scholarly journals Computer-aided medical microbiology monitoring tool: a strategy to adapt to the SARS-CoV-2 epidemic and that highlights RT-PCR consistency

2020 ◽  
Author(s):  
Linda Mueller ◽  
Valentin Scherz ◽  
Gilbert Greub ◽  
Katia Jaton ◽  
Onya Opota
Keyword(s):  
Turnaround Time ◽  
Quality Monitoring ◽  
Rt Pcr ◽  
Monitoring Tool ◽  
Diagnostic Laboratory ◽  
Health Authorities ◽  
Important Health ◽  
Public Health Authorities ◽  
Automated Processes ◽  
Case Validation

Since the beginning of the COVID-19 pandemic, important health and regulatory decisions relied on the SARS-CoV-2 reverse transcription polymerase chain reaction (RT-PCR) results. Our diagnostic laboratory faced a rapid increase in the number of SARS-CoV-2 RT-PCR, with up to 1,007 tests per day. To maintain a rapid turnaround time to support patient management and public health authorities' decisions, we moved from a case-by-case validation of RT-PCR to an automated validation and immediate transmission of the results to clinicians. To maintain high quality and to track possible aberrant results, we developed a quality-monitoring tool based on a homemade algorithm coded in R. We present the results of this quality-monitoring tool applied to 35,137 RT-PCR results corresponding to 30,198 patients. Patients tested several times led to 4,939 pairwise comparisons; 88% concordant and 12% discrepant. Among the 573 discrepancies, 428 were automatically solved by the algorithm. The most likely explanation for these 573 discrepancies was related for 44.9% of the situations to "Clinical evolution", 27.9% to "Preanalytical" problems, and 25.3% to "Stochastic". Finally, 11 discrepant results could not be explained, including 8 received from external partners for which clinical data were not available. The implemented quality-monitoring strategy allowed to: i) assist the investigation of discrepant results ii) focus the attention of medical microbiologists onto results requiring a specific expertise and iii) maintain an acceptable TAT. This work highlighted the high RT-PCR consistency for the detection of SARS-CoV-2 and the importance of automated processes to handle a huge number of samples while preserving quality.

scholarly journals Computer-Aided Medical Microbiology Monitoring Tool: A Strategy to Adapt to the SARS-CoV-2 Epidemic and That Highlights RT-PCR Consistency

2021 ◽  
Vol 11 ◽  
Author(s):  
Linda Mueller ◽  
Valentin Scherz ◽  
Gilbert Greub ◽  
Katia Jaton ◽  
Onya Opota
Keyword(s):  
Turnaround Time ◽  
Quality Monitoring ◽  
Rt Pcr ◽  
Monitoring Tool ◽  
Diagnostic Laboratory ◽  
Important Health ◽  
Polymerase Chain ◽  
Automated Processes ◽  
Regulatory Decisions ◽  
Case Validation

Since the beginning of the COVID-19 pandemic, important health and regulatory decisions relied on SARS-CoV-2 reverse transcription polymerase chain reaction (RT-PCR) results. Our diagnostic laboratory faced a rapid increase in the number of SARS-CoV-2 RT-PCR. To maintain a rapid turnaround time, we moved from a case-by-case validation of RT-PCR results to an automated validation and immediate results transmission to clinicians. A quality-monitoring tool based on a homemade algorithm coded in R was developed, to preserve high quality and to track aberrant results. We present the results of this quality-monitoring tool applied to 35,137 RT-PCR results. Patients tested several times led to 4,939 pairwise comparisons: 88% concordant and 12% discrepant. The algorithm automatically solved 428 out of 573 discrepancies. The most likely explanation for these 573 discrepancies was related for 44.9% of the situations to the clinical evolution of the disease, 27.9% to preanalytical factors, and 25.3% to stochasticity of the assay. Finally, 11 discrepant results could not be explained, including 8 for which clinical data was not available. For patients repeatedly tested on the same day, the second result confirmed a first negative or positive result in 99.2% or 88.9% of cases, respectively. The implemented quality-monitoring strategy allowed to: i) assist the investigation of discrepant results ii) focus the attention of medical microbiologists onto results requiring a specific expertise and iii) maintain an acceptable turnaround time. This work highlights the high RT-PCR consistency for the detection of SARS-CoV-2 and the necessity for automated processes to handle a huge number of microbiological results while preserving quality.

scholarly journals Rapid spread of the SARS-CoV-2 Delta variant in some French regions, June 2021

