592 hot topic(s) found with the query "Surveillance"
Dynamic SARS-CoV-2 surveillance model combining seroprevalence and wastewater concentrations for post-vaccine disease burden estimates
RH Holm et al, Comm Med, April 9, 2024
(Posted: Apr 10, 2024 8AM)
From the abstract: "We used weekly SARS-CoV-2 wastewater concentration with a stratified random sampling of seroprevalence, and linked vaccination and hospitalization data, from April 2021–August 2021 in Jefferson County, Kentucky (USA). We show the 64% county vaccination rate translate into about a 61% decrease in SARS-CoV-2 incidence. The estimated effect of SARS-CoV-2 Delta variant emergence is a 24-fold increase of infection counts, which correspond to an over 9-fold increase in wastewater concentration. Hospitalization burden and wastewater concentration have the strongest correlation (r?=?0.95) at 1 week lag."
Genomics reveals heterogeneous Plasmodium falciparum transmission and selection signals in Zambia.
Abebe A Fola et al. Commun Med (Lond) 2024 4 (1) 67
(Posted: Apr 10, 2024 8AM)
From the abstract: "We conducted genomic surveillance of Plasmodium falciparum parasites from the 2018 Malaria Indicator Survey in Zambia, a nationally representative household survey of children under five years of age. We whole-genome sequenced and analyzed 241?P. falciparum genomes from regions with varying levels of malaria transmission across Zambia and estimated genetic metrics that are informative about transmission intensity, genetic relatedness between parasites, and selection. We provide genomic evidence of widespread within-host polygenomic infections, regardless of epidemiological characteristics, underscoring the extensive and ongoing endemic malaria transmission in Zambia. Our analysis reveals country-level clustering of parasites from Zambia and neighboring regions, with distinct separation in West Africa. "
Concerted efforts toward genomic surveillance of viral pathogens in immunocompromised individuals.
Matheus Filgueira Bezerra et al. Lancet Microbe 2024 4
(Posted: Apr 08, 2024 9AM)
From the article: "A recent study underscores the crucial need to closely monitor immunocompromised individuals with prolonged SARS-CoV-2 infections for emerging variants and investigate their phenotypic implications. Sequencing the genomes of the viruses from these cases would marginally elevate the cost in the whole COVID-19 genomic surveillance effort, and many countries with universal health systems could effectively integrate the tracking of prolonged COVID-19 infections in people living with HIV into their primary care programmes. "
Viral genome sequencing to decipher in-hospital SARS-CoV-2 transmission events.
Elisabeth Esser et al. Sci Rep 2024 3 (1) 5768
(Posted: Mar 11, 2024 8AM)
From the abstract: "The SARS-CoV-2 pandemic has highlighted the need to better define in-hospital transmissions, a need that extends to all other common infectious diseases encountered in clinical settings. To evaluate how whole viral genome sequencing can contribute to deciphering nosocomial SARS-CoV-2 transmission 926 SARS-CoV-2 viral genomes from 622 staff members and patients were collected. Bioinformatically defined transmission clusters inferred from viral genome sequencing were compared to those inferred from interview-based contact tracing. Clustering analysis of SARS-CoV-2 whole genome sequences can reveal cryptic transmission events missed by classical, interview-based contact tracing, helping to decipher in-hospital transmissions. These results, in line with other studies, advocate for viral genome sequencing as a pathogen transmission surveillance tool in hospitals. "
Prevalence of persistent SARS-CoV-2 in a large community surveillance study.
Mahan Ghafari et al. Nature 2024 2
(Posted: Feb 23, 2024 3PM)
From the abstract: "Persistent SARS-CoV-2 infections may act as viral reservoirs that could seed future outbreaks1,2,3,4,5, give rise to highly divergent lineages6,7,8 and contribute to cases with post-acute COVID-19 sequelae (long COVID)9,10. However, the population prevalence of persistent infections, their viral load kinetics and evolutionary dynamics over the course of infections remain largely unknown. Here, using viral sequence data collected as part of a national infection survey, we identified 381 individuals with SARS-CoV-2 RNA at high titre persisting for at least 30 days, of which 54 had viral RNA persisting at least 60 days. "
Non-SARS-CoV-2 respiratory viral detection and whole genome sequencing from COVID-19 rapid antigen test devices: a laboratory evaluation study
MA Moso et al, Lancet Microbe, February 2024
(Posted: Feb 13, 2024 9AM)
From the abstract: " There has been high uptake of rapid antigen test device use for point-of-care COVID-19 diagnosis. Individuals who are symptomatic but test negative on COVID-19 rapid antigen test devices might have a different respiratory viral infection. We aimed to detect and sequence non-SARS-CoV-2 respiratory viruses from rapid antigen test devices, which could assist in the characterisation and surveillance of circulating respiratory viruses in the community."
Maximizing scarce colonoscopy resources: the crucial role of Stool-Based tests.
Gloria D Coronado et al. J Natl Cancer Inst 2024 2
(Posted: Feb 04, 2024 4PM)
From the abstract: "During the COVID-19 pandemic, health systems, including federally qualified health centers (FQHCs), experienced disruptions in colorectal cancer (CRC) screening. National organizations called for greater use of at-home stool-based testing followed by colonoscopy for those with abnormal test results to limit (in-person) colonoscopy exams to people with acute symptoms, or who were high-risk. This ‘stool-test-first’ strategy may also be useful for adults with low-risk adenomas who are due for surveillance colonoscopy. "
Notes from the Field: The National Wastewater Surveillance System's Centers of Excellence Contributions to Public Health Action During the Respiratory Virus Season - Four U.S. Jurisdictions, 2022-23.
Diana Valencia et al. MMWR Morb Mortal Wkly Rep 2023 11 (48) 1309-1312
(Posted: Dec 01, 2023 7AM)
From the article: "NWSS Centers of Excellence have reported correlation between WWS data and clinical surveillance with WWS allowing localized, timely coverage, and in some situations, valuable lead time notification. In Wisconsin, WWS detected increases in influenza and RSV weeks before increases in related emergency department visits were observed. NWSS data, together with clinical surveillance data, have guided jurisdictional partner decisions regarding allocation of resources, deployment of vaccination clinics, updating clinical guidance, and sending respiratory disease notifications and alerts when trends exceed baseline thresholds. During the 2022–23 respiratory disease season, NWSS Centers of Excellence translated WWS data into real-time public health action for multiple respiratory pathogens, highlighting the contribution of WWS in monitoring disease circulation and helping guide public health response. "
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. "
Inferring bacterial transmission dynamics using deep sequencing genomic surveillance data.
