,119 cases have been confirmed as of August 19, 2022. However, and based on the wastewater data, the reported clinical cases seem to be underestimated and asymptomatic infections may be more frequent than expected.
Population Normalization in SARS-CoV-2 Wastewater-Based Epidemiology: Implications from Statewide Wastewater Monitoring in Missouri
C Li et al, MEDRXIV, September 10, 2022
(Posted: Sep 11, 2022 9AM)
A 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.
Genomic epidemiology of SARS-CoV-2 infections in The Gambia, March 2020 to Jan 2022
A Kanteh et al, MEDRXIV, September 9, 2022
(Posted: Sep 10, 2022 10AM)
Tools for assessing quality and risk of bias in Mendelian randomization studies: a systematic review.
Spiga Francesca et al. International journal of epidemiology 2022 7
(Posted: Aug 06, 2022 7AM)
We present an overview of tools and methods to assess risk of bias/quality of evidence in MR analysis. Issues commonly addressed relate to the three standard assumptions of instrumental variables analyses, the choice of genetic instrument(s) and features of the population(s) from which the data are collected (particularly in two-sample MR), in addition to more traditional non-MR-specific epidemiological biases. The identified tools should be tested and validated for general use before recommendations can be made on their widespread use.
The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2
JE Pekar et al, Science, July 26, 2022
(Posted: Jul 26, 2022 6PM)
We show that SARS-CoV-2 genomic diversity before February 2020 likely comprised only two distinct viral lineages, denoted A and B. Phylodynamic rooting methods, coupled with epidemic simulations, reveal that these lineages were the result of at least two separate cross-species transmission events into humans. The first zoonotic transmission likely involved lineage B viruses around 18 November 2019 (23 October–8 December), while the separate introduction of lineage A likely occurred within weeks of this event. These findings indicate that it is unlikely that SARS-CoV-2 circulated widely in humans prior to November 2019 and define the narrow window between when SARS-CoV-2 first jumped into humans and when the first cases of COVID-19 were reported.
Genomic epidemiology and phylodynamics for county-to-county transmission of SARS-CoV-2 in Minnesota, from 19A to Omicron
M Scotch et al, MEDRXIV, July 25, 2022
(Posted: Jul 26, 2022 6AM)
We sequenced virus genomes from over 22,000 patients tested at Mayo Clinic Laboratories between 2020-2022 and leveraged detailed patient metadata to describe county-to-county spread in Minnesota. Our findings indicate that spread in the state was mostly dominated by viruses from Hennepin County, which contains the largest metropolis. For many counties, we found that state government restrictions eventually led to a decrease in the diversity of circulating viruses from other counties and that their complete removal in May of 2021 saw a drastic revert to levels at or greater than those observed during the months before.
The Role of Children in SARS-CoV-2 Variant of Concerns Transmission within Households: A Meta-analysis
Y Zuo et al, MEDRXIV, July 22, 2022
(Posted: Jul 23, 2022 7AM)
We perform a meta-analysis of the role of children in the household transmission of both ancestral SARS-CoV-2 and SARS-CoV-2 VOCs. Unlike the ancestral virus, children infected with VOCs spread SARS-CoV-2 to an equivalent number of household contacts as infected adults. Similarly, unlike the ancestral virus, children within a household were equally as likely as adults to acquire SARS-CoV-2 from an infected family member. Interestingly, this same observation was noted when unvaccinated children exposed to VOCs were compared to unvaccinated adults exposed to VOCs. Together, these data suggest that the emergence of VOCs were associated with a fundamental shift in the epidemiology of SARS-CoV-2.
Wastewater-Based Epidemiology for SARS-CoV-2 Biomarkers: Evaluation of Normalization Methods in Small and Large Communities in Southern Germany
A Mitranescu et al, MEDRXIV, July 7, 2022
(Posted: Jul 08, 2022 7AM)
Making cough count in tuberculosis care
AJ Zimmer et al, Comm Medicine, July 6, 2022
(Posted: Jul 07, 2022 7AM)
Acoustic epidemiology is an emerging field that uses technology to detect cough sounds and analyze cough patterns to improve health outcomes among people with respiratory conditions linked to cough. This field is increasingly exploring the potential of artificial intelligence (AI) for more advanced applications, such as analyzing cough sounds as a biomarker for disease screening. While much of the data are preliminary, objective cough assessment could potentially transform disease control programs, including TB, and support individual patient management.
