scholarly journals VarLOCK - sequencing independent, rapid detection of SARS-CoV-2 variants of concern for point-of-care testing, qPCR pipelines and national wastewater surveillance

2022 ◽  
Author(s):  
Xinsheng Nan ◽  
Sven Hoehn ◽  
Patrick Hardinge ◽  
Shrinivas N Dighe ◽  
John Ukeri ◽  
...  
Keyword(s):  
Point Of Care ◽  
Vaccination Strategy ◽  
Population Level ◽  
Rapid Identification ◽  
Public Health Response ◽  
Vaccination Programs ◽  
The Public ◽  
Detection Technology ◽  
Health Response ◽  
Wastewater Samples

The COVID-19 pandemic continues to pose a threat to the general population. The ongoing vaccination programs provide protection to individuals and facilitate the opening of society and a return to normality. However, emergent and existing SARS-CoV-2 variants capable of evading the immune system endanger the efficacy of the vaccination strategy. To preserve the efficacy of SARS-CoV-2 vaccination globally, aggressive and effective surveillance for known and emerging SARS-CoV-2 Variants of Concern (VOC) is required. Rapid and specific molecular diagnostics can provide speed and coverage advantages compared to genomic sequencing alone, benefitting the public health response and facilitating VOC containment. In this work, we expand the recently developed SARS-CoV-2 CRISPR-Cas detection technology (SHERLOCK) to allow rapid and sensitive discrimination of VOCs, that can be used at point of care and/or implemented in the pipelines of small or large testing facilities, and even determine proportion of VOCs in pooled population-level wastewater samples. This technology aims to complement the ongoing sequencing efforts to allow facile and, crucially, rapid identification of individuals infected with VOCs to help break infection chains. Here, we show the optimisation of our VarLOCK assays (Variant-specific SHERLOCK) for multiple specific mutations in the S gene of SARS-CoV-2 and validation with samples from the Cardiff University Testing Service. We also show the applicability of VarLOCK to national wastewater surveillance of SARS-CoV-2 variants. In addition, we show the rapid adaptability of the technique for new and emerging VOCs such as Omicron.

scholarly journals Detection of SARS-CoV-2 at the point of care

Bioanalysis ◽  
2021 ◽  
Author(s):  
Michael J Loeffelholz ◽  
Yi-Wei Tang
Keyword(s):  
New Technologies ◽  
Point Of Care ◽  
Etiologic Agent ◽  
Critical Element ◽  
Public Health Response ◽  
Rna Sequences ◽  
Future Directions ◽  
The Public ◽  
Health Response ◽  
Epidemiological Impact

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiologic agent of COVID-19. Testing for SARS-CoV-2 infection is a critical element of the public health response to COVID-19. Point-of-care (POC) tests can drive patient management decisions for infectious diseases, including COVID-19. POC tests are available for the diagnosis of SARS-CoV-2 infections and include those that detect SARS-CoV-2 antigens as well as amplified RNA sequences. We provide a review of SARS-CoV-2 POC tests including their performance, settings for which they might be used, their impact and future directions. Further optimization and validation, new technologies as well as studies to determine clinical and epidemiological impact of SARS-CoV-2 POC tests are needed.

scholarly journals Estimation of the Actual Incidence of Coronavirus Disease (COVID-19) in Emergent Hotspots: The Example of Hokkaido, Japan during February–March 2020

2021 ◽  
Vol 10 (11) ◽  
pp. 2392
Author(s):  
Andrei R. Akhmetzhanov ◽  
Kenji Mizumoto ◽  
Sung-Mok Jung ◽  
Natalie M. Linton ◽  
Ryosuke Omori ◽  
...  
Keyword(s):  
Cumulative Incidence ◽  
Surveillance System ◽  
Negative Binomial ◽  
Actual Number ◽  
Public Health Response ◽  
The Public ◽  
Health Response ◽  
Using Data ◽  
Insight Into ◽  
Actual Incidence

Following the first report of the coronavirus disease 2019 (COVID-19) in Sapporo city, Hokkaido Prefecture, Japan, on 14 February 2020, a surge of cases was observed in Hokkaido during February and March. As of 6 March, 90 cases were diagnosed in Hokkaido. Unfortunately, many infected persons may not have been recognized due to having mild or no symptoms during the initial months of the outbreak. We therefore aimed to predict the actual number of COVID-19 cases in (i) Hokkaido Prefecture and (ii) Sapporo city using data on cases diagnosed outside these areas. Two statistical frameworks involving a balance equation and an extrapolated linear regression model with a negative binomial link were used for deriving both estimates, respectively. The estimated cumulative incidence in Hokkaido as of 27 February was 2,297 cases (95% confidence interval (CI): 382–7091) based on data on travelers outbound from Hokkaido. The cumulative incidence in Sapporo city as of 28 February was estimated at 2233 cases (95% CI: 0–4893) based on the count of confirmed cases within Hokkaido. Both approaches resulted in similar estimates, indicating a higher incidence of infections in Hokkaido than were detected by the surveillance system. This quantification of the gap between detected and estimated cases helped to inform the public health response at the beginning of the pandemic and provided insight into the possible scope of undetected transmission for future assessments.

scholarly journals United States response to the COVID-19 pandemic, January–November 2020

2021 ◽  
pp. 1-14
Author(s):  
Mathew Alexander ◽  
Lynn Unruh ◽  
Andriy Koval ◽  
William Belanger
Keyword(s):  
United States ◽  
The United States ◽  
Contact Tracing ◽  
Public Health Response ◽  
The Public ◽  
The Past ◽  
Health Response ◽  
Physical Infrastructure ◽  
Key Policy ◽  
United States Healthcare