Madikay Senghore et al. Nat Commun 2023 11 (1) 6397
(Posted: Nov 01, 2023 7AM)
From the abstract: "In this work, we assess the utility of deep-sequenced genomic surveillance (where genomic regions are sequenced hundreds to thousands of times) using a mouse transmission model involving controlled spread of the pathogenic bacterium Citrobacter rodentium from infected to naïve female animals. We observe that within-host single nucleotide variants (iSNVs) are maintained over multiple transmission steps and present a model for inferring the likelihood that a given pair of sequenced samples are linked by transmission. "
Circulating Tumor HPV DNA for Surveillance of HPV-Positive Oropharyngeal Squamous Cell Carcinoma: A Narrative Review.
Krystle A Lang Kuhs et al. JAMA Oncol 2023 10
(Posted: Oct 13, 2023 1PM)
From the abstract: "This article reviews the current state of knowledge, highlights existing knowledge gaps, and suggests research that should be prioritized to understand the association between biomarker-based surveillance and patient outcomes. Specific attention is paid to the commercially available tumor tissue–modified viral HPV DNA assay, given its increasing clinical use. This review may serve as a road map for future research and a guide for clinicians considering its adoption in practice. Enrollment of patients into clinical trials incorporating biomarker-based surveillance should be prioritized. "
Genomic surveillance for antimicrobial resistance - a One Health perspective.
Steven P Djordjevic et al. Nat Rev Genet 2023 9
(Posted: Sep 29, 2023 7AM)
From the abstract: "To understand and manage the threat posed to health (human, animal, plant and environmental) and security (food and water security and biosecurity), a multifaceted ‘One Health’ approach to AMR surveillance is required. Genomic technologies have enabled monitoring of the mobilization, persistence and abundance of AMR genes and mutations within and between microbial populations. Their adoption has also allowed source-tracing of AMR pathogens and modelling of AMR evolution and transmission. "
Engaging a national-scale cohort of smart thermometer users in participatory surveillance
YJ Tseng et al, NPJ Digital Medicine, September 20, 2023
(Posted: Sep 21, 2023 2PM)
From the abstract: "Participatory surveillance systems crowdsource individual reports to rapidly assess population health phenomena. The value of these systems increases when more people join and persistently contribute. We examine the level of and factors associated with engagement in participatory surveillance among a retrospective, national-scale cohort of individuals using smartphone-connected thermometers with a companion app that allows them to report demographic and symptom information. Between January 1, 2020 and October 29, 2022, 1,325,845 participants took 20,617,435 temperature readings, yielding 3,529,377 episodes of consecutive readings. There were 1,735,805 (49.2%) episodes with self-reported symptoms (including reports of no symptoms). "
“I don’t need any more unknowns hanging over my head”: Cancer patients’ views on variants of uncertain significance and low/moderate risk results from genomic sequencing
S Shickh et al, Genet in Medicine, August 11, 2023
(Posted: Aug 11, 2023 11AM)
We sought to explore patient-reported utility of all types of cancer results from genomic sequencing (GS). This was a qualitative study, using semi-structured interviews with patients who underwent GS within a trial. Patients’ perceptions of the utility of cancer GS results hinged on whether they triggered clinical action. For example, when patients were enrolled into high-risk breast cancer surveillance programs for low/moderate risk breast cancer genes, they perceived the results to be very “useful” and of moderate-high utility. In contrast, patients receiving low/moderate risk or primary VUS results without clinical action perceived results as “concerning”, leading to harms such as hypervigilance about cancer symptoms.
Management of individuals with germline pathogenic/likely pathogenic variants in CHEK2: A clinical practice resource of the American College of Medical Genetics and Genomics (ACMG)
H Hanson et al, Genetics in Medicine, July 25, 2023
(Posted: Jul 26, 2023 8AM)
Although CHEK2 is considered a moderate penetrance gene, cancer risks may be considered as a continuous variable, which are influenced by family history and other modifiers. Consequently, early cancer detection and prevention for CHEK2 heterozygotes should be guided by personalized risk estimates. Such estimates may result in both downgrading lifetime breast cancer risks to those similar to the general population or upgrading lifetime risk to a level at which CHEK2 heterozygotes are offered high-risk breast surveillance according to country-specific guidelines.
A new era of pathogen surveillance using genomic sequencing
Open Access Government, July 19, 2023
(Posted: Jul 21, 2023 7AM)
Genomic sequencing is a method scientists use to decipher the genetic material found in organisms or viruses. The significance of genomic sequencing tools was truly brought to the fore during the COVID-19 pandemic as researchers were able to observe any sudden changes (or mutations) in a virus’s genetic code which may give it an advantage over other variants of itself, for example, spreading faster or causing more harm to those it infects.
Utility of Exome Sequencing for Diagnosis in Unexplained Pediatric-Onset Epilepsy.
Hyun Yong Koh et al. JAMA Netw Open 2023 7 (7) e2324380
(Posted: Jul 21, 2023 7AM)
What are the diagnostic yield and clinical utility of genetic sequencing for patients with unexplained pediatric epilepsy? This cohort study of 522 children with previously unexplained epilepsy used exome sequencing to identify and clinically confirm diagnostic results for 100 children, including 89 with single nucleotide variants and 11 with copy number variants. Individuals with earlier seizure onset, intellectual disability, and motor impairment were more likely to have diagnostic results, and at least 29 patients had changes in treatment, surveillance, or prognosis based on their genetic diagnoses.
Tackling covid-19 variants.
Kayoko Shioda et al. BMJ 2023 7 p1603
(Posted: Jul 16, 2023 9AM)
SARS-CoV-2 is probably here to stay. The question is whether countries have the necessary tools and capacity to detect new variants and evaluate their severity so that we can act quickly to protect the most vulnerable populations. Surveillance is the obvious essential tool, but is it robust enough? What is our current situation, and where are we headed? Genomic surveillance has a critical role in detecting new variants, but 32% of countries lacked this capacity in January 2022, despite the scale-up during the covid-19 pandemic.
Global, regional, and national prevalence and mortality burden of sickle cell disease, 2000-2021: a systematic analysis from the Global Burden of Disease Study 2021.
et al. Lancet Haematol 2023 6
(Posted: Jul 12, 2023 9AM)
We estimated cause-specific sickle cell disease mortality using standardised GBD approaches, in which each death is assigned to a single underlying cause, to estimate mortality rates from the International Classification of Diseases (ICD)-coded vital registration, surveillance, and verbal autopsy data. In parallel, our goal was to estimate a more accurate account of sickle cell disease health burden using four types of epidemiological data on sickle cell disease: birth incidence, age-specific prevalence, with-condition mortality (total deaths), and excess mortality (excess deaths). Our findings show a strikingly high contribution of sickle cell disease to all-cause mortality that is not apparent when each death is assigned to only a single cause. Sickle cell disease mortality burden is highest in children, especially in countries with the greatest under-5 mortality rates.