Smartphone apps in the COVID-19 pandemic
JA Pandit et al, Nature Biotechnology, June 20,2022
(Posted: Jun 20, 2022 6PM)
Smartphone apps, given accessibility in the time of physical distancing, were widely used for tracking, tracing and educating the public about COVID-19. Despite limitations, such as concerns around data privacy, data security, digital health illiteracy and structural inequities, there is ample evidence that apps are beneficial for understanding outbreak epidemiology, individual screening and contact tracing. While there were successes and failures in each category, outbreak epidemiology and individual screening were substantially enhanced by the reach of smartphone apps and accessory wearables.
Mendelian randomization analysis for attention deficit/hyperactivity disorder: studying a broad range of exposures and outcomes.
Soler Artigas María et al. International journal of epidemiology 2022 6
(Posted: Jun 18, 2022 10AM)
We used genome-wide association study (GWAS) summary statistics for ADHD (n?=?53?293) and 124 traits related to anthropometry, cognitive function and intelligence, early life exposures, education and employment, lifestyle and environment, longevity, neurological, and psychiatric and mental health or personality and psychosocial factors available in the MR-Base database (16?067 =n?=766?345). Our findings strengthen previous evidence of a causal effect of ADHD liability on smoking and major depression, and are consistent with a causal effect on odds of decreased average total household income [odds ratio (OR)?=?0.966, 95% credible interval (CrI)?=?(0.954, 0.979)] and increased lifetime number of sexual partners [OR?=?1.023, 95% CrI?=?(1.013, 1.033)].
Mendelian randomization study of maternal coffee consumption and its influence on birthweight, stillbirth, miscarriage, gestational age and pre-term birth.
Brito Nunes Caroline et al. International journal of epidemiology 2022 6
(Posted: Jun 12, 2022 8AM)
Immuno-epidemiology and the predictability of viral evolution
CM Saad-Roy et al, Science, June 9, 2022
(Posted: Jun 10, 2022 6AM)
Despite much recent progress in modeling the epidemiology and evolution of acute viruses, a full quantitative synthesis of viral eco-evolutionary dynamics remains elusive. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has stimulated vast research efforts into measuring viral dynamics and genetics, across scales from individual hosts to global circulation. In parallel, understanding determinants of individual immune protection against infection and severe disease has been a major research focus. However, the interaction between population immunity and viral dynamics has been much less studied—a crucial gap because this interaction will strongly influence SARS-CoV-2 evolution over time.
Development of a COVID-19 warning system for neighborhood-scale wastewater-based epidemiology in low incidence situations
C Oh et al, MEDRXIV, June 8, 2022
(Posted: Jun 09, 2022 6AM)
This study applied WBE to seven neighborhood-scale sewersheds (average population 1,471) from January to November 2021. Community testing data showed an average of 0.004% incidence rate in these sewersheds (97% of monitoring periods reported two or fewer daily infections). In 92% of sewage samples, SARS-CoV-2 N gene fragments were below the limit of quantification. COVID-19 cases poorly correlated with SARS-CoV-2 N gene concentrations except for one location where frequent COVID-19 testing was required.
Comparison of variant callers for wastewater-based epidemiology
V Ramachandran et al, MEDRXIV, June 6, 2022
(Posted: Jun 08, 2022 6AM)
Extended human papillomavirus genotyping to predict progression to high-grade cervical precancer: A prospective cohort study in the southeastern United States.