Abstract As of November 2020, the United States leads the world in confirmed coronavirus disease 2019 (COVID-19) cases and deaths. Over the past 10 months, the United States has experienced three peaks in new cases, with the most recent spike in November setting new records. Inaction and the lack of a scientifically informed, unified response have contributed to the sustained spread of COVID-19 in the United States. This paper describes major events and findings from the domestic response to COVID-19 from January to November 2020, including on preventing transmission, COVID-19 testing and contact tracing, ensuring sufficient physical infrastructure and healthcare workforce, paying for services, and governance. We further reflect on the public health response to-date and analyse the link between key policy decisions (e.g. closing, reopening) and COVID-19 cases in three states that are representative of the broader regions that have experienced spikes in cases. Finally, as we approach the winter months and undergo a change in national leadership, we highlight some considerations for the ongoing COVID-19 response and the broader United States healthcare system. These findings describe why the United States has failed to contain COVID-19 effectively to-date and can serve as a reference in the continued response to COVID-19 and future pandemics.

scholarly journals Toward a critical race analysis of the COVID-19 crisis in US carceral institutions

2021 ◽  
pp. 026101832110014
Author(s):  
Paddy Farr
Keyword(s):  
Critical Race Theory ◽  
Racial Justice ◽  
Critical Race ◽  
Public Health Response ◽  
The Public ◽  
Detention Centers ◽  
Health Response ◽  
Increased Risk ◽  
History Of ◽  
Race Analysis

People in carceral institutions are at increased risk for COVID-19 infection. Applying critical race theory to the problem of COVID-19 provides tools to analyze the risk of infection and evaluate the public health response within the imprisoned, jailed, and detained population. On the surface, this is due to factors related to a lack of hygiene products, an inability to physically distance, a low quality and inaccessible health care, and poor health. However, at root, the increased risk for infection is directly linked to the legacy of slavery and colonization within the history of US prisons, jails, and detention centers. As a solution to the crisis of COVID-19 and prevention of future pandemics within prisons, jails and detention centers, a critical race orientation provides reason and direction for mass decarceration and racial justice.

scholarly journals Effect of COVID-19 on childhood Mycoplasma pneumoniae infection in Chengdu, China

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Ying Zhang ◽  
Yijie Huang ◽  
Tao Ai ◽  
Jun Luo ◽  
Hanmin Liu
Keyword(s):  
Public Health ◽  
Mycoplasma Pneumoniae ◽  
Close Contact ◽  
Serum Antibody ◽  
Pathogen Transmission ◽  
Western China ◽  
Public Health Response ◽  
The Public ◽  
Health Response ◽  
The Impact

Abstract Background Following the outbreak of the COVID-19 pandemic, a change in the incidence and transmission of respiratory pathogens was observed. Here, we retrospectively analyzed the impact of COVID-19 on the epidemiologic characteristics of Mycoplasma pneumoniae infection among children in Chengdu, one of the largest cities of western China. Method M. pneumoniae infection was diagnosed in 33,345 pediatric patients with respiratory symptoms at the Chengdu Women’s & Children’s Central Hospital between January 2017 and December 2020, based on a serum antibody titer of ≥1:160 measured by the passive agglutination assay. Differences in infection rates were examined by sex, age, and temporal distribution. Results Two epidemic outbreaks occurred between October-December 2017 and April-December 2019, and two infection peaks were detected in the second and fourth quarters of 2017, 2018, and 2019. Due to the public health response to COVID-19, the number of positive M. pneumoniae cases significantly decreased in the second quarter of 2020. The number of M. pneumoniae infection among children aged 3–6 years was higher than that in other age groups. Conclusions Preschool children are more susceptible to M. pneumoniae infection and close contact appears to be the predominant factor favoring pathogen transmission. The public health response to COVID-19 can effectively control the transmission of M. pneumoniae.

scholarly journals The Australian industrial system in the era of COVID-19

2021 ◽  
pp. 002218562110128
Author(s):  
Michele O’Neil
Keyword(s):  
Industrial Relations ◽  
National Level ◽  
Recovery Phase ◽  
Public Health Response ◽  
The Public ◽  
Paid Leave ◽  
Union Movement ◽  
Health Response ◽  
Decentralised Systems ◽  
Australian Economy

COVID-19 caused sudden and serious damage to the Australian economy. The effects have been spread unevenly, and highlighted the shortcomings of over-reliance on insecure forms of work. The lack of any form of paid leave for casual and other insecure workers undermined the public health response, and was emblematic of the broader consequences of insecurity. Despite its limitations, Australia’s industrial relations system responded to the challenges of the pandemic in a way that less regulated and ‘decentralised’ systems would not have been able to. This article argues that the union movement was critical to Australia’s successful response, and that the award system proved to be an adaptable mechanism to deliver change at a national level while ensuring that the representative voice of workers was heard, and basic industrial protections were not jettisoned. Industry bargaining would have also been a beneficial tool to deal with economy-wide issues of this kind. The article urges that the lessons of the pandemic be learned as we move to a recovery phase and that we ensure there are more secure jobs, better bargaining rights and improvements to basic protections to ensure that workers’ rights are not eroded.

Survey on the Populationʼs Needs and the Public Health Response During Floods in Germany 2002

2007 ◽  
Vol 13 (5) ◽  
pp. 461-464 ◽  
Author(s):  
Johannes Schnitzler ◽  
Justus Benzler ◽  
Doris Altmann ◽  
Inge Mücke ◽  
Gérard Krause
Keyword(s):  
Public Health ◽  
Public Health Response ◽  
The Public ◽  
Health Response
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