Community Counts: Understanding Hemophilia and Other Bleeding Disorders through Public Health Surveillance
CDC webinar, August 24, 2023
(Posted: Jul 11, 2023 8AM)
Over the past 20 years, CDC has conducted public health surveillance to better understand the characteristics and complications that impact the bleeding disorders population. Community Counts is a public health surveillance program that gathers and shares information about common health issues, medical complications, and causes of death that affect people with bleeding disorders cared for in U.S. Hemophilia Treatment Centers.
Performance of Liquid Biopsy for Diagnosis and Surveillance of Human Papillomavirus-Associated Oropharyngeal Cancer.
Rocco M Ferrandino et al. JAMA Otolaryngol Head Neck Surg 2023 7
(Posted: Jul 10, 2023 11AM)
What is the accuracy of tumor tissue–modified human papillomavirus DNA (TTMV-HPV DNA) liquid biopsy in the diagnosis and surveillance of HPV-associated oropharyngeal squamous cell carcinoma (OPSCC)? In this cohort study of 399 patients in a contemporary clinical setting, TTMV-HPV DNA testing at the time of OPSCC diagnosis demonstrated excellent sensitivity and specificity of 91.5% and 100%, respectively. With respect to surveillance, the TTMV-HPV DNA test had a sensitivity of 88.4% and specificity of 100% for detecting a recurrence.
A new network for pathogen surveillance.
Talha Burki et al. Lancet Infect Dis 2023 7 (7) 792-793
(Posted: Jul 05, 2023 7AM)
A Critical Opportunity to Improve Public Health Data.
David Blumenthal et al. N Engl J Med 2023 6
(Posted: Jun 29, 2023 7AM)
In a country as large and heterogeneous as the United States, the decentralization of public health may seem appropriate. But during an infectious health emergency, in which disease spreads with no respect for political jurisdictions, fragmentation carries huge risks. States and localities develop their own data systems using their own definitions of critical terms and methods of data collection.
Traveler-based Genomic Surveillance for Early Detection of New SARS-CoV-2 Variants
CDC, June 2023
(Posted: Jun 26, 2023 8AM)
The Traveler Genomic Surveillance program (TGS), run by the Travelers’ Health Branch at CDC in partnership with Ginkgo Bioworks and XpresCheck, plays an important role in U.S. national surveillance by testing travelers to detect new variants entering the country and fill gaps in global surveillance. In September 2021, during the Delta wave, the program began collecting samples from travelers arriving at three major U.S. international airports, John F. Kennedy in New York City, Newark Liberty, and San Francisco.
Description of the first global outbreak of mpox: an analysis of global surveillance data
HLS Schafer et al, Lancet Global Health, July 2023
(Posted: Jun 26, 2023 8AM)
In this analysis of global surveillance data we analysed data for all confirmed mpox cases reported by WHO Member States through the global surveillance system from Jan 1, 2022, to Jan 29, 2023. Data from 82?807 cases were included in the analysis. Cases were primarily due to clade IIb MPXV (mainly lineage B.1, followed by lineage A.2). The outbreak was driven by transmission among males (73?560 [96·4%] of 76?293 cases) who self-identify as men who have sex with men (25?938 [86·9%] of 29?854 cases). The most common reported route of transmission was sexual contact (14?941 [68·7%] of 21?749).
WHO Introduces Worldwide Pathogen Surveillance Network
E Harris, JAMA, June 20, 2023
(Posted: Jun 21, 2023 7AM)
A global collaboration, known as the International Pathogen Surveillance Network, will harness pathogen genomics to improve disease surveillance and identify and respond to disease-causing agents before they become pandemics or epidemics, the World Health Organization (WHO) announced. The Network will connect members of different countries to improve sample collection and analysis and facilitate public health decision-making, among other goals.
Pathogen genomics—which involves analyzing the genomes of viruses, bacteria, and other contagions to understand their infectivity, deadliness, and transmission—has played a key role in the world’s ability to respond to diseases, from COVID-19 to HIV.
ReporTree: a surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data.
Verónica Mixão et al. Genome Med 2023 6 (1) 43
(Posted: Jun 20, 2023 7AM)
We developed ReporTree, a flexible bioinformatics pipeline that allows diving into the complexity of pathogen diversity to rapidly identify genetic clusters at any (or all) distance threshold(s) or cluster stability regions and to generate surveillance-oriented reports based on the available metadata, such as timespan, geography, or vaccination/clinical status.
Genomic Surveillance for SARS-CoV-2 Variants: Circulation of Omicron Lineages - United States, January 2022-May 2023.
Kevin C Ma et al. MMWR Morb Mortal Wkly Rep 2023 6 (24) 651-656
(Posted: Jun 16, 2023 7AM)
CDC has used national genomic surveillance since December 2020 to monitor SARS-CoV-2 variants that have emerged throughout the COVID-19 pandemic, including the Omicron variant. This report summarizes U.S. trends in variant proportions from national genomic surveillance during January 2022-May 2023. During this period, the Omicron variant remained predominant, with various descendant lineages reaching national predominance (>50% prevalence).
Generation of SARS-CoV-2 escape mutations by monoclonal antibody therapy
MR Cronin et al, Nat Comm, June 7, 2023
(Posted: Jun 07, 2023 1PM)
COVID-19 patients at risk of severe disease may be treated with neutralising monoclonal antibodies (mAbs). To minimise virus escape from neutralisation these are administered as combinations e.g. casirivimab+imdevimab or, for antibodies targeting relatively conserved regions, individually e.g. sotrovimab. Unprecedented genomic surveillance of SARS-CoV-2 in the UK has enabled a genome-first approach to detect emerging drug resistance in Delta and Omicron cases treated with casirivimab+imdevimab and sotrovimab respectively.
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.
Use of digital technologies for public health surveillance during the COVID-19 pandemic: A scoping review.
Lorie Donelle et al. Digit Health 2023 5 20552076231173220
(Posted: May 24, 2023 9AM)
The most frequently used technologies included mobile phone devices and applications, location tracking technologies, drones, temperature scanning technologies, and wearable devices. The utility of digital technologies for public health surveillance was impacted by factors including uptake of digital technologies across targeted populations, technological capacity and errors, scope, validity and accuracy of data, guiding legal frameworks, and infrastructure to support technology use.
Wastewater monitoring can anchor global disease surveillance systems.