Bukowski Alexandra et al. Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology 2022 6
(Posted: Jun 05, 2022 7AM)
We assessed a US-based prospective, multiracial, clinical cohort of 343 colposcopy patients with normal histology (n=226) or CIN1 (n=117). Baseline cervical samples underwent HPV DNA genotyping, and participants were followed up to five years. Non-16/18 hrHPV types are associated with differential CIN2+ progression rates. HPV16, 33, and 58 exhibited the highest rates over five years. HPV risk groups warrant further investigation in diverse US populations
Descriptive Epidemiology of SARS-CoV-2 Gamma (P.1/501Y.V3) variant cases in England, August 2021
N Iwani et al, MEDRXIV, May 31, 2022
(Posted: Jun 01, 2022 7AM)
The human genetic epidemiology of COVID-19
MEK Niemi et al, Nature Rev Genetics, May 2, 2022
(Posted: May 03, 2022 11AM)
Large-scale genetic association studies, encompassing both rare and common genetic variants, have used different study designs and multiple disease phenotype definitions to identify several genomic regions associated with COVID-19. Along with a multitude of follow-up studies, these findings have increased our understanding of disease aetiology and provided routes for management of COVID-19. Important emergent opportunities include the clinical translatability of genetic risk prediction, the repurposing of existing drugs, exploration of variable host effects of different viral strains, study of inter-individual variability in vaccination response and understanding the long-term consequences of SARS-CoV-2 infection.
COVID-19 Genomic Epidemiology Toolkit
CDC, April 2022
(Posted: Apr 29, 2022 8AM)
The CDC Office of Advanced Molecular Detection presents this toolkit to address topics related to the application of genomics to epidemiologic investigations and public health response to SARS-CoV-2. The COVID-19 Genomic Epidemiology Toolkit is meant to further the use of genomics in responding to COVID-19 at the state and local level. Each module includes a dedicated survey to inform future training development.
Regional replacement of SARS-CoV-2 variant BA.1 with BA.2 as observed through wastewater surveillance
A Boehm et al, MEDRXIV, April 25, 2022
(Posted: Apr 26, 2022 7AM)
An understanding of circulating SARS-CoV-2 variants can inform pandemic response, vaccine development, disease epidemiology, and use of monoclonal antibody treatments. We developed custom assays targeting characteristic mutations in SARS-CoV-2 variants Omicron BA.1 and BA.2 and confirmed their sensitivity and specificity in silico and in vitro. We then applied these assays to daily wastewater solids samples from eight publicly owned treatment works in the greater Bay Area of California, USA, over four months to obtain a spatially and temporally intensive data set. We documented regional replacement of BA.1 with BA.2 in agreement with, and ahead of, clinical sequencing data
The Evolution and Biology of SARS-CoV-2 Variants
A Telenti et al, Cold Spring Harbor Persp Medicine, April 19, 2022
(Posted: Apr 21, 2022 7AM)
Our understanding of the still unfolding severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic would have been extremely limited without the study of the genetics and evolution of this new human coronavirus. Large-scale genome-sequencing efforts have provided close to real-time tracking of the global spread and diversification of SARS-CoV-2 since its entry into the human population in late 2019. These data have underpinned analysis of its origins, epidemiology, and adaptations to the human population: principally immune evasion and increasing transmissibility. SARS-CoV-2, despite being a new human pathogen, was highly capable of human-to-human transmission.
Effect of SARS-CoV-2 digital droplet RT-PCR assay sensitivity on COVID-19 wastewater based epidemiology
S Kim et al, MEDRXIV, April 18, 2022
(Posted: Apr 19, 2022 7AM)
Epidemiology of infections with SARS-CoV-2 Omicron BA.2 variant in Hong Kong, January-March 2022
Y Mefsin et al, MEDRXIV, April 14, 2022
(Posted: Apr 16, 2022 1PM)
From elimination to suppression: genomic epidemiology of a large Delta SARS-CoV-2 outbreak in Aotearoa New Zealand
L Jelley et al, MEDRXIV, April 12, 2022
(Posted: Apr 12, 2022 0PM)
Impact of technological developments on infectious disease epidemiology: Lessons from the first 100 years of AJE.
