scholarly journals Supplementing SARS-CoV-2 genomic surveillance with PCR-based variant detection for real-time actionable information, the Netherlands, June to July 2021

2021 ◽  
Vol 26 (40) ◽  
Author(s):  
Richard Molenkamp ◽  
Ewout Fanoy ◽  
Leonie Derickx ◽  
Theun de Groot ◽  
Marcel Jonges ◽  
...  

We evaluated routine testing with SARS-CoV-2 Delta variant-specific RT-PCR in regional hospital laboratories in addition to centralised national genomic surveillance in the Netherlands during June and July 2021. The increase of the Delta variant detected by RT-PCR correlated well with data from genomic surveillance and was available ca 2 weeks earlier. This rapid identification of the relative abundance and increase of SARS-CoV-2 variants of concern may have important benefits for implementation of local public health measures.

2021 ◽  
Author(s):  
Ryan Badman ◽  
Ace X. Wang ◽  
Martin Skrodzki ◽  
Hengchin Cho ◽  
David Aguilar-Lleyda ◽  
...  

A core assumption often heard in public health discourse is that increasing trust in national political leaders is essential for securing public health compliance during crises like the Covid-19 pandemic (2019-ongoing). However, studies of national government trust typically are too coarse-grained to differentiate between the trust in institutions versus more interpersonal trust in political leaders. Here, we present multiscale trust measurements for twelve countries and territories across the West, Oceania and East Asia. These trust results are used to identify which specific domains of government and social trust were most crucial for securing public health compliance (frequency of mask wearing and social distancing), and understanding the reasons for following the health measures (belief in effectiveness of public health measures). Our cross-cultural survey-based analysis (12 countries/territories, N=3369 subjects) reveals that higher trust in national and local public health institutions were a universally consistent predictor of public health compliance, while trust in national political leaders was actually not predictive of compliance across cultures and geographical regions. Institutional trust was mediated by multiple types of transparency, including providing rationale, securing public feedback, and honestly expressing uncertainty. These measures of transparency in public health communications, in turn, influence the public’s compliance behavior and beliefs. In total, these results highlight the importance of distinguishing between components of government trust, to better understand which entities the public give the most attention to during crises. Our findings may contribute to better planning and improvement of society-level cooperation, especially under highly uncertain disaster contexts.


Author(s):  
Kelvin Kai-Wang To ◽  
Xin Li ◽  
David Christopher Lung ◽  
Jonathan Daniel Ip ◽  
Wan-Mui Chan ◽  
...  

Abstract A false-positive SARS-CoV-2 RT-PCR result can lead to unnecessary public-health measures. We report two individuals whose respiratory specimens were contaminated by inactivated SARS-CoV-2 vaccine strain(CoronaVac), likely at vaccination premises. Incidentally, whole-genome sequencing of CoronaVac showed adaptive deletions on the spike protein, which do not result in observable changes of antigenicity.


Author(s):  
Narelle Campbell ◽  
Sandra C. Thompson ◽  
Anna Tynan ◽  
Louise Townsin ◽  
Lauren A. Booker ◽  
...  

This national study investigated the positives reported by residents experiencing the large-scale public health measures instituted in Australia to manage the first wave of the COVID-19 pandemic in 2020. Most Australians had not previously experienced the traditional public health measures used (social distancing, hand hygiene and restriction of movement) and which could potentially impact negatively on mental well-being. The research design included qualitative semi-structured phone interviews where participants described their early pandemic experiences. Data analysis used a rapid identification of themes technique, well-suited to large-scale qualitative research. The ninety participants (mean age 48 years; 70 women) were distributed nationally. Analysis revealed five themes linked with mental well-being and the concept of silver linings: safety and security, gratitude and appreciation, social cohesion and connections, and opportunities to reset priorities and resilience. Participants demonstrated support for the public health measures and evidence of individual and community resilience. They were cognisant of positives despite personal curtailment and negative impacts of public health directives. Stories of hope, strength, and acceptance, innovative connections with others and focusing on priorities and opportunities within the hardship were important strategies that others could use in managing adversity.