Aparna Keshaviah et al. Lancet Glob Health 2023 5 (6) e976-e981
(Posted: May 21, 2023 9AM)
To inform the development of global wastewater monitoring systems, we surveyed programmes in 43 countries. Most programmes monitored predominantly urban populations. In high-income countries (HICs), composite sampling at centralised treatment plants was most common, whereas grab sampling from surface waters, open drains, and pit latrines was more typical in low-income and middle-income countries (LMICs). Almost all programmes analysed samples in-country, with an average processing time of 2·3 days in HICs and 4·5 days in LMICs.
As Covid Emergency Ends, Surveillance Shifts to the Sewers
A ANtnes NY Times, May 11, 2023
(Posted: May 12, 2023 6AM)
With other virus tracking efforts winding down, wastewater data is likely to become increasingly important in the months ahead, scientists say.
This approach expanded rapidly during the pandemic. The National Wastewater Surveillance System, which the C.D.C. established in late 2020, now includes data from more than 1,400 sampling sites, distributed across 50 states, three territories and 12 tribal communities.
Wasting no time: CDC adapts wastewater surveillance to stay vigilant for emerging threats
A Kirby, CDC, May 2023
(Posted: May 10, 2023 6AM)
The COVID-19 pandemic made the value of sewage clear. For epidemiologists, CDC’s National Wastewater Surveillance System (NWSS) provides invaluable insights by helping identify community infection trends before they appear in clinical cases. In 2022, NWSS enhanced detection of SARS-CoV-2 and its variants. But perhaps equally critical were efforts to adapt wastewater surveillance for other emerging infectious disease challenges.
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.
Genome-based surveillance offers new hope in the fight against healthcare-associated infections
P Bose, News Medical, May 2, 2023
(Posted: May 05, 2023 10AM)
Large volumes of high-quality data can be created by high-throughput bacterial genomic sequencing. Simultaneous developments in sequencing technology and bioinformatics have made it easier to use genomics to analyze outbreaks and conduct broader public health surveillance. Pathogen or AMR dissemination could prevail for years if they went unnoticed or prevention and control strategies were less effective. From a public health perspective, the focus of hospital pathogen surveillance is, to a large extent, AMR surveillance, which needs a greater adoption of long-read sequencing.
A break from Covid waves and a breakthrough for preventing Long Covid
E Topol, Ground Truths, May 1, 2023
(Posted: May 01, 2023 10AM)
All indications from genomic surveillance of the virus, wastewater. and the clinical outcomes that are still being tracked (albeit more limited and less periodicity as time goes on), that we’ve (finally) entered an endemic phase (think smaller “wavelets”). There are no new SARS-CoV-2 variants that have yet cropped up with a growth advantage over XBB.1.5 (the recombinant with 2 significant mutations added on) which is dominant throughout much of the world, or its cousin, XBB.1.9.1.
Mainstreaming Wastewater Surveillance for Infectious Disease.
Michelle M Mello et al. N Engl J Med 2023 4 (16) 1441-1444
(Posted: Apr 20, 2023 11AM)
During the Covid-19 pandemic, valuable intelligence on trends in the infection rates, variants, and distribution of SARS-CoV-2 in the United States was obtained from the humblest of assets: the country’s sewage. Analyzing fragments of viral RNA shed into sewers, organizations including universities and the Centers for Disease Control and Prevention (CDC) used wastewater to understand disease dynamics. This information became especially important as new variants emerged and use of home antigen testing exacerbated the reporting bias present in traditional testing systems.
Utilization of Circulating Tumor Cells in the Management of Solid Tumors
PC Kumiali et al, J Per Med, April 20., 2023
(Posted: Apr 20, 2023 10AM)
CTCs may play significant roles in cancer screening, diagnosis, treatment navigation, including prognostication and precision medicine, and surveillance. In cancer screening, capturing and evaluating CTCs from peripheral blood could be a strategy to detect cancer at its earliest stage. Cancer diagnosis using liquid biopsy could also have tremendous benefits. Full utilization of CTCs in the clinical management of malignancies may be feasible in the near future; however, several challenges still exist.
A global aircraft-based wastewater genomic surveillance network for early warning of future pandemics.
Jiaying Li et al. Lancet Glob Health 2023 4 (5) e791-e795
(Posted: Apr 16, 2023 6AM)
We propose the development of a global aircraft-based wastewater genomic surveillance network, with the busiest international airports as central nodes and continuing air travel journeys as vectors. This surveillance program requires routinely collecting aircraft wastewater samples for microbiological analysis and sequencing and linking the resulting data with associated international air traffic information. With the creation of a strong international alliance between the airline industry and health authorities, this surveillance network will potentially complement public health systems with a true early warning ability to inform decision making for new variants and future global health risks.
Tracking early lung cancer metastatic dissemination in TRACERx using ctDNA.
Christopher Abbosh et al. Nature 2023 4
(Posted: Apr 14, 2023 7AM)
Landmark analyses of plasma samples collected within 120?days after surgery revealed ctDNA detection in 25% of patients, including 49% of all patients who experienced clinical relapse; 3 to 6 monthly ctDNA surveillance identified impending disease relapse in an additional 20% of landmark-negative patients. We developed a bioinformatic tool (ECLIPSE) for non-invasive tracking of subclonal architecture at low ctDNA levels. ECLIPSE identified patients with polyclonal metastatic dissemination, which was associated with a poor clinical outcome.
The evolution and international spread of extensively drug resistant Shigella sonnei.
Lewis C E Mason et al. Nature communications 2023 4 (1) 1983
(Posted: Apr 10, 2023 7AM)
Our genomic epidemiological analyses of 3,304 isolates from the United Kingdom, Australia, Belgium, France, and the United States of America revealed an internationally connected outbreak with a most recent common ancestor in 2018 carrying a low-fitness cost resistance plasmid, previously observed in travel associated sublineages of S. flexneri. Our results highlight the persistent threat of horizontally transmitted antimicrobial resistance and the value of continuing to work towards early and open international sharing of genomic surveillance data.
Surveillance of SARS-CoV-2 at the Huanan Seafood Market
WJ Liu et al, Nature, April 5, 2023
(Posted: Apr 05, 2023 5AM)
SARS-CoV-2, the causative agent of COVID-19, emerged in December 2019. Its origins remain uncertain. It has been reported that a number of the early human cases had a history of contact with the Huanan Seafood Market. Here we present the results of surveillance for SARS-CoV-2 within the market. From January 1st 2020, after closure of the market, 923 samples were collected from the environment. From 18th January, 457 samples were collected from 18 species of animals, comprising of unsold contents of refrigerators and freezers, swabs from stray animals, and the contents of a fish tank. Using RT-qPCR, SARS-CoV-2 was detected in 73 environmental samples, but none of the animal samples.