Foxman Betsy et al. American journal of epidemiology 2022 4
(Posted: Apr 03, 2022 7AM)
Technological developments in laboratory and epidemiology methods combined with increasing computing power have synergistically increased our understanding of the epidemiology of infectious disease. Using historic examples from the first 100 years of AJE to illustrate how these developments provided the foundation for the rapid detection of the agent causing COVID-19, SARS-CoV-2, from its transmission efficiency and modalities, risk factors and natural history to the evaluation of new vaccines and treatments to control its spread and impact.
Genomic Epidemiology of SARS-CoV-2 in Seychelles, 2020-2021
JM Morobe et al, MEDRXIV, March 29, 2022
(Posted: Mar 30, 2022 6AM)
Coronavirus Host Genetics South Africa (COHG-SA) database—a variant database for gene regions associated with SARS-CoV-2 outcomes
F Barmania et al, EJHG, March 29, 2022
(Posted: Mar 29, 2022 7AM)
The SARS-CoV-2 virus is responsible for the COVID-19 global public health emergency, and the disease it causes is highly variable in its clinical presentation. Clinical phenotypes are heterogeneous both in terms of presentation of symptoms in the host and response to therapy. Several studies and initiatives have been established to analyse and review host genetic epidemiology associated with COVID-19. Our research group curated these articles into a web-based database using the python application-server framework Django. The database provides a searchable research tool describing current literature surrounding COVID-19 host genetic factors associated with disease outcome.
Genomic epidemiology reveals the impact of national and international restrictions measures on the SARS-CoV-2 epidemic in Brazil
M Giovanetti et al, MEDRXIV, March 28 2022
(Posted: Mar 29, 2022 6AM)
We show that the early stage of the pandemic in Brazil was characterised by the co-circulation of multiple viral lineages, linked to multiple importations predominantly from Europe, and subsequently characterized by large local transmission clusters. As the epidemic progressed under an absence of effective restriction measures, there was a local emergence and onward international spread of Variants of Concern (VOC) and Variants Under Monitoring (VUM), including Gamma (P.1) and Zeta (P.2). In addition, we provide a preliminary genomic overview of the epidemic in Paraguay, showing evidence of importation from Brazil. These data reinforce the usefulness and need for the implementation of widespread genomic surveillance in South America as a toolkit for pandemic monitoring.
Biomarkers Selection for Population Normalization in SARS-CoV-2 Wastewater-based Epidemiology
SY Hsu et al, MEDRXIV, March 15, 2022
(Posted: Mar 16, 2022 8AM)
The changing epidemiology of SARS-CoV-2.
Koelle Katia et al. Science (New York, N.Y.) 2022 3 (6585) 1116-1121
(Posted: Mar 12, 2022 8AM)
We have ome a long way in understanding the complex and changing dynamics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19. In this Review, we retrace our steps through the questions that this community faced as the pandemic unfolded. We focus on the key roles that mathematical modeling and quantitative analyses of empirical data have played in allowing us to address these questions and ultimately to better understand and control the pandemic.
Impact of BNT162b2 vaccination and isolation on SARS-CoV-2 transmission in Israeli households: an observational study.
Layan Maylis et al. American journal of epidemiology 2022 3
(Posted: Mar 07, 2022 9AM)
Compared with unvaccinated and unisolated adult/teenager contacts, vaccination reduced the risk of infection among unisolated adult/teenager contacts above 12 (RR=0.21, 95% CrI credible interval 0.08-0.44) and isolation reduced the risk of infection among unvaccinated adult/teenager (RR=0.12, 95% CrI 0.06-0.21) and child contacts (RR=0.17, 95% CrI 0.08-0.32). Infectivity was reduced in vaccinated cases (RR=0.25, 95% CrI 0.06-0.77). Within households, vaccination reduces both the risk of infection and of transmission if infected.
Factors associated with SARS-CoV-2 transmission in setting of high COVID-19 vaccination coverage: a case-control study.
