An open-source, automated, and cost-effective platform for COVID-19 diagnosis and rapid portable genomic surveillance using nanopore sequencing.

The COVID-19 pandemic, caused by SARS-CoV-2, has emphasized the necessity for scalable diagnostic workflows using locally produced reagents and basic laboratory equipment with minimal dependence on global supply chains. We introduce an open-source automated platform for high-throughput RNA extraction and pathogen diagnosis, which uses reagents almost entirely produced in-house. This platform integrates our methods for self-manufacturing magnetic nanoparticles and qRT-PCR reagents-both of which have received regulatory approval for clinical use-with an in-house, open-source robotic extraction protocol. It also incorporates our "Nanopore Sequencing of Isothermal Rapid Viral Amplification for Near Real-time Analysis" (NIRVANA) technology, designed for tracking SARS-CoV-2 mutations and variants. The platform exhibits high reproducibility and consistency without cross-contamination, and its limit of detection, sensitivity, and specificity are comparable to commercial assays. Automated NIRVANA effectively identifies circulating SARS-CoV-2 variants. Our in-house, cost-effective reagents, automated diagnostic workflows, and portable genomic surveillance strategies provide a scalable and rapid solution for COVID-19 diagnosis and variant tracking, essential for current and future pandemic responses.

Impact of the SARS-CoV-2 nucleocapsid 203K/204R mutations on the inflammatory immune response in COVID-19 severity.

BACKGROUND: The excessive inflammatory responses provoked by SARS-CoV-2 infection are critical factors affecting the severity and mortality of COVID-19. Previous work found that two adjacent co-occurring mutations R203K and G204R (KR) on the nucleocapsid (N) protein correlate with increased disease severity in COVID-19 patients. However, links with the host immune response remain unclear. METHODS: Here, we grouped nasopharyngeal swab samples of COVID-19 patients into two cohorts based on the presence and absence of SARS-CoV-2 nucleocapsid KR mutations. We performed nasopharyngeal transcriptome analysis of age, gender, and ethnicity-matched COVID-19 patients infected with either SARS-CoV-2 with KR mutations in the N protein (KR patients n = 39) or with the wild-type N protein (RG patients n = 39) and compared to healthy controls (n = 34). The impact of KR mutation on immune response was further characterized experimentally by transcriptomic and proteomic profiling of virus-like-particle (VLP) incubated cells. RESULTS: We observed markedly elevated expression of proinflammatory cytokines, chemokines, and interferon-stimulated (ISGs) genes in the KR patients compared to RG patients. Using nasopharyngeal transcriptome data, we found significantly higher levels of neutrophils and neutrophil-to-lymphocyte (NLR) ratio in KR patients than in the RG patients. Furthermore, transcriptomic and proteomic profiling of VLP incubated cells confirmed a similar hyper-inflammatory response mediated by the KR variant. CONCLUSIONS: Our data demonstrate an unforeseen connection between nucleocapsid KR mutations and augmented inflammatory immune response in severe COVID-19 patients. These findings provide insights into how mutations in SARS-CoV-2 modulate host immune output and pathogenesis and may contribute to more efficient therapeutics and vaccine development.

Rapid single-molecule detection of COVID-19 and MERS antigens via nanobody-functionalized organic electrochemical transistors.

The coronavirus disease 2019 (COVID-19) pandemic has highlighted the need for rapid and sensitive protein detection and quantification in simple and robust formats for widespread point-of-care applications. Here, we report on nanobody-functionalized organic electrochemical transistors with a modular architecture for the rapid quantification of single-molecule-to-nanomolar levels of specific antigens in complex bodily fluids. The sensors combine a solution-processable conjugated polymer in the transistor channel and high-density and orientation-controlled bioconjugation of nanobody-SpyCatcher fusion proteins on disposable gate electrodes. The devices provide results after 10 min of exposure to 5 µl of unprocessed samples, maintain high specificity and single-molecule sensitivity in human saliva and serum, and can be reprogrammed to detect any protein antigen if a corresponding specific nanobody is available. We used the sensors to detect green fluorescent protein, and severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and Middle East respiratory syndrome coronavirus (MERS-CoV) spike proteins, and for the COVID-19 screening of unprocessed clinical nasopharyngeal swab and saliva samples with a wide range of viral loads.

Screening for High Risk of Sleep Apnea in an Ambulatory Care Setting in Saudi Arabia.

Sleep apnea is a potentially serious but under-diagnosed sleep disorder. Saudi Arabia has a high prevalence of hypertension, diabetes, obesity, and smoking, which are all major risk factors for sleep apnea. However, few studies report screening for sleep apnea in Saudi Arabia. A three-month prospective, questionnaire-based study, using the Berlin Questionnaire (BQ) and the Epworth Sleepiness Scale (ESS), screened 319 patients attending a family medicine clinic in Saudi Arabia for risk of sleep apnea. The results showed that when using the BQ and the ESS, 95 (29.8%) and 102 (32.0%) respondents were at high risk of sleep apnea. Taken together, the BQ and the ESS combined measure showed that 41 (12.9%) respondents were classified as high risk for sleep apnea. Logistic regression revealed that the high risk of sleep apnea was statistically significantly (p < 0.05) associated with respondent characteristics of obesity and hypertension. No associations were found between high risk for sleep apnea and: Smoking, diabetes mellitus, hypothyroidism or hyperlipidemia. Screening for sleep apnea using the BQ and ESS questionnaires, particularly among those who are obese or hypertensive, can be a fast, valid and acceptable way of alerting the physician to this disorder among patients.

A global perspective for managing obesity and improving health: conventional treatment and surgical options: 4th Annual Obesity Summit, London, April 2016.

4th Annual Obesity Summit, London, 12-14 April 2016 There are more than 1.9 billion overweight people worldwide, culminating in high rates of Type 2 diabetes; and cardiovascular, digestive and other health problems. This makes obesity a startling phenomenon and a significant global health epidemic. To address this, The 2016 Obesity Summit, 4th in the series of obesity-related annual events organized by EuroSciCon, was held from 12 to 14 April 2016 at Cineworld, The O2 in London. This conference set the stage for three days of stimulating high-quality presentations on the advancements in obesity in an informal academic setting. Approximately 156 delegates including students, researchers, healthcare professionals and scientists from 36 countries around the world attended the event. This meeting report summarizes some of the most outstanding presentations.