Mortality by age, gene and gender in carriers of pathogenic mismatch repair gene variants receiving surveillance for early cancer diagnosis and treatment: a report from the prospective Lynch syndrome database
MD Valentin et al, EClinicalMedicine, March 2023
(Posted: Mar 22, 2023 7AM)
The Prospective Lynch Syndrome Database (PLSD) collates information on carriers of pathogenic or likely pathogenic MMR variants (path_MMR) who are receiving medical follow-up, including colonoscopy surveillance, which aims to the achieve early diagnosis and treatment of cancers. In path_MMR carriers undergoing colonoscopy surveillance, non-colorectal Lynch syndrome cancers were associated with more deaths than were colorectal cancers. Reducing deaths from non-colorectal cancers presents a key challenge in contemporary medical care in Lynch syndrome.
Viruses in sewage help to pinpoint typhoid hotspots Targeting the virus that infects the disease-causing bacterium could be a cheap way to prioritize populations for vaccination campaigns.
S Mallapaty, Nature, March 22, 2023
(Posted: Mar 22, 2023 7AM)
Public-health officials typically rely on numbers of infected people to identify communities to prioritize for vaccination campaigns, but these data are limited because they rely on testing at health facilities, to which many people in resource-poor regions don’t have access. Some researchers have tried to improve surveillance by testing for the presence of S. Typhi in wastewater, but isolating the bacterium requires collecting large amounts of water and often doesn’t work. Molecular approaches that involve sequencing segments of DNA using a technique called polymerase chain reaction (PCR) are expensive.
Utility of non-invasive Saline Gargle SARS-CoV-2 genome surveillance in post-pandemic scenario and limitations of wastewater surveillance
K Khairmar et al, MEDRXIV, March 7, 2023
(Posted: Mar 07, 2023 6PM)
Spatially-resolved wastewater-based surveillance enables COVID-19 case localization across a university campus, and confirms lower SARS-CoV-2 RNA burden relative to the surrounding community
J Lee et al, MEDRXIV, March 6, 2023
(Posted: Mar 06, 2023 6PM)
Wastewater-based surveillance (WBS) has been established as a powerful tool that can guide health policy at multiple levels of government. However, this technology has not been well assessed at more granular scales, including large work sites such as University campuses.
Genomic surveillance reveals early detection and transition of Delta to Omicron Lineages of SARS-CoV-2 Variants in wastewater treatment plants of Pune, India
V Rajput et al, MEDRXIV, February 24, 2023
(Posted: Feb 26, 2023 8AM)
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.
Effect of Predeparture Testing on Postarrival SARS-CoV-2-Positive Test Results Among International Travelers - CDC Traveler-Based Genomic Surveillance Program, Four U.S. Airports, March-September 2022.
Stephen M Bart et al. MMWR. Morbidity and mortality weekly report 2023 2 (8) 206-209
(Posted: Feb 24, 2023 7AM)
During December 6, 2021–June 11, 2022, SARS-CoV-2 testing =1 day before departure or proof of recent COVID-19 recovery were required for passengers boarding U.S.-bound flights. Mathematical models have estimated predeparture testing effectiveness in preventing travel-associated transmission.
CDC’s Traveler-based Genomic Surveillance Program collects postarrival nasal swabs for SARS-CoV-2 testing from volunteering international air travelers. Among 3,049 pooled (28,056 individual) samples collected during March 20–September 3, 2022, the predeparture testing requirement was associated with 52% lower postarrival SARS-CoV-2 positivity.
Notes from the Field: Aircraft Wastewater Surveillance for Early Detection of SARS-CoV-2 Variants — John F. Kennedy International Airport, New York City, August–September 2022
RS Morfino et al, MMWR, February 24, 2023
(Posted: Feb 23, 2023 1PM)
As SARS-CoV-2 testing declines worldwide, surveillance of international travelers for SARS-CoV-2 enables detection of emerging variants and fills gaps in global genomic surveillance. Because SARS-CoV-2 can be detected in feces and urine of some infected persons, wastewater surveillance in airports and on aircraft has been proposed by the global public health community† as a low-cost mechanism to monitor SARS-CoV-2 variants entering the United States. Sampling wastewater directly from aircraft can be used to link SARS-CoV-2 lineage data with flight origin countries without active engagement of travelers.
A systematic review of economic evaluations of whole-genome sequencing for the surveillance of bacterial pathogens.
Vivien Price et al. Microbial genomics 2023 2 (2)
(Posted: Feb 17, 2023 9AM)
Six hundred and eighty-one articles were identified, of which 49 proceeded to full-text screening, with 9 selected for inclusion. All had been published since 2019. Heterogeneity was high. Five studies assessed WGS for hospital surveillance and four analyzed foodborne pathogens. Four were cost-benefit analyses, one was a cost-utility analysis, one was a cost-effectiveness analysis, one was a combined cost-effectiveness and cost-utility analysis, one combined cost-effectiveness and cost-benefit analyses and one was a partial analysis. All studies supported the use of WGS as a surveillance tool on economic grounds.
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.
Wastewater genomic surveillance tracks the spread of the SARS-CoV-2 Omicron variant across England
F Bruner et al, MEDRXIV, February 16, 2023
(Posted: Feb 17, 2023 6AM)
We analyzed more than 19,000 samples from 524 wastewater sites across England at least twice a week between November 2021 and February 2022, capturing sewage from >70% of the English population. We show that wastewater data can reconstruct the spread of the Omicron variant across England since November 2021 in close detail and aligns closely with epidemiological estimates from individual testing data. We also show the temporal and spatial spread of Omicron within London.
Sample Size Calculations for Variant Surveillance in the Presence of Biological and Systematic Biases
S Wohl et al, MEDRXIV, February 8, 2023
(Posted: Feb 09, 2023 6AM)
Characterisation of SARS-CoV-2 variants in Beijing during 2022: an epidemiological and phylogenetic analysis
Y Pan et al, The Lancet, February 8, 2023
(Posted: Feb 08, 2023 0PM)
With soaring growth in the number of COVID-19 cases in China recently, there are concerns that there might be an emergence of novel SARS-CoV-2 variants. Routine surveillance of viral genomes has been carried out in Beijing over the last 3 years. From Nov 14 to Dec 20, we sequenced 413 new samples, including 350 local cases and 63 imported cases. All of these genomes belong to the existing 123 Pango lineages, showing there are no persistently dominant variants or novel lineages.
Benefits, Harms and Costs of Newborn Genetic Screening for Hypertrophic Cardiomyopathy: Estimates from the PreEMPT Model
KD Chrisiensen et al, Genetics in Medicine, January 31, 2023
(Posted: Feb 01, 2023 6AM)
In a cohort of 3.7 million newborns, newborn genetic screening would reduce HCM-related deaths through age 20 by 44 (95% uncertainty interval (95% UI): 10 to 103) but increase the numbers of children undergoing surveillance by 8,127 (95% UI, 6,308 to 9,664). Compared to usual care, newborn genetic screening costs $267,000 per life-year saved (95% UI, $106,000 to $919,000 per life-year saved). Newborn genetic screening for HCM could prevent deaths but at a high cost and would require many healthy children to undergo surveillance.
High number of SARS-CoV-2 persistent infections uncovered through genetic analysis of samples from a large community-based surveillance study
M Ghafari et al, MEDRXIV, January 30, 2023
(Posted: Jan 31, 2023 8AM)
We identified 381 infections lasting at least 30 days, of which 54 lasted at least 60 days. These persistently infected individuals had more than 50% higher odds of self-reporting Long Covid compared to the infected controls, and we estimate that 0.09-0.5% of SARS-CoV-2 infections can become persistent and last for at least 60 days. In nearly 70% of the persistent infections we identified, there were long periods during which there were no consensus changes in virus sequences, consistent with prolonged presence of non-replicating virus.
Genomic surveillance of SARS-CoV-2 in COVID-19 vaccinated healthcare workers in Lebanon.
Habib AlKalamouni et al. BMC medical genomics 2023 1 (1) 14
(Posted: Jan 30, 2023 6AM)
Spike Gene Target Amplification in a Diagnostic Assay as a Marker for Public Health Monitoring of Emerging SARS-CoV-2 Variants — United States, November 2021–January 2023
HM Scobie et al, MMWR, January 25, 2023
(Posted: Jan 26, 2023 7AM)
When early nowcast estimates of rapidly emerging variants lacked precision and geographic resolution because of lags in genomic sequencing results, SGTF/SGTP estimates were used as complementary data by CDC and the SARS-CoV-2 Interagency Group to support guidance on the use of monoclonal antibody therapies. SGTF/SGTP data were also used as proxy markers in several early studies of vaccine effectiveness and severity of emerging variants (3,5,6). Continued monitoring of SGTF/SGTP patterns will likely serve as a useful complement to genomic surveillance of SARS-CoV-2 lineages.
The next worrisome coronavirus variant could come from China — will it get detected?
D Lewis, Nature, January 24, 2023
(Posted: Jan 24, 2023 8AM)
Fears that the massive surge of coronavirus infections in China could immediately spark the emergence of a troubling new variant are unfounded, say researchers. But that could change in the coming months as more people in the country acquire some natural immunity from infection. More widespread immunity could drive the virus SARS-CoV-2 to evolve ways to evade these immune protections. It remains crucial that variants be tracked, yet scientists question how quickly the next variant of concern will be detected as many countries wind down surveillance efforts.
Wastewater-based surveillance can be used to model COVID-19-associated workforce absenteeism
N Acosta et al, MEDRXIV< January 23, 2023
(Posted: Jan 24, 2023 7AM)
Wastewater-based Disease Surveillance for Public Health Action
National Academies Consensus Report, January 2023
(Posted: Jan 22, 2023 8AM)
The report concludes that wastewater surveillance is and will continue to be a valuable component of infectious disease management. This report presents a vision for a national wastewater surveillance system that would track multiple pathogens simultaneously and pivot quickly to detect emerging pathogens, and it offers recommendations to ensure that the system is flexible, equitable, and economically sustainable for informing public health actions. The report also recommends approaches to address ethical and privacy concerns and develop a more representative wastewater surveillance system. Predictable and sustained federal funding as well as ongoing coordination and collaboration among many partners will be critical to the effectiveness of efforts moving forward.
Use of Wastewater for Mpox Outbreak Surveillance in California.
Wolfe Marlene K et al. The New England journal of medicine 2023 1
(Posted: Jan 19, 2023 6AM)
As part of the response to the spread of MPXV infection, we adapted and deployed polymerase-chain-reaction assays targeting MPXV genomic DNA5 as part of our ongoing wastewater surveillance program. Testing was implemented within a month after the first identified case of MPXV infection in the United States, and the results were used in real time for the public health response in California.
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.
Wastewater surveillance for public health.
Levy Joshua I et al. Science (New York, N.Y.) 2023 1 (6627) 26-27
(Posted: Jan 09, 2023 5AM)
Wastewater monitoring enables rapid pathogen detection and community prevalence quantification. At sites where wastewater from the population collects and mixes, so too do a diverse array of microbes shed from individuals. The resulting mixture is representative of local infections, and with now-standard laboratory processing and quantitative polymerase chain reaction (qPCR), sensitive concentration measurements of specific pathogens can be obtained affordably and in only a few hours.
An ISO-certified genomics workflow for identification and surveillance of antimicrobial resistance
NL Sherry et al, Nature Comm, January 4, 2023
(Posted: Jan 05, 2023 5AM)
Here, we report the creation and validation of abritAMR, an ISO-certified bioinformatics platform for genomics-based bacterial AMR gene detection. The abritAMR platform utilises NCBI’s AMRFinderPlus, as well as additional features that classify AMR determinants into antibiotic classes and provide customised reports. We validate abritAMR by comparing with PCR or reference genomes, representing 1500 different bacteria and 415 resistance alleles.
Infectiousness of SARS-CoV-2 breakthrough infections and reinfections during the Omicron wave
ST Tan et al, Nature Medicine, January 2, 2023
(Posted: Jan 02, 2023 0PM)
Analyzing SARS-CoV-2 surveillance data from December 2021 to May 2022 across 35 California state prisons with a predominately male population, we estimate that unvaccinated Omicron cases had a 36% (95% confidence interval (CI): 31–42%) risk of transmitting infection to close contacts, as compared to a 28% (25–31%) risk among vaccinated cases. In adjusted analyses, we estimated that any vaccination, prior infection alone and both vaccination and prior infection reduced an index case’s risk of transmitting infection by 22%, 23% and 40%, respectively.
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.
Parents’ decision-making regarding whether to receive adult-onset only genetic findings for their children: Findings from the BabySeq Project
S Pereira et al, Genetics in Medicine, December 20, 2022
(Posted: Dec 20, 2022 8AM)
Parents noted several motivations to receive and reasons to decline adult-onset only results. Most commonly, parents cited early intervention/surveillance (n=11), implications for family heath (n=7), and the ability to prepare (n=6) as motivations to receive these results. The most common reasons to decline were protection of the child’s future autonomy (n=4), negative impact on parenting (n=3), and anxiety about future disease (n=3).
Infectious diseases genomic surveillance capacity in the Caribbean: A retrospective analysis of SARS-CoV-2
MA Ber Lucien et al, Lancet Regional Health, December 19, 2022
(Posted: Dec 20, 2022 8AM)
As of August 6, 2022, the number of SARS-CoV-2 sequences from the Caribbean are underrepresented with only 40,190 (1.07%) of the over 3.76 million documented cases sequenced, which is further exacerbated by a disparity based not only on the country's income but also on its political status (sovereign country versus dependent or integrated) and accessibility to sequencing technologies.