Reid Michael J A et al. American journal of epidemiology 2022 3
(Posted: Mar 07, 2022 9AM)
Genomic epidemiology offers high resolution estimates of serial intervals for COVID-19
JE Stockdale et al, MEDRXIV, March 3, 2022
(Posted: Mar 04, 2022 8AM)
Association of Titin Variations With Late-Onset Dilated Cardiomyopathy
A Cannata et al, JAMA Cardiology, February 9, 2022
(Posted: Feb 09, 2022 4PM)
Is dilated cardiomyopathy diagnosed in individuals older than 60 years characterized by a specific genetic background and have similar clinical characteristics to the known epidemiology? In this cohort study of 184 patients with late-onset dilated cardiomyopathy, compared with the current epidemiology, a high genetic variation burden was identified, largely due to titin-truncating variants. Patients with a positive genetic test had higher mortality than genotype-negative patients.
Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission
D Aggarwal et al, Nature Comms, February 8, 2022
(Posted: Feb 08, 2022 8AM)
We sequenced 482 SARS-CoV-2 isolates from the University of Cambridge from 5 October to 6 December 2020. We perform a detailed phylogenetic comparison with 972 isolates from the surrounding community, complemented with epidemiological and contact tracing data, to determine transmission dynamics. We observe limited viral introductions into the university; the majority of student cases were linked to a single genetic cluster, likely following social gatherings at a venue outside the university
Genomic epidemiology of SARS-CoV-2 under an elimination strategy in Hong Kong
H Gu et al, Nature Comms, February 8, 2022
(Posted: Feb 08, 2022 8AM)
Hong Kong employed a strategy of intermittent public health and social measures alongside increasingly stringent travel regulations to eliminate domestic SARS-CoV-2 transmission. By analyzing 1899 genome sequences (>18% of confirmed cases) from 23-January-2020 to 26-January-2021, we reveal the effects of fluctuating control measures on the evolution and epidemiology of SARS-CoV-2 lineages in Hong Kong. Despite numerous importations, only three introductions were responsible for 90% of locally-acquired cases.
Molecular epidemiology of AY.28 and AY.104 delta sub-lineages in Sri Lanka
D Ranasinghe et al, MEDRXIV, February 7, 2022
(Posted: Feb 08, 2022 7AM)
Spatio-temporal epidemiology of SARS-CoV-2 virus lineages in Teesside, UK, in 2020: effects of social deprivation, weather and lockdown on lineage dynamics
S Rushton et al, MEDRXIV, February 8, 2022
(Posted: Feb 08, 2022 7AM)
What has the pandemic revealed about the shortcomings of modern epidemiology? What can we fix or do better?
Dimitris Michelle C et al. American journal of epidemiology 2022 1
(Posted: Jan 29, 2022 11AM)
In this commentary, we discuss themes that emerged from the symposium about what modern epidemiology as a science may learn from the coronavirus disease 19 (COVID-19) pandemic. We reflect on the successes and limitations of this discipline from multiple perspectives, including junior and senior epidemiologists and scientists on the front lines of generating evidence for the COVID-19 pandemic response from Wuhan, China to Ontario, Canada.
Using Genomic Epidemiology to Advance Public Health Action
CDC Preventive Medicine Grand Rounds, February 22, 2022
(Posted: Jan 25, 2022 8AM)
Rapid advances in genomic technologies, such as genomic sequencing, are transforming how we respond to public health threats. Scientists use genomic sequencing to identify and prevent a wide variety of pathogens, including those that cause foodborne illness, tuberculosis, and COVID-19. Combining genomics and epidemiology—coined “genomic epidemiology”—provides a powerful tool for surveillance, outbreak detection, as well as response, and indicates a future where the human genome can direct public health action.
COVID-19 wastewater epidemiology: a model to estimate infected populations
CS McMahan et al, Lancet Planetary Health, December 2021
(Posted: Dec 10, 2021 7AM)
This is a wastewater-based epidemiology study using wastewater samples that were collected weekly or twice a week from three sewersheds in South Carolina, USA, between either May 27 or June 16, 2020, and Aug 25, 2020, and tested for SARS-CoV-2 RNA. We developed a susceptible-exposed-infectious-recovered (SEIR) model based on the mass rate of SARS-CoV-2 RNA in the wastewater to predict the number of infected individuals, and have also provided a simplified equation to predict this. Model predictions were compared with the number of confirmed cases. We found that the SEIR model provides a robust method to estimate the total number of infected individuals in a sewershed on the basis of the mass rate of RNA copies released per day.