2021 ◽  
Vol 26 (28) ◽  
Author(s):  
Samuel Alizon ◽  
Stéphanie Haim-Boukobza ◽  
Vincent Foulongne ◽  
Laura Verdurme ◽  
Sabine Trombert-Paolantoni ◽  
...  
Keyword(s):  
Public Health ◽  
Confidence Interval ◽  
Rapid Growth ◽  
Rt Pcr ◽  
Health Authorities ◽  
Rapid Spread ◽  
Public Health Authorities ◽  
Alpha Variant

We analysed 9,030 variant-specific RT-PCR tests performed on SARS-CoV-2-positive samples collected in France between 31 May and 21 June 2021. This analysis revealed rapid growth of the Delta variant in three of the 13 metropolitan French regions and estimated a +79% (95% confidence interval: 52–110%) transmission advantage compared with the Alpha variant. The next weeks will prove decisive and the magnitude of the estimated transmission advantages of the Delta variant could represent a major challenge for public health authorities.

scholarly journals The Delta Variant Had Negligible Impact on COVID-19 Vaccine Effectiveness in the USA

2021 ◽  
Author(s):  
Ben Blaiszik ◽  
Carlo Graziani ◽  
James L. Olds ◽  
Ian Foster
Keyword(s):  
Age Distribution ◽  
Vaccine Effectiveness ◽  
Vaccination Status ◽  
Rt Pcr ◽  
Factors Affecting ◽  
A Value ◽  
Health Authorities ◽  
Public Health Authorities ◽  
The Usa ◽  
Zero Baseline

The SARS-CoV-2 Delta variant (B.1.617.2) was initially identified in India in December 2020. Due to its high transmissibility, its prevalence in the U.S.A. grew from a near-zero baseline in early May 2021 to nearly 100% by late August 2021, according to CDC tracking. We accessed openly available data sources from the public health authorities of seven U.S. states, five U.S. counties, and the District of Columbia on RT-PCR COVID-19 tests split by the COVID-19 vaccination status of individuals tested during this period. Together, these time series enable estimation and tracking of COVID-19 vaccine effectiveness (VE∗) (against RT-PCR diagnosed infection) concurrently with the growth of Delta variant prevalence in those locations. Our analyses reveal that in each locality the VE∗ for the combined set of all three US vaccines remained relatively stable and quite well-performing, despite the dramatic concurrent rise of Delta variant prevalence. We conclude that the Delta variant does not significantly evade vaccine-induced immunity. The variations in our measured VE∗ appear to be driven by demographic factors affecting the composition of the vaccinated cohorts, particularly as pertains to age distribution. We report that the measured VE∗, aggregated across the collected sites, began at a value of about 0.9 in mid-May, declined to about 0.76 by mid-July, and recovered to about 0.9 by mid-September.SummaryWe estimated local COVID-19 vaccine effectiveness using RT-PCR COVID-19 test data broken out by vaccination status from select localities in the U.S.A. between 15 May and 15 September 2021 while the SARS-CoV-2 Delta variant (B.1.617.2) was ascending from essentially zero prevalence to total dominance of the genome, and showed that the rise of the Delta variant had negligible effect on vaccine effectiveness.

scholarly journals Massive SARS-CoV-2 RT-PCR Testing on Rural Communities in Manabi Province (Ecuador) Reveals Severe COVID-19 Outbreaks

2021 ◽  
Vol 104 (4) ◽  
pp. 1493-1494
Author(s):  
Esteban Ortiz-Prado ◽  
Aquiles R. Henriquez-Trujillo ◽  
Ismar A. Rivera-Olivero ◽  
Byron Freire-Paspuel ◽  
Alexander Paolo Vallejo-Janeta ◽  
...  
Keyword(s):  
Public Health ◽  
Rural Communities ◽  
Coastal Region ◽  
Contact Tracing ◽  
Rt Pcr ◽  
The Public ◽  
Health Infrastructure ◽  
Health Authorities ◽  
Public Health Authorities ◽  
The Impact

ABSTRACTRural communities from Latin America are particularly susceptible to develop serious outbreaks of infectious diseases. Inadequate diagnosis and poor health infrastructure jeopardize proper contact tracing and other actions to reduce the impact of COVID-19 in the region. We herein describe the preliminary data of our ongoing fieldwork of massive testing among nonhospitalized rural population in Manabi Province of the coastal region of Ecuador. A total of 1,479 people from six different rural communities were tested for SARS-CoV-2 by RT-qPCR following the CDC protocol; 350 individuals tested positive, resulting in an overall attack rate of 23.7% for SARS-CoV-2 infection. This ultrahigh prevalence must urge to the public health authorities from Ecuador to take immediate actions to counteract this dramatic scenario in Manabi Province and to improve SARS-CoV-2 testing countrywide.