Detection of Monkeypox Virus DNA in Airport Wastewater, Rome, Italy.
La Rosa Giuseppina et al. Emerging infectious diseases 2022 12 (1)
(Posted: Dec 10, 2022 7AM)
Wastewater surveillance for SARS-CoV-2 was adapted for MPX virus detection from the wastewater treatment plant of an international airport with >3M passengers monthly (Rome, Italy, May–Aug 2022). Real-time and nested PCR assays were modified to detect mpox DNA in 24hr composite wastewater samples collected 2x/week. Among 20 samples, 3 had detectable MPXV. Average quantification cycle (Cq) ranged from 38.37–40.18, indicating relatively low DNA concentrations. Consensus sequences found 100% similarity with MPXV strains available in GenBank.
Implementation-effectiveness trial of systematic family health history based risk assessment and impact on clinical disease prevention and surveillance activities.
Wu R Ryanne et al. BMC health services research 2022 12 (1) 1486
(Posted: Dec 09, 2022 2PM)
19 primary care clinics at four geographically and culturally diverse U.S. healthcare systems. Participants: any English or Spanish-speaking adult with an upcoming appointment at an enrolling clinic. A personal and family health history based HRA with integrated guideline-based clinical decision support (CDS) was completed by each participant prior to their appointment. Risk reports were provided to patients and providers to discuss at their clinical encounter.
Systematic health risk assessment revealed that almost half the population were at increased disease risk based on guidelines. Risk identification resulted in shared discussions between participants and providers but variable clinical action uptake depending upon the recommendation.
The new Covid wave It's across most of the planet now. Delving into why, what to expect, and what we can do about it.
E Topol, Ground Truths, December 3, 2022
(Posted: Dec 04, 2022 9AM)
Things are once again going in the wrong direction in the United States. Hospitalizations have jumped by 25% in recent days, along with ICUs, test positivity, wastewater surveillance virus levels, and even cases, which have been grossly under-diagnosed because of home rapid antigen testing or no testing.
Seniors, particularly those without a booster or one in the past 6 months, are bearing most of the brunt with the sharp ascent seen below, already surpassing the summer BA.5 wave nationally.
Reemergence of Cholera in Haiti.
Rubin Daniel H F et al. The New England journal of medicine 2022 11
(Posted: Dec 01, 2022 8AM)
To decipher the relationship between the current outbreak strain and other toxigenic O1 El Tor strains from the ongoing seventh pandemic of cholera, we sequenced the isolate obtained on September 30, 2022, along with four isolates obtained in 2021 and 2022 from Dhaka, Bangladesh. Phylogenetic analysis of more than 1200 isolates revealed that the 2022 Haiti isolate was closely related to the 2010 Nepal isolate that was the origin of the initial outbreak. These analyses suggest that the reemergence of cholera in Haiti in 2022 was caused, at least in part, by a descendant of the V. cholerae strain that caused the 2010 epidemic. However, no cases of cholera were confirmed between 2019 and 2022, despite ongoing surveillance.
Wastewater genomic surveillance captures early detection of Omicron in Utah
P Gupta et al, MEDRXIV, November 29, 2022
(Posted: Nov 30, 2022 8AM)
Here, we investigated the spread of SARS-CoV-2 infections across Utah by characterizing lineages and mutations detected in wastewater samples. We sequenced over 1,200 samples from 32 sewersheds collected between November 2021 and March 2022. Wastewater sequencing confirmed the presence of Omicron (B.1.1.529) in Utah in samples collected on November 19, 2021, up to seven days before its corresponding detection via clinical sequencing.
Global disparities in SARS-CoV-2 genomic surveillance.
Brito Anderson F et al. Nature communications 2022 11 (1) 7003
(Posted: Nov 19, 2022 7AM)
In the first two years of the pandemic, 78% of high-income countries sequenced >0.5% of their COVID-19 cases, while 42% of low- and middle-income countries reached that mark. Around 25% of the genomes from high income countries were submitted within 21 days, a pattern observed in 5% of the genomes from low- and middle-income countries. We found that sequencing around 0.5% of the cases, with a turnaround time <21 days, could provide a benchmark for SARS-CoV-2 genomic surveillance. Socioeconomic inequalities undermine the global pandemic preparedness.
Exploration of wastewater surveillance for Monkeypox virus
EM Meijia et al, MEDRXIV, November 14, 2022
(Posted: Nov 15, 2022 7AM)
Protection against infection with the Omicron BA.5 subvariant among people with previous SARS-CoV-2 infection - surveillance results from southern Sweden, June to August 2022
F Kahn et al, MEDRXIV, November 14, 2022
(Posted: Nov 15, 2022 7AM)
Big data and AI in pandemic preparedness
The Lancet Summit: October 27-28, 2022
(Posted: Oct 27, 2022 0PM)
Managing COVID-19 and infectious disease is a global priority over the next few decades. Clinical and research communities are committed to reviewing the global response to the COVID-19 pandemic and a key part has been the unprecedented use and rapid scale of technology. This conference will allow diverse stakeholders to discuss opportunities for new pandemic warning systems based on modelling approaches using AI; advances in real-world surveillance and tracking of disease spread; AI for drug screening and rapid diagnostics; and advances in remote treatment and telehealth.
NPCR’s 30th Anniversary
CDC, October 2022,
(Posted: Oct 24, 2022 11AM)
The need for timely, accurate cancer data is greater than ever. While we have data on every cancer case that can be reported in the United States, we need to improve our systems so we can collect data faster at every step. Real-time data would provide a current, more complete picture of cancer trends at all levels, from local to national. This would also help public health professionals make decisions faster to save lives. To accomplish this goal, CDC is working with central cancer registries to move toward a cloud-based computing platform and to use electronic reporting from laboratories and electronic health records. We’re starting to build and test the cloud-based platform now.
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.
An updated counseling framework for moderate-penetrance colorectal cancer susceptibility genes
KE Breen et al, Genetics in Medicine, October 12, 2022
(Posted: Oct 12, 2022 9AM)
When an individual at average risk would initiate colonoscopy at age 45 years, a CRC risk of 0.39% is reached. For CHEK2 1100delC, CHEK2 I157T, and APC I1307K heterozygotes, this same level of risk is reached (or nearly reached) by age 40 to 45 years. For individuals with a monoallelic MUTYH variant, the CRC risk is 0.46% by age 45 to 49 years, similar to individuals at average risk. These updated calculations support recommendations to initiate earlier colonoscopy surveillance for CHEK2 and APC I1307K germline variant heterozygotes. However, earlier surveillance is not indicated for individuals with monoallelic MUTYH germline variants in the absence of family history.