Epidemiology of myocarditis and pericarditis following mRNA vaccines in Ontario, Canada: by vaccine product, schedule and interval
SA Buchan et al, MEDRXIV, December 5, 2021
(Posted: Dec 06, 2021 6AM)
Classification of Omicron (B.1.1.529): SARS-CoV-2 Variant of Concern
WHO, November 26, 2021
(Posted: Nov 27, 2021 9AM)
Countries are asked to do the following: enhance surveillance and sequencing efforts to better understand circulating SARS-CoV-2 variants; submit complete genome sequences and associated metadata to a publicly available database, such as GISAID.
report initial cases/clusters associated with VOC infection to WHO through the IHR mechanism; where capacity exists and in coordination with the international community, perform field investigations and laboratory assessments to improve understanding of the potential impacts of the VOC on COVID-19 epidemiology, severity, effectiveness of public health and social measures, diagnostic methods, immune responses, antibody neutralization, or other relevant characteristics.
Reporting guidelines for human microbiome research: the STORMS checklist
C Mirzayi et al, Nature Medicine, November 17, 2021
(Posted: Nov 18, 2021 5AM)
A multidisciplinary group of microbiome epidemiology researchers adapted guidelines for observational and genetic studies to culture-independent human microbiome studies, and also developed new reporting elements for laboratory, bioinformatics and statistical analyses tailored to microbiome studies. The resulting tool, called ‘Strengthening The Organization and Reporting of Microbiome Studies’ (STORMS), is composed of a 17-item checklist organized into six sections that correspond to the typical sections of a scientific publication, presented as an editable table for inclusion in supplementary materials.
Transdisciplinary Conference for Future Leaders in Precision Public Health
Speakers Slide Presentations, November 2021
(Posted: Nov 12, 2021 7AM)
This virtual event held in October 2021 connected future research leaders around the world interested in the role of genetics and precision health in the promotion of public health. The speakers provided opportunities for early career investigators to discuss new developments in precision public health with leading experts in the field. Attendees heard from expert epidemiologists, behavioral scientists, statisticians, and global public health leaders about topics such as health equity in genetic epidemiology, genetic risk communication in cancer care, and biostatistics and modeling.
The value of vaccine programme impact monitoring during the COVID-19 pandemic
JR Ortiz et al, The Lancet, November 3, 2021
(Posted: Nov 05, 2021 6PM)
Observational assessments of vaccine performance have taken on increased importance as populations targeted for vaccination expand, the epidemiology of the pandemic evolves, and randomized placebo-controlled trials become less feasible and ethical to conduct.7, 8 It will be important to assess public health outcomes in diverse settings, given differences in circulation and emergence of viral variants, the heterogeneity of vaccines and vaccination schedules, and the diversity of populations targeted.
Elimination versus mitigation of SARS-CoV-2 in the presence of effective vaccines
MO Barton, The Lancet Global Health, November 2, 2021
(Posted: Nov 03, 2021 11AM)
There is increasing evidence that elimination strategies have resulted in better outcomes for public health, the economy, and civil liberties than have mitigation strategies throughout the first year of the COVID-19 pandemic. With vaccines that offer high protection against severe forms of COVID-19, and increasing vaccination coverage, policy makers have had to reassess the trade-offs between different options. The desirability and feasibility of eliminating SARS-CoV-2 compared with other strategies should also be re-evaluated from the perspective of different fields, including epidemiology, public health, and economics.