scholarly journals Users’ Beliefs Toward Physical Distancing in Facebook Pages of Public Health Authorities During COVID-19 Pandemic in Early 2020

2021 ◽  
pp. 109019812110144
Author(s):  
Soon Guan Tan ◽  
Aravind Sesagiri Raamkumar ◽  
Hwee Lin Wee
Keyword(s):  
Public Health ◽  
Health Belief Model ◽  
United States Public Health ◽  
Health Belief ◽  
The United States ◽  
Health Authorities ◽  
Public Health Authorities ◽  
Control And Prevention ◽  
Belief Model ◽  
The Health Belief Model

This study aims to describe Facebook users’ beliefs toward physical distancing measures implemented during the Coronavirus disease (COVID-19) pandemic using the key constructs of the health belief model. A combination of rule-based filtering and manual classification methods was used to classify user comments on COVID-19 Facebook posts of three public health authorities: Centers for Disease Control and Prevention of the United States, Public Health England, and Ministry of Health, Singapore. A total of 104,304 comments were analyzed for posts published between 1 January, 2020, and 31 March, 2020, along with COVID-19 cases and deaths count data from the three countries. Findings indicate that the perceived benefits of physical distancing measures ( n = 3,463; 3.3%) was three times higher than perceived barriers ( n = 1,062; 1.0%). Perceived susceptibility to COVID-19 ( n = 2,934; 2.8%) was higher compared with perceived severity ( n = 2,081; 2.0%). Although susceptibility aspects of physical distancing were discussed more often at the start of the year, mentions on the benefits of intervention emerged stronger toward the end of the analysis period, highlighting the shift in beliefs. The health belief model is useful for understanding Facebook users’ beliefs at a basic level, and it provides a scope for further improvement.

scholarly journals Fueling the Covid-19 pandemic: summer school holidays and incidence rates in German districts

2021 ◽  
Author(s):  
Thomas Plümper ◽  
Eric Neumayer
Keyword(s):  
Public Health ◽  
Fixed Effects ◽  
Summer School ◽  
Incidence Rates ◽  
Contact Tracing ◽  
Robert Koch Institute ◽  
Cross Sectional ◽  
Holiday Period ◽  
Health Authorities ◽  
Public Health Authorities

AbstractBackgroundThe Robert-Koch-Institute reports that during the summer holiday period a foreign country is stated as the most likely place of infection for an average of 27 and a maximum of 49% of new SARS-CoV-2 infections in Germany.MethodsCross-sectional study on observational data. In Germany, summer school holidays are coordinated between states and spread out over 13 weeks. Employing a dynamic model with district fixed effects, we analyze the association between these holidays and weekly incidence rates across 401 German districts.ResultsWe find effects of the holiday period of around 45% of the average district incidence rates in Germany during their respective final week of holidays and the 2 weeks after holidays end. Western states tend to experience stronger effects than Eastern states. We also find statistically significant interaction effects of school holidays with per capita taxable income and the share of foreign residents in a district’s population.ConclusionsOur results suggest that changed behavior during the holiday season accelerated the pandemic and made it considerably more difficult for public health authorities to contain the spread of the virus by means of contact tracing. Germany’s public health authorities did not prepare adequately for this acceleration.

scholarly journals EHEC O111:H8 strain and norovirus GII.4 Sydney [P16] causing an outbreak in a daycare center, Brazil, 2019

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Liliana Cruz Spano ◽  
Caroline Gastaldi Guerrieri ◽  
Lays Paula Bondi Volpini ◽  
Ricardo Pinto Schuenck ◽  
Jaqueline Pegoretti Goulart ◽  
...  
Keyword(s):  
Southeastern Brazil ◽  
Viral Pathogens ◽  
Daycare Center ◽  
Staff Members ◽  
Health Authorities ◽  
Single Locus Variant ◽  
Public Health Authorities ◽  
Uremic Syndrome ◽  
Norovirus Gii ◽  
Relationship Of