Pandemic origins and a One Health approach to preparedness and prevention: Solutions based on SARS-CoV-2 and other RNA viruses
GD Keusch et al, PNAS, October 10, 2022
(Posted: Oct 10, 2022 5PM)
We identify three primary targets for pandemic prevention and preparedness: first, smart surveillance coupled with epidemiological risk assessment across wildlife–livestock–human (One Health) spillover interfaces; second, research to enhance pandemic preparedness and expedite development of vaccines and therapeutics; and third, strategies to reduce underlying drivers of spillover risk and spread and reduce the influence of misinformation. For all three, continued efforts to improve and integrate biosafety and biosecurity with the implementation of a One Health approach are essential.
COVID-19 Symptoms and Duration of Rapid Antigen Test Positivity at a Community Testing and Surveillance Site During Pre-Delta, Delta, and Omicron BA.1 Periods
C Marquez et al, JAMA Network Open, October 10, 2022
(Posted: Oct 10, 2022 0PM)
In this cross-sectional study of 63?277 participants conducted at a walk-up community testing site, patients more commonly reported COVID-19 upper respiratory tract symptoms during the Omicron BA.1 period than the pre-Delta and Delta periods, with differences by vaccination status and age. During the Omicron BA.1 period, 5 days after symptom onset, 80% of participants remained positive via a rapid antigen test. These findings indicate differences in symptoms in the BA.1 Omicron period vs the pre-Delta and Delta periods, which may be associated with rising population immunity as well as different SARS-CoV-2 variants, and positivity remained high 5 days after symptom onset in the BA.1 Omicron period.
The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance.
Tegally Houriiyah et al. Science (New York, N.Y.) 2022 9 (6615) eabq5358
(Posted: Oct 09, 2022 10AM)
Tegally et al. show how the coordinated efforts of talented African scientists have in a short time made great contributions to pandemic surveillance and data gathering. Their efforts and initiatives have provided early warning that has likely benefited wealthier countries more than their own. Genomic surveillance identified the emergence of the highly transmissible Beta and Omicron variants and now the appearance of Omicron sublineages in Africa.
100,000 coronavirus genomes reveal COVID's evolution in Africa.
Kwon Diana et al. Nature 2022 10
(Posted: Oct 07, 2022 6AM)
New SARS-CoV-2 variants arise and spread with great stealth, but that hasn’t stopped Africa’s genomic sleuths from spotting a host of these threats — and alerting the rest of the world. Now an analysis details how the rapid growth in Africa’s sequencing capacity has aided global SARS-CoV-2 surveillance. It also reveals that most variants were imported into Africa more often than they were exported from the continent.
Long-term Protection Associated With COVID-19 Vaccination and Prior Infection
MM Tenforde et al, JAMA, September 26, 2022
(Posted: Sep 26, 2022 4PM)
Developing the best strategies to reduce the morbidity and mortality associated with future COVID-19 surges warrants a strategic approach to monitor vaccine effectiveness. Monitoring will require complementary surveillance systems that can generate timely vaccine effectiveness estimates with accuracy and precision to guide policies and research.
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
(Posted: Sep 24, 2022 7AM)
Outcomes at least 90 days since onset of myocarditis after mRNA COVID-19 vaccination in adolescents and young adults in the USA: a follow-up surveillance study
I Kracalik et al, The Lancet Infectious Diseases, September 2022
(Posted: Sep 22, 2022 10AM)
After at least 90 days since onset of myocarditis after mRNA COVID-19 vaccination, most individuals in our cohort were considered recovered by health-care providers, and quality of life measures were comparable to those in pre-pandemic and early pandemic populations of a similar age.
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.
SARS-CoV-2 diagnostic testing rates determine the sensitivity of genomic surveillance programs
AX Han et al, MEDRXIV, September 16, 2022
(Posted: Sep 18, 2022 5AM)
We simulated COVID-19 epidemics in a prototypical LMIC to investigate how testing rates, sampling strategies, and sequencing proportions jointly impact surveillance outcomes and showed that low testing rates and spatiotemporal biases delay time-to-detection of new variants by weeks-to-months and can lead to unreliable estimates of variant prevalence even when the proportion of samples sequenced is increased.
Time to redefine a primary vaccination series?
MD Tanriover et al, The Lancet Infectious Diseases, September 13, 2022
(Posted: Sep 15, 2022 6AM)
In the third year of the COVID-19 pandemic, it is getting harder to define what a full-dose COVID-19 vaccination series is, especially in the era of emerging variants such as omicron (B.1.1.529). The definition might differ depending on the dominant variant in circulation, the availability of vaccines, the risk factors of vaccine recipients, and the availability of surveillance and COVID-19 vaccine safety and effectiveness data.
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.
Wastewater Surveillance for Monkeypox Virus in Nine California Communities
MK Wolfe et al, MEDRXIV, September 9, 2022
(Posted: Sep 10, 2022 10AM)
MPXV DNA was detected at all nine sites between June 19 and August 1, 2022; 5 of 9 sites detected MPXV DNA prior to or within a day of the first case identified in the source sewershed. At the four sites with >10 positive detections, we observed a positive, statistically significant correlation (p <0.001) between MPXV DNA in wastewater solids and incidence rate of reported cases.
Higher sensitivity monitoring of reactions to COVID-19 vaccination using smartwatches
G Guan et al, NPJ Digital Medicine, September 9, 2022
(Posted: Sep 09, 2022 8AM)
Wearable devices were more sensitive than questionnaires in determining when participants returned to baseline levels. We conclude that wearable devices can detect physiological responses following vaccination that may not be captured by patient self-reporting. More broadly, the ubiquity of smartwatches provides an opportunity to gather improved data on patient health, including active surveillance of vaccine safety.
Application of Statistical Learning to Identify Omicron Mutations in SARS-CoV-2 Viral Genome Sequence Data From Populations in Africa and the United States
LP Zhao et al, JAMA Network Open, September 8, 2022
(Posted: Sep 08, 2022 1PM)
Could the SARS-CoV-2 Omicron variant have been detected earlier with existing surveillance data and a state-of-the-art statistical learning strategy?
In this case series of 2698 Omicron cases in Africa and 12?141 Omicron cases in the United States, a statistical learning strategy found that Omicron was dynamically expanding in Africa and the United States with trackable expansion over time. The results indicated that Omicron could have been detected 20 days earlier in Africa; similarly, 8 Omicron cases were detected in the United States by November 25, 2021, prior to the official US Centers for Disease Control and Prevention declaration.