Analysis of Sociodemographic, Clinical, and Genomic Factors Associated With Breast Cancer Mortality in the Linked Surveillance, Epidemiology, and End Results and Medicare Database
TJ Robinson et al, JAMA Network Open, October 29,2021
(Posted: Nov 01, 2021 4PM)
EER-Medicare data were available for 3522 women (mean [SD] age, 70.9 [2.6] years; 3049 [86.6%] White), of whom 1555 (44.2%) were diagnosed by screening mammogram. In the SEER-Medicare cohort, factors associated with increased BCS mortality included symptomatic detection (hazard ratio [HR], 1.49 [95% CI, 1.16-1.91]), advanced disease stage (HR for stage III, 2.33 [95% CI, 1.41-3.85]), and high-grade disease (HR, 1.85 [95% CI, 1.46-2.34]). The molecular cohort of 130 cases with luminal A/B cancer further revealed increased all-cause mortality associated with genomic upregulation of transforming growth factor ß activation and p53 dysregulation (eg, p53 dysregulation: HR, 2.15 [95% CI, 1.20-3.86]) and decreased mortality associated with androgen receptor, macrophage, cytotoxicity, and Treg signaling (eg, androgen receptor signaling: HR, 0.23 [95% CI, 0.12-0.45]).
Strengthening the Reporting of Observational Studies in Epidemiology Using Mendelian Randomization
The STROBE-MR Statement
V Skrivankova et al, JAMA October 26, 2021
(Posted: Oct 26, 2021 0PM)
An international expert committee, informed by the methodological framework for guideline development of the Enhancing the Quality and Transparency of Health Research (EQUATOR) Network and using a consensus process, developed the STROBE-MR checklist, which includes 20 main items and 30 subitems for reporting the results of MR studies. Use of the STROBE-MR reporting guideline for MR studies could facilitate evaluation by editors, peer reviewers, researchers, clinicians, and other readers, and enhance the interpretation of their results.
Genomic epidemiology and the role of international and regional travel in the SARS-CoV-2 epidemic in Zimbabwe: a retrospective study of routinely collected surveillance data
T Mashe et al, Lancet Global Health, October 2021
(Posted: Oct 25, 2021 1PM)
Advances in SARS-CoV-2 sequencing have enabled identification of new variants, tracking of its evolution, and monitoring of its spread. We aimed to use whole genome sequencing to describe the molecular epidemiology of the SARS-CoV-2 outbreak and to inform the implementation of effective public health interventions for control in Zimbabwe. We found that initial public health interventions delayed onset of SARS-CoV-2 community transmission after the introduction of the virus from international and regional migration in Zimbabwe. Global whole genome sequence data are essential to reveal major routes of spread and guide intervention strategies.
Trans-ethnic Mendelian-randomization study reveals causal relationships between cardiometabolic factors and chronic kidney disease.
Zheng Jie et al. International journal of epidemiology 2021 10
(Posted: Oct 24, 2021 6PM)
51, 672 CKD cases and 958 102 controls of European ancestry from CKDGen, UK Biobank and HUNT, and 13 093 CKD cases and 238 118 controls of East Asian ancestry from Biobank Japan, China Kadoorie Biobank and Japan-Kidney-Biobank/ToMMo were included. Eight risk factors showed reliable evidence of causal effects on CKD in Europeans, including genetically predicted body mass index (BMI), hypertension, systolic blood pressure, high-density lipoprotein cholesterol, apolipoprotein A-I, lipoprotein(a), type 2 diabetes (T2D) and nephrolithiasis. In East Asians, BMI, T2D and nephrolithiasis showed evidence of causality on CKD.
A prospective evaluation of AI-augmented epidemiology to forecast COVID-19 in the USA and Japan
SA Arik et al,NPJ Digital Medicine, October 8, 2021
(Posted: Oct 09, 2021 7AM)
We present an international, prospective evaluation of our models’ performance across all states and counties in the USA and prefectures in Japan. Nationally, incident mean absolute percentage error (MAPE) for predicting COVID-19 associated deaths during prospective deployment remained consistently <8% (US) and <29% (Japan), while cumulative MAPE remained <2% (US) and <10% (Japan). We show that our models perform well even during periods of considerable change in population behavior, and are robust to demographic differences across different geographic locations. We further demonstrate that our framework provides meaningful explanatory insights with the models accurately adapting to local and national policy interventions.
Using genomic epidemiology of SARS-CoV-2 to support contact tracing and public health surveillance in rural Humboldt County, California.