2021 ◽  
Author(s):  
Clare L Fasching ◽  
Venice Servellita ◽  
Bridget McKay ◽  
Vaishnavi Nagesh ◽  
James P Broughton ◽  
...  

Laboratory tests for the accurate and rapid identification of SARS-CoV-2 variants have the potential to guide the treatment of COVID-19 patients and inform infection control and public health surveillance efforts. Here we present the development and validation of a COVID-19 variant DETECTR assay incorporating loop-mediated isothermal amplification (LAMP) followed by CRISPR-Cas12 based identification of single nucleotide polymorphism (SNP) mutations in the SARS-CoV-2 spike (S) gene. This assay targets the L452R, E484K, and N501Y mutations associated with nearly all circulating viral lineages. In a comparison of three different Cas12 enzymes, only the newly identified enzyme CasDx1 was able to accurately identify all three targeted SNP mutations. We developed a data analysis pipeline for CRISPR-based SNP identification using the assay from 91 clinical samples (Ct < 30), yielding an overall SNP concordance and agreement with SARS-CoV-2 lineage classification of 100% compared to viral whole-genome sequencing. These findings highlight the potential utility of CRISPR-based mutation detection for clinical and public health diagnostics.


Health Policy ◽  
2008 ◽  
Vol 86 (2-3) ◽  
pp. 295-307 ◽  
Author(s):  
Maria W.J. Jansen ◽  
Nanne K. De Vries ◽  
Gerjo Kok ◽  
Hans A.M. Van Oers

2019 ◽  
Vol 57 (8) ◽  
Author(s):  
Satheesh Nair ◽  
Vineet Patel ◽  
Tadgh Hickey ◽  
Clare Maguire ◽  
David R. Greig ◽  
...  

ABSTRACT Rapid and accurate differentiation of Salmonella spp. causing enteric fever from nontyphoidal Salmonella is essential for clinical management of cases, laboratory risk management, and implementation of public health measures. Current methods used for confirmation of identification, including biochemistry and serotyping as well as whole-genome sequencing analyses, take several days. Here we report the development and evaluation of a real-time PCR assay that can be performed directly on crude DNA extracts from bacterial colonies for the rapid identification of typhoidal and nontyphoidal Salmonella.


PLoS ONE ◽  
2021 ◽  
Vol 16 (12) ◽  
pp. e0260862
Author(s):  
Rachel E. Pollreis ◽  
Clay Roscoe ◽  
Rachel J. Phinney ◽  
Surabhi S. Malesha ◽  
Matthew C. Burns ◽  
...  

SARS-CoV-2 RT-PCR, the gold standard for diagnostic testing, may not be readily available or logistically applicable for routine COVID-19 testing in many rural communities in the United States. In this validation study, we compared the BinaxNOW™ COVID-19 Test Ag Card with SARS-CoV-2 RT-PCR in 214 participants who sought COVID-19 testing from a local public health district in Idaho, USA. The median age of participants was 35 and 82.7% were symptomatic. Thirty-seven participants (17.3%) had positive RT-PCR results. Results between the two tests were 94.4% concordant. The sensitivity of the BinaxNOW™ COVID-19 Test Ag Card was 67.6% (95% CI: 50.2–81.9%), and the specificity was 100.0% (95% CI: 97.9–100.0%). The positive predictive value (PPV) for the BinaxNOW™ COVID-19 Test Ag Card was 100.0% (95% CI: 86.2–100.0%), and the negative predictive value (NPV) was 93.6% (95% CI: 89.1–96.6%). Although the sensitivity of BinaxNOW™ COVID-19 Test Ag Card was lower than RT-PCR, rapid results and high specificity support its use for early detection of COVID-19, especially in settings where SARS-CoV-2 RT-PCR testing is not readily available. Rapid antigen tests, such as the BinaxNOW™ COVID-19 Test Ag Card, may be a more convenient tool in quickly identifying and preventing COVID-19 transmission, especially in rural settings.


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