Abstract Background This study describes the investigation of an outbreak of diarrhea, hemorrhagic colitis (HC), and hemolytic uremic syndrome (HUS) at a daycare center in southeastern Brazil, involving fourteen children, six staff members, six family members, and one nurse. All bacterial and viral pathogens detected were genetically characterized. Results Two isolates of a strain of enterohemorrhagic Escherichia coli (EHEC) serotype O111:H8 were recovered, one implicated in a case of HUS and the other in a case of uncomplicated diarrhea. These isolates had a clonal relationship of 94% and carried the stx2a and eae virulence genes and the OI-122 pathogenicity island. The EHEC strain was determined to be a single-locus variant of sequence type (ST) 327. EHEC isolates were resistant to ofloxacin, doxycycline, tetracycline, ampicillin, and trimethoprim-sulfamethoxazole and intermediately resistant to levofloxacin and ciprofloxacin. Rotavirus was not detected in any samples, and norovirus was detected in 46.7% (14/30) of the stool samples, three of which were from asymptomatic staff members. The noroviruses were classified as the recombinant GII.4 Sydney [P16] by gene sequencing. Conclusion In this outbreak, it was possible to identify an uncommon stx2a + EHEC O111:H8 strain, and the most recent pandemic norovirus strain GII.4 Sydney [P16]. Our findings reinforce the need for surveillance and diagnosis of multiple enteric pathogens by public health authorities, especially during outbreaks.

scholarly journals The effect of COVID19 pandemic restrictions on an urban rodent population

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Miguel A. Bedoya-Pérez ◽  
Michael P. Ward ◽  
Max Loomes ◽  
Iain S. McGregor ◽  
Mathew S. Crowther
Keyword(s):  
Binary Data ◽  
Sampling Interval ◽  
Resource Scarcity ◽  
Health Authorities ◽  
Before And After ◽  
Directional Change ◽  
Public Health Authorities ◽  
Bait Stations ◽  
Rodent Populations ◽  
The City

AbstractShortly after the enactment of restrictions aimed at limiting the spread of COVID-19, various local government and public health authorities around the world reported an increased sighting of rats. Such reports have yet to be empirically validated. Here we combined data from multi-catch rodent stations (providing data on rodent captures), rodent bait stations (providing data on rodent activity) and residents’ complaints to explore the effects of a six week lockdown period on rodent populations within the City of Sydney, Australia. The sampling interval encompassed October 2019 to July 2020 with lockdown defined as the interval from April 1st to May 15th, 2020. Rodent captures and activity (visits to bait stations) were stable prior to lockdown. Captures showed a rapid increase and then decline during the lockdown, while rodent visits to bait stations declined throughout this period. There were no changes in the frequency of complaints during lockdown relative to before and after lockdown. There was a non-directional change in the geographical distribution of indices of rodent abundance suggesting that rodents redistributed in response to resource scarcity. We hypothesize that lockdown measures initially resulted in increased rodent captures due to sudden shortage of human-derived food resources. Rodent visits to bait stations might not show this pattern due to the nature of the binary data collected, namely the presence or absence of a visit. Relocation of bait stations driven by pest management goals may also have affected the detection of any directional spatial effect. We conclude that the onset of COVID-19 may have disrupted commensal rodent populations, with possible implications for the future management of these ubiquitous urban indicator species.

scholarly journals Indoor Environmental Quality in Dwellings and Lifestyle Behaviors during the COVID-19 Pandemic: Russian Perspective

2021 ◽  
Vol 18 (11) ◽  
pp. 5975
Author(s):  
Vladimir Reshetnikov ◽  
Oleg Mitrokhin ◽  
Elena Belova ◽  
Victor Mikhailovsky ◽  
Maria Mikerova ◽  
...  
Keyword(s):  
Public Health ◽  
Medical Students ◽  
Environmental Quality ◽  
Indoor Environmental Quality ◽  
Lifestyle Behaviors ◽  
Contagious Diseases ◽  
Health Authorities ◽  
Public Health Authorities ◽  
Isolation Index ◽  
Novel Coronavirus

The novel coronavirus (COVID-19) outbreak is a public health emergency of international concern, and as a response, public health authorities started enforcing preventive measures like self-isolation and social distancing. The enforcement of isolation has consequences that may affect the lifestyle-related behavior of the general population. Quarantine encompasses a range of strategies that can be used to detain, isolate, or conditionally release individuals or populations infected or exposed to contagious diseases and should be tailored to circumstances. Interestingly, medical students may represent an example of how the COVID-19 pandemic can form new habits and change lifestyle behaviors. We conducted a web-based survey to assess changes in lifestyle-related behavior of self-isolated medical students during the COVID-19 pandemic. Then we analyzed the sanitary-hygienic regulations of the Russian Federation to determine the requirements for healthy buildings. Results showed that during the pandemic, the enforcement of isolation affects medical students’ lifestyle-related behavior and accompanies an increase in non-communicable diseases (NCDs). Indoor environmental quality (IEQ) and healthy buildings are cutting-edge factors in preventing COVID-19 and NCDs. The Russian sanitary-hygienic regulations support improving this factor with suitable requirements for ventilation, sewage, waste management, and disinfection. Herein, assessing isolation is possible through the hygienic self-isolation index.

Sign in / Sign up

Export Citation Format

Share Document