G Stoddard et al, MEDRXIV, September 27, 2021
(Posted: Sep 27, 2021 7AM)
853 whole SARS-CoV-2 genomes were generated, representing ~58% of the 1,449 SARS-CoV-2-positive cases detected in Humboldt County as of March 12, 2021. Phylogenetic analysis of these data was used to develop a comprehensive understanding of SARS-CoV-2 introductions to the county and to support contact tracing and epidemiologic investigations of all large outbreaks in the county. In the case of an outbreak on a commercial farm, viral genomic data were used to validate reported epidemiologic links and link additional cases within the community who did not report a farm exposure to the outbreak.
Tracking the temporal variation of COVID-19 surges through wastewater-based epidemiology during the peak of the pandemic: a six-month long study in Charlotte, North Carolina
VB Barua et al, MEDRXIV, September 24, 2021
(Posted: Sep 26, 2021 7AM)
Impact of paternal education on epigenetic ageing in adolescence and mid-adulthood: a multi-cohort study in the USA and Mexico.
Joyce Brian T et al. International journal of epidemiology 2021 9
(Posted: Sep 19, 2021 10AM)
Both parental and neighbourhood socio-economic status (SES) are linked to poorer health independently of personal SES measures, but the biological mechanisms are unclear. Our objective was to examine these influences via epigenetic age acceleration (EAA)—the discrepancy between chronological and epigenetic ages.We examined three USA-based [Coronary Artery Risk Disease in Adults (CARDIA) study, Fragile Families and Child Wellbeing Study (FFCWS) and Programming Research in Obesity, Growth, Environment and Social Stressors (PROGRESS)] and one Mexico-based (Project Viva) cohort. Our findings suggest that EAA captures epigenetic impacts of paternal education independently of personal SES later in life.
State-wide Genomic Epidemiology Investigations of COVID-19 Infections in Healthcare Workers: Insights for Future Pandemic Preparedness
AE Watts et al, MEDRXIV, September 13, 2021
(Posted: Sep 14, 2021 7AM)
Genomic sequencing was successful for 612 (80%) cases. Thirty-six investigations were undertaken across 12 HCFs. Genomic analysis revealed that multiple introductions of COVID-19 into facilities (31/36) were more common than single introductions (5/36). Major contributors to HCW acquisitions included mobility of staff and patients between wards and facilities, and characteristics and behaviors of individual patients including super-spreading events.
A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa
E Wilkinson et al, Science, September 10, 2021
(Posted: Sep 12, 2021 5PM)
Progression of the SARS-CoV-2 pandemic in Africa has so far been heterogeneous and the full impact is not yet well understood. Here, we describe the genomic epidemiology using a dataset of 8746 genomes from 33 African countries and two overseas territories. We show that the epidemics in most countries were initiated by importations predominantly from Europe, which diminished following the early introduction of international travel restrictions. As the pandemic progressed, ongoing transmission in many countries and increasing mobility led to the emergence and spread within the continent of many variants of concern and interest.
The next phase of SARS-CoV-2 surveillance: real-time molecular epidemiology
BBO Munnink et al, Nature Medicine, September 9, 2021
(Posted: Sep 10, 2021 7AM)
To prepare for the next phase of the pandemic, a systematic approach is needed to link global genomic surveillance and timely assessment of the phenotypic characteristics of novel variants, which will support the development and updating of diagnostics, vaccines, therapeutics and nonpharmaceutical interventions. This Review summarizes the current knowledge on key viral mutations and variants and looks to the next phase of surveillance of the evolving pandemic.
Assessment of COVID-19 intervention strategies in the Nordic countries using genomic epidemiology
S Duchene et al, MEDRXIV, September 8, 2021
(Posted: Sep 09, 2021 8AM)
Wastewater-Based Epidemiology and Whole-Genome Sequencing for Community-Level Surveillance of SARS-CoV-2 in Selected Urban Communities of Davao City, Philippines: A Pilot Study
MCB Otero et al, MEDRXIV, September 3, 2021
(Posted: Sep 04, 2021 8AM)
Sensitivity of wastewater-based epidemiology for detection of SARS-CoV-2 RNA in a low prevalence setting
J Hewitt et al, MEDRXIV, August 26, 2021
(Posted: Aug 27, 2021 6